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Nicholas H. Putnam, Ph.D. - Publications

Affiliations: 
Ecology and Evolution Rice University, Houston, TX 
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38 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 Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, ... ... Putnam NH, et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 592: 737-746. PMID 33911273 DOI: 10.1038/s41586-021-03451-0  0.668
2020 Mitros T, Session AM, James BT, Wu GA, Belaffif MB, Clark LV, Shu S, Dong H, Barling A, Holmes JR, Mattick JE, Bredeson JV, Liu S, Farrar K, Głowacka K, ... ... Putnam NH, et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nature Communications. 11: 5442. PMID 33116128 DOI: 10.1038/s41467-020-18923-6  0.662
2020 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. Nature Ecology & Evolution. PMID 32313176 DOI: 10.1038/S41559-020-1156-Z  0.833
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  0.359
2016 Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, ... ... Putnam N, et al. Genome evolution in the allotetraploid frog Xenopus laevis. Nature. 538: 336-343. PMID 27762356 DOI: 10.1038/Nature19840  0.838
2016 Yue JX, Kozmikova I, Ono H, Nossa CW, Kozmik Z, Putnam NH, Yu JK, Holland LZ. Conserved non-coding elements in the most distant genera of cephalochordates: the Goldilocks principle. Genome Biology and Evolution. PMID 27412606 DOI: 10.1093/Gbe/Evw158  0.799
2016 Long KA, Nossa CW, Sewell MA, Putnam NH, Ryan JF. Low coverage sequencing of three echinoderm genomes: the brittle star Ophionereis fasciata, the sea star Patiriella regularis, and the sea cucumber Australostichopus mollis. Gigascience. 5: 20. PMID 27175279 DOI: 10.1186/S13742-016-0125-6  0.549
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  0.683
2015 Zwarycz AS, Nossa CW, Putnam NH, Ryan JF. Timing and scope of genomic expansion within Annelida: evidence from homeoboxes in the genome of the earthworm Eisenia fetida. Genome Biology and Evolution. PMID 26659921 DOI: 10.1093/Gbe/Evv243  0.753
2015 Simakov O, Kawashima T, Marlétaz F, Jenkins J, Koyanagi R, Mitros T, Hisata K, Bredeson J, Shoguchi E, Gyoja F, Yue JX, Chen YC, Freeman RM, Sasaki A, Hikosaka-Katayama T, ... ... Putnam NH, et al. Hemichordate genomes and deuterostome origins. Nature. PMID 26580012 DOI: 10.1038/Nature16150  0.841
2015 Warren CR, Kassir E, Spurlin J, Martinez J, Putnam NH, Farach-Carson MC. Evolution of the perlecan/HSPG2 gene and its activation in regenerating Nematostella vectensis. Plos One. 10: e0124578. PMID 25876075 DOI: 10.1371/Journal.Pone.0124578  0.6
2014 Maxwell EK, Schnitzler CE, Havlak P, Putnam NH, Nguyen AD, Moreland RT, Baxevanis AD. Evolutionary profiling reveals the heterogeneous origins of classes of human disease genes: implications for modeling disease genetics in animals. Bmc Evolutionary Biology. 14: 212. PMID 25281000 DOI: 10.1186/S12862-014-0212-1  0.446
2014 Yue JX, Yu JK, Putnam NH, Holland LZ. The transcriptome of an amphioxus, Asymmetron lucayanum, from the Bahamas: a window into chordate evolution. Genome Biology and Evolution. 6: 2681-96. PMID 25240057 DOI: 10.1093/Gbe/Evu212  0.787
2014 Nossa CW, Havlak P, Yue JX, Lv J, Vincent KY, Brockmann HJ, Putnam NH. Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication. Gigascience. 3: 9. PMID 24987520 DOI: 10.1186/2047-217X-3-9  0.855
2013 Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT, Simmons DK, Koch BJ, Francis WR, Havlak P, Smith SA, Putnam NH, Haddock SH, Dunn CW, Wolfsberg TG, et al. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science (New York, N.Y.). 342: 1242592. PMID 24337300 DOI: 10.1126/Science.1242592  0.576
2013 Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, Kuo DH, Larsson T, Lv J, Arendt D, Savage R, Osoegawa K, de Jong P, Grimwood J, Chapman JA, ... ... Putnam NH, et al. Insights into bilaterian evolution from three spiralian genomes. Nature. 493: 526-31. PMID 23254933 DOI: 10.1038/Nature11696  0.86
2012 Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research. 40: D1178-86. PMID 22110026 DOI: 10.1093/Nar/Gkr944  0.757
2011 Lv J, Havlak P, Putnam NH. Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes. Bmc Bioinformatics. 12: S11. PMID 22151646 DOI: 10.1186/1471-2105-12-S9-S11  0.772
2011 Katayama T, Wilkinson MD, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y, Chun HW, Yamaguchi A, Kawano S, Aerts J, Aoki-Kinoshita KF, Arakawa K, Aranda B, Bonnal RJ, ... ... Putnam N, et al. The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. Journal of Biomedical Semantics. 2: 4. PMID 21806842 DOI: 10.1186/2041-1480-2-4  0.353
2011 Sucgang R, Kuo A, Tian X, Salerno W, Parikh A, Feasley CL, Dalin E, Tu H, Huang E, Barry K, Lindquist E, Shapiro H, Bruce D, Schmutz J, Salamov A, ... ... Putnam NH, et al. Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biology. 12: R20. PMID 21356102 DOI: 10.1186/Gb-2011-12-2-R20  0.384
