Publications

Researchers associated with the UC Santa Cruz Genomics Institute write publications in genomics, bioinformatics, and a variety of other related fields.

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Complete Bibliography

2019 | 2018 | 2017 | 2016 | 2015 | 2014 |2013 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 2004 | 2003 2002 | 2001 2000 | 1999 19981997 1996 1995 1994 1993 1992 1991 1990 1989 | Other

2019

Wolfgang Beyer, Adam M Novak, Glenn Hickey, Jeffrey Chan, Vanessa Tan, Benedict Paten, Daniel R Zerbino. Sequence tube maps: making graph genomes intuitive to commuters. Bioinformatics, 01 August 2019.

Chiara Barbieri, Rodrigo Barquera, Leonardo Arias, José R Sandoval, Oscar Acosta, Camilo Zurita, Abraham Aguilar-Campos, Ana M Tito-Álvarez, Ricardo Serrano-Osuna, Russell Gray, Fabrizio Mafessoni, Paul Heggarty, Kentaro K Shimizu, Ricardo Fujita, Mark Stoneking, Irina Pugach, Lars Fehren-Schmitz, The current genomic landscape of western South America: Andes, Amazonia and Pacific Coast, Molecular Biology and Evolution (2019). DOI: 10.1093/molbev/msz174

Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E. Olsen, Colleen Bosworth, Joel Armstrong, Kristof Tigyi, Nicholas Maurer, Sergey Koren, Fritz J. Sedlazeck, Tobias Marschall, Simon Mayes, Vania Costa, Justin M. Zook, Kelvin J. Liu, Duncan Kilburn, Melanie Sorensen, Katy M. Munson, Mitchell R. Vollger, Evan E. Eichler, Sofie Salama, David Haussler, Richard E. Green, Mark Akeson, Adam Phillippy, Karen H. Miga, Paolo Carnevali, Miten Jain, Benedict Paten. Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit. bioRxiv preprint, July 26, 2019. 715722; doi: 10.1101/715722

Anthony D. Long, James Baldwin-Brown, Yuan Tao, Vanessa J. Cook, Gabriela Balderrama-Gutierrez, Russell Corbett-Detig, Ali Mortazavi, Alan G. Barbour. The genome of Peromyscus leucopus, natural host for Lyme disease and other emerging infections. 24 July 2019.

Schirmer L, Velmeshev D, Holmqvist S, Kaufmann M, Werneburg S, Jung D, Vistnes S, Stockley JH, Young A, Steindel M, Tung B, Goyal N, Bhaduri A, Mayer S, Engler, JB, Bayraktar, OA, Franklin Robin JM, Haeussler M, et al. Neuronal vulnerability and multilineage diversity in multiple sclerosis. Nature. 17 July 2019.

Learned K, Durbin A, Currie R, Kephart E, Beale H, Sanders L, Pfeil J, Goldstein T, Salama S, Haussler D, Morozova Vaske O, Bjork I. Barriers to accessing public cancer genomic data. Scientific Data. 20 June 2019.

Sanders L, Cheney A, Beale H, Kephart E, Bjork I, Pfeil J, Salama S, Haussler D, Morozova O. Shared dysregulation of long non-coding RNA and developmental gene networks in histone H3 K27M gliomas and PF-A ependymomas. Journal of Clinical Oncology 2019 37:15_suppl, e21523-e21523

Smith AM, Jain M, Mulroney L, Garalde DR, Akeson M. Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing. PLoS One. 2019 May 16;14(5) 

Velmeshev D, Schirmer L, Jung D, Haeussler M, Perez Y, Mayer S, Bhaduri A, Goyal N, Rowitch DH, Kriegstein AR. Single-cell genomics identifies cell type-specific molecular changes in autism. Science. 2019 May 17;364(6441):685-689. 

Aggarwal R, Huang J, Alumkal J, Feng FY, Zhang L, Stuart JM, Small EJ. Transformation of Prostate Adenocarcinoma Into Small-Cell Neuroendocrine Cancer Under Androgen Deprivation Therapy: Much Is Achieved But More Information Is Needed Reply. DOI: 10.1200/JCO.18.01487 Journal of Clinical Oncology 37, no. 4 (February 1 2019) 351-352., PMID: 30557523

Armstrong JFiddes ITDiekhans MPaten B. Whole-Genome Alignment and Comparative Annotation. Annual Review of Animal Biosciences. 2019 Feb. doi: 10.1146/annurev-animal-020518-115005.

Bernardi G, Crane N. Benthic coverage data collected from 2012 to 2014 in the Federated States of Micronesia and the Caroline Islands (Disturb Impacts Coral project). 2019 Apr 4. doi: 10.1575/1912/bco-dmo.684031.1, https://hdl.handle.net/1912/23958.

Bernardi G, Crane N. Fish count data from the Caroline Islands and the Federal States of Micronesia collected from 2012-2014. 2019 Apr 4. doi: 10.1575/1912/bco-dmo.684177.1.

Bittman D, Alvaro P, Long D, Miller EL.Optimizing systems for byte-addressable NVM by reducing bit flipping. In Proceedings of the 17th USENIX Conference on File and Storage Technologies (FAST’19). USENIX Association, Berkeley, CA, USA, 17-30.

Byrne ASupple MAVolden RLaidre KLShapiro BVollmers C. Depletion of hemoglobin transcripts and long read sequencing improves the transcriptome annotation of the polar bear (Ursus maritimus). bioRxiv. 2019 Jan 27. doi: 10.1101/527978.

Corbett‐Detig R, Medina P, Frérot H, Blassiau C, Castric V. Bulk pollen sequencing reveals rapid evolution of segregation distortion in the male germline of Arabidopsis hybrids. Evolution Letters, 3: 93-103. 2019 Jan 30. doi: 10.1002/evl3.96.

