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Journal Articles
- 2019
[j25]Anna-Leigh Brown
, Minghui Li, Alexander Goncearenco, Anna R. Panchenko:
Finding driver mutations in cancer: Elucidating the role of background mutational processes. PLoS Comput. Biol. 15(4) (2019)- 2018
- [j24]Igor B. Rogozin, Youri I. Pavlov, Alexander Goncearenco, Subhajyoti De, Artem G. Lada, Eugenia Poliakov, Anna R. Panchenko, David N. Cooper:
Mutational signatures and mutable motifs in cancer genomes. Briefings Bioinform. 19(6): 1085-1101 (2018) - 2017
- [j23]Alexander Goncearenco, Stephanie L. Rager, Minghui Li, Qing-Xiang Sang, Igor B. Rogozin, Anna R. Panchenko:
Exploring background mutational processes to decipher cancer genetic heterogeneity. Nucleic Acids Res. 45(Webserver-Issue): W514-W522 (2017) - 2016
- [j22]Eli J. Draizen, Alexey K. Shaytan, Leonardo Mariño-Ramírez, Paul B. Talbert, David Landsman, Anna R. Panchenko:
HistoneDB 2.0: a histone database with variants - an integrated resource to explore histones and their variants. Database J. Biol. Databases Curation 2016 (2016) - [j21]Minghui Li, Franco L. Simonetti, Alexander Goncearenco, Anna R. Panchenko:
MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions. Nucleic Acids Res. 44(Webserver-Issue): W494-W501 (2016) - 2012
- [j20]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:
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 40(Database-Issue): 13-25 (2012) - [j19]Thomas Madej, Kenneth J. Addess, Jessica H. Fong, Lewis Y. Geer, Renata C. Geer, Christopher J. Lanczycki, Chunlei Liu, Shennan Lu, Aron Marchler-Bauer, Anna R. Panchenko, Jie Chen, Paul A. Thiessen, Yanli Wang, Dachuan Zhang, Stephen H. Bryant:
MMDB: 3D structures and macromolecular interactions. Nucleic Acids Res. 40(Database-Issue): 461-464 (2012) - [j18]Benjamin A. Shoemaker, Dachuan Zhang, Manoj Tyagi, Ratna R. Thangudu, Jessica H. Fong, Aron Marchler-Bauer, Stephen H. Bryant, Thomas Madej, Anna R. Panchenko:
IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. Nucleic Acids Res. 40(Database-Issue): 834-840 (2012) - [j17]Abhijit Chakraborty, Sapan Mandloi, Christopher J. Lanczycki, Anna R. Panchenko, Saikat Chakrabarti:
SPEER-SERVER: a web server for prediction of protein specificity determining sites. Nucleic Acids Res. 40(Web-Server-Issue): 242-248 (2012) - 2011
- [j16]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:
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 39(Database-Issue): 38-51 (2011) - 2010
- [j15]Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka, Paul A. Thiessen, Stephen H. Bryant:
State of the art: refinement of multiple sequence alignments. BMC Bioinform. 11: 3 (2010) - [j14]Ratna R. Thangudu, Manoj Tyagi, Benjamin A. Shoemaker, Stephen H. Bryant, Anna R. Panchenko, Thomas Madej:
Knowledge-based annotation of small molecule binding sites in proteins. BMC Bioinform. 11: 365 (2010) - [j13]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:
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 38(Database-Issue): 5-16 (2010) - [j12]Michail Yu. Lobanov, Benjamin A. Shoemaker, Sergiy O. Garbuzynskiy, Jessica H. Fong, Anna R. Panchenko, Oxana V. Galzitskaya:
ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder. Nucleic Acids Res. 38(Database-Issue): 283-287 (2010) - [j11]Benjamin A. Shoemaker, Dachuan Zhang, Ratna R. Thangudu, Manoj Tyagi, Jessica H. Fong, Aron Marchler-Bauer, Stephen H. Bryant, Tom Madej, Anna R. Panchenko:
