Adam Godzik

Natalie Castellana, Andrey Lushnikov, Piotr Rotkiewicz, Natasha Sefcovic, Pavel A. Pevzner, Adam Godzik, Kira Vyatkina: MORPH-PRO: A Novel Algorithm and Web Server for Protein Morphing. WABI 2012: 262-273

Kyle Ellrott, Christian M. Zmasek, Dana Weekes, S. Sri Krishna, Constantina Bakolitsa, Adam Godzik, John C. Wooley: TOPSAN: a dynamic web database for structural genomics. Nucleic Acids Research 39(Database-Issue): 494-496 (2011)

Lukasz Jaroszewski, Zhanwen Li, Xiao-hui Cai, Christoph Weber, Adam Godzik: FFAS server: novel features and applications. Nucleic Acids Research 39(Web-Server-Issue): 38-44 (2011)

Ying Zhang, Olga Zagnitko, Irina Rodionova, Andrei Osterman, Adam Godzik: The FGGY Carbohydrate Kinase Family: Insights into the Evolution of Functional Specificities. PLoS Computational Biology 7(12) (2011)

Andreas Prlic, Spencer Bliven, Peter W. Rose, Wolfgang Bluhm, Chris Bizon, Adam Godzik, Philip E. Bourne: Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics 26(23): 2983-2985 (2010)

Dana Weekes, S. Sri Krishna, Constantina Bakolitsa, Ian A. Wilson, Adam Godzik, John C. Wooley: TOPSAN: a collaborative annotation environment for structural genomics. BMC Bioinformatics 11: 426 (2010)

John C. Wooley, Adam Godzik, Iddo Friedberg: A Primer on Metagenomics. PLoS Computational Biology 6(2) (2010)

Kyle Ellrott, Lukasz Jaroszewski, Weizhong Li, John C. Wooley, Adam Godzik: Expansion of the Protein Repertoire in Newly Explored Environments: Human Gut Microbiome Specific Protein Families. PLoS Computational Biology 6(6) (2010)

Yoshinobu Igarashi, Emily Heureux, Kutbuddin S. Doctor, Priti Talwar, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Michael L. Blinov, Salmaz S. Ibragimova, Sarah Boyd, Boris Ratnikov, Piotr Cieplak, Adam Godzik, Jeffrey W. Smith, Andrei Osterman, Alexey M. Eroshkin: PMAP: databases for analyzing proteolytic events and pathways. Nucleic Acids Research 37(Database-Issue): 611-618 (2009)

Mallika Veeramalai, Yuzhen Ye, Adam Godzik: TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model. BMC Bioinformatics 9 (2008)

Iddo Friedberg, Tim Harder, Rachel Kolodny, Einat Sitbon, Zhanwen Li, Adam Godzik: Using an alignment of fragment strings for comparing protein structures. Bioinformatics 23(2): 219-224 (2007)

Lukasz Slabinski, Lukasz Jaroszewski, Leszek Rychlewski, Ian A. Wilson, Scott A. Lesley, Adam Godzik: XtalPred: a web server for prediction of protein crystallizability. Bioinformatics 23(24): 3403-3405 (2007)

Ana P. C. Rodrigues, Barry J. Grant, Adam Godzik, Iddo Friedberg: The 2006 Automated Function Prediction Meeting. BMC Bioinformatics 8(S-4) (2007)

Yoshinobu Igarashi, Alexey M. Eroshkin, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Jeffrey W. Smith, Andrei Osterman, Adam Godzik: CutDB: a proteolytic event database. Nucleic Acids Research 35(Database-Issue): 546-549 (2007)

Lukasz Slabinski, Adam Godzik, Leszek Rychlewski: TOM - Task and Object Management for Grid Clusters. GCA 2007: 199-205

Weizhong Li, Adam Godzik: VISSA: a program to visualize structural features from structure sequence alignment. Bioinformatics 22(7): 887-888 (2006)

Weizhong Li, Adam Godzik: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22(13): 1658-1659 (2006)