Ding H, Blair A, Stuart J. Cross-Species Alignment of Single Cell States with Biological Process Activity. bioRxiv. 2019 Feb 19; doi: https://doi.org/10.1101/555268.

Field AR, Jacobs FMJ, Fiddes IT, Phillips APR, Reyes-Ortiz AM, LaMontagne E, Whitehead L, Meng V, Rosenkrantz JL, Olsen M, Hauessler M, Katzman S, Salama SR, Haussler D. Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes. Stem Cell Reports. 2019 Feb 12;12(2):245-257. doi: 10.1016/j.stemcr.2018.12.006. Epub 2019 Jan 10.

Fiume M, Cupak M, Keenan S, Rambla J, de la Torre S, Dyke SOM, Brookes AJ, Carey K, Lloyd D, Goodhand P, Haeussler M, Baudis M, Stockinger H, Dolman L, Lappalainen I, Törnroos J, Linden M, Spalding JD, Ur-Rehman S, Page A, Flicek P, Sherry S, et al. Federated discovery and sharing of genomic data using Beacons. Nat Biotechnol. 2019 Mar;37(3):220-224. doi: 10.1038/s41587-019-0046-x.

Fregel R, Ordóñez AC, Santana-Cabrera J, et al. Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary IslandsPLoS One. 2019;14(3):e0209125. Published 2019 Mar 20. doi:10.1371/journal.pone.0209125

Fulton TL, Shapiro B. Setting Up an Ancient DNA Laboratory. Springer. 2019 Mar 16. doi: 10.1007/978-1-4939-9176-1_1.

Galvén-Peña S, Carroll RG, Newman C, Hinchy EC, Palsson-McDermott E, Robinson EK, Covarrubias S, Nadin A, James AM, Haneklaus M, Carpenter S, Kelly VP, Murphy MP, Modis LK, O’Neill LA. Malonylation of GAPDH is an inflammatory signal in macrophages. Nat Commun. 2019 Jan 18;10(1):338. doi: 10.1038/s41467-018-08187-6.

Goldman MCraft BHastie MRepečka KKamath AMcDade FRogers DBrooks ANZhu JHaussler D. The UCSC Xena platform for public and private cancer genomics data visualization and interpretation. bioRxiv. 2019 Mar 5. doi: https://doi.org/10.1101/326470.

Graim K, Friedl V, Houlahan KE, Stuart JM. PLATYPUS: A Multiple-View Learning Predictive Framework for Cancer Drug Sensitivity PredictionPac Symp Biocomput. 2019;24:136–147.

Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, Gibson D, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2019 update. Nucleic Acids Res. 2019 Jan 8;47(D1):D853-D858. doi: 10.1093/nar/gky1095.

Horns F, Vollmers C, Dekker CL, Quake SR. Signatures of selection in the human antibody repertoire: Selective sweeps, competing subclones, and neutral drift. Proc Natl Acad Sci U S A. 2019 Jan 22;116(4):1261-1266. doi: 10.1073/pnas.1814213116. Epub 2019 Jan 8.

Hu D, Feng D, Xie Y, Xu G, Gu X, Long D. Efficient Provenance Management via Clustering and Hybrid Storage in Big Data EnvironmentsIEEE Transactions on Big Datadoi: 10.1109/TBDATA.2019.2907116.

Jung E, Ly V, Buderi A, Appleton E, Teodorescu M. Design and Selection of Muscle Excitation Patterns for Modeling a Lower Extremity Joint Inspired Tensegrity.  IEEE International Conference on Robotic Computing (IRC). 2019 Feb. doi: 10.1109/IRC.2019.00053.

Mesa KA, Yu B, Wrin T, Petropoulos CJ, Pogson GH, Alexander DL, Perez G, O’Rourke SM, Sinangil F, Robinson J, Conant MA, Berman PW.
Ancestral sequences from an elite neutralizer proximal to the development of neutralization resistance as a potential source of HIV vaccine immunogens. PLoS One. 2019 Apr 10;14(4):e0213409. doi: 10.1371/journal.pone.0213409. eCollection 2019.

Meyer RCurd EESchweizer TGold ZRamos DRShirazi SKandlikar GKwan WLin MFriese AMoberg-Parker JRamos MMShapiro BSexton JPipes LVedrenne AGMejia MP, Aronson EMoore TNielsen RLewin H, Barber PWall JKraft NWayne R. The California Environmental DNA “CALeDNA” Program. bioRxiv. 2019 Jan 4. doi: 10.1101/503383.

New B, Spradley M, Fehren-Schmitz L. A Forensic Anthropological Perspective on Latin American Genetic Diversity. 2019 Mar. doi: 10.13140/RG.2.2.24217.47207.

Nichols RV, Curd E, Heintzman PD, Shapiro B. Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA. Methods Mol Biol. 2019;1963:149-161. doi: 10.1007/978-1-4939-9176-1_16.

Nickols NG, Nazarian R, Zhao SG, Tan V, Uzunangelov V, Xia Z, Baertsch R, Neeman E, Gao AC, Thomas GV, Howard L, De Hoedt AM, Stuart J, Goldstein T, Chi K, Gleave ME, Graff JN, Beer TM, Drake JM, Evans CP, Aggarwal R, Foye A, et al. MEK-ERK signaling is a therapeutic target in metastatic castration resistant prostate cancer. Prostate Cancer Prostatic Dis. 2019 Feb 25. doi: 10.1038/s41391-019-0134-5. [Epub ahead of print].

O’Rourke SM, Yu B, Morales JF, Didinger CM, Alexander DL, Vollmers C, Berman PW. Production of a recombinant monoclonal antibody to Herpes Simplex Virus glycoprotein D for immunoaffinity purification of tagged proteins. J Immunol Methods. 2019 Feb;465:31-38. doi: 10.1016/j.jim.2018.11.015. Epub 2018 Nov 28.

