Search Results - "Brover, Vyacheslav"

AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence by Feldgarden, Michael, Brover, Vyacheslav, Gonzalez-Escalona, Narjol, Frye, Jonathan G., Haendiges, Julie, Haft, Daniel H., Hoffmann, Maria, Pettengill, James B., Prasad, Arjun B., Tillman, Glenn E., Tyson, Gregory H., Klimke, William

“…Antimicrobial resistance (AMR) is a significant public health threat. With the rise of affordable whole genome sequencing, in silico approaches to assessing…”
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Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates by Feldgarden, Michael, Brover, Vyacheslav, Haft, Daniel H, Prasad, Arjun B, Slotta, Douglas J, Tolstoy, Igor, Tyson, Gregory H, Zhao, Shaohua, Hsu, Chih-Hao, McDermott, Patrick F, Tadesse, Daniel A, Morales, Cesar, Simmons, Mustafa, Tillman, Glenn, Wasilenko, Jamie, Folster, Jason P, Klimke, William

“…Antimicrobial resistance (AMR) is a major public health problem that requires publicly available tools for rapid analysis. To identify AMR genes in…”
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Insights into corn genes derived from large-scale cDNA sequencing by Alexandrov, Nickolai N, Brover, Vyacheslav V, Freidin, Stanislav, Troukhan, Maxim E, Tatarinova, Tatiana V, Zhang, Hongyu, Swaller, Timothy J, Lu, Yu-Ping, Bouck, John, Flavell, Richard B, Feldmann, Kenneth A

“…We present a large portion of the transcriptome of Zea mays, including ESTs representing 484,032 cDNA clones from 53 libraries and 36,565 fully sequenced cDNA…”
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Deletions across the SARS-CoV-2 Genome: Molecular Mechanisms and Putative Functional Consequences of Deletions in Accessory Genes by Rogozin, Igor B, Saura, Andreu, Bykova, Anastassia, Brover, Vyacheslav, Yurchenko, Vyacheslav

“…The analysis of deletions may reveal evolutionary trends and provide new insight into the surprising variability and rapidly spreading capability that…”
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Curation of the AMRFinderPlus databases: applications, functionality and impact by Feldgarden, Michael, Brover, Vyacheslav, Fedorov, Boris, Haft, Daniel H, Prasad, Arjun B, Klimke, William

“…Antimicrobial resistance (AMR) is a significant public health threat. Low-cost whole-genome sequencing, which is often used in surveillance programmes,…”
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Features of Arabidopsis Genes and Genome Discovered using Full-length cDNAs by Alexandrov, N.N, Troukhan, M.E, Brover, V.V, Tatarinova, T, Flavell, R.B, Feldmann, K.A

“…Arabidopsis is currently the reference genome for higher plants. A new, more detailed statistical analysis of Arabidopsis gene structure is presented including…”
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RefSeq: an update on prokaryotic genome annotation and curation by Haft, Daniel H, DiCuccio, Michael, Badretdin, Azat, Brover, Vyacheslav, Chetvernin, Vyacheslav, O'Neill, Kathleen, Li, Wenjun, Chitsaz, Farideh, Derbyshire, Myra K, Gonzales, Noreen R, Gwadz, Marc, Lu, Fu, Marchler, Gabriele H, Song, James S, Thanki, Narmada, Yamashita, Roxanne A, Zheng, Chanjuan, Thibaud-Nissen, Françoise, Geer, Lewis Y, Marchler-Bauer, Aron, Pruitt, Kim D

“…Abstract The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) provides annotation for over 95 000 prokaryotic…”
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Phylogenomic analysis of the family Peptostreptococcaceae (Clostridium cluster XI) and proposal for reclassification of Clostridium litorale (Fendrich et al. 1991) and Eubacterium acidaminophilum (Zindel et al. 1989) as Peptoclostridium litorale gen. nov. comb. nov. and Peptoclostridium acidaminophilum comb. nov by Galperin, Michael Y, Brover, Vyacheslav, Tolstoy, Igor, Yutin, Natalya

“…In 1994, analyses of clostridial 16S rRNA gene sequences led to the assignment of 18 species to Clostridium cluster XI, separating them from Clostridium sensu…”
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Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation by O'Leary, Nuala A, Wright, Mathew W, Brister, J Rodney, Ciufo, Stacy, Haddad, Diana, McVeigh, Rich, Rajput, Bhanu, Robbertse, Barbara, Smith-White, Brian, Ako-Adjei, Danso, Astashyn, Alexander, Badretdin, Azat, Bao, Yiming, Blinkova, Olga, Brover, Vyacheslav, Chetvernin, Vyacheslav, Choi, Jinna, Cox, Eric, Ermolaeva, Olga, Farrell, Catherine M, Goldfarb, Tamara, Gupta, Tripti, Haft, Daniel, Hatcher, Eneida, Hlavina, Wratko, Joardar, Vinita S, Kodali, Vamsi K, Li, Wenjun, Maglott, Donna, Masterson, Patrick, McGarvey, Kelly M, Murphy, Michael R, O'Neill, Kathleen, Pujar, Shashikant, Rangwala, Sanjida H, Rausch, Daniel, Riddick, Lillian D, Schoch, Conrad, Shkeda, Andrei, Storz, Susan S, Sun, Hanzhen, Thibaud-Nissen, Francoise, Tolstoy, Igor, Tully, Raymond E, Vatsan, Anjana R, Wallin, Craig, Webb, David, Wu, Wendy, Landrum, Melissa J, Kimchi, Avi, Tatusova, Tatiana, DiCuccio, Michael, Kitts, Paul, Murphy, Terence D, Pruitt, Kim D

