Identifying proteins controlling key disease signaling pathways

Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem

(2013) Nurcan Tuncbag et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions

(2013) Martin H. Schaefer et al.   PLoS Computational Biology

An unbiased evaluation of gene prioritization tools

(2012) Daniela Börnigen et al.   BIOINFORMATICS

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

(2012) Marcel H Schulz et al.   BMC Systems Biology

Computational approaches to disease-gene prediction: rationale, classification and successes

(2012) Rosario M. Piro et al.   FEBS Journal

Complexity in the signaling network: insights from the use of targeted inhibitors in cancer therapy

(2012) J. S. Logue et al.   GENES & DEVELOPMENT

Linking the signaling cascades and dynamic regulatory networks controlling stress responses

(2012) A. Gitter et al.   GENOME RESEARCH

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

Single-cell analysis of population context advances RNAi screening at multiple levels

(2012) Berend Snijder et al.   Molecular Systems Biology

Computational tools for prioritizing candidate genes: boosting disease gene discovery

(2012) Yves Moreau et al.   NATURE REVIEWS GENETICS

Adaptations of Avian Flu Virus Are a Cause for Concern

(2012) K. I. Berns et al.   SCIENCE

Generation and Comprehensive Analysis of an Influenza Virus Polymerase Cellular Interaction Network

(2011) L. Tafforeau et al.   JOURNAL OF VIROLOGY

Host Regulatory Network Response to Infection with Highly Pathogenic H5N1 Avian Influenza Virus

(2011) C. Li et al.   JOURNAL OF VIROLOGY

Uncovering the global host cell requirements for influenza virus replication via RNAi screening

(2011) Silke Stertz et al.   MICROBES AND INFECTION

PINTA: a web server for network-based gene prioritization from expression data

(2011) D. Nitsch et al.   NUCLEIC ACIDS RESEARCH

Host- and Strain-Specific Regulation of Influenza Virus Polymerase Activity by Interacting Cellular Proteins

(2011) E. Bortz et al.   mBio

Identifying Causal Genes and Dysregulated Pathways in Complex Diseases

(2011) Yoo-Ah Kim et al.   PLoS Computational Biology

Dissecting Inflammatory Complications in Critically Injured Patients by Within-Patient Gene Expression Changes: A Longitudinal Clinical Genomics Study

(2011) Keyur H. Desai et al.   PLOS MEDICINE

Genomic Screening with RNAi: Results and Challenges

(2010) Stephanie Mohr et al.   Annual Review of Biochemistry

Integrating multiple evidence sources to predict transcription factor binding in the human genome

(2010) J. Ernst et al.   GENOME RESEARCH

Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication

(2010) Alexander Karlas et al.   NATURE

TLR activation of the transcription factor XBP1 regulates innate immune responses in macrophages

(2010) Fabio Martinon et al.   NATURE IMMUNOLOGY

Analysing biological pathways in genome-wide association studies

(2010) Kai Wang et al.   NATURE REVIEWS GENETICS

Discovering pathways by orienting edges in protein interaction networks

(2010) Anthony Gitter et al.   NUCLEIC ACIDS RESEARCH

Transcriptomics and Proteomics in the Study of H1N1 2009

(2010) Lijun Zhang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection

(2009) Sagi D. Shapira et al.   CELL

The IFITM Proteins Mediate Cellular Resistance to Influenza A H1N1 Virus, West Nile Virus, and Dengue Virus

(2009) Abraham L. Brass et al.   CELL

Human host factors required for influenza virus replication

(2009) Renate König et al.   NATURE

Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity

(2009) Esti Yeger-Lotem et al.   NATURE GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Network Analysis of Differential Expression for the Identification of Disease-Causing Genes

(2009) Daniela Nitsch et al.   PLoS One

Comprehensive Characterization of Genes Required for Protein Folding in the Endoplasmic Reticulum

(2009) M. C. Jonikas 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

Host Cell Factors in HIV Replication: Meta-Analysis of Genome-Wide Studies

(2009) Frederic D. Bushman et al.   PLoS Pathogens

Coactivator function of RIP140 for NF B/RelA-dependent cytokine gene expression

(2008) I. Zschiedrich et al.   BLOOD

Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions

(2008) Y. Qi et al.   GENOME RESEARCH

Personal genomes: The case of the missing heritability

(2008) Brendan Maher   NATURE

ENDEAVOUR update: a web resource for gene prioritization in multiple species

(2008) L.-C. Tranchevent et al.   NUCLEIC ACIDS RESEARCH

VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus–host interaction networks

(2008) Vincent Navratil et al.   NUCLEIC ACIDS RESEARCH

Genetic Mapping in Human Disease

(2008) D. Altshuler et al.   SCIENCE

Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen

(2008) Abraham L. Brass et al.   SCIENCE