Finding driver mutations in cancer: Elucidating the role of background mutational processes. - Brown, Anna-Leigh; Li, Minghui; Goncearenco, Alexander; Panchenko, Anna R. (PLoS Comput. Biol., 2019)

Mutational signatures and mutable motifs in cancer genomes. - Rogozin, Igor B.; Pavlov, Youri I.; Goncearenco, Alexander; De, Subhajyoti; Lada, Artem G.; Poliakov, Eugenia; Panchenko, Anna R.; Cooper, David N. (Briefings Bioinform., 2018)

Exploring background mutational processes to decipher cancer genetic heterogeneity. - Goncearenco, Alexander; Rager, Stephanie L.; Li, Minghui; Sang, Qing-Xiang; Rogozin, Igor B.; Panchenko, Anna R. (Nucleic Acids Res., 2017)

HistoneDB 2.0: a histone database with variants - an integrated resource to explore histones and their variants. - Draizen, Eli J.; Shaytan, Alexey K.; Mariño-Ramírez, Leonardo; Talbert, Paul B.; Landsman, David; Panchenko, Anna R. (Database J. Biol. Databases Curation, 2016)

MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions. - Li, Minghui; Simonetti, Franco L.; Goncearenco, Alexander; Panchenko, Anna R. (Nucleic Acids Res., 2016)

Database resources of the National Center for Biotechnology Information. - 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.; et al. (Nucleic Acids Res., 2012)

MMDB: 3D structures and macromolecular interactions. - Madej, Thomas; Addess, Kenneth J.; Fong, Jessica H.; Geer, Lewis Y.; Geer, Renata C.; Lanczycki, Christopher J.; Liu, Chunlei; Lu, Shennan; Marchler-Bauer, Aron; Panchenko, Anna R.; Chen, Jie; Thiessen, Paul A.; et al. (Nucleic Acids Res., 2012)

IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. - Shoemaker, Benjamin A.; Zhang, Dachuan; Tyagi, Manoj; Thangudu, Ratna R.; Fong, Jessica H.; Marchler-Bauer, Aron; Bryant, Stephen H.; Madej, Thomas; Panchenko, Anna R. (Nucleic Acids Res., 2012)

SPEER-SERVER: a web server for prediction of protein specificity determining sites. - Chakraborty, Abhijit; Mandloi, Sapan; Lanczycki, Christopher J.; Panchenko, Anna R.; Chakrabarti, Saikat (Nucleic Acids Res., 2012)

Database resources of the National Center for Biotechnology Information. - 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.; et al. (Nucleic Acids Res., 2011)

State of the art: refinement of multiple sequence alignments. - Chakrabarti, Saikat; Lanczycki, Christopher J.; Panchenko, Anna R.; Przytycka, Teresa M.; Thiessen, Paul A.; Bryant, Stephen H. (BMC Bioinform., 2010)

Knowledge-based annotation of small molecule binding sites in proteins. - Thangudu, Ratna R.; Tyagi, Manoj; Shoemaker, Benjamin A.; Bryant, Stephen H.; Panchenko, Anna R.; Madej, Thomas (BMC Bioinform., 2010)

Database resources of the National Center for Biotechnology Information. - 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; Geer, Lewis Y.; et al. (Nucleic Acids Res., 2010)

ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder. - Lobanov, Michail Yu.; Shoemaker, Benjamin A.; Garbuzynskiy, Sergiy O.; Fong, Jessica H.; Panchenko, Anna R.; Galzitskaya, Oxana V. (Nucleic Acids Res., 2010)

Inferred Biomolecular Interaction Server - a web server to analyze and predict protein interacting partners and binding sites. - Shoemaker, Benjamin A.; Zhang, Dachuan; Thangudu, Ratna R.; Tyagi, Manoj; Fong, Jessica H.; Marchler-Bauer, Aron; Bryant, Stephen H.; Madej, Tom; Panchenko, Anna R. (Nucleic Acids Res., 2010)

Ensemble approach to predict specificity determinants: benchmarking and validation. - Chakrabarti, Saikat; Panchenko, Anna R. (BMC Bioinform., 2009)

Intrinsic Disorder in Protein Interactions: Insights From a Comprehensive Structural Analysis. - Fong, Jessica H.; Shoemaker, Benjamin A.; Garbuzynskiy, Sergiy O.; Lobanov, Michail Yu.; Galzitskaya, Oxana V.; Panchenko, Anna R. (PLoS Comput. Biol., 2009)

Advances in Bioinformatics and Computational Biology, 4th Brazilian Symposium on Bioinformatics, BSB 2009, Porto Alegre, Brazil, July 29-31, 2009. Proceedings (Springer, 2009)

Handling Diverse Protein Interaction Data: Integration, Storage and Retrieval. - Shoemaker, Benjamin A.; Panchenko, Anna R. (2008)

Protein-protein Interactions and Networks: Identification, Computer Analysis, and Prediction (Springer, 2008)

Deciphering Protein-Protein Interactions. Part I. Experimental Techniques and Databases. - Shoemaker, Benjamin A.; Panchenko, Anna R. (PLoS Comput. Biol., 2007)

Deciphering Protein-Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners. - Shoemaker, Benjamin A.; Panchenko, Anna R. (PLoS Comput. Biol., 2007)

State of the art: refinement of multiple sequence alignments. - Chakrabarti, Saikat; Lanczycki, Christopher J.; Panchenko, Anna R.; Przytycka, Teresa M.; Thiessen, Paul A.; Bryant, Stephen H. (BMC Bioinform., 2006)

A structure-based method for protein sequence alignment. - Kann, Maricel G.; Thiessen, Paul A.; Panchenko, Anna R.; Schäffer, Alejandro A.; Altschul, Stephen F.; Bryant, Stephen H. (Bioinform., 2005)

CDD: a curated Entrez database of conserved domain alignments. - Marchler-Bauer, Aron; Anderson, John B.; DeWeese-Scott, Carol; Fedorova, Natalie D.; Geer, Lewis Y.; He, Siqian; Hurwitz, David I.; Jackson, John D.; Jacobs, Aviva R.; Lanczycki, Christopher J.; Liebert, Cynthia A.; Liu, Chunlei; et al. (Nucleic Acids Res., 2003)

MMDB: Entrez's 3D-structure database. - Chen, Jie; Anderson, John B.; DeWeese-Scott, Carol; Fedorova, Natalie D.; Geer, Lewis Y.; He, Siqian; Hurwitz, David I.; Jackson, John D.; Jacobs, Aviva R.; Lanczycki, Christopher J.; Liebert, Cynthia A.; Liu, Chunlei; et al. (Nucleic Acids Res., 2003)

MMDB: Entrez's 3D-structure database. - Wang, Yanli; Anderson, John B.; Chen, Jie; Geer, Lewis Y.; He, Siqian; Hurwitz, David I.; Liebert, Cynthia A.; Madej, Thomas; Marchler, Gabriele H.; Marchler-Bauer, Aron; Panchenko, Anna R.; Shoemaker, Benjamin A.; et al. (Nucleic Acids Res., 2002)

CDD: a database of conserved domain alignments with links to domain three-dimensional structure. - Marchler-Bauer, Aron; Panchenko, Anna R.; Shoemaker, Benjamin A.; Thiessen, Paul A.; Geer, Lewis Y.; Bryant, Stephen H. (Nucleic Acids Res., 2002)