Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models

by Brandes, Aaron, Lun, Desmond S., Ip, Kuhn, Zucker, Jeremy, Colijn, Caroline, Weiner, Brian, Galagan, James E.
Published 2012

Correction: Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models

by Brandes, Aaron, Lun, Desmond S., Ip, Kuhn, Zucker, Jeremy, Colijn, Caroline, Weiner, Brian, Galagan, James E.
Published 2012

Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM

by Dreyfuss, Jonathan M., Zucker, Jeremy D., Hood, Heather M., Ocasio, Linda R., Sachs, Matthew S., Galagan, James E.
Published 2013

Microbial Community Metabolic Modeling: A Community Data‐Driven Network Reconstruction

by Henry, Christopher S., Bernstein, Hans C., Weisenhorn, Pamela, Taylor, Ronald C., Lee, Joon‐Yong, Zucker, Jeremy, Song, Hyun‐Seob
Published 2016

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

by Colijn, Caroline, Brandes, Aaron, Zucker, Jeremy, Lun, Desmond S., Weiner, Brian, Farhat, Maha R., Cheng, Tan-Yun, Moody, D. Branch, Murray, Megan, Galagan, James E.
Published 2009

Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

by Kettler, Gregory C, Martiny, Adam C, Huang, Katherine, Zucker, Jeremy, Coleman, Maureen L, Rodrigue, Sebastien, Chen, Feng, Lapidus, Alla, Ferriera, Steven, Johnson, Justin, Steglich, Claudia, Church, George M, Richardson, Paul, Chisholm, Sallie W
Published 2007

Comparative Genomics of Enterococci: Variation in Enterococcus faecalis, Clade Structure in E. faecium, and Defining Characteristics of E. gallinarum and E. casseliflavus

by Palmer, Kelli L., Godfrey, Paul, Griggs, Allison, Kos, Veronica N., Zucker, Jeremy, Desjardins, Christopher, Cerqueira, Gustavo, Gevers, Dirk, Walker, Suzanne, Wortman, Jennifer, Feldgarden, Michael, Haas, Brian, Birren, Bruce, Gilmore, Michael S.
Published 2012

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

by 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
Published 2012

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes

by White, Richard Allen, Bottos, Eric M., Roy Chowdhury, Taniya, Zucker, Jeremy D., Brislawn, Colin J., Nicora, Carrie D., Fansler, Sarah J., Glaesemann, Kurt R., Glass, Kevin, Jansson, Janet K.
Published 2016

Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models

by Karr, Jonathan R., Williams, Alex H., Zucker, Jeremy D., Raue, Andreas, Steiert, Bernhard, Timmer, Jens, Kreutz, Clemens, Wilkinson, Simon, Allgood, Brandon A., Bot, Brian M., Hoff, Bruce R., Kellen, Michael R., Covert, Markus W., Stolovitzky, Gustavo A., Meyer, Pablo
Published 2015

Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa

by Wu, Cheng, Yang, Fei, Smith, Kristina M., Peterson, Matthew, Dekhang, Rigzin, Zhang, Ying, Zucker, Jeremy, Bredeweg, Erin L., Mallappa, Chandrashekara, Zhou, Xiaoying, Lyubetskaya, Anna, Townsend, Jeffrey P., Galagan, James E., Freitag, Michael, Dunlap, Jay C., Bell-Pedersen, Deborah, Sachs, Matthew S.
Published 2014

Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development

by Holder, Jason W., Ulrich, Jil C., DeBono, Anthony C., Godfrey, Paul A., Desjardins, Christopher A., Zucker, Jeremy, Zeng, Qiandong, Leach, Alex L. B., Ghiviriga, Ion, Dancel, Christine, Abeel, Thomas, Gevers, Dirk, Kodira, Chinnappa D., Desany, Brian, Affourtit, Jason P., Birren, Bruce W., Sinskey, Anthony J.
Published 2011

Comparative analysis of mycobacterium and related actinomycetes yields insight into the evolution of mycobacterium tuberculosis pathogenesis

by McGuire, Abigail Manson, Weiner, Brian, Park, Sang Tae, Wapinski, Ilan, Raman, Sahadevan, Dolganov, Gregory, Peterson, Matthew, Riley, Robert, Zucker, Jeremy, Abeel, Thomas, White, Jared, Sisk, Peter, Stolte, Christian, Koehrsen, Mike, Yamamoto, Robert T, Iacobelli-Martinez, Milena, Kidd, Matthew J, Maer, Andreia M, Schoolnik, Gary K, Regev, Aviv, Galagan, James
Published 2012

Microbial community function and biomarker discovery in the human microbiome

by 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
Published 2011

Genomics of Loa loa, a Wolbachia-free filarial parasite of humans

by Desjardins, Christopher A., Cerqueira, Gustavo C., Goldberg, Jonathan M., Hotopp, Julie C. Dunning, Haas, Brian J., Zucker, Jeremy, Ribeiro, Jose’ M.C., Saif, Sakina, Levin, Joshua Z., Fan, Lin, Zeng, Qiandong, Russ, Carsten, Wortman, Jennifer R., Fink, Doran L., Birren, Bruce W., Nutman, Thomas B.
Published 2013

Comparative Genomic Analysis of Human Fungal Pathogens Causing Paracoccidioidomycosis

by Desjardins, Christopher A., Champion, Mia D., Holder, Jason W., Muszewska, Anna, Goldberg, Jonathan, Bailão, Alexandre M., Brigido, Marcelo Macedo, Ferreira, Márcia Eliana da Silva, Garcia, Ana Maria, Grynberg, Marcin, Gujja, Sharvari, Heiman, David I., Henn, Matthew R., Kodira, Chinnappa D., León-Narváez, Henry, Longo, Larissa V. G., Ma, Li-Jun, Malavazi, Iran, Matsuo, Alisson L., Morais, Flavia V., Pereira, Maristela, Rodríguez-Brito, Sabrina, Sakthikumar, Sharadha, Salem-Izacc, Silvia M., Sykes, Sean M., Teixeira, Marcus Melo, Vallejo, Milene C., Walter, Maria Emília Machado Telles, Yandava, Chandri, Young, Sarah, Zeng, Qiandong, Zucker, Jeremy, Felipe, Maria Sueli, Goldman, Gustavo H., Haas, Brian J., McEwen, Juan G., Nino-Vega, Gustavo, Puccia, Rosana, San-Blas, Gioconda, Soares, Celia Maria de Almeida, Birren, Bruce W., Cuomo, Christina A.
Published 2011

A framework for human microbiome research

by Methé, Barbara A., Nelson, Karen E., Pop, Mihai, Creasy, Heather H., Giglio, Michelle G., Huttenhower, Curtis, Gevers, Dirk, Petrosino, Joseph F., Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Vivien Bonazzi, J., Brooks, Paul, Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Wm. Michael, Durkin, A. Scott, Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry, Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, Kinder-Haake, Susan, King, Nicholas B., Knight, Rob, Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, R. Dwayne, Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavrommatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Pamela Sankar, J., Sathirapongsasuti, Fah, Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Chris S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, Yuan Qing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Weinstock, George M., Wilson, Richard K., White, Owen
Published 2012