Genome wide survey, discovery and evolution of repetitive elements in three Entamoeba species

por Lorenzi, Hernan, Thiagarajan, Mathangi, Haas, Brian, Wortman, Jennifer, Hall, Neil, Caler, Elisabet
Publicado 2008

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

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

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

por Goll, Johannes, Rusch, Douglas B., Tanenbaum, David M., Thiagarajan, Mathangi, Li, Kelvin, Methé, Barbara A., Yooseph, Shibu
Publicado 2010

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

por Tanenbaum, David M., Goll, Johannes, Murphy, Sean, Kumar, Prateek, Zafar, Nikhat, Thiagarajan, Mathangi, Madupu, Ramana, Davidsen, Tanja, Kagan, Leonid, Kravitz, Saul, Rusch, Douglas B., Yooseph, Shibu
Publicado 2010

Metagenomic Exploration of Viruses throughout the Indian Ocean

por 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
Publicado 2012

Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic

por Allen, Lisa Zeigler, Allen, Eric E, Badger, Jonathan H, McCrow, John P, Paulsen, Ian T, Elbourne, Liam DH, Thiagarajan, Mathangi, Rusch, Doug B, Nealson, Kenneth H, Williamson, Shannon J, Venter, J Craig, Allen, Andrew E
Publicado 2012

A Metagenomic Framework for the Study of Airborne Microbial Communities

por Yooseph, Shibu, Andrews-Pfannkoch, Cynthia, Tenney, Aaron, McQuaid, Jeff, Williamson, Shannon, Thiagarajan, Mathangi, Brami, Daniel, Zeigler-Allen, Lisa, Hoffman, Jeff, Goll, Johannes B., Fadrosh, Douglas, Glass, John, Adams, Mark D., Friedman, Robert, Venter, J. Craig
Publicado 2013

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

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

Microbial community function and biomarker discovery in the human microbiome

por Segata, Nicola, Abubucker, Sahar, Goll, Johannes, Schubert, Alyxandria M, Izard, Jacques, Cantarel, Brandi L, Rodriguez-Mueller, Beltran, Waldron, Levi, Zucker, Jeremy, Thiagarajan, Mathangi, Henrissat, Bernard, White, Owen, Kelley, Scott T, Methé, Barbara, Schloss, Patrick D, Garrett, Wendy S, Gevers, Dirk, Mitreva, Makedonka, Huttenhower, Curtis
Publicado 2011

Comparative genomic analysis and phylogenetic position of Theileria equi

por Kappmeyer, Lowell S, Thiagarajan, Mathangi, Herndon, David R, Ramsay, Joshua D, Caler, Elisabet, Djikeng, Appolinaire, Gillespie, Joseph J, Lau, Audrey OT, Roalson, Eric H, Silva, Joana C, Silva, Marta G, Suarez, Carlos E, Ueti, Massaro W, Nene, Vishvanath M, Mealey, Robert H, Knowles, Donald P, Brayton, Kelly A
Publicado 2012

Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure

por Coyne, Robert S, Thiagarajan, Mathangi, Jones, Kristie M, Wortman, Jennifer R, Tallon, Luke J, Haas, Brian J, Cassidy-Hanley, Donna M, Wiley, Emily A, Smith, Joshua J, Collins, Kathleen, Lee, Suzanne R, Couvillion, Mary T, Liu, Yifan, Garg, Jyoti, Pearlman, Ronald E, Hamilton, Eileen P, Orias, Eduardo, Eisen, Jonathan A, Methé, Barbara A
Publicado 2008

Neoplastic cell enrichment of tumor tissues using coring and laser microdissection for proteomic and genomic analyses of pancreatic ductal adenocarcinoma

por Li, Qing Kay, Hu, Yingwei, Chen, Lijun, Schnaubelt, Michael, Cui Zhou, Daniel, Li, Yize, Lu, Rita Jui-Hsien, Thiagarajan, Mathangi, Hostetter, Galen, Newton, Chelsea J., Jewell, Scott D., Omenn, Gil, Robles, Ana I., Mesri, Mehdi, Bathe, Oliver F., Zhang, Bing, Ding, Li, Hruban, Ralph H., Chan, Daniel W., Zhang, Hui
Publicado 2022

Pathema: a clade-specific bioinformatics resource center for pathogen research

por Brinkac, Lauren M., Davidsen, Tanja, Beck, Erin, Ganapathy, Anuradha, Caler, Elisabet, Dodson, Robert J., Durkin, A. Scott, Harkins, Derek M., Lorenzi, Hernan, Madupu, Ramana, Sebastian, Yinong, Shrivastava, Susmita, Thiagarajan, Mathangi, Orvis, Joshua, Sundaram, Jaideep P., Crabtree, Jonathon, Galens, Kevin, Zhao, Yongmei, Inman, Jason M., Montgomery, Robert, Schobel, Seth, Galinsky, Kevin, Tanenbaum, David M., Resnick, Adam, Zafar, Nikhat, White, Owen, Sutton, Granger
Publicado 2010

Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition

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

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

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

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

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

Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens

por Whiteaker, Jeffrey R., Lundeen, Rachel A., Zhao, Lei, Schoenherr, Regine M., Burian, Aura, Huang, Dongqing, Voytovich, Ulianna, Wang, Tao, Kennedy, Jacob J., Ivey, Richard G., Lin, Chenwei, Murillo, Oscar D., Lorentzen, Travis D., Thiagarajan, Mathangi, Colantonio, Simona, Caceres, Tessa W., Roberts, Rhonda R., Knotts, Joseph G., Reading, Joshua J., Kaczmarczyk, Jan A., Richardson, Christopher W., Garcia-Buntley, Sandra S., Bocik, William, Hewitt, Stephen M., Murray, Karen E., Do, Nhan, Brophy, Mary, Wilz, Stephen W., Yu, Hongbo, Ajjarapu, Samuel, Boja, Emily, Hiltke, Tara, Rodriguez, Henry, Paulovich, Amanda G.
Publicado 2021

Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy

por Krug, Karsten, Jaehnig, Eric J., Satpathy, Shankha, Blumenberg, Lili, Karpova, Alla, Anurag, Meenakshi, Miles, George, Mertins, Philipp, Geffen, Yifat, Tang, Lauren C., Heiman, David I., Cao, Song, Maruvka, Yosef E., Lei, Jonathan T., Huang, Chen, Kothadia, Ramani B., Colaprico, Antonio, Birger, Chet, Wang, Jarey, Dou, Yongchao, Wen, Bo, Shi, Zhiao, Liao, Yuxing, Wiznerowicz, Maciej, Wyczalkowski, Matthew A., Chen, Xi Steven, Kennedy, Jacob J., Paulovich, Amanda G., Thiagarajan, Mathangi, Kinsinger, Christopher R., Hiltke, Tara, Boja, Emily S., Mesri, Mehdi, Robles, Ana I., Rodriguez, Henry, Westbrook, Thomas F., Ding, Li, Getz, Gad, Clauser, Karl R., Fenyö, David, Ruggles, Kelly V., Zhang, Bing, Mani, D.R., Carr, Steven A., Ellis, Matthew J., Gillette, Michael A.
Publicado 2020

Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote

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

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

por Clark, David J., Dhanasekaran, Saravana M., Petralia, Francesca, Pan, Jianbo, Song, Xiaoyu, Hu, Yingwei, da Veiga Leprevost, Felipe, Reva, Boris, Lih, Tung-Shing M., Chang, Hui-Yin, Ma, Weiping, Huang, Chen, Ricketts, Christopher J., Chen, Lijun, Krek, Azra, Li, Yize, Rykunov, Dmitry, Li, Qing Kay, Chen, Lin S., Ozbek, Umut, Vasaikar, Suhas, Wu, Yige, Yoo, Seungyeul, Chowdhury, Shrabanti, Wyczalkowski, Matthew A., Ji, Jiayi, Schnaubelt, Michael, Kong, Andy, Sethuraman, Sunantha, Avtonomov, Dmitry M., Ao, Minghui, Colaprico, Antonio, Cao, Song, Cho, Kyung-Cho, Kalayci, Selim, Ma, Shiyong, Liu, Wenke, Ruggles, Kelly, Calinawan, Anna, Gümüş, Zeynep H., Geiszler, Daniel, Kawaler, Emily, Teo, Guo Ci, Wen, Bo, Zhang, Yuping, Keegan, Sarah, Li, Kai, Chen, Feng, Edwards, Nathan, Pierorazio, Phillip M., Chen, Xi Steven, Pavlovich, Christian P., Hakimi, A. Ari, Brominski, Gabriel, Hsieh, James J., Antczak, Andrzej, Omelchenko, Tatiana, Lubinski, Jan, Wiznerowicz, Maciej, Linehan, W. Marston, Kinsinger, Christopher R., Thiagarajan, Mathangi, Boja, Emily S., Mesri, Mehdi, Hiltke, Tara, Robles, Ana I., Rodriguez, Henry, Qian, Jiang, Fenyö, David, Zhang, Bing, Ding, Li, Schadt, Eric, Chinnaiyan, Arul M., Zhang, Zhen, Omenn, Gilbert S., Cieslik, Marcin, Chan, Daniel W., Nesvizhskii, Alexey I., Wang, Pei, Zhang, Hui
Publicado 2019