Multi-study inference of regulatory networks for more accurate models of gene regulation

Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks

(2018) Konstantine Tchourine et al.   Cell Reports

Inference and Evolutionary Analysis of Genome-Scale Regulatory Networks in Large Phylogenies

(2017) Christopher Koch et al.   Cell Systems

Batch effects and the effective design of single-cell gene expression studies

(2017) Po-Yuan Tung et al.   Scientific Reports

Toward Accurate and Quantitative Comparative Metagenomics

(2016) Stephen Nayfach et al.   CELL

A prior-based integrative framework for functional transcriptional regulatory network inference

(2016) Alireza F. Siahpirani et al.   NUCLEIC ACIDS RESEARCH

Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens

(2016) Deborah Chasman et al.   PLoS Computational Biology

Fused Regression for Multi-source Gene Regulatory Network Inference

(2016) Kari Y. Lam et al.   PLoS Computational Biology

Removing Batch Effects from Longitudinal Gene Expression - Quantile Normalization Plus ComBat as Best Approach for Microarray Transcriptome Data

(2016) Christian Müller et al.   PLoS One

Gene regulatory network inference using fused LASSO on multiple data sets

(2016) Nooshin Omranian et al.   Scientific Reports

Integrative random forest for gene regulatory network inference

(2015) Francesca Petralia et al.   BIOINFORMATICS

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

(2015) Alicia N. Schep et al.   GENOME RESEARCH

An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network

(2015) M. L. Arrieta-Ortiz et al.   Molecular Systems Biology

SubtiWiki 2.0—an integrated database for the model organismBacillus subtilis

(2015) Raphael H. Michna et al.   NUCLEIC ACIDS RESEARCH

TRRUST: a reference database of human transcriptional regulatory interactions

(2015) Heonjong Han et al.   Scientific Reports

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Inferring gene regulatory networks by integrating ChIP-seq/chip and transcriptome data via LASSO-type regularization methods

(2014) Jing Qin et al.   METHODS

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Regulation of transcription factor activity by interconnected post-translational modifications

(2014) Theresa M. Filtz et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Chromatin accessibility: a window into the genome

(2014) Maria Tsompana et al.   Epigenetics & Chromatin

Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu

(2014) Siddhartha Jain et al.   PLoS Computational Biology

Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks

(2013) Alex Greenfield et al.   BIOINFORMATICS

Dynamic regulatory network controlling TH17 cell differentiation

(2013) Nir Yosef et al.   NATURE

The big challenges of big data

(2013) Vivien Marx   NATURE

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Saccharomycesgenome database provides new regulation data

(2013) Maria C. Costanzo et al.   NUCLEIC ACIDS RESEARCH

A Validated Regulatory Network for Th17 Cell Specification

(2012) Maria Ciofani et al.   CELL

Reconstruction of Transcriptional Regulatory Networks by Stability-Based Network Component Analysis

(2012) Xi Chen et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Reuse of public genome-wide gene expression data

(2012) Johan Rung et al.   NATURE REVIEWS GENETICS

MicroRNA profiling: approaches and considerations

(2012) Colin C. Pritchard et al.   NATURE REVIEWS GENETICS

Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

(2012) P. Nicolas et al.   SCIENCE

YeastMine—an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit

(2012) Rama Balakrishnan et al.   Database-The Journal of Biological Databases and Curation

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities

(2011) Yao Fu et al.   BMC BIOINFORMATICS

A computational framework for gene regulatory network inference that combines multiple methods and datasets

(2011) Rita Gupta et al.   BMC Systems Biology

Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression

(2011) L. T. MacNeil et al.   GENOME RESEARCH

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

(2011) C. G. de Boer et al.   NUCLEIC ACIDS RESEARCH

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Statistical Design and Analysis of RNA Sequencing Data

(2010) P. L. Auer et al.   GENETICS

Stability selection

(2010) Nicolai Meinshausen et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Multi-species integrative biclustering

(2010) Peter Waltman et al.   GENOME BIOLOGY

Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: A quantitative analysis of a compendium of chemostat-based transcriptome data

(2009) Theo A Knijnenburg et al.   BMC GENOMICS

Extended Bayesian information criteria for model selection with large model spaces

(2008) J. Chen et al.   BIOMETRIKA

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

(2008) Michael Hecker et al.   BIOSYSTEMS

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Gene–Environment Interaction in Yeast Gene Expression

(2008) Erin N Smith et al.   PLOS BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY