Lab & Research Group Publications

Looking for publications from a particular UC Santa Cruz Genomics Institute researcher or investigator?

  • Bibliographies for individual faculty scholars may be found by visiting their Google Scholar profile.
  • Bibliographies from our labs and projects may be found by visiting their lab websites.

Farshidfar, Farshad and Zheng, Siyuan and Gingras, Marie-Claude and Newton, Yulia and Shih, Juliann and Robertson, A Gordon and Hinoue, Toshinori and Hoadley, Katherine A and Gibb, Ewan A and Roszik, Jason and others; Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell reports. 18-11. 2780–2794 (2017) Elsevier

Beale, Holly and Lam, Du Linh and Vivian, John and Newton, Yulia and Shah, Avanthi Tayi and Bjork, Isabel and Goldstein, Ted and Brooks, Angela N and Stuart, Josh and Salama, Sofie and others; Identifying confidently measured genes in single pediatric cancer patient samples using RNA sequencing. (2017) AACR

Morozova, Olena and Newton, Yulia and Shah, Avanthi Tayi and Beale, Holly and Lam, Du Linh and Vivian, John and Bjork, Isabel and Goldstein, Theodore and Stuart, Josh and Salama, Sofie and others; A pan-cancer analysis framework for incorporating gene expression information into clinical interpretation of pediatric cancer genomic data. (2017) AACR

Cai, Binghuang and Li, Biao and Kiga, Nikki and Thusberg, Janita and Bergquist, Timothy and Chen, Yun-Ching and Niknafs, Noushin and Carter, Hannah and Tokheim, Collin and Beleva-Guthrie, Violeta and others; Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges. Human Mutation. (2017) Wiley Online Library

de Bourcy, Charles FA and Angel, Cesar J Lopez and Vollmers, Christopher and Dekker, Cornelia L and Davis, Mark M and Quake, Stephen R; Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging. Proceedings of the National Academy of Sciences. 114-5. 1105–1110 (2017) National Acad Sciences

Casper, Jonathan and Newport, Dave and Pfahl, Michael; Is” Going Green” Worth It? Assessing Fan Engagement and Perceptions of Athletic Department Environmental Efforts. Journal of Applied Sport Management. 9-1. (2017) Sagamore Publishing LLC

Kellison, Timothy B and Bunds, Kyle S and Casper, Jonathan M and Newman, Joshua I; Public parks usage near hydraulic fracturing operations. Journal of Outdoor Recreation and Tourism. 18. 75–80 (2017) Elsevier

Kellison, Timothy B and Casper, Jonathan M; 8 Environmental legacy of mega sport events. Legacies and Mega Events: Fact or Fairy Tales?. (2017) Routledge

Ceccarelli, Michele and Barthel, Floris P and Malta, Tathiane M and Sabedot, Thais S and Salama, Sofie R and Murray, Bradley A and Morozova, Olena and Newton, Yulia and Radenbaugh, Amie and Pagnotta, Stefano M and others; Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma. Cell. 164-3. 550–563 (2016) Elsevier

Putnam, Nicholas H and O’Connell, Brendan L and Stites, Jonathan C and Rice, Brandon J and Blanchette, Marco and Calef, Robert and Troll, Christopher J and Fields, Andrew and Hartley, Paul D and Sugnet, Charles W and others; Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome research. 26-3. 342–350 (2016) Cold Spring Harbor Lab

Gordon, David and Huddleston, John and Chaisson, Mark JP and Hill, Christopher M and Kronenberg, Zev N and Munson, Katherine M and Malig, Maika and Raja, Archana and Fiddes, Ian and Hillier, LaDeana W and others; Long-read sequence assembly of the gorilla genome. Science. 352-6281. aae0344 (2016) American Association for the Advancement of Science

Siu, Lillian L and Lawler, Mark and Haussler, David and Knoppers, Bartha Maria and Lewin, Jeremy and Vis, Daniel J and Liao, Rachel G and Andre, Fabrice and Banks, Ian and Barrett, J Carl and others; Facilitating a culture of responsible and effective sharing of cancer genome data. Nature medicine. 22-5. 464 (2016) NIH Public Access

Small, Eric Jay and Aggarwal, Rahul Raj and Huang, Jiaoti and Sokolov, Artem and Zhang, Li and Alumkal, Joshi J and Youngren, Jack and Ryan, Charles J and Foye, Adam and Reiter, Robert Evan and others; Clinical and genomic characterization of metastatic small cell/neuroendocrine prostate cancer (SCNC) and intermediate atypical prostate cancer (IAC): Results from the SU2C/PCF/AACRWest Coast Prostate Cancer Dream Team (WCDT).. (2016) American Society of Clinical Oncology

Liu, Tiffany T and Achrol, Achal S and Mitchell, Lex A and Rodriguez, Scott A and Feroze, Abdullah and Iv, Michael and Kim, Christine and Chaudhary, Navjot and Gevaert, Olivier and Stuart, Josh M and others; Magnetic resonance perfusion image features uncover an angiogenic subgroup of glioblastoma patients with poor survival and better response to antiangiogenic treatment. Neuro-oncology. now270 (2016) Oxford University Press US

Morozova, Olena and Newton, Yulia and Cline, Melissa and Yip, Stephen and Rao, Arjun and Stuart, Josh and Goldstein, Ted and Salama, Sofie and Deyell, Rebecca and Rassekh, S Rod and others; Abstract PR14: Harnessing the power of big data to advance pediatric cancer care. (2016) AACR

Kim, Won and Ryan, Charles J and Zhang, Li and Youngren, Jack and Wilton, John and Alumkal, Joshi J and Beer, Tomasz M and Baertsch, Robert and Stuart, Josh and Chi, Kim N and others; Dehydroepiandrosterone in metastatic castration-resistant prostate cancer: Preliminary results from the SU2C-PCF West Coast Dream Team (WCDT).. (2016) American Society of Clinical Oncology

Tyner, Cath and Barber, Galt P and Casper, Jonathan and Clawson, Hiram and Diekhans, Mark and Eisenhart, Christopher and Fischer, Clayton M and Gibson, David and Gonzalez, Jairo Navarro and Guruvadoo, Luvina and others; The UCSC Genome Browser database: 2017 update. Nucleic acids research. 45-D1. D626–D634 (2016) Oxford University Press

Hinrichs, Angie S and Raney, Brian J and Speir, Matthew L and Rhead, Brooke and Casper, Jonathan and Karolchik, Donna and Kuhn, Robert M and Rosenbloom, Kate R and Zweig, Ann S and Haussler, David and others; UCSC data integrator and variant annotation integrator. Bioinformatics. 32-9. 1430–1432 (2016) Oxford University Press

Gordon, David and Huddleston, John and Chaisson, Mark JP and Hill, Christopher M and Kronenberg, Zev N and Munson, Katherine M and Malig, Maika and Raja, Archana and Fiddes, Ian and Hillier, Ladeana W and others; Nonhuman Genomics: Long-read sequence assembly of the gorilla genome. Science. 352-6281. 52 (2016)

Lee, Jiwon and Boutz, Daniel R and Chromikova, Veronika and Joyce, M Gordon and Vollmers, Christopher and Leung, Kwanyee and Horton, Andrew P and DeKosky, Brandon J and Lee, Chang-Han and Lavinder, Jason J and others; Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination. Nature medicine. 22-12. 1456 (2016) NIH Public Access

Horns, Felix and Vollmers, Christopher and Croote, Derek and Mackey, Sally F and Swan, Gary E and Dekker, Cornelia L and Davis, Mark M and Quake, Stephen R; Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching. Elife. 5. e16578 (2016) eLife Sciences Publications Limited

Nair, Nitya and Newell, Evan W and Vollmers, Christopher and Quake, Stephen R and Morton, John M and Davis, Mark M and He, Xiao-Song and Greenberg, Harry B; High-dimensional immune profiling of total and rotavirus VP6-specific intestinal and circulating B cells by mass cytometry. Mucosal immunology. 9-1. 68 (2016) NIH Public Access

Cole, Charles and Volden, Roger and Dharmadhikari, Sumedha and Scelfo-Dalbey, Camille and Vollmers, Christopher; Highly Accurate Sequencing of Full-Length Immune Repertoire Amplicons Using Tn5-Enabled and Molecular Identifier–Guided Amplicon Assembly. The Journal of Immunology. 196-6. 2902–2907 (2016) Am Assoc Immnol

Okayasu, Isao and Nogawa, Haruo and Casper, Jonathan M and Morais, Duarte B; Recreational sports event participants’ attitudes and satisfaction: cross-cultural comparisons between runners in Japan and the USA. Managing Sport and Leisure. 21-3. 164–180 (2016) Taylor \& Francis

Jeon, Jung-Hwan and Casper, Jonathan; Psychological antecedents of youth versus adult participation: An examination based on the Sport Commitment Model. Journal of Amateur Sport. 2-2. 103–125 (2016)

Peterson, Megan L and Kay, Kathleen M and Angert, Amy L; The scale of local adaptation in Mimulus guttatus: comparing life history races, ecotypes, and populations. New Phytologist. 211-1. 345–356 (2016) Wiley Online Library

Kundaje, Anshul and Meuleman, Wouter and Ernst, Jason and Bilenky, Misha and Yen, Angela and Kheradpour, Pouya and Zhang, Zhizhuo and Heravi-Moussavi, Alireza and Liu, Yaping and Amin, Viren and others; Integrative analysis of 111 reference human epigenomes. Nature. 518-7539. 317 (2015) NIH Public Access

Speir, Matthew L and Zweig, Ann S and Rosenbloom, Kate R and Raney, Brian J and Paten, Benedict and Nejad, Parisa and Lee, Brian T and Learned, Katrina and Karolchik, Donna and Hinrichs, Angie S and others; The UCSC genome browser database: 2016 update. Nucleic acids research. 44-D1. D717–D725 (2015) Oxford University Press

Ewing, Adam D and Houlahan, Kathleen E and Hu, Yin and Ellrott, Kyle and Caloian, Cristian and Yamaguchi, Takafumi N and Bare, J Christopher and P’ng, Christine and Waggott, Daryl and Sabelnykova, Veronica Y and others; Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nature methods. 12-7. 623–630 (2015) Nature Research

Paten, Benedict and Diekhans, Mark and Druker, Brian J and Friend, Stephen and Guinney, Justin and Gassner, Nadine and Guttman, Mitchell and James Kent, W and Mantey, Patrick and Margolin, Adam A and others; The NIH BD2K center for big data in translational genomics. Journal of the American Medical Informatics Association. 22-6. 1143–1147 (2015) Oxford University Press

Nguyen, Ngan and Hickey, Glenn and Zerbino, Daniel R and Raney, Brian and Earl, Dent and Armstrong, Joel and Kent, W James and Haussler, David and Paten, Benedict; Building a pan-genome reference for a population. Journal of Computational Biology. 22-5. 387–401 (2015) Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA

Small, Eric Jay and Huang, Jiaoti and Youngren, Jack and Sokolov, Artem and Aggarwal, Rahul Raj and Thomas, George and True, Lawrence D and Zhang, Li and Foye, Adam and Alumkal, Joshi J and others; Characterization of neuroendocrine prostate cancer (NEPC) in patients with metastatic castration resistant prostate cancer (mCRPC) resistant to abiraterone (Abi) or enzalutamide (Enz): Preliminary results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT).. (2015) American Society of Clinical Oncology

Aggarwal, Rahul Raj and Thomas, George and Youngren, Jack and Foye, Adam and Olson, Susan and Paris, Pamela and Beer, Tomasz M and Ryan, Charles J and Witte, Owen and Evans, Christopher P and others; Androgen receptor (AR) amplification in patients (pts) with metastatic castration resistant prostate cancer (mCRPC) resistant to abiraterone (Abi) and enzalutamide (Enz): Preliminary results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT).. (2015) American Society of Clinical Oncology

Woodward, Josha and King, Carly and Coleman, Daniel and Lisac, Robert and Schwartzman, Jacob and Wang, Nicholas and Gleave, Martin and Gray, Joe and Thomas, George and Beer, Tomasz M and others; Integrative genomic analysis to identify emergent enzalutamide resistance mechanisms in castration-resistant prostate cancer. (2015) AACR

Morozova, Olena and Ng, Sam and Rao, Arjun and Stuart, Josh and Haussler, David and Salama, Sofie; Abstract A2-52: Pan-cancer analysis reveals distinct effects of receptor tyrosine kinase mutations on downstream pathway activities. (2015) AACR

Hafner, Marc and Niepel, Mario and Duan, Qiaonan and Paull, Evan and Stuart, Josh and Subramanian, Aravind and Ma’ayan, Avi and Sorger, Peter; Abstract B20: Transcriptional landscape of drug response guides the design of specific and potent drug combinations. (2015) AACR

Stuart, Josh and Boutros, Paul and Lee, Anna Ying-Wah and Ellrott, Kyle and Margolin, Adam and Dang, Kristen and Houlahan, Kathleen and Bare, Christopher and Guinney, Justin and Espiritu, Shadrielle and others; Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic variant detection. F1000Research. 4. (2015)

Baertsch, Robert and Wong, Chris and Youngren, Jack and Stuart, Josh and Small, Eric and Goldstein, Ted; Abstract A1-46: Using Medbook Workbench to create evidence streams to guide medical decisions. (2015) AACR

Dobrynin, Pavel and Liu, Shiping and Tamazian, Gaik and Xiong, Zijun and Yurchenko, Andrey A and Krasheninnikova, Ksenia and Kliver, Sergey and Schmidt-K{\”u}ntzel, Anne and Koepfli, Klaus-Peter and Johnson, Warren and others; Genomic legacy of the African cheetah, Acinonyx jubatus. Genome biology. 16-1. 277 (2015) BioMed Central

Zhu, Jingchun and Craft, Brian and Goldman, Mary and Cline, Melissa and Diekhans, Mark and Haussler, David; Abstract B1-07: Using the UCSC Xena Platform to integrate, visualize, and analyze your own data in the context of large external genomic datasets. (2015) AACR

Vollmers, Christopher and De Vlaminck, Iwijn and Valantine, Hannah A and Penland, Lolita and Luikart, Helen and Strehl, Calvin and Cohen, Garrett and Khush, Kiran K and Quake, Stephen R; Monitoring pharmacologically induced immunosuppression by immune repertoire sequencing to detect acute allograft rejection in heart transplant patients: a proof-of-concept diagnostic accuracy study. PLoS medicine. 12-10. e1001890 (2015) Public Library of Science

Vollmers, Christopher and Penland, Lolita and Kanbar, Jad N and Quake, Stephen R; Novel exons and splice variants in the human antibody heavy chain identified by single cell and single molecule sequencing. PloS one. 10-1. e0117050 (2015) Public Library of Science

Pfahl, Michael and Casper, Jonathan and Trendafilova, Sylvia and McCullough, Brian P and Nguyen, Sheila N; Crossing boundaries: An examination of sustainability department and athletics department collaboration regarding environmental issues. Communication \& Sport. 3-1. 27–56 (2015) Sage Publications Sage CA: Los Angeles, CA

Casper, Jonathan M and Pfahl, Michael E; Sport Management and the Natural Environment: Theory and Practice. (2015) Routledge

Casper, Jonathan M and Pfahl, Michael E; Environmental sustainability practices in US NCAA Division III athletics departments. International Journal of Event Management Research. 10-1. (2015)

Mayer, Jessica and Seekamp, Erin and Casper, Jonathan and Blank, Gary; An examination of behavior change theories to predict behavioral intentions of organisms-in-trade hobbyists. Human Ecology Review. 21-2. 65–92 (2015) JSTOR

Peterson, Megan L and Miller, Timothy J and Kay, Kathleen M; An ultraviolet floral polymorphism associated with life history drives pollinator discrimination in Mimulus guttatus. American journal of botany. 102-3. 396–406 (2015) Botanical Soc America

Biletch, Barry and Kay, Kathleen and Yu, Hongji; An Analysis of Mathematical Notations: For Better or For Worse. (2015)

Jarvis, Erich D and Mirarab, Siavash and Aberer, Andre J and Li, Bo and Houde, Peter and Li, Cai and Ho, Simon YW and Faircloth, Brant C and Nabholz, Benoit and Howard, Jason T and others; Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 346-6215. 1320–1331 (2014) American Association for the Advancement of Science

Rosenbloom, Kate R and Armstrong, Joel and Barber, Galt P and Casper, Jonathan and Clawson, Hiram and Diekhans, Mark and Dreszer, Timothy R and Fujita, Pauline A and Guruvadoo, Luvina and Haeussler, Maximilian and others; The UCSC genome browser database: 2015 update. Nucleic acids research. 43-D1. D670–D681 (2014) Oxford University Press

Zhang, Guojie and Li, Cai and Li, Qiye and Li, Bo and Larkin, Denis M and Lee, Chul and Storz, Jay F and Antunes, Agostinho and Greenwold, Matthew J and Meredith, Robert W and others; Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 346-6215. 1311–1320 (2014) American Association for the Advancement of Science

Jacobs, Frank MJ and Greenberg, David and Nguyen, Ngan and Haeussler, Maximilian and Ewing, Adam D and Katzman, Sol and Paten, Benedict and Salama, Sofie R and Haussler, David; An evolutionary arms race between KRAB zinc finger genes 91/93 and SVA/L1 retrotransposons. Nature. 516-7530. 242 (2014) NIH Public Access

Green, Richard E and Braun, Edward L and Armstrong, Joel and Earl, Dent and Nguyen, Ngan and Hickey, Glenn and Vandewege, Michael W and John, John A St and Capella-Guti{\’e}rrez, Salvador and Castoe, Todd A and others; Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science. 346-6215. 1254449 (2014) American Association for the Advancement of Science

Wilks, Christopher and Cline, Melissa S and Weiler, Erich and Diehkans, Mark and Craft, Brian and Martin, Christy and Murphy, Daniel and Pierce, Howdy and Black, John and Nelson, Donavan and others; The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. Database. 2014. (2014) Oxford University Press

Goldman, Mary and Craft, Brian and Swatloski, Teresa and Cline, Melissa and Morozova, Olena and Diekhans, Mark and Haussler, David and Zhu, Jingchun; The UCSC cancer genomics browser: update 2015. Nucleic acids research. 43-D1. D812–D817 (2014) Oxford University Press

Earl, Dent and Nguyen, Ngan and Hickey, Glenn and Harris, Robert S and Fitzgerald, Stephen and Beal, Kathryn and Seledtsov, Igor and Molodtsov, Vladimir and Raney, Brian J and Clawson, Hiram and others; Alignathon: a competitive assessment of whole-genome alignment methods. Genome research. 24-12. 2077–2089 (2014) Cold Spring Harbor Lab

Lowe, Craig B and Clarke, Julia A and Baker, Allan J and Haussler, David and Edwards, Scott V; Feather development genes and associated regulatory innovation predate the origin of Dinosauria. Molecular biology and evolution. 32-1. 23–28 (2014) Oxford University Press

Paten, Benedict and Novak, Adam and Haussler, David; Mapping to a reference genome structure. arXiv preprint arXiv:1404.5010. (2014)

Haeussler, Maximilian and Raney, Brian J and Hinrichs, Angie S and Clawson, Hiram and Zweig, Ann S and Karolchik, Donna and Casper, Jonathan and Speir, Matthew L and Haussler, David and Kent, W James; Navigating protected genomics data with UCSC Genome Browser in a Box. Bioinformatics. 31-5. 764–766 (2014) Oxford University Press

Radenbaugh, Amie J and Ma, Singer and Ewing, Adam and Stuart, Joshua M and Collisson, Eric A and Zhu, Jingchun and Haussler, David; RADIA: RNA and DNA integrated analysis for somatic mutation detection. PloS one. 9-11. e111516 (2014) Public Library of Science

Yuan, Yuan and Van Allen, Eliezer M and Omberg, Larsson and Wagle, Nikhil and Amin-Mansour, Ali and Sokolov, Artem and Byers, Lauren A and Xu, Yanxun and Hess, Kenneth R and Diao, Lixia and others; Assessing the clinical utility of cancer genomic and proteomic data across tumor types. Nature biotechnology. 32-7. 644–652 (2014) Nature Research

Small, Eric Jay and Youngren, Jack and Thomas, George and Olson, Susan and Toschi, Alexandria and Foye, Adam and Alumkal, Joshi J and Rettig, Matthew and Gleave, Martin Edwin and Evans, Christopher P and others; Androgen receptor (AR) amplification in patients with metastatic castration-resistant prostate cancer (mCRPC) refractory to therapy with abiraterone acetate or enzalutamide: Preliminary results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT).. (2014) American Society of Clinical Oncology

Yau, Christina and Benz, Stephen and Vaske, Charles and Ng, Sam and Stuart, Josh and Benz, Christopher C; Differential pathway activation associated with domain-specific PIK3CA mutations. (2014) AACR

Wolf, Denise M and Fan, Cheng and Hoadley, Katherine A and Yau, Christina and Sokolov, Artem and Network, TCGA and Stuart, Josh and Perou, Charles and van’t Veer, Laura; Thousands of published cancer signatures and pathways can be collapsed into a handful of non-redundant gene programs: a TCGA pan-cancer analysis. (2014) AACR

Spellman, Paul T and Stuart, Josh and Gray, Joe W; Understanding and Using Information about Cancer Genomes. (2014) Elsevier Inc.

Bivol, Adrian and Graim, Kiley and Paull, Evan and Carlin, Dan and Baertsch, Robert and Sokolov, Artem and Stuart, Josh; Identification of pathways relevant for metastatic site prediction in prostate cancer. (2014) AACR

Alumkal, Joshi J and Heiser, Laura and Beer, Tomasz M and Small, Eric Jay and Baertsch, Robert and Stuart, Josh and King, Carly and Korkola, James and Cetnar, Jeremy and Graff, Julie Nicole and others; Identifying enzalutamide resistance mechanisms in men with castration-resistant prostate cancer.. (2014) American Society of Clinical Oncology

Nguyen, Ngan and Hickey, Glenn and Raney, Brian J and Armstrong, Joel and Clawson, Hiram and Zweig, Ann and Karolchik, Donna and Kent, William James and Haussler, David and Paten, Benedict; Comparative assembly hubs: web-accessible browsers for comparative genomics. Bioinformatics. 30-23. 3293–3301 (2014) Oxford University Press

Haeussler, Maximilian and Karolchik, Donna and Clawson, Hiram and Raney, Brian J and Rosenbloom, Kate R and Fujita, Pauline A and Hinrichs, Angie S and Speir, Matthew L and Eisenhart, Chris and Zweig, Ann S and others; The UCSC Ebola genome portal. PLoS currents. 6. (2014) Public Library of Science

Ezkurdia, Iakes and Juan, David and Rodriguez, Jose Manuel and Frankish, Adam and Diekhans, Mark and Harrow, Jennifer and Vazquez, Jesus and Valencia, Alfonso and Tress, Michael L; Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes. Human molecular genetics. 23-22. 5866–5878 (2014) Oxford University Press

Sisu, Cristina and Pei, Baikang and Leng, Jing and Frankish, Adam and Zhang, Yan and Balasubramanian, Suganthi and Harte, Rachel and Wang, Daifeng and Rutenberg-Schoenberg, Michael and Clark, Wyatt and others; Comparative analysis of pseudogenes across three phyla. Proceedings of the National Academy of Sciences. 111-37. 13361–13366 (2014) National Acad Sciences

Casper, Jonathan M and Pfahl, Michael E and McCullough, Brian and others; Intercollegiate sport and the environment: Examining fan engagement based on athletics department sustainability efforts. Journal of Issues in Intercollegiate Athletics. 7. 65–91 (2014) College Sport Research Institute

Bocarro, Jason N and Kanters, Michael A and Edwards, Michael B and Casper, Jonathan M and McKenzie, Thomas L; Prioritizing school intramural and interscholastic programs based on observed physical activity. American Journal of Health Promotion. 28-3\_suppl. S65–S71 (2014) SAGE Publications Sage CA: Los Angeles, CA

Kelley, Katharine and Harrolle, Michelle G and Casper, Jonathan M; Estimating Consumer Spending on Tickets, Merchandise, and Food and Beverage: A Case Study of a NHL Team. Journal of Sport Management. 28-3. 253–265 (2014)

Trendafilova, Sylvia and McCullough, Brian and Pfahl, Michael and Nguyen, Sheila N and Casper, Jonathan and Picariella, M; Environmental sustainability in sport: Current state and future trends. Global Journal on Advances in Pure and Applied Sciences. 3. 9–14 (2014)

Frick, Winifred F and Shipley, J Ryan and Kelly, Jeffrey F and Heady, Paul A and Kay, Kathleen M; Seasonal reliance on nectar by an insectivorous bat revealed by stable isotopes. Oecologia. 174-1. 55–65 (2014) Springer

Peterson, Megan L and Kay, Kathleen M; Mating system plasticity promotes persistence and adaptation of colonizing populations of hermaphroditic angiosperms. The American Naturalist. 185-1. 28–43 (2014) University of Chicago Press Chicago, IL

Brennan, Cameron W and Verhaak, Roel GW and McKenna, Aaron and Campos, Benito and Noushmehr, Houtan and Salama, Sofie R and Zheng, Siyuan and Chakravarty, Debyani and Sanborn, J Zachary and Berman, Samuel H and others; The somatic genomic landscape of glioblastoma. Cell. 155-2. 462–477 (2013) Elsevier

Karolchik, Donna and Barber, Galt P and Casper, Jonathan and Clawson, Hiram and Cline, Melissa S and Diekhans, Mark and Dreszer, Timothy R and Fujita, Pauline A and Guruvadoo, Luvina and Haeussler, Maximilian and others; The UCSC genome browser database: 2014 update. Nucleic acids research. 42-D1. D764–D770 (2013) Oxford University Press

Bradnam, Keith R and Fass, Joseph N and Alexandrov, Anton and Baranay, Paul and Bechner, Michael and Birol, Inan{\c{c}} and Boisvert, S{\’e}bastien and Chapman, Jarrod A and Chapuis, Guillaume and Chikhi, Rayan and others; Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience. 2-1. 10 (2013) BioMed Central

Cline, Melissa S and Craft, Brian and Swatloski, Teresa and Goldman, Mary and Ma, Singer and Haussler, David and Zhu, Jingchun; Exploring TCGA pan-cancer data at the UCSC cancer genomics browser. Scientific reports. 3. (2013) Nature Publishing Group

Farrell, Catherine M and O’Leary, Nuala A and Harte, Rachel A and Loveland, Jane E and Wilming, Laurens G and Wallin, Craig and Diekhans, Mark and Barrell, Daniel and Searle, Stephen MJ and Aken, Bronwen and others; Current status and new features of the Consensus Coding Sequence database. Nucleic acids research. 42-D1. D865–D872 (2013) Oxford University Press

Paull, Evan O and Carlin, Daniel E and Niepel, Mario and Sorger, Peter K and Haussler, David and Stuart, Joshua M; Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). Bioinformatics. 29-21. 2757–2764 (2013) Oxford University Press

Ewing, Adam D and Ballinger, Tracy J and Earl, Dent and Harris, Christopher C and Ding, Li and Wilson, Richard K and Haussler, David; Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome biology. 14-3. R22 (2013) BioMed Central

Sanborn, J Zachary and Salama, Sofie R and Grifford, Mia and Brennan, Cameron W and Mikkelsen, Tom and Jhanwar, Suresh and Katzman, Sol and Chin, Lynda and Haussler, David; Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons. Cancer research. 73-19. 6036–6045 (2013) AACR

Hickey, Glenn and Paten, Benedict and Earl, Dent and Zerbino, Daniel and Haussler, David; HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics. 29-10. 1341–1342 (2013) Oxford University Press

Wong, Christopher K and Vaske, Charles J and Ng, Sam and Sanborn, J Zachary and Benz, Stephen C and Haussler, David and Stuart, Joshua M; The UCSC Interaction Browser: multidimensional data views in pathway context. Nucleic acids research. 41-W1. W218–W224 (2013) Oxford University Press

Omberg, Larsson and Ellrott, Kyle and Yuan, Yuan and Kandoth, Cyriac and Wong, Chris and Kellen, Michael R and Friend, Stephen H and Stuart, Josh and Liang, Han and Margolin, Adam A; Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. Nature genetics. 45-10. 1121–1126 (2013) Nature Research

Raney, Brian J and Dreszer, Timothy R and Barber, Galt P and Clawson, Hiram and Fujita, Pauline A and Wang, Ting and Nguyen, Ngan and Paten, Benedict and Zweig, Ann S and Karolchik, Donna and others; Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics. 30-7. 1003–1005 (2013) Oxford University Press

Douville, Christopher and Carter, Hannah and Kim, Rick and Niknafs, Noushin and Diekhans, Mark and Stenson, Peter D and Cooper, David N and Ryan, Michael and Karchin, Rachel; CRAVAT: cancer-related analysis of variants toolkit. Bioinformatics. 29-5. 647–648 (2013) Oxford University Press

Niknafs, Noushin and Kim, Dewey and Kim, RyangGuk and Diekhans, Mark and Ryan, Michael and Stenson, Peter D and Cooper, David N and Karchin, Rachel; MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures. Human genetics. 132-11. 1235–1243 (2013) Springer

Ezkurdia, Iakes and Juan, David and Rodriguez, Jose Manuel and Frankish, Adam and Diekhans, Mark and Harrow, Jennifer and Vazquez, Jesus and Valencia, Alfonso and Tress, Michael L; The shrinking human protein coding complement: are there now fewer than 20,000 genes?. arXiv preprint arXiv:1312.7111. (2013)

Wilks, Christopher and Maltbie, Dan and Diekhans, Mark and Haussler, David; Cghub: Kick-starting the worldwide genome web. Proceedings of the Asia-Pacific Advanced Network. 35. 1–13 (2013)

Diekhans, Mark and Team, UCSC CGHub; CGHub Client Security Guide. (2013)

Vollmers, Christopher and Sit, Rene V and Weinstein, Joshua A and Dekker, Cornelia L and Quake, Stephen R; Genetic measurement of memory B-cell recall using antibody repertoire sequencing. Proceedings of the National Academy of Sciences. 110-33. 13463–13468 (2013) National Acad Sciences

Plikus, Maksim V and Vollmers, Christopher and de la Cruz, Damon and Chaix, Amandine and Ramos, Raul and Panda, Satchidananda and Chuong, Cheng-Ming; Local circadian clock gates cell cycle progression of transient amplifying cells during regenerative hair cycling. Proceedings of the National Academy of Sciences. 110-23. E2106–E2115 (2013) National Acad Sciences

Kanters, Michael A and Bocarro, Jason N and Edwards, Michael B and Casper, Jonathan M and Floyd, Myron F; School sport participation under two school sport policies: comparisons by race/ethnicity, gender, and socioeconomic status. Annals of behavioral medicine. 45-1. 113–121 (2013) Springer

Casper, Jonathan M and Harrolle, Michelle Gacio; Perceptions of constraints to leisure time physical activity among Latinos in Wake County, North Carolina. American Journal of Health Promotion. 27-3. 139–142 (2013) SAGE Publications Sage CA: Los Angeles, CA

Trendafilova, Sylvia and Pfahl, Michael E and Casper, Jonathan; The case of NCAA athletic departments. Routledge Handbook of Sport and Corporate Social Responsibility. 105 (2013) Routledge

Casper, Jonathan M and Harrolle, Michelle Gacio and Kelley, Katharine; Gender differences in self-report physical activity and park and recreation facility use among Latinos in Wake County, North Carolina. Annals of behavioral medicine. 45-1. 49–54 (2013) Springer

Harrolle, Michelle Gacio and Floyd, Myron F and Casper, Jonathan M and Kelley, Katharine E and Bruton, Candice M; Physical activity constraints among Latinos: Identifying clusters and acculturation differences. Journal of Leisure Research. 45-1. 74 (2013) Sagamore Publishing LLC

Casper, Jonathan and Larson, Derek R and Stock, Tom and Howe-Veenstra, Carol and Sinn, Brad; Sustainability and Sports: Lecture \& Panel. (2013)

Casper, Jonathan M and Harrolle, Michelle Gacio and Kelley, Katharine; Background Physical activity (PA) is associated with reduced morbidity and mortality in individuals with type 2 diabetes mellitus (T2DM); however, most T2DM adults are insufficiently active. Purpose To explore the effectiveness of two innovative/theoretically based behavioral-change strategies to increase PA and reduce hemoglobin A1c (A1c) in T2DM adults. Methods Participants (n= 287) were randomly…. Annals of Behavioral Medicine. 45-1. 121–131 (2013)

Kowal, Emma and Radin, Joanna and Reardon, Jenny; Indigenous body parts, mutating temporalities, and the half-lives of postcolonial technoscience. Social Studies of Science. 43-4. 465–483 (2013) Sage Publications Sage UK: London, England

Reardon, Jenny; On the emergence of science and justice. Science, Technology, \& Human Values. 38-2. 176–200 (2013) Sage Publications Sage CA: Los Angeles, CA

Lancaster, Lesley T and Kay, Kathleen M; Origin and diversification of the California Flora: Re-examining classic hypotheses with molecular phylogenies. Evolution. 67-4. 1041–1054 (2013) Wiley Online Library

Surget-Groba, Yann and Kay, Kathleen M; Restricted gene flow within and between rapidly diverging Neotropical plant species. Molecular ecology. 22-19. 4931–4942 (2013) Wiley Online Library

Miller, Timothy J and Raguso, Robert A and Kay, Kathleen M; Novel adaptation to hawkmoth pollinators in Clarkia reduces efficiency, not attraction of diurnal visitors. Annals of botany. 113-2. 317–329 (2013) Oxford University Press

Yost, Jenn M and Bontrager, Megan and McCabe, Stephen Ward and Burton, Darren and Simpson, Michael G and Kay, Kathleen M and Ritter, Matt; Phylogenetic relationships and evolution in Dudleya (Crassulaceae). Systematic Botany. 38-4. 1096–1104 (2013) BioOne

Kay, Kathleen M and Picklum, Devon A; Drought alters the expression of mating system traits in two species of Clarkia. Evolutionary Ecology. 27-5. 899–910 (2013) Springer

Harrow, Jennifer and Frankish, Adam and Gonzalez, Jose M and Tapanari, Electra and Diekhans, Mark and Kokocinski, Felix and Aken, Bronwen L and Barrell, Daniel and Zadissa, Amonida and Searle, Stephen and others; GENCODE: the reference human genome annotation for The ENCODE Project. Genome research. 22-9. 1760–1774 (2012) Cold Spring Harbor Lab

Meyer, Laurence R and Zweig, Ann S and Hinrichs, Angie S and Karolchik, Donna and Kuhn, Robert M and Wong, Matthew and Sloan, Cricket A and Rosenbloom, Kate R and Roe, Greg and Rhead, Brooke and others; The UCSC Genome Browser database: extensions and updates 2013. Nucleic acids research. 41-D1. D64–D69 (2012) Oxford University Press

Rosenbloom, Kate R and Sloan, Cricket A and Malladi, Venkat S and Dreszer, Timothy R and Learned, Katrina and Kirkup, Vanessa M and Wong, Matthew C and Maddren, Morgan and Fang, Ruihua and Heitner, Steven G and others; ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic acids research. 41-D1. D56–D63 (2012) Oxford University Press

Heiser, Laura M and Sadanandam, Anguraj and Kuo, Wen-Lin and Benz, Stephen C and Goldstein, Theodore C and Ng, Sam and Gibb, William J and Wang, Nicholas J and Ziyad, Safiyyah and Tong, Frances and others; Subtype and pathway specific responses to anticancer compounds in breast cancer. Proceedings of the National Academy of Sciences. 109-8. 2724–2729 (2012) National Acad Sciences

Kuhn, Robert M and Haussler, David and Kent, W James; The UCSC genome browser and associated tools. Briefings in bioinformatics. 14-2. 144–161 (2012) Oxford University Press

Goldman, Mary and Craft, Brian and Swatloski, Teresa and Ellrott, Kyle and Cline, Melissa and Diekhans, Mark and Ma, Singer and Wilks, Chris and Stuart, Josh and Haussler, David and others; The UCSC cancer genomics browser: update 2013. Nucleic acids research. 41-D1. D949–D954 (2012) Oxford University Press

Kristensen, Vessela N and Vaske, Charles J and Ursini-Siegel, Josie and Van Loo, Peter and Nordgard, Silje H and Sachidanandam, Ravi and S{\o}rlie, Therese and W{\”a}rnberg, Fredrik and Haakensen, Vilde D and Helland, {\AA}slaug and others; Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling. Proceedings of the National Academy of Sciences. 109-8. 2802–2807 (2012) National Acad Sciences

Raab, Jesse R and Chiu, Jonathan and Zhu, Jingchun and Katzman, Sol and Kurukuti, Sreenivasulu and Wade, Paul A and Haussler, David and Kamakaka, Rohinton T; Human tRNA genes function as chromatin insulators. The EMBO journal. 31-2. 330–350 (2012) EMBO Press

Ng, Sam and Collisson, Eric A and Sokolov, Artem and Goldstein, Theodore and Gonzalez-Perez, Abel and Lopez-Bigas, Nuria and Benz, Christopher and Haussler, David and Stuart, Joshua M; PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis. Bioinformatics. 28-18. i640–i646 (2012) Oxford University Press

Bernardi, Giacomo and Wiley, Edward O and Mansour, Hicham and Miller, Michael R and Orti, Guillermo and Haussler, David and O’Brien, Stephen J and Ryder, Oliver A and Venkatesh, Byrappa; The fishes of Genome 10K. Marine genomics. 7. 3–6 (2012) Elsevier

Lowe, Craig B and Haussler, David; 29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. PLoS One. 7-8. e43128 (2012) Public Library of Science

Wong, Pamela BY and Wiley, Edward O and Johnson, Warren E and Ryder, Oliver A and O’Brien, Stephen J and Haussler, David and Koepfli, Klaus-Peter and Houck, Marlys L and Perelman, Polina and Mastromonaco, Gabriela and others; Tissue sampling methods and standards for vertebrate genomics. GigaScience. 1-1. 8 (2012) BioMed Central

Onodera, Courtney S and Underwood, Jason G and Katzman, Sol and Jacobs, Frank and Greenberg, David and Salama, Sofie R and Haussler, David; Gene isoform specificity through enhancer-associated antisense transcription. PloS one. 7-8. e43511 (2012) Public Library of Science

Pei, Baikang and Sisu, Cristina and Frankish, Adam and Howald, C{\’e}dric and Habegger, Lukas and Mu, Xinmeng Jasmine and Harte, Rachel and Balasubramanian, Suganthi and Tanzer, Andrea and Diekhans, Mark and others; The GENCODE pseudogene resource. Genome biology. 13-9. R51 (2012) BioMed Central

Harte, Rachel A and Farrell, Catherine M and Loveland, Jane E and Suner, Marie-Marthe and Wilming, Laurens and Aken, Bronwen and Barrell, Daniel and Frankish, Adam and Wallin, Craig and Searle, Steve and others; Tracking and coordinating an international curation effort for the CCDS Project. Database. 2012. bas008 (2012) Oxford University Press

Hatori, Megumi and Vollmers, Christopher and Zarrinpar, Amir and DiTacchio, Luciano and Bushong, Eric A and Gill, Shubhroz and Leblanc, Mathias and Chaix, Amandine and Joens, Matthew and Fitzpatrick, James AJ and others; Time-restricted feeding without reducing caloric intake prevents metabolic diseases in mice fed a high-fat diet. Cell metabolism. 15-6. 848–860 (2012) Elsevier

Vollmers, Christopher and Schmitz, Robert J and Nathanson, Jason and Yeo, Gene and Ecker, Joseph R and Panda, Satchidananda; Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome. Cell metabolism. 16-6. 833–845 (2012) Elsevier

Zarrinpar, Amir and Vollmers, Christopher and Panda, Satchidananda; 52 Temporally Restricted Feeding Prevents Obesity and Other Metabolic Disorders Associated With High Fat Diet in Mice. Gastroenterology. 142-5. S–14 (2012) WB Saunders

Bocarro, Jason N and Kanters, Michael A and Cerin, Ester and Floyd, Myron F and Casper, Jonathan M and Suau, Luis J and McKenzie, Thomas L; School sport policy and school-based physical activity environments and their association with observed physical activity in middle school children. Health \& Place. 18-1. 31–38 (2012) Elsevier

Casper, Jonathan and Pfahl, Michael and McSherry, Mark; Athletics department awareness and action regarding the environment: A study of NCAA athletics department sustainability practices. Journal of Sport Management. 26-1. 11–29 (2012)

Henderson, Karla A and Casper, Jonathan and Wilson, Beth E and Dern, Liana; Behaviors, reasons, and outcomes perceived by senior games participants. Journal of Park and Recreation Administration. 30-1. (2012) Sagamore Publishing LLC

Casper, Jonathan M and Pfahl, Michael E; Environmental behavior frameworks of sport and recreation undergraduate students. Sport Management Education Journal. 6-1. 8–20 (2012)

Kanters, Michael A and Bocarro, Jason N and Greenwood, P Brian and Casper, Jonathan M and Suau, Luis and McKenzie, Thomas L; Determinants of middle school sport participation: a comparison of different models for school sport delivery. International Journal of Sport Management and Marketing. 12-3-4. 159–179 (2012) Inderscience Publishers Ltd

Reardon, Jenny and TallBear, Kim; “Your DNA Is Our History” Genomics, Anthropology, and the Construction of Whiteness as Property. Current Anthropology. 53-S5. S233–S245 (2012) University of Chicago Press Chicago, IL

Reardon, Jenny; The democratic, anti-racist genome? Technoscience at the limits of liberalism. Science as Culture. 21-1. 25–47 (2012) Taylor \& Francis

Yost, Jenn M and Barry, Teri and Kay, Kathleen M and Rajakaruna, Nishanta; Edaphic adaptation maintains the coexistence of two cryptic species on serpentine soils. American Journal of Botany. 99-5. 890–897 (2012) Botanical Soc America

Abreu, Aluana G and Albaina, A and Alpermann, Tilman J and Apkenas, Vanessa E and BANKHEAD-DRONNET, St{\’e}phanie and Bergek, Sara and Berumen, Michael L and CHO, CHANG-HUNG and Clobert, Jean and Coulon, Aur{\’e}lie and others; Permanent genetic resources added to molecular ecology resources database 1 October 2011–30 November 2011. Molecular ecology resources. 12-2. 374–376 (2012) Wiley Online Library

Frick, Winifred F and Price, Ryan D and Heady III, Paul A and Kay, Kathleen M; Insectivorous bat pollinates columnar cactus more effectively per visit than specialized nectar bat. The American Naturalist. 181-1. 137–144 (2012) University of Chicago Press Chicago, IL

Earl, Dent and Bradnam, Keith and John, John St and Darling, Aaron and Lin, Dawei and Fass, Joseph and Yu, Hung On Ken and Buffalo, Vince and Zerbino, Daniel R and Diekhans, Mark and others; Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome research. 21-12. 2224–2241 (2011) Cold Spring Harbor Lab

Alf{\”o}ldi, Jessica and Di Palma, Federica and Grabherr, Manfred and Williams, Christina and Kong, Lesheng and Mauceli, Evan and Russell, Pamela and Lowe, Craig B and Glor, Richard and Jaffe, Jacob D and others; The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature. 477-7366. 587 (2011) NIH Public Access

Locke, Devin P and Hillier, LaDeana W and Warren, Wesley C and Worley, Kim C and Nazareth, Lynne V and Muzny, Donna M and Yang, Shiaw-Pyng and Wang, Zhengyuan and Chinwalla, Asif T and Minx, Pat and others; Comparative and demographic analysis of orangutan genomes. Nature. 469-7331. 529 (2011) NIH Public Access

Dreszer, Timothy R and Karolchik, Donna and Zweig, Ann S and Hinrichs, Angie S and Raney, Brian J and Kuhn, Robert M and Meyer, Laurence R and Wong, Mathew and Sloan, Cricket A and Rosenbloom, Kate R and others; The UCSC Genome Browser database: extensions and updates 2011. Nucleic acids research. 40-D1. D918–D923 (2011) Oxford University Press

Gravel, Simon and Henn, Brenna M and Gutenkunst, Ryan N and Indap, Amit R and Marth, Gabor T and Clark, Andrew G and Yu, Fuli and Gibbs, Richard A and Bustamante, Carlos D and Altshuler, David L and others; Demographic history and rare allele sharing among human populations. Proceedings of the National Academy of Sciences. 108-29. 11983–11988 (2011) National Acad Sciences

Wang, Nicholas J and Sanborn, Zachary and Arnett, Kelly L and Bayston, Laura J and Liao, Wilson and Proby, Charlotte M and Leigh, Irene M and Collisson, Eric A and Gordon, Patricia B and Jakkula, Lakshmi and others; Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma. Proceedings of the National Academy of Sciences. 108-43. 17761–17766 (2011) National Acad Sciences

Rosenbloom, Kate R and Dreszer, Timothy R and Long, Jeffrey C and Malladi, Venkat S and Sloan, Cricket A and Raney, Brian J and Cline, Melissa S and Karolchik, Donna and Barber, Galt P and Clawson, Hiram and others; ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic acids research. 40-D1. D912–D917 (2011) Oxford University Press

Zhou, Xin and Maricque, Brett and Xie, Mingchao and Li, Daofeng and Sundaram, Vasavi and Martin, Eric A and Koebbe, Brian C and Nielsen, Cydney and Hirst, Martin and Farnham, Peggy and others; The human epigenome browser at Washington University. Nature methods. 8-12. 989–990 (2011) Nature Research

Lowe, Craig B and Kellis, Manolis and Siepel, Adam and Raney, Brian J and Clamp, Michele and Salama, Sofie R and Kingsley, David M and Lindblad-Toh, Kerstin and Haussler, David; Three periods of regulatory innovation during vertebrate evolution. science. 333-6045. 1019–1024 (2011) American Association for the Advancement of Science

Paten, Benedict and Diekhans, Mark and Earl, Dent and John, John St and Ma, Jian and Suh, Bernard and Haussler, David; Cactus graphs for genome comparisons. Journal of Computational Biology. 18-3. 469–481 (2011) Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA

Katzman, Sol and Capra, John A and Haussler, David and Pollard, Katherine S; Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots. Genome biology and evolution. 3. 614–626 (2011) Oxford University Press

Roskin, Krishna M and Paten, Benedict and Haussler, David; Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization. BMC bioinformatics. 12-1. 144 (2011) BioMed Central

Craft, Brian and Ellrott, Kyle and Goldman, Mary and Wilks, Christopher and Szeto, Christopher and Ma, Singer and Stuart, Josh and Zhu, Jingchun and Haussler, David; Abstract A39: The UCSC Cancer Genomics Browser. (2011) AACR

Karolchik, Donna and Hinrichs, Angie S and Kent, W James; The UCSC genome browser. Current protocols in human genetics. 18–6 (2011) Wiley Online Library

Raney, Melissa S Cline and Karolchik, Donna and Barber, Galt P and Clawson, Hiram and others; Encode whole-genome 751 data in the ucsc genome browser: update 2012. Nucleic acids research, page gkr1012. 752. (2011)

Wong, Wing Chung and Kim, Dewey and Carter, Hannah and Diekhans, Mark and Ryan, Michael C and Karchin, Rachel; CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. Bioinformatics. 27-15. 2147–2148 (2011) Oxford University Press

DiTacchio, Luciano and Le, Hiep D and Vollmers, Christopher and Hatori, Megumi and Witcher, Michael and Secombe, Julie and Panda, Satchidananda; Histone lysine demethylase JARID1a activates CLOCK-BMAL1 and influences the circadian clock. Science. 333-6051. 1881–1885 (2011) American Association for the Advancement of Science

Casper, Jonathan M and Bocarro, Jason N and Kanters, Michael A and Floyd, Myron F; “Just let me play!”—understanding constraints that limit adolescent sport participation. Journal of Physical Activity and Health. 8-s1. S32–S39 (2011)

Casper, Jonathan M and Bocarro, Jason N and Kanters, Michael A and Floyd, Myron F; Measurement properties of constraints to sport participation: A psychometric examination with adolescents. Leisure Sciences. 33-2. 127–146 (2011) Taylor \& Francis

Edwards, Michael B and Bocarro, Jason N and Kanters, Michael and Casper, Jonathan; Participation in interscholastic and intramural sport programs in middle schools: An exploratory investigation of race and gender. Recreational Sports Journal. 35-2. 157–173 (2011)

Bruton, Candice M and Floyd, Myron F and Bocarro, Jason N and Henderson, Karla A and Casper, Jonathan M and Kanters, Michael A; Physical activity and health partnerships among park and recreation departments in North Carolina. Journal of Park and Recreation Administration. 29-2. (2011) Sagamore Publishing LLC

Menefee, W Chadwick and Casper, Jonathan M; Professional basketball fans in China: A comparison of National Basketball Association and Chinese Basketball Association team identification. International Journal of Sport Management and Marketing. 9-3-4. 185–200 (2011) Inderscience Publishers

Jonathan, Casper; Measurement Properties of Constraints to Sport Participation: A Psychometric Examination with Adolescents/Jonathan M. Casper, Jason N. Bocarro, Michael A. Kanters, Myron F. Floyd. Leisure Sciences. 33. (2011)

Casper, Jonathan and Pfahl, Michael and McSherry, Mark; Journal of Sport Management. Journal of Sport Management. (2011)

Reardon, Jenny; The ‘persons’ and ‘genomics’ of personal genomics. Personalized Medicine. 8-1. 95–107 (2011) Future Medicine

Kay, Kathleen M and Ward, Kimiora L and Watt, Lorna R and Schemske, Douglas W; Plant speciation. Serpentine: Evolution and Ecology in a Model System (SP Harrison \& N. Rajakaruna, eds). 71–96 (2011)

Louthan, Allison M and Kay, Kathleen M; Comparing the adaptive landscape across trait types: larger QTL effect size in traits under biotic selection. BMC evolutionary biology. 11-1. 60 (2011) BioMed Central

Maunakea, Alika K and Nagarajan, Raman P and Bilenky, Mikhail and Ballinger, Tracy J and D’Souza, Cletus and Fouse, Shaun D and Johnson, Brett E and Hong, Chibo and Nielsen, Cydney and Zhao, Yongjun and others; Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 466-7303. 253 (2010) NIH Public Access

Fujita, Pauline A and Rhead, Brooke and Zweig, Ann S and Hinrichs, Angie S and Karolchik, Donna and Cline, Melissa S and Goldman, Mary and Barber, Galt P and Clawson, Hiram and Coelho, Antonio and others; The UCSC genome browser database: update 2011. Nucleic acids research. 39-suppl\_1. D876–D882 (2010) Oxford University Press

Harris, R Alan and Wang, Ting and Coarfa, Cristian and Nagarajan, Raman P and Hong, Chibo and Downey, Sara L and Johnson, Brett E and Fouse, Shaun D and Delaney, Allen and Zhao, Yongjun and others; Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature biotechnology. 28-10. 1097–1105 (2010) Nature Research

Vaske, Charles J and Benz, Stephen C and Sanborn, J Zachary and Earl, Dent and Szeto, Christopher and Zhu, Jingchun and Haussler, David and Stuart, Joshua M; Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics. 26-12. i237–i245 (2010) Oxford University Press

Underwood, Jason G and Uzilov, Andrew V and Katzman, Sol and Onodera, Courtney S and Mainzer, Jacob E and Mathews, David H and Lowe, Todd M and Salama, Sofie R and Haussler, David; FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nature methods. 7-12. 995–1001 (2010) Nature Research

Raney, Brian J and Cline, Melissa S and Rosenbloom, Kate R and Dreszer, Timothy R and Learned, Katrina and Barber, Galt P and Meyer, Laurence R and Sloan, Cricket A and Malladi, Venkat S and Roskin, Krishna M and others; ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic acids research. 39-suppl\_1. D871–D875 (2010) Oxford University Press

Sanborn, J Zachary and Benz, Stephen C and Craft, Brian and Szeto, Christopher and Kober, Kord M and Meyer, Laurence and Vaske, Charles J and Goldman, Mary and Smith, Kayla E and Kuhn, Robert M and others; The UCSC cancer genomics browser: update 2011. Nucleic acids research. 39-suppl\_1. D951–D959 (2010) Oxford University Press

Katzman, Sol and Kern, Andrew D and Pollard, Katherine S and Salama, Sofie R and Haussler, David; GC-biased evolution near human accelerated regions. PLoS genetics. 6-5. e1000960 (2010) Public Library of Science

Kern, Andrew D and Haussler, David; A population genetic hidden Markov model for detecting genomic regions under selection. Molecular biology and evolution. 27-7. 1673–1685 (2010) Oxford University Press

Lowe, Craig B and Bejerano, Gill and Salama, Sofie R and Haussler, David; Endangered species hold clues to human evolution. Journal of heredity. 101-4. 437–447 (2010) Oxford University Press

Marshall, Heather and Stuart, Josh and Jaunzens, Tatiana; Community organizing goes green. Social Policy. 39-4. 8–10 (2010)

Kent, W James and Zweig, Ann S and Barber, G and Hinrichs, Angie S and Karolchik, Donna; BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 26-17. 2204–2207 (2010) Oxford University Press

Paten, Benedict and Diekhans, Mark and Earl, Dent; John St. John, Jian Ma, Bernard Suh, and David Haussler. 410–425 (2010)

Miller, David T and Adam, Margaret P and Aradhya, Swaroop and Biesecker, Leslie G and Brothman, Arthur R and Carter, Nigel P and Church, Deanna M and Crolla, John A and Eichler, Evan E and Epstein, Charles J and others; Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. The American Journal of Human Genetics. 86-5. 749–764 (2010) Elsevier

Jones, Matthew A and Covington, Michael F and DiTacchio, Luciano and Vollmers, Christopher and Panda, Satchidananda and Harmer, Stacey L; Jumonji domain protein JMJD5 functions in both the plant and human circadian systems. Proceedings of the National Academy of Sciences. 107-50. 21623–21628 (2010) National Acad Sciences

Casper, Jonathan M and Menefee, W Chadwick; Prior sport participation and spectator sport consumption: Socialization and soccer. European Sport Management Quarterly. 10-5. 595–611 (2010) Taylor \& Francis

Casper, Jonathan and Pfahl, Michael; Athletic Department Awareness and Action Regarding the Environment: An Exploratory Study of Athletic Department Sustainability Practices. (2010)

LaJeunesse, Dennis R and Johnson, Brooke and Presnell, Jason S and Catignas, Kathleen Kay and Zapotoczny, Grzegorz; Peristalsis in the junction region of the Drosophila larval midgut is modulated by DH31 expressing enteroendocrine cells. BMC physiology. 10-1. 14 (2010) BioMed Central

Rhead, Brooke and Karolchik, Donna and Kuhn, Robert M and Hinrichs, Angie S and Zweig, Ann S and Fujita, Pauline A and Diekhans, Mark and Smith, Kayla E and Rosenbloom, Kate R and Raney, Brian J and others; The UCSC genome browser database: update 2010. Nucleic acids research. 38-suppl\_1. D613–D619 (2009) Oxford University Press

Pruitt, Kim D and Harrow, Jennifer and Harte, Rachel A and Wallin, Craig and Diekhans, Mark and Maglott, Donna R and Searle, Steve and Farrell, Catherine M and Loveland, Jane E and Ruef, Barbara J and others; The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes (vol 19, pg 1316, 2009). Genome Research. 19-8. 1506–1506 (2009) COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2924 USA

Han, Jinju and Pedersen, Jakob S and Kwon, S Chul and Belair, Cassandra D and Kim, Young-Kook and Yeom, Kyu-Hyeon and Yang, Woo-Young and Haussler, David and Blelloch, Robert and Kim, V Narry; Posttranscriptional crossregulation between Drosha and DGCR8. Cell. 136-1. 75–84 (2009) Elsevier

Rosenbloom, Kate R and Dreszer, Timothy R and Pheasant, Michael and Barber, Galt P and Meyer, Laurence R and Pohl, Andy and Raney, Brian J and Wang, Ting and Hinrichs, Angie S and Zweig, Ann S and others; ENCODE whole-genome data in the UCSC Genome Browser. Nucleic acids research. 38-suppl\_1. D620–D625 (2009) Oxford University Press

Haussler, David and O’Brien, Stephen J and Ryder, Oliver A and Barker, F Keith and Clamp, Michele and Crawford, Andrew J and Hanner, Robert and Hanotte, Olivier and Johnson, Warren E and McGuire, Jimmy A and others; Genome 10K: a proposal to obtain whole-genome sequence for 10 000 vertebrate species. (2009)

Zhu, Jingchun and Sanborn, J Zachary and Benz, Stephen and Szeto, Christopher and Hsu, Fan and Kuhn, Robert M and Karolchik, Donna and Archie, John and Lenburg, Marc E and Esserman, Laura J and others; The UCSC cancer genomics browser. Nature methods. 6-4. 239–240 (2009) Nature Publishing Group

Temple, Gary and Gerhard, Daniela S and Rasooly, Rebekah and Feingold, Elise A and Good, Peter J and Robinson, Cristen and Mandich, Allison and Derge, Jeffrey G and Lewis, Jeanne and Shoaf, Debonny and others; The completion of the mammalian gene collection (MGC). Genome research. 19-12. 2324–2333 (2009) Cold Spring Harbor Lab

Koeva, Martina and Forsberg, E Camilla and Stuart, Josh M; Core stemness mechanisms revealed through homology. BMC Bioinformatics. 10-S13. O4 (2009) Springer

Karolchik, Donna and Hinrichs, Angie S and Kent, W James; The UCSC genome browser. Current protocols in bioinformatics. 1–4 (2009) Wiley Online Library

Ryan, Michael and Diekhans, Mark and Lien, Stephanie and Liu, Yun and Karchin, Rachel; LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Bioinformatics. 25-11. 1431–1432 (2009) Oxford University Press

Pruitt, Kim D and Harrow, Jennifer and Harte, Rachel A and Wallin, Craig and Diekhans, Mark and Maglott, Donna R and Searle, Steve and Farrell, Catherine M and Loveland, Jane E and Ruef, Barbara J; Clara Amid, Garth Brown, Oksana Dukhanina, Adam Frankish, Jennifer Hart, Bonnie L. (2009)

Flume, Patrick A and Mogayzel Jr, Peter J and Robinson, Karen A and Goss, Christopher H and Rosenblatt, Randall L and Kuhn, Robert J and Marshall, Bruce C and Clinical Practice Guidelines for Pulmonary Therapies Committee*; Cystic fibrosis pulmonary guidelines: treatment of pulmonary exacerbations. American journal of respiratory and critical care medicine. 180-9. 802–808 (2009) Am Thoracic Soc

Hartnig, Christoph and Manke, Ingo and Kuhn, Robert and Kleinau, Sebastian and Goebbels, J{\”u}rgen and Banhart, John; High-resolution in-plane investigation of the water evolution and transport in PEM fuel cells. Journal of Power Sources. 188-2. 468–474 (2009) Elsevier

Hughes, Michael E and DiTacchio, Luciano and Hayes, Kevin R and Vollmers, Christopher and Pulivarthy, S and Baggs, Julie E and Panda, Satchidananda and Hogenesch, John B; Harmonics of circadian gene transcription in mammals. PLoS genetics. 5-4. e1000442 (2009) Public Library of Science

Vollmers, Christopher and Gill, Shubhroz and DiTacchio, Luciano and Pulivarthy, Sandhya R and Le, Hiep D and Panda, Satchidananda; Time of feeding and the intrinsic circadian clock drive rhythms in hepatic gene expression. Proceedings of the National Academy of Sciences. 106-50. 21453–21458 (2009) National Acad Sciences

Bocarro, Jason N and Casper, Jonathan and Henderson, Karla A and Floyd, Myron F and Moore, Roger and Kanters, Michael A and Laven, Kevin and Edwards, Michael B; Physical Activity Promotion in North Carolina: Perceptions of Public Park and Recreation Directors.. Journal of Park \& Recreation Administration. 27-1. (2009)

Reardon, Jenny; Race to the Finish: Identity and Governance in an Age of Genomics. (2009) Princeton University Press

Kay, Kathleen M and Sargent, Risa D; The role of animal pollination in plant speciation: integrating ecology, geography, and genetics. Annual Review of Ecology, Evolution, and Systematics. 40. 637–656 (2009) Annual Reviews

Yost, Jenn M and Kay, Kathleen M; The evolution of postpollination reproductive isolation in Costus. Sexual plant reproduction. 22-4. 247–255 (2009) Springer

Kuhn, Robert M and Karolchik, Donna and Zweig, Ann S and Wang, Ting and Smith, Kayla E and Rosenbloom, Kate R and Rhead, B and Raney, Brian J and Pohl, Andy and Pheasant, Michael and others; The UCSC genome browser database: update 2009. Nucleic acids research. 37-suppl\_1. D755–D761 (2008) Oxford University Press

Stanke, Mario and Diekhans, Mark and Baertsch, Robert and Haussler, David; Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 24-5. 637–644 (2008) Oxford University Press

Baertsch, Robert and Diekhans, Mark and Kent, W James and Haussler, David and Brosius, J{\”u}rgen; Retrocopy contributions to the evolution of the human genome. BMC genomics. 9-1. 466 (2008) BioMed Central

Ma, Jian and Ratan, Aakrosh and Raney, Brian J and Suh, Bernard B and Miller, Webb and Haussler, David; The infinite sites model of genome evolution. Proceedings of the National Academy of Sciences. 105-38. 14254–14261 (2008) National Acad Sciences

Zweig, Ann S and Karolchik, Donna and Kuhn, Robert M and Haussler, David and Kent, W James; UCSC genome browser tutorial. Genomics. 92-2. 75–84 (2008) Elsevier

Ma, Jian and Ratan, Aakrosh and Raney, Brian J and Suh, Bernard B and Zhang, Louxin and Miller, Webb and Haussler, David; DUPCAR: reconstructing contiguous ancestral regions with duplications. Journal of computational biology. 15-8. 1007–1027 (2008) Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA

Blanchette, Mathauieu and Diallo, Abdoulaye Banir{\’e} and Green, Eric D and Miller, Webb and Haussler, David; Computational reconstruction of ancestral DNA sequences. Phylogenomics. 171–184 (2008) Springer

Karolchik, Donna and Bejerano, Gill and Hinrichs, Angie S and Kuhn, Robert M and Miller, Webb and Rosenbloom, Kate R and Zweig, Ann S and Haussler, David and Kent, W James; Comparative genomic analysis using the UCSC genome browser. Comparative Genomics. 17–33 (2008) Springer

Rosenbloom, Kate and Taylor, James and Schaeffer, Stephen and Kent, Jim and Haussler, David and Miller, Webb; Phylogenomic resources at the UCSC Genome Browser. Phylogenomics. 133–144 (2008) Springer

Twigger, Simon N and Pruitt, Kim D and Fern{\’a}ndez-Su{\’a}rez, Xos{\’e} M and Karolchik, Donna and Worley, Kim C and Maglott, Donna R and Brown, Garth and Weinstock, George and Gibbs, Richard A and Kent, Jim and others; What everybody should know about the rat genome and its online resources. Nature genetics. 40-5. 523–527 (2008) Nature Publishing Group

Mangan, Mary E and Williams, Jennifer M and Lathe, Scott M and Karolchik, Donna and Lathe, Warren C; UCSC genome browser: deep support for molecular biomedical research. Biotechnology annual review. 14. 63–108 (2008) Elsevier

Harte, Rachel and Diekhans, Mark; Fishing for Genes in the UCSC Browser A Tutorial. (2008)

Hartnig, Christoph and Manke, Ingo and Kuhn, Robert and Kardjilov, Nikolay and Banhart, John and Lehnert, Werner; Cross-sectional insight in the water evolution and transport in polymer electrolyte fuel cells. Applied Physics Letters. 92-13. 134106 (2008) AIP

Hatori, Megumi and Le, Hiep and Vollmers, Christopher and Keding, Sheena Racheal and Tanaka, Nobushige and Schmedt, Christian and Jegla, Timothy and Panda, Satchidananda; Inducible ablation of melanopsin-expressing retinal ganglion cells reveals their central role in non-image forming visual responses. PloS one. 3-6. e2451 (2008) Public Library of Science

Vollmers, Christopher and Panda, Satchidananda and DiTacchio, Luciano; A high-throughput assay for siRNA-based circadian screens in human U2OS cells. PloS one. 3-10. e3457 (2008) Public Library of Science

Kanters, Michael A and Bocarro, Jason and Casper, Jonathan; Supported or pressured? An examination of agreement among parent’s and children on parent’s role in youth sports. Journal of sport behavior. 31-1. 64 (2008) Journal of Sport Behavior

Bocarro, Jason and Kanters, Michael A and Casper, Jonathan and Forrester, Scott; School physical education, extracurricular sports, and lifelong active living. Journal of Teaching in Physical Education. 27-2. 155–166 (2008)

Casper, Jonathan M and Andrew, Damon PS; Sport commitment differences among tennis players on the basis of participation outlet and skill level. Journal of Sport Behavior. 31-3. 201 (2008) Journal of Sport Behavior

Casper, Jonathan M and Stellino, Megan Babkes; Demographic Predictors of Recreational Tennis Participants’ Sport Commitment.. Journal of Park \& Recreation Administration. 26-3. (2008)

Casper, Jonathan M and Kanters, Michael A and James, Jeffrey D; Perceptions of constraints to NHL spectatorship. International Journal of Sport Management and Marketing. 5-1-2. 55–72 (2008) Inderscience Publishers

Kanters, Michael and Bocarro, Jason and Casper, Jonathan and Forrester, Scott; Determinants of sport participation in middle school children and the impact of intramural sports. Recreational sports journal. 32-2. 134–151 (2008)

Prainsack, Barbara and Reardon, Jenny and Hindmarsh, Richard and Gottweis, Herbert and Naue, Ursula and Lunshof, Jeantine E; Personal genomes: misdirected precaution. Nature. 456-7218. 34–35 (2008) Nature Publishing Group

Reardon, Jenny; Race without Salvation. Revisiting Race in a Genomic Age (New Brunswick: Rutgers University Press, 2008). 304–19 (2008)

Bolnick, Deborah A and Fullwiley, Duana and Marks, Jonathan and Reverby, Susan M and Kahn, Jonathan and Tallbear, Kimberly and Reardon, Jenny and Cooper, Richard S and Duster, Troy and Fujimura, Joan H and others; The legitimacy of genetic ancestry tests-Response. Science. 319-5866. 1039–1040 (2008) AMER ASSOC ADVANCEMENT SCIENCE 1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA

Kay, Kathleen M and Schemske, Douglas W; Natural selection reinforces speciation in a radiation of neotropical rainforest plants. Evolution. 62-10. 2628–2642 (2008) Wiley Online Library

Rogers, Kathleen Kay; Editorial in English: Innovation, risk-taking, and collaboration: A celebration and history of CADE/ACED and distance education in Canada. International Journal of E-Learning \& Distance Education. 8-1. 1–7 (2008)

Gibbs, Richard A and Rogers, Jeffrey and Katze, Michael G and Bumgarner, Roger and Weinstock, George M and Mardis, Elaine R and Remington, Karin A and Strausberg, Robert L and Venter, J Craig and Wilson, Richard K and others; Evolutionary and biomedical insights from the rhesus macaque genome. science. 316-5822. 222–234 (2007) American Association for the Advancement of Science

Karolchik, Donna and Kuhn, Robert M and Baertsch, Robert and Barber, Galt P and Clawson, Hiram and Diekhans, Mark and Giardine, Belinda and Harte, Rachel A and Hinrichs, Angela S and Hsu, Fan and others; The UCSC genome browser database: 2008 update. Nucleic acids research. 36-suppl\_1. D773–D779 (2007) Oxford University Press

Miller, Webb and Rosenbloom, Kate and Hardison, Ross C and Hou, Minmei and Taylor, James and Raney, Brian and Burhans, Richard and King, David C and Baertsch, Robert and Blankenberg, Daniel and others; 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome research. 17-12. 1797–1808 (2007) Cold Spring Harbor Lab

Margulies, Elliott H and Cooper, Gregory M and Asimenos, George and Thomas, Daryl J and Dewey, Colin N and Siepel, Adam and Birney, Ewan and Keefe, Damian and Schwartz, Ariel S and Hou, Minmei and others; Analyses of deep mammalian sequence alignments and constraint predictions for 1\% of the human genome. Genome research. 17-6. 760–774 (2007) Cold Spring Harbor Lab

Wang, Ting and Zeng, Jue and Lowe, Craig B and Sellers, Robert G and Salama, Sofie R and Yang, Min and Burgess, Shawn M and Brachmann, Rainer K and Haussler, David; Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proceedings of the National Academy of Sciences. 104-47. 18613–18618 (2007) National Acad Sciences

Lowe, Craig B and Bejerano, Gill and Haussler, David; Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proceedings of the National Academy of Sciences. 104-19. 8005–8010 (2007) National Acad Sciences

Katzman, Sol and Kern, Andrew D and Bejerano, Gill and Fewell, Ginger and Fulton, Lucinda and Wilson, Richard K and Salama, Sofie R and Haussler, David; Human genome ultraconserved elements are ultraselected. Science. 317-5840. 915–915 (2007) American Association for the Advancement of Science

Yeang, Chen-Hsiang and Darot, Jeremy FJ and Noller, Harry F and Haussler, David; Detecting the coevolution of biosequences—an example of RNA interaction prediction. Molecular biology and evolution. 24-9. 2119–2131 (2007) Oxford University Press

Ohlson, Johan and Pedersen, Jakob Skou and Haussler, David and {\”O}hman, Marie; Editing modifies the GABAA receptor subunit $\alpha$3. Rna. 13-5. 698–703 (2007) Cold Spring Harbor Lab

Zhu, Jingchun and Sanborn, J Zachary and Diekhans, Mark and Lowe, Craig B and Pringle, Tom H and Haussler, David; Comparative genomics search for losses of long-established genes on the human lineage. PLoS computational biology. 3-12. e247 (2007) Public Library of Science

Dreszer, Timothy R and Wall, Gregory D and Haussler, David and Pollard, Katherine S; Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion. Genome research. 17-10. 1420–1430 (2007) Cold Spring Harbor Lab

Siepel, Adam and Diekhans, Mark and Brejov{\’a}, Bro{\v{n}}a and Langton, Laura and Stevens, Michael and Comstock, Charles LG and Davis, Colleen and Ewing, Brent and Oommen, Shelly and Lau, Christopher and others; Targeted discovery of novel human exons by comparative genomics. Genome research. 17-12. 1763–1773 (2007) Cold Spring Harbor Lab

Zeng, Jue and Yan, Jizhou and Wang, Ting and Mosbrook-Davis, Deborah and Dolan, Kyle T and Christensen, Ryan and Stormo, Gary D and Haussler, David and Lathrop, Richard H and Brachmann, Rainer K and others; Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins. Nucleic acids research. 36-1. e8–e8 (2007) Oxford University Press

Salomonis, Nathan and Hanspers, Kristina and Zambon, Alexander C and Vranizan, Karen and Lawlor, Steven C and Dahlquist, Kam D and Doniger, Scott W and Stuart, Josh and Conklin, Bruce R and Pico, Alexander R; GenMAPP 2: new features and resources for pathway analysis. BMC bioinformatics. 8-1. 217 (2007) BioMed Central

Casper, Jonathan; Sport commitment, participation frequency and purchase intention segmentation based on age, gender, income and skill level with US tennis participants. European Sport Management Quarterly. 7-3. 269–282 (2007) Taylor \& Francis

Casper, Jonathan and Kanters, Michael A and Bocarro, Jason and Forrester, Scott and Greenwood, P Brian; Youth Sport Market Segmentation with the Theory of Planned Behavior. (2007)

Kanters, Michael and Bocarro, Jason and Casper, Jonathan and Forrester, Scott and Ballard, Kymm; Middle School Intramurals in Promoting Lifelong Active Living. (2007)

Bolnick, Deborah A and Fullwiley, Duana and Duster, Troy and Cooper, Richard S and Fujimura, Joan H and Kahn, Jonathan and Kaufman, Jay S and Marks, Jonathan and Morning, Ann and Nelson, Alondra and others; The science and business of genetic ancestry testing. SCIENCE-NEW YORK THEN WASHINGTON-. 318-5849. 399 (2007) American Association for the Advancement of Science

Reardon, Jenny; Democratic mis-haps: the problem of democratization in a time of biopolitics. BioSocieties. 2-2. 239–256 (2007) Springer

Hinrichs, Angela S and Karolchik, Donna and Baertsch, Robert and Barber, Galt P and Bejerano, Gill and Clawson, Hiram and Diekhans, Mark and Furey, Terrence S and Harte, Rachel A and Hsu, Fan and others; The UCSC genome browser database: update 2006. Nucleic acids research. 34-suppl\_1. D590–D598 (2006) Oxford University Press

Pedersen, Jakob Skou and Bejerano, Gill and Siepel, Adam and Rosenbloom, Kate and Lindblad-Toh, Kerstin and Lander, Eric S and Kent, Jim and Miller, Webb and Haussler, David; Identification and classification of conserved RNA secondary structures in the human genome. PLoS computational biology. 2-4. e33 (2006) Public Library of Science

Hsu, Fan and Kent, W James and Clawson, Hiram and Kuhn, Robert M and Diekhans, Mark and Haussler, David; The UCSC known genes. Bioinformatics. 22-9. 1036–1046 (2006) Oxford University Press

Bejerano, Gill and Lowe, Craig B and Ahituv, Nadav and King, Bryan and Siepel, Adam and Salama, Sofie R and Rubin, Edward M and Kent, W James and Haussler, David; A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 441-7089. 87 (2006) Nature Publishing Group

Kuhn, Robert M and Karolchik, Donna and Zweig, Ann S and Trumbower, Heather and Thomas, Daryl J and Thakkapallayil, Archana and Sugnet, Charles W and Stanke, Mario and Smith, Kayla E and Siepel, A and others; The UCSC genome browser database: update 2007. Nucleic acids research. 35-suppl\_1. D668–D673 (2006) Oxford University Press

Pollard, Katherine S and Salama, Sofie R and King, Bryan and Kern, Andrew D and Dreszer, Tim and Katzman, Sol and Siepel, Adam and Pedersen, Jakob S and Bejerano, Gill and Baertsch, Robert and others; Forces shaping the fastest evolving regions in the human genome. PLoS genetics. 2-10. e168 (2006) Public Library of Science

Ma, Jian and Zhang, Louxin and Suh, Bernard B and Raney, Brian J and Burhans, Richard C and Kent, W James and Blanchette, Mathieu and Haussler, David and Miller, Webb; Reconstructing contiguous regions of an ancestral genome. Genome research. 16-12. 1557–1565 (2006) Cold Spring Harbor Lab

Sugnet, Charles W and Srinivasan, Karpagam and Clark, Tyson A and O’Brien, Georgeann and Cline, Melissa S and Wang, Hui and Williams, Alan and Kulp, David and Blume, John E and Haussler, David and others; Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS computational biology. 2-1. e4 (2006) Public Library of Science

Siepel, Adam and Pollard, Katherine S and Haussler, David; New methods for detecting lineage-specific selection. Lecture Notes in Computer Science. 3909. 190–205 (2006) Springer

Thomas, Daryl J and Rosenbloom, Kate R and Clawson, Hiram and Hinrichs, Angie S and Trumbower, Heather and Raney, Brian J and Karolchik, Donna and Barber, Galt P and Harte, Rachel A and Hillman-Jackson, Jennifer and others; The ENCODE project at UC santa cruz. Nucleic acids research. 35-suppl\_1. D663–D667 (2006) Oxford University Press

Thomas, Daryl J and Trumbower, Heather and Kern, Andrew D and Rhead, Brooke L and Kuhn, Robert M and Haussler, David and Kent, W James; Variation resources at UC Santa Cruz. Nucleic acids research. 35-suppl\_1. D716–D720 (2006) Oxford University Press

Wu, Jing and Haussler, David; Coding exon detection using comparative sequences. Journal of Computational Biology. 13-6. 1148–1164 (2006) Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA

Schattner, Peter and Diekhans, Mark; Regions of extreme synonymous codon selection in mammalian genes. Nucleic acids research. 34-6. 1700–1710 (2006) Oxford University Press

Sanborn, J Zachary and Zhu, Jing and Diekhans, Mark and Haussler, David; A Novel Method for Discovering Primate Gene Loss using the Ancestral Genome. (2006)

Smith, David I and Zhu, Yu and McAvoy, Sarah and Kuhn, Robert; Common fragile sites, extremely large genes, neural development and cancer. Cancer letters. 232-1. 48–57 (2006) Elsevier

Brian Greenwood, P and Kanters, Michael A and Casper, Jonathan M; Sport fan team identification formation in mid-level professional sport. European Sport Management Quarterly. 6-3. 253–265 (2006) Taylor \& Francis

Casper, Jonathan; You Can’t be Serious, that Ball was IN: An Investigation of Junior Tennis Cheating Behavior. The qualitative report. 11-1. 20–36 (2006)

Casper, Jonathan D; Eminent Domain: Property Rights vs. Redevelopment. (2006)

Kay, Kathleen M and Whittall, Justen B and Hodges, Scott A; A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects. BMC Evolutionary Biology. 6-1. 36 (2006) BioMed Central

Kay, Kathleen M; Reproductive isolation between two closely related hummingbird-pollinated neotropical gingers. Evolution. 60-3. 538–552 (2006) BioOne

Kay, Kathleen M and Voelckel, Claudia and Yang, Ji Y and Hufford, Kristina M and Kaska, Debora D and Hodges, Scott A; Floral characters and species diversification. Ecology and evolution of flowers. 311–25 (2006) Oxford Univ. Press Oxford

Siepel, Adam and Bejerano, Gill and Pedersen, Jakob S and Hinrichs, Angie S and Hou, Minmei and Rosenbloom, Kate and Clawson, Hiram and Spieth, John and Hillier, LaDeana W and Richards, Stephen and others; Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome research. 15-8. 1034–1050 (2005) Cold Spring Harbor Lab

Karchin, Rachel and Diekhans, Mark and Kelly, Libusha and Thomas, Daryl J and Pieper, Ursula and Eswar, Narayanan and Haussler, David and Sali, Andrej; LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics. 21-12. 2814–2820 (2005) Oxford University Press

Siepel, Adam and Haussler, David; Phylogenetic hidden Markov models. 325–351 (2005) Springer

Kent, WJ and Hsu, Fan and Karolchik, Donna and Kuhn, Robert M and Clawson, Hiram and Trumbower, Heather and Haussler, David; Exploring relationships and mining data with the UCSC Gene Sorter. Genome research. 15-5. 737–741 (2005) Cold Spring Harbor Lab

Bejerano, Gill and Siepel, Adam C and Kent, W James and Haussler, David; Computational screening of conserved genomic DNA in search of functional noncoding elements. Nature Methods. 2-7. 535–545 (2005) Nature Publishing Group

Hsu, Fan and Pringle, Tom H and Kuhn, Robert M and Karolchik, Donna and Diekhans, Mark and Haussler, David and Kent, W James; The UCSC proteome browser. Nucleic acids research. 33-suppl\_1. D454–D458 (2005) Oxford University Press

Lucena, Brian and Haussler, David; Counterexample to a claim about the reconstruction of ancestral character states. Systematic biology. 54-4. 693–695 (2005) Society of Systematic Zoology

Forsberg, E Camilla and Prohaska, Susan S and Katzman, Sol and Heffner, Garrett C and Stuart, Josh M and Weissman, Irving L; Differential expression of novel potential regulators in hematopoietic stem cells. PLoS genetics. 1-3. e28 (2005) Public Library of Science

Di Bias, A and Dahle, David M and Diekhans, Mark and Grate, Leslie and Hirschberg, Jeffrey and Karplus, Kevin and Keller, Hansj{\”o}rg and Kendrick, Mark and Mesa-Martinez, Francisco J and Pease, David and others; The UCSC Kestrel parallel processor. IEEE Transactions on Parallel and Distributed Systems. 16-1. 80–92 (2005) IEEE

Kay, Kathleen M and Reeves, Patrick A and Olmstead, Richard G and Schemske, Douglas W; Rapid speciation and the evolution of hummingbird pollination in neotropical Costus subgenus Costus (Costaceae): evidence from nrDNA ITS and ETS sequences. American Journal of Botany. 92-11. 1899–1910 (2005) Botanical Soc America

Hillier, LaDeana W and Miller, Webb and Birney, Ewan and Warren, Wesley and Hardison, Ross C and Ponting, Chris P and Bork, Peer and Burt, David W and Groenen, Martien AM and Delany, Mary E and others; Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 432-7018. 695–716 (2004) Nature Publishing Group

Gibbs, Richard A and Weinstock, George M and Metzker, Michael L and Muzny, Donna M and Sodergren, Erica J and Scherer, Steven and Scott, Graham and Steffen, David and Worley, Kim C and Burch, Paula E and others; Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428-6982. 493–521 (2004) Nature Publishing Group

Bejerano, Gill and Pheasant, Michael and Makunin, Igor and Stephen, Stuart and Kent, W James and Mattick, John S and Haussler, David; Ultraconserved elements in the human genome. Science. 304-5675. 1321–1325 (2004) American Association for the Advancement of Science

Karolchik, Donna and Hinrichs, Angela S and Furey, Terrence S and Roskin, Krishna M and Sugnet, Charles W and Haussler, David and Kent, W James; The UCSC Table Browser data retrieval tool. Nucleic acids research. 32-suppl\_1. D493–D496 (2004) Oxford University Press

Blanchette, Mathieu and Kent, W James and Riemer, Cathy and Elnitski, Laura and Smit, Arian FA and Roskin, Krishna M and Baertsch, Robert and Rosenbloom, Kate and Clawson, Hiram and Green, Eric D and others; Aligning multiple genomic sequences with the threaded blockset aligner. Genome research. 14-4. 708–715 (2004) Cold Spring Harbor Lab

Gerhard, Daniela S and Wagner, Lukas and Feingold, Elise A and Shenmen, Carolyn M and Grouse, Lynette H and Schuler, Greg and Klein, Steven L and Old, Susan and Rasooly, Rebekah and Good, Peter and others; The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).. Genome research. 14-10B. 2121–2127 (2004) Cold Spring Harbor Laboratory Press

Jensen-Seaman, Michael I and Furey, Terrence S and Payseur, Bret A and Lu, Yontao and Roskin, Krishna M and Chen, Chin-Fu and Thomas, Michael A and Haussler, David and Jacob, Howard J; Comparative recombination rates in the rat, mouse, and human genomes. Genome research. 14-4. 528–538 (2004) Cold Spring Harbor Lab

Siepel, Adam and Haussler, David; Combining phylogenetic and hidden Markov models in biosequence analysis. Journal of Computational Biology. 11-2-3. 413–428 (2004) Mary Ann Liebert, Inc.