Pollock DD. Society for Molecular Biology and Evolution, Council and Business Meetings, 2018, Yokohama, JapanMol Biol Evol. 2019;36(1):204–206. doi: 10.1093/molbev/msy240.

Prieto G, Verano JW, Goepfert N, Kennett D, Quilter J, LeBlanc S, Fehren-Schmitz L, Forst J, Lund M, Dement B, Dufour E, Tombret O, Calmon M, Gadison D, Tschinkel K. A mass sacrifice of children and camelids at the Huanchaquito-Las Llamas site, Moche Valley, Peru. PLoS One. 2019 Mar 6;14(3):e0211691. doi: 10.1371/journal.pone.0211691.

Ratjen A, Au J, Carpenter S, John P, Ratjen F. Growth of Pulmonary Arteriovenous Malformations in Pediatric Patients with Hereditary Hemorrhagic Telangiectasia. J Pediatr. 2019 May;208:279-281. doi: 10.1016/j.jpeds.2018.12.069. Epub 2019 Mar 8.

Rosen YM, Paten BJ. An average-case sublinear forward algorithm for the haploid Li and Stephens model. Algorithms Mol Biol. 2019 Apr 2;14:11. doi: 10.1186/s13015-019-0144-9. eCollection 2019.

Sarsani VK, Raghupathy N, Fiddes IT, Armstrong J, Thibaud-Nissen F, Zinder O, Bolisetty M, Howe K, Hinerfeld D, Ruan X, Rowe L, Barter M, Ananda G, Paten B, Weinstock GM, Churchill GA, Wiles MV, Schneider VA, Srivastava A, Reinholdt LG. The Genome of C57BL/6J “Eve”, the Mother of the Laboratory Mouse Genome Reference Strain. G3 (Bethesda). 2019 Apr 17. pii: g3.400071.2019. doi: 10.1534/g3.119.400071. [Epub ahead of print].

Sirén JGarrison ENovak AMPaten BDurbin R. Haplotype-aware graph indexes. bioRxiv. 2019 Feb 24. doi: 10.1101/559583.

Vaske OM, Haussler D. Data sharing for pediatric cancers. Science. 2019 Mar 15;363(6432):1125. doi: 10.1126/science.aax2739. No abstract available.

Yin S, Gambe RG, Sun J, Martinez AZ, Cartun ZJ, Regis FFD, Wan Y, Fan J, Brooks AN, Herman SEM, Ten Hacken E, Taylor-Weiner A, Rassenti LZ, Ghia EM, Kipps TJ, Obeng EA, Cibulskis CL, Neuberg D, Campagna DR, Fleming MD, Ebert BL, Wiestner A, et al. A Murine Model of Chronic Lymphocytic Leukemia Based on B Cell-Restricted Expression of Sf3b1 Mutation and Atm Deletion. Cancer Cell. 2019 Feb 11;35(2):283-296.e5. doi: 10.1016/j.ccell.2018.12.013. Epub 2019 Jan 31.

2018

Aggarwal R, Huang J, Alumkal JJ, Zhang L, Feng FY, Thomas GV, Weinstein AS, Friedl V, Zhang C, Witte ON, Lloyd P, Gleave M, Evans CP, Youngren J, Beer TM, Rettig M, Wong CK, True L, Foye A, Playdle D, Ryan CJ, Lara P, et al.; Clinical and Genomic Characterization of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer: A Multi-institutional Prospective Study. J Clin Oncol. 2018 Aug 20;36(24):2492-2503. doi: 10.1200/JCO.2017.77.6880. Epub 2018 Jul 9. PMID:29985747

Anbar A, Elgin S, Jez J, O’Dowd D, Shapiro B, Zaman M; Improving societies’ harassment policies. Science. 2018 Sep 7;361(6406):984-985. doi: 10.1126/science.aav1362. No abstract available. PMID:30190397

Barlow A, Cahill JA, Hartmann S, Theunert C, Xenikoudakis G, Fortes GG, Paijmans JLA, Rabeder G, Frischauf C, Grandal-d’Anglade A, García-Vázquez A, Murtskhvaladze M, Saarma U, Anijalg P, Skrbinšek T, Bertorelle G, Gasparian B, Bar-Oz G, Pinhasi R, Slatkin M, Dalén L, Shapiro B, et al.; Partial genomic survival of cave bears in living brown bears. Nat Ecol Evol. 2018 Oct;2(10):1563-1570. doi: 10.1038/s41559-018-0654-8. Epub 2018 Aug 27. PMID:30150744

Bulbul G, Chaves G, Olivier J, Ozel RE, Pourmand N; Nanopipettes as Monitoring Probes for the Single Living Cell: State of the Art and Future Directions in Molecular Biology. Cells. 2018 Jun 6;7(6). pii: E55. doi: 10.3390/cells7060055. Review. PMID:29882813 | PMCID:PMC6024992 

Cahill JA, Heintzman PD, Harris K, Teasdale MD, Kapp J, Soares AER, Stirling I, Bradley D, Edwards CJ, Graim K, Kisleika AA, Malev AV, Monaghan N, Green RE, Shapiro B; Genomic Evidence of Widespread Admixture from Polar Bears into Brown Bears during the Last Ice Age. Mol Biol Evol. 2018 May 1;35(5):1120-1129. doi: 10.1093/molbev/msy018. PMID:29471451

Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, et al.; Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Rep. 2018 Apr 3;23(1):194-212.e6. doi: 10.1016/j.celrep.2018.03.063. PMID:29617660 | PMCID:PMC6002769

