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Richard E. Green, Ph.D. - Publications

Affiliations: 
2005 University of California, Berkeley, Berkeley, CA, United States 
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57 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Warren WC, Harris RA, Haukness M, Fiddes IT, Murali SC, Fernandes J, Dishuck PC, Storer JM, Raveendran M, Hillier LW, Porubsky D, Mao Y, Gordon D, Vollger MR, Lewis AP, ... ... Green RE, et al. Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. Science (New York, N.Y.). 370. PMID 33335035 DOI: 10.1126/science.abc6617  0.319
2020 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 Research. PMID 32491177 DOI: 10.1093/Nar/Gkaa450  0.313
2019 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 Biology and Evolution. PMID 31821505 DOI: 10.1093/Gbe/Evz269  0.396
2018 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 30201725 DOI: 10.1073/Pnas.1806447115  0.376
2017 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. 8. PMID 29261166 DOI: 10.3390/Genes8120403  0.685
2017 Rice ES, Kohno S, St John J, Pham S, Howard J, Lareau L, O'Connell BL, Hickey G, Armstrong J, Deran A, Fiddes I, Platt RN, Gresham C, McCarthy F, Kern C, ... ... Green RE, et al. Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling. Genome Research. PMID 28137821 DOI: 10.1101/Gr.213595.116  0.708
2016 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, et al. Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley. Nature Genetics. PMID 27428749 DOI: 10.1038/Ng.3611  0.36
2016 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). Marine Genomics. PMID 26994927 DOI: 10.1016/J.Margen.2016.03.006  0.373
2015 Suh A, Churakov G, Ramakodi MP, Platt RN, 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 Biology and Evolution. 7: 205-17. PMID 25503085 DOI: 10.1093/Gbe/Evu256  0.33
2014 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, et al. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science (New York, N.Y.). 346: 1254449. PMID 25504731 DOI: 10.1126/Science.1254449  0.376
2014 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, ... ... Green RE, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science (New York, N.Y.). 346: 1320-31. PMID 25504713 DOI: 10.1126/Science.1253451  0.385
2014 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, ... ... Green RE, et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science (New York, N.Y.). 346: 1311-20. PMID 25504712 DOI: 10.1126/Science.1251385  0.406
2014 Suh A, Weber CC, Kehlmaier C, Braun EL, Green RE, Fritz U, Ray DA, Ellegren H. Early mesozoic coexistence of amniotes and hepadnaviridae. Plos Genetics. 10: e1004559. PMID 25501991 DOI: 10.1371/Journal.Pgen.1004559  0.356
2014 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. Proceedings of the National Academy of Sciences of the United States of America. 111: 2937-41. PMID 24516122 DOI: 10.1073/Pnas.1318678111  0.305
2014 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, ... ... Green RE, et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 505: 43-9. PMID 24352235 DOI: 10.1038/Nature12886  0.388
2013 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, ... ... Green RE, et al. Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs. Science (New York, N.Y.). 342: 871-4. PMID 24233726 DOI: 10.1126/Science.1243650  0.31
2013 Green RE, Shapiro B. Human evolution: turning back the clock. Current Biology : Cb. 23: R286-8. PMID 23578879 DOI: 10.1016/J.Cub.2013.02.050  0.335
2013 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, ... ... Green RE, et al. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology. 14: R28. PMID 23537068 DOI: 10.1186/Gb-2013-14-3-R28  0.421
2013 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. Molecular Biology and Evolution. 30: 964-76. PMID 23329688 DOI: 10.1093/Molbev/Mst005  0.42
2012 Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, ... ... Green RE, et al. A high-coverage genome sequence from an archaic Denisovan individual. Science (New York, N.Y.). 338: 222-6. PMID 22936568 DOI: 10.1126/Science.1224344  0.376
2012 Burbano HA, Green RE, Maricic T, Lalueza-Fox C, de la Rasilla M, Rosas A, Kelso J, Pollard KS, Lachmann M, Pääbo S. Analysis of human accelerated DNA regions using archaic hominin genomes. Plos One. 7: e32877. PMID 22412940 DOI: 10.1371/Journal.Pone.0032877  0.3