Siepel, Adam and Haussler, David; Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Molecular biology and evolution. 21-3. 468–488 (2004) Oxford University Press

Bailey, Jeffrey A and Baertsch, Robert and Kent, W James and Haussler, David and Eichler, Evan E; Hotspots of mammalian chromosomal evolution. Genome biology. 5-4. R23 (2004) BioMed Central

Sugnet, Charles W and Kent, W James and Ares, Manuel and Haussler, David; Transcriptome and genome conservation of alternative splicing events in humans and mice.. 9. 66–77 (2004)

Blanchette, Mathieu and Green, Eric D and Miller, Webb and Haussler, David; Reconstructing large regions of an ancestral mammalian genome in silico. Genome research. 14-12. 2412–2423 (2004) Cold Spring Harbor Lab

Bejerano, Gill and Haussler, David and Blanchette, Mathieu; Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics. 20-suppl\_1. i40–i48 (2004) Oxford University Press

Yang, Shan and Smit, Arian F and Schwartz, Scott and Chiaromonte, Francesca and Roskin, Krishna M and Haussler, David and Miller, Webb and Hardison, Ross C; Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. Genome research. 14-4. 517–527 (2004) Cold Spring Harbor Lab

Robertson, Michael P and Igel, Haller and Baertsch, Robert and Haussler, David and Ares Jr, Manuel and Scott, William G; The structure of a rigorously conserved RNA element within the SARS virus genome. PLoS biology. 3-1. e5 (2004) Public Library of Science

Jojic, Vladimir and Jojic, Nebojsa and Meek, Chris and Geiger, Dan and Siepel, Adam and Haussler, David and Heckerman, David; Efficient approximations for learning phylogenetic HMM models from data. Bioinformatics. 20-suppl\_1. i161–i168 (2004) Oxford University Press

Furey, Terrence S and Diekhans, Mark and Lu, Yontao and Graves, Tina A and Oddy, Lachlan and Randall-Maher, Jennifer and Hillier, LaDeana W and Wilson, Richard K and Haussler, David; Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing. Genome research. 14-10b. 2034–2040 (2004) Cold Spring Harbor Lab

Roskin, Krishna M and Diekhans, Mark and Haussler, David; Score functions for determining regional conservation in two-species local alignments. Journal of Computational Biology. 11-2-3. 395–411 (2004) Mary Ann Liebert, Inc.

Br{\”a}ndlein, Stephanie and Pohle, Tina and Vollmers, Christopher and Wozniak, Ewa and Ruoff, Nele and M{\”u}ller-Hermelink, Hans Konrad and Vollmers, H Peter; CFR-1 receptor as target for tumor-specific apoptosis induced by the natural human monoclonal antibody PAM-1. Oncology reports. 11-4. 777–784 (2004) Spandidos Publications

Casper, Jonathan; Explaining adult tennis participants’ participation frequency and purchase intention with the sport commitment model.. (2004)

Casper, Jonathan and Finley, Peter S and others; Teams web sites as aids in the recruiting process: NCAA Tennis coaches attitudes toward their use.. The Sport Journal. 7-1. (2004) United States Sports Academy

Reardon, Jenny; Decoding race and human difference in a genomic age. Differences: A journal of feminist cultural studies. 15-3. 38–65 (2004) Duke University Press

Kay, Kathleen M and Schemske, Douglas W; Geographic patterns in plant-pollinator mutualistic networks: comment. Ecology. 875–878 (2004) JSTOR

Karolchik, Donna and Baertsch, Robert and Diekhans, Mark and Furey, Terrence S and Hinrichs, Angie and Lu, YT and Roskin, Krishna M and Schwartz, Matthias and Sugnet, Charles W and Thomas, Daryl J and others; The UCSC genome browser database. Nucleic acids research. 31-1. 51–54 (2003) Oxford University Press

Schwartz, Scott and Kent, W James and Smit, Arian and Zhang, Zheng and Baertsch, Robert and Hardison, Ross C and Haussler, David and Miller, Webb; Human–mouse alignments with BLASTZ. Genome research. 13-1. 103–107 (2003) Cold Spring Harbor Lab

Kent, W James and Baertsch, Robert and Hinrichs, Angie and Miller, Webb and Haussler, David; Evolution’s cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proceedings of the National Academy of Sciences. 100-20. 11484–11489 (2003) National Acad Sciences

Margulies, Elliott H and Blanchette, Mathieu and Haussler, David and Green, Eric D and NISC Comparative Sequencing Program and others; Identification and characterization of multi-species conserved sequences. Genome research. 13-12. 2507–2518 (2003) Cold Spring Harbor Lab

Hardison, Ross C and Roskin, Krishna M and Yang, Shan and Diekhans, Mark and Kent, W James and Weber, Ryan and Elnitski, Laura and Li, Jia and O’Connor, Michael and Kolbe, Diana and others; Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome research. 13-1. 13–26 (2003) Cold Spring Harbor Lab

Wang, Hui and Hubbell, Earl and Hu, Jing-shan and Mei, Gangwu and Cline, Melissa and Lu, Gang and Clark, Tyson and Siani-Rose, Michael A and Ares, Manuel and Kulp, David C and others; Gene structure-based splice variant deconvolution using a microarry platform. Bioinformatics. 19-suppl\_1. i315–i322 (2003) Oxford University Press

Winters-Hilt, Stephen and Vercoutere, Wenonah and DeGuzman, Veronica S and Deamer, David and Akeson, Mark and Haussler, David; Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules. Biophysical Journal. 84-2. 967–976 (2003) Elsevier

Furey, Terrence S and Haussler, David; Integration of the cytogenetic map with the draft human genome sequence. Human Molecular Genetics. 12-9. 1037–1044 (2003) Oxford University Press

Owen, Art B and Stuart, Josh and Mach, Kathy and Villeneuve, Anne and Kim, Stuart; A Gene Recommender for C. elegans. (2003)

Picone, Joseph and Johnson, Wesley and Dyess, Matthew and Stuart, Josh and Trobough, Chris and Parker, Brock and Tate, Kevin and Riddell, Shaw and Anderson, Matthew; KARMA: A Mobile Acquisition Unit. (2003)

Karplus, Kevin and Karchin, Rachel and Draper, Jenny and Casper, Jonathan and Mandel-Gutfreund, Yael and Diekhans, Mark and Hughey, Richard; Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins: Structure, Function, and Bioinformatics. 53-S6. 491–496 (2003) Wiley Online Library

Diekhans, Mark and Grate, Leslie and Barrett, Christian and Brown, Michael and Casper, Jonathan and Cline, Melissa and Figel, Terry and Karchin, Rachel and Sj{\”o}lander, Kimmen and Tarnas, Christopher; Sequence Alignment and Modeling Software System. (2003)

Kay, Kathleen M and Schemske, Douglas W; Pollinator assemblages and visitation rates for 11 species of Neotropical Costus (Costaceae). Biotropica. 35-2. 198–207 (2003) BioOne

Beauregard, Mary A and Deck, Dinah S and Kay, Kathleen Coughlin and Haynes, Jodi and Inman, Ruth and Perry, Martha and Richardson, Sharon and Rose, Beverly A and Silver, Kimberly N and White, Cathy and others; Improving our image a nurse at a time. Journal of nursing administration. 33-10. 510–511 (2003) LWW

Kent, W James and Sugnet, Charles W and Furey, Terrence S and Roskin, Krishna M and Pringle, Tom H and Zahler, Alan M and Haussler, David; The human genome browser at UCSC. Genome research. 12-6. 996–1006 (2002) Cold Spring Harbor Lab

Karchin, Rachel and Karplus, Kevin and Haussler, David; Classifying G-protein coupled receptors with support vector machines. Bioinformatics. 18-1. 147–159 (2002) Oxford University Press

Asif T, Chinwalla and Lisa L, Cook and Kimberly D, Delehaunty and Ginger A, Fewell and Lucinda A, Fulton and Robert S, Fulton and Tina A, Graves and LaDeana W, Hillier and Elaine R, Mardis and Tracie L, Miner and others; Initial sequencing and comparative analysis of the mouse genome. Nature. 420-6915. (2002) Joint Genome Institute (JGI)

Cline, Melissa S and Karplus, Kevin and Lathrop, Richard H and Smith, Temple F and Rogers, Robert G and Haussler, David; Information-theoretic dissection of pairwise contact potentials. Proteins: Structure, Function, and Bioinformatics. 49-1. 7–14 (2002) Wiley Online Library

McPherson, John D and Marra, Marco and Hillier, LaDeana and Waterston, Robert H and Chinwalla, Asif and Wallis, John and Sekhon, Mandeep and Wylie, Kristine and Mardis, Elaine R and Wilson, Richard K and others; A physical map of the human genome. Nature. 409-6822. 934–941 (2001) Nature Publishing Group

Vercoutere, Wenonah and Winters-Hilt, Stephen and Olsen, Hugh and Deamer, David and Haussler, David and Akeson, Mark; Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nature biotechnology. 19-3. 248 (2001) Nature Publishing Group

Kent, W James and Haussler, David; Assembly of the working draft of the human genome with GigAssembler. Genome Research. 11-9. 1541–1548 (2001) Cold Spring Harbor Lab

Marra, Marco and Hillier, LaDeana and Waterston, Robert H and Chinwalla, Asif and Wallis, John and Sekhon, Mandeep and Wylie, Kristine and Mardis, Elaine R and Wilson, Richard K and Fulton, Robert and others; A physical map of the human genome. Nature. 409. 934–941 (2001)

Karplus, Kevin and Karchin, Rachel and Barrett, Christian and Tu, Spencer and Cline, Melissa and Diekhans, Mark and Grate, Leslie and Casper, Jonathan and Hughey, Richard; What is the value added by human intervention in protein structure prediction?. Proteins: Structure, Function, and Bioinformatics. 45-S5. 86–91 (2001) Wiley Online Library

Reardon, Jenny; The human genome diversity project: a case study in coproduction. Social studies of science. 31-3. 357–388 (2001) Sage Publications London

Brown, Michael PS and Grundy, William Noble and Lin, David and Cristianini, Nello and Sugnet, Charles Walsh and Furey, Terrence S and Ares, Manuel and Haussler, David; Knowledge-based analysis of microarray gene expression data by using support vector machines. Proceedings of the National Academy of Sciences. 97-1. 262–267 (2000) National Acad Sciences

Furey, Terrence S and Cristianini, Nello and Duffy, Nigel and Bednarski, David W and Schummer, Michel and Haussler, David; Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics. 16-10. 906–914 (2000) Oxford University Press

Jaakkola, Tommi and Diekhans, Mark and Haussler, David; A discriminative framework for detecting remote protein homologies. Journal of computational biology. 7-1-2. 95–114 (2000) Mary Ann Liebert, Inc.

Reese, Martin G and Kulp, David and Tammana, Hari and Haussler, David; Genie—gene finding in Drosophila melanogaster. Genome Research. 10-4. 529–538 (2000) Cold Spring Harbor Lab

Grate, Leslie and Diekhans, Mark and Dahle, David and Hughey, Richard; Sequence analysis with the Kestrel SIMD parallel processor. 2001. 263–274 (2000)

Mandelberg, Joshua H and Kuhn, Robert E and Kohn, Michael A; Epidemiologic analysis of an urban, public emergency department’s frequent users. Academic emergency medicine. 7-6. 637–646 (2000) Wiley Online Library

Jaakkola, Tommi and Haussler, David; Exploiting generative models in discriminative classifiers. 487–493 (1999)

Jaakkola, Tommi S and Diekhans, Mark and Haussler, David; Using the Fisher kernel method to detect remote protein homologies.. 99. 149–158 (1999)

Jaakkola, Tommi S and Haussler, David; Probabilistic kernel regression models.. (1999)

SPINGOLA, MARC and GRATE, LESLIE and HAUSSLER, DAVID and ARES, MANUEL; Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. Rna. 5-2. 221–234 (1999) Cambridge University Press

Brown, Michael PS and Grundy, William Noble and Lin, David and Cristianini, Nello and Sugnet, Charles and Ares, Manuel and Haussler, David; Support vector machine classification of microarray gene expression data. University of California, Santa Cruz, Technical Report UCSC-CRL-99-09. (1999)

Opper, Manfred and Haussler, David; Worst case prediction over sequences under log loss. 81–90 (1999) Springer

Haussler, David; Technical Report UCSC-CRL-99-10. Computer Science Department, UC Santa Cruz. (1999)

Karplus, Kevin and Barrett, Christian and Cline, Melissa and Diekhans, Mark and Grate, Leslie and Hughey, Richard; Predicting protein structure using only sequence information. Proteins: Structure, Function, and Bioinformatics. 37-S3. 121–125 (1999) Wiley Online Library

Kuhn, D Robert and Shibley, Nofa J and Austin, William M and Yochum, Terry R; Radiographic evaluation of weight-bearing orthotics and their effect on flexible pes planus. Journal of manipulative and physiological therapeutics. 22-4. 221–226 (1999) Elsevier

Roskin, Krish M and Casper, Jonathan B; From chaos to cryptography. Disposn{\’\i}vel em:< http://www. gaianxaos. com/pdf/unsorted/chaos\_and\_cryptography. pdf>. Acesso em. 10. (1999)

Park, Jong and Karplus, Kevin and Barrett, Christian and Hughey, Richard and Haussler, David and Hubbard, Tim and Chothia, Cyrus; Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. Journal of molecular biology. 284-4. 1201–1210 (1998) Elsevier

Haussler, David and Kivinen, Jyrki and Warmuth, Manfred K; Sequential prediction of individual sequences under general loss functions. IEEE Transactions on Information Theory. 44-5. 1906–1925 (1998) IEEE

Haussler, David; Computational genefinding. Trends in biotechnology. 16. 12–15 (1998) Elsevier

Casper, Jonathan D; Remembering Herbert Jacob. Law \& Soc. Inquiry. 23. 745 (1998) HeinOnline

CASPER, JONATHAN D; Crossing Boundaries in Sociolegal Research. Crossing boundaries: traditions and transformations in law and society research. 4. 81 (1998) Northwestern University Press

Abram, Karen and Gilsinan, James and Applebaum, Paul S and Golding, Jonathan M and Bagby, Michael and Golding, Stephen L and Bersoff, Donald N and Goldner, Jesse and Borgida, Eugene and Goodman, Gail S and others; Reviewers for Volume 22. Law and Human Behavior. 22-6. (1998) Springer

Treseder, Kathleen Kay; Plant-soil interactions across a fertility gradient in Hawaii: nutrient acquisition strategies and effects of genetic variation on ecosystem function. (1998) Stanford University

Reese, Martin G and Eeckman, Frank H and Kulp, David and Haussler, David; Improved splice site detection in Genie. Journal of computational biology. 4-3. 311–323 (1997)

Cesa-Bianchi, Nicolo and Freund, Yoav and Haussler, David and Helmbold, David P and Schapire, Robert E and Warmuth, Manfred K; How to use expert advice. Journal of the ACM (JACM). 44-3. 427–485 (1997) ACM

Alon, Noga and Ben-David, Shai and Cesa-Bianchi, Nicolo and Haussler, David; Scale-sensitive dimensions, uniform convergence, and learnability. Journal of the ACM (JACM). 44-4. 615–631 (1997) ACM

Karplus, Kevin and Sj{\”o}lander, Kimmen and Barrett, Christian and Cline, Melissa and Haussler, David and Hughey, Richard and Holm, Liisa and Sander, Chris; Predicting protein structure using hidden Markov models. Proteins Structure Function and Genetics. 29-s 1. 134–139 (1997)

Haussler, David and Opper, Manfred and others; Mutual information, metric entropy and cumulative relative entropy risk. The Annals of Statistics. 25-6. 2451–2492 (1997) Institute of Mathematical Statistics

Haussler, David; A general minimax result for relative entropy. IEEE Transactions on Information Theory. 43-4. 1276–1280 (1997) IEEE

Kulp, David and Haussler, David and Reese, Martin G and Eeckman, Frank H; Integrating database homology in a probabilistic gene structure model. 2. 232–244 (1997)

Harrison, Mark and Brighton, Allan and Clarke, De and Crowley, Charles and Diekhans, Mark and Greenberg, Saul and Hill, D Richard and Howlett, George A and Lam, Ioi and Libes, Don and others; Tcl/Tk Tools. (1997) O’Reilly \& Associates, Inc.

