Thomas L. Madden

29 papers Journal 29
YearRankTypeTitle / Venue / Authors
2023 J jnl
Database resources of the National Center for Biotechnology Information in 2023.
Nucleic Acids Res.
Eric W. Sayers, Evan E. Bolton, J. Rodney Brister, Kathi Canese, Jessica Chan, Donald C. Comeau, Catherine M. Farrell, Michael Feldgarden, Anna M. Fine, Kathryn Funk, Eneida Hatcher, Sivakumar Kannan, Christopher Kelly, Sunghwan Kim, William Klimke, Melissa J. Landrum, Stacy Lathrop, Zhiyong Lu, Thomas L. Madden, Adriana J. Malheiro, Aron Marchler-Bauer, Terence D. Murphy, Lon Phan, Shashikant Pujar, Sanjida H. Rangwala, Valerie A. Schneider, Tony Tse, Jiyao Wang, Jian Ye, Barton W. Trawick, Kim D. Pruitt, Stephen T. Sherry
2023 J jnl
ElasticBLAST: accelerating sequence search via cloud computing.
BMC Bioinform.
Christiam Camacho, Grzegorz M. Boratyn, Victor Joukov, Roberto Vera Alvarez, Thomas L. Madden
2021 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
Eric W. Sayers, Jeffrey Beck, Evan Bolton, Devon Bourexis, James R. Brister, Kathi Canese, Donald C. Comeau, Kathryn Funk, Sunghwan Kim, William Klimke, Aron Marchler-Bauer, Melissa J. Landrum, Stacy Lathrop, Zhiyong Lu, Thomas L. Madden, Nuala A. O'Leary, Lon Phan, Sanjida H. Rangwala, Valerie A. Schneider, Yuri Skripchenko, Jiyao Wang, Jian Ye, Barton W. Trawick, Kim D. Pruitt, Stephen T. Sherry
2020 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
Eric W. Sayers, Jeffrey Beck, J. Rodney Brister, Evan Bolton, Kathi Canese, Donald C. Comeau, Kathryn Funk, Anne Ketter, Sunghwan Kim, Avi Kimchi, Paul A. Kitts, Anatoliy Kuznetsov, Stacy Lathrop, Zhiyong Lu, Kelly M. McGarvey, Thomas L. Madden, Terence D. Murphy, Nuala A. O'Leary, Lon Phan, Valerie A. Schneider, Françoise Thibaud-Nissen, Barton W. Trawick, Kim D. Pruitt, James Ostell
2019 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
Eric W. Sayers, Richa Agarwala, Evan Bolton, J. Rodney Brister, Kathi Canese, Karen Clark, Ryan Connor, Nicolas Fiorini, Kathryn Funk, Timothy Hefferon, J. Bradley Holmes, Sunghwan Kim, Avi Kimchi, Paul A. Kitts, Stacy Lathrop, Zhiyong Lu, Thomas L. Madden, Aron Marchler-Bauer, Lon Phan, Valerie A. Schneider, Conrad L. Schoch, Kim D. Pruitt, James Ostell
2019 J jnl
Magic-BLAST, an accurate RNA-seq aligner for long and short reads.
BMC Bioinform.
Grzegorz M. Boratyn, Jean Thierry-Mieg, Danielle Thierry-Mieg, Ben Busby, Thomas L. Madden
2019 J jnl
Reply to the paper: Misunderstood parameters of NCBI BLAST impacts the correctness of bioinformatics workflows.
Bioinform.
Thomas L. Madden, Ben Busby, Jian Ye
2013 J jnl
BLAST: a more efficient report with usability improvements.
Nucleic Acids Res.
Grzegorz M. Boratyn, Christiam Camacho, Peter S. Cooper, George Coulouris, Amelia Fong, Ning Ma, Thomas L. Madden, Wayne T. Matten, Scott D. McGinnis, Yuri Merezhuk, Yan Raytselis, Eric W. Sayers, Tao Tao, Jian Ye, Irena Zaretskaya
2013 J jnl
IgBLAST: an immunoglobulin variable domain sequence analysis tool.
Nucleic Acids Res.
