List of works by Shibu Yooseph

A Microbiomic Analysis in African Americans with Colonic Lesions Reveals Streptococcus sp.VT162 as a Marker of Neoplastic Transformation.

scientific article

A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP)

scientific article

A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome

scientific article

A framework for human microbiome research

scientific article

A metagenomic framework for the study of airborne microbial communities

scientific article

A note on efficient computation of haplotypes via perfect phylogeny.

scientific article

A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome

scientific article

A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes.

scientific article

ANDES: Statistical tools for the ANalyses of DEep Sequencing

scientific article

An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome

scientific article published on 02 October 2013

Analyses of the microbial diversity across the human microbiome

scientific article

Better methods for solving parsimony and compatibility.

scientific article published in January 1998

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

scientific article

Co-occurrence of Anaerobes in Human Chronic Wounds

scientific article published on 23 August 2018

Comparative genome analysis of 19 Ureaplasma urealyticum and Ureaplasma parvum strains

scientific article

Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics

scientific article published on 9 January 2015

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

scientific article published in February 2018

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

article

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

scientific article

Detection and characterization of human Ureaplasma species and serovars by real-time PCR.

scientific article

Diet and feeding pattern affect the diurnal dynamics of the gut microbiome

scientific article

Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection With Human Rhinovirus and Respiratory Syncytial Virus in Infancy

scientific article

Discovery of [NiFe] hydrogenase genes in metagenomic DNA: cloning and heterologous expression in Thiocapsa roseopersicina

scientific article published on 24 July 2009

Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters

scientific article published on 16 June 2016

Effect of Macondo Prospect 252 Oil on Microbiota Associated with Pelagic Sargassum in the Northern Gulf of Mexico.

scientific article published on 4 November 2016

Essential genes of a minimal bacterium

scientific article

Evaluation of 16S rDNA-based community profiling for human microbiome research

scientific article

Evaluation of the upper airway microbiome and immune response with nasal epithelial lining fluid absorption and nasal washes

scientific article published on 26 November 2020

Evolution of allostery in the cyclic nucleotide binding module

scientific article

Exploring expression data: identification and analysis of coexpressed genes

scientific article

Foregut microbiome in development of esophageal adenocarcinoma

From bacterial to microbial ecosystems (metagenomics).

scientific article published on January 2012

Functional tradeoffs underpin salinity-driven divergence in microbial community composition

scientific article

GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data

scientific article published on 06 June 2019

GRASP: guided reference-based assembly of short peptides

scientific article

GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly

scientific article

Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis.

scientific article

Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering

scientific article

Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease

scientific article published on 18 January 2018

Genomic and functional adaptation in surface ocean planktonic prokaryotes

scientific article

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

scientific article

Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: geochemical controls on microbial community structure and function

scientific article

Global biogeography of Prochlorococcus genome diversity in the surface ocean.

scientific article published on 2 February 2016

Global ecotypes in the ubiquitous marine clade SAR86

scientific article published on 14 October 2019

Going deeper: metagenome of a hadopelagic microbial community

scientific article

Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease

scientific article published on May 2017

Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease

scientific article published on 01 September 2019

Gut microbiota dependent anti-tumor immunity restricts melanoma growth in Rnf5 mice

scientific article published on 02 April 2019

Haplotyping as perfect phylogeny: a direct approach

scientific article (publication date: 2003)

Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets

scientific article

Learning a mixture of microbial networks using minorization-maximization

scientific article published on 01 July 2019

Library preparation methodology can influence genomic and functional predictions in human microbiome research

scientific article published on 28 October 2015

METAREP: JCVI metagenomics reports--an open source tool for high-performance comparative metagenomics.

scientific article

Meta-omic analyses of Baltic Sea cyanobacteria: diversity, community structure and salt acclimation.

scientific article published on 21 November 2016

Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism

scientific article published on 29 May 2015

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles

scientific article

Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution

scientific article

Metagenomic exploration of viruses throughout the Indian Ocean

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Metagenomic investigation of microbes and viruses in patients with jaw osteonecrosis associated with bisphosphonate therapy.

scientific article published on December 2012

Microbial diversity in individuals and their household contacts following typical antibiotic courses.

scientific article published on 30 July 2016

Microbiome analysis of stool samples from African Americans with colon polyps.

scientific article

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

scientific article

Papio spp. Colon microbiome and its link to obesity in pregnancy

scientific article published on 24 July 2018

Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea

scientific article published on 13 March 2014

SFA-SPA: a suffix array based short peptide assembler for metagenomic data

scientific article published on 30 January 2015

SPA: a short peptide assembler for metagenomic data

scientific article

Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees

scientific article (publication date: 18 March 2011)

Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection

scientific article published on 22 August 2015

Structure, function and diversity of the healthy human microbiome

scientific article

The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data

scientific article

The Sequence of the Human Genome

scientific article

The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples

scientific article

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families

scientific article published in March 2007

The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific

scientific article published in March 2007

ThurGood: Evaluating Assembly-to-Assembly Mapping

scientific article published on 01 January 2004

Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation

scientific article published on 06 December 2018

Using DGGE profiling to develop a novel culture medium suitable for oral microbial communities

scientific article

Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies

scientific article

Variational Approximation-Based Model Selection for Microbial Network Inference

scientific article published in 2022

Viral photosynthetic reaction center genes and transcripts in the marine environment

scientific article

Whole-genome shotgun assembly and comparison of human genome assemblies

scientific article

Zinc finger gene clusters and tandem gene duplication

scientific article published on 01 January 2002

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