A Decade of Systems Biology

Mechanism of Radiosensitization by the Chk1/2 Inhibitor AZD7762 Involves Abrogation of the G2Checkpoint and Inhibition of Homologous Recombinational DNA Repair

(2010) Meredith A. Morgan et al.   CANCER RESEARCH

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

NAViGaTOR: Network Analysis, Visualization and Graphing Toronto

(2009) Kevin R. Brown et al.   BIOINFORMATICS

Synthetic Lethal Interaction between Oncogenic KRAS Dependency and STK33 Suppression in Human Cancer Cells

(2009) Claudia Scholl et al.   CELL

A Genome-wide RNAi Screen Identifies Multiple Synthetic Lethal Interactions with the Ras Oncogene

(2009) Ji Luo et al.   CELL

A Genome-Scale RNAi Screen for Oct4 Modulators Defines a Role of the Paf1 Complex for Embryonic Stem Cell Identity

(2009) Li Ding et al.   Cell Stem Cell

Synthetic lethal targeting ofPTENmutant cells with PARP inhibitors

(2009) Ana M. Mendes-Pereira et al.   EMBO Molecular Medicine

Gene and pathway-based second-wave analysis of genome-wide association studies

(2009) Gang Peng et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal

(2009) G. Hu et al.   GENES & DEVELOPMENT

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells

(2009) Kai Wang et al.   NATURE BIOTECHNOLOGY

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

(2009) I. Amit et al.   SCIENCE

Genome-Wide Association Data Reveal a Global Map of Genetic Interactions among Protein Complexes

(2009) Gregory Hannum et al.   PLoS Genetics

Systematic Mapping of Genetic Interaction Networks

(2008) Scott J. Dixon et al.   Annual Review of Genetics

Gene Expression Profiling of Breast Cancer

(2008) Maggie C.U. Cheang et al.   Annual Review of Pathology-Mechanisms of Disease

Local coherence in genetic interaction patterns reveals prevalent functional versatility

(2008) Shuye Pu et al.   BIOINFORMATICS

VisANT: an integrative framework for networks in systems biology

(2008) Z. Hu et al.   BRIEFINGS IN BIOINFORMATICS

Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells

(2008) Alexander Marson et al.   CELL

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells

(2008) Jonghwan Kim et al.   CELL

Yamanaka factors critically regulate the developmental signaling network in mouse embryonic stem cells

(2008) Xiaosong Liu et al.   CELL RESEARCH

Unraveling Epigenetic Regulation in Embryonic Stem Cells

(2008) Marina Bibikova et al.   Cell Stem Cell

Promoter CpG Methylation Contributes to ES Cell Gene Regulation in Parallel with Oct4/Nanog, PcG Complex, and Histone H3 K4/K27 Trimethylation

(2008) Shaun D. Fouse et al.   Cell Stem Cell

Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells

(2008) M. F. Cole et al.   GENES & DEVELOPMENT

Pathway analysis of seven common diseases assessed by genome-wide association

(2008) Ali Torkamani et al.   GENOMICS

Discovery and Scoring of Protein Interaction Subnetworks Discriminative of Late Stage Human Colon Cancer

(2008) Rod K. Nibbe et al.   MOLECULAR & CELLULAR PROTEOMICS

A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas

(2008) Kartik M Mani et al.   Molecular Systems Biology

From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions

(2008) Igor Ulitsky et al.   Molecular Systems Biology

Personal genomes: The case of the missing heritability

(2008) Brendan Maher   NATURE

Regulatory networks define phenotypic classes of human stem cell lines

(2008) Franz-Josef Müller et al.   NATURE

Progress and challenges in genome-wide association studies in humans

(2008) Peter Donnelly   NATURE

A core Klf circuitry regulates self-renewal of embryonic stem cells

(2008) Jianming Jiang et al.   NATURE CELL BIOLOGY

Stat3 and c-Myc Genome-Wide Promoter Occupancy in Embryonic Stem Cells

(2008) Benjamin L. Kidder et al.   PLoS One

CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks

(2008) A. Funahashi et al.   PROCEEDINGS OF THE IEEE

Kinase requirements in human cells: III. Altered kinase requirements in VHL-/- cancer cells detected in a pilot synthetic lethal screen

(2008) A. Bommi-Reddy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Defining genetic interaction

(2008) R. Mani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes

(2008) S. J. Dixon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phosphorylation Networks Regulating JNK Activity in Diverse Genetic Backgrounds

(2008) C. Bakal et al.   SCIENCE

From Genotype to Phenotype: Systems Biology Meets Natural Variation

(2008) P. N. Benfey et al.   SCIENCE

The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes

(2008) M. E. Hillenmeyer et al.   SCIENCE

Conservation and Rewiring of Functional Modules Revealed by an Epistasis Map in Fission Yeast

(2008) A. Roguev et al.   SCIENCE

REST Regulates Distinct Transcriptional Networks in Embryonic and Neural Stem Cells

(2008) Rory Johnson et al.   PLOS BIOLOGY

Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data

(2008) Sourav Bandyopadhyay et al.   PLoS Computational Biology

Inferring Pathway Activity toward Precise Disease Classification

(2008) Eunjung Lee et al.   PLoS Computational Biology

Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET

(2008) Divya Mathur et al.   GENOME BIOLOGY

Inhibition of casein kinase 1-epsilon induces cancer-cell-selective, PERIOD2-dependent growth arrest

(2008) Wan Seok Yang et al.   GENOME BIOLOGY