Towards Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine

APoc: large-scale identification of similar protein pockets

(2013) Mu Gao et al.   BIOINFORMATICS

Drug–target interaction prediction through domain-tuned network-based inference

(2013) Salvatore Alaimo et al.   BIOINFORMATICS

Antibacterial mechanisms identified through structural systems pharmacology

(2013) Roger L Chang et al.   BMC Systems Biology

Structural Systems Pharmacology: The Role of 3D Structures in Next-Generation Drug Development

(2013) Miquel Duran-Frigola et al.   CHEMISTRY & BIOLOGY

Trendspotting in the Protein Data Bank

(2013) Helen M. Berman et al.   FEBS LETTERS

The why and how of phenotypic small-molecule screens

(2013) Ulrike S Eggert   Nature Chemical Biology

Target identification and mechanism of action in chemical biology and drug discovery

(2013) Monica Schenone et al.   Nature Chemical Biology

Signalling bias in new drug discovery: detection, quantification and therapeutic impact

(2013) Terry Kenakin et al.   NATURE REVIEWS DRUG DISCOVERY

The role of tumour–stromal interactions in modifying drug response: challenges and opportunities

(2013) Douglas W. McMillin et al.   NATURE REVIEWS DRUG DISCOVERY

Cytochrome P450 enzymes in drug metabolism: Regulation of gene expression, enzyme activities, and impact of genetic variation

(2013) Ulrich M. Zanger et al.   PHARMACOLOGY & THERAPEUTICS

Predicting Drug-Target Interactions for New Drug Compounds Using a Weighted Nearest Neighbor Profile

(2013) Twan van Laarhoven et al.   PLoS One

Integrative Structural Biology

(2013) A. B. Ward et al.   SCIENCE

Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

(2013) R. L. Chang et al.   SCIENCE

A vitamin B12 transporter in Mycobacterium tuberculosis

(2013) K. Gopinath et al.   Open Biology

Prediction of the P. falciparum Target Space Relevant to Malaria Drug Discovery

(2013) Andreas Spitzmüller et al.   PLoS Computational Biology

Combinatorial Clustering of Residue Position Subsets Predicts Inhibitor Affinity across the Human Kinome

(2013) Drew H. Bryant et al.   PLoS Computational Biology

Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis

(2013) Francisco Martínez-Jiménez et al.   PLoS Computational Biology

Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling

(2013) Shao-shan Carol Huang et al.   PLoS Computational Biology

Systematic Prediction of Pharmacodynamic Drug-Drug Interactions through Protein-Protein-Interaction Network

(2013) Jialiang Huang et al.   PLoS Computational Biology

Panitumumab combined with irinotecan for patients with KRAS wild-type metastatic colorectal cancer refractory to standard chemotherapy: a GERCOR efficacy, tolerance, and translational molecular study

(2012) T. André et al.   ANNALS OF ONCOLOGY

Systems pharmacology of complex diseases

(2012) Jens Hansen et al.   Annals of the New York Academy of Sciences

G-protein-coupled receptor dynamics: dimerization and activation models compared with experiment

(2012) Bruck Taddese et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

ReLiance: a machine learning and literature-based prioritization of receptor—ligand pairings

(2012) Ernesto Iacucci et al.   BIOINFORMATICS

Drug target prediction using adverse event report systems: a pharmacogenomic approach

(2012) M. Takarabe et al.   BIOINFORMATICS

Drug–target interaction prediction by learning from local information and neighbors

(2012) Jian-Ping Mei et al.   BIOINFORMATICS

Multiscale modeling of macromolecular biosystems

(2012) S. C. Flores et al.   BRIEFINGS IN BIOINFORMATICS

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Constructing structural networks of signaling pathways on the proteome scale

(2012) Guray Kuzu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

INDI: a computational framework for inferring drug interactions and their associated recommendations

