My Bibliography

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Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, Vollger MR, Monlong J, Garrison E, Eichler EE, Salama S, Haussler D, Green RE, Akeson M, Phillippy A, Miga KH, Carnevali P, Jain M, Paten B. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nat Biotechnol. 2020 Sep;38(9):1044-1053. doi: 10.1038/s41587-020-0503-6. Epub 2020 May 4. PubMed PMID: 32686750; PubMed Central PMCID: PMC7483855.

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Adams M, McBroome J, Maurer N, Pepper-Tunick E, Saremi NF, Green RE, Vollmers C, Corbett-Detig RB. One fly-one genome: chromosome-scale genome assembly of a single outbred Drosophila melanogaster. Nucleic Acids Res. 2020 Jul 27;48(13):e75. doi: 10.1093/nar/gkaa450. PubMed PMID: 32491177; PubMed Central PMCID: PMC7367183.

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Simakov O, Marlétaz F, Yue JX, O'Connell B, Jenkins J, Brandt A, Calef R, Tung CH, Huang TK, Schmutz J, Satoh N, Yu JK, Putnam NH, Green RE, Rokhsar DS. Deeply conserved synteny resolves early events in vertebrate evolution. Nat Ecol Evol. 2020 Jun;4(6):820-830. doi: 10.1038/s41559-020-1156-z. Epub 2020 Apr 20. PubMed PMID: 32313176; PubMed Central PMCID: PMC7269912.

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Harkins KM, Schaefer NK, Troll CJ, Rao V, Kapp J, Naughton C, Shapiro B, Green RE. A novel NGS library preparation method to characterize native termini of fragmented DNA. Nucleic Acids Res. 2020 May 7;48(8):e47. doi: 10.1093/nar/gkaa128. PubMed PMID: 32112100; PubMed Central PMCID: PMC7192605.

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Rice ES, Koren S, Rhie A, Heaton MP, Kalbfleisch TS, Hardy T, Hackett PH, Bickhart DM, Rosen BD, Ley BV, Maurer NW, Green RE, Phillippy AM, Petersen JL, Smith TPL. Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle. Gigascience. 2020 Apr 1;9(4). doi: 10.1093/gigascience/giaa029. PubMed PMID: 32242610; PubMed Central PMCID: PMC7118895.

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Ghosh A, Johnson MG, Osmanski AB, Louha S, Bayona-Vásquez NJ, Glenn TC, Gongora J, Green RE, Isberg S, Stevens RD, Ray DA. A High-Quality Reference Genome Assembly of the Saltwater Crocodile, Crocodylus porosus, Reveals Patterns of Selection in Crocodylidae. Genome Biol Evol. 2020 Jan 1;12(1):3635-3646. doi: 10.1093/gbe/evz269. PubMed PMID: 31821505; PubMed Central PMCID: PMC6946029.

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Troll CJ, Kapp J, Rao V, Harkins KM, Cole C, Naughton C, Morgan JM, Shapiro B, Green RE. A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos. BMC Genomics. 2019 Dec 27;20(1):1023. doi: 10.1186/s12864-019-6355-0. PubMed PMID: 31881841; PubMed Central PMCID: PMC6935139.

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Saremi NF, Supple MA, Byrne A, Cahill JA, Coutinho LL, Dalén L, Figueiró HV, Johnson WE, Milne HJ, O'Brien SJ, O'Connell B, Onorato DP, Riley SPD, Sikich JA, Stahler DR, Villela PMS, Vollmers C, Wayne RK, Eizirik E, Corbett-Detig RB, Green RE, Wilmers CC, Shapiro B. Puma genomes from North and South America provide insights into the genomic consequences of inbreeding. Nat Commun. 2019 Oct 18;10(1):4769. doi: 10.1038/s41467-019-12741-1. PubMed PMID: 31628318; PubMed Central PMCID: PMC6800433.