Casper, Jonathan D; Herbert Jacob. PS: Political Science \& Politics. 30-1. 88–89 (1997) Cambridge University Press

Haussler, David Kulp David and Eeckman, Martin G Reese Frank H; A generalized hidden Markov model for the recognition of human genes in DNA. 134–142 (1996)

Sj{\”o}lander, Kimmen and Karplus, Kevin and Brown, Michael and Hughey, Richard and Krogh, Anders and Mian, I Saira and Haussler, David; Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Bioinformatics. 12-4. 327–345 (1996) Oxford University Press

Fayyad, Usama and Haussler, David and Stolorz, Paul; Mining scientific data. Communications of the ACM. 39-11. 51–57 (1996) ACM

Haussler, David and Kearns, Michael and Seung, H Sebastian and Tishby, Naftali; Rigorous learning curve bounds from statistical mechanics. Machine Learning. 25-2-3. 195–236 (1996) Springer

Fayyad, Usama M and Haussler, David and Stolorz, Paul E; KDD for Science Data Analysis: Issues and Examples.. 50–56 (1996)

Haussler, David; Probably Approximately Correct learning and decision-theoretic generalizations. Mathematical perspectives on neural networks. Hillsdale, NJ: Lawrence Erlbaum Publishers. (1996)

Wagner, Doris and Fairchild, Craig D and Kuhn, Robert M and Quail, Peter H; Chromophore-bearing NH2-terminal domains of phytochromes A and B determine their photosensory specificity and differential light lability. Proceedings of the National Academy of Sciences. 93-9. 4011–4015 (1996) National Acad Sciences

Diamond, Shari Seidman and Casper, Jonathan D and Heiert, Cami L and Marshall, Anna-Maria; Juror reactions to attorneys at trial. The Journal of Criminal Law and Criminology (1973-). 87-1. 17–47 (1996) JSTOR

Haussler, David; Sphere packing numbers for subsets of the Boolean n-cube with bounded Vapnik-Chervonenkis dimension. Journal of Combinatorial Theory, Series A. 69-2. 217–232 (1995) Elsevier

Bendavid, Shai and Cesabianchi, Nicolo and Haussler, David and Long, Philip M; Characterizations of Learnability for Classes of $\{$0,…, n)-Valued Functions. Journal of Computer and System Sciences. 50-1. 74–86 (1995) Elsevier

Haussler, David and Long, Philip M; A generalization of Sauer’s lemma. Journal of Combinatorial Theory, Series A. 71-2. 219–240 (1995) Elsevier

Opper, Manfred and Haussler, David; Bounds for predictive errors in the statistical mechanics of supervised learning. Physical Review Letters. 75-20. 3772 (1995) APS

Goldstein, Susan T and Watkins, G Todd and Kuhn, Robert M; Microhabitats of salt marsh foraminifera: St. Catherines island, Georgia, USA. Marine Micropaleontology. 26-1-4. 17–29 (1995) Elsevier

Baume, Peter and Kay, Kathleen; Working solution: Report of the strategic review of the Commonwealth Disability Services Program. (1995) Australian Government Pub. Service

Krogh, Anders and Mian, I Saira and Haussler, David; A hidden Markov model that finds genes in E. coli DNA. Nucleic Acids Research. 22-22. 4768–4778 (1994) Oxford University Press

Sakakibara, Yasubumi and Brown, Michael and Hughey, Richard and Mian, I Saira and Sj{\”o}lander, Kimmen and Underwood, Rebecca C and Haussler, David; Stochastic context-free grammers for tRNA modeling. Nucleic acids research. 22-23. 5112–5120 (1994) Oxford University Press

Haussler, David and Kearns, Michael and Schapire, Robert E; Bounds on the sample complexity of Bayesian learning using information theory and the VC dimension. Machine learning. 14-1. 83–113 (1994) Springer

Haussler, David and Littlestone, Nick and Warmuth, Manfred K; Predicting $\{$0, 1$\}$-functions on randomly drawn points. Information and Computation. 115-2. 248–292 (1994) Elsevier

Grate, Leslie and Herbster, Mark and Hughey, Richard and Haussler, David and Mian, I Saira and Noller, Harry; RNA modeling using Gibbs sampling and stochastic context free grammars.. 2. 138–146 (1994)

Stormo, Gary D and Haussler, David; Optimally parsing a sequence into different classes based on multiple types of evidence.. 2. 369–375 (1994)

Diamond, Shari Seidman and Casper, Jonathan D; Empirical evidence and the death penalty: Past and future. Journal of Social Issues. 50-2. 177–197 (1994) Wiley Online Library

Adams, Kenneth and Adler, Jeffrey and Ageton, Suzanne and Agnew, Robert and Akers, Ronald and Albonetti, Celesta and Allen, Harry and Alpert, Geoffrey and Anderson, Patrick and Andrews, Don and others; Justice quarterly 1994 reviewers. Justice Quarterly. 11-4. (1994) Taylor \& Francis

Abel, Richard and Albonetti, Celesta and Alfieri, Anthony and Alschuler, Albert and Aleson, James and Banks, Taunya L and Barak, Gregg and Barkai, John and Barreto, Emilcar and Baumgartner, Mary P and others; the Trustees, and the Editorial Advisory Board, as well as the following individuals who reviewed manuscripts for Volume 28.. Law \& Society Review. 28-5. (1994) HeinOnline

Brown, Michael and Hughey, Richard and Krogh, Anders and Mian, I Saira and Sj{\”o}lander, Kimmen and Haussler, David; Using Dirichlet mixture priors to derive hidden Markov models for protein families.. 1. 47–55 (1993)

Haussler, David and Warmuth, Manfred; The probably approximately correct (PAC) and other learning models. KLUWER INTERNATIONAL SERIES IN ENGINEERING AND COMPUTER SCIENCE. 291–291 (1993) Springer

Casper, Jonathan D and Benedict, Kennette M; The influence of outcome information and attitudes on juror decision making in search and seizure cases. Inside the juror. 65–83 (1993) Cambridge University Press Cambridge,, UK

Casper, Jonathan D; Restructuring the traditional civil jury: The effects of changes in composition and procedures. Verdict: Assessing the civil jury system. 414–459 (1993)

Casper, Jonathan D and Diamond, Shari Seidman; Estimating damages and predicting violence: The influence of experts in the courtroom. (1993)

Ambuel, Bruce and Casper, Jonathan and Clark, Charles and Dvoskin, Joel and Ewing, Charles P and Faigman, David and FoUingstad, Diane and Fulero, Solomon and Greer, Alexander and Griffin, Patty and others; Reviewers for volume 17. Law and Human Behavior. 17-6. (1993) Springer

O’Neil, Kathleen Kay; An evaluation of student retention efforts at a small college. NASPA Journal. 31-1. 36–40 (1993) Routledge

Haussler, David; Decision theoretic generalizations of the PAC model for neural net and other learning applications. Information and computation. 100-1. 78–150 (1992) Elsevier

Freund, Yoav and Haussler, David; Unsupervised learning of distributions on binary vectors using two layer networks. 912–919 (1992)

Haussler, David and Barron, Andrew; How well do Bayes methods work for on-line prediction of f+ 1; 1g values. (1992)

Haussler, David and Kearns, Michael and Opper, Manfred and Schapire, Robert; Estimating average-case learning curves using Bayesian, statistical physics and VC dimension methods. 855–862 (1992)

Diamond, Shari and Casper, Jonathan; Blindfolding the Jury to Verdict Consequences, 26L. \& Soc’y Rev. 513. 553 (1992)

Abel, Richard and Adler, Patricia and Albonetti, Celesta and Atleson, James B and Banks, Taunya L and Barkai, John and Barnett, Laurence and Baum, Lawrence and Baumgartner, Mary P and Beattie, John and others; 0 1993 by The Law and Society Association. All rights reserved.. Law \& Society Review. 27-4. (1992) HeinOnline

Burstein, James Acker Paul and Buzawa, Patricia Adler Eva and Cahn, Celesta Albonetti Naomi and Caiger, Francis Allen Andrew and Call, Albert Alschuler Jack and Canan, Anthony Amsterdam Penelope and Cannell, Andrew Arno Fenella and Carp, Burton Atkins Robert and Carroll, James Atleson John and Carson, Dianne Avery William and others; The Law \& Society Review would like to thank the Officers, Trustees, and Editorial Board, as well as the following individu-als who reviewed manuscripts for Volume 26.. Law \& Society Review. 26-4. (1992) JSTOR

Schutte, Kathleen Kay; Personality and social support: A proposed causal model.. (1992)

Haussler, David and Kearns, Michael and Littlestone, Nick and Warmuth, Manfred K; Equivalence of models for polynomial learnability. Information and Computation. 95-2. 129–161 (1991) Elsevier

Opper, Manfred and Haussler, David; Generalization performance of Bayes optimal classification algorithm for learning a perceptron. Physical Review Letters. 66-20. 2677 (1991) APS

Opper, Manfred and Haussler, David; Calculation of the learning curve of Bayes optimal classification algorithm for learning a perceptron with noise. 5-07. 75–87 (1991)

Sabatino, Frank and Masoro, Edward J and McMahan, C Alex and Kuhn, Robert W; Assessment of the role of the glucocorticoid system in aging processes and in the action of food restriction. Journal of gerontology. 46-5. B171–B179 (1991) The Gerontological Society of America

Mann, Jonathan M and Kay, Kathleen; Confronting the pandemic: the world health organization’s global programme on AIDS, 1986–1989. Aids. 5-2. 221–229 (1991) LWW

Bagallo, Giulia and Haussler, David; Boolean feature discovery in empirical learning. Machine learning. 5-1. 71–99 (1990) Springer

Haussler, David; Probably approximately correct learning. (1990) University of California, Santa Cruz, Computer Research Laboratory

Haussler, David; Applying valiant’s learning framework to Al concept-learning problems. (1990) Morgan Kaufmann Publishers Inc.

Haussler, David and Long, Philip M; A generalization of Sauer’s lemma. (1990) University of California, Santa Cruz, Computer Research Laboratory

Haussler, David; Decision theoretic generalizations of the PAC learning model. (1990) University of California, Santa Cruz, Computer Research Laboratory

Mann, Jonathan and Dam, Marjorie and Kay, Kathleen; Global Coordination of National Public Health Strategies. The Journal of Law, Medicine \& Ethics. 18-1-2. 20–28 (1990) Wiley Online Library

Stromer, Kathleen Kay; GAO report: A long way from equality (promotion for men and women in the US military). Armed Forces Journal International. 127-8. 56 (1990)

Marcus, Ruthanne and Kay, Kathleen and Mann, Jonathan M; Transmisi{\’o}n del virus de la inmunodeficiencia humana (VIH) en establecimientos de atenci{\’o}n de salud de todo el mundo. (1990)

Baum, Eric B and Haussler, David; What size net gives valid generalization?. 81–90 (1989)

Blumer, Anselm and Ehrenfeucht, Andrzej and Haussler, David and Warmuth, Manfred K; Learnability and the Vapnik-Chervonenkis dimension. Journal of the ACM (JACM). 36-4. 929–965 (1989) ACM

Ehrenfeucht, Andrzej and Haussler, David and Kearns, Michael and Valiant, Leslie; A general lower bound on the number of examples needed for learning. Information and Computation. 82-3. 247–261 (1989) Elsevier

Haussler, David; Learning conjunctive concepts in structural domains. Machine learning. 4-1. 7–40 (1989) Springer

Ehrenfeucht, Andrzej and Haussler, David; Learning decision trees from random examples. Information and Computation. 82-3. 231–246 (1989) Elsevier

Blumer, Anselm and Ehrenfeucht, Andrzej and Haussler, David; Average sizes of suffix trees and dawgs. Discrete Applied Mathematics. 24-1-3. 37–45 (1989) Elsevier

Haussler, David; Generalizing the PAC model for neural net and other learning applications. (1989) University of California, Santa Cruz, Computer Research Laboratory

Pagallo, Giulia and Haussler, David; A Greedy Method for Learning [mu] DNF Functions Under the Uniform Distribution. (1989) University of California, Santa Cruz, Computer Research Laboratory

DALLMAN, MARY F and LEVIN, NANCY and CASCIO, CAREN S and AKANA, SUSAN F and JACOBSON, LAUREN and KUHN, ROBERT W; Pharmacological evidence that the inhibition of diurnal adrenocorticotropin secretion by corticosteroids is mediated via type I corticosterone-preferring receptors. Endocrinology. 124-6. 2844–2850 (1989) The Endocrine Society

Tyler, Tom R and Casper, Jonathan D and Fisher, Bonnie; Maintaining allegiance toward political authorities: The role of prior attitudes and the use of fair procedures. American Journal of Political Science. 629–652 (1989) JSTOR

Casper, Jonathan D and Benedict, Kennette and Perry, Jo L; Juror Decision Making, Attitudes, and the Hindsight Bias, 13 LAW \& HUM. BEHAV. 291. 300 (1989)

Diamond, Shari Seidman and Casper, Jonathan D and Ostergren, Lynne; Blindfolding the jury. Law and Contemporary Problems. 52-4. 247–267 (1989) JSTOR

Casper, Jonathan D; Public Opinion and the Supreme Court: Introductory Remarks. Nw. UL Rev.. 84. 983 (1989) HeinOnline

Casper, Jonathan D and Tyler, Tom R and Fisher, Bonnie; Maintaining allegiance toward political authorities. American Journal of Political Science. 33. 629–625 (1989)

Marcus, Ruthanne and Kay, Kathleen and Mann, Jonathan M; Transmission of human immunodeficiency virus (HIV) in health-care settings worldwide.. Bulletin of the World Health Organization. 67-5. 577 (1989) World Health Organization

O’neil, Kathleen Kay and Gajdostik, Karen Lee; The head nurse’s managerial role.. Nursing management. 20-6. 39–41 (1989) LWW

Kay, Kathleen; AIDS—a global concern. Midwifery. 5-2. 84–95 (1989) Elsevier

Haussler, David; Quantifying inductive bias: AI learning algorithms and Valiant’s learning framework. Artificial intelligence. 36-2. 177–221 (1988) Elsevier

Ehrenfeucht, Andrzej and Haussler, David; A new distance metric on strings computable in linear time. Discrete Applied Mathematics. 20-3. 191–203 (1988) Elsevier

Haussler, David; Space efficient learning algorithms. (1988) University of California, Santa Cruz, Computer Research Laboratory

Pagallo, Giulia M and Haussler, David; Feature discovery in empirical learning. 88-8. (1988) Computer Research Laboratory,[University of California, Santa Cruz

Solish, Sharyn B and Picado-Leonard, James and Morel, Yves and Kuhn, Robert W and Mohandas, TK and Hanukoglu, Israel and Miller, Walter L; Human adrenodoxin reductase: two mRNAs encoded by a single gene on chromosome 17cen—-q25 are expressed in steroidogenic tissues. Proceedings of the National Academy of Sciences. 85-19. 7104–7108 (1988) National Acad Sciences

Casper, Jonathan D and Tyler, Tom and Fisher, Bonnie; Procedural justice in felony cases. Law and Society Review. 483–507 (1988) JSTOR

Casper, Jonathan D and Benedict, Kennette and Kelly, Janice R; Cognitions, Attitudes and Decision-Making in Search and Seizure Cases. Journal of Applied Social Psychology. 18-2. 93–113 (1988) Wiley Online Library

Casper, Jonathan D and Benedict, Kennette and Perry, Jo L; The tort remedy in search and seizure cases: a case study in juror decision making. Law \& Social Inquiry. 13-2. 279–303 (1988) Wiley Online Library

Tyler, Tom R and Casper, Jonathan D and Fisher, Bonnie; Maintaining allegiance toward legal authorities: The role of prior attitudes and the use of fair procedures. (1988) American Bar Foundation

Benedict, Kennette and Casper, Jonathan D and Bright Jr, Joseph C and Kadane, Joseph B; Index to Volume 13. (1988) Wiley Online Library

Kay, Kathleen; The global struggle against AIDS: WHO’s strategy.. International nursing review. 35-2. 35–40 (1988)

Blumer, Anselm and Ehrenfeucht, Andrzej and Haussler, David and Warmuth, Manfred K; Occam’s razor. Information processing letters. 24-6. 377–380 (1987) Elsevier

Haussler, David and Welzl, Emo; ɛ-nets and simplex range queries. Discrete \& Computational Geometry. 2-2. 127–151 (1987) Springer

Blumer, Anselm and Blumer, Janet and Haussler, David and McConnell, Ross and Ehrenfeucht, Andrzej; Complete inverted files for efficient text retrieval and analysis. Journal of the ACM (JACM). 34-3. 578–595 (1987) ACM

Haussler, David; Bias, version spaces and valiant’s learning framework. 324–336 (1987)

Haussler, David and Littlestone, Nick and Warmuth, MK; Expected mistake bounds for on-line learning algorithms. Unpublished manuscript. (1987)

Ehrenfeucht, Andrzej and Haemer, Jeffrey and Haussler, David; Quasi-monotonic sequences: theory, algorithms and applications. SIAM Journal on Algebraic Discrete Methods. 8-3. 410–429 (1987) SIAM

O’Neil, Kathleen Kay and Gajdostik, Karen Lee; Nurse perceptions of problems in meeting the health needs of youth. Journal of School Health. 57-6. 244–245 (1987) Wiley Online Library