Inferred Biomolecular Interaction Server - a web server to analyze and predict protein interacting partners and binding sites. Nucleic Acids Res. 38(Database-Issue): 518-524 (2010) - 2009
- [j10]Saikat Chakrabarti, Anna R. Panchenko:
Ensemble approach to predict specificity determinants: benchmarking and validation. BMC Bioinform. 10 (2009) - [j9]Jessica H. Fong, Benjamin A. Shoemaker, Sergiy O. Garbuzynskiy, Michail Yu. Lobanov, Oxana V. Galzitskaya, Anna R. Panchenko:
Intrinsic Disorder in Protein Interactions: Insights From a Comprehensive Structural Analysis. PLoS Comput. Biol. 5(3) (2009) - 2007
- [j8]Benjamin A. Shoemaker, Anna R. Panchenko:
Deciphering Protein-Protein Interactions. Part I. Experimental Techniques and Databases. PLoS Comput. Biol. 3(3) (2007) - [j7]Benjamin A. Shoemaker, Anna R. Panchenko:
Deciphering Protein-Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners. PLoS Comput. Biol. 3(4) (2007) - 2006
- [j6]Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka, Paul A. Thiessen, Stephen H. Bryant:
State of the art: refinement of multiple sequence alignments. BMC Bioinform. 7: 499 (2006) - 2005
- [j5]Maricel G. Kann, Paul A. Thiessen, Anna R. Panchenko, Alejandro A. Schäffer, Stephen F. Altschul, Stephen H. Bryant:
A structure-based method for protein sequence alignment. Bioinform. 21(8): 1451-1456 (2005) - 2003
- [j4]Aron Marchler-Bauer, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Anna R. Panchenko, Bachoti S. Rao, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, Stephen H. Bryant:
CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res. 31(1): 383-387 (2003) - [j3]Jie Chen, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Aron Marchler-Bauer, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Bachoti S. Rao, Anna R. Panchenko, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, Stephen H. Bryant:
MMDB: Entrez's 3D-structure database. Nucleic Acids Res. 31(1): 474-477 (2003) - 2002
- [j2]Yanli Wang, John B. Anderson, Jie Chen, Lewis Y. Geer, Siqian He, David I. Hurwitz, Cynthia A. Liebert, Thomas Madej, Gabriele H. Marchler, Aron Marchler-Bauer, Anna R. Panchenko, Benjamin A. Shoemaker, James S. Song, Paul A. Thiessen, Roxanne A. Yamashita, Stephen H. Bryant:
MMDB: Entrez's 3D-structure database. Nucleic Acids Res. 30(1): 249-252 (2002) - [j1]Aron Marchler-Bauer, Anna R. Panchenko, Benjamin A. Shoemaker, Paul A. Thiessen, Lewis Y. Geer, Stephen H. Bryant:
CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res. 30(1): 281-283 (2002)
Parts in Books or Collections
- 2008
- [p1]Benjamin A. Shoemaker, Anna R. Panchenko:
Handling Diverse Protein Interaction Data: Integration, Storage and Retrieval. Protein-protein Interactions and Networks 2008: 33-51
Editorship
- 2009
- [e2]Katia S. Guimarães, Anna R. Panchenko, Teresa M. Przytycka:
Advances in Bioinformatics and Computational Biology, 4th Brazilian Symposium on Bioinformatics, BSB 2009, Porto Alegre, Brazil, July 29-31, 2009. Proceedings. Lecture Notes in Computer Science 5676, Springer 2009, ISBN 978-3-642-03222-6 [contents] - 2008
- [e1]Anna R. Panchenko, Teresa M. Przytycka:
Protein-protein Interactions and Networks: Identification, Computer Analysis, and Prediction. Computational Biology 9, Springer 2008, ISBN 978-1-84800-124-4 [contents]
Coauthor Index
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