LASSIM—A network inference toolbox for genome-wide mechanistic modeling

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

(2016) Daniel Marbach et al.   NATURE METHODS

Analysis of computational footprinting methods for DNase sequencing experiments

(2016) Eduardo G Gusmao et al.   NATURE METHODS

Avoiding pitfalls in L1-regularised inference of gene networks

(2015) Andreas Tjärnberg et al.   Molecular BioSystems

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

(2015) Ivan V. Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

A validated gene regulatory network and GWAS identifies early regulators of T cell–associated diseases

(2015) Mika Gustafsson et al.   Science Translational Medicine

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions

(2014) Maxwell A. Hume et al.   NUCLEIC ACIDS RESEARCH

Physiologically Realistic and Validated Mathematical Liver Model Revels Hepatobiliary Transfer Rates for Gd-EOB-DTPA Using Human DCE-MRI Data

(2014) Mikael Fredrik Forsgren et al.   PLoS One

A Generally Applicable Translational Strategy Identifies S100A4 as a Candidate Gene in Allergy

(2014) S. Bruhn et al.   Science Translational Medicine

DNA Methylation Changes Separate Allergic Patients from Healthy Controls and May Reflect Altered CD4+ T-Cell Population Structure

(2014) Colm E. Nestor et al.   PLoS Genetics

Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0

(2013) Michael Weber et al.   BMC Systems Biology

Early signaling events that underlie fate decisions of naive CD4+T cells toward distinct T-helper cell subsets

(2013) Hidehiro Yamane et al.   IMMUNOLOGICAL REVIEWS

Insulin Signaling in Type 2 Diabetes

(2013) Cecilia Brännmark et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models

(2013) Emanuel Gonçalves et al.   Molecular BioSystems

The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes

(2012) Sebastian Vlaic et al.   BMC Systems Biology

Mechanistic explanations for counter-intuitive phosphorylation dynamics of the insulin receptor and insulin receptor substrate-1 in response to insulin in murine adipocytes

(2012) Elin Nyman et al.   FEBS Journal

Tyrosine Phosphorylation of c-Maf Enhances the Expression of IL-4 Gene

(2012) C.-Y. Lai et al.   JOURNAL OF IMMUNOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements

(2012) Aditi Kanhere et al.   Nature Communications

Increased expression of IRF4 and ETS1 in CD4+ cells from patients with intermittent allergic rhinitis

(2011) S. Bruhn et al.   ALLERGY

Gene Regulatory Network Reconstruction Using Bayesian Networks, the Dantzig Selector, the Lasso and Their Meta-Analysis

(2011) Matthieu Vignes et al.   PLoS One

Diverse Targets of the Transcription Factor STAT3 Contribute to T Cell Pathogenicity and Homeostasis

(2010) Lydia Durant et al.   IMMUNITY

Peripheral CD4+ T-cell differentiation regulated by networks of cytokines and transcription factors

(2010) Jinfang Zhu et al.   IMMUNOLOGICAL REVIEWS

Improved Reconstruction of In Silico Gene Regulatory Networks by Integrating Knockout and Perturbation Data

(2010) Kevin Y. Yip et al.   PLoS One

Gene Regulatory Networks from Multifactorial Perturbations Using Graphical Lasso: Application to the DREAM4 Challenge

(2010) Patricia Menéndez et al.   PLoS One

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Covering a Broad Dynamic Range: Information Processing at the Erythropoietin Receptor

(2010) V. Becker et al.   SCIENCE

Combining Network Modeling and Gene Expression Microarray Analysis to Explore the Dynamics of Th1 and Th2 Cell Regulation

(2010) Marco Pedicini et al.   PLoS Computational Biology

Reverse Engineering of Gene Networks with LASSO and Nonlinear Basis Functions

(2009) Mika Gustafsson et al.   Annals of the New York Academy of Sciences

Integrative modeling of transcriptional regulation in response to antirheumatic therapy

(2009) Michael Hecker et al.   BMC BIOINFORMATICS

Systems biology: model based evaluation and comparison of potential explanations for given biological data

(2009) Gunnar Cedersund et al.   FEBS Journal

Genome-wide system analysis reveals stable yet flexible network dynamics in yeast

(2009) M. Gustafsson et al.   IET Systems Biology