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Joshua Orvis

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Address9500 Gilman Drive #
La Jolla CA 92093
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. A Curated Compendium of Transcriptomic Data for the Exploration of Neocortical Development. bioRxiv. 2024 Aug 07. Sonthalia S, Adkins RS, Orvis J, Li G, Mato Blanco X, Casella A, Liu J, Stein-O'Brien G, Caffo B, Hertzano R, Mahurkar A, Gillis J, Werner J, Ma S, Micali N, Sestan N, Rakic P, Santpere G, Ament SA, Colantuoni C. PMID: 38464021; PMCID: PMC10925183.
      View in: PubMed   Mentions:
    2. A guide to the BRAIN Initiative Cell Census Network data ecosystem. PLoS Biol. 2023 06; 21(6):e3002133. Hawrylycz M, Martone ME, Ascoli GA, Bjaalie JG, Dong HW, Ghosh SS, Gillis J, Hertzano R, Haynor DR, Hof PR, Kim Y, Lein E, Liu Y, Miller JA, Mitra PP, Mukamel E, Ng L, Osumi-Sutherland D, Peng H, Ray PL, Sanchez R, Regev A, Ropelewski A, Scheuermann RH, Tan SZK, Thompson CL, Tickle T, Tilgner H, Varghese M, Wester B, White O, Zeng H, Aevermann B, Allemang D, Ament S, Athey TL, Baker C, Baker KS, Baker PM, Bandrowski A, Banerjee S, Bishwakarma P, Carr A, Chen M, Choudhury R, Cool J, Creasy H, D'Orazi F, Degatano K, Dichter B, Ding SL, Dolbeare T, Ecker JR, Fang R, Fillion-Robin JC, Fliss TP, Gee J, Gillespie T, Gouwens N, Zhang GQ, Halchenko YO, Harris NL, Herb BR, Hintiryan H, Hood G, Horvath S, Huo B, Jarecka D, Jiang S, Khajouei F, Kiernan EA, Kir H, Kruse L, Lee C, Lelieveldt B, Li Y, Liu H, Liu L, Markuhar A, Mathews J, Mathews KL, Mezias C, Miller MI, Mollenkopf T, Mufti S, Mungall CJ, Orvis J, Puchades MA, Qu L, Receveur JP, Ren B, Sjoquist N, Staats B, Tward D, van Velthoven CTJ, Wang Q, Xie F, Xu H, Yao Z, Yun Z, Zhang YR, Zheng WJ, Zingg B. PMID: 37390046; PMCID: PMC10313015.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimalsCells
    3. The Neuroscience Multi-Omic Archive: a BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain. Nucleic Acids Res. 2023 01 06; 51(D1):D1075-D1085. Ament SA, Adkins RS, Carter R, Chrysostomou E, Colantuoni C, Crabtree J, Creasy HH, Degatano K, Felix V, Gandt P, Garden GA, Giglio M, Herb BR, Khajouei F, Kiernan E, McCracken C, McDaniel K, Nadendla S, Nickel L, Olley D, Orvis J, Receveur JP, Schor M, Sonthalia S, Tickle TL, Way J, Hertzano R, Mahurkar AA, White OR. PMID: 36318260; PMCID: PMC9825473.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    4. The evolution of synaptic and cognitive capacity: Insights from the nervous system transcriptome of Aplysia. Proc Natl Acad Sci U S A. 2022 07 12; 119(28):e2122301119. Orvis J, Albertin CB, Shrestha P, Chen S, Zheng M, Rodriguez CJ, Tallon LJ, Mahurkar A, Zimin AV, Kim M, Liu K, Kandel ER, Fraser CM, Sossin W, Abrams TW. PMID: 35867761; PMCID: PMC9282427.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    5. Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature. 2022 Apr; 604(7904):E8. Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, Bertagnolli D, Casper T, Castanon RG, Crichton K, Daigle TL, Dalley R, Dee N, Dembrow N, Diep D, Ding SL, Dong W, Fang R, Fischer S, Goldman M, Goldy J, Graybuck LT, Herb BR, Hou X, Kancherla J, Kroll M, Lathia K, van Lew B, Li YE, Liu CS, Liu H, Lucero JD, Mahurkar A, McMillen D, Miller JA, Moussa M, Nery JR, Nicovich PR, Niu SY, Orvis J, Osteen JK, Owen S, Palmer CR, Pham T, Plongthongkum N, Poirion O, Reed NM, Rimorin C, Rivkin A, Romanow WJ, Sedeño-Cortés AE, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Wang X, Xie F, Yanny AM, Zhang R, Ament SA, Behrens MM, Bravo HC, Chun J, Dobin A, Gillis J, Hertzano R, Hof PR, Höllt T, Horwitz GD, Keene CD, Kharchenko PV, Ko AL, Lelieveldt BP, Luo C, Mukamel EA, Pinto-Duarte A, Preiss S, Regev A, Ren B, Scheuermann RH, Smith K, Spain WJ, White OR, Koch C, Hawrylycz M, Tasic B, Macosko EZ, McCarroll SA, Ting JT, Zeng H, Zhang K, Feng G, Ecker JR, Linnarsson S, Lein ES. PMID: 35319013; PMCID: PMC8986536.
      View in: PubMed   Mentions: 3     Fields:    
    6. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature. 2021 10; 598(7879):111-119. Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, Bertagnolli D, Casper T, Castanon RG, Crichton K, Daigle TL, Dalley R, Dee N, Dembrow N, Diep D, Ding SL, Dong W, Fang R, Fischer S, Goldman M, Goldy J, Graybuck LT, Herb BR, Hou X, Kancherla J, Kroll M, Lathia K, van Lew B, Li YE, Liu CS, Liu H, Lucero JD, Mahurkar A, McMillen D, Miller JA, Moussa M, Nery JR, Nicovich PR, Niu SY, Orvis J, Osteen JK, Owen S, Palmer CR, Pham T, Plongthongkum N, Poirion O, Reed NM, Rimorin C, Rivkin A, Romanow WJ, Sedeño-Cortés AE, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Wang X, Xie F, Yanny AM, Zhang R, Ament SA, Behrens MM, Bravo HC, Chun J, Dobin A, Gillis J, Hertzano R, Hof PR, Höllt T, Horwitz GD, Keene CD, Kharchenko PV, Ko AL, Lelieveldt BP, Luo C, Mukamel EA, Pinto-Duarte A, Preissl S, Regev A, Ren B, Scheuermann RH, Smith K, Spain WJ, White OR, Koch C, Hawrylycz M, Tasic B, Macosko EZ, McCarroll SA, Ting JT, Zeng H, Zhang K, Feng G, Ecker JR, Linnarsson S, Lein ES. PMID: 34616062; PMCID: PMC8494640.
      View in: PubMed   Mentions: 356     Fields:    Translation:HumansAnimalsCells
    7. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature. 2021 10; 598(7879):103-110. Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, Casper T, Colantuoni C, Crabtree J, Creasy H, Crichton K, Crow M, Dee N, Dougherty EL, Doyle WI, Dudoit S, Fang R, Felix V, Fong O, Giglio M, Goldy J, Hawrylycz M, Herb BR, Hertzano R, Hou X, Hu Q, Kancherla J, Kroll M, Lathia K, Li YE, Lucero JD, Luo C, Mahurkar A, McMillen D, Nadaf NM, Nery JR, Nguyen TN, Niu SY, Ntranos V, Orvis J, Osteen JK, Pham T, Pinto-Duarte A, Poirion O, Preissl S, Purdom E, Rimorin C, Risso D, Rivkin AC, Smith K, Street K, Sulc J, Svensson V, Tieu M, Torkelson A, Tung H, Vaishnav ED, Vanderburg CR, van Velthoven C, Wang X, White OR, Huang ZJ, Kharchenko PV, Pachter L, Ngai J, Regev A, Tasic B, Welch JD, Gillis J, Macosko EZ, Ren B, Ecker JR, Zeng H, Mukamel EA. PMID: 34616066; PMCID: PMC8494649.
      View in: PubMed   Mentions: 176     Fields:    Translation:AnimalsCells
    8. A cell-type-specific atlas of the inner ear transcriptional response to acoustic trauma. Cell Rep. 2021 09 28; 36(13):109758. Milon B, Shulman ED, So KS, Cederroth CR, Lipford EL, Sperber M, Sellon JB, Sarlus H, Pregernig G, Shuster B, Song Y, Mitra S, Orvis J, Margulies Z, Ogawa Y, Shults C, Depireux DA, Palermo AT, Canlon B, Burns J, Elkon R, Hertzano R. PMID: 34592158; PMCID: PMC8709734.
      View in: PubMed   Mentions: 51     Fields:    Translation:AnimalsCellsPHPublic Health
    9. gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration. Nat Methods. 2021 08; 18(8):843-844. Orvis J, Gottfried B, Kancherla J, Adkins RS, Song Y, Dror AA, Olley D, Rose K, Chrysostomou E, Kelly MC, Milon B, Matern MS, Azaiez H, Herb B, Colantuoni C, Carter RL, Ament SA, Kelley MW, White O, Bravo HC, Mahurkar A, Hertzano R. PMID: 34172972; PMCID: PMC8996439.
      View in: PubMed   Mentions: 97     Fields:    Translation:HumansCells
    10. HMPDACC: a Human Microbiome Project Multi-omic data resource. Nucleic Acids Res. 2021 01 08; 49(D1):D734-D742. Creasy HH, Felix V, Aluvathingal J, Crabtree J, Ifeonu O, Matsumura J, McCracken C, Nickel L, Orvis J, Schor M, Giglio M, Mahurkar A, White O. PMID: 33305317; PMCID: PMC7778886.
      View in: PubMed   Mentions: 16     Fields:    Translation:Humans
    11. Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity. PLoS Negl Trop Dis. 2020 10; 14(10):e0008781. Palmateer NC, Tretina K, Orvis J, Ifeonu OO, Crabtree J, Drabék E, Pelle R, Awino E, Gotia HT, Munro JB, Tallon L, Morrison WI, Daubenberger CA, Nene V, Knowles DP, Bishop RP, Silva JC. PMID: 33119590; PMCID: PMC7654785.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    12. De novo assembly and annotation of transcriptomes from two cultivars of Cannabis sativa with different cannabinoid profiles. Gene. 2020 Dec 15; 762:145026. McGarvey P, Huang J, McCoy M, Orvis J, Katsir Y, Lotringer N, Nesher I, Kavarana M, Sun M, Peet R, Meiri D, Madhavan S. PMID: 32781193.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    13. Characterization of the development of the mouse cochlear epithelium at the single cell level. Nat Commun. 2020 05 13; 11(1):2389. Kolla L, Kelly MC, Mann ZF, Anaya-Rocha A, Ellis K, Lemons A, Palermo AT, So KS, Mays JC, Orvis J, Burns JC, Hertzano R, Driver EC, Kelley MW. PMID: 32404924; PMCID: PMC7221106.
      View in: PubMed   Mentions: 164     Fields:    Translation:AnimalsCells
    14. Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms. BMC Genomics. 2020 Apr 03; 21(1):279. Tretina K, Pelle R, Orvis J, Gotia HT, Ifeonu OO, Kumari P, Palmateer NC, Iqbal SBA, Fry LM, Nene VM, Daubenberger CA, Bishop RP, Silva JC. PMID: 32245418; PMCID: PMC7126163.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    15. Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project. Nature. 2017 11 09; 551(7679):256. Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C. PMID: 29022944; PMCID: PMC7608344.
      View in: PubMed   Mentions: 14     Fields:    
    16. Strains, functions and dynamics in the expanded Human Microbiome Project. Nature. 2017 10 05; 550(7674):61-66. Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C. PMID: 28953883; PMCID: PMC5831082.
      View in: PubMed   Mentions: 647     Fields:    Translation:Humans
    17. Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions. Sci Rep. 2016 10 18; 6:35284. Silva JC, Cornillot E, McCracken C, Usmani-Brown S, Dwivedi A, Ifeonu OO, Crabtree J, Gotia HT, Virji AZ, Reynes C, Colinge J, Kumar V, Lawres L, Pazzi JE, Pablo JV, Hung C, Brancato J, Kumari P, Orvis J, Tretina K, Chibucos M, Ott S, Sadzewicz L, Sengamalay N, Shetty AC, Su Q, Tallon L, Fraser CM, Frutos R, Molina DM, Krause PJ, Ben Mamoun C. PMID: 27752055; PMCID: PMC5082761.
      View in: PubMed   Mentions: 50     Fields:    Translation:HumansAnimals
    18. Annotated draft genome sequences of three species of Cryptosporidium: Cryptosporidium meleagridis isolate UKMEL1, C. baileyi isolate TAMU-09Q1 and C. hominis isolates TU502_2012 and UKH1. Pathog Dis. 2016 10; 74(7). Ifeonu OO, Chibucos MC, Orvis J, Su Q, Elwin K, Guo F, Zhang H, Xiao L, Sun M, Chalmers RM, Fraser CM, Zhu G, Kissinger JC, Widmer G, Silva JC. PMID: 27519257; PMCID: PMC5407061.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansAnimalsCells
    19. An integrated genomic and transcriptomic survey of mucormycosis-causing fungi. Nat Commun. 2016 07 22; 7:12218. Chibucos MC, Soliman S, Gebremariam T, Lee H, Daugherty S, Orvis J, Shetty AC, Crabtree J, Hazen TH, Etienne KA, Kumari P, O'Connor TD, Rasko DA, Filler SG, Fraser CM, Lockhart SR, Skory CD, Ibrahim AS, Bruno VM. PMID: 27447865; PMCID: PMC4961843.
      View in: PubMed   Mentions: 77     Fields:    Translation:HumansAnimalsCells
    20. The genome sequence of four isolates from the family Lichtheimiaceae. Pathog Dis. 2015 Jul; 73(5). Chibucos MC, Etienne KA, Orvis J, Lee H, Daugherty S, Lockhart SR, Ibrahim AS, Bruno VM. PMID: 25857734; PMCID: PMC4467520.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsPHPublic Health
    21. Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys. BMC Genomics. 2014 Aug 29; 15:738. Ioannidis P, Lu Y, Kumar N, Creasy T, Daugherty S, Chibucos MC, Orvis J, Shetty A, Ott S, Flowers M, Sengamalay N, Tallon LJ, Pick L, Dunning Hotopp JC. PMID: 25168586; PMCID: PMC4174608.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    22. Draft Genome Sequence of Mortierella alpina Isolate CDC-B6842. Genome Announc. 2014 Jan 23; 2(1). Etienne KA, Chibucos MC, Su Q, Orvis J, Daugherty S, Ott S, Sengamalay NA, Fraser CM, Lockhart SR, Bruno VM. PMID: 24459263; PMCID: PMC3900895.
      View in: PubMed   Mentions: 5  
    23. The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res. 2014 Jan; 42(Database issue):D705-10. Cerqueira GC, Arnaud MB, Inglis DO, Skrzypek MS, Binkley G, Simison M, Miyasato SR, Binkley J, Orvis J, Shah P, Wymore F, Sherlock G, Wortman JR. PMID: 24194595; PMCID: PMC3965050.
      View in: PubMed   Mentions: 156     Fields:    Translation:Animals
    24. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013 Aug; 8(8):1494-512. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A. PMID: 23845962; PMCID: PMC3875132.
      View in: PubMed   Mentions: 4068     Fields:    Translation:AnimalsCells
    25. Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities. PLoS One. 2012; 7(6):e36427. Martin J, Sykes S, Young S, Kota K, Sanka R, Sheth N, Orvis J, Sodergren E, Wang Z, Weinstock GM, Mitreva M. PMID: 22719831; PMCID: PMC3374613.
      View in: PubMed   Mentions: 32     Fields:    Translation:Humans
    26. Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses. BMC Genomics. 2011 Nov 23; 12:570. Siddaramappa S, Challacombe JF, Duncan AJ, Gillaspy AF, Carson M, Gipson J, Orvis J, Zaitshik J, Barnes G, Bruce D, Chertkov O, Detter JC, Han CS, Tapia R, Thompson LS, Dyer DW, Inzana TJ. PMID: 22111657; PMCID: PMC3339403.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    27. The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources. Nucleic Acids Res. 2012 Jan; 40(Database issue):D653-9. Arnaud MB, Cerqueira GC, Inglis DO, Skrzypek MS, Binkley J, Chibucos MC, Crabtree J, Howarth C, Orvis J, Shah P, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G, Wortman JR. PMID: 22080559; PMCID: PMC3245136.
      View in: PubMed   Mentions: 99     Fields:    Translation:Animals
    28. The IGS Standard Operating Procedure for Automated Prokaryotic Annotation. Stand Genomic Sci. 2011 Apr 29; 4(2):244-51. Galens K, Orvis J, Daugherty S, Creasy HH, Angiuoli S, White O, Wortman J, Mahurkar A, Giglio MG. PMID: 21677861; PMCID: PMC3111993.
      View in: PubMed   Mentions: 106  
    29. Draft genome sequence of the oilseed species Ricinus communis. Nat Biotechnol. 2010 Sep; 28(9):951-6. Chan AP, Crabtree J, Zhao Q, Lorenzi H, Orvis J, Puiu D, Melake-Berhan A, Jones KM, Redman J, Chen G, Cahoon EB, Gedil M, Stanke M, Haas BJ, Wortman JR, Fraser-Liggett CM, Ravel J, Rabinowicz PD. PMID: 20729833; PMCID: PMC2945230.
      View in: PubMed   Mentions: 213     Fields:    Translation:AnimalsCells
    30. A catalog of reference genomes from the human microbiome. Science. 2010 May 21; 328(5981):994-9. Human Microbiome Jumpstart Reference Strains Consortium, 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, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, FitzGerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D. PMID: 20489017; PMCID: PMC2940224.
