Adam Godzik, Ph.D.

Adam Godzik's Research Focus

Cancer, Inflammatory/Autoimmune Disease

Our research is focused on biological systems and their evolution. We try to combine insights from mathematics and physics to answer basic questions about biological systems and to use them to develop new computational tools that could allow us to find new regularities and trends in biological data. In particular we are trying to understand how the topology, structure, and function of proteins and protein networks has evolved and how it reacts to perturbation, such as disease mutations or other genomics perturbations. 

By combining structural information about proteins with data on cellular networks formed by these proteins in an approach we call structural systems biology we can explicitly model the networks in their perturbed state and try to predict their behavior. We study systems from bacterial metabolic and virulence networks, to human immunity, apoptosis and cancer networks.

Adam Godzik's Research Report

Cancer3D Website

Cancer3D is a database that unites information on somatic missense mutations from TCGA and CCLE, allowing users to explore two different cancer-related problems at the same time: drug sensitivity/biomarker identification and prediction of cancer drivers. The database is an interface to two novel algorithms, e-Driver and e-Drug, that make use of information about the internal structure of a protein to predict novel cancer drivers or drug biomarkers respectively. Moreover, it maps somatic missense mutations from over 18,000 human proteins to more than 25,000 protein structures from PDB.

Cancer 3d website image

Adam Godzik's Bio

Dr. Adam Godzik earned his Ph.D. in physics from the Department of Physics, University of Warsaw, Poland in 1990. After postdoctoral work in the European Molecular Biology Laboratory in Heidelberg and The Scripps Research Institute in San Diego, he became an Assistant Professor at The Scripps Research Institute. In 1999 he joined Sanford-Burnham Medical Research Institute as an Associate Professor.



This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes.

Zmasek CM, Godzik A

PLoS Comput Biol 2012 ;8(11):e1002701

PDBFlex: exploring flexibility in protein structures.

Hrabe T, Li Z, Sedova M, Rotkiewicz P, Jaroszewski L, Godzik A

Nucleic Acids Res 2016 Jan 4 ;44(D1):D423-8

Comparison of algorithms for the detection of cancer drivers at subgene resolution.

Porta-Pardo E, Kamburov A, Tamborero D, Pons T, Grases D, Valencia A, Lopez-Bigas N, Getz G, Godzik A

Nat Methods 2017 Aug ;14(8):782-788

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The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins.

Jaroszewski L, Iyer M, Alisoltani A, Sedova M, Godzik A

PLoS Comput Biol 2021 Jul ;17(7):e1009147

ModFlex: Towards Function Focused Protein Modeling.

Sedova M, Jaroszewski L, Iyer M, Li Z, Godzik A

J Mol Biol 2021 May 28 ;433(11):166828

FATCAT 2.0: towards a better understanding of the structural diversity of proteins.

Li Z, Jaroszewski L, Iyer M, Sedova M, Godzik A

Nucleic Acids Res 2020 Jul 2 ;48(W1):W60-W64

Difference contact maps: From what to why in the analysis of the conformational flexibility of proteins.

Iyer M, Li Z, Jaroszewski L, Sedova M, Godzik A

PLoS One 2020 ;15(3):e0226702

Structures of single-layer β-sheet proteins evolved from β-hairpin repeats.

Xu Q, Biancalana M, Grant JC, Chiu HJ, Jaroszewski L, Knuth MW, Lesley SA, Godzik A, Elsliger MA, Deacon AM, Wilson IA

Protein Sci 2019 Sep ;28(9):1676-1689

Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets.

Sedova M, Iyer M, Li Z, Jaroszewski L, Post KW, Hrabe T, Porta-Pardo E, Godzik A

Nucleic Acids Res 2019 Jan 8 ;47(D1):D895-D899

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