Search Results - "Madden, L."

BLAST: at the core of a powerful and diverse set of sequence analysis tools by McGinnis, Scott, Madden, Thomas L.

“…Basic Local Alignment Search Tool (BLAST) is one of the most heavily used sequence analysis tools available in the public domain. There is now a wide choice of…”
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Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction by Ye, Jian, Coulouris, George, Zaretskaya, Irena, Cutcutache, Ioana, Rozen, Steve, Madden, Thomas L

“…Choosing appropriate primers is probably the single most important factor affecting the polymerase chain reaction (PCR). Specific amplification of the intended…”
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Magic-BLAST, an accurate RNA-seq aligner for long and short reads by Boratyn, Grzegorz M, Thierry-Mieg, Jean, Thierry-Mieg, Danielle, Busby, Ben, Madden, Thomas L

“…Next-generation sequencing technologies can produce tens of millions of reads, often paired-end, from transcripts or genomes. But few programs can align RNA on…”
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BLAST+: architecture and applications by Camacho, Christiam, Coulouris, George, Avagyan, Vahram, Ma, Ning, Papadopoulos, Jason, Bealer, Kevin, Madden, Thomas L

“…Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its…”
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Database resources of the National Center for Biotechnology Information by Sayers, Eric W, Beck, Jeffrey, Bolton, Evan E, Bourexis, Devon, Brister, James R, Canese, Kathi, Comeau, Donald C, Funk, Kathryn, Kim, Sunghwan, Klimke, William, Marchler-Bauer, Aron, Landrum, Melissa, Lathrop, Stacy, Lu, Zhiyong, Madden, Thomas L, O’Leary, Nuala, Phan, Lon, Rangwala, Sanjida H, Schneider, Valerie A, Skripchenko, Yuri, Wang, Jiyao, Ye, Jian, Trawick, Barton W, Pruitt, Kim D, Sherry, Stephen T

“…Abstract The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the…”
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Database resources of the National Center for Biotechnology Information by Sayers, Eric W, Agarwala, Richa, Bolton, Evan E, Brister, J Rodney, Canese, Kathi, Clark, Karen, Connor, Ryan, Fiorini, Nicolas, Funk, Kathryn, Hefferon, Timothy, Holmes, J Bradley, Kim, Sunghwan, Kimchi, Avi, Kitts, Paul A, Lathrop, Stacy, Lu, Zhiyong, Madden, Thomas L, Marchler-Bauer, Aron, Phan, Lon, Schneider, Valerie A, Schoch, Conrad L, Pruitt, Kim D, Ostell, James

“…Abstract The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the…”
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Is it too hard? Promoting equitable work-life balance by Brewster, L Madden, Bruce, Christina D

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Database resources of the National Center for Biotechnology Information by Sayers, Eric W, Beck, Jeff, Brister, J Rodney, Bolton, Evan E, Canese, Kathi, Comeau, Donald C, Funk, Kathryn, Ketter, Anne, Kim, Sunghwan, Kimchi, Avi, Kitts, Paul A, Kuznetsov, Anatoliy, Lathrop, Stacy, Lu, Zhiyong, McGarvey, Kelly, Madden, Thomas L, Murphy, Terence D, O’Leary, Nuala, Phan, Lon, Schneider, Valerie A, Thibaud-Nissen, Françoise, Trawick, Bart W, Pruitt, Kim D, Ostell, James

“…Abstract The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the…”
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ElasticBLAST: accelerating sequence search via cloud computing by Camacho, Christiam, Boratyn, Grzegorz M, Joukov, Victor, Vera Alvarez, Roberto, Madden, Thomas L

“…Biomedical researchers use alignments produced by BLAST (Basic Local Alignment Search Tool) to categorize their query sequences. Producing such alignments is…”
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Predicting plant disease epidemics from functionally represented weather series by Shah, D A, Paul, P A, De Wolf, E D, Madden, L V

“…Epidemics are often triggered by specific weather patterns favouring the pathogen on susceptible hosts. For plant diseases, models predicting epidemics have…”
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Meta-Analysis for Evidence Synthesis in Plant Pathology: An Overview by Madden, L.V, Paul, P.A

“…Meta-analysis is the analysis of the results of multiple studies, which is typically performed in order to synthesize evidence from many possible sources in a…”
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Natural Occurrence of Maize Gibberella Ear Rot and Contamination of Grain with Mycotoxins in Association with Weather Variables by Dalla Lana, F, Madden, L V, Paul, P A