(2012) Assaf Gottlieb et al.   Molecular Systems Biology

Systematic identification of genomic markers of drug sensitivity in cancer cells

(2012) Mathew J. Garnett et al.   NATURE

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

Crystal structure of the multidrug transporter P-glycoprotein from Caenorhabditis elegans

(2012) Mi Sun Jin et al.   NATURE

Structure of AMP-PNP-bound vitamin B12 transporter BtuCD–F

(2012) Vladimir M. Korkhov et al.   NATURE

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

(2012) Jordi Barretina et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2012) Ravid Straussman et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

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

(2012) Xiujuan Wang et al.   NATURE BIOTECHNOLOGY

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Systems-pharmacology dissection of a drug synergy in imatinib-resistant CML

(2012) Georg E Winter et al.   Nature Chemical Biology

Evidence for dynamics in proteins as a mechanism for ligand dissociation

(2012) Mary J Carroll et al.   Nature Chemical Biology

Developing predictive molecular maps of human disease through community-based modeling

(2012) Jonathan M J Derry et al.   NATURE GENETICS

Treatment-induced damage to the tumor microenvironment promotes prostate cancer therapy resistance through WNT16B

(2012) Yu Sun et al.   NATURE MEDICINE

Interactome3D: adding structural details to protein networks

(2012) Roberto Mosca et al.   NATURE METHODS

The GPCR Network: a large-scale collaboration to determine human GPCR structure and function

(2012) Raymond C. Stevens et al.   NATURE REVIEWS DRUG DISCOVERY

PrePPI: a structure-informed database of protein–protein interactions

(2012) Qiangfeng Cliff Zhang et al.   NUCLEIC ACIDS RESEARCH

Biased Signaling Pathways in  2-Adrenergic Receptor Characterized by 19F-NMR

(2012) J. J. Liu et al.   SCIENCE

Network Context and Selection in the Evolution to Enzyme Specificity

(2012) H. Nam et al.   SCIENCE

Pseudogenes: Newly Discovered Players in Human Cancer

(2012) L. Poliseno   Science Signaling

Data-Driven Prediction of Drug Effects and Interactions

(2012) N. P. Tatonetti et al.   Science Translational Medicine

A Structural Systems Biology Approach for Quantifying the Systemic Consequences of Missense Mutations in Proteins

(2012) Tammy M. K. Cheng et al.   PLoS Computational Biology

Kinetic Rate Constant Prediction Supports the Conformational Selection Mechanism of Protein Binding

(2012) Iain H. Moal et al.   PLoS Computational Biology

Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference

(2012) Feixiong Cheng et al.   PLoS Computational Biology

Integrating Cellular Metabolism into a Multiscale Whole-Body Model

(2012) Markus Krauss et al.   PLoS Computational Biology

Prediction of a Ligand-Binding Niche within a Human Olfactory Receptor by Combining Site-Directed Mutagenesis with Dynamic Homology Modeling

(2011) Lian Gelis et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Novel Computational Approaches to Polypharmacology as a Means to Define Responses to Individual Drugs

(2011) Lei Xie et al.   Annual Review of Pharmacology and Toxicology

Systems Pharmacology: Network Analysis to Identify Multiscale Mechanisms of Drug Action

(2011) Shan Zhao et al.   Annual Review of Pharmacology and Toxicology

Hierarchical graphs for rule-based modeling of biochemical systems

(2011) Nathan W Lemons et al.   BMC BIOINFORMATICS

Three-dimensional modeling of protein interactions and complexes is going ‘omics

(2011) Amelie Stein et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure-based systems biology for analyzing off-target binding

(2011) Lei Xie et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Toward in silico structure-based ADMET prediction in drug discovery

(2011) Gautier Moroy et al.   DRUG DISCOVERY TODAY

Conformational adaptation in drug–target interactions and residence time

(2011) Robert A Copeland   Future Medicinal Chemistry

Prioritizing candidate disease genes by network-based boosting of genome-wide association data

