Search Results - "Sevinsky, Joel R"

Comparison of Label-free Methods for Quantifying Human Proteins by Shotgun Proteomics by Old, William M, Meyer-Arendt, Karen, Aveline-Wolf, Lauren, Pierce, Kevin G, Mendoza, Alex, Sevinsky, Joel R, Resing, Katheryn A, Ahn, Natalie G

“…Measurements of mass spectral peak intensities and spectral counts are promising methods for quantifying protein abundance changes in shotgun proteomic…”
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The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern Nevada by Gorzalski, Andrew, Ambrosio, 3rd, Frank J, Massic, Lauryn, Scribner, Michelle R, Siao, Danielle Denise, Hua, Chi, Dykema, Phillip, Schneider, Emily, Njoku, Chidinma, Libuit, Kevin, Sevinsky, Joel R, Van Hooser, Stephanie, Pandori, Mark, Hess, David

“…A outbreak has been ongoing in Southern Nevada since August 2021. In this manuscript we describe the sequencing of over 200 isolates from patients at several…”
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TheiaEuk: a species-agnostic bioinformatics workflow for fungal genomic characterization by Ambrosio, Frank J., Scribner, Michelle R., Wright, Sage M., Otieno, James R., Doughty, Emma L., Gorzalski, Andrew, Siao, Danielle Denise, Killian, Steve, Hua, Chi, Schneider, Emily, Tran, Michael, Varghese, Vici, Libuit, Kevin G., Pandori, Mark, Sevinsky, Joel R., Hess, David

“…Introduction The clinical incidence of antimicrobial-resistant fungal infections has dramatically increased in recent years. Certain fungal pathogens colonize…”
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Genomic evidence for reinfection with SARS-CoV-2: a case study by Tillett, Richard L, Sevinsky, Joel R, Hartley, Paul D, Kerwin, Heather, Crawford, Natalie, Gorzalski, Andrew, Laverdure, Chris, Verma, Subhash C, Rossetto, Cyprian C, Jackson, David, Farrell, Megan J, Van Hooser, Stephanie, Pandori, Mark

“…The degree of protective immunity conferred by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently unknown. As such, the…”
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Implementation of California COVIDNet - a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance by Wadford, Debra A, Baumrind, Nikki, Baylis, Elizabeth F, Bell, John M, Bouchard, Ellen L, Crumpler, Megan, Foote, Eric M, Gilliam, Sabrina, Glaser, Carol A, Hacker, Jill K, Ledin, Katya, Messenger, Sharon L, Morales, Christina, Smith, Emily A, Sevinsky, Joel R, Corbett-Detig, Russell B, DeRisi, Joseph, Jacobson, Kathleen

“…The SARS-CoV-2 pandemic represented a formidable scientific and technological challenge to public health due to its rapid spread and evolution. To meet these…”
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Systematic comparison of the human saliva and plasma proteomes by Yan, Weihong, Apweiler, Rolf, Balgley, Brian M., Boontheung, Pinmanee, Bundy, Jonathan L., Cargile, Benjamin J., Cole, Steve, Fang, Xueping, Gonzalez‐Begne, Mireya, Griffin, Timothy J., Hagen, Fred, Hu, Shen, Wolinsky, Lawrence E., Lee, Cheng S., Malamud, Daniel, Melvin, James E., Menon, Rajasree, Mueller, Michael, Qiao, Renli, Rhodus, Nelson L., Sevinsky, Joel R., States, David, Stephenson, James L., Than, Shawn, Yates, John R., Yu, Weixia, Xie, Hongwei, Xie, Yongming, Omenn, Gilbert S., Loo, Joseph A., Wong, David T.

“…The proteome of human salivary fluid has the potential to open new doors for disease biomarker discovery. A recent study to comprehensively identify and…”
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Proteomic Analysis Reveals Virus-Specific Hsp25 Modulation in Cardiac Myocytes by Li, Lianna, Sevinsky, Joel R, Rowland, Megan D, Bundy, Jonathan L, Stephenson, James L, Sherry, Barbara

“…Viruses frequently infect the heart but clinical myocarditis is rare, suggesting that the cardiac antiviral response is uniquely effective. Indeed, the Type I…”
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QIIME allows analysis of high-throughput community sequencing data by Knight, Rob, Caporaso, J Gregory, Kuczynski, Justin, Stombaugh, Jesse, Bittinger, Kyle, Bushman, Frederic D, Costello, Elizabeth K, Fierer, Noah, Peña, Antonio Gonzalez, Goodrich, Julia K, Gordon, Jeffrey I, Huttley, Gavin A, Kelley, Scott T, Knights, Dan, Koenig, Jeremy E, Ley, Ruth E, Lozupone, Catherine A, McDonald, Daniel, Muegge, Brian D, Pirrung, Meg, Reeder, Jens, Sevinsky, Joel R, Turnbaugh, Peter J, Walters, William A, Widmann, Jeremy, Yatsunenko, Tanya, Zaneveld, Jesse

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Analysis of Membrane Proteins from Human Chronic Myelogenous Leukemia Cells:  Comparison of Extraction Methods for Multidimensional LC−MS/MS by Ruth, Mariah C, Old, William M, Emrick, Michelle A, Meyer-Arendt, Karen, Aveline-Wolf, Lauren D, Pierce, Kevin G, Mendoza, Alex M, Sevinsky, Joel R, Hamady, Micah, Knight, Robin D, Resing, Katheryn A, Ahn, Natalie G

“…An important strategy for “shotgun proteomics” profiling involves solution proteolysis of proteins, followed by peptide separation using multidimensional…”
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Extracellular Signal-Regulated Kinase Induces the Megakaryocyte GPIIb/CD41 Gene through MafB/Kreisler by Sevinsky, Joel R., Whalen, Anne M., Ahn, Natalie G.

