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
Published 2012-01-01

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
Published 2012-01-01

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
Published 2013-01-01

Metabolic reconstruction for metagenomic data and its application to the human microbiome.

by Sahar Abubucker, Nicola Segata, Johannes Goll, Alyxandria M Schubert, Jacques Izard, Brandi L Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat, Owen White, Scott T Kelley, Barbara Methé, Patrick D Schloss, Dirk Gevers, Makedonka Mitreva, Curtis Huttenhower
Published 2012-01-01

Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

by Chris L Dupont, John Larsson, Shibu Yooseph, Karolina Ininbergs, Johannes Goll, Johannes Asplund-Samuelsson, John P McCrow, Narin Celepli, Lisa Zeigler Allen, Martin Ekman, Andrew J Lucas, Åke Hagström, Mathangi Thiagarajan, Björn Brindefalk, Alexander R Richter, Anders F Andersson, Aaron Tenney, Daniel Lundin, Andrey Tovchigrechko, Johan A A Nylander, Daniel Brami, Jonathan H Badger, Andrew E Allen, Douglas B Rusch, Jeff Hoffman, Erling Norrby, Robert Friedman, Jarone Pinhassi, J Craig Venter, Birgitta Bergman
Published 2014-01-01

Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability

by Jason E. McDermott, Osama A. Arshad, Vladislav A. Petyuk, Yi Fu, Marina A. Gritsenko, Therese R. Clauss, Ronald J. Moore, Athena A. Schepmoes, Rui Zhao, Matthew E. Monroe, Michael Schnaubelt, Chia-Feng Tsai, Samuel H. Payne, Chen Huang, Liang-Bo Wang, Steven Foltz, Matthew Wyczalkowski, Yige Wu, Ehwang Song, Molly A. Brewer, Mathangi Thiagarajan, Christopher R. Kinsinger, Ana I. Robles, Emily S. Boja, Henry Rodriguez, Daniel W. Chan, Bing Zhang, Zhen Zhang, Li Ding, Richard D. Smith, Tao Liu, Karin D. Rodland
Published 2020-08-01

Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability

by Jason E. McDermott, Osama A. Arshad, Vladislav A. Petyuk, Yi Fu, Marina A. Gritsenko, Therese R. Clauss, Ronald J. Moore, Athena A. Schepmoes, Rui Zhao, Matthew E. Monroe, Michael Schnaubelt, Chia-Feng Tsai, Samuel H. Payne, Chen Huang, Liang-Bo Wang, Steven Foltz, Matthew Wyczalkowski, Yige Wu, Ehwang Song, Molly A. Brewer, Mathangi Thiagarajan, Christopher R. Kinsinger, Ana I. Robles, Emily S. Boja, Henry Rodriguez, Daniel W. Chan, Bing Zhang, Zhen Zhang, Li Ding, Richard D. Smith, Tao Liu, Karin D. Rodland
Published 2020-04-01

Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.

by Jonathan A Eisen, Robert S Coyne, Martin Wu, Dongying Wu, Mathangi Thiagarajan, Jennifer R Wortman, Jonathan H Badger, Qinghu Ren, Paolo Amedeo, Kristie M Jones, Luke J Tallon, Arthur L Delcher, Steven L Salzberg, Joana C Silva, Brian J Haas, William H Majoros, Maryam Farzad, Jane M Carlton, Roger K Smith, Jyoti Garg, Ronald E Pearlman, Kathleen M Karrer, Lei Sun, Gerard Manning, Nels C Elde, Aaron P Turkewitz, David J Asai, David E Wilkes, Yufeng Wang, Hong Cai, Kathleen Collins, B Andrew Stewart, Suzanne R Lee, Katarzyna Wilamowska, Zasha Weinberg, Walter L Ruzzo, Dorota Wloga, Jacek Gaertig, Joseph Frankel, Che-Chia Tsao, Martin A Gorovsky, Patrick J Keeling, Ross F Waller, Nicola J Patron, J Michael Cherry, Nicholas A Stover, Cynthia J Krieger, Christina del Toro, Hilary F Ryder, Sondra C Williamson, Rebecca A Barbeau, Eileen P Hamilton, Eduardo Orias
Published 2006-09-01

Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma

by Yingwei Hu, Jianbo Pan, Punit Shah, Minghui Ao, Stefani N. Thomas, Yang Liu, Lijun Chen, Michael Schnaubelt, David J. Clark, Henry Rodriguez, Emily S. Boja, Tara Hiltke, Christopher R. Kinsinger, Karin D. Rodland, Qing Kay Li, Jiang Qian, Zhen Zhang, Daniel W. Chan, Hui Zhang, Akhilesh Pandey, Amanda Paulovich, Andrew Hoofnagle, Bing Zhang, D.R. Mani, Daniel C. Liebler, David F. Ransohoff, David Fenyo, David L. Tabb, Douglas A. Levine, Eric Kuhn, Forest M. White, Gordon A. Whiteley, Heng Zhu, Ie-Ming Shih, Jasmin Bavarva, Jason E. McDermott, Jeffrey Whiteaker, Karen A. Ketchum, Karl R. Clauser, Kelly Ruggles, Kimberly Elburn, Li Ding, Linda Hannick, Lisa J. Zimmerman, Mark Watson, Mathangi Thiagarajan, Matthew J.C. Ellis, Mauricio Oberti, Mehdi Mesri, Melinda E. Sanders, Melissa Borucki, Michael A. Gillette, Michael Snyder, Nathan J. Edwards, Negin Vatanian, Paul A. Rudnick, Peter B. McGarvey, Philip Mertins, R. Reid Townsend, Ratna R. Thangudu, Richard D. Smith, Robert C. Rivers, Robert J.C. Slebos, Samuel H. Payne, Sherri R. Davies, Shuang Cai, Stephen E. Stein, Steven A. Carr, Steven J. Skates, Subha Madhavan, Tao Liu, Xian Chen, Yingming Zhao, Yue Wang, Zhiao Shi
Published 2020-10-01

Genomic insights into the Ixodes scapularis tick vector of Lyme disease

by Monika Gulia-Nuss, Andrew B. Nuss, Jason M. Meyer, Daniel E. Sonenshine, R. Michael Roe, Robert M. Waterhouse, David B. Sattelle, José de la Fuente, Jose M. Ribeiro, Karine Megy, Jyothi Thimmapuram, Jason R. Miller, Brian P. Walenz, Sergey Koren, Jessica B. Hostetler, Mathangi Thiagarajan, Vinita S. Joardar, Linda I. Hannick, Shelby Bidwell, Martin P. Hammond, Sarah Young, Qiandong Zeng, Jenica L. Abrudan, Francisca C. Almeida, Nieves Ayllón, Ketaki Bhide, Brooke W. Bissinger, Elena Bonzon-Kulichenko, Steven D. Buckingham, Daniel R. Caffrey, Melissa J. Caimano, Vincent Croset, Timothy Driscoll, Don Gilbert, Joseph J. Gillespie, Gloria I. Giraldo-Calderón, Jeffrey M. Grabowski, David Jiang, Sayed M. S. Khalil, Donghun Kim, Katherine M. Kocan, Juraj Koči, Richard J. Kuhn, Timothy J. Kurtti, Kristin Lees, Emma G. Lang, Ryan C. Kennedy, Hyeogsun Kwon, Rushika Perera, Yumin Qi, Justin D. Radolf, Joyce M. Sakamoto, Alejandro Sánchez-Gracia, Maiara S. Severo, Neal Silverman, Ladislav Šimo, Marta Tojo, Cristian Tornador, Janice P. Van Zee, Jesús Vázquez, Filipe G. Vieira, Margarita Villar, Adam R. Wespiser, Yunlong Yang, Jiwei Zhu, Peter Arensburger, Patricia V. Pietrantonio, Stephen C. Barker, Renfu Shao, Evgeny M. Zdobnov, Frank Hauser, Cornelis J. P. Grimmelikhuijzen, Yoonseong Park, Julio Rozas, Richard Benton, Joao H. F. Pedra, David R. Nelson, Maria F. Unger, Jose M. C. Tubio, Zhijian Tu, Hugh M. Robertson, Martin Shumway, Granger Sutton, Jennifer R. Wortman, Daniel Lawson, Stephen K. Wikel, Vishvanath M. Nene, Claire M. Fraser, Frank H. Collins, Bruce Birren, Karen E. Nelson, Elisabet Caler, Catherine A. Hill
Published 2016-02-01