Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach

Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy

(2015) Feixiong Cheng et al.   Oncotarget

A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations

(2014) Gregory A Ryslik et al.   BMC BIOINFORMATICS

A spatial simulation approach to account for protein structure when identifying non-random somatic mutations

(2014) Gregory A Ryslik et al.   BMC BIOINFORMATICS

Patterns and processes of somatic mutations in nine major cancers

(2014) Peilin Jia et al.   BMC Medical Genomics

Studying Tumorigenesis through Network Evolution and Somatic Mutational Perturbations in the Cancer Interactome

(2014) Feixiong Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Structure-energy-based predictions and network modelling of RASopathy and cancer missense mutations

(2014) C. Kiel et al.   Molecular Systems Biology

Deriving a Mutation Index of Carcinogenicity Using Protein Structure and Protein Interfaces

(2014) Octavio Espinosa et al.   PLoS One

VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data

(2014) Peilin Jia et al.   PLoS Computational Biology

mCSM: predicting the effects of mutations in proteins using graph-based signatures

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

Utilizing protein structure to identify non-random somatic mutations

(2013) Gregory A Ryslik et al.   BMC BIOINFORMATICS

Oncogenic ERBB3 Mutations in Human Cancers

(2013) Bijay S. Jaiswal et al.   CANCER CELL

Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome

(2013) Teresa Davoli et al.   CELL

Personalized Cancer Medicine: Molecular Diagnostics, Predictive biomarkers, and Drug Resistance

(2013) D Gonzalez de Castro et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Loss of DOK2 induces carboplatin resistance in ovarian cancer via suppression of apoptosis

(2013) Elena Lum et al.   GYNECOLOGIC ONCOLOGY

Network-Based Interpretation of Genomic Variation Data

(2013) Bjarni V. Halldórsson et al.   JOURNAL OF MOLECULAR BIOLOGY

The Effects of Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs) on Protein–Protein Interactions

(2013) Christopher M. Yates et al.   JOURNAL OF MOLECULAR BIOLOGY

Targeting the Vav3 oncogene enhances docetaxel-induced apoptosis through the inhibition of androgen receptor phosphorylation in LNCaP prostate cancer cells under chronic hypoxia

(2013) Takeo Nomura et al.   Molecular Cancer

Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers

(2013) J. Reimand et al.   Molecular Systems Biology

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Interaction-based discovery of functionally important genes in cancers

(2013) Dario Ghersi et al.   NUCLEIC ACIDS RESEARCH

Mice Lacking NCF1 Exhibit Reduced Growth of Implanted Melanoma and Carcinoma Tumors

(2013) Tiina Kelkka et al.   PLoS One

Interplay of physics and evolution in the likely origin of protein biochemical function

(2013) Jeffrey Skolnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Pocket-Based Drug Design: Exploring Pocket Space

(2012) Xiliang Zheng et al.   AAPS Journal

Vav3-Rac1 Signaling Regulates Prostate Cancer Metastasis with Elevated Vav3 Expression Correlating with Prostate Cancer Progression and Posttreatment Recurrence

(2012) K.-T. Lin et al.   CANCER RESEARCH

Systematic identification of genomic markers of drug sensitivity in cancer cells

(2012) Mathew J. Garnett et al.   NATURE

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

(2012) Xiujuan Wang et al.   NATURE BIOTECHNOLOGY

Interactome3D: adding structural details to protein networks

(2012) Roberto Mosca et al.   NATURE METHODS

PSC: protein surface classification

(2012) Y. Y. Tseng et al.   NUCLEIC ACIDS RESEARCH

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

Classification of protein functional surfaces using structural characteristics

(2012) Y. Y. Tseng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia

(2012) Peilin Jia et al.   PLoS Computational Biology

The Protein Data Bank in Europe (PDBe): bringing structure to biology

(2011) Sameer Velankar et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

(2011) Wing Chung Wong et al.   BIOINFORMATICS

Multi-institutional phase 2 study of the farnesyltransferase inhibitor tipifarnib (R115777) in patients with relapsed and refractory lymphomas

(2011) T. E. Witzig et al.   BLOOD

Improving the prediction of disease-related variants using protein three-dimensional structure

(2011) Emidio Capriotti et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Elevated C-reactive protein in the diagnosis, prognosis, and cause of cancer

(2011) Kristine H. Allin et al.   CRITICAL REVIEWS IN CLINICAL LABORATORY SCIENCES

The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors

(2011) Henning Stehr et al.   Molecular Cancer

Cancer genomics: from discovery science to personalized medicine

(2011) Lynda Chin et al.   NATURE MEDICINE

PINA v2.0: mining interactome modules

(2011) Mark J. Cowley et al.   NUCLEIC ACIDS RESEARCH

Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor

(2010) Y. Benita et al.   BLOOD

Phase IIB Trial of Oral Midostaurin (PKC412), the FMS-Like Tyrosine Kinase 3 Receptor (FLT3) and Multi-Targeted Kinase Inhibitor, in Patients With Acute Myeloid Leukemia and High-Risk Myelodysplastic Syndrome With Either Wild-Type or Mutated FLT3

(2010) Thomas Fischer et al.   JOURNAL OF CLINICAL ONCOLOGY

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Edgetic perturbation models of human inherited disorders

(2009) Quan Zhong et al.   Molecular Systems Biology

Structure of the DNA deaminase domain of the HIV-1 restriction factor APOBEC3G

(2008) Kuan-Ming Chen et al.   NATURE

Hypermutation by intersegmental transfer of APOBEC3G cytidine deaminase

(2008) Roni Nowarski et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY