Mugsy: fast multiple alignment of closely related whole genomes

Por Angiuoli, Samuel V., Salzberg, Steven L.
Publicado em 2011

Improving pan-genome annotation using whole genome multiple alignment

Por Angiuoli, Samuel V, Dunning Hotopp, Julie C, Salzberg, Steven L, Tettelin, Hervé
Publicado em 2011

Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing

Por Angiuoli, Samuel V., White, James R., Matalka, Malcolm, White, Owen, Fricke, W. Florian
Publicado em 2011

CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota

Por White, James Robert, Maddox, Cynthia, White, Owen, Angiuoli, Samuel V, Fricke, W Florian
Publicado em 2013

Using Sybil for interactive comparative genomics of microbes on the web

Por Riley, David R., Angiuoli, Samuel V., Crabtree, Jonathan, Dunning Hotopp, Julie C., Tettelin, Hervé
Publicado em 2012

The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists

Por Heinicke, Sven, Livstone, Michael S., Lu, Charles, Oughtred, Rose, Kang, Fan, Angiuoli, Samuel V., White, Owen, Botstein, David, Dolinski, Kara
Publicado em 2007

A Comparative Genomic Analysis of Diverse Clonal Types of Enterotoxigenic Escherichia coli Reveals Pathovar-Specific Conservation

Por Sahl, Jason W., Steinsland, Hans, Redman, Julia C., Angiuoli, Samuel V., Nataro, James P., Sommerfelt, Halvor, Rasko, David A.
Publicado em 2011

The IGS Standard Operating Procedure for Automated Prokaryotic Annotation

Por Galens, Kevin, Orvis, Joshua, Daugherty, Sean, Creasy, Heather H., Angiuoli, Sam, White, Owen, Wortman, Jennifer, Mahurkar, Anup, Giglio, Michelle Gwinn
Publicado em 2011

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

Por Angiuoli, Samuel V, Matalka, Malcolm, Gussman, Aaron, Galens, Kevin, Vangala, Mahesh, Riley, David R, Arze, Cesar, White, James R, White, Owen, Fricke, W Florian
Publicado em 2011

GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database

Por Schriml, Lynn M., Arze, Cesar, Nadendla, Suvarna, Ganapathy, Anu, Felix, Victor, Mahurkar, Anup, Phillippy, Katherine, Gussman, Aaron, Angiuoli, Sam, Ghedin, Elodie, White, Owen, Hall, Neil
Publicado em 2010

Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta) genomic Annotation

Por 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
Publicado em 2008

CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline

Por Agrawal, Sonia, Arze, Cesar, Adkins, Ricky S., Crabtree, Jonathan, Riley, David, Vangala, Mahesh, Galens, Kevin, Fraser, Claire M., Tettelin, Hervé, White, Owen, Angiuoli, Samuel V., Mahurkar, Anup, Fricke, W. Florian
Publicado no BMC Genomics (2017)

Notch1 mutations are drivers of oral tumorigenesis

Por 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
Publicado no Cancer Prev Res (Phila) (2014)

Ergatis: a web interface and scalable software system for bioinformatics workflows

Por 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.
Publicado em 2010

Genomic analyses of gynaecologic carcinosarcomas reveal frequent mutations in chromatin remodelling genes

Por 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.
Publicado no Nat Commun (2014)

Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination

Por 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
Publicado em 2011

The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1

Por Rasko, David A., Ravel, Jacques, Økstad, Ole Andreas, Helgason, Erlendur, Cer, Regina Z., Jiang, Lingxia, Shores, Kelly A., Fouts, Derrick E., Tourasse, Nicolas J., Angiuoli, Samuel V., Kolonay, James, Nelson, William C., Kolstø, Anne-Brit, Fraser, Claire M., Read, Timothy D.
Publicado em 2004

Personalized genomic analyses for cancer mutation discovery and interpretation

Por Jones, Siân, Anagnostou, Valsamo, Lytle, Karli, Parpart-Li, Sonya, Nesselbush, Monica, Riley, David R., Shukla, Manish, Chesnick, Bryan, Kadan, Maura, Papp, Eniko, Galens, Kevin G., Murphy, Derek, Zhang, Theresa, Kann, Lisa, Sausen, Mark, Angiuoli, Samuel V., Diaz, Luis A., Velculescu, Victor E.
Publicado no Sci Transl Med (2015)

Integrated Next-Generation Sequencing and Avatar Mouse Models for Personalized Cancer Treatment

Por Garralda, Elena, Paz, Keren, López-Casas, Pedro P., Jones, Siân, Katz, Amanda, Kann, Lisa M., López-Rios, Fernando, Sarno, Francesca, Al-Shahrour, Fátima, Vasquez, David, Bruckheimer, Elizabeth, Angiuoli, Samuel V., Calles, Antonio, Diaz, Luis A., Velculescu, Victor E., Valencia, Alfonso, Sidransky, David, Hidalgo, Manuel
Publicado no Clin Cancer Res (2014)

Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

Por 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
Publicado em 2010