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Kalbfleisch TS, Rice ES, DePriest MS Jr, Walenz BP, Hestand MS, Vermeesch JR, O'Connell BL, Fiddes IT, Vershinina AO, Saremi NF, Petersen JL, Finno CJ, Bellone RR, McCue ME, Brooks SA, Bailey E, Orlando L, Green RE, Miller DC, Antczak DF, MacLeod JN. Erratum: Author Correction: Improved reference genome for the domestic horse increases assembly contiguity and composition. Commun Biol. 2019;2:342. doi: 10.1038/s42003-019-0591-3. eCollection 2019. PubMed PMID: 31531403; PubMed Central PMCID: PMC6739301.

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Troll CJ, Putnam NH, Hartley PD, Rice B, Blanchette M, Siddiqui S, Ganbat JO, Powers MP, Ramakrishnan R, Kunder CA, Bustamante CD, Zehnder JL, Green RE, Costa HA. Structural Variation Detection by Proximity Ligation from Formalin-Fixed, Paraffin-Embedded Tumor Tissue. J Mol Diagn. 2019 May;21(3):375-383. doi: 10.1016/j.jmoldx.2018.11.003. Epub 2018 Dec 31. PubMed PMID: 30605765.

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Rice ES, Green RE. New Approaches for Genome Assembly and Scaffolding. Annu Rev Anim Biosci. 2019 Feb 15;7:17-40. doi: 10.1146/annurev-animal-020518-115344. Epub 2018 Nov 28. Review. PubMed PMID: 30485757.

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Kalbfleisch TS, Rice ES, DePriest MS Jr, Walenz BP, Hestand MS, Vermeesch JR, O Connell BL, Fiddes IT, Vershinina AO, Saremi NF, Petersen JL, Finno CJ, Bellone RR, McCue ME, Brooks SA, Bailey E, Orlando L, Green RE, Miller DC, Antczak DF, MacLeod JN. Improved reference genome for the domestic horse increases assembly contiguity and composition. Commun Biol. 2018;1:197. doi: 10.1038/s42003-018-0199-z. eCollection 2018. PubMed PMID: 30456315; PubMed Central PMCID: PMC6240028.

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Volden R, Palmer T, Byrne A, Cole C, Schmitz RJ, Green RE, Vollmers C. Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA. Proc Natl Acad Sci U S A. 2018 Sep 25;115(39):9726-9731. doi: 10.1073/pnas.1806447115. Epub 2018 Sep 10. PubMed PMID: 30201725; PubMed Central PMCID: PMC6166824.

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Tucci S, Vohr SH, McCoy RC, Vernot B, Robinson MR, Barbieri C, Nelson BJ, Fu W, Purnomo GA, Sudoyo H, Eichler EE, Barbujani G, Visscher PM, Akey JM, Green RE. Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science. 2018 Aug 3;361(6401):511-516. doi: 10.1126/science.aar8486. PubMed PMID: 30072539; PubMed Central PMCID: PMC6709593.

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Lazar NH, Nevonen KA, O'Connell B, McCann C, O'Neill RJ, Green RE, Meyer TJ, Okhovat M, Carbone L. Epigenetic maintenance of topological domains in the highly rearranged gibbon genome. Genome Res. 2018 Jul;28(7):983-997. doi: 10.1101/gr.233874.117. Epub 2018 Jun 18. PubMed PMID: 29914971; PubMed Central PMCID: PMC6028127.

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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] PubMed PMID: 29797549.

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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. PubMed PMID: 29471451.

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Schweizer RM, Durvasula A, Smith J, Vohr SH, Stahler DR, Galaverni M, Thalmann O, Smith DW, Randi E, Ostrander EA, Green RE, Lohmueller KE, Novembre J, Wayne RK. Natural Selection and Origin of a Melanistic Allele in North American Gray Wolves. Mol Biol Evol. 2018 May 1;35(5):1190-1209. doi: 10.1093/molbev/msy031. PubMed PMID: 29688543; PubMed Central PMCID: PMC6455901.