Cline MS, Liao RG, Parsons MT, Paten B, Alquaddoomi F, Antoniou A, Baxter S, Brody L, Cook-Deegan R, Coffin A, Couch FJ, Craft B, Currie R, Dlott CC, Dolman L, den Dunnen JT, Dyke SOM, Domchek SM, Easton D, Fischmann Z, Foulkes WD, Garber J, et al. BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2. PLoS Genet. 2018 Dec 26;14(12):e1007752. doi: 10.1371/journal.pgen.1007752. eCollection 2018 Dec. PMID:30586411 | PMCID:PMC6324924

Cooper CI, Yao D, Sendorek DH, Yamaguchi TN, P’ng C, Houlahan KE, Caloian C, Fraser M; SMC-DNA Challenge Participants., Ellrott K, Margolin AA, Bristow RG, Stuart JM, Boutros PC; Valection: design optimization for validation and verification studies. BMC Bioinformatics. 2018 Sep 25;19(1):339. doi: 10.1186/s12859-018-2391-z. PMID:30253747

Coulter ME, Dorobantu CM, Lodewijk GA, Delalande F, Cianferani S, Ganesh VS, Smith RS, Lim ET, Xu CS, Pang S, Wong ET, Lidov HGW, Calicchio ML, Yang E, Gonzalez DM, Schlaeger TM, Mochida GH, Hess H, Lee WA, Lehtinen MK, Kirchhausen T, Haussler D, et al.; The ESCRT-III Protein CHMP1A Mediates Secretion of Sonic Hedgehog on a Distinctive Subtype of Extracellular VesiclesCell Rep. 2018 Jul 24;24(4):973-986.e8. doi: 10.1016/j.celrep.2018.06.100. PMID: 30044992

Dang LT, Tondl M, Chiu MHH, Revote J, Paten B, Tano V, Tokolyi A, Besse F, Quaife-Ryan G, Cumming H, Drvodelic MJ, Eichenlaub MP, Hallab JC, Stolper JS, Rossello FJ, Bogoyevitch MA, Jans DA, Nim HT, Porrello ER, Hudson JE, Ramialison M; TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets. BMC Genomics. 2018 Apr 5;19(1):238. doi: 10.1186/s12864-018-4630-0. PMID:29621972 | PMCID:PMC5887194

Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, et al.; Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell. 2018 Apr 5;173(2):305-320.e10. doi: 10.1016/j.cell.2018.03.033. PMID:29625049 | PMCID:PMC5916814

Eerkens JW, Nichols RV, Murray GGR, Perez K, Murga E, Kaijankoski P, Rosenthal JS, Engbring L, Shapiro B; A probable prehistoric case of meningococcal disease from San Francisco Bay: Next generation sequencing of Neisseria meningitidis from dental calculus and osteological evidence. Int J Paleopathol. 2018 Sep;22:173-180. doi: 10.1016/j.ijpp.2018.05.001. Epub 2018 May 25. PMID:29807684

Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B; Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. Genome Res. 2018 Jul;28(7):1029-1038. doi: 10.1101/gr.233460.117. Epub 2018 Jun 8. PMID:29884752 | PMCID:PMC6028123

Fiddes IT, Lodewijk GA, Mooring M, Bosworth CM, Ewing AD, Mantalas GL, Novak AM, van den Bout A, Bishara A, Rosenkrantz JL, Lorig-Roach R, Field AR, Haeussler M, Russo L, Bhaduri A, Nowakowski TJ, Pollen AA, Dougherty ML, Nuttle X, Addor MC, Zwolinski S, Katzman S, et al.; Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis. Cell. 2018 May 31;173(6):1356-1369.e22. doi: 10.1016/j.cell.2018.03.051. Epub 2018 May 31. PMID:29856954 | PMCID:PMC5986104

Fregel R, Méndez FL, Bokbot Y, Martín-Socas D, Camalich-Massieu MD, Santana J, Morales J, Ávila-Arcos MC, Underhill PA, Shapiro B, Wojcik G, Rasmussen M, Soares AER, Kapp J, Sockell A, Rodríguez-Santos FJ, Mikdad A, Trujillo-Mederos A, Bustamante CD; Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe. Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):6774-6779. doi: 10.1073/pnas.1800851115. Epub 2018 Jun 12. Erratum in: Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):E7231. PMID:29895688 | PMCID:PMC6042094

Garrison E, Sirén J, Novak AM, Hickey G, Eizenga JM, Dawson ET, Jones W, Garg S, Markello C, Lin MF, Paten B, Durbin R; Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nat Biotechnol. 2018 Oct;36(9):875-879. doi: 10.1038/nbt.4227. Epub 2018 Aug 20. PMID:30125266 | PMCID:PMC6126949

Haussler D, Smuga-Otto M, Eizenga JM, Paten B, Novak AM, Nikitin S, Zueva M, Miagkov D; A Flow Procedure for Linearization of Genome Sequence Graphs. J Comput Biol. 2018 Jul;25(7):664-676. doi: 10.1089/cmb.2017.0248. Epub 2018 May 24. PMID:29792514 | PMCID:PMC6067104

Hoadley, Katherine A.Caesar-Johnson, Samantha J; Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of CancerCell. (5 April 2018)

Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, Shen R, Taylor AM, Cherniack AD, Thorsson V, Akbani R, Bowlby R, Wong CK, Wiznerowicz M, Sanchez-Vega F, Robertson AG, Schneider BG, Lawrence MS, Noushmehr H, Malta TM; Cancer Genome Atlas Network., Stuart JM, et al.; Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell. 2018 Apr 5;173(2):291-304.e6. doi: 10.1016/j.cell.2018.03.022. PMID:29625048 | PMCID:PMC5957518