      View in: PubMed   Mentions: 352     Fields:    Translation:HumansCells
    31. Ergatis: a web interface and scalable software system for bioinformatics workflows. Bioinformatics. 2010 Jun 15; 26(12):1488-92. Orvis J, Crabtree J, Galens K, Gussman A, Inman JM, Lee E, Nampally S, Riley D, Sundaram JP, Felix V, Whitty B, Mahurkar A, Wortman J, White O, Angiuoli SV. PMID: 20413634; PMCID: PMC2881353.
      View in: PubMed   Mentions: 62     Fields:    
    32. Transcriptional and functional analysis of the Neisseria gonorrhoeae Fur regulon. J Bacteriol. 2010 Jan; 192(1):77-85. Jackson LA, Ducey TF, Day MW, Zaitshik JB, Orvis J, Dyer DW. PMID: 19854902; PMCID: PMC2798271.
      View in: PubMed   Mentions: 40     Fields:    Translation:Cells
    33. Pathema: a clade-specific bioinformatics resource center for pathogen research. Nucleic Acids Res. 2010 Jan; 38(Database issue):D408-14. Brinkac LM, Davidsen T, Beck E, Ganapathy A, Caler E, Dodson RJ, Durkin AS, Harkins DM, Lorenzi H, Madupu R, Sebastian Y, Shrivastava S, Thiagarajan M, Orvis J, Sundaram JP, Crabtree J, Galens K, Zhao Y, Inman JM, Montgomery R, Schobel S, Galinsky K, Tanenbaum DM, Resnick A, Zafar N, White O, Sutton G. PMID: 19843611; PMCID: PMC2808925.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    34. The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community. Nucleic Acids Res. 2010 Jan; 38(Database issue):D420-7. Arnaud MB, Chibucos MC, Costanzo MC, Crabtree J, Inglis DO, Lotia A, Orvis J, Shah P, Skrzypek MS, Binkley G, Miyasato SR, Wortman JR, Sherlock G. PMID: 19773420; PMCID: PMC2808984.
      View in: PubMed   Mentions: 69     Fields:    Translation:AnimalsCells
    35. Transcript analysis of nrrF, a Fur repressed sRNA of Neisseria gonorrhoeae. Microb Pathog. 2009 Mar; 46(3):166-70. Ducey TF, Jackson L, Orvis J, Dyer DW. PMID: 19162160; PMCID: PMC4890603.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    36. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet. 2008 Apr 11; 4(4):e1000046. Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, Anderson MJ, Crabtree J, Silva JC, Badger JH, Albarraq A, Angiuoli S, Bussey H, Bowyer P, Cotty PJ, Dyer PS, Egan A, Galens K, Fraser-Liggett CM, Haas BJ, Inman JM, Kent R, Lemieux S, Malavazi I, Orvis J, Roemer T, Ronning CM, Sundaram JP, Sutton G, Turner G, Venter JC, White OR, Whitty BR, Youngman P, Wolfe KH, Goldman GH, Wortman JR, Jiang B, Denning DW, Nierman WC. PMID: 18404212; PMCID: PMC2289846.
      View in: PubMed   Mentions: 242     Fields:    Translation:HumansAnimalsCells
    37. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 2008 Jan 11; 9(1):R7. Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR. PMID: 18190707; PMCID: PMC2395244.
      View in: PubMed   Mentions: 2030     Fields:    Translation:HumansAnimals
    38. Genome sequence of Aedes aegypti, a major arbovirus vector. Science. 2007 Jun 22; 316(5832):1718-23. 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, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, Debruyn B, Decaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, Labutti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CF, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JM, Vanzee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, Severson DW. PMID: 17510324; PMCID: PMC2868357.
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    39. The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res. 2007 Jan; 35(Database issue):D883-7. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR. PMID: 17145706; PMCID: PMC1751532.
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    40. Genomic distribution and functions of uptake signal sequences in Actinobacillus actinomycetemcomitans. Microbiology (Reading). 2006 Nov; 152(Pt 11):3319-3325. Wang Y, Orvis J, Dyer D, Chen C. PMID: 17074902.
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    41. Identification of the iron-responsive genes of Neisseria gonorrhoeae by microarray analysis in defined medium. J Bacteriol. 2005 Jul; 187(14):4865-74. Ducey TF, Carson MB, Orvis J, Stintzi AP, Dyer DW. PMID: 15995201; PMCID: PMC1169496.
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    42. Regulation and autoregulation of the promoter for the latency-associated nuclear antigen of Kaposi's sarcoma-associated herpesvirus. J Biol Chem. 2004 Apr 16; 279(16):16822-31. Jeong JH, Orvis J, Kim JW, McMurtrey CP, Renne R, Dittmer DP. PMID: 14742422.
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