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Jarrod A. Chapman, PhD - Publications

Affiliations: 
Computational Genomics Joint Genome Institute, Walnut Creek, CA, United States 
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35 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
2016 Morales J, Kokkori S, Weidauer D, Chapman J, Goltsman E, Rokhsar D, Grossman AR, Nowack EC. Development of a toolbox to dissect host-endosymbiont interactions and protein trafficking in the trypanosomatid Angomonas deanei. Bmc Evolutionary Biology. 16: 247. PMID 27835948 DOI: 10.1186/S12862-016-0820-Z  0.573
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, et al. Genome evolution in the allotetraploid frog Xenopus laevis. Nature. 538: 336-343. PMID 27762356 DOI: 10.1038/Nature19840  0.829
2015 Chapman JA, Mascher M, Buluç A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L, Schmutz J, Yelick KA, Scholz U, Waugh R, Poland JA, et al. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biology. 16: 26. PMID 25637298 DOI: 10.1186/S13059-015-0582-8  0.721
2015 Lowry DB, Hernandez K, Taylor SH, Meyer E, Logan TL, Barry KW, Chapman JA, Rokhsar DS, Schmutz J, Juenger TE. The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii. The New Phytologist. 205: 402-14. PMID 25252269 DOI: 10.1111/Nph.13027  0.559
2014 Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, Perrier X, Ruiz M, Scalabrin S, Terol J, Takita MA, Labadie K, Poulain J, Couloux A, Jabbari K, ... ... Chapman J, et al. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nature Biotechnology. 32: 656-62. PMID 24908277 DOI: 10.1038/Nbt.2906  0.71
2014 Lukaszewski AJ, Alberti A, Sharpe A, Kilian A, Stanca AM, Keller B, Clavijo BJ, Friebe B, Gill B, Wulff B, Chapman B, Steuernagel B, Feuillet C, Viseux C, Pozniak C, ... ... Chapman J, et al. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome Science. 345. DOI: 10.1126/science.1251788  0.693
2014 Georganas E, Buluç A, Chapman J, Oliker L, Rokhsar D, Yelick K. Parallel de Bruijn Graph Construction and Traversal for de Novo Genome Assembly International Conference For High Performance Computing, Networking, Storage and Analysis, Sc. 2015: 437-448. DOI: 10.1109/SC.2014.41  0.617
2014 Strnadová V, Buluc A, Chapman J, Gilbert JR, Gonzalez J, Jegelka S, Rokhsar D, Oliker L. Efficient and accurate clustering for large-scale genetic mapping Proceedings - 2014 Ieee International Conference On Bioinformatics and Biomedicine, Ieee Bibm 2014. 3-10. DOI: 10.1109/BIBM.2014.6999119  0.435
2013 Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, Muñoz-Amatriaín M, Close TJ, Wise RP, Schulman AH, Himmelbach A, Mayer KF, Scholz U, Poland JA, Stein N, et al. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). The Plant Journal : For Cell and Molecular Biology. 76: 718-27. PMID 23998490 DOI: 10.1111/Tpj.12319  0.752
2013 Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2: 10. PMID 23870653 DOI: 10.1186/2047-217X-2-10  0.738
2013 Slotte T, Hazzouri KM, Ã…gren JA, Koenig D, Maumus F, Guo YL, Steige K, Platts AE, Escobar JS, Newman LK, Wang W, Mandáková T, Vello E, Smith LM, Henz SR, ... ... Chapman J, et al. The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nature Genetics. 45: 831-5. PMID 23749190 DOI: 10.1038/Ng.2669  0.707
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, et al. Insights into bilaterian evolution from three spiralian genomes. Nature. 493: 526-31. PMID 23254933 DOI: 10.1038/Nature11696  0.836
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, ... ... Chapman JA, 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  0.675
2011 Chapman JA, Ho I, Sunkara S, Luo S, Schroth GP, Rokhsar DS. Meraculous: de novo genome assembly with short paired-end reads. Plos One. 6: e23501. PMID 21876754 DOI: 10.1371/Journal.Pone.0023501  0.7
2010 Ingle JN, Schaid DJ, Goss PE, Liu M, Mushiroda T, Chapman JA, Kubo M, Jenkins GD, Batzler A, Shepherd L, Pater J, Wang L, Ellis MJ, Stearns V, Rohrer DC, et al. Genome-wide associations and functional genomic studies of musculoskeletal adverse events in women receiving aromatase inhibitors. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 28: 4674-82. PMID 20876420 DOI: 10.1200/Jco.2010.28.5064  0.367
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  0.837
2010 Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T, Fritz-Laylin LK, Hellsten U, Chapman J, Simakov O, Rensing SA, Terry A, et al. Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science (New York, N.Y.). 329: 223-6. PMID 20616280 DOI: 10.1126/Science.1188800  0.651
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, et al. The dynamic genome of Hydra. Nature. 464: 592-6. PMID 20228792 DOI: 10.1038/Nature08830  0.832
2010 Fritz-Laylin LK, Prochnik SE, Ginger ML, Dacks JB, Carpenter ML, Field MC, Kuo A, Paredez A, Chapman J, Pham J, Shu S, Neupane R, Cipriano M, Mancuso J, Tu H, et al. The genome of Naegleria gruberi illuminates early eukaryotic versatility. Cell. 140: 631-42. PMID 20211133 DOI: 10.1016/J.Cell.2010.01.032  0.772
2010 Srivastava M, Larroux C, Lu DR, Mohanty K, Chapman J, Degnan BM, Rokhsar DS. Early evolution of the LIM homeobox gene family. Bmc Biology. 8: 4. PMID 20082688 DOI: 10.1186/1741-7007-8-4  0.647
2009 Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, ... ... Chapman J, et al. The Sorghum bicolor genome and the diversification of grasses. Nature. 457: 551-6. PMID 19189423 DOI: 10.1038/Nature07723  0.757
2008 Sela DA, Chapman J, Adeuya A, Kim JH, Chen F, Whitehead TR, Lapidus A, Rokhsar DS, Lebrilla CB, German JB, Price NP, Richardson PM, Mills DA. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Proceedings of the National Academy of Sciences of the United States of America. 105: 18964-9. PMID 19033196 DOI: 10.1073/Pnas.0809584105  0.648
2008 Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, Shen L, Donahue WF, Tusneem N, Stromberg MP, Stewart DA, Zhang L, Ranade SS, Warner JB, Lee CC, ... ... Chapman J, et al. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Research. 18: 1638-42. PMID 18775913 DOI: 10.1101/Gr.077776.108  0.622
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  0.849
2008 Hwang JS, Takaku Y, Chapman J, Ikeo K, David CN, Gojobori T. Cilium evolution: identification of a novel protein, nematocilin, in the mechanosensory cilium of Hydra nematocytes. Molecular Biology and Evolution. 25: 2009-17. PMID 18635678 DOI: 10.1093/Molbev/Msn154  0.532
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  0.822
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  0.833
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, ... ... Chapman J, 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  0.818
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, 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 Martinez D, Larrondo LF, Putnam N, Gelpke MD, Huang K, Chapman J, Helfenbein KG, Ramaiya P, Detter JC, Larimer F, Coutinho PM, Henrissat B, Berka R, Cullen D, Rokhsar D. Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nature Biotechnology. 22: 695-700. PMID 15122302 DOI: 10.1038/Nbt967  0.718
2004 Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 428: 37-43. PMID 14961025 DOI: 10.1038/Nature02340  0.715
2003 Richardson PM, Chapman J. The Xenopus tropicalis genome project Current Genomics. 4: 645-652. DOI: 10.2174/1389202033490088  0.441
2002 Detter JC, Jett JM, Lucas SM, Dalin E, Arellano AR, Wang M, Nelson JR, Chapman J, Lou Y, Rokhsar D, Hawkins TL, Richardson PM. Isothermal strand-displacement amplification applications for high-throughput genomics Genomics. 80: 691-698. PMID 12523365 DOI: 10.1006/Geno.2002.7020  0.678
2002 Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KE, Ho I, Hotta K, Huang W, et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science (New York, N.Y.). 298: 2157-67. PMID 12481130 DOI: 10.1126/Science.1080049  0.767
2002 Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MD, Roach J, Oh T, Ho IY, Wong M, et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science (New York, N.Y.). 297: 1301-10. PMID 12142439 DOI: 10.1126/Science.1072104  0.763
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