Degui Zhi, S. Sri Krishna, Haibo Cao, Pavel A. Pevzner, Adam Godzik: Representing and comparing protein structures as paths in three-dimensional space. BMC Bioinformatics 7: 460 (2006)

Zhanwen Li, Yuzhen Ye, Adam Godzik: Flexible Structural Neighborhood - a database of protein structural similarities and alignments. Nucleic Acids Research 34(Database-Issue): 277-280 (2006)

Iddo Friedberg, Tim Harder, Adam Godzik: JAFA: a protein function annotation meta-server. Nucleic Acids Research 34(Web-Server-Issue): 379-381 (2006)

Yuzhen Ye, Zhanwen Li, Adam Godzik: Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins. Pacific Symposium on Biocomputing 2006: 439-450

Yuzhen Ye, Adam Godzik: Multiple flexible structure alignment using partial order graphs. Bioinformatics 21(10): 2362-2369 (2005)

Iddo Friedberg, Adam Godzik: Fragnostic: walking through protein structure space. Nucleic Acids Research 33(Web-Server-Issue): 249-251 (2005)

Lukasz Jaroszewski, Leszek Rychlewski, Zhanwen Li, Weizhong Li, Adam Godzik: FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Research 33(Web-Server-Issue): 284-288 (2005)

Yuzhen Ye, Andrei Osterman, Ross A. Overbeek, Adam Godzik: Automatic detection of subsystem/pathway variants in genome analysis. ISMB (Supplement of Bioinformatics) 2005: 478-486

Dariusz Plewczynski, Leszek Rychlewski, Yuzhen Ye, Lukasz Jaroszewski, Adam Godzik: Integrated web service for improving alignment quality based on segments comparison. BMC Bioinformatics 5: 98 (2004)

Yuzhen Ye, Adam Godzik: FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Research 32(Web-Server-Issue): 582-585 (2004)

Philip E. Bourne, C. K. J. Allerston, Werner G. Krebs, Wilfred W. Li, Ilya N. Shindyalov, Adam Godzik, Iddo Friedberg, Tong Liu, David L. Wild, Seungwoo Hwang, Zoubin Ghahramani, Li Chen, John D. Westbrook: The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures. Pacific Symposium on Biocomputing 2004: 375-386

Yuzhen Ye, Lukasz Jaroszewski, Weizhong Li, Adam Godzik: A segment alignment approach to protein comparison. Bioinformatics 19(6): 742-749 (2003)

Marcin Grynberg, Lukasz Jaroszewski, Adam Godzik: Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization. BMC Bioinformatics 4: 46 (2003)

Yuzhen Ye, Adam Godzik: Flexible structure alignment by chaining aligned fragment pairs allowing twists. ECCB 2003: 246-255

Weizhong Li, Lukasz Jaroszewski, Adam Godzik: Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 18(1): 77-82 (2002)

Baohong Zhang, Adam Godzik: The Meaning and Limitations of Protein Structure Alignments. 3DPVT 2002: 729-736

Weizhong Li, Lukasz Jaroszewski, Adam Godzik: Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 17(3): 282-283 (2001)

Weizhong Li, Frederic Pio, Krzysztof Pawlowski, Adam Godzik: Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. Bioinformatics 16(12): 1105-1110 (2000)

Krzysztof Pawlowski, Leszek Rychlewski, John C. Reed, Adam Godzik: From Fold to Function Predictions: An Apoptosis Regulator Protein BID. Computers & Chemistry 24(3-4): 511-517 (2000)

Lukasz Jaroszewski, Adam Godzik: Search for a New Description of Protein Topology and Local Structure. ISMB 2000: 211-217

Adam Godzik, Jeffrey Skolnick: Flexible algorithm for direct multiple alignment of protein structures and sequences. Computer Applications in the Biosciences 10(6): 587-596 (1994)

Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick: De novo and inverse folding predictions of protein structure and dynamics. Journal of Computer-Aided Molecular Design 7(4): 397-438 (1993)