“…The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic,…”
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Publicly Available and Validated DNA Reference Sequences Are Critical to Fungal Identification and Global Plant Protection Efforts: A Use-Case in Colletotrichum by Kennedy, Aaron H, Schoch, Conrad L, Marrero, Glorimar, Brover, Vyacheslav, Robbertse, Barbara

“…Publicly available and validated DNA reference sequences useful for phylogeny estimation and identification of fungal pathogens are an increasingly important…”
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Widespread CRISPR-derived RNA regulatory elements in CRISPR-Cas systems by Shmakov, Sergey A, Barth, Zachary K, Makarova, Kira S, Wolf, Yuri I, Brover, Vyacheslav, Peters, Joseph E, Koonin, Eugene V

“…Abstract CRISPR-cas loci typically contain CRISPR arrays with unique spacers separating direct repeats. Spacers along with portions of adjacent repeats are…”
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NCBI RefSeq: reference sequence standards through 25 years of curation and annotation by Goldfarb, Tamara, Kodali, Vamsi K, Pujar, Shashikant, Brover, Vyacheslav, Robbertse, Barbara, Farrell, Catherine M, Oh, Dong-Ha, Astashyn, Alexander, Ermolaeva, Olga, Haddad, Diana, Hlavina, Wratko, Hoffman, Jinna, Jackson, John D, Joardar, Vinita S, Kristensen, David, Masterson, Patrick, McGarvey, Kelly M, McVeigh, Richard, Mozes, Eyal, Murphy, Michael R, Schafer, Susan S, Souvorov, Alexander, Spurrier, Brett, Strope, Pooja K, Sun, Hanzhen, Vatsan, Anjana R, Wallin, Craig, Webb, David, Brister, J Rodney, Hatcher, Eneida, Kimchi, Avi, Klimke, William, Marchler-Bauer, Aron, Pruitt, Kim D, Thibaud-Nissen, Françoise, Murphy, Terence D

“…Abstract Reference sequences and annotations serve as the foundation for many lines of research today, from organism and sequence identification to providing a…”
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Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation by O'Leary, Nuala A., Wright, Mathew W., Brister, J. Rodney, Ciufo, Stacy, Haddad, Diana, McVeigh, Rich, Rajput, Bhanu, Robbertse, Barbara, Smith-White, Brian, Ako-Adjei, Danso, Astashyn, Alexander, Badretdin, Azat, Bao, Yiming, Blinkova, Olga, Brover, Vyacheslav, Chetvernin, Vyacheslav, Choi, Jinna, Cox, Eric, Ermolaeva, Olga, Farrell, Catherine M., Goldfarb, Tamara, Gupta, Tripti, Haft, Daniel, Hatcher, Eneida, Hlavina, Wratko, Joardar, Vinita S., Kodali, Vamsi K., Li, Wenjun, Maglott, Donna, Masterson, Patrick, McGarvey, Kelly M., Murphy, Michael R., O'Neill, Kathleen, Pujar, Shashikant, Rangwala, Sanjida H., Rausch, Daniel, Riddick, Lillian D., Schoch, Conrad, Shkeda, Andrei, Storz, Susan S., Sun, Hanzhen, Thibaud-Nissen, Francoise, Tolstoy, Igor, Tully, Raymond E., Vatsan, Anjana R., Wallin, Craig, Webb, David, Wu, Wendy, Landrum, Melissa J., Kimchi, Avi, Tatusova, Tatiana, DiCuccio, Michael, Kitts, Paul, Murphy, Terence D., Pruitt, Kim D.

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Erratum for Feldgarden et al., "Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates" by Feldgarden, Michael, Brover, Vyacheslav, Haft, Daniel H, Prasad, Arjun B, Slotta, Douglas J, Tolstoy, Igor, Tyson, Gregory H, Zhao, Shaohua, Hsu, Chih-Hao, McDermott, Patrick F, Tadesse, Daniel A, Morales, Cesar, Simmons, Mustafa, Tillman, Glenn, Wasilenko, Jamie, Folster, Jason P, Klimke, William

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Lessons learned in virulence factor identification and data management from a hackathon on microbial virulence [version 1; peer review: 1 approved with reservations] by Pickett, Brett E, Connor, Ryan, Berhanu-Denka, Tamiru, Bhalla, Sherry, Brover, Vyacheslav, Chambers, Michael James, Chaudhary, Kumardeep, Cissé, Ousmane H, Dillman, Allissa, Elmassry, Moamen M, Feldgarden, Michael, Holloway, Eric, Huang, Xin, Klimke, William, Inês Mendes, Catarina, Norred, S. Elizabeth, Parkinson, Jonathan, Sevilla, Samantha, Garcia Solache, Monica, Surujon, Defne, Torian, Udana, Zalunin, Vadim, Busby, Ben

“…Virulence is a complex mix of microbial traits and host susceptibility that could ultimately lead to disease. The increased prevalence of multidrug resistant…”
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Skew in CG content near the transcription start site in Arabidopsis thaliana by Tatarinova, Tatiana, Brover, Vyacheslav, Troukhan, Maxim, Alexandrov, Nickolai

“…We have discovered a novel statistical feature of Arabidopsis thaliana genome that remarkably correlates with a position of transcription start site--CG skew…”
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Skew in CG content near the transcription start site inArabidopsis thaliana by Tatarinova, Tatiana, Brover, Vyacheslav, Troukhan, Maxim, Alexandrov, Nickolai

“…We have discovered a novel statistical feature of Arabidopsis thaliana genome that remarkably correlates with a position of transcription start site—CG skew…”
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