Jain, Miten and Koren, Sergey and Miga, Karen H and Quick, Josh and Rand, Arthur C and Sasani, Thomas A and Tyson, John R and Beggs, Andrew D and Dilthey, Alexander T and Fiddes, Ian T and others; Nanopore sequencing and assembly of a human genome with ultra-long readsNature Biotechnology. (2018) Nature Publishing Group

Jain, Miten and Olsen, Hugh E and Turner, Daniel J and Stoddart, David and Bulazel, Kira V and Paten, Benedict and Haussler, David and Willard, Huntington F and Akeson, Mark and Miga, Karen H; Linear Assembly of a Human Y CentromerebioRxiv.170373 (2018) Cold Spring Harbor Laboratory

Jain M, Olsen HE, Turner DJ, Stoddart D, Bulazel KV, Paten B, Haussler D, Willard HF, Akeson M, Miga KH. Linear assembly of a human centromere on the Y chromosome. Nat Biotechnol. 2018 Apr;36(4):321-323. doi: 10.1038/nbt.4109. Epub 2018 Mar 19.PMID:29553574 | PMCID:PMC5886786

Khan SY, Ali M, Kabir F, Chen R, Na CH, Lee MW, Pourmand N, Hackett SF, Riazuddin SA; Identification of novel transcripts and peptides in developing murine lens. Sci Rep. 2018 Jul 24;8(1):11162. doi: 10.1038/s41598-018-28727-w. PMID:30042402 | PMCID:PMC6057992

Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, Hoekzema K, Qiu R, Clark K, Raja A, Welch AE, Sorensen M, Baker C, et al.; High-resolution comparative analysis of great ape genomes. Science. 2018 Jun 8;360(6393). pii: eaar6343. doi: 10.1126/science.aar6343. PMID:29880660

Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN; ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants., Kellen MR, Chen K, Norman TC, Friend SH, Guinney J, Stolovitzky G, Haussler D, Margolin AA, Stuart JM, et al. Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection. Genome Biol. 2018 Nov 6;19(1):188. doi: 10.1186/s13059-018-1539-5.

Lewin HA, Robinson GE, Kress WJ, Baker WJ, Coddington J, Crandall KA, Durbin R, Edwards SV, Forest F, Gilbert MTP, Goldstein MM, Grigoriev IV, Hackett KJ, Haussler D, Jarvis ED, Johnson WE, Patrinos A, Richards S, Castilla-Rubio JC, van Sluys MA, Soltis PS, Xu X, et al.; Earth BioGenome Project: Sequencing life for the future of life. Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4325-4333. doi: 10.1073/pnas.1720115115. PMID:29686065 | PMCID:PMC5924910

Li J, Choi PS, Chaffer CL, Labella K, Hwang JH, Giacomelli AO, Kim JW, Ilic N, Doench JG, Ly SH, Dai C, Hagel K, Hong AL, Gjoerup O, Goel S, Ge JY, Root DE, Zhao JJ, Brooks AN, Weinberg RA, Hahn WC; An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer. Elife. 2018 Jul 30;7. pii: e37184. doi: 10.7554/eLife.37184. PMID:30059005 | PMCID:PMC6103745

Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert J, Goodstadt L, Harrow J, Howe K, Ibarra-Soria X, Kolmogorov M, Lelliott CJ, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S, Navarro FCP, Odom DT, Park N, Pelan S, Pham SK, Quail M, Reinholdt L, Romoth L, Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold G, Thybert D, Torrance J, Wong K, Wood J, Yalcin B, Yang F, Adams DJ, Paten B, Keane TM. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. Nat Genet. 2018 Oct 1.

M. Ryan Corces, Jeffrey M. Granja, Shadi Shams, Bryan H. Louie, Jose A. Seoane, Wanding Zhou, Tiago C. Silva, Clarice Groeneveld, Christopher K. Wong, Seung Woo Cho, Ansuman T. Satpathy, Maxwell R. Mumbach, Katherine A. Hoadley, A. Gordon Robertson, Nathan C. Sheffield, Ina Felau, Mauro A. A. Castro, Benjamin P. Berman, Louis M. Staudt, Jean C. Zenklusen, Peter W. Laird, Christina Curtis, The Cancer Genome Atlas Analysis Network, William J. Greenleaf, Howard Y. Chang. The chromatin accessibility landscape of primary human cancers. SCIENCE 26 OCT 2018

Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kamińska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwińska P, Mazurek S, Mishra L, Heyn H, Krasnitz A, Godwin AK, Lazar AJ; Cancer Genome Atlas Research Network., Stuart JM, Hoadley KA, Laird PW, et al.; Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. Cell. 2018 Apr 5;173(2):338-354.e15. doi: 10.1016/j.cell.2018.03.034. PMID:29625051 | PMCID:PMC5902191

Mann DH, Groves P, Gaglioti BV, Shapiro BA; Climate-driven ecological stability as a globally shared cause of Late Quaternary megafaunal extinctions: the Plaids and Stripes Hypothesis. Biol Rev Camb Philos Soc. 2018 Aug 22. doi: 10.1111/brv.12456. [Epub ahead of print] PMID:30136433

Nichols RV, Vollmers C, Newsom LA, Wang Y, Heintzman PD, Leighton M, Green RE, Shapiro B; Minimizing polymerase biases in metabarcoding. Mol Ecol Resour. 2018 May 24. doi: 10.1111/1755-0998.12895. [Epub ahead of print] PMID:29797549

Ozel RE, Bulbul G, Perez J, Pourmand N; Functionalized Quartz Nanopipette for Intracellular Superoxide Sensing: A Tool for Monitoring Reactive Oxygen Species Levels in Single Living Cell. ACS Sens. 2018 Jul 27;3(7):1316-1321. doi: 10.1021/acssensors.8b00185. Epub 2018 Jun 25. PMID:29893547

