SPA: a short peptide assembler for metagenomic data

by Yang, Youngik, Yooseph, Shibu
Published 2013

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

by Zhong, Cuncong, Yang, Youngik, Yooseph, Shibu
Published 2016

GRASP: Guided Reference-based Assembly of Short Peptides

by Zhong, Cuncong, Yang, Youngik, Yooseph, Shibu
Published 2015

Analyses of the Microbial Diversity across the Human Microbiome

by Li, Kelvin, Bihan, Monika, Yooseph, Shibu, Methé, Barbara A.
Published 2012

Evolution of allostery in the cyclic nucleotide binding module

by Kannan, Natarajan, Wu, Jian, Anand, Ganesh S, Yooseph, Shibu, Neuwald, Andrew F, Venter, J Craig, Taylor, Susan S
Published 2007

A Case Study for Large-Scale Human Microbiome Analysis Using JCVI’s Metagenomics Reports (METAREP)

by Goll, Johannes, Thiagarajan, Mathangi, Abubucker, Sahar, Huttenhower, Curtis, Yooseph, Shibu, Methé, Barbara A.
Published 2012

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

by Larsson, John, Celepli, Narin, Ininbergs, Karolina, Dupont, Christopher L, Yooseph, Shibu, Bergman, Bigitta, Ekman, Martin
Published 2014

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles

by Zhong, Cuncong, Edlund, Anna, Yang, Youngik, McLean, Jeffrey S., Yooseph, Shibu
Published 2016

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

by Wu, Dongying, Wu, Martin, Halpern, Aaron, Rusch, Douglas B., Yooseph, Shibu, Frazier, Marvin, Venter, J. Craig, Eisen, Jonathan A.
Published 2011

Microbiome Analysis of Stool Samples from African Americans with Colon Polyps

by Brim, Hassan, Yooseph, Shibu, Zoetendal, Erwin G., Lee, Edward, Torralbo, Manolito, Laiyemo, Adeyinka O., Shokrani, Babak, Nelson, Karen, Ashktorab, Hassan
Published 2013

Metagenomic Exploration of Viruses throughout the Indian Ocean

by Williamson, Shannon J., Allen, Lisa Zeigler, Lorenzi, Hernan A., Fadrosh, Douglas W., Brami, Daniel, Thiagarajan, Mathangi, McCrow, John P., Tovchigrechko, Andrey, Yooseph, Shibu, Venter, J. Craig
Published 2012

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

by Edlund, Anna, Yang, Youngik, Hall, Adam P, Guo, Lihong, Lux, Renate, He, Xuesong, Nelson, Karen E, Nealson, Kenneth H, Yooseph, Shibu, Shi, Wenyuan, McLean, Jeffrey S
Published 2013

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

by Anderson, Ericka L., Li, Weizhong, Klitgord, Niels, Highlander, Sarah K., Dayrit, Mark, Seguritan, Victor, Yooseph, Shibu, Biggs, William, Venter, J. Craig, Nelson, Karen E., Jones, Marcus B.
Published 2016

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

by Abeles, Shira R., Jones, Marcus B., Santiago-Rodriguez, Tasha M., Ly, Melissa, Klitgord, Niels, Yooseph, Shibu, Nelson, Karen E., Pride, David T.
Published 2016

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

by Díez, Beatriz, Nylander, Johan A. A., Ininbergs, Karolina, Dupont, Christopher L., Allen, Andrew E., Yooseph, Shibu, Rusch, Douglas B., Bergman, Birgitta
Published 2016

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

by Edlund, Anna, Yang, Youngik, Yooseph, Shibu, Hall, Adam P, Nguyen, Don D, Dorrestein, Pieter C, Nelson, Karen E, He, Xuesong, Lux, Renate, Shi, Wenyuan, McLean, Jeffrey S
Published 2015

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

by Llorens-Marès, Tomàs, Yooseph, Shibu, Goll, Johannes, Hoffman, Jeff, Vila-Costa, Maria, Borrego, Carles M, Dupont, Chris L, Casamayor, Emilio O
Published 2015

The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples

by Williamson, Shannon J., Rusch, Douglas B., Yooseph, Shibu, Halpern, Aaron L., Heidelberg, Karla B., Glass, John I., Andrews-Pfannkoch, Cynthia, Fadrosh, Douglas, Miller, Christopher S., Sutton, Granger, Frazier, Marvin, Venter, J. Craig
Published 2008

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

by Dupont, Chris L, Rusch, Douglas B, Yooseph, Shibu, Lombardo, Mary-Jane, Alexander Richter, R, Valas, Ruben, Novotny, Mark, Yee-Greenbaum, Joyclyn, Selengut, Jeremy D, Haft, Dan H, Halpern, Aaron L, Lasken, Roger S, Nealson, Kenneth, Friedman, Robert, Craig Venter, J
Published 2012

Going Deeper: Metagenome of a Hadopelagic Microbial Community

by Eloe, Emiley A., Fadrosh, Douglas W., Novotny, Mark, Zeigler Allen, Lisa, Kim, Maria, Lombardo, Mary-Jane, Yee-Greenbaum, Joyclyn, Yooseph, Shibu, Allen, Eric E., Lasken, Roger, Williamson, Shannon J., Bartlett, Douglas H.
Published 2011