Integrative Multi-omics Module Network Inference with Lemon-Tree

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

The Somatic Genomic Landscape of Glioblastoma

(2013) Cameron W. Brennan et al.   CELL

Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules

(2013) S. Roy et al.   GENOME RESEARCH

Androgen receptor-induced tumor suppressor, KLLN, inhibits breast cancer growth and transcriptionally activates p53/p73-mediated apoptosis in breast carcinomas

(2013) Yu Wang et al.   HUMAN MOLECULAR GENETICS

Transcription Factor KLLN Inhibits Tumor Growth byARSuppression, Induces Apoptosis byTP53/TP73Stimulation in Prostate Carcinomas, and Correlates With Cellular Differentiation

(2013) Yu Wang et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

The integrated landscape of driver genomic alterations in glioblastoma

(2013) Veronique Frattini et al.   NATURE GENETICS

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks

(2013) Sushmita Roy et al.   PLoS Computational Biology

Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells

(2012) Mingzhu Zhu et al.   BMC GENOMICS

Alignment and integration of complex networks by hypergraph-based spectral clustering

(2012) Tom Michoel et al.   PHYSICAL REVIEW E

Physical Module Networks: an integrative approach for reconstructing transcription regulation

(2011) N. Novershtern et al.   BIOINFORMATICS

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

(2011) Noa Novershtern et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data

(2010) E. Bonnet et al.   BIOINFORMATICS

Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

(2010) Roel G.W. Verhaak et al.   CANCER CELL

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

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

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

Module Network Inference from a Cancer Gene Expression Data Set Identifies MicroRNA Regulated Modules

(2010) Eric Bonnet et al.   PLoS One

Cerebral cavernous malformation protein CCM1 inhibits sprouting angiogenesis by activating DELTA-NOTCH signaling

(2010) Joycelyn Wüstehube et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules

(2010) Wei Zhang et al.   PLoS Computational Biology

Module networks revisited: computational assessment and prioritization of model predictions

(2009) A. Joshi et al.   BIOINFORMATICS

Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

(2009) Tom Michoel et al.   BMC Systems Biology

Insulin Receptor Isoforms and Insulin Receptor/Insulin-Like Growth Factor Receptor Hybrids in Physiology and Disease

(2009) Antonino Belfiore et al.   ENDOCRINE REVIEWS

The role of microglia in central nervous system immunity and glioma immunology

(2009) Isaac Yang et al.   JOURNAL OF CLINICAL NEUROSCIENCE

Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development

(2009) Vanessa Vermeirssen et al.   Molecular BioSystems

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

(2009) I. Amit et al.   SCIENCE

Learning a Prior on Regulatory Potential from eQTL Data

(2009) Su-In Lee et al.   PLoS Genetics

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

Killin is a p53-regulated nuclear inhibitor of DNA synthesis

(2008) Y.-j. Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Integrated Genomic Analysis of Human Glioblastoma Multiforme

(2008) D. W. Parsons et al.   SCIENCE

A Functional and Regulatory Map of Asthma

(2007) Noa Novershtern et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY