Joshua Orvis
Joshua Orvis
Institute for Genome Sciences & Johns Hopkins
Verified email at - Homepage
Cited by
Cited by
Structure, function and diversity of the healthy human microbiome
Human Microbiome Project Consortium
nature 486 (7402), 207, 2012
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
BJ Haas, A Papanicolaou, M Yassour, M Grabherr, PD Blood, J Bowden, ...
Nature protocols 8 (8), 1494-1512, 2013
A framework for human microbiome research
BA Methé, KE Nelson, M Pop, HH Creasy, MG Giglio, C Huttenhower, ...
nature 486 (7402), 215, 2012
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
BJ Haas, SL Salzberg, W Zhu, M Pertea, JE Allen, J Orvis, O White, ...
Genome biology 9 (1), 1-22, 2008
Genome sequence of Aedes aegypti, a major arbovirus vector
V Nene, JR Wortman, D Lawson, B Haas, C Kodira, ZJ Tu, B Loftus, Z Xi, ...
Science 316 (5832), 1718-1723, 2007
The TIGR rice genome annotation resource: improvements and new features
S Ouyang, W Zhu, J Hamilton, H Lin, M Campbell, K Childs, ...
Nucleic acids research 35 (suppl_1), D883-D887, 2007
A catalog of reference genomes from the human microbiome
Human Microbiome Jumpstart Reference Strains Consortium, KE Nelson, ...
Science 328 (5981), 994-999, 2010
Strains, functions and dynamics in the expanded Human Microbiome Project
J Lloyd-Price, A Mahurkar, G Rahnavard, J Crabtree, J Orvis, AB Hall, ...
Nature 550 (7674), 61-66, 2017
Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus
ND Fedorova, N Khaldi, VS Joardar, R Maiti, P Amedeo, MJ Anderson, ...
PLoS genetics 4 (4), e1000046, 2008
Draft genome sequence of the oilseed species Ricinus communis
AP Chan, J Crabtree, Q Zhao, H Lorenzi, J Orvis, D Puiu, ...
Nature biotechnology 28 (9), 951-956, 2010
The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations
GC Cerqueira, MB Arnaud, DO Inglis, MS Skrzypek, G Binkley, M Simison, ...
Nucleic acids research 42 (D1), D705-D710, 2014
The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources
MB Arnaud, GC Cerqueira, DO Inglis, MS Skrzypek, J Binkley, ...
Nucleic acids research 40 (D1), D653-D659, 2012
The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community
MB Arnaud, MC Chibucos, MC Costanzo, J Crabtree, DO Inglis, A Lotia, ...
Nucleic acids research 38 (suppl_1), D420-D427, 2010
The IGS standard operating procedure for automated prokaryotic annotation
K Galens, J Orvis, S Daugherty, HH Creasy, S Angiuoli, O White, ...
Standards in genomic sciences 4 (2), 244-251, 2011
Identification of the Iron-Responsive Genes of Neisseria gonorrhoeae by Microarray Analysis in Defined Medium
TF Ducey, MB Carson, J Orvis, AP Stintzi, DW Dyer
Journal of bacteriology 187 (14), 4865-4874, 2005
Ergatis: a web interface and scalable software system for bioinformatics workflows
J Orvis, J Crabtree, K Galens, A Gussman, JM Inman, E Lee, S Nampally, ...
Bioinformatics 26 (12), 1488-1492, 2010
The Staphylococcus aureus NCTC 8325 Genome
AF Gillaspy, V Worrell, J Orvis, BA Roe, DW Dyer, JJ Iandolo
Gram‐Positive Pathogens, 381-412, 2006
An integrated genomic and transcriptomic survey of mucormycosis-causing fungi
MC Chibucos, S Soliman, T Gebremariam, H Lee, S Daugherty, J Orvis, ...
Nature communications 7 (1), 1-11, 2016
Transcriptional and Functional Analysis of the Neisseria gonorrhoeae Fur Regulon
LA Jackson, TF Ducey, MW Day, JB Zaitshik, J Orvis, DW Dyer
Journal of bacteriology 192 (1), 77-85, 2010
Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities
J Martin, S Sykes, S Young, K Kota, R Sanka, N Sheth, J Orvis, ...
PloS one 7 (6), e36427, 2012
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