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Douglas B. Rusch - Publications

Affiliations: 
J. Craig Venter Institute, San Diego, CA, United States 
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56 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 McKay LJ, Nigro OD, Dlakić M, Luttrell KM, Rusch DB, Fields MW, Inskeep WP. Sulfur cycling and host-virus interactions in Aquificales-dominated biofilms from Yellowstone's hottest ecosystems. The Isme Journal. PMID 34650231 DOI: 10.1038/s41396-021-01132-4  0.31
2019 Simpson CA, Podicheti R, Rusch DB, Dalia AB, van Kessel JC. Diversity in Natural Transformation Frequencies and Regulation across Species. Mbio. 10. PMID 31848285 DOI: 10.1128/Mbio.02788-19  0.326
2019 Chaparian RR, Tran MLN, Miller Conrad LC, Rusch DB, van Kessel JC. Global H-NS counter-silencing by LuxR activates quorum sensing gene expression. Nucleic Acids Research. PMID 31745565 DOI: 10.1093/Nar/Gkz1089  0.325
2019 Bentz AB, Thomas GWC, Rusch DB, Rosvall KA. Tissue-specific expression profiles and positive selection analysis in the tree swallow (Tachycineta bicolor) using a de novo transcriptome assembly. Scientific Reports. 9: 15849. PMID 31676844 DOI: 10.1038/S41598-019-52312-4  0.356
2019 Barton IS, Platt TG, Rusch DB, Fuqua C. Destabilization of the Tumor-Inducing Plasmid from an Octopine-Type Lineage Drives a Large Deletion in the Co-resident At Megaplasmid. G3 (Bethesda, Md.). PMID 31451548 DOI: 10.1534/G3.119.400554  0.344
2019 McKay LJ, Dlakić M, Fields MW, Delmont TO, Eren AM, Jay ZJ, Klingelsmith KB, Rusch DB, Inskeep WP. Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota. Nature Microbiology. PMID 30833730 DOI: 10.1038/S41564-019-0362-4  0.322
2019 Ellison CK, Rusch DB, Brun YV. Flagellar mutants have reduced pilus synthesis in . Journal of Bacteriology. PMID 30833355 DOI: 10.1128/Jb.00031-19  0.339
2019 Sinha D, Zimmer K, Cameron TA, Rusch DB, Winkler ME, De Lay NR. Redefining the sRNA Transcriptome in Serotype 2 Strain D39. Journal of Bacteriology. PMID 30833353 DOI: 10.1128/Jb.00764-18  0.327
2018 Jay ZJ, Beam JP, Dlakić M, Rusch DB, Kozubal MA, Inskeep WP. Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats. Nature Microbiology. PMID 29760463 DOI: 10.1038/S41564-018-0163-1  0.339
2017 Rusch DB, Rowe-Magnus DA. Complete Genome Sequence of the Pathogenic Vibrio vulnificus Type Strain ATCC 27562. Genome Announcements. 5. PMID 28860258 DOI: 10.1128/Genomea.00907-17  0.356
2017 Orsini L, Brown JB, Shams Solari O, Li D, He S, Podicheti R, Stoiber MH, Spanier KI, Gilbert D, Jansen M, Rusch D, Pfrender ME, Colbourne JK, Frilander MJ, Kvist J, et al. Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean specific genes. Molecular Ecology. PMID 28746735 DOI: 10.1111/Mec.14261  0.317
2017 Miller DF, Yan P, Fang F, Buechlein A, Kroll K, Frankhouser D, Stump C, Stump P, Ford JB, Tang H, Michaels S, Matei D, Huang TH, Chien J, Liu Y, ... Rusch DB, et al. Complete Transcriptome RNA-Seq. Methods in Molecular Biology (Clifton, N.J.). 1513: 141-162. PMID 27807835 DOI: 10.1007/978-1-4939-6539-7_10  0.346
2016 Llorens-Marès T, Liu Z, Allen LZ, Rusch DB, Craig MT, Dupont CL, Bryant DA, Casamayor EO. Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly. The Isme Journal. PMID 27392085 DOI: 10.1038/Ismej.2016.93  0.395
2016 Díez B, Nylander JA, Ininbergs K, Dupont CL, Allen AE, Yooseph S, Rusch DB, Bergman B. Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution. Plos One. 11: e0155757. PMID 27196065 DOI: 10.1371/Journal.Pone.0155757  0.393