2010 Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME, Mitros T, Richards GS, Conaco C, Dacre M, Hellsten U, Larroux C, Putnam NH, Stanke M, Adamska M, Darling A, et al. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature. 466: 720-6. PMID 20686567 DOI: 10.1038/Nature09201  0.851
2010 Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, et al. The genome of the Western clawed frog Xenopus tropicalis. Science (New York, N.Y.). 328: 633-6. PMID 20431018 DOI: 10.1126/Science.1183670  0.86
2010 Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, Rattei T, Balasubramanian PG, Borman J, Busam D, Disbennett K, Pfannkoch C, Sumin N, Sutton GG, Viswanathan LD, ... ... Putnam NH, et al. The dynamic genome of Hydra. Nature. 464: 592-6. PMID 20228792 DOI: 10.1038/Nature08830  0.841
2009 Kawashima T, Kawashima S, Tanaka C, Murai M, Yoneda M, Putnam NH, Rokhsar DS, Kanehisa M, Satoh N, Wada H. Domain shuffling and the evolution of vertebrates. Genome Research. 19: 1393-403. PMID 19443856 DOI: 10.1101/Gr.087072.108  0.554
2008 Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, Kuo A, Mitros T, Salamov A, Carpenter ML, Signorovitch AY, Moreno MA, Kamm K, Grimwood J, Schmutz J, et al. The Trichoplax genome and the nature of placozoans. Nature. 454: 955-60. PMID 18719581 DOI: 10.1038/Nature07191  0.866
2008 Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiérrez EL, Dubchak I, Garcia-Fernàndez J, Gibson-Brown JJ, Grigoriev IV, et al. The amphioxus genome and the evolution of the chordate karyotype. Nature. 453: 1064-71. PMID 18563158 DOI: 10.1038/Nature06967  0.829
2008 Holland LZ, Albalat R, Azumi K, Benito-Gutiérrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DE, Garcia-Fernàndez J, Gibson-Brown JJ, Gissi C, Godzik A, ... ... Putnam NH, et al. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Research. 18: 1100-11. PMID 18562680 DOI: 10.1101/Gr.073676.107  0.77
2008 Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Grigoriev IV, Harris P, Jackson M, Kubicek CP, ... ... Putnam N, et al. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nature Biotechnology. 26: 553-60. PMID 18454138 DOI: 10.1038/Nbt1403  0.736
2008 King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, Marr M, Pincus D, Putnam N, Rokas A, Wright KJ, et al. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature. 451: 783-8. PMID 18273011 DOI: 10.1038/Nature06617  0.828
2008 Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EGJ, Grigoriev IV, Harris P, Jackson M, Kubicek CP, ... ... Putnam N, et al. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina) (Nature Biotechnology (2008) 26, (553-560)) Nature Biotechnology. 26: 1193. DOI: 10.1038/Nbt1008-1193A  0.774
2008 Holland LZ, Albalat R, Azumi K, Benito-Gutiérrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DEK, Garcia-Fernàndez J, Gibson-Brown JJ, Gissi C, Godzik A, ... ... Putnam NH, et al. The amphioxus genome illuminates vertebrate origins and cephalochordate biology (Genome Research (2008) 18, (1100-1111)) Genome Research. 18: 1380.  0.763
2007 Kawashima S, Kawashima T, Putnam NH, Rokhsar DS, Wada H, Kanehisa M. Comparative pair-wise domain-combinations for screening the clade specific domain-architectures in metazoan genomes. Genome Informatics. International Conference On Genome Informatics. 19: 50-60. PMID 18546504 DOI: 10.11234/Gi1990.19.50  0.643
2007 Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Grigoriev IV, Lucas SM, Steele RE, et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science (New York, N.Y.). 317: 86-94. PMID 17615350 DOI: 10.1126/Science.1139158  0.846
2007 Kelleher CT, Chiu R, Shin H, Bosdet IE, Krzywinski MI, Fjell CD, Wilkin J, Yin T, DiFazio SP, Ali J, Asano JK, Chan S, Cloutier A, Girn N, Leach S, ... ... Putnam NH, et al. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. The Plant Journal : For Cell and Molecular Biology. 50: 1063-78. PMID 17488239 DOI: 10.1111/J.1365-313X.2007.03112.X  0.722
2007 Palenik B, Grimwood J, Aerts A, Rouzé P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, et al. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proceedings of the National Academy of Sciences of the United States of America. 104: 7705-10. PMID 17460045 DOI: 10.1073/Pnas.0611046104  0.704
2006 Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science (New York, N.Y.). 313: 1596-604. PMID 16973872 DOI: 10.1126/Science.1128691  0.822
2006 Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, ... ... Putnam NH, et al. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science (New York, N.Y.). 313: 1261-6. PMID 16946064 DOI: 10.1126/Science.1128796  0.815
2004 Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, et al. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science (New York, N.Y.). 306: 79-86. PMID 15459382 DOI: 10.1126/Science.1101156  0.729
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