2012 St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B, Abzhanov A, Burgess SC, Cooksey AM, Castoe TA, Crawford NG, Densmore LD, ... ... Green RE, et al. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology. 13: 415. PMID 22293439 DOI: 10.1186/Gb-2012-13-1-415  0.345
2011 Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, ... ... Green RE, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Research. 21: 2224-41. PMID 21926179 DOI: 10.1101/Gr.126599.111  0.318
2011 Taliaferro JM, Alvarez N, Green RE, Blanchette M, Rio DC. Evolution of a tissue-specific splicing network. Genes & Development. 25: 608-20. PMID 21406555 DOI: 10.1101/Gad.2009011  0.447
2011 Albert FW, Hodges E, Jensen JD, Besnier F, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Good JM, Green RE, Burbano HA, Plyusnina IZ, Trut L, Andersson L, Schöneberg T, et al. Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection. Heredity. 107: 205-14. PMID 21304545 DOI: 10.1038/Hdy.2011.4  0.333
2011 Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, ... ... Green RE, et al. The developmental transcriptome of Drosophila melanogaster. Nature. 471: 473-9. PMID 21179090 DOI: 10.1038/Nature09715  0.606
2010 Rohland N, Reich D, Mallick S, Meyer M, Green RE, Georgiadis NJ, Roca AL, Hofreiter M. Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants. Plos Biology. 8: e1000564. PMID 21203580 DOI: 10.1371/Journal.Pbio.1000564  0.385
2010 Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 468: 1053-60. PMID 21179161 DOI: 10.1038/Nature09710  0.361
2010 Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PL, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Albert FW, de la Rasilla M, et al. Targeted investigation of the Neandertal genome by array-based sequence capture. Science (New York, N.Y.). 328: 723-5. PMID 20448179 DOI: 10.1126/Science.1188046  0.409
2010 Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, et al. A draft sequence of the Neandertal genome. Science (New York, N.Y.). 328: 710-22. PMID 20448178 DOI: 10.1126/Science.1188021  0.384
2010 Prüfer K, Stenzel U, Hofreiter M, Pääbo S, Kelso J, Green RE. Computational challenges in the analysis of ancient DNA. Genome Biology. 11: R47. PMID 20441577 DOI: 10.1186/Gb-2010-11-5-R47  0.374
2009 Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Pääbo S. Primer extension capture: targeted sequence retrieval from heavily degraded DNA sources. Journal of Visualized Experiments : Jove. 1573. PMID 19730410 DOI: 10.3791/1573  0.369
2009 Green RE, Briggs AW, Krause J, Prüfer K, Burbano HA, Siebauer M, Lachmann M, Pääbo S. The Neandertal genome and ancient DNA authenticity. The Embo Journal. 28: 2494-502. PMID 19661919 DOI: 10.1038/Emboj.2009.222  0.405
2009 Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Schmitz R, Doronichev VB, Golovanova LV, de la Rasilla M, et al. Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science (New York, N.Y.). 325: 318-21. PMID 19608918 DOI: 10.1126/Science.1174462  0.37
2009 Hansen KD, Lareau LF, Blanchette M, Green RE, Meng Q, Rehwinkel J, Gallusser FL, Izaurralde E, Rio DC, Dudoit S, Brenner SE. Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila. Plos Genetics. 5: e1000525. PMID 19543372 DOI: 10.1371/Journal.Pgen.1000525  0.768
2009 Blanchette M, Green RE, MacArthur S, Brooks AN, Brenner SE, Eisen MB, Rio DC. Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Molecular Cell. 33: 438-49. PMID 19250905 DOI: 10.1016/J.Molcel.2009.01.022  0.576
2009 Haussler D, O'Brien SJ, Ryder OA, Keith Barker F, Clamp M, Crawford AJ, Hanner R, Hanotte O, Johnson WE, McGuire JA, Miller W, Murphy RW, Murphy WJ, Sheldon FH, Sinervo B, ... ... Green RE, et al. Genome 10K: A proposal to obtain whole-genome sequence for 10000 vertebrate species Journal of Heredity. 100: 659-674. DOI: 10.1093/Jhered/Esp086  0.327
2008 Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PL, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano HA, Ronan M, Rothberg JM, et al. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell. 134: 416-26. PMID 18692465 DOI: 10.1016/J.Cell.2008.06.021  0.361