(2011) I. Lee et al.   GENOME RESEARCH

Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs

(2011) Alessia David et al.   HUMAN MUTATION

Multi-scale modelling and simulation in systems biology

(2011) Joseph O. Dada et al.   Integrative Biology

A Multiscale Simulation System for the Prediction of Drug-Induced Cardiotoxicity

(2011) Cristian Obiol-Pardo et al.   Journal of Chemical Information and Modeling

Characterization of the Ligand Receptor Encounter Complex and Its Potential for in Silico Kinetics-Based Drug Development

(2011) Karim M. ElSawy et al.   Journal of Chemical Theory and Computation

Structural and Functional Impact of Cancer-Related Missense Somatic Mutations

(2011) Zhen Shi et al.   JOURNAL OF MOLECULAR BIOLOGY

Human Proteome-scale Structural Modeling of E2–E3 Interactions Exploiting Interface Motifs

(2011) Gozde Kar et al.   JOURNAL OF PROTEOME RESEARCH

Associating Drugs, Targets and Clinical Outcomes into an Integrated Network Affords a New Platform for Computer-Aided Drug Repurposing

(2011) Tudor I. Oprea et al.   Molecular Informatics

PREDICT: a method for inferring novel drug indications with application to personalized medicine

(2011) A. Gottlieb et al.   Molecular Systems Biology

Transforming binding affinities from three dimensions to two with application to cadherin clustering

(2011) Yinghao Wu et al.   NATURE

An active role for machine learning in drug development

(2011) Robert F Murphy   Nature Chemical Biology

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM

(2011) Nurcan Tuncbag et al.   Nature Protocols

Probing the links between in vitro potency, ADMET and physicochemical parameters

(2011) M. Paul Gleeson et al.   NATURE REVIEWS DRUG DISCOVERY

The modENCODE guide to the genome

(2011) Mary Muers   NATURE REVIEWS GENETICS

ProtChemSI: a network of protein-chemical structural interactions

(2011) O. V. Kalinina et al.   NUCLEIC ACIDS RESEARCH

Pocketome: an encyclopedia of small-molecule binding sites in 4D

(2011) Irina Kufareva et al.   NUCLEIC ACIDS RESEARCH

DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical–protein interactome

(2011) Heng Luo et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: a large-scale bioactivity database for drug discovery

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

Using Functional Annotation for the Empirical Determination of Bayes Factors for Genome-Wide Association Study Analysis

(2011) Jo Knight et al.   PLoS One

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET

(2011) A. Schlessinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural principles within the human-virus protein-protein interaction network

(2011) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CASP9 results compared to those of previous casp experiments

(2011) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison

(2011) Lee Sael et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Integrating Multiple Types of Data for Signaling Research: Challenges and Opportunities

(2011) H. S. Wiley   Science Signaling

Allo-network drugs: harnessing allostery in cellular networks

(2011) Ruth Nussinov et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir

(2011) Li Xie et al.   PLoS Computational Biology

Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding

(2011) Tianyun Liu et al.   PLoS Computational Biology

BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server

(2010) Bing Xiong et al.   BMC BIOINFORMATICS

Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data

(2010) Bin Chen et al.   BMC BIOINFORMATICS

Long-lasting target binding and rebinding as mechanisms to prolong in vivo drug action

(2010) Georges Vauquelin et al.   BRITISH JOURNAL OF PHARMACOLOGY

Identification of Optimal Drug Combinations Targeting Cellular Networks: Integrating Phospho-Proteomics and Computational Network Analysis

(2010) S. Iadevaia et al.   CANCER RESEARCH

Dissecting Variability in Responses to Cancer Chemotherapy Through Systems Pharmacology

(2010) R Yang et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Drug–target residence time: critical information for lead optimization

(2010) Hao Lu et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

PubChem as a public resource for drug discovery

(2010) Qingliang Li et al.   DRUG DISCOVERY TODAY

Progress and Promise of Genome-Wide Association Studies for Human Complex Trait Genetics

