Integrated systems‐genetic analyses reveal a network target for delaying glioma progression

The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders

(2018) A. Jeremy Willsey et al.   CELL

A systems-level framework for drug discovery identifies Csf1R as an anti-epileptic drug target

(2018) Prashant K. Srivastava et al.   Nature Communications

Integrated genomic analyses of de novo pathways underlying atypical meningiomas

(2017) Akdes Serin Harmancı et al.   Nature Communications

The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary

(2016) David N. Louis et al.   ACTA NEUROPATHOLOGICA

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information

(2016) Alexander Lachmann et al.   BIOINFORMATICS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Current Management of Adult Diffuse Infiltrative Low Grade Gliomas

(2016) Emilie Le Rhun et al.   Current Neurology and Neuroscience Reports

Investigational new drugs for brain cancer

(2016) Verena Staedtke et al.   EXPERT OPINION ON INVESTIGATIONAL DRUGS

Glioblastoma vaccine therapy disappointment in Phase III trial

(2016) Hemi Malkki   Nature Reviews Neurology

A Systems-Level Analysis of the Peripheral Nerve Intrinsic Axonal Growth Program

(2016) Vijayendran Chandran et al.   NEURON

Radiation plus Procarbazine, CCNU, and Vincristine in Low-Grade Glioma

(2016) Jan C. Buckner et al.   NEW ENGLAND JOURNAL OF MEDICINE

Toward a Shared Vision for Cancer Genomic Data

(2016) Robert L. Grossman et al.   NEW ENGLAND JOURNAL OF MEDICINE

Integration of TP53, DREAM, MMB-FOXM1 and RB-E2F target gene analyses identifies cell cycle gene regulatory networks

(2016) Martin Fischer et al.   NUCLEIC ACIDS RESEARCH

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki

(2016) Imad Abugessaisa et al.   Database-The Journal of Biological Databases and Curation

Direct molecular targets of resveratrol: identifying key interactions to unlock complex mechanisms

(2015) Robert G. Britton et al.   Annals of the New York Academy of Sciences

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors

(2015) Tali Mazor et al.   CANCER CELL

Deregulation of the FOXM1 target gene network and its coregulatory partners in oesophageal adenocarcinoma

(2015) Elizabeth F Wiseman et al.   Molecular Cancer

Mutational landscape and clonal architecture in grade II and III gliomas

(2015) Hiromichi Suzuki et al.   NATURE GENETICS

Integrated genomic characterization of IDH1-mutant glioma malignant progression

(2015) Hanwen Bai et al.   NATURE GENETICS

A randomized, double-blind, placebo-controlled trial of resveratrol for Alzheimer disease

(2015) R. Scott Turner et al.   NEUROLOGY

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

(2015)   NEW ENGLAND JOURNAL OF MEDICINE

Properties of Resveratrol:In VitroandIn VivoStudies about Metabolism, Bioavailability, and Biological Effects in Animal Models and Humans

(2015) J. Gambini et al.   Oxidative Medicine and Cellular Longevity

Resveratrol inhibits oral squamous cell carcinoma through induction of apoptosis and G2/M phase cell cycle arrest

(2015) Xiao-Dong Yu et al.   TUMOR BIOLOGY

Systems genetics identifies Sestrin 3 as a regulator of a proconvulsant gene network in human epileptic hippocampus

(2015) Michael R. Johnson et al.   Nature Communications

Patterns and functional implications of rare germline variants across 12 cancer types

(2015) Charles Lu et al.   Nature Communications

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Conducting Meta-Analyses inRwith themetaforPackage

(2015) Wolfgang Viechtbauer   Journal of Statistical Software

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Cross-Species Regulatory Network Analysis Identifies a Synergistic Interaction between FOXM1 and CENPF that Drives Prostate Cancer Malignancy