2008 Myles S, Tang K, Somel M, Green RE, Kelso J, Stoneking M. Identification and analysis of genomic regions with large between-population differentiation in humans. Annals of Human Genetics. 72: 99-110. PMID 18184145 DOI: 10.1111/J.1469-1809.2007.00390.X  0.323
2007 Krause J, Lalueza-Fox C, Orlando L, Enard W, Green RE, Burbano HA, Hublin JJ, Hänni C, Fortea J, de la Rasilla M, Bertranpetit J, Rosas A, Pääbo S. The derived FOXP2 variant of modern humans was shared with Neandertals. Current Biology : Cb. 17: 1908-12. PMID 17949978 DOI: 10.1016/J.Cub.2007.10.008  0.307
2007 Briggs AW, Stenzel U, Johnson PL, Green RE, Kelso J, Prüfer K, Meyer M, Krause J, Ronan MT, Lachmann M, Pääbo S. Patterns of damage in genomic DNA sequences from a Neandertal. Proceedings of the National Academy of Sciences of the United States of America. 104: 14616-21. PMID 17715061 DOI: 10.1073/Pnas.0704665104  0.366
2007 Chen H, Green RE, Pääbo S, Slatkin M. The joint allele-frequency spectrum in closely related species. Genetics. 177: 387-98. PMID 17603120 DOI: 10.1534/Genetics.107.070730  0.316
2007 Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature. 446: 926-9. PMID 17361132 DOI: 10.1038/Nature05676  0.774
2006 Green RE, Krause J, Ptak SE, Briggs AW, Ronan MT, Simons JF, Du L, Egholm M, Rothberg JM, Paunovic M, Pääbo S. Analysis of one million base pairs of Neanderthal DNA. Nature. 444: 330-6. PMID 17108958 DOI: 10.1038/Nature05336  0.39
2006 Khaitovich P, Kelso J, Franz H, Visagie J, Giger T, Joerchel S, Petzold E, Green RE, Lachmann M, Pääbo S. Functionality of intergenic transcription: an evolutionary comparison. Plos Genetics. 2: e171. PMID 17040132 DOI: 10.1371/Journal.Pgen.0020171  0.425
2006 Stiller M, Green RE, Ronan M, Simons JF, Du L, He W, Egholm M, Rothberg JM, Keates SG, Keats SG, Ovodov ND, Antipina EE, Baryshnikov GF, Kuzmin YV, Vasilevski AA, et al. Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA. Proceedings of the National Academy of Sciences of the United States of America. 103: 13578-84. PMID 16938852 DOI: 10.1073/Pnas.0605327103  0.353
2005 Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, ... ... Green RE, et al. The transcriptional landscape of the mammalian genome. Science (New York, N.Y.). 309: 1559-63. PMID 16141072 DOI: 10.1126/Science.1112014  0.765
2005 Crooks GE, Green RE, Brenner SE. Pairwise alignment incorporating dipeptide covariation Bioinformatics. 21: 3704-3710. PMID 16123116 DOI: 10.1093/Bioinformatics/Bti616  0.509
2005 Price GA, Crooks GE, Green RE, Brenner SE. Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap Bioinformatics. 21: 3824-3831. PMID 16105900 DOI: 10.1093/Bioinformatics/Bti627  0.537
2005 Blanchette M, Green RE, Brenner SE, Rio DC. Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. Genes & Development. 19: 1306-14. PMID 15937219 DOI: 10.1101/Gad.1314205  0.559
2004 Blanchette M, Labourier E, Green RE, Brenner SE, Rio DC. Genome-wide analysis reveals an unexpected function for the Drosophila splicing factor U2AF50 in the nuclear export of intronless mRNAs. Molecular Cell. 14: 775-86. PMID 15200955 DOI: 10.1016/J.Molcel.2004.06.012  0.59
2004 Lareau LF, Green RE, Bhatnagar RS, Brenner SE. The evolving roles of alternative splicing. Current Opinion in Structural Biology. 14: 273-82. PMID 15193306 DOI: 10.1016/J.Sbi.2004.05.002  0.771
2004 Hillman RT, Green RE, Brenner SE. An unappreciated role for RNA surveillance. Genome Biology. 5: R8. PMID 14759258 DOI: 10.1186/Gb-2004-5-2-R8  0.591
2003 Green RE, Lewis BP, Hillman RT, Blanchette M, Lareau LF, Garnett AT, Rio DC, Brenner SE. Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. Bioinformatics (Oxford, England). 19: i118-21. PMID 12855447 DOI: 10.1093/Bioinformatics/Btg1015  0.749
2003 Lewis BP, Green RE, Brenner SE. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proceedings of the National Academy of Sciences of the United States of America. 100: 189-92. PMID 12502788 DOI: 10.1073/Pnas.0136770100  0.608
2002 Mougous JD, Green RE, Williams SJ, Brenner SE, Bertozzi CR. Sulfotransferases and sulfatases in mycobacteria. Chemistry & Biology. 9: 767-76. PMID 12144918 DOI: 10.1016/S1074-5521(02)00175-8  0.539
2002 Green RE, Brenner SE. Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison Proceedings of the Ieee. 90: 1834-1847. DOI: 10.1109/JPROC.2002.805303  0.453
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