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Author Details

Jennifer R Wortman
Broad Institute of MIT and Harvard
1999
89
66
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
35045228SER-109, an Oral Microbiome Therapy for Recurrent <i>Clostridioides difficile</i> Infection.N Engl J Med2022
32255488SER-109, an Investigational Microbiome Drug to Reduce Recurrence After Clostridioides difficile Infection: Lessons Learned From a Phase 2 Trial.Clin Infect Dis2021
32763240A Phase 1b Safety Study of SER-287, a Spore-Based Microbiome Therapeutic, for Active Mild to Moderate Ulcerative Colitis.Gastroenterology2021
29500637RNA-Seq Profile Reveals Th-1 and Th-17-Type of Immune Responses in Mice Infected Systemically with Aspergillus fumigatus.Mycopathologia2018
27775185Discovery of McrA, a master regulator of Aspergillus secondary metabolism.Mol Microbiol2017
28196534Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.Genome Biol2017
28329759Corrigendum: Mobile genes in the human microbiome are structured from global to individual scales.Nature2017
28096418Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks.Proc Natl Acad Sci U S A2017
28874473Revitalization of a Forward Genetic Screen Identifies Three New Regulators of Fungal Secondary Metabolism in the Genus Aspergillus.mBio2017
27064254Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance.Nat Genet2016
27892853Structure of the germline genome of <i>Tetrahymena thermophila</i> and relationship to the massively rearranged somatic genome.Elife2016
27409808Mobile genes in the human microbiome are structured from global to individual scales.Nature2016
26856261Genomic insights into the Ixodes scapularis tick vector of Lyme disease.Nat Commun2016
26418737Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal.PLoS Med2015
26380633Toward a standard in structural genome annotation for prokaryotes.Stand Genomic Sci2015
24194595The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations.Nucleic Acids Res2014
25416206Illumina identification of RsrA, a conserved C2H2 transcription factor coordinating the NapA mediated oxidative stress signaling pathway in Aspergillus.BMC Genomics2014
25409509Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.PLoS One2014
25313016The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences.Genome Biol Evol2014
24936976Standardized metadata for human pathogen/vector genomic sequences.PLoS One2014
24277043Identification of 50 class D β-lactamases and 65 Acinetobacter-derived cephalosporinases in Acinetobacter spp.Antimicrob Agents Chemother2014
23341549Comparative genomics of recent Shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen.mBio2013
23904509Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily.Bioinformatics2013
23963180Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains.mBio2013
23617571Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae.BMC Microbiol2013
23525074Genomics of Loa loa, a Wolbachia-free filarial parasite of humans.Nat Genet2013
22080559The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources.Nucleic Acids Res2012
23479789Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany.Proc Natl Acad Sci U S A2012
22617140Comparative genomics of vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with Methicillin-resistant S. aureus hospital-acquired infection in the United States.mBio2012
22315421Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011.Proc Natl Acad Sci U S A2012
22354958Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus.mBio2012
21677861The IGS Standard Operating Procedure for Automated Prokaryotic Annotation.Stand Genomic Sci2011
22059117Approaches to Fungal Genome Annotation.Mycology2011
21974739New resources for functional analysis of omics data for the genus Aspergillus.BMC Genomics2011
21552244Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.Nat Biotechnol2011
19773420The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community.Nucleic Acids Res2010
20729833Draft genome sequence of the oilseed species Ricinus communis.Nat Biotechnol2010
20929810Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.Science2010
20489017A catalog of reference genomes from the human microbiome.Science2010
20413634Ergatis: a web interface and scalable software system for bioinformatics workflows.Bioinformatics2010
19146970The 2008 update of the Aspergillus nidulans genome annotation: a community effort.Fungal Genet Biol2009
20003475Unraveling the genomic diversity of small eukaryotes.Genome Biol2009
19606141The genome of the blood fluke Schistosoma mansoni.Nature2009
19717792Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives.Genome Res2009
18190707Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.Genome Biol2008
19077187Genome wide survey, discovery and evolution of repetitive elements in three Entamoeba species.BMC Genomics2008
18820685Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum.Nat Biotechnol2008
18843361Comparative genomics of the neglected human malaria parasite Plasmodium vivax.Nature2008
19036158Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure.BMC Genomics2008
18404212Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus.PLoS Genet2008
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Collaborators

Broad Institute of MIT and Harvard
Co-authored papers 38
Institute for Genome Sciences, University of Maryland School of Medicine
Co-authored papers 27
Broad Institute of MIT and Harvard
Co-authored papers 20
Center for Computational Biology, Johns Hopkins University
Co-authored papers 18
Institute for Genome Sciences, University of Maryland School of Medicine
Co-authored papers 17
Institute for Genome Sciences, University of Maryland School of Medicine
Co-authored papers 16
Center for Computational Biology, Johns Hopkins School of Medicine
Co-authored papers 12
Institute for Genome Sciences, University of Maryland School of Medicine
Co-authored papers 11
GE Global Research Center
Co-authored papers 9
Inc., Frederick National Laboratory for Cancer Research
Co-authored papers 9
Yunnan Institute of Tropical Crops
Co-authored papers 9
Personal Genome Diagnostics Inc.
Co-authored papers 9
Macquarie University
Co-authored papers 8
Center for Computational Biology, Johns Hopkins University
Co-authored papers 8
International Livestock Research Institute (ILRI)
Co-authored papers 7
Center for Cancer Research, National Cancer Institute, National Institutes of Health
Co-authored papers 7
University of Utah
Co-authored papers 6
J. Craig Venter Institute
Co-authored papers 6
The J. Craig Venter Institute
Co-authored papers 6
Broad Institute
Co-authored papers 6
Institute of Technology, Broad Institute of Harvard and Massachusetts
Co-authored papers 5
Institut fur Mathematik und Informatik, Universitat Greifswald
Co-authored papers 5
National Institute of Allergy and Infectious Diseases, National Institutes of Health
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Case Western Reserve University School of Medicine
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Center for Genomics and Bioinformatics, Indiana University
Co-authored papers 5
Center for Genomics and Systems Biology
Co-authored papers 5
College of Veterinary Medicine, Sichuan Agricultural University
Co-authored papers 5
Wellcome Sanger Institute
Co-authored papers 5
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