(2010) B. E. Stranger et al.   GENETICS

Association of KRAS p.G13D Mutation With Outcome in Patients With Chemotherapy-Refractory Metastatic Colorectal Cancer Treated With Cetuximab

(2010) Wendy De Roock et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Predicting Polypharmacology by Binding Site Similarity: From Kinases to the Protein Universe

(2010) Francesca Milletti et al.   Journal of Chemical Information and Modeling

When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values

(2010) Pierre Baldi et al.   Journal of Chemical Information and Modeling

Development of a stochastic model for the efficacy of NRTIs using known mechanisms of action

(2010) Samira Khalili et al.   JOURNAL OF THEORETICAL BIOLOGY

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

(2010) Aarash Bordbar et al.   Molecular Systems Biology

Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism

(2010) Livnat Jerby et al.   Molecular Systems Biology

Thousands of chemical starting points for antimalarial lead identification

(2010) Francisco-Javier Gamo et al.   NATURE

Chemical genetics of Plasmodium falciparum

(2010) W. Armand Guiguemde et al.   NATURE

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

The challenges of integrating multi-omic data sets

(2010) Bernhard Palsson et al.   Nature Chemical Biology

Coupling of receptor conformation and ligand orientation determine graded activity

(2010) John B Bruning et al.   Nature Chemical Biology

SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison

(2010) J. Ren et al.   NUCLEIC ACIDS RESEARCH

Pharmacometabonomics as an effector for personalized medicine

(2010) Jeremy K Nicholson et al.   PHARMACOGENOMICS

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

(2010) J. B. Kinney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Blueprint for antimicrobial hit discovery targeting metabolic networks

(2010) Y. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting kinetic constants of protein-protein interactions based on structural properties

(2010) Hongjun Bai et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Systems Pharmacology of Arrhythmias

(2010) S. I. Berger et al.   Science Signaling

The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications

(2010) Sarah L. Kinnings et al.   PLoS Computational Biology

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model

(2010) Roger L. Chang et al.   PLoS Computational Biology

Correlated Mutations: A Hallmark of Phenotypic Amino Acid Substitutions

(2010) Andreas Kowarsch et al.   PLoS Computational Biology

Drug-Induced Regulation of Target Expression

(2010) Murat Iskar et al.   PLoS Computational Biology

Slow-Onset Inhibition of the FabI Enoyl Reductase fromFrancisella tularensis: Residence Time andin VivoActivity

(2009) Hao Lu et al.   ACS Chemical Biology

Efavirenz Binding to HIV-1 Reverse Transcriptase Monomers and Dimers

(2009) Valerie A. Braz et al.   BIOCHEMISTRY

A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery

(2009) L. Xie et al.   BIOINFORMATICS

Network analyses in systems pharmacology

(2009) S. I. Berger et al.   BIOINFORMATICS

Structure-based Drug Metabolism Predictions for Drug Design

(2009) Hao Sun et al.   Chemical Biology & Drug Design

Systematic Evaluation of Drug–Disease Relationships to Identify Leads for Novel Drug Uses

(2009) A P Chiang et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Nuance in the double-helix and its role in protein–DNA recognition

(2009) Remo Rohs et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws - a promising method for speeding up the kinetic modelling of complex metabolic networks

(2009) Sascha Bulik et al.   FEBS Journal

Multiscale modeling of biomedical, biological, and behavioral systems (part 2) [Introduction to special issue

(2009) R.J. White et al.   IEEE ENGINEERING IN MEDICINE AND BIOLOGY MAGAZINE

Multiscale modeling of biomedical, biological, and behavioral systems (Part 1) [Introduction to the special issue

(2009) R.J. White et al.   IEEE ENGINEERING IN MEDICINE AND BIOLOGY MAGAZINE

Influence Relevance Voting: An Accurate And Interpretable Virtual High Throughput Screening Method

