TNF-insulin crosstalk at the transcription factor GATA6 is revealed by a model that links signaling and transcriptomic data tensors

IGF1 stimulates crypt expansion via differential activation of 2 intestinal stem cell populations

(2015) Laurianne Van Landeghem et al.   FASEB JOURNAL

Gata6 potently initiates reprograming of pluripotent and differentiated cells to extraembryonic endoderm stem cells

(2015) Sissy E. Wamaitha et al.   GENES & DEVELOPMENT

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Phosphorylation of GATA-6 is required for vascular smooth muscle cell differentiation after mTORC1 inhibition

(2015) Yi Xie et al.   Science Signaling

An analysis of critical factors for quantitative immunoblotting

(2015) Kevin A. Janes   Science Signaling

MAPK feedback encodes a switch and timer for tunable stress adaptation in yeast

(2015) J. G. English et al.   Science Signaling

Phosphorylation of GATA-6 is required for vascular smooth muscle cell differentiation after mTORC1 inhibition

(2015) Yi Xie et al.   Science Signaling

An analysis of critical factors for quantitative immunoblotting

(2015) Kevin A. Janes   Science Signaling

MAPK feedback encodes a switch and timer for tunable stress adaptation in yeast

(2015) J. G. English et al.   Science Signaling

Tensor GSVD of Patient- and Platform-Matched Tumor and Normal DNA Copy-Number Profiles Uncovers Chromosome Arm-Wide Patterns of Tumor-Exclusive Platform-Consistent Alterations Encoding for Cell Transformation and Predicting Ovarian Cancer Survival

(2015) Preethi Sankaranarayanan et al.   PLoS One

A Pak1/Erk Signaling Module Acts through Gata6 to Regulate Cardiovascular Development in Zebrafish

(2014) Mollie L. Kelly et al.   DEVELOPMENTAL CELL

The transcription factor GATA6 enables self-renewal of colon adenoma stem cells by repressing BMP gene expression

(2014) Gavin Whissell et al.   NATURE CELL BIOLOGY

Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles

(2014) Sameer S. Bajikar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

An ERK-p38 Subnetwork Coordinates Host Cell Apoptosis and Necrosis during Coxsackievirus B3 Infection

(2013) Karin J. Jensen et al.   Cell Host & Microbe

Models of signalling networks - what cell biologists can gain from them and give to them

(2013) K. A. Janes et al.   JOURNAL OF CELL SCIENCE

Profiles of Basal and Stimulated Receptor Signaling Networks Predict Drug Response in Breast Cancer Lines

(2013) M. Niepel et al.   Science Signaling

Using Partial Least Squares Regression to Analyze Cellular Response Data

(2013) P. K. Kreeger   Science Signaling

Simultaneous Profiling of 194 Distinct Receptor Transcripts in Human Cells

(2013) B. H. Kang et al.   Science Signaling

Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling

(2013) Shao-shan Carol Huang et al.   PLoS Computational Biology

cAMP-dependent proteolysis of GATA-6 is linked to JNK-signaling pathway

(2012) Hironori Ushijima et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Sequential Application of Anticancer Drugs Enhances Cell Death by Rewiring Apoptotic Signaling Networks

(2012) Michael J. Lee et al.   CELL

Cross-talk between Receptor Tyrosine Kinase and Tumor Necrosis Factor-α Signaling Networks Regulates Apoptosis but not Proliferation

(2012) Elsa M. Beyer et al.   MOLECULAR & CELLULAR PROTEOMICS

Combined experimental and computational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis and G1/S arrest after genotoxic stress

(2012) Andrea R Tentner et al.   Molecular Systems Biology

Modeling the latent dimensions of multivariate signaling datasets

(2012) Karin J Jensen et al.   PHYSICAL BIOLOGY

Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers

(2011) Edward Y. Chen et al.   BIOINFORMATICS

Single-vector inducible lentiviral RNAi system for oncology target validation

(2011) Dmitri Wiederschain et al.   CELL CYCLE

Tumor necrosis factor-α increases angiopoietin-like protein 2 gene expression by activating Foxo1 in 3T3-L1 adipocytes

(2011) Jiao-Yang Zheng et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

What's wrong with correlative experiments?