(2014) Alvaro Aytes et al.   CANCER CELL

Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks

(2014) James C. Chen et al.   CELL

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

(2014) P. J. Balwierz et al.   GENOME RESEARCH

Realizing the promise of cancer predisposition genes

(2014) Nazneen Rahman   NATURE

Detecting and correcting systematic variation in large-scale RNA sequencing data

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

NF- B, an Active Player in Human Cancers

(2014) Y. Xia et al.   Cancer Immunology Research

Leveraging gene co-expression networks to pinpoint the regulation of complex traits and disease, with a focus on cardiovascular traits

(2013) M. Rotival et al.   Briefings in Functional Genomics

Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites

(2013) Jian Yan et al.   CELL

Personalizing Oncology: Perspectives and Prospects

(2013) John Mendelsohn   JOURNAL OF CLINICAL ONCOLOGY

Effects ofTP53mutational status on gene expression patterns across 10 human cancer types

(2013) Neha Parikh et al.   JOURNAL OF PATHOLOGY

Control of cell cycle transcription during G1 and S phases

(2013) Cosetta Bertoli et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013

(2013) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

MELK-Dependent FOXM1 Phosphorylation is Essential for Proliferation of Glioma Stem Cells

(2013) Kaushal Joshi et al.   STEM CELLS

Large-Scale Quality Analysis of Published ChIP-seq Data

(2013) Georgi K. Marinov et al.   G3-Genes Genomes Genetics

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A resveratrol analog, phoyunbene B, induces G2/M cell cycle arrest and apoptosis in HepG2 liver cancer cells

(2012) Guanghui Wang et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

The MuvB complex sequentially recruits B-Myb and FoxM1 to promote mitotic gene expression

(2012) S. Sadasivam et al.   GENES & DEVELOPMENT

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

The Forkhead Transcription Factor FOXM1 Controls Cell Cycle-Dependent Gene Expression through an Atypical Chromatin Binding Mechanism

(2012) X. Chen et al.   MOLECULAR AND CELLULAR BIOLOGY

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

(2012) Boris Lenhard et al.   NATURE REVIEWS GENETICS

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Addressing Diffuse Glioma as a Systemic Brain Disease With Single-Cell Analysis

(2011) David Capper   ARCHIVES OF NEUROLOGY

Phase I Randomized, Double-Blind Pilot Study of Micronized Resveratrol (SRT501) in Patients with Hepatic Metastases--Safety, Pharmacokinetics, and Pharmacodynamics

(2011) L. M. Howells et al.   Cancer Prevention Research

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

A Decade of the Human Genome Sequence-How Does the Medicinal Chemist Benefit?

(2011) Andreas Brunschweiger et al.   ChemMedChem

In Silico Screening Reveals Structurally Diverse, Nanomolar Inhibitors of NQO2 That Are Functionally Active in Cells and Can Modulate NF- B Signaling

(2011) K. A. Nolan et al.   MOLECULAR CANCER THERAPEUTICS

Chromosome 9p and 10q losses predict unfavorable outcome in low-grade gliomas

(2011) C. Houillier et al.   NEURO-ONCOLOGY

Autophagy Interplay with Apoptosis and Cell Cycle Regulation in the Growth Inhibiting Effect of Resveratrol in Glioma Cells

(2011) Eduardo C. Filippi-Chiela et al.   PLoS One

Is My Network Module Preserved and Reproducible?

(2011) Peter Langfelder et al.   PLoS Computational Biology

DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules

(2010) Bruno M Tesson et al.   BMC BIOINFORMATICS

Clinical Pharmacology of Resveratrol and Its Metabolites in Colorectal Cancer Patients

(2010) K. R. Patel et al.   CANCER RESEARCH

High dose methotrexate for pediatric high grade glioma: results of the HIT-GBM-D Pilot study

(2010) Johannes E. Wolff et al.   JOURNAL OF NEURO-ONCOLOGY

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers

(2010) Celine Lefebvre et al.   Molecular Systems Biology

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

Resveratrol: One molecule, many targets

(2008) Luciano Pirola et al.   IUBMB LIFE

CUX1 and E2F1 Regulate Coordinated Expression of the Mitotic Complex Genes Ect2, MgcRacGAP, and MKLP1 in S Phase

(2008) L. Seguin et al.   MOLECULAR AND CELLULAR BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY