Mugsy: fast multiple alignment of closely related whole genomes von ANGIUOLI, Samuel V, SALZBERG, Steven L

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CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing von Angiuoli, Samuel V, Matalka, Malcolm, Gussman, Aaron, Galens, Kevin, Vangala, Mahesh, Riley, David R, Arze, Cesar, White, James R, White, Owen, Fricke, W Florian

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Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing von Angiuoli, Samuel V, White, James R, Matalka, Malcolm, White, Owen, Fricke, W Florian

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Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells von van 't Erve, Iris, Medina, Jamie E, Leal, Alessandro, Papp, Eniko, Phallen, Jillian, Adleff, Vilmos, Chiao, Elaine Jiayuee, Arun, Adith S, Bolhuis, Karen, Simmons, John K, Karandikar, Aanavi, Valkenburg, Kenneth C, Sausen, Mark, Angiuoli, Samuel V, Scharpf, Robert B, Punt, Cornelis J A, Meijer, Gerrit A, Velculescu, Victor E, Fijneman, Remond J A

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Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation von Angiuoli, Samuel V., Gussman, Aaron, Klimke, William, Cochrane, Guy, Field, Dawn, Garrity, George M., Kodira, Chinnappa D., Kyrpides, Nikos, Madupu, Ramana, Markowitz, Victor, Tatusova, Tatiana, Thomson, Nick, White, Owen

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Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species von Donati, Claudio, Hiller, N Luisa, Tettelin, Hervé, Muzzi, Alessandro, Croucher, Nicholas J, Angiuoli, Samuel V, Oggioni, Marco, Dunning Hotopp, Julie C, Hu, Fen Z, Riley, David R, Covacci, Antonello, Mitchell, Tim J, Bentley, Stephen D, Kilian, Morgens, Ehrlich, Garth D, Rappuoli, Rino, Moxon, E Richard, Masignani, Vega

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Integrated Next-Generation Sequencing and Avatar Mouse Models for Personalized Cancer Treatment von GARRALDA, Elena, PAZ, Keren, BRUCKHEIMER, Elizabeth, ANGIUOLI, Samuel V, CALLES, Antonio, DIAZ, Luis A, VELCULESCU, Victor E, VALENCIA, Alfonso, SIDRANSKY, David, HIDALGO, Manuel, LOPEZ-CASAS, Pedro P, JONES, Siân, KATZ, Amanda, KANN, Lisa M, LOPEZ-RIOS, Fernando, SARNO, Francesca, AL-SHAHROUR, Fátima, VASQUEZ, David

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Comparative genomics of emerging human ehrlichiosis agents von Dunning Hotopp, Julie C, Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan A, Eisen, Jonathan, Seshadri, Rekha, Ren, Qinghu, Wu, Martin, Utterback, Teresa R, Smith, Shannon, Lewis, Matthew, Khouri, Hoda, Zhang, Chunbin, Niu, Hua, Lin, Quan, Ohashi, Norio, Zhi, Ning, Nelson, William, Brinkac, Lauren M, Dodson, Robert J, Rosovitz, M J, Sundaram, Jaideep, Daugherty, Sean C, Davidsen, Tanja, Durkin, Anthony S, Gwinn, Michelle, Haft, Daniel H, Selengut, Jeremy D, Sullivan, Steven A, Zafar, Nikhat, Zhou, Liwei, Benahmed, Faiza, Forberger, Heather, Halpin, Rebecca, Mulligan, Stephanie, Robinson, Jeffrey, White, Owen, Rikihisa, Yasuko, Tettelin, Hervé

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Genomic analyses of gynaecologic carcinosarcomas reveal frequent mutations in chromatin remodelling genes von Jones, Siân, Stransky, Nicolas, McCord, Christine L., Cerami, Ethan, Lagowski, James, Kelly, Devon, Angiuoli, Samuel V., Sausen, Mark, Kann, Lisa, Shukla, Manish, Makar, Rosemary, Wood, Laura D., Diaz, Luis A., Lengauer, Christoph, Velculescu, Victor E.

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Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination von Budroni, Sonia, Siena, Emilio, Hotopp, Julie C. Dunning, Seib, Kate L., Serruto, Davide, Nofroni, Chiara, Comanducci, Maurizio, Riley, David R., Daugherty, Sean C., Angiuoli, Samuel V., Covacci, Antonello, Pizza, Mariagrazia, Rappuoli, Rino, Moxon, E. Richard, Tettelin, Hervé, Medini, Duccio

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Comparative Genomic Analysis of Diverse Clonal Types of Enterotoxigenic Escherichia coli Reveals Pathovar-Specific Conservation von Sahl, Jason W, Steinsland, Hans, Redman, Julia C, Angiuoli, Samuel V, Nataro, James P, Sommerfelt, Halvor, Rasko, David A

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The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists von Heinicke, Sven, Livstone, Michael S, Lu, Charles, Oughtred, Rose, Kang, Fan, Angiuoli, Samuel V, White, Owen, Botstein, David, Dolinski, Kara

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Notch1 mutations are drivers of oral tumorigenesis von Izumchenko, Evgeny, Sun, Kai, Jones, Sian, Brait, Mariana, Agrawal, Nishant, Koch, Wayne, McCord, Christine L, Riley, David R, Angiuoli, Samuel V, Velculescu, Victor E, Jiang, Wei-Wen, Sidransky, David

