Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm

Normalizing single-cell RNA sequencing data: challenges and opportunities

(2017) Catalina A Vallejos et al.   NATURE METHODS

A computational systems approach identifies synergistic specification genes that facilitate lineage conversion to prostate tissue

(2017) Flaminia Talos et al.   Nature Communications

Beta-Poisson model for single-cell RNA-seq data analyses

(2016) Trung Nghia Vu et al.   BIOINFORMATICS

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

(2016) Michele Ceccarelli et al.   CELL

Functional characterization of somatic mutations in cancer using network-based inference of protein activity

(2016) Mariano J Alvarez et al.   NATURE GENETICS

Identification of an NKX3.1-G9a-UTY transcriptional regulatory network that controls prostate differentiation

(2016) A. Dutta et al.   SCIENCE

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Elucidation and Pharmacological Targeting of Novel Molecular Drivers of Follicular Lymphoma Progression

(2015) B. Bisikirska et al.   CANCER RESEARCH

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

(2015) Aleksandra A. Kolodziejczyk et al.   Cell Stem Cell

Inhibition of the autocrine IL-6–JAK2–STAT3–calprotectin axis as targeted therapy for HR−/HER2+breast cancers

(2015) Ruth Rodriguez-Barrueco et al.   GENES & DEVELOPMENT

Identification of neurodegenerative factors using translatome–regulatory network analysis

(2015) Lars Brichta et al.   NATURE NEUROSCIENCE

Interrogation of a Context-Specific Transcription Factor Network Identifies Novel Regulators of Pluripotency

(2015) Ritu Kushwaha et al.   STEM CELLS

The Regulatory Machinery of Neurodegeneration in In Vitro Models of Amyotrophic Lateral Sclerosis

(2015) Burcin Ikiz et al.   Cell Reports

Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks

(2015) Vez Repunte-Canonigo et al.   GENOME BIOLOGY

Assembly and Interrogation of Alzheimer’s Disease Genetic Networks Reveal Novel Regulators of Progression

(2015) Soline Aubry et al.   PLoS One

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

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

ZFHX4 Interacts with the NuRD Core Member CHD4 and Regulates the Glioblastoma Tumor-Initiating Cell State

(2014) Yakov Chudnovsky et al.   Cell Reports

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

Direct Reversal of Glucocorticoid Resistance by AKT Inhibition in Acute Lymphoblastic Leukemia

(2013) Erich Piovan et al.   CANCER CELL

Murine cell line model of proneural glioma for evaluation of anti-tumor therapies

(2013) Adam M. Sonabend et al.   JOURNAL OF NEURO-ONCOLOGY

Pancreatic β Cell Dedifferentiation as a Mechanism of Diabetic β Cell Failure

(2012) Chutima Talchai et al.   CELL

Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL

(2012) Giusy Della Gatta et al.   NATURE MEDICINE

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Glioblastoma Models Reveal the Connection between Adult Glial Progenitors and the Proneural Phenotype

(2011) Liang Lei et al.   PLoS One

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann 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

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

A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate

(2010) Yin C Lin et al.   NATURE IMMUNOLOGY

An Early T Cell Lineage Commitment Checkpoint Dependent on the Transcription Factor Bcl11b

(2010) L. Li et al.   SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Epithelial-Mesenchymal Transitions in Development and Disease

(2009) Jean Paul Thiery et al.   CELL

The transcriptional network for mesenchymal transformation of brain tumours

(2009) Maria Stella Carro et al.   NATURE

Correlating measurements across samples improves accuracy of large-scale expression profile experiments

(2009) Mariano Alvarez et al.   GENOME BIOLOGY

lumi: a pipeline for processing Illumina microarray

(2008) P. Du et al.   BIOINFORMATICS

Gene regulatory network inference: Data integration in dynamic models—A review

(2008) Michael Hecker et al.   BIOSYSTEMS