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Cotoras DD, Murray GGR, Kapp J, Gillespie RG, Griswold C, Simison WB, Green RE, Shapiro B. Ancient DNA Resolves the History of Tetragnatha (Araneae, Tetragnathidae) Spiders on Rapa Nui. Genes (Basel). 2017 Dec 20;8(12). doi: 10.3390/genes8120403. PubMed PMID: 29261166; PubMed Central PMCID: PMC5748721.

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Murray GGR, Soares AER, Novak BJ, Schaefer NK, Cahill JA, Baker AJ, Demboski JR, Doll A, Da Fonseca RR, Fulton TL, Gilbert MTP, Heintzman PD, Letts B, McIntosh G, O'Connell BL, Peck M, Pipes ML, Rice ES, Santos KM, Sohrweide AG, Vohr SH, Corbett-Detig RB, Green RE, Shapiro B. Natural selection shaped the rise and fall of passenger pigeon genomic diversity. Science. 2017 Nov 17;358(6365):951-954. doi: 10.1126/science.aao0960. PubMed PMID: 29146814.

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Kuderna LFK, Tomlinson C, Hillier LW, Tran A, Fiddes IT, Armstrong J, Laayouni H, Gordon D, Huddleston J, Garcia Perez R, Povolotskaya I, Serres Armero A, Gómez Garrido J, Ho D, Ribeca P, Alioto T, Green RE, Paten B, Navarro A, Betranpetit J, Herrero J, Eichler EE, Sharp AJ, Feuk L, Warren WC, Marques-Bonet T. A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0). Gigascience. 2017 Nov 1;6(11):1-6. doi: 10.1093/gigascience/gix098. PubMed PMID: 29092041; PubMed Central PMCID: PMC5714192.

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Eerkens JW, Hull B, Goodman J, Evoy A, Kapp JD, Hussain S, Green RE. Stable C and N isotope analysis of hair suggest undernourishment as a factor in the death of a mummified girl from late 19th century San Francisco, CA. PLoS One. 2017;12(9):e0184921. doi: 10.1371/journal.pone.0184921. eCollection 2017. PubMed PMID: 28922420; PubMed Central PMCID: PMC5602664.

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Vohr SH, Gordon R, Eizenga JM, Erlich HA, Calloway CD, Green RE. A phylogenetic approach for haplotype analysis of sequence data from complex mitochondrial mixtures. Forensic Sci Int Genet. 2017 Sep;30:93-105. doi: 10.1016/j.fsigen.2017.05.007. Epub 2017 May 29. PubMed PMID: 28667863.

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Rice ES, Kohno S, John JS, Pham S, Howard J, Lareau LF, O'Connell BL, Hickey G, Armstrong J, Deran A, Fiddes I, Platt RN 2nd, Gresham C, McCarthy F, Kern C, Haan D, Phan T, Schmidt C, Sanford JR, Ray DA, Paten B, Guillette LJ Jr, Green RE. Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling. Genome Res. 2017 May;27(5):686-696. doi: 10.1101/gr.213595.116. Epub 2017 Jan 30. PubMed PMID: 28137821; PubMed Central PMCID: PMC5411764.

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Schaefer NK, Shapiro B, Green RE. AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data. BMC Bioinformatics. 2017 Apr 4;18(1):203. doi: 10.1186/s12859-017-1613-0. PubMed PMID: 28376731; PubMed Central PMCID: PMC5381037.

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Mascher M, Schuenemann VJ, Davidovich U, Marom N, Himmelbach A, Hübner S, Korol A, David M, Reiter E, Riehl S, Schreiber M, Vohr SH, Green RE, Dawson IK, Russell J, Kilian B, Muehlbauer GJ, Waugh R, Fahima T, Krause J, Weiss E, Stein N. Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley. Nat Genet. 2016 Sep;48(9):1089-93. doi: 10.1038/ng.3611. Epub 2016 Jul 18. PubMed PMID: 27428749.

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Longo GC, O'Connell B, Green RE, Bernardi G. The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae). Mar Genomics. 2016 Aug;28:107-112. doi: 10.1016/j.margen.2016.03.006. Epub 2016 Mar 16. PubMed PMID: 26994927.

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Cahill JA, Soares AE, Green RE, Shapiro B. Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data. Philos Trans R Soc Lond B Biol Sci. 2016 Jul 19;371(1699). doi: 10.1098/rstb.2015.0138. PubMed PMID: 27325835; PubMed Central PMCID: PMC4920339.

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Schaefer NK, Shapiro B, Green RE. Detecting hybridization using ancient DNA. Mol Ecol. 2016 Jun;25(11):2398-412. doi: 10.1111/mec.13556. Epub 2016 Mar 23. Review. PubMed PMID: 26826668; PubMed Central PMCID: PMC5063030.

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Putnam NH, O'Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R, Troll CJ, Fields A, Hartley PD, Sugnet CW, Haussler D, Rokhsar DS, Green RE. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. 2016 Mar;26(3):342-50. doi: 10.1101/gr.193474.115. Epub 2016 Feb 4. PubMed PMID: 26848124; PubMed Central PMCID: PMC4772016.

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Schweizer RM, Robinson J, Harrigan R, Silva P, Galverni M, Musiani M, Green RE, Novembre J, Wayne RK. Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves. Mol Ecol. 2016 Jan;25(1):357-79. doi: 10.1111/mec.13467. Epub 2015 Dec 24. PubMed PMID: 26562361.

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Vohr SH, Buen Abad Najar CF, Shapiro B, Green RE. A method for positive forensic identification of samples from extremely low-coverage sequence data. BMC Genomics. 2015 Dec 7;16:1034. doi: 10.1186/s12864-015-2241-6. PubMed PMID: 26643904; PubMed Central PMCID: PMC4672566.

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Schulze CJ, Donia MS, Siqueira-Neto JL, Ray D, Raskatov JA, Green RE, McKerrow JH, Fischbach MA, Linington RG. Genome-Directed Lead Discovery: Biosynthesis, Structure Elucidation, and Biological Evaluation of Two Families of Polyene Macrolactams against Trypanosoma brucei. ACS Chem Biol. 2015 Oct 16;10(10):2373-81. doi: 10.1021/acschembio.5b00308. Epub 2015 Aug 13. PubMed PMID: 26270237; PubMed Central PMCID: PMC7505085.

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Vohr SH, Green RE. Development. Aneuploidy and mother's genes. Science. 2015 Apr 10;348(6231):180-1. doi: 10.1126/science.aab0877. PubMed PMID: 25859029.

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Cahill JA, Stirling I, Kistler L, Salamzade R, Ersmark E, Fulton TL, Stiller M, Green RE, Shapiro B. Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears. Mol Ecol. 2015 Mar;24(6):1205-17. doi: 10.1111/mec.13038. Epub 2015 Feb 5. PubMed PMID: 25490862; PubMed Central PMCID: PMC4409089.

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Koepfli KP, Paten B, O'Brien SJ. The Genome 10K Project: a way forward. Annu Rev Anim Biosci. 2015;3:57-111. doi: 10.1146/annurev-animal-090414-014900. Review. PubMed PMID: 25689317; PubMed Central PMCID: PMC5837290.

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Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J, Jarvis ED, Gilbert MT, Wang J. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014 Dec 12;346(6215):1311-20. doi: 10.1126/science.1251385. Epub 2014 Dec 11. PubMed PMID: 25504712; PubMed Central PMCID: PMC4390078.

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Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW Jr, Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock DD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabaldón T, Paten B, Ray DA. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science. 2014 Dec 12;346(6215):1254449. doi: 10.1126/science.1254449. Epub 2014 Dec 11. PubMed PMID: 25504731; PubMed Central PMCID: PMC4386873.

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Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451. PubMed PMID: 25504713; PubMed Central PMCID: PMC4405904.

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Suh A, Weber CC, Kehlmaier C, Braun EL, Green RE, Fritz U, Ray DA, Ellegren H. Early mesozoic coexistence of amniotes and hepadnaviridae. PLoS Genet. 2014 Dec;10(12):e1004559. doi: 10.1371/journal.pgen.1004559. eCollection 2014 Dec. PubMed PMID: 25501991; PubMed Central PMCID: PMC4263362.

