Nicholas H. Putnam, Ph.D. - Publications

Affiliations: 
Ecology and Evolution Rice University, Houston, TX 

27 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
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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.  1
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  1
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  1
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  1
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  1
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  1
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