A systematic approach to identify novel cancer drug targets using machine learning, inhibitor design and high-throughput screening

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

Aiding and abetting cancer: mRNA export and the nuclear pore

(2013) Biljana Culjkovic-Kraljacic et al.   TRENDS IN CELL BIOLOGY

CancerDR: Cancer Drug Resistance Database

(2013) Rahul Kumar et al.   Scientific Reports

A randomised phase II trial of the Polo-like kinase inhibitor BI 2536 in chemo-naïve patients with unresectable exocrine adenocarcinoma of the pancreas – a study within the Central European Society Anticancer Drug Research (CESAR) collaborative network

(2012) K Mross et al.   BRITISH JOURNAL OF CANCER

A Landscape of Driver Mutations in Melanoma

(2012) Eran Hodis et al.   CELL

Molecular Pathways: Dysregulated Glutamatergic Signaling Pathways in Cancer

(2012) T. D. Prickett et al.   CLINICAL CANCER RESEARCH

Machine Learning Techniques and Drug Design

(2012) J.C. Gertrudes et al.   CURRENT MEDICINAL CHEMISTRY

Targeting the insulin-like growth factor 1 receptor (IGF1R) signaling pathway for cancer therapy

(2012) Cristina E Tognon et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

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

(2012) Jordi Barretina et al.   NATURE

Semaphorin 3A lytic hybrid peptide binding to neuropilin-1 as a novel anti-cancer agent in pancreatic cancer

(2011) Hanae Ueyama et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Correlation of Somatic Mutation and Expression Identifies Genes Important in Human Glioblastoma Progression and Survival

(2011) D. L. Masica et al.   CANCER RESEARCH

Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency

(2011) L. Wang et al.   GENOME RESEARCH

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(2011) Michalis Karamouzis et al.   MOLECULAR MEDICINE

Targeting ATR and Chk1 kinases for cancer treatment: A new model for new (and old) drugs

(2011) Luis I. Toledo et al.   Molecular Oncology

Predicting selective drug targets in cancer through metabolic networks

(2011) O. Folger et al.   Molecular Systems Biology

Beyond natural antibodies: the power of in vitro display technologies

(2011) Andrew R M Bradbury et al.   NATURE BIOTECHNOLOGY

Trends in the exploitation of novel drug targets

(2011) Mathias Rask-Andersen et al.   NATURE REVIEWS DRUG DISCOVERY

Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis

(2011) J. Lees et al.   NUCLEIC ACIDS RESEARCH

STITCH 3: zooming in on protein-chemical interactions

(2011) M. Kuhn et al.   NUCLEIC ACIDS RESEARCH

SMART 7: recent updates to the protein domain annotation resource

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

A New Methodology to Associate SNPs with Human Diseases According to Their Pathway Related Context

(2011) Burcu Bakir-Gungor et al.   PLoS One

Essential Gene Profiles in Breast, Pancreatic, and Ovarian Cancer Cells

(2011) Richard Marcotte et al.   Cancer Discovery

UniProt Knowledgebase: a hub of integrated protein data

(2011) M. Magrane et al.   Database-The Journal of Biological Databases and Curation

Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data

(2011) Xing-Ming Zhao et al.   PLoS Computational Biology

Identifying essential genes in bacterial metabolic networks with machine learning methods

(2010) Kitiporn Plaimas et al.   BMC Systems Biology

Integrative Genomic Profiling of Human Prostate Cancer

(2010) Barry S. Taylor et al.   CANCER CELL

Dasatinib Inhibits the Development of Metastases in a Mouse Model of Pancreatic Ductal Adenocarcinoma

(2010) Jennifer P. Morton et al.   GASTROENTEROLOGY

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

(2010) C. Knox et al.   NUCLEIC ACIDS RESEARCH

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

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

WD40 proteins propel cellular networks

(2010) Christian U. Stirnimann et al.   TRENDS IN BIOCHEMICAL SCIENCES

Combining tissue transcriptomics and urine metabolomics for breast cancer biomarker identification

(2009) Hojung Nam et al.   BIOINFORMATICS

Peptide Inhibitors Targeting Protein Kinases

(2009) Hagit Eldar-Finkelman et al.   CURRENT PHARMACEUTICAL DESIGN

Targeting cancer with phosphodiesterase inhibitors

(2009) Rajkumar Savai et al.   EXPERT OPINION ON INVESTIGATIONAL DRUGS

Cancer genome sequencing: a review

(2009) E. R. Mardis et al.   HUMAN MOLECULAR GENETICS

Identification of a novel antitumor peptide based on the screening of an Ala-library derived from the LALF32–51 region

(2009) Maribel G. Vallespi et al.   JOURNAL OF PEPTIDE SCIENCE

The Aurora kinase inhibitor SNS-314 shows broad therapeutic potential with chemotherapeutics and synergy with microtubule-targeted agents in a colon carcinoma model

(2009) E. C. VanderPorten et al.   MOLECULAR CANCER THERAPEUTICS

Tissue specificity and the human protein interaction network

(2009) Alice Bossi et al.   Molecular Systems Biology

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

PepX: a structural database of non-redundant protein–peptide complexes

(2009) Peter Vanhee et al.   NUCLEIC ACIDS RESEARCH

The role of COX-2 in intestinal inflammation and colorectal cancer

(2009) D Wang et al.   ONCOGENE

Human Disease-Drug Network Based on Genomic Expression Profiles

(2009) Guanghui Hu et al.   PLoS One

SVMs Modeling for Highly Imbalanced Classification

(2008) Yuchun Tang et al.   IEEE TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART B-CYBERNETICS

An integrated approach to inferring gene-disease associations in humans

(2008) Predrag Radivojac et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

(2008) S. Jones et al.   SCIENCE

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE

Targeting FLT3 for the Treatment of Leukemia

(2008) Donald Small   SEMINARS IN HEMATOLOGY

Effects of α-adrenoreceptor antagonists on apoptosis and proliferation of pancreatic cancer cells in vitro

(2008) Su-Gang Shen et al.   WORLD JOURNAL OF GASTROENTEROLOGY

PTTG: an important target gene for ovarian cancer therapy

(2008) Siva Panguluri et al.   Journal of Ovarian Research