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Richard E. Green, Ph.D. - Publications

Affiliations: 
2005 University of California, Berkeley, Berkeley, CA 
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60 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
2021 Trujillo CA, Rice ES, Schaefer NK, Chaim IA, Wheeler EC, Madrigal AA, Buchanan J, Preissl S, Wang A, Negraes PD, Szeto RA, Herai RH, Huseynov A, Ferraz MSA, Borges FS, ... ... Green RE, et al. Reintroduction of the archaic variant of in cortical organoids alters neurodevelopment. Science (New York, N.Y.). 371. PMID 33574182 DOI: 10.1126/science.aax2537  0.36
2018 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. The Journal of Molecular Diagnostics : Jmd. PMID 30605765 DOI: 10.1016/j.jmoldx.2018.11.003  0.44
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  0.56
2016 Cahill JA, Soares AE, Green RE, Shapiro B. Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 371. PMID 27325835 DOI: 10.1098/rstb.2015.0138  0.56
2016 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 Research. PMID 26848124 DOI: 10.1101/gr.193474.115  0.44
2016 Schaefer NK, Shapiro B, Green RE. Detecting hybridization using ancient DNA. Molecular Ecology. PMID 26826668 DOI: 10.1111/mec.13556  0.56
2015 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. 16: 1034. PMID 26643904 DOI: 10.1186/s12864-015-2241-6  0.56
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  0.56
2015 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. Molecular Ecology. 24: 1205-17. PMID 25490862 DOI: 10.1111/mec.13038  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2013 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 Genetics. 9: e1003345. PMID 23516372 DOI: 10.1371/journal.pgen.1003345  0.56
2013 Vohr SH, Green RE. A mouse following in the footsteps of human prehistory. Cell. 152: 667-8. PMID 23415216 DOI: 10.1016/j.cell.2013.01.039  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2011 Abi-Rached L, Jobin MJ, Kulkarni S, McWhinnie A, Dalva K, Gragert L, Babrzadeh F, Gharizadeh B, Luo M, Plummer FA, Kimani J, Carrington M, Middleton D, Rajalingam R, Beksac M, ... ... Green RE, et al. The shaping of modern human immune systems by multiregional admixture with archaic humans. Science (New York, N.Y.). 334: 89-94. PMID 21868630 DOI: 10.1126/science.1209202  0.56
2011 Brett CL, Kallay L, Hua Z, Green R, Chyou A, Zhang Y, Graham TR, Donowitz M, Rao R. Genome-wide analysis reveals the vacuolar pH-stat of Saccharomyces cerevisiae. Plos One. 6: e17619. PMID 21423800 DOI: 10.1371/journal.pone.0017619  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2008 Prüfer K, Stenzel U, Dannemann M, Green RE, Lachmann M, Kelso J. PatMaN: rapid alignment of short sequences to large databases. Bioinformatics (Oxford, England). 24: 1530-1. PMID 18467344 DOI: 10.1093/bioinformatics/btn223  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2005 Crooks GE, Green RE, Brenner SE. Pairwise alignment incorporating dipeptide covariation Bioinformatics. 21: 3704-3710. PMID 16123116 DOI: 10.1093/bioinformatics/bti616  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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