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Automated next-generation profiling of genomic alterations in human cancers von Keefer, Laurel A., White, James R., Wood, Derrick E., Gerding, Kelly M. R., Valkenburg, Kenneth C., Riley, David, Gault, Christopher, Papp, Eniko, Vollmer, Christine M., Greer, Amy, Hernandez, James, McGregor, Paul M., Zingone, Adriana, Ryan, Bríd M., Deak, Kristen, McCall, Shannon J., Datto, Michael B., Prescott, James L., Thompson, John F., Cerqueira, Gustavo C., Jones, Siân, Simmons, John K., McElhinny, Abigail, Dickey, Jennifer, Angiuoli, Samuel V., Diaz, Luis A., Velculescu, Victor E., Sausen, Mark

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Genome Analysis of Multiple Pathogenic Isolates of Streptococcus agalactiae: Implications for the Microbial "Pan-Genome" von Tettelin, Hervé, Masignani, Vega, Cieslewicz, Michael J., Donati, Claudio, Medini, Duccio, Ward, Naomi L., Angiuoli, Samuel V., Crabtree, Jonathan, Jones, Amanda L., Durkin, A. Scott, DeBoy, Robert T., Davidsen, Tanja M., Mora, Marirosa, Scarselli, Maria, Immaculada Margarit y Ros, Peterson, Jeremy D., Hauser, Christopher R., Sundaram, Jaideep P., Nelson, William C., Madupu, Ramana, Brinkac, Lauren M., Dodson, Robert J., Rosovitz, Mary J., Sullivan, Steven A., Daugherty, Sean C., Haft, Daniel H., Selengut, Jeremy, Gwinn, Michelle L., Zhou, Liwei, Zafar, Nikhat, Khouri, Hoda, Radune, Diana, Dimitrov, George, Watkins, Kisha, Kevin J. B. O'Connor, Smith, Shannon, Utterback, Teresa R., White, Owen, Rubens, Craig E., Grandi, Guido, Madoff, Lawrence C., Kasper, Dennis L., Telford, John L., Wessels, Michael R., Rappuoli, Rino, Fraser, Claire M.

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Comparative genomics of the neglected human malaria parasite Plasmodium vivax von Sargeant, Tobias J, Gueye, Amy H, Salzberg, Steven L, Essien, Kobby, Kooij, Taco W. A, Angiuoli, Samuel V, del Portillo, Hernando A, Gardner, Malcolm J, Nene, Vish, Korsinczky, Michael, Stoeckert, Christian J, Meyer, Esmeralda V.-S, Wortman, Jennifer R, Barnwell, John W, Yamamoto, Marcio M, Crabb, Brendan S, Ralph, Stuart A, Sullivan, Steven A, Coulson, Richard M. R, Merino, Emilio F, Bidwell, Shelby L, Adams, John H, Ren, Qinghu, Fernandez-Becerra, Carmen, Fraser-Liggett, Claire M, Kang'a, Simon, Guo, Xiang, Cheng, Qin, Crabtree, Jonathan, Hoffman, Stephen L, Silva, Joana C, Galinski, Mary R, Caler, Elisabet, Amedeo, Paolo, Paulsen, Ian, Feldblyum, Tamara V, Gilson, Paul R, White, Owen, Lorenzi, Hernan, Carlton, Jane M

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Improving pan-genome annotation using whole genome multiple alignment von Angiuoli, Samuel V, Dunning Hotopp, Julie C, Salzberg, Steven L, Tettelin, Hervé

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Insights on Evolution of Virulence and Resistance from the Complete Genome Analysis of an Early Methicillin-Resistant Staphylococcus aureus Strain and a Biofilm-Producing Methicill... von GILL, Steven R, FOUTS, Derrick E, DODSON, Robert J, DAUGHERTY, Sean C, MADUPU, Ramana, ANGIUOLI, Samuel V, DURKIN, A. Scott, HAFT, Daniel H, VAMATHEVAN, Jessica, KHOURI, Hoda, UTTERBACK, Terry, LEE, Chris, ARCHER, Gordon L, DIMITROV, George, LINGXIA JIANG, HAIYING QIN, JAN WEIDMAN, TRAN, Kevin, KANG, Kathy, HANCE, Ioana R, NELSON, Karen E, FRASER, Claire M, MONGODIN, Emmanuel F, DEBOY, Robert T, RAVEL, Jacques, PAULSEN, Ian T, KOLONAY, James F, BRINKAC, Lauren, BEANAN, Mauren

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CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota von White, James Robert, Maddox, Cynthia, White, Owen, Angiuoli, Samuel V, Fricke, W Florian

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Ergatis: a web interface and scalable software system for bioinformatics workflows von Orvis, Joshua, Crabtree, Jonathan, Galens, Kevin, Gussman, Aaron, Inman, Jason M., Lee, Eduardo, Nampally, Sreenath, Riley, David, Sundaram, Jaideep P., Felix, Victor, Whitty, Brett, Mahurkar, Anup, Wortman, Jennifer, White, Owen, Angiuoli, Samuel V.

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