(2011) Marco Vilela et al.   NATURE CELL BIOLOGY

Adaptive informatics for multifactorial and high-content biological data

(2011) Bjorn L Millard et al.   NATURE METHODS

A public genome-scale lentiviral expression library of human ORFs

(2011) Xiaoping Yang et al.   NATURE METHODS

Intersection of FOXO- and RUNX1-mediated gene expression programs in single breast epithelial cells during morphogenesis and tumor progression

(2011) L. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phosphoproteomic Analysis Identifies Grb10 as an mTORC1 Substrate That Negatively Regulates Insulin Signaling

(2011) Y. Yu et al.   SCIENCE

In Vivo Systems Analysis Identifies Spatial and Temporal Aspects of the Modulation of TNF- -Induced Apoptosis and Proliferation by MAPKs

(2011) K. S. Lau et al.   Science Signaling

PTEN differentially regulates expressions of ICAM-1 and VCAM-1 through PI3K/Akt/GSK-3β/GATA-6 signaling pathways in TNF-α-activated human endothelial cells

(2010) Konstantin Tsoyi et al.   ATHEROSCLEROSIS

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

(2010) Alexander Lachmann et al.   BIOINFORMATICS

Protein Dynamics in Drug Combinations: a Linear Superposition of Individual-Drug Responses

(2010) Naama Geva-Zatorsky et al.   CELL

Cytokine-associated drug toxicity in human hepatocytes is associated with signaling network dysregulation

(2010) Benjamin D. Cosgrove et al.   Molecular BioSystems

Single-cell NF-κB dynamics reveal digital activation and analogue information processing

(2010) Savaş Tay et al.   NATURE

Paring down signaling complexity

(2010) Kevin A Janes   NATURE BIOTECHNOLOGY

Pairwise agonist scanning predicts cellular signaling responses to combinatorial stimuli

(2010) Manash S Chatterjee et al.   NATURE BIOTECHNOLOGY

Identifying single-cell molecular programs by stochastic profiling

(2010) Kevin A Janes et al.   NATURE METHODS

RAS Mutations Affect Tumor Necrosis Factor-Induced Apoptosis in Colon Carcinoma Cells via ERK-Modulatory Negative and Positive Feedback Circuits Along with Non-ERK Pathway Effects

(2009) P. K. Kreeger et al.   CANCER RESEARCH

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Defining Network Topologies that Can Achieve Biochemical Adaptation

(2009) Wenzhe Ma et al.   CELL

Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression

(2009) Larsson Omberg et al.   Molecular Systems Biology

Linear combinations of docking affinities explain quantitative differences in RTK signaling

(2009) Andrew Gordus et al.   Molecular Systems Biology

Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

(2009) Julio Saez-Rodriguez et al.   Molecular Systems Biology

Pulsatile Stimulation Determines Timing and Specificity of NF- B-Dependent Transcription

(2009) L. Ashall et al.   SCIENCE

Cell-Specific Information Processing in Segregating Populations of Eph Receptor Ephrin-Expressing Cells

(2009) C. Jorgensen et al.   SCIENCE

Deciphering Signaling Outcomes from a System of Complex Networks

(2009) R. C. Hsueh et al.   Science Signaling

Tensor Decompositions and Applications

(2009) Tamara G. Kolda et al.   SIAM REVIEW

Cytokine-Induced Signaling Networks Prioritize Dynamic Range over Signal Strength

(2008) Kevin A. Janes et al.   CELL

Quantitative Analysis of Pathways Controlling Extrinsic Apoptosis in Single Cells

(2008) John G. Albeck et al.   MOLECULAR CELL

DiRE: identifying distant regulatory elements of co-expressed genes

(2008) V. Gotea et al.   NUCLEIC ACIDS RESEARCH

Oncogenic Ras upregulates NADPH oxidase 1 gene expression through MEK-ERK-dependent phosphorylation of GATA-6

(2008) Y Adachi et al.   ONCOGENE

Design Logic of a Cannabinoid Receptor Signaling Network That Triggers Neurite Outgrowth

(2008) K. D. Bromberg et al.   SCIENCE

Modeling a Snap-Action, Variable-Delay Switch Controlling Extrinsic Cell Death

(2008) John G Albeck et al.   PLOS BIOLOGY