2016 Jay ZJ, Beam JP, Kozubal MA, deM Jennings R, Rusch DB, Inskeep WP. The distribution, diversity and function of predominant Thermoproteales in high-temperature environments of Yellowstone National Park. Environmental Microbiology. PMID 27130276 DOI: 10.1111/1462-2920.13366  0.356
2016 Colman DR, Jay ZJ, Inskeep WP, Jennings Rd, Maas KR, Rusch DB, Takacs-Vesbach CD. Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes. Frontiers in Microbiology. 7: 304. PMID 27014227 DOI: 10.3389/Fmicb.2016.00304  0.397
2016 Hahn NM, Cramer HM, Badve SS, Cheng L, Gokmen-Polar Y, Miller DF, Buechlein A, Rusch DB, Fang F, Frankhouser D, Bundschu R, Javkhlan-Ochir G, Koch MO, Bihrle R, Foster R, et al. Identification of novel immunomodulatory tumor biology through comprehensive characterization of a metastases-specific epigenome in patients with metachronous primary and metastatic urothelial carcinoma (UC) tumor pairs. Journal of Clinical Oncology. 34: 452-452. DOI: 10.1200/Jco.2016.34.2_Suppl.452  0.321
2015 Melendrez MC, Becraft ED, Wood JM, Olsen MT, Bryant DA, Heidelberg JF, Rusch DB, Cohan FM, Ward DM. Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat. Frontiers in Microbiology. 6: 1540. PMID 26834710 DOI: 10.3389/Fmicb.2015.01540  0.357
2015 Liu J, Zimmer K, Rusch DB, Paranjape N, Podicheti R, Tang H, Calvi BR. DNA sequence templates adjacent nucleosome and ORC sites at gene amplification origins in Drosophila. Nucleic Acids Research. PMID 26227968 DOI: 10.1093/Nar/Gkv766  0.361
2015 Olsen MT, Nowack S, Wood JM, Becraft ED, LaButti K, Lipzen A, Martin J, Schackwitz WS, Rusch DB, Cohan FM, Bryant DA, Ward DM. The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat. Frontiers in Microbiology. 6: 604. PMID 26157428 DOI: 10.3389/Fmicb.2015.00604  0.367
2015 Becraft ED, Wood JM, Rusch DB, Kühl M, Jensen SI, Bryant DA, Roberts DW, Cohan FM, Ward DM. The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park. Frontiers in Microbiology. 6: 590. PMID 26157420 DOI: 10.3389/Fmicb.2015.00590  0.355
2015 Beam JP, Jay ZJ, Schmid MC, Rusch DB, Romine MF, M Jennings R, Kozubal MA, Tringe SG, Wagner M, Inskeep WP. Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous 'streamer' community. The Isme Journal. PMID 26140529 DOI: 10.1038/Ismej.2015.83  0.386
2015 Rynkiewicz EC, Hemmerich C, Rusch DB, Fuqua C, Clay K. Concordance of bacterial communities of two tick species and blood of their shared rodent host. Molecular Ecology. 24: 2566-79. PMID 25847197 DOI: 10.1111/Mec.13187  0.347
2015 Wheeler EC, Washburn MC, Major F, Rusch DB, Hundley HA. Noncoding regions of C. elegans mRNA undergo selective adenosine to inosine deamination and contain a small number of editing sites per transcript. Rna Biology. 12: 162-74. PMID 25826568 DOI: 10.1080/15476286.2015.1017220  0.324
2015 Matei D, Fang F, Cardenas H, Miller DF, Buechlein A, Yu Q, Perkins SM, Liu Y, Jiang G, Taverna P, Keer HN, Rusch DB, Nephew KP. Epigenome and genome alterations in platinum resistant ovarian cancer. Journal of Clinical Oncology. 33: 5555-5555. DOI: 10.1200/Jco.2015.33.15_Suppl.5555  0.306
2014 Dupont CL, Larsson J, Yooseph S, Ininbergs K, Goll J, Asplund-Samuelsson J, McCrow JP, Celepli N, Allen LZ, Ekman M, Lucas AJ, Hagström Å, Thiagarajan M, Brindefalk B, Richter AR, ... ... Rusch DB, et al. Functional tradeoffs underpin salinity-driven divergence in microbial community composition. Plos One. 9: e89549. PMID 24586863 DOI: 10.1371/Journal.Pone.0089549  0.359
2014 Jay ZJ, Rusch DB, Tringe SG, Bailey C, Jennings RM, Inskeep WP. Predominant Acidilobus-like populations from geothermal environments in yellowstone national park exhibit similar metabolic potential in different hypoxic microbial communities. Applied and Environmental Microbiology. 80: 294-305. PMID 24162572 DOI: 10.1128/Aem.02860-13  0.307
2013 Klatt CG, Inskeep WP, Herrgard MJ, Jay ZJ, Rusch DB, Tringe SG, Niki Parenteau M, Ward DM, Boomer SM, Bryant DA, Miller SR. Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. Frontiers in Microbiology. 4: 106. PMID 23761787 DOI: 10.3389/Fmicb.2013.00106  0.404
2013 Takacs-Vesbach C, Inskeep WP, Jay ZJ, Herrgard MJ, Rusch DB, Tringe SG, Kozubal MA, Hamamura N, Macur RE, Fouke BW, Reysenbach AL, McDermott TR, Jennings Rd, Hengartner NW, Xie G. Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages. Frontiers in Microbiology. 4: 84. PMID 23755042 DOI: 10.3389/Fmicb.2013.00084  0.4
2013 Inskeep WP, Jay ZJ, Herrgard MJ, Kozubal MA, Rusch DB, Tringe SG, Macur RE, Jennings Rd, Boyd ES, Spear JR, Roberto FF. Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry. Frontiers in Microbiology. 4: 95. PMID 23720654 DOI: 10.3389/Fmicb.2013.00095  0.412
2013 Inskeep WP, Jay ZJ, Tringe SG, Herrgård MJ, Rusch DB. The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem. Frontiers in Microbiology. 4: 67. PMID 23653623 DOI: 10.3389/Fmicb.2013.00067  0.407
2013 Rusch DB, Lombardo MJ, Yee-Greenbaum J, Novotny M, Brinkac LM, Lasken RS, Dupont CL. Draft Genome Sequence of a Single Cell of SAR86 Clade Subgroup IIIa. Genome Announcements. 1. PMID 23405308 DOI: 10.1128/Genomea.00030-12  0.374
2012 Zeigler Allen L, Allen EE, Badger JH, McCrow JP, Paulsen IT, Elbourne LD, Thiagarajan M, Rusch DB, Nealson KH, Williamson SJ, Venter JC, Allen AE. Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. The Isme Journal. 6: 1403-14. PMID 22278668 DOI: 10.1038/Ismej.2011.201  0.31
2012 Dupont CL, Rusch DB, Yooseph S, Lombardo MJ, Richter RA, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH, Halpern AL, Lasken RS, Nealson K, Friedman R, Venter JC. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. The Isme Journal. 6: 1186-99. PMID 22170421 DOI: 10.1038/Ismej.2011.189  0.401
2011 Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RS. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nature Biotechnology. 29: 915-21. PMID 21926975 DOI: 10.1038/Nbt.1966  0.38
2011 Liu Z, Klatt CG, Wood JM, Rusch DB, Ludwig M, Wittekindt N, Tomsho LP, Schuster SC, Ward DM, Bryant DA. Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat. The Isme Journal. 5: 1279-90. PMID 21697962 DOI: 10.1038/Ismej.2011.37  0.436
2011 Klatt CG, Wood JM, Rusch DB, Bateson MM, Hamamura N, Heidelberg JF, Grossman AR, Bhaya D, Cohan FM, Kühl M, Bryant DA, Ward DM. Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential. The Isme Journal. 5: 1262-78. PMID 21697961 DOI: 10.1038/Ismej.2011.73  0.441
2011 Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA. Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. Plos One. 6: e18011. PMID 21437252 DOI: 10.1371/Journal.Pone.0018011  0.405
2010 Tanenbaum DM, Goll J, Murphy S, Kumar P, Zafar N, Thiagarajan M, Madupu R, Davidsen T, Kagan L, Kravitz S, Rusch DB, Yooseph S. The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data. Standards in Genomic Sciences. 2: 229-37. PMID 21304707 DOI: 10.4056/Sigs.651139  0.397
2010 Yooseph S, Nealson KH, Rusch DB, McCrow JP, Dupont CL, Kim M, Johnson J, Montgomery R, Ferriera S, Beeson K, Williamson SJ, Tovchigrechko A, Allen AE, Zeigler LA, Sutton G, et al. Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature. 468: 60-6. PMID 21048761 DOI: 10.1038/Nature09530  0.408
2010 Rusch DB, Martiny AC, Dupont CL, Halpern AL, Venter JC. Characterization of Prochlorococcus clades from iron-depleted oceanic regions. Proceedings of the National Academy of Sciences of the United States of America. 107: 16184-9. PMID 20733077 DOI: 10.1073/Pnas.1009513107  0.313
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, 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  0.427
2010 Inskeep WP, Rusch DB, Jay ZJ, Herrgard MJ, Kozubal MA, Richardson TH, Macur RE, Hamamura N, Jennings Rd, Fouke BW, Reysenbach AL, Roberto F, Young M, Schwartz A, Boyd ES, et al. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. Plos One. 5: e9773. PMID 20333304 DOI: 10.1371/Journal.Pone.0009773  0.378
2010 Selengut JD, Rusch DB, Haft DH. Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function. Bmc Bioinformatics. 11: 52. PMID 20102603 DOI: 10.1186/1471-2105-11-52  0.357
2009 Pearson A, Rusch DB. Distribution of microbial terpenoid lipid cyclases in the global ocean metagenome. The Isme Journal. 3: 352-63. PMID 19037261 DOI: 10.1038/Ismej.2008.116  0.374
2008 Williamson SJ, Rusch DB, Yooseph S, Halpern AL, Heidelberg KB, Glass JI, Andrews-Pfannkoch C, Fadrosh D, Miller CS, Sutton G, Frazier M, Venter JC. The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples. Plos One. 3: e1456. PMID 18213365 DOI: 10.1371/Journal.Pone.0001456  0.416
2007 Sharon I, Tzahor S, Williamson S, Shmoish M, Man-Aharonovich D, Rusch DB, Yooseph S, Zeidner G, Golden SS, Mackey SR, Adir N, Weingart U, Horn D, Venter JC, Mandel-Gutfreund Y, et al. Viral photosynthetic reaction center genes and transcripts in the marine environment. The Isme Journal. 1: 492-501. PMID 18043651 DOI: 10.1038/Ismej.2007.67  0.372
2007 Yutin N, Suzuki MT, Teeling H, Weber M, Venter JC, Rusch DB, Béjà O. Assessing diversity and biogeography of aerobic anoxygenic phototrophic bacteria in surface waters of the Atlantic and Pacific Oceans using the Global Ocean Sampling expedition metagenomes. Environmental Microbiology. 9: 1464-75. PMID 17504484 DOI: 10.1111/J.1462-2920.2007.01265.X  0.319
2007 Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. Plos Biology. 5: e77. PMID 17355176 DOI: 10.1371/Journal.Pbio.0050077  0.454
2007 Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, et al. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. Plos Biology. 5: e16. PMID 17355171 DOI: 10.1371/Journal.Pbio.0050016  0.328
2003 Kirkness EF, Bafna V, Halpern AL, Levy S, Remington K, Rusch DB, Delcher AL, Pop M, Wang W, Fraser CM, Venter JC. The dog genome: survey sequencing and comparative analysis. Science (New York, N.Y.). 301: 1898-903. PMID 14512627 DOI: 10.1126/Science.1086432  0.388
2003 Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD, Salzberg SL, White O. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Research. 31: 5654-66. PMID 14500829 DOI: 10.1093/Nar/Gkg770  0.411
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, 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  0.407
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, ... ... Rusch DB, 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  0.364
2001 Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, ... ... Rusch DB, et al. The sequence of the human genome. Science (New York, N.Y.). 291: 1304-51. PMID 11181995 DOI: 10.1126/Science.1058040  0.404
1998 Popadic A, Abzhanov A, Rusch D, Kaufman TC. Understanding the genetic basis of morphological evolution: the role of homeotic genes in the diversification of the arthropod bauplan. The International Journal of Developmental Biology. 42: 453-461. DOI: 10.1387/Ijdb.9654031  0.321
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