Computational algorithms for in silico profiling of activating mutations in cancer

Worldwide Frequency of Commonly Detected EGFR Mutations

(2018) Rondell P. Graham et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

SMOTE for Learning from Imbalanced Data: Progress and Challenges, Marking the 15-year Anniversary

(2018) Alberto Fernandez et al.   JOURNAL OF ARTIFICIAL INTELLIGENCE RESEARCH

Cell signaling heterogeneity is modulated by both cell-intrinsic and -extrinsic mechanisms: An integrated approach to understanding targeted therapy

(2018) Eunjung Kim et al.   PLOS BIOLOGY

A method of high-throughput functional evaluation of EGFR gene variants of unknown significance in cancer

(2017) Shinji Kohsaka et al.   Science Translational Medicine

Dual Characteristics of Novel HER2 Kinase Domain Mutations in Response to HER2-Targeted Therapies in Human Breast Cancer

(2016) W.-J. Zuo et al.   CLINICAL CANCER RESEARCH

A Functional Landscape of Resistance to ALK Inhibition in Lung Cancer

(2015) Frederick H. Wilson et al.   CANCER CELL

HER2 Activating Mutations Are Targets for Colorectal Cancer Treatment

(2015) S. M. Kavuri et al.   Cancer Discovery

ALK Mutations Confer Differential Oncogenic Activation and Sensitivity to ALK Inhibition Therapy in Neuroblastoma

(2014) Scott C. Bresler et al.   CANCER CELL

Multiscale computational models in physical systems biology of intracellular trafficking

(2014) Richard W. Tourdot et al.   IET Systems Biology

How does conformational flexibility influence key structural features involved in activation of anaplastic lymphoma kinase?

(2014) Tatyana G. Karabencheva et al.   Molecular BioSystems

Molecular modeling of ErbB4/HER4 kinase in the context of the HER4 signaling network helps rationalize the effects of clinically identified HER4 somatic mutations on the cell phenotype

(2013) Shannon E. Telesco et al.   Biotechnology Journal

Novel Modeling of Cancer Cell Signaling Pathways Enables Systematic Drug Repositioning for Distinct Breast Cancer Metastases

(2013) H. Zhao et al.   CANCER RESEARCH

Network-based drug repositioning

(2013) Zikai Wu et al.   Molecular BioSystems

The causes and consequences of genetic heterogeneity in cancer evolution

(2013) Rebecca A. Burrell et al.   NATURE

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

Personalized medicine in oncology: where have we come from and where are we going?

(2013) Fabrice André et al.   PHARMACOGENOMICS

The Role of Balanced Training and Testing Data Sets for Binary Classifiers in Bioinformatics

(2013) Qiong Wei et al.   PLoS One

Explaining why Gleevec is a specific and potent inhibitor of Abl kinase

(2013) Y.-L. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase

(2013) L. Sutto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic Reprogramming in Cancer

(2013) M. L. Suva et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

The mutational landscape of phosphorylation signaling in cancer

(2013) Jüri Reimand et al.   Scientific Reports

The Technologically Integrated Oncosimulator: Combining Multiscale Cancer Modeling With Information Technology in the In Silico Oncology Context

(2013) Georgios Stamatakos et al.   IEEE Journal of Biomedical and Health Informatics

Structural Systems Biology and Multiscale Signaling Models

(2012) Shannon E. Telesco et al.   ANNALS OF BIOMEDICAL ENGINEERING

Erlotinib binds both inactive and active conformations of the EGFR tyrosine kinase domain

(2012) Jin H. Park et al.   BIOCHEMICAL JOURNAL

Prioritization of pathogenic mutations in the protein kinase superfamily

(2012) Jose MG Izarzugaza et al.   BMC GENOMICS

Domain landscapes of somatic mutations in cancer

(2012) Nathan L Nehrt et al.   BMC GENOMICS

Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization

(2012) Yibing Shan et al.   CELL

A Landscape of Driver Mutations in Melanoma

(2012) Eran Hodis et al.   CELL

Coarse-graining of multiprotein assemblies

(2012) Marissa G Saunders et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

MuSiC: Identifying mutational significance in cancer genomes

(2012) N. D. Dees et al.   GENOME RESEARCH

Molecular diagnostics and personalized medicine in oncology: Challenges and opportunities

(2012) Nicola Normanno et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

The landscape of cancer genes and mutational processes in breast cancer

(2012) Philip J. Stephens et al.   NATURE

Tumour micro-environment elicits innate resistance to RAF inhibitors through HGF secretion

(2012) Ravid Straussman et al.   NATURE

Widespread potential for growth-factor-driven resistance to anticancer kinase inhibitors

(2012) Timothy R. Wilson et al.   NATURE

Crystal structures of the JAK2 pseudokinase domain and the pathogenic mutant V617F

(2012) Rajintha M Bandaranayake et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Activating HER2 Mutations in HER2 Gene Amplification Negative Breast Cancer

(2012) Ron Bose et al.   Cancer Discovery

Circumventing Cancer Drug Resistance in the Era of Personalized Medicine

(2012) Levi A. Garraway et al.   Cancer Discovery

Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics

(2012) Alfonso Valencia et al.   Genome Medicine

Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score, Condel

(2011) Abel González-Pérez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Multiscale Cancer Modeling

(2011) Thomas S. Deisboeck et al.   Annual Review of Biomedical Engineering

Molecular dynamics analysis of conserved hydrophobic and hydrophilic bond-interaction networks in ErbB family kinases

(2011) Andrew J. Shih et al.   BIOCHEMICAL JOURNAL

Old friends in new guise: repositioning of known drugs with structural bioinformatics

(2011) V. J. Haupt et al.   BRIEFINGS IN BIOINFORMATICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Role of BRAF in Thyroid Oncogenesis

(2011) L. M. Caronia et al.   CLINICAL CANCER RESEARCH

Model-based global sensitivity analysis as applied to identification of anti-cancer drug targets and biomarkers of drug resistance in the ErbB2/3 network

(2011) Galina Lebedeva et al.   EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES

A new disease-specific machine learning approach for the prediction of cancer-causing missense variants

(2011) Emidio Capriotti et al.   GENOMICS

Systems biology and physical biology of clathrin-mediated endocytosis

(2011) Vyas Ramanan et al.   Integrative Biology

Predictive mathematical models of cancer signalling pathways

(2011) J. Bachmann et al.   JOURNAL OF INTERNAL MEDICINE

A multiscale modeling approach to investigate molecular mechanisms of pseudokinase activation and drug resistance in the HER3/ErbB3 receptor tyrosine kinase signaling network

(2011) Shannon E. Telesco et al.   Molecular BioSystems

Why don't we get more cancer? A proposed role of the microenvironment in restraining cancer progression

(2011) Mina J Bissell et al.   NATURE MEDICINE

Personalized medicine in oncology: next generation

(2011) Alex Chiang et al.   NATURE REVIEWS DRUG DISCOVERY

The pseudokinase domain of JAK2 is a dual-specificity protein kinase that negatively regulates cytokine signaling

(2011) Daniela Ungureanu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

Changes in Gene Expression and Cellular Architecture in an Ovarian Cancer Progression Model

(2011) Amy L. Creekmore et al.   PLoS One

Analysis of Somatic Mutations in Cancer: Molecular Mechanisms of Activation in the ErbB Family of Receptor Tyrosine Kinases

(2011) Andrew J. Shih et al.   Cancers

Cell Signaling by Receptor Tyrosine Kinases

(2010) Mark A. Lemmon et al.   CELL

Anti-cancer drug resistance: Understanding the mechanisms through the use of integrative genomics and functional RNA interference

(2010) Daniel S.-W. Tan et al.   EUROPEAN JOURNAL OF CANCER

The origins of cancer robustness and evolvability

(2010) Tianhai Tian et al.   Integrative Biology

Future of Personalized Medicine in Oncology: A Systems Biology Approach

(2010) Ana Maria Gonzalez-Angulo et al.   JOURNAL OF CLINICAL ONCOLOGY

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Automated inference of molecular mechanisms of disease from amino acid substitutions

(2009) B. Li et al.   BIOINFORMATICS

Atomistic Insights into Regulatory Mechanisms of the HER2 Tyrosine Kinase Domain: A Molecular Dynamics Study

(2009) Shannon E. Telesco et al.   BIOPHYSICAL JOURNAL

Computational Modeling of Structurally Conserved Cancer Mutations in the RET and MET Kinases: The Impact on Protein Structure, Dynamics, and Stability

(2009) Anshuman Dixit et al.   BIOPHYSICAL JOURNAL

Cancer systems biology: a network modeling perspective

(2009) P. K. Kreeger et al.   CARCINOGENESIS

The D816V Mutation of c-Kit Circumvents a Requirement for Src Family Kinases in c-Kit Signal Transduction

(2009) Jianmin Sun et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

KIT kinase mutants show unique mechanisms of drug resistance to imatinib and sunitinib in gastrointestinal stromal tumor patients

(2009) K. S. Gajiwala et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of Network Branching in Eliciting Differential Short-Term Signaling Responses in the Hypersensitive Epidermal Growth Factor Receptor Mutants Implicated in Lung Cancer

(2008) J. Purvis et al.   BIOTECHNOLOGY PROGRESS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations

(2008) Anna Berteotti et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular systems biology of ErbB1 signaling: bridging the gap through multiscale modeling and high-performance computing

(2008) Andrew J. Shih et al.   Molecular BioSystems

Molecular Basis of Inactive B-RAFWTand B-RAFV600ELigand Inhibition, Selectivity and Conformational Stability: Anin SilicoStudy

(2008) Filip Fratev et al.   MOLECULAR PHARMACEUTICS

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology

Activation of tyrosine kinases by mutation of the gatekeeper threonine

(2008) Mohammad Azam et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP

(2008) C.-H. Yun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational dynamics of the EGFR kinase domain reveals structural features involved in activation

(2008) Athanasios Papakyriakou et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases

(2008) Nilesh K. Banavali et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms

(2008) Sichun Yang et al.   PLoS Computational Biology