“…Article Usage Stats Services MCB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene by Hartley, Paul D., Tillett, Richard L., AuCoin, David P., Sevinsky, Joel R., Xu, Yanji, Gorzalski, Andrew, Pandori, Mark, Buttery, Erin, Hansen, Holly, Picker, Michael A., Rossetto, Cyprian C., Verma, Subhash C.

“…Patients with signs of COVID-19 were tested through diagnostic RT-PCR for SARS-CoV-2 using RNA extracted from the nasopharyngeal/nasal swabs. To determine the…”
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Accelerating bioinformatics implementation in public health by Libuit, Kevin G, Doughty, Emma L, Otieno, James R, Ambrosio, Frank, Kapsak, Curtis J, Smith, Emily A, Wright, Sage M, Scribner, Michelle R, Petit Iii, Robert A, Mendes, Catarina Inês, Huergo, Marcela, Legacki, Gregory, Loreth, Christine, Park, Daniel J, Sevinsky, Joel R

“…We have adopted an open bioinformatics ecosystem to address the challenges of bioinformatics implementation in public health laboratories (PHLs)…”
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Pathogen genomics in public health laboratories: successes, challenges, and lessons learned from California's SARS-CoV-2 Whole-Genome Sequencing Initiative, California COVIDNet by Smith, Emily A, Libuit, Kevin G, Kapsak, Curtis J, Scribner, Michelle R, Wright, Sage M, Bell, John, Morales, Christina, Crumpler, Megan, Messenger, Sharon, Hacker, Jill K, Ledin, Katya, Glaser, Carol, Jacobson, Kathleen, Sevinsky, Joel R, Wadford, Debra A

“…The capacity for pathogen genomics in public health expanded rapidly during the coronavirus disease 2019 (COVID-19) pandemic, but many public health…”
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Detection and Validation of Non-synonymous Coding SNPs from Orthogonal Analysis of Shotgun Proteomics Data by Bunger, Maureen K, Cargile, Benjamin J, Sevinsky, Joel R, Deyanova, Ekaterina, Yates, Nathan A, Hendrickson, Ronald C, Stephenson, James L

“…Orthogonal analysis of amino acid substitutions as a result of SNPs in existing proteomic datasets provides a critical foundation for the emerging field of…”
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Proteomics of Pyrococcus furiosus, a Hyperthermophilic Archaeon Refractory to Traditional Methods by Lee, Alice M., Sevinsky, Joel R., Bundy, Jonathan L., Grunden, Amy M., Stephenson, James L.

“…Pyrococcus furiosus is one of the most extensively studied hyperthermophilic archaea. Proteins from this hyperthemophile organism are extremely thermostable…”
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Immobilized pH gradient isoelectric focusing as a first-dimension separation in shotgun proteomics by Cargile, Benjamin J, Sevinsky, Joel R, Essader, Amal S, Stephenson, Jr, James L, Bundy, Jonathan L

“…Shotgun proteomics, where a tryptic digest of a complex proteome sample is directly analyzed by either single dimensional or multidimensional liquid…”
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Whole Genome Searching with Shotgun Proteomic Data: Applications for Genome Annotation by Sevinsky, Joel R, Cargile, Benjamin J, Bunger, Maureen K, Meng, Fanyu, Yates, Nathan A, Hendrickson, Ronald C, Stephenson, Jr, James L

“…High-throughput genome sequencing continues to accelerate the rate at which complete genomes are available for biological research. Many of these new genome…”
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Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects by Cargile, Benjamin J, Sevinsky, Joel R, Essader, Amal S, Eu, Jerry P, Stephenson, James L. Jr

“…Current algorithms for the calculation of peptide or protein pI, based on the charge associated with individual amino acids, can calculate pI values to within…”
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Ligand-Induced Protease Receptor Translocation into Caveolae: A Mechanism for Regulating Cell Surface Proteolysis of the Tissue Factor-Dependent Coagulation Pathway by Sevinsky, Joel R., L. Vijay Mohan Rao, Ruf, Wolfram

“…The ability to regulate proteolytic functions is critical to cell biology. We describe events that regulate the initiation of the coagulation cascade on…”
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Incorporating expression data in metabolic modeling: A case study of lactate dehydrogenase by Downer, Joshua, Sevinsky, Joel R., Ahn, Natalie G., Resing, Katheryn A., Betterton, M.D.

“…Integrating biological information from different sources to understand cellular processes is an important problem in systems biology. We use data from mRNA…”
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