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Suh A, Churakov G, Ramakodi MP, Platt RN 2nd, Jurka J, Kojima KK, Caballero J, Smit AF, Vliet KA, Hoffmann FG, Brosius J, Green RE, Braun EL, Ray DA, Schmitz J. Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes. Genome Biol Evol. 2014 Dec 11;7(1):205-17. doi: 10.1093/gbe/evu256. PubMed PMID: 25503085; PubMed Central PMCID: PMC4316615.

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Kistler L, Montenegro A, Smith BD, Gifford JA, Green RE, Newsom LA, Shapiro B. Transoceanic drift and the domestication of African bottle gourds in the Americas. Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):2937-41. doi: 10.1073/pnas.1318678111. Epub 2014 Feb 10. PubMed PMID: 24516122; PubMed Central PMCID: PMC3939861.

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Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PL, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 2014 Jan 2;505(7481):43-9. doi: 10.1038/nature12886. Epub 2013 Dec 18. PubMed PMID: 24352235; PubMed Central PMCID: PMC4031459.

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Thalmann O, Shapiro B, Cui P, Schuenemann VJ, Sawyer SK, Greenfield DL, Germonpré MB, Sablin MV, López-Giráldez F, Domingo-Roura X, Napierala H, Uerpmann HP, Loponte DM, Acosta AA, Giemsch L, Schmitz RW, Worthington B, Buikstra JE, Druzhkova A, Graphodatsky AS, Ovodov ND, Wahlberg N, Freedman AH, Schweizer RM, Koepfli KP, Leonard JA, Meyer M, Krause J, Pääbo S, Green RE, Wayne RK. Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs. Science. 2013 Nov 15;342(6160):871-4. doi: 10.1126/science.1243650. PubMed PMID: 24233726.

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Jeanes C, Vaughan-Higgins R, Green RE, Sainsbury AW, Marshall RN, Blake DP. Two new Eimeria species parasitic in corncrakes (Crex crex) (Gruiformes: Rallidae) in the United Kingdom. J Parasitol. 2013 Aug;99(4):634-8. doi: 10.1645/12-52.1. Epub 2013 Jan 24. PubMed PMID: 23347228.

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Green RE, Shapiro B. Human evolution: turning back the clock. Curr Biol. 2013 Apr 8;23(7):R286-8. doi: 10.1016/j.cub.2013.02.050. PubMed PMID: 23578879.

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Good JM, Wiebe V, Albert FW, Burbano HA, Kircher M, Green RE, Halbwax M, André C, Atencia R, Fischer A, Pääbo S. Comparative population genomics of the ejaculate in humans and the great apes. Mol Biol Evol. 2013 Apr;30(4):964-76. doi: 10.1093/molbev/mst005. Epub 2013 Jan 16. PubMed PMID: 23329688.

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Shaffer HB, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, Capel B, Castoe TA, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hernandez O, Hillier LW, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning AP, Li Y, Literman R, McGaugh SE, Mork L, O'Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Spinks PQ, Storey KB, Thane N, Vinar T, Zimmerman LM, Warren WC, Mardis ER, Wilson RK. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol. 2013 Mar 28;14(3):R28. doi: 10.1186/gb-2013-14-3-r28. PubMed PMID: 23537068; PubMed Central PMCID: PMC4054807.

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Cahill JA, Green RE, Fulton TL, Stiller M, Jay F, Ovsyanikov N, Salamzade R, St John J, Stirling I, Slatkin M, Shapiro B. Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution. PLoS Genet. 2013;9(3):e1003345. doi: 10.1371/journal.pgen.1003345. Epub 2013 Mar 14. PubMed PMID: 23516372; PubMed Central PMCID: PMC3597504.

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Vohr SH, Green RE. A mouse following in the footsteps of human prehistory. Cell. 2013 Feb 14;152(4):667-8. doi: 10.1016/j.cell.2013.01.039. PubMed PMID: 23415216.