Clift, B and Haussler, David and McConnell, R\_ and Schneider, Thomas D and Stormo, Gary D; Sequence landscapes. Nucleic Acids Research. 14-1. 141–158 (1986) Oxford University Press

Haussler, David; Quantifying the inductive bias in concept learning. 485–489 (1986)

Edelsbrunner, Herbert and Haussler, David; The complexity of cells in three-dimensional arrangements. Discrete mathematics. 60. 139–146 (1986) Elsevier

Blumer, Anselm and Blumer, Janet and Haussler, David and Ehrenfeucht, Andrzej and Chen, Mu-Tian and Seiferas, Joel; The smallest automation recognizing the subwords of a text. Theoretical computer science. 40. 31–55 (1985) Elsevier

Bucher, Walter and Ehrenfeucht, Andrzej and Haussler, David; On total regulators generated by derivation relations. Theoretical Computer Science. 40. 131–148 (1985) Elsevier

Haussler, David; Another generalization of Higman’s well quasi order result on $\Sigma$∗. Discrete Mathematics. 57-3. 237–243 (1985) Elsevier

Kay, Kathleen; History of Poetsch and Peterson Tannery. On file, History Room, South San Francisco Library, South San Francisco. (1985)

Warmuth, Manfred K and Haussler, David; On the complexity of iterated shuffle. Journal of Computer and System Sciences. 28-3. 345–358 (1984) Elsevier

Blumer, Anselm and Blumer, J and Ehrenfeucht, Andrzej and Haussler, David and McConnell, R; Building the minimal DFA for the set of all subwords of a word on-line in linear time. Automata, Languages and Programming. 109–118 (1984) Springer

Casper, Jonathan D and Brereton, David; Evaluating criminal justice reforms. Law \& Soc’y Rev.. 18. 121 (1984) HeinOnline

Casper, Jonathan D; Determinate sentencing and prison crowding in Illinois. U. Ill. L. Rev.. 231 (1984) HeinOnline

Thompson, James R and Blumstein, Alfred and Casper, Jonathan D and Cohen, Jacqueline and Gottfredson, Michael R and Gottfredson, Don M and Harland, Alan T and Harris, Philip W; Peter F. Nardulli \& Rod Smolla.. U. Ill. L. Rev.. 1984. 203–421 (1984)

Brereton, David and Casper, Jonathan; Evaluating Criminal Justice Reforms,”. Law and Society Review (. 18. 1984 (1984)

Kay, Kathleen; Alimony Pendente Life and Earning Capacity. La. L. Rev.. 45. 79 (1984) HeinOnline

Ehrenfeucht, Andrzej and Haussler, David and Rozenberg, Grzegorz; On regularity of context-free languages. Theoretical Computer Science. 27-3. 311–332 (1983) Elsevier

Blumer, Anselm and Blumer, Janet and Ehrenfeucht, Andrzej and Haussler, David and McConnell, Ross M.; Linear size finite automata for the set of all subwords of a word – an outline of results. Bulletin of the EATCS. 21. 12–20 (1983)

Haussler, David; Insertion languages. Information Sciences. 31-1. 77–89 (1983) Elsevier

Casper, Jonathan D and Brereton, David and Neal, David; The California Determinate Sentence Law. Criminal Law Bulletin. 19-5. 405–433 (1983)

Casper, Jonathan D; The Impact of Criminal Justice Innovation: Feeley on Court Reform. Law \& Social Inquiry. 8-4. 959–965 (1983) Wiley Online Library

Haussler, David Henry; Insertion and iterated insertion as operations on formal languages. (1982) University of Colorado at Boulder

Ehrenfeucht, Andrzej and Haussler, David and Rozenberg, Grzegorz; Conditions enforcing regularity of context-free languages. Automata, Languages and Programming. 187–191 (1982) Springer

Siiteri, Pentti K and Murai, James T and Hammond, GL and Nisker, Jeffrey A and Raymoure, WJ and Kuhn, Robert W; The serum transport of steroid hormones. Recent progress in hormone research. 38. 457–510 (1982)

Gajski, Daniel D and Padua, David A. and Kuck, David J. and Kuhn, Robert H.; Second opinion on data flow machines and languages. Computer;(United States). 2. (1982) Univ. of Illinois, Chicago

Casper, Jonathan D and Brereton, David and Neal, David J; The implementation of the California determinate sentencing law. 1. (1982) US Dept. of Justice, National Institute of Justice, Office of Research Programs

Brereton, David and Casper, Jonathan D; Does it pay to plead guilty? Differential sentencing and the functioning of criminal courts. Law and Society Review. 45–70 (1981) JSTOR

Casper, Jonathan D and Brereton, David and Neal, David J; The Implementation of the California Determinate Sentence Law. (1981) Department of Political Science, Stanford University

Casper, Jonathan D; The public defender: man in the middle. Courts. Law. And Judicial Processes, ed. S. Ulmer. 87–94 (1981)

Kay, Nelson Kathleen; Iris check list of registered cultivar names, 1970-1979.. (1981)

Haussler, David and Zeiger, H Paul; Very special languages and representations of recursively enumerable languages via computation histories. Information and Control. 47-3. 201–212 (1980) Elsevier

Kuck, David J and Kuhn, Robert H and Leasure, Bruce and Wolfe, Michael; The structure of an advanced vectorizer for pipelined processors. 207–218 (1980)

Kuhn, Robert Henry; Optimization and interconnection complexity for: parallel processors, single-stage networks, and decision trees. (1980) University of Illinois at Urbana-Champaign

Dy, AJ and Kay, Kathleen E; The marketing of mental health services. The Journal of Behavioral Health Services and Research. 7-1. 21–24 (1980) Springer

Scholl, Kathleen Kay Boop; INTERFAMILY ECONOMIC TRANSFERS.. (1980)

Casper, Jonathan D; Reformers v. Abolitionists: Some Notes for Further Research on Plea Bargaining. Law \& Society Review. 13-2. 567–572 (1979) JSTOR

Casper, Jonathan D; Having their day in court: Defendant evaluations of the fairness of their treatment. Law and Society Review. 237–251 (1978) JSTOR

Casper, Jonathan D; Criminal courts: The defendant’s perspective. (1978) National Institute of Law Enforcement and Criminal Justice, Law Enforcement Assistance Administration, US Dept. of Justice: for sale by the Supt. of Docs., US Govt. Print. Off.

Casper, Jonathan D; The Supreme Court and national policy making. The American Political Science Review. 70-1. 50–63 (1976) JSTOR

Casper, Jonathan; Men in Prison. Psyccritiques. 21-4. 303–304 (1976)

Brumbaugh, Peter F and Haussler, David H and Bressler, Rubin and Haussler, Mark R; Radioreceptor assay for 1$\alpha$, 25-dihydroxyvitamin D 3. Science. 183-4129. 1089–1091 (1974) American Association for the Advancement of Science

Brumbaugh, Peter F and Haussler, David H and Bursac, Kristine M and Haussler, Mark R; Filter assay for 1$\alpha$, 25-dihydroxyvitamin D3. Utilization of the hormone’s target tissue chromatin receptor. Biochemistry. 13-20. 4091–4097 (1974) ACS Publications

Zerwekh, Joseph E and Brumbaugh, Peter F and Haussler, David H and Cork, Douglas J and Haussler, Mark R; 1$\alpha$-Hydroxyvitamin D3. Analog of vitamin D which apparently acts by metabolism to 1$\alpha$, 25-dihydroxyvitamin D3. Biochemistry. 13-20. 4097–4102 (1974) ACS Publications

Ryan, Clarence A and Hass, G Michael and Kuhn, Robert W; Purification and properties of a carboxypeptidase inhibitor from potatoes. Journal of Biological Chemistry. 249-17. 5495–5499 (1974) ASBMB

Kuhn, Robert W and Walsh, Kenneth A and Neurath, Hans; Isolation and partial characterization of an acid carboxypeptidase from yeast. Biochemistry. 13-19. 3871–3877 (1974) ACS Publications

Hermodson, Mark A and Kuhn, Robert W and Walsh, Kenneth A and Neurath, Hans and Eriksen, Nils and Benditt, Earl P; Amino acid sequence of monkey amyloid protein A. Biochemistry. 11-16. 2934–2938 (1972) ACS Publications

Casper, Jonathan; American Criminal Justice (Englewood Cliffs, NJ: Pren-tice-Hall). (1972)

Casper, Jonathan D; Lawyers before the Warren Court: Civil liberties and civil rights, 1957-66. (1972) Urbana: University of Illinois Press

Casper, Jonathan D; The politics of civil liberties. (1972) HarperCollins Publishers

Casper, Jonathan D; Criminal Justice–the Consumer’s Perspective. 72-9. (1972) US National Institute of Law Enforcement and Criminal Justice

Mautz, Robert Kuhn and Neumann, Frederick L; Corporate audit committees. -94. (1970) Bureau of Economic and Business Research, University of Illinois

Casper, Jonathan D; Did You Have a Lawyer When You Went to Court-No, I Had a Public Defender. Yale Rev. L. \& Soc. Action. 1. 4 (1970) HeinOnline

Casper, Jonathan D; LAWYERS IN DEFENSE OF LIBERTY: LAWYERS BEFORE THE SUPREME COURT IN CIVIL LIBERTIES AND CIVIL RIGHTS CASES, 1957-1966.. (1970)

Casper, Jonathan D; With All Deliberate Speed. Ed. by McCordJohn H..(Urbana: University of Illinois Press, 1969. Pp. 205. $7.50.). American Political Science Review. 64-3. 943–944 (1970) Cambridge University Press

Casper, Jonathan D; Lawyers and Loyalty-Security Litigation. Law and Society Review. 575–596 (1969) JSTOR

YEGGE, ROBERT B and SCHWARTZ, RICHARD D and LEFSTEIN, NORMAN and STAPIETON, VAUGHAN and TEITELBAUM, LEE and COHEN, MICHAEL and CASPER, JONATHAN D and SCHWITZGEBEL, RALPH K and BECK, BERNARD and ZEISEL, HANS and others; LAW S SOCIETY Review. (1969) HeinOnline

Kuhn, Robert J; Control of anterior vertical dimension and proper selection of extraoral anchorage. The Angle Orthodontist. 38-4. 340–349 (1968)

Mautz, Robert Kuhn; Financial reporting by diversified companies. (1968) Financial Executives Research Foundation

Routtenberg, Aryeh and Kay, Kathleen E; Effect of one electroconvulsive seizure on rat behavior.. Journal of comparative and physiological psychology. 59-2. 285 (1965) American Psychological Association

Kuhn, Robert A and Kugler, Hermann; False aneurysms of the middle meningeal artery. Journal of neurosurgery. 21-2. 92–96 (1964) Journal of Neurosurgery Publishing Group

Holme, Molly and Casper, Jonathan D; NASA historical report. First six years of NASA: A concise chronology. (1964)

Mautz, Robert Kuhn and Sharaf, Hussein Amer; The philosophy of auditing. -6. (1961) American Accounting Association

Kuhn, Robert A; Organization of tactile dermatomes in cat and monkey. Journal of neurophysiology. 16-2. 169–182 (1953) Am Physiological Soc

Kuhn, Robert A; FUNCTITONAL CAPACITY OF THE ISOLATED HUMAN SPINAL CORD. Brain. 73-1. 1–51 (1950) Oxford University Press

Johnson, Wesley and Dyess, Matthew and Stuart, Josh and Trobough, Chris and Parker, Brock and Tate, Kevin and Riddell, Shaw and Anderson, Matthew; Professor Joseph Picone E-mail: picone@ isip. msstate. edu ECE 4542: Senior Design II Department of Electrical and Computer Engineering Mississippi State University.

Stuart, Josh and Koller, Daphne and Friedman, Nir; Graphical Models for Joint Learning, Part II..

Craft, Brian and Swatloski, Teresa and Goldman, Mary and Ellrott, Kyle and Ma, Singer and Wilks, Chris and Stuart, Josh and Haussler, David and Zhu, Jingchun; The New UCSC Cancer Genomics Browser.

Jaakkola, Tommi and Diekhans, Mark and Haussler, David; A discriminative framework for detecting remote protein homologies, 1998. Unpublished, available from http://www. cse. ucsc. edu/research/compbio/research. html.

Diekhans, Mark and Lehenbauer, Karl; TclX-Extended Tcl.

ROSKIN, KRISHNA M and DIEKHANS, MARK and KENT, W JAMES and HAUSSLER, DAVID; SCORE FUNCTIONS FOR ASSESSING CONSERVATION IN LOCALLY ALIGNED REGIONS OF DNA FROM TWO SPECIES UCSC TECH REPORT UCSC-CRL-02-30.

Nguyen, Ngan and Diekhans, Mark; Genome 10K Data Submission Guidelines.

Hsu, Fan and Pringle, Tom H and Kuhn, Robert M and Karolchik, Donna and Diekhans, Mark and Haussler, David and Kent, W James; Nucleic acids research Volume: 33 ISSN: 1362-4962 ISO Abbreviation: Nucleic Acids Res. Publication Date: 2005 Jan. Detail:.

Ableson, A and Akmaev, Viatcheslav R and Anantharaman, Thomas and Andersen, Claus A and Andrade, Miguel A and Ankerst, Mihael and Benson, Gary and Blackwell, Thomas W and Blaschke, Christian and Brass, Andy and others; From: ISMB-99 Proceedings. Copyright{\copyright} 1999, AAAI (www. aaai. org). All rights reserved..

Ezkurdia, Iakes and Juan, David and Rodriguez, Jose Manuel and Frankish, Adam and Diekhans, Mark and Harrow, Jennifer and Vazquez, Jesus and Valencia, Alfonso and Tress, Michael L; 1. The potential non-coding set, expanded version, page 3. 2. Detecting expression of proteins in the non-coding set from other sources, page 6. 3. Coding genes not in GENCODE 19, page 8. 4. Supplementary figures, page 9..

Rosenbloom, Kate and Dreszer, Timothy and Malladi, Venkat and Long, Jeffrey and Sloan, Cricket and Raney, Brian and Cline, Melissa and Karolchik, Donna and Barber, Galt and Clawson, Hiram and others; ENCODE Project at UCSC.

Casper, Jonathan; D.(1972) American Criminal Justice: The Defendant’s Perspective. Englewood Cliffs, NJ: Prentice-Hall

Casper, Jonathan and Tyler, Tom and Fisher, Bonnie; Procedural Justice in Felony Cases'(1988). Law and Society Review. 22. 483–483

Diamond, Shari Seidman and Casper, Jonathan D; Blindfolding the Jury to Verdict Consequences: Damages, Experts and the Civil Jury’(1992). Law \& Society Review. 26. 513

Casper, Jonathan D and Sentencing, Determinate; Prison Crowding in Illinois, 1984 U. L Rev. 111. 231–236

Casper, Jonathan D; Tom R. Tyler, \& Bonnie Fisher (1988)” Procedural Justice in Felony Cases,” 22 Law \&. Society Rev. 483. 507

Casper, Jonathan D; Tom R. Tyler, and Bonnie Fisher. 1988. Procedural Justice in Felony Cases. Law and Society Review. 22-3. 483–507

Casper, Jonathan D; Having their Day in Court: Defendant Evaluation of the Fairness of their Treatment”(1978). Law and Soc’y Rev.. 12. 237

Casper, Jonathan D; Kennette Benedict \&Jo L. Perry, Juror Decision Making, Attitudes, and the Hindsight Bias. 13. 294–96

Casper, Jonathan D and Benedict, Kennette and Perry, Jo L; Juror Decision Making, Attitudes and Hindsight Bias,(1989). Law and Human Behavior. 13. 291

Casper, Jonathan D and Benedict, Kennette and Perry, Jo L; Juror Decision Making. Attitudes, and the Hindsight Bias (American Bar Foundation Working Paper 8702)(” Casper, Benedict, \& Perry”).

Casper, Jonathan; D.(1976)” The Supreme Court and National Policymaking,” 70. American Political Science Rev. 50. 66

Casper, Jonathan; David Brereton and David Neal. The Implementation of the California DeterminateSentencing Law (Washington, DC: US Department of Justice, 1982).

AARONSON, David E and ALEXANDER, Sue C and BARONTI, Giancarlo and PITCH, Tamar and BAYER, Ronald and Decriminalization, Heroin and BOLAND, Barbara and BREDA, Jef and VAN HOUTTE, Jean and CASPER, Jonathan D and others; ” Race as a Determinant of Criminal Sentences: A Methodologi-cal Critique and a Case Study,” Gibson, 455.” Rationalist and Normative Approaches to the Sociological Study of Law”(review essay on Donald Black, The Behav-ior of Law, and Roberto Mangabeira Unger, Law in Mod. HeinOnline