Paten B, Eizenga JM, Rosen YM, Novak AM, Garrison E, Hickey G; Superbubbles, Ultrabubbles, and Cacti. J Comput Biol. 2018 Jul;25(7):649-663. doi: 10.1089/cmb.2017.0251. Epub 2018 Feb 20. PMID:29461862 | PMCID:PMC6067107

Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, Cieslik MP, Parolia A, Beer TM, Thomas G, Chi KN, Gleave M, Lack NA, et al.; Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer. Cell. 2018 Jul 26;174(3):758-769.e9. doi: 10.1016/j.cell.2018.06.039. Epub 2018 Jul 19. PMID:30033370

Sasha A. LangleyKaren MigaGary H. KarpenCharles H. Langley; Diverse haplotypes span human centromeres and include archaic lineages within and out of Africa. bioRxiv (2018)

Sendorek DH, Caloian C, Ellrott K, Bare JC, Yamaguchi TN, Ewing AD, Houlahan KE, Norman TC, Margolin AA, Stuart JM, Boutros PC; Germline contamination and leakage in whole genome somatic single nucleotide variant detection. BMC Bioinformatics. 2018 Jan 31;19(1):28. doi: 10.1186/s12859-018-2046-0. PMID:29385983 | PMCID:PMC5793408

Shen H, Shih J, Hollern DP, Wang L, Bowlby R, Tickoo SK, Thorsson V, Mungall AJ, Newton Y, Hegde AM, Armenia J, Sánchez-Vega F, Pluta J, Pyle LC, Mehra R, Reuter VE, Godoy G, Jones J, Shelley CS, Feldman DR, Vidal DO, Lessel D, et al.; Integrated Molecular Characterization of Testicular Germ Cell TumorsCell Rep. 2018 Jun 12;23(11):3392-3406. doi: 10.1016/j.celrep.2018.05.039. PMID:29898407 | PMCID:PMC6075738

Supple MA, Shapiro B; Conservation of biodiversity in the genomics era. Genome Biol. 2018 Sep 11;19(1):131. doi: 10.1186/s13059-018-1520-3. Review. PMID:30205843 | PMCID:PMC6131752

Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, et al.; Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes. Genome Res. 2018 Apr;28(4):448-459. doi: 10.1101/gr.234096.117. Epub 2018 Mar 21. PMID:29563166 | PMCID:PMC5880236

Toor, Jugmohit S and Rao, Arjun A and McShan, Andrew C and Yarmarkovich, Mark and Nerli, Santrupti and Yamaguchi, Karissa and Madejska, Ada A and Nguyen, Son and Tripathi, Sarvind and Maris, John M and others; A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope ConformationsFrontiers in Immunology9. 99 (2018) Frontiers

Toor JS, Rao AA, McShan AC, Yarmarkovich M, Nerli S, Yamaguchi K, Madejska AA, Nguyen S, Tripathi S, Maris JM, Salama SR, Haussler D, Sgourakis NG. A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations. Front Immunol. 2018 Jan 30;9:99. doi: 10.3389/fimmu.2018.00099. eCollection 2018. PMID:29441070 | PMCID:PMC5797543

Tóth EN, Lohith A, Mondal M, Guo J, Fukamizu A, Pourmand N; Single-cell nanobiopsy reveals compartmentalization of mRNAs within neuronal cells. J Biol Chem. 2018 Mar 30;293(13):4940-4951. doi: 10.1074/jbc.M117.800763. Epub 2018 Jan 29. PMID:29378846 | PMCID:PMC5880154

Tunstall T, Kock R, Vahala J, Diekhans M, Fiddes I, Armstrong J, Paten B, Ryder OA, Steiner CC; Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells. Genome Res. 2018 Jun;28(6):780-788. doi: 10.1101/gr.227603.117. Epub 2018 May 24. PMID:29798851 | PMCID:PMC5991516

 

2017

Adema, Coen M and Hillier, LaDeana W and Jones, Catherine S and Loker, Eric S and Knight, Matty and Minx, Patrick and Oliveira, Guilherme and Raghavan, Nithya and Shedlock, Andrew and Do Amaral, Laurence Rodrigues and others; Whole genome analysis of a schistosomiasis-transmitting freshwater snailNature communications8. 15451 (2017) Nature Publishing Group

Benazzo, Andrea and Trucchi, Emiliano and Cahill, James A and Delser, Pierpaolo Maisano and Mona, Stefano and Fumagalli, Matteo and Bunnefeld, Lynsey and Cornetti, Luca and Ghirotto, Silvia and Girardi, Matteo and others; Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglersProceedings of the National Academy of Sciences114-45. E9589–E9597 (2017) National Acad Sciences

Cahill, James A and Heintzman, Peter D and Harris, Kelley and Teasdale, Matthew and Kapp, Joshua and Soares, Andre E Rodrigues and Stirling, Ian and Bradley, Daniel and Edwards, Ceiridwen J and Kisleika, Aliaksandr A and others; Genomic evidence of globally widespread admixture from polar bears into brown bears during the last ice agebioRxiv. 154773 (2017) Cold Spring Harbor Laboratory

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 challengesHuman mutation.(2017) Wiley Online Library

Casper, Jonathan and Zweig, Ann S and Villarreal, Chris and Tyner, Cath and Speir, Matthew L and Rosenbloom, Kate R and Raney, Brian J and Lee, Christopher M and Lee, Brian T and Karolchik, Donna and others; The UCSC Genome Browser database: 2018 updateNucleic acids research46-D1. D762–D769 (2017) Oxford University Press

Chang, Dan and Knapp, Michael and Enk, Jacob and Lippold, Sebastian and Kircher, Martin and Lister, Adrian and MacPhee, Ross DE and Widga, Christopher and Czechowski, Paul and Sommer, Robert and others; The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysisScientific reports7. 44585 (2017) Nature Publishing Group