“…Gibberella ear rot (GER) severity (percent area of the ear diseased) and associated grain contamination with mycotoxins were quantified in plots of 15 to 16…”
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Database resources of the National Center for Biotechnology Information in 2023 by Sayers, Eric W, Bolton, Evan E, Brister, J Rodney, Canese, Kathi, Chan, Jessica, Comeau, Donald C, Farrell, Catherine M, Feldgarden, Michael, Fine, Anna M, Funk, Kathryn, Hatcher, Eneida, Kannan, Sivakumar, Kelly, Christopher, Kim, Sunghwan, Klimke, William, Landrum, Melissa J, Lathrop, Stacy, Lu, Zhiyong, Madden, Thomas L, Malheiro, Adriana, Marchler-Bauer, Aron, Murphy, Terence D, Phan, Lon, Pujar, Shashikant, Rangwala, Sanjida H, Schneider, Valerie A, Tse, Tony, Wang, Jiyao, Ye, Jian, Trawick, Barton W, Pruitt, Kim D, Sherry, Stephen T

“…The National Center for Biotechnology Information (NCBI) provides online information resources for biology, including the GenBank® nucleic acid sequence…”
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NCBI BLAST: a better web interface by Johnson, Mark, Zaretskaya, Irena, Raytselis, Yan, Merezhuk, Yuri, McGinnis, Scott, Madden, Thomas L

“…Basic Local Alignment Search Tool (BLAST) is a sequence similarity search program. The public interface of BLAST, http://www.ncbi.nlm.nih.gov/blast, at the…”
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mTOR Complex 1 Regulates Lipin 1 Localization to Control the SREBP Pathway by Peterson, Timothy R., Sengupta, Shomit S., Harris, Thurl E., Carmack, Anne E., Kang, Seong A., Balderas, Eric, Guertin, David A., Madden, Katherine L., Carpenter, Anne E., Finck, Brian N., Sabatini, David M.

“…The nutrient- and growth factor-responsive kinase mTOR complex 1 (mTORC1) regulates many processes that control growth, including protein synthesis, autophagy,…”
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Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software by KAMENTSKY, Lee, JONAS, Thouis R, FRAMER, Adam, BRAY, Mark-Anthony, LOGAN, David J, MADDEN, Katherine L, LJOSA, Vebjorn, RUEDEN, Curtis, ELICEIRI, Kevin W, CARPENTER, Anne E

“…There is a strong and growing need in the biology research community for accurate, automated image analysis. Here, we describe CellProfiler 2.0, which has been…”
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Database resources of the National Center for Biotechnology Information by Sayers, Eric W., Barrett, Tanya, Benson, Dennis A., Bolton, Evan, Bryant, Stephen H., Canese, Kathi, Chetvernin, Vyacheslav, Church, Deanna M., DiCuccio, Michael, Federhen, Scott, Feolo, Michael, Fingerman, Ian M., Geer, Lewis Y., Helmberg, Wolfgang, Kapustin, Yuri, Krasnov, Sergey, Landsman, David, Lipman, David J., Lu, Zhiyong, Madden, Thomas L., Madej, Tom, Maglott, Donna R., Marchler-Bauer, Aron, Miller, Vadim, Karsch-Mizrachi, Ilene, Ostell, James, Panchenko, Anna, Phan, Lon, Pruitt, Kim D., Schuler, Gregory D., Sequeira, Edwin, Sherry, Stephen T., Shumway, Martin, Sirotkin, Karl, Slotta, Douglas, Souvorov, Alexandre, Starchenko, Grigory, Tatusova, Tatiana A., Wagner, Lukas, Wang, Yanli, Wilbur, W. John, Yaschenko, Eugene, Ye, Jian

“…In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and…”
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Database indexing for production MegaBLAST searches by Morgulis, Aleksandr, Coulouris, George, Raytselis, Yan, Madden, Thomas L., Agarwala, Richa, Schäffer, Alejandro A.

“…Motivation: The BLAST software package for sequence comparison speeds up homology search by preprocessing a query sequence into a lookup table. Numerous…”
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Nonparametric analysis of ordinal data in designed factorial experiments by SHAH, D. A, MADDEN, L. V

“…ABSTRACT Plant disease severity often is assessed using an ordinal rating scale rather than a continuous scale of measurement. Although such data usually…”
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Statistical Models and Methods for Network Meta-Analysis by Madden, L V, Piepho, H-P, Paul, P A

“…Meta-analysis, the methodology for analyzing the results from multiple independent studies, has grown tremendously in popularity over the last four decades…”
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