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  • Our Institute is retiring the following domains in web and email:
    ljcf.edu
    burnham-inst.org
    sanford-burnham.org
    sbmri.org
    burnham.org
    sanfordburnham.org


    Please replace them by sbpdiscovery.org
PubMed   Google Scholar   Faculty of 1000   2017   2016   2015   2014   2013   2012   2011   2010   2009   ALL

Selected Publications

  • Porta-Pardo E, Kamburov A, Tamborero D, Pons T, Grases D, Valencia A, Lopez-Bigas N, Getz G, Godzik A. Comparison of algorithms for the detection of cancer drivers at subgene resolution. Nat Methods. 2017 Aug;14(8):782-788. PubMed
  • Derewenda ZS, Godzik A. The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability. Methods Mol Biol. 2017;1607:77-115. PubMed
  • Porta-Pardo E, Godzik A., Mutation drivers of immunological responses to cancer. Cancer Immunol Res. 2016 Jul 11. PubMed
  • Thomas Hrabe, Lukasz Jaroszewski and Adam Godzik, Revealing aperiodic aspects of solenoid proteins from sequence information. Bioinformatics. 2016 Jun 9. PubMed
  • Thomas Hrabe, Zhanwen Li, Mayya Sedova, Piotr Rotkiewicz, Lukasz Jaroszewski and Adam Godzik, PDBFlex: exploring flexibility in protein structures. Nucl. Acids Res. (2015) doi: 10.1093/nar/gkv1316
  • Jahandideh S, Sharifi F, Jaroszewski L, Godzik A. PROPER: Performance visualization for optimizing and comparing ranking classifiers in MATLAB. Source Code Biol Med. 2015 Dec 3;10:15. doi: 10.1186/s13029-015-0047-1. PubMed
  • Sedova M, Jaroszewski L, Godzik A. Protael: protein data visualization library for the web. Bioinformatics. 2015 Oct 29. pii: btv605. [Epub ahead of print] PubMed
  • Porta-Pardo E, Garcia-Alonso L, Hrabe T, Dopazo J, Godzik A. A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces. PLoS Comput Biol. 2015 Oct 20;11(10):e1004518. doi: 10.1371/journal.pcbi.1004518. PubMed
  • Xu D, Jaroszewski L, Li Z, Godzik A. AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction. Bioinformatics. 2015 Feb 19. pii: btv092. [Epub ahead of print] PubMed
  • Porta-Pardo E, Godzik A. Analysis of Individual Protein Regions Provides Novel Insights on Cancer Pharmacogenomics. PLoS Comput Biol. 2015 Jan 8;11(1):e1004024. doi:10.1371/journal.pcbi.1004024. PubMed
  • Porta-Pardo E, Hrabe T and Godzik A. Cancer3D: understanding cancer mutations through protein structures. Nucl. Acids Res. (2014) doi: 10.1093/nar/gku1140. Download
  • Hwang WC, Golden JW, Pascual J, Xu D, Cheltsov A, Godzik A. Site-specific recombination of nitrogen-fixation genes in cyanobacteria by XisF-XisH-XisI complex: Structures and models. Proteins. 2014 Sep 1. doi: 10.1002/prot.24679. PubMed
  • Zmasek CM, Godzik A. Phylogenomic analysis of glycogen branching and debranching enzymatic duo. BMC Evol Biol. 2014 Aug 23;14(1):183. PubMed
  • Hwang WC, Xu Q, Wu B, Godzik A. Crystal structure of a Baeyer-Villiger flavin-containing monooxygenase from Staphylococcus aureus MRSA strain MU50. Proteins. 2014 Aug 5. doi: 10.1002/prot.2466 PubMed
  • Porta-Pardo E, Godzik A. e-Driver: a novel method to identify protein regions driving cancer. Bioinformatics. 2014 Jul 26. pii: btu499. PubMed
  • Jaroszewski L, Koska L, Sedova M, Godzik A. PubServer: literature searches by homology. Nucleic Acids Res. 2014 Jun 23. doi:pii: gku450. PubMed
  • Rigden DJ, Eberhardt RY, Gilbert HJ, Xu Q, Chang Y, Godzik A. Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase. BMC Bioinformatics. 2014 Jun 17;15:196. doi: 10.1186/1471-2105-15-196. PubMed
  • Li Z, Natarajan P, Ye Y, Hrabe T, Godzik A. POSA: a user-driven, interactive multiple protein structure alignment server. Nucleic Acids Res. 2014 May 16. doi:pii: gku394. PubMed
  • Xu D, Jaroszewski L, Li Z, Godzik A. AIDA: ab initio domain assembly server. Nucleic Acids Res. 2014 May 15. doi:pii: gku369. PubMed
  • Hrabe T, Godzik A. ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures. BMC Bioinformatics. 2014 Apr 27;15(1):119. doi: 10.1186/1471-2105-15-119. PubMed
  • Sheydina A, Eberhardt RY, Rigden DJ, Chang Y, Li Z, Zmasek CC, Axelrod HL, Godzik A. Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase. BMC Bioinformatics. 2014 Apr 17;15(1):112. doi: 10.1186/1471-2105-15-112. PubMed
  • Jahandideh S, Jaroszewski L, Godzik A. Improving the chances of successful protein structure determination with a random forest classifier. Acta Crystallogr D Biol Crystallogr. 2014 Mar;70(Pt 3):627-35. doi: 10.1107/S1399004713032070. Epub 2014 Feb 15. PubMed
  • Hwang WC, Bakolitsa C, Punta M, Coggill PC, Bateman A, Axelrod HL, Rawlings ND, Sedova M, Peterson SN, Eberhardt RY, Aravind L, Pascual J, Godzik A. LUD, a new protein domain associated with lactate utilization. BMC Bioinformatics. 2013 Nov 26;14:341. doi: 10.1186/1471-2105-14-341. PubMed
  • Eroshkin AM, Leblanc A, Weekes D, Post K, Li Z, Rajput A, Butera ST, Burton DR, Godzik A. bNAber: database of broadly neutralizing HIV antibodies. Nucleic Acids Res. 2013 Nov 7. PubMed
  • Bhabha G, Ekiert DC, Jennewein M, Zmasek CM, Tuttle LM, Kroon G, Dyson HJ, Godzik A, Wilson IA, Wright PE. Divergent evolution of protein conformational dynamics in dihydrofolate reductase. Nat Struct Mol Biol. 2013 Nov;20(11):1243-9. doi: 10.1038/nsmb.2676. Epub 2013 Sep 29. PubMed
  • Xu D, Jaroszewski L, Li Z, Godzik A. FFAS-3D: Improving Fold Recognition by Including Optimized Structural Features and Template Re-ranking. Bioinformatics (2013) doi: 10.1093/bioinformatics/btt578 First published online: October 15, 2013. PubMed
  • Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson BO. Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. Science. 2013 Jun 7;340(6137):1220-3. doi: 10.1126/science.1234012. PubMed
  • Zmasek CM, Godzik A. Evolution of the animal apoptosis network. Cold Spring Harb Perspect Biol. 2013 Mar 1;5(3):a008649. doi: 10.1101/cshperspect.a008649. PubMed
  • Zmasek CM, Godzik A. This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes. PLoS Comput Biol. 2012;8(11):e1002701. doi: 10.1371/journal.pcbi.1002701. Epub 2012 Nov 15. PubMed
  • Zhang Y, Zagnitko O, Rodionova I, Osterman A, Godzik A. The FGGY carbohydrate kinase family: insights into the evolution of functional specificities. PLoS Comput Biol. 2011 Dec;7(12):e1002318. Epub 2011 Dec 22. PubMed
  • Jaroszewski L, Li Z, Cai XH, Weber C, Godzik A. FFAS server: novel features and applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W38-44. PubMed
  • Godzik A. Metagenomics and the protein universe. Curr Opin Struct Biol. 2011 Jun;21(3):398-403. Epub 2011 Apr 14. Review. PubMed
  • Zmasek CM, Godzik A. Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires. Genome Biol. 2011;12(1):R4. Epub 2011 Jan 17. PubMed
  • Ellrott K, Zmasek CM, Weekes D, Sri Krishna S, Bakolitsa C, Godzik A, Wooley J. TOPSAN: a dynamic web database for structural genomics. Nucleic Acids Res. 2011 Jan;39(Database issue):D494-6. Epub 2010 Oct 20. PubMed
  • Ellrott K, Jaroszewski L, Li W, Wooley JC, Godzik A. Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families. PLoS Comput Biol. 2010 Jun 3;6(6):e1000798. PubMed
  • Zhang Q, Zmasek CM, Godzik A. Domain architecture evolution of pattern-recognition receptors. Immunogenetics. 2010 May;62(5):263-72. Epub 2010 Mar 2. PubMed
  • Wooley JC, Godzik A, Friedberg I. A primer on metagenomics. PLoS Comput Biol. 2010 Feb 26;6(2):e1000667. Review. PubMed
  • Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A, Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science, 2009 Sep 18;325(5947):1544-9. PubMed
  • Lukasz Jaroszewski, Zhanwen Li, S. Sri Krishna, Constantina Bakolitsa, John Wooley, Ashley M. Deacon, Ian A. Wilson, Adam Godzik, Exploration of Uncharted Regions of the Protein Universe. Plos Biology. 2009 Sep. 7(9):e1000205
  • Jaroszewski L, Slabinski L, Wooley J, Deacon AM, Lesley SA, Wilson IA, Godzik A. Genome pool strategy for structural coverage of protein families. Structure. 2008 Nov 12;16(11):1659-67. PubMed
  • Zhang Q, Zmasek CM, Dishaw LJ, Mueller MG, Ye Y, Litman GW, Godzik A. Novel genes dramatically alter regulatory network topology in amphioxus. Genome Biol. 2008 Aug 4;9(8):R123.    PubMed
  • Zmasek CM, Zhang Q, Ye Y, Godzik A. Surprising complexity of the ancestral apoptosis network. Genome Biol. 2007 Oct 24;8(10):R226    PubMed
  • Slabinski L, Jaroszewski L, Rychlewski L, Wilson IA, Lesley SA, Godzik A. XtalPred: a web server for prediction of protein crystallizability. Bioinformatics. 2007 Dec 15;23(24):3403-5. Epub 2007 Oct 5.   PubMed
  • Zhang Y, Stec B, Godzik A. Between order and disorder in protein structures: analysis of "dual personality" fragments in proteins. Structure. 2007 Sep;15(9):1141-7.   PubMed
  • Friedberg I, Godzik A. Functional differentiation of proteins: implications for structural genomics. Structure. 2007 Apr;15(4):405-15.   PubMed
  • Friedberg I, Harder T, Kolodny R, Sitbon E, Li Z, Godzik A. Using an alignment of fragment strings for comparing protein structures. Bioinformatics. 2007 Jan 15;23(2):e219-24.    PubMed
  • Li W, Godzik A, Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Bioinformatics. 2006 Jul 1;22(13):1658-9. Epub 2006 May 26    PubMed
  • Ye Y, Godzik A, Multiple flexible structure alignment using partial order graphs. Bioinformatics. 2005 May 15;21(10):2362-9. Epub 2005 Mar 3. PubMed,
  • Ye Y, Godzik A, Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics. 2003 Oct;19 Suppl 2:ii246-55. PubMed,

Faculty of 1000

Publications By Years

2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 and before