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 agingProceedings of the National Academy of Sciences114-5. 1105–1110 (2017) National Acad Sciences

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 profilesCell reports18-11. 2780–2794 (2017) Elsevier

Fehren-Schmitz, Lars and Harkins, Kelly M and Llamas, Bastien; A paleogenetic perspective on the early population history of the high altitude AndesQuaternary International. (2017) Elsevier

Fiddes, Ian T and Armstrong, Joel and Diekhans, Mark and Nachtweide, Stefanie and Kronenberg, Zev N and Underwood, Jason G and Gordon, David and Earl, Dent and Keane, Thomas and Eichler, Evan E and others; Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotationbioRxiv. 231118 (2017) Cold Spring Harbor Laboratory

Fiddes, Ian T and Lodewijk, Gerrald A and Mooring, Meghan M and Bosworth, Colleen M and Ewing, Adam D and Mantalas, Gary L and Novak, Adam M and van den Bout, Anouk and Bishara, Alex and Rosenkrantz, Jimi L and others; Human-specific NOTCH-like genes in a region linked to neurodevelopmental disorders affect cortical neurogenesisbioRxiv. 221226 (2017) Cold Spring Harbor Laboratory

Field, Andrew R and Jacobs, Frank MJ and Fiddes, Ian T and Phillips, Alex PR and Reyes-Ortiz, Andrea M and LaMontagne, Erin and Whitehead, Lila and Meng, Vincent and Rosenkrantz, Jimi L and Haeussler, Maximillian and others; Structurally conserved primate lncRNAs are transiently expressed during human cortical differentiation and influence cell type specific genesbioRxiv. 232553 (2017) Cold Spring Harbor Laboratory

Froese, Duane and Stiller, Mathias and Heintzman, Peter D and Reyes, Alberto V and Zazula, Grant D and Soares, Andr{\\’e} ER and Meyer, Matthias and Hall, Elizabeth and Jensen, Britta JL and Arnold, Lee J and others; Fossil and genomic evidence constrains the timing of bison arrival in North AmericaProceedings of the National Academy of Sciences114-13. 3457–3462 (2017) National Acad Sciences

Garrison, Erik and Sir{\\’e}n, Jouni and Novak, Adam M and Hickey, Glenn and Eizenga, Jordan M and Dawson, Eric T and Jones, William and Lin, Michael F and Paten, Benedict and Durbin, Richard; Sequence variation aware genome references and read mapping with the variation graph toolkitbioRxiv. 234856 (2017) Cold Spring Harbor Laboratory

Hamilton, Scott L and Logan, Cheryl A and Fennie, Hamilton W and Sogard, Susan M and Barry, James P and Makukhov, April D and Tobosa, Lauren R and Boyer, Kirsten and Lovera, Christopher F and Bernardi, Giacomo; Species-Specific Responses of Juvenile Rockfish to Elevated pCO2: From Behavior to GenomicsPloS one12-1. e0169670 (2017) Public Library of Science

Hrabeta-Robinson, Eva and Marcus, Erin and Cozen, Aaron E and Phizicky, Eric M and Lowe, Todd M; High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-Seq)RNA Methylation: Methods and Protocols. 231–243 (2017) Springer

Jain, Miten and Koren, Sergey and Quick, Josh and Rand, Arthur C and Sasani, Thomas A and Tyson, John R and Beggs, Andrew D and Dilthey, Alexander T and Fiddes, Ian T and Malla, Sunir and others; Nanopore sequencing and assembly of a human genome with ultra-long readsbioRxiv. 128835 (2017) Cold Spring Harbor Labs Journals

Kuderna, Lukas FK and Tomlinson, Chad and Hillier, LaDeana W and Tran, Annabel and Fiddes, Ian and Armstrong, Joel and Laayouni, Hafid and Gordon, David and Huddleston, John and Perez, Raquel Garcia and others; A 3-way hybrid approach to generate a new high quality chimpanzee reference genome (Pan\\_tro\\_3. 0)GigaScience. (2017)

Lee, Anna Ying-Wah and Ewing, Adam D and Ellrott, Kyle and Hu, Yin and Houlahan, Kathleen E and Bare, J Christopher and Espiritu, Shadrielle Melijah G and Huang, Vincent and Dang, Kristen and Chong, Zechen and others; Combining accurate tumour genome simulation with crowd sourcing to benchmark somatic structural variant detectionbioRxiv. 224733 (2017) Cold Spring Harbor Laboratory

Lincoln, Stephen E and Yang, Shan and Cline, Melissa S and Kobayashi, Yuya and Zhang, Can and Topper, Scott and Haussler, David and Paten, Benedict and Nussbaum, Robert L; Consistency of BRCA1 and BRCA2 variant classifications among clinical diagnostic laboratoriesJCO Precision Oncology1. 1–10 (2017) American Society of Clinical Oncology

Lui, Lauren M and Uzilov, Andrew V and Bernick, David L and Corredor, Andrea and Lowe, Todd M and Dennis, Patrick P; Evolutionary Insights On The Structure And Function Of Archaeal C/D Box sRNAs As Revealed By A Comprehensive Set From Six Pyrobaculum SpeciesbioRxiv. 121921 (2017) Cold Spring Harbor Labs Journals

Lui, Lauren M and Uzilov, Andrew V and Bernick, David L and Corredor, Andrea and Lowe, Todd M and Dennis, Patrick P; Methylation guide RNA evolution in archaea: structure, function, and genomic organization of 110 C/D box sRNA families across six Pyrobaculum speciesbioRxiv. 121921 (2017) Cold Spring Harbor Laboratory

