Skip to Main Content

Author Details

Shibu Yooseph
University of Central Florida
1998
89
41
PMIDPaper TitleJournal TitlePublished Year
36915411Integrated <i>de novo</i> gene prediction and peptide assembly of metagenomic sequencing data.NAR Genom Bioinform2023
36195733Species-specific transcriptomic changes upon respiratory syncytial virus infection in cotton rats.Sci Rep2022
35549398Variational Approximation-Based Model Selection for Microbial Network Inference.J Comput Biol2022
35670514De Novo Genome Assembly Highlights the Role of Lineage-Specific Gene Duplications in the Evolution of Venom in Fea's Viper (Azemiops feae).Genome Biol Evol2022
35692084Maternal binge alcohol consumption leads to distinctive acute perturbations in embryonic cardiac gene expression profiles.Alcohol Clin Exp Res2022
33408227Identification of Nasal Gammaproteobacteria with Potent Activity against Staphylococcus aureus: Novel Insights into the "Noncarrier" State.mSphere2021
33546321Peroxidized Linoleic Acid, 13-HPODE, Alters Gene Expression Profile in Intestinal Epithelial Cells.Foods2021
33789570Bacterial community structure alterations within the colorectal cancer gut microbiome.BMC Microbiol2021
33644803Pulmonary Microbiome of Patients Receiving Mechanical Ventilation: Changes Over Time.Am J Crit Care2021
33531651Bacterial associations in the healthy human gut microbiome across populations.Sci Rep2021
33863395Microbial community structure and composition is associated with host species and sex in Sigmodon cotton rats.Anim Microbiome2021
34790908Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples.Cell Rep Methods2021
34349736Linking Inflammatory Bowel Disease Symptoms to Changes in the Gut Microbiome Structure and Function.Front Microbiol2021
31611653Global ecotypes in the ubiquitous marine clade SAR86.ISME J2020
33244064Evaluation of the upper airway microbiome and immune response with nasal epithelial lining fluid absorption and nasal washes.Sci Rep2020
31167633GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data.BMC Bioinformatics2019
30141127Co-occurrence of Anaerobes in Human Chronic Wounds.Microb Ecol2019
31484056Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease.Cell Metab2019
31510709Learning a mixture of microbial networks using minorization-maximization.Bioinformatics2019
29345635Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease.Clin Transl Gastroenterol2018
30039863Papio spp. Colon microbiome and its link to obesity in pregnancy.J Med Primatol2018
29979671Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.Nat Biotechnol2018
30522530Uncovering complex microbiome activities via metatranscriptomics during 24â¿¿hours of oral biofilm assembly and maturation.Microbiome2018
29406516Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.Nat Biotechnol2018
27871145Meta-omic analyses of Baltic Sea cyanobacteria: diversity, community structure and salt acclimation.Environ Microbiol2017
28407798Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies.BMC Genomics2017
28467925Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease.Cell Metab2017
29120399A Microbiomic Analysis in African Americans with Colonic Lesions Reveals Streptococcus sp.VT162 as a Marker of Neoplastic Transformation.Genes (Basel)2017
28787424Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.Nat Biotechnol2017
27815589Effect of Macondo Prospect 252 Oil on Microbiota Associated with Pelagic Sargassum in the Northern Gulf of Mexico.Microb Ecol2017
26836261Global biogeography of Prochlorococcus genome diversity in the surface ocean.ISME J2016
27585568GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly.BMC Bioinformatics2016
27923952Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection With Human Rhinovirus and Respiratory Syncytial Virus in Infancy.J Infect Dis2016
27306515Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters.Environ Microbiol2016
27558918A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome.Sci Rep2016
27196065Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.PLoS One2016
27473422Microbial diversity in individuals and their household contacts following typical antibiotic courses.Microbiome2016
27527070Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis.BMC Genomics2016
27400380Metagenome and Metatranscriptome Analyses Using Protein Family Profiles.PLoS Comput Biol2016
25535390Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle.Proc Natl Acad Sci U S A2015
26512100Library preparation methodology can influence genomic and functional predictions in human microbiome research.Proc Natl Acad Sci U S A2015
26296559Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection.BMC Genomics2015
26579074Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: geochemical controls on microbial community structure and function.Front Microbiol2015
26023872Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism.ISME J2015
25637561SFA-SPA: a suffix array based short peptide assembler for metagenomic data.Bioinformatics2015
25414351GRASP: guided reference-based assembly of short peptides.Nucleic Acids Res2015
25575307Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics.ISME J2015
24522917Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets.J Virol2014
25470548Diet and feeding pattern affect the diurnal dynamics of the gut microbiome.Cell Metab2014
24586863Functional tradeoffs underpin salinity-driven divergence in microbial community composition.PLoS One2014
  • 1 - 50 of 89