Jian Ye, Ning Ma, Thomas L. Madden, James M. Ostell
2012 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Ian M. Fingerman, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, Sergey Krasnov, David Landsman, David J. Lipman, Zhiyong Lu, Thomas L. Madden, Tom Madej, Donna R. Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Karsch-Mizrachi, James Ostell, Anna R. Panchenko, Lon Phan, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Douglas J. Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Yanli Wang, W. John Wilbur, Eugene Yaschenko, Jian Ye
2012 J jnl
Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction.
BMC Bioinform.
Jian Ye, George Coulouris, Irena Zaretskaya, Ioana Cutcutache, Steve Rozen, Thomas L. Madden
2011 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Ian M. Fingerman, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J. Lipman, Zhiyong Lu, Thomas L. Madden, Tom Madej, Donna R. Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Mizrachi, James Ostell, Anna R. Panchenko, Lon Phan, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Douglas J. Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Yanli Wang, W. John Wilbur, Eugene Yaschenko, Jian Ye
2010 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J. Lipman, Zhiyong Lu, Thomas L. Madden, Tom Madej, Donna R. Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Mizrachi, James Ostell, Anna R. Panchenko, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Douglas J. Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Yanli Wang, W. John Wilbur, Eugene Yaschenko, Jian Ye
2009 J jnl
BLAST+: architecture and applications.
BMC Bioinform.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason S. Papadopoulos, Kevin Bealer, Thomas L. Madden
2009 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Michael Feolo, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J. Lipman, Thomas L. Madden, Donna R. Maglott, Vadim Miller, Ilene Karsch-Mizrachi, James Ostell, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko, Jian Ye
2008 J jnl
Database indexing for production MegaBLAST searches.
Bioinform.
Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, Alejandro A. Schäffer
2008 J jnl
Database indexing for production MegaBLAST searches.
Bioinform.
Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, Alejandro A. Schäffer
2008 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Michael Feolo, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, Oleg Khovayko, David Landsman, David J. Lipman, Thomas L. Madden, Donna R. Maglott, Vadim Miller, James Ostell, Kim D. Pruitt, Gregory D. Schuler, Martin Shumway, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko
2008 J jnl
NCBI BLAST: a better web interface.
Nucleic Acids Res.
Mark Johnson, Irena Zaretskaya, Yan Raytselis, Yuri Merezhuk, Scott D. McGinnis, Thomas L. Madden
2007 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Lewis Y. Geer, Yuri Kapustin, Oleg Khovayko, David Landsman, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Vadim Miller, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko
2006 J jnl
BLAST: improvements for better sequence analysis.
Nucleic Acids Res.
Jian Ye, Scott D. McGinnis, Thomas L. Madden
2006 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David L. Kenton, Oleg Khovayko, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Kim D. Pruitt, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Stephen T. Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Tugba O. Suzek, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko
2005 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Wolfgang Helmberg, David L. Kenton, Oleg Khovayko, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Joan U. Pontius, Kim D. Pruitt, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Grigory Starchenko, Tugba O. Suzek, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko
2004 J jnl
BLAST: at the core of a powerful and diverse set of sequence analysis tools.
Nucleic Acids Res.
Scott D. McGinnis, Thomas L. Madden
2004 J jnl
atabase resources of the National Center for Biotechnology Information: update.
Nucleic Acids Res.
David L. Wheeler, Deanna M. Church, Ron Edgar, Scott Federhen, Wolfgang Helmberg, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Tugba O. Suzek, Tatiana A. Tatusova, Lukas Wagner
2003 J jnl
Database resources of the National Center for Biotechnology.
Nucleic Acids Res.
David L. Wheeler, Deanna M. Church, Scott Federhen, Alex E. Lash, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Tatiana A. Tatusova, Lukas Wagner
2002 J jnl
Database resources of the National Center for Biotechnology Information: 2002 update.
Nucleic Acids Res.
David L. Wheeler, Deanna M. Church, Alex E. Lash, Detlef D. Leipe, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Tatiana A. Tatusova, Lukas Wagner, Barbara A. Rapp
2001 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
David L. Wheeler, Deanna M. Church, Alex E. Lash, Detlef D. Leipe, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Tatiana A. Tatusova, Lukas Wagner, Barbara A. Rapp
2000 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
David L. Wheeler, Colombe Chappey, Alex E. Lash, Detlef D. Leipe, Thomas L. Madden, Gregory D. Schuler, Tatiana A. Tatusova, Barbara A. Rapp