Murray, Gemma GR and Soares, Andr{\\’e} ER and Novak, Ben J and Schaefer, Nathan K and Cahill, James A and Baker, Allan J and Demboski, John R and Doll, Andrew and Da Fonseca, Rute R and Fulton, Tara L and others; Natural selection shaped the rise and fall of passenger pigeon genomic diversitybioRxiv. 154294 (2017) Cold Spring Harbor Laboratory

Novak, Adam M and Garrison, Erik and Paten, Benedict; A graph extension of the positional Burrows–Wheeler transform and its applicationsAlgorithms for Molecular Biology12-1. 18 (2017) BioMed Central

O’Connor, Brian D and Yuen, Denis and Chung, Vincent and Duncan, Andrew G and Liu, Xiang Kun and Patricia, Janice and Paten, Benedict and Stein, Lincoln and Ferretti, Vincent; The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflowsF1000Research6. (2017) Faculty of 1000 Ltd

Paten, Benedict and Novak, Adam M and Eizenga, Jordan M and Garrison, Erik; Genome graphs and the evolution of genome inferenceGenome research27-5. 665–676 (2017) Cold Spring Harbor Lab

Pujar, Shashikant and O’Leary, Nuala A and Farrell, Catherine M and Loveland, Jane E and Mudge, Jonathan M and Wallin, Craig and Gir{\\’o}n, Carlos G and Diekhans, Mark and Barnes, If and Bennett, Ruth and others; Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curationNucleic acids research46-D1. D221–D228 (2017) Oxford University Press

Rand, Arthur C and Jain, Miten and Eizenga, Jordan M and Musselman-Brown, Audrey and Olsen, Hugh E and Akeson, Mark and Paten, Benedict; Mapping DNA methylation with high-throughput nanopore sequencingnature methods14-4. 411–413 (2017) Nature Research

Rand, Arthur C and Jain, Miten and Eizenga, Jordan M and Musselman-Brown, Audrey and Olsen, Hugh E and Akeson, Mark and Paten, Benedict; Mapping DNA methylation with high-throughput nanopore sequencingNature methods14-4. 411 (2017) Nature Publishing Group

Rice, Edward S and Kohno, Satomi and John, John St and Pham, Son and Howard, Jonathan and Lareau, Liana F and O’Connell, Brendan L and Hickey, Glenn and Armstrong, Joel and Deran, Alden and others; Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signalingGenome Research27-5. 686–696 (2017) Cold Spring Harbor Lab

Rosen, Yohei and Eizenga, Jordan and Paten, Benedict; Modelling haplotypes with respect to reference cohort variation graphsBioinformatics33-14. i118–i123 (2017) Oxford University Press

Rosen, Yohei and Eizenga, Jordan and Paten, Benedict; Supplement to “Modelling haplotypes with respect to reference cohort variation graphs”. (2017)

Shapiro, Beth; Pathways to de-extinction: how close can we get to resurrection of an extinct species?Functional Ecology31-5. 996–1002 (2017) Wiley Online Library

Thornlow, Bryan and Hough, Josh and Roger, Jackie and Gong, Henry and Lowe, Todd and Corbett-Detig, Russell; Transfer RNA genes experience exceptionally elevated mutation ratesbioRxiv. 229906 (2017) Cold Spring Harbor Laboratory

Thybert, David and Roller, Ma{\\v{s}}a and Navarro, F{\\’a}bio CP and Fiddes, Ian and Streeter, Ian and Feig, Christine and Martin-Galvez, David and Kolmogorov, Mikhail and Janou{\\v{s}}ek, V{\\’a}clav and Akanni, Wasiu and others; Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomesbioRxiv. 158659 (2017) Cold Spring Harbor Laboratory

Verdugo, Cristina and Kassadjikova, Kalina and Washburn, Eden and Harkins, KM and Fehren-Schmitz, Lars; Ancient DNA Clarifies Osteological Analyses of Commingled Remains from Midnight Terror Cave, BelizeInternational Journal of Osteoarchaeology27-3. 495–499 (2017) Wiley Online Library

Vivian, John and Rao, Arjun Arkal and Nothaft, Frank Austin and Ketchum, Christopher and Armstrong, Joel and Novak, Adam and Pfeil, Jacob and Narkizian, Jake and Deran, Alden D and Musselman-Brown, Audrey and others; Toil enables reproducible, open source, big biomedical data analysesNature biotechnology35-4. 314 (2017) Nature Publishing Group

Vohr, Samuel H and Gordon, Rachel and Eizenga, Jordan M and Erlich, Henry A and Calloway, Cassandra D and Green, Richard E; A phylogenetic approach for haplotype analysis of sequence data from complex mitochondrial mixturesForensic Science International: Genetics30. 93–105 (2017) Elsevier

Vohr, Samuel H and Gordon, Rachel and Eizenga, Jordan M and Erlich, Henry A and Calloway, Cassandra D and Green, Richard E; A phylogenetic approach for haplotype analysis of sequence data from complex mitochondrial mixturesForensic Science International: Genetics. (2017) Elsevier

Wang, Yue and Heintzman, Peter D and Newsom, Lee and Bigelow, Nancy H and Wooller, Matthew J and Shapiro, Beth and Williams, John W; The southern coastal Beringian land bridge: cryptic refugium or pseudorefugium for woody plants during the Last Glacial Maximum?Journal of Biogeography44-7. 1559–1571 (2017) Wiley Online Library

Zazula, Grant D and Hall, Elizabeth and Hare, P Gregory and Thomas, Christian and Mathewes, Rolf and La Farge, Catherine and Martel, Andr{\\’e} L and Heintzman, Peter D and Shapiro, Beth; A middle Holocene steppe bison and paleoenvironments from the Versleuce Meadows, Whitehorse, Yukon, CanadaCanadian Journal of Earth Sciences-999. 1–15 (2017) NRC Research Press

2016

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 gliomaCell164-3. 550–563 (2016) Elsevier

Putnam, Nicholas H and