Recommended Authors

Migun Shakya
Los Alamos National Laboratory
Career Start Year 2012
Number of shared co-authors 3
Neha Varghese
Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
Career Start Year 2011
Number of shared co-authors 7
Chien-Chi Lo
Los Alamos National Laboratory
Career Start Year 2009
Number of shared co-authors 4
Nicola Segata
University of Trento
Career Start Year 2008
Number of shared co-authors 9
Daniel McDonald
University of California San Diego
Career Start Year 2007
Number of shared co-authors 15
Bonnie L Hurwitz
The University of Arizona
Career Start Year 2006
Number of shared co-authors 11
Gail L Rosen
Drexel University
Career Start Year 2006
Number of shared co-authors 1
Davide Albanese
Fondazione Edmund Mach
Career Start Year 2006
Number of shared co-authors 1
Brandi L Cantarel
University of Texas Southwestern Medical Center
Career Start Year 2006
Number of shared co-authors 6
Morgan G I Langille
Dalhousie University
Career Start Year 2004
Number of shared co-authors 6
Katherine Huang
Broad Institute of MIT and Harvard
Career Start Year 2004
Number of shared co-authors 9
Paul Wilmes
University of Luxembourg
Career Start Year 2004
Number of shared co-authors 5
Manimozhiyan Arumugam
Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen
Career Start Year 2004
Number of shared co-authors 29
Matthieu Pichaud
Novartis Institute for Biomedical Research
Career Start Year 2004
Number of shared co-authors 2
Patrick D Schloss
University of Michigan ann arbor
Career Start Year 2003
Number of shared co-authors 15
Alice C McHardy
Computational Biology of Infection Research, Helmholtz Centre for Infection Research
Career Start Year 2003
Number of shared co-authors 15
Jeroen Raes
KU Leuven - University of Leuven
Career Start Year 2002
Number of shared co-authors 15
Paramvir S Dehal
Lawrence Berkeley National Laboratory
Career Start Year 2001
Number of shared co-authors 10
Aaron A Best
Hope College
Career Start Year 2001
Number of shared co-authors 6
Jo??o C Setubal
Chemistry Institute, Universidade de Sao Paulo - USP
Career Start Year 2000
Number of shared co-authors 12
Patrick S G Chain
Los Alamos National Laboratory
Career Start Year 2000
Number of shared co-authors 27
Alexander Sczyrba
Center for Biotechnology (CeBiTec), Bielefeld University, Universitatsstrasse 27
Career Start Year 2000
Number of shared co-authors 5
Aye Wollam
McDonnell Genome Institute, Washington University School of Medicine
Career Start Year 2000
Number of shared co-authors 15
Jonathan Crabtree
Institute for Genome Sciences, University of Maryland School of Medicine
Career Start Year 1998
Number of shared co-authors 27
Eric J Alm
Massachusetts Institute of Technology 21 Ames St. Cambridge
Career Start Year 1998
Number of shared co-authors 8
James A Foster
University of Idaho
Career Start Year 1996
Number of shared co-authors 1
Thomas Brettin
University of Chicago
Career Start Year 1996
Number of shared co-authors 13
John Parkinson
The Hospital for Sick Children
Career Start Year 1994
Number of shared co-authors 6
Lee Ann McCue
Pacific Northwest National Laboratory
Career Start Year 1991
Number of shared co-authors 8
Owen White
Institute for Genome Sciences, University of Maryland School of Medicine
Career Start Year 1988
Number of shared co-authors 51

Collaborators

J C Venter
The J. Craig Venter Institute
Co-authored papers 23
Karen E Nelson
J. Craig Venter Institute, 9605 Medical Center Drive
Co-authored papers 20
Douglas B Rusch
Center for Genomics and Bioinformatics, Indiana University
Co-authored papers 13
Shannon J Williamson
J. Craig Venter Institute
Co-authored papers 10
Weizhong Li
J. Craig Venter Institute
Co-authored papers 8
Aaron L Halpern
Illumina Inc.
Co-authored papers 8
Mathangi Thiagarajan
Co-authored papers 7
Andrey Tovchigrechko
J. Craig Venter Institute, 9605 Medical Center Dr
Co-authored papers 7
Robert Friedman
University of South Carolina
Co-authored papers 7
Jonathan A Eisen
McLean Hospital
Co-authored papers 6
Granger G Sutton
J. Craig Venter Institute
Co-authored papers 6
Marvin Frazier
Co-authored papers 6
Granger Sutton
J. Craig Venter Institute
Co-authored papers 6
Johannes B Goll
.The Emmes Corporation
Co-authored papers 6
Douglas W Fadrosh
University of California san francisco
Co-authored papers 5
Saul Kravitz
Co-authored papers 5
Hamilton O Smith
J. Craig Venter Institute
Co-authored papers 5
Karin A Remington
The J. Craig Venter Institute.
Co-authored papers 5
Seesandra V Rajagopala
Vanderbilt University Medical Center
Co-authored papers 5
Cynthia Andrews-Pfannkoch
Mayo Clinic
Co-authored papers 5
Emiley A Eloe-Fadrosh
DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
Co-authored papers 4
Mark D Adams
Case Western Reserve University School of Medicine
Co-authored papers 4
Yu-Hui Rogers
Johns Hopkins Bayview Research Campus
Co-authored papers 4
Karen Beeson
J. Craig Venter Institute
Co-authored papers 4
Vineet Bafna
University of California San Diego
Co-authored papers 4
Clark Mobarry
Co-authored papers 4
Bixiong Chris Shue
Co-authored papers 3
Thomas Rattei
Co-authored papers 3
Lynn M Schriml
University of Maryland School of Medicine, Institute for Genome Sciences
Co-authored papers 3
Eli Venter
Vanderbilt University, Columbia University Medical Center
Co-authored papers 3
Release 1.2