(2009) S. Joshua Swamidass et al.   Journal of Chemical Information and Modeling

Systems biology, the Physiome Project and oriental medicine

(2009) Denis Noble   Journal of Physiological Sciences

Substrate Binding Mechanism of HIV-1 Protease from Explicit-Solvent Atomistic Simulations

(2009) Fabio Pietrucci et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Fast predictions of thermodynamics and kinetics of protein–protein recognition from structures: from molecular design to systems biology

(2009) Daniele Dell’Orco   Molecular BioSystems

Alignment-Free Prediction of a Drug−Target Complex Network Based on Parameters of Drug Connectivity and Protein Sequence of Receptors

(2009) Dolores Viña et al.   MOLECULAR PHARMACEUTICS

Conformational Toggle Switches Implicated in Basal Constitutive and Agonist-Induced Activated States of 5-Hydroxytryptamine-4 Receptors

(2009) L. P. Pellissier et al.   MOLECULAR PHARMACOLOGY

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Estimation of the Warfarin Dose with Clinical and Pharmacogenetic Data

(2009)   NEW ENGLAND JOURNAL OF MEDICINE

f POP: footprinting functional pockets of proteins by comparative spatial patterns

(2009) Yan Yuan Tseng et al.   NUCLEIC ACIDS RESEARCH

An overview of the PubChem BioAssay resource

(2009) Yanli Wang et al.   NUCLEIC ACIDS RESEARCH

SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions

(2009) Saskia Preissner et al.   NUCLEIC ACIDS RESEARCH

PubChem: a public information system for analyzing bioactivities of small molecules

(2009) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Absorption of montelukast is transporter mediated: a common variant of OATP2B1 is associated with reduced plasma concentrations and poor response

(2009) Edward B. Mougey et al.   Pharmacogenetics and Genomics

A multiscale model linking ion-channel molecular dynamics and electrostatics to the cardiac action potential

(2009) J. R. Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Drugs, bugs, and personalized medicine: Pharmacometabonomics enters the ring

(2009) I. D. Wilson   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism

(2009) T. A. Clayton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima

(2009) Y. Zhang et al.   SCIENCE

Integrating Proteomic, Transcriptional, and Interactome Data Reveals Hidden Components of Signaling and Regulatory Networks

(2009) S.-s. C. Huang et al.   Science Signaling

PSI-2: Structural Genomics to Cover Protein Domain Family Space

(2009) Benoît H. Dessailly et al.   STRUCTURE

Large scale study of multiple-molecule queries

(2009) Ramzi J Nasr et al.   Journal of Cheminformatics

Systems pharmacology and genome medicine: a future perspective

(2009) Aislyn D Wist et al.   Genome Medicine

Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening

(2009) Nobuyoshi Nagamine et al.   PLoS Computational Biology

Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors

(2009) Li Xie et al.   PLoS Computational Biology

Analyzing Protein Interaction Networks Using Structural Information

(2008) Christina Kiel et al.   Annual Review of Biochemistry

Prediction of drug-target interaction networks from the integration of chemical and genomic spaces

(2008) Y. Yamanishi et al.   BIOINFORMATICS

Bioinformatics, multiscale modeling and the IUPS Physiome Project

(2008) P. J. Hunter et al.   BRIEFINGS IN BIOINFORMATICS

Rewiring the Specificity of Two-Component Signal Transduction Systems

(2008) Jeffrey M. Skerker et al.   CELL

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Wild-TypeKRASIs Required for Panitumumab Efficacy in Patients With Metastatic Colorectal Cancer

(2008) Rafael G. Amado et al.   JOURNAL OF CLINICAL ONCOLOGY

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

(2008) Rommie E. Amaro et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Finding multiple target optimal intervention in disease-related molecular network

(2008) Kun Yang et al.   Molecular Systems Biology

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments

(2008) L. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS

Surface Sites for Engineering Allosteric Control in Proteins

(2008) J. Lee et al.   SCIENCE

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology