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Jason R. Miller - Publications

Affiliations: 
The J. Craig Venter Institute, San Diego, CA, United States 
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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 Miller JR, Koren S, Dilley KA, Harkins DM, Stockwell TB, Shabman RS, Sutton GG. A draft genome sequence for the cell line, ISE6. F1000research. 7: 297. PMID 29707202 DOI: 10.12688/F1000Research.13635.1  0.327
2017 Moll KM, Zhou P, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, Stupar RM, Tiffin P, Miller JR, Young ND, Silverstein KAT, Mudge J. Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula. Bmc Genomics. 18: 578. PMID 28778149 DOI: 10.1186/S12864-017-3971-4  0.413
2017 Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, et al. Hybrid assembly with long and short reads improves discovery of gene family expansions. Bmc Genomics. 18: 541. PMID 28724409 DOI: 10.1186/S12864-017-3927-8  0.404
2017 Miller JR, Dilley KA, Harkins DM, Torralba MG, Moncera KJ, Beeri K, Goglin K, Stockwell TB, Sutton GG, Shabman RS. Initial genome sequencing of the sugarcane CP 96-1252 complex hybrid. F1000research. 6: 688. PMID 28721204 DOI: 10.12688/F1000Research.11629.1  0.384
2017 Zhou P, Silverstein KA, Ramaraj T, Guhlin J, Denny R, Liu J, Farmer AD, Steele KP, Stupar RM, Miller JR, Tiffin P, Mudge J, Young ND. Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes. Bmc Genomics. 18: 261. PMID 28347275 DOI: 10.1186/S12864-017-3654-1  0.415
2017 Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research. PMID 28298431 DOI: 10.1101/Gr.215087.116  0.411
2017 Tørresen OK, Star B, Jentoft S, Reinar WB, Grove H, Miller JR, Walenz BP, Knight J, Ekholm JM, Peluso P, Edvardsen RB, Tooming-Klunderud A, Skage M, Lien S, Jakobsen KS, et al. An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. Bmc Genomics. 18: 95. PMID 28100185 DOI: 10.1186/S12864-016-3448-X  0.435
2016 Krishnakumar V, Contrino S, Cheng CY, Belyaeva I, Ferlanti ES, Miller JR, Vaughn MW, Micklem G, Town CD, Chan AP. ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery. Plant & Cell Physiology. PMID 28013278 DOI: 10.1093/Pcp/Pcw200  0.331
2016 Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A, Grammes F, Grove H, Gjuvsland A, Walenz B, Hermansen RA, et al. The Atlantic salmon genome provides insights into rediploidization. Nature. PMID 27088604 DOI: 10.1038/Nature17164  0.416
2016 Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J, Ribeiro JM, Megy K, Thimmapuram J, Miller JR, Walenz BP, Koren S, Hostetler JB, et al. Genomic insights into the Ixodes scapularis tick vector of Lyme disease. Nature Communications. 7: 10507. PMID 26856261 DOI: 10.1038/Ncomms10507  0.349
2015 Krishnakumar V, Hanlon MR, Contrino S, Ferlanti ES, Karamycheva S, Kim M, Rosen BD, Cheng CY, Moreira W, Mock SA, Stubbs J, Sullivan JM, Krampis K, Miller JR, Micklem G, et al. Araport: the Arabidopsis information portal. Nucleic Acids Research. 43: D1003-9. PMID 25414324 DOI: 10.1093/Nar/Gku1200  0.327
2012 Choi Y, Sims GE, Murphy S, Miller JR, Chan AP. Predicting the functional effect of amino acid substitutions and indels. Plos One. 7: e46688. PMID 23056405 DOI: 10.1371/Journal.Pone.0046688  0.328
2012 Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, et al. The bonobo genome compared with the chimpanzee and human genomes. Nature. 486: 527-31. PMID 22722832 DOI: 10.1038/Nature11128  0.384
