GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data by Cuncong Zhong, Youngik Yang, Shibu Yooseph

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Bacterial community structure alterations within the colorectal cancer gut microbiome by Mark Loftus, Sayf Al-Deen Hassouneh, Shibu Yooseph

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Linking Inflammatory Bowel Disease Symptoms to Changes in the Gut Microbiome Structure and Function by Sayf Al-Deen Hassouneh, Mark Loftus, Shibu Yooseph

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Bacterial associations in the healthy human gut microbiome across populations by Mark Loftus, Sayf Al-Deen Hassouneh, Shibu Yooseph

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Analyses of the microbial diversity across the human microbiome. by Kelvin Li, Monika Bihan, Shibu Yooseph, Barbara A Methé

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Effect of 13-Hydroperoxyoctadecadienoic Acid (13-HPODE) Treatment on the Transcriptomic Profile of Poorly-Differentiated Caco-2 Cells by Nisreen Faizo, Chandrakala Aluganti Narasimhulu, Anna Forsman, Shibu Yooseph, Sampath Parthasarathy

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Peroxidized Linoleic Acid, 13-HPODE, Alters Gene Expression Profile in Intestinal Epithelial Cells by Nisreen Faizo, Chandrakala Aluganti Narasimhulu, Anna Forsman, Shibu Yooseph, Sampath Parthasarathy

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Metagenome and Metatranscriptome Analyses Using Protein Family Profiles. by Cuncong Zhong, Anna Edlund, Youngik Yang, Jeffrey S McLean, Shibu Yooseph

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A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP). by Johannes Goll, Mathangi Thiagarajan, Sahar Abubucker, Curtis Huttenhower, Shibu Yooseph, Barbara A Methé

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Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation by Anna Edlund, Youngik Yang, Shibu Yooseph, Xuesong He, Wenyuan Shi, Jeffrey S. McLean

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Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies by William W. Greenwald, Niels Klitgord, Victor Seguritan, Shibu Yooseph, J. Craig Venter, Chad Garner, Karen E. Nelson, Weizhong Li

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Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. by Dongying Wu, Martin Wu, Aaron Halpern, Douglas B Rusch, Shibu Yooseph, Marvin Frazier, J Craig Venter, Jonathan A Eisen

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Microbiome analysis of stool samples from African Americans with colon polyps. by Hassan Brim, Shibu Yooseph, Erwin G Zoetendal, Edward Lee, Manolito Torralbo, Adeyinka O Laiyemo, Babak Shokrani, Karen Nelson, Hassan Ashktorab

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Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution. by Beatriz Díez, Johan A A Nylander, Karolina Ininbergs, Christopher L Dupont, Andrew E Allen, Shibu Yooseph, Douglas B Rusch, Birgitta Bergman

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Species-specific transcriptomic changes upon respiratory syncytial virus infection in cotton rats by Britton A. Strickland, Seesandra V. Rajagopala, Arash Kamali, Meghan H. Shilts, Suman B. Pakala, Marina S. Boukhvalova, Shibu Yooseph, Jorge C. G. Blanco, Suman R. Das

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Metagenomic exploration of viruses throughout the Indian Ocean. by Shannon J Williamson, Lisa Zeigler Allen, Hernan A Lorenzi, Douglas W Fadrosh, Daniel Brami, Mathangi Thiagarajan, John P McCrow, Andrey Tovchigrechko, Shibu Yooseph, J Craig Venter

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The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples. by Shannon J Williamson, Douglas B Rusch, Shibu Yooseph, Aaron L Halpern, Karla B Heidelberg, John I Glass, Cynthia Andrews-Pfannkoch, Douglas Fadrosh, Christopher S Miller, Granger Sutton, Marvin Frazier, J Craig Venter

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Going deeper: metagenome of a hadopelagic microbial community. by Emiley A Eloe, Douglas W Fadrosh, Mark Novotny, Lisa Zeigler Allen, Maria Kim, Mary-Jane Lombardo, Joyclyn Yee-Greenbaum, Shibu Yooseph, Eric E Allen, Roger Lasken, Shannon J Williamson, Douglas H Bartlett

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Microbial community structure and composition is associated with host species and sex in Sigmodon cotton rats by Britton A. Strickland, Mira C. Patel, Meghan H. Shilts, Helen H. Boone, Arash Kamali, Wei Zhang, Daniel Stylos, Marina S. Boukhvalova, Christian Rosas-Salazar, Shibu Yooseph, Seesandra V. Rajagopala, Jorge C. G. Blanco, Suman R. Das

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A metagenomic framework for the study of airborne microbial communities. by Shibu Yooseph, Cynthia Andrews-Pfannkoch, Aaron Tenney, Jeff McQuaid, Shannon Williamson, Mathangi Thiagarajan, Daniel Brami, Lisa Zeigler-Allen, Jeff Hoffman, Johannes B Goll, Douglas Fadrosh, John Glass, Mark D Adams, Robert Friedman, J Craig Venter

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