2011 Miller W, Hayes VM, Ratan A, Petersen DC, Wittekindt NE, Miller J, Walenz B, Knight J, Qi J, Zhao F, Wang Q, Bedoya-Reina OC, Katiyar N, Tomsho LP, Kasson LM, et al. Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proceedings of the National Academy of Sciences of the United States of America. 108: 12348-53. PMID 21709235 DOI: 10.1073/Pnas.1102838108  0.364
2011 Ye L, Hillier LW, Minx P, Thane N, Locke DP, Martin JC, Chen L, Mitreva M, Miller JR, Haub KV, Dooling DJ, Mardis ER, Wilson RK, Weinstock GM, Warren WC. A vertebrate case study of the quality of assemblies derived from next-generation sequences. Genome Biology. 12: R31. PMID 21453517 DOI: 10.1186/Gb-2011-12-3-R31  0.41
2010 Koren S, Miller JR, Walenz BP, Sutton G. An algorithm for automated closure during assembly. Bmc Bioinformatics. 11: 457. PMID 20831800 DOI: 10.1186/1471-2105-11-457  0.378
2010 Lorenzi HA, Puiu D, Miller JR, Brinkac LM, Amedeo P, Hall N, Caler EV. New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information. Plos Neglected Tropical Diseases. 4: e716. PMID 20559563 DOI: 10.1371/Journal.Pntd.0000716  0.403
2010 Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, ... ... Miller J, et al. A catalog of reference genomes from the human microbiome. Science (New York, N.Y.). 328: 994-9. PMID 20489017 DOI: 10.1126/Science.1183605  0.415
2010 Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics. 95: 315-27. PMID 20211242 DOI: 10.1016/J.Ygeno.2010.03.001  0.389
2008 Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics (Oxford, England). 24: 2818-24. PMID 18952627 DOI: 10.1093/Bioinformatics/Btn548  0.394
2008 Denisov G, Walenz B, Halpern AL, Miller J, Axelrod N, Levy S, Sutton G. Consensus generation and variant detection by Celera Assembler. Bioinformatics (Oxford, England). 24: 1035-40. PMID 18321888 DOI: 10.1093/Bioinformatics/Btn074  0.385
2007 Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, ... ... Miller JR, et al. Genome sequence of Aedes aegypti, a major arbovirus vector. Science (New York, N.Y.). 316: 1718-23. PMID 17510324 DOI: 10.1126/Science.1138878  0.384
2005 Florea L, Di Francesco V, Miller J, Turner R, Yao A, Harris M, Walenz B, Mobarry C, Merkulov GV, Charlab R, Dew I, Deng Z, Istrail S, Li P, Sutton G. Gene and alternative splicing annotation with AIR. Genome Research. 15: 54-66. PMID 15632090 DOI: 10.1101/Gr.2889405  0.376
2004 Shatkay H, Miller J, Mobarry C, Flanigan M, Yooseph S, Sutton G. ThurGood: evaluating assembly-to-assembly mapping. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 800-11. PMID 15700403 DOI: 10.1089/Cmb.2004.11.800  0.346
2004 Istrail S, Sutton GG, Florea L, Halpern AL, Mobarry CM, Lippert R, Walenz B, Shatkay H, Dew I, Miller JR, Flanigan MJ, Edwards NJ, Bolanos R, Fasulo D, Halldorsson BV, et al. Whole-genome shotgun assembly and comparison of human genome assemblies. Proceedings of the National Academy of Sciences of the United States of America. 101: 1916-21. PMID 14769938 DOI: 10.1073/Pnas.0307971100  0.432
2002 Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, ... ... Miller J, et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science (New York, N.Y.). 298: 129-49. PMID 12364791 DOI: 10.1126/Science.1076181  0.404
2002 Mural RJ, Adams MD, Myers EW, Smith HO, Miklos GL, Wides R, Halpern A, Li PW, Sutton GG, Nadeau J, Salzberg SL, Holt RA, Kodira CD, Lu F, Chen L, ... ... Miller JR, et al. A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (New York, N.Y.). 296: 1661-71. PMID 12040188 DOI: 10.1126/Science.1069193  0.391
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