TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data

Off the Clock: From Circadian Disruption to Metabolic Disease

(2019) Eleonore Maury   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Interspecies analysis of MYC targets identifies tRNA synthetases as mediators of growth and survival in MYC-overexpressing cells

(2019) Jonathan Zirin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TuxNet: A simple interface to process RNA sequencing data and infer gene regulatory networks

(2019) Ryan J. Spurney et al.   PLANT JOURNAL

Time-Course Transcriptome Analysis for Drug Repositioning in Fusobacterium nucleatum-Infected Human Gingival Fibroblasts

(2019) Wenyan Kang et al.   Frontiers in Cell and Developmental Biology

Fusobacterium nucleatum Facilitates Apoptosis, ROS Generation, and Inflammatory Cytokine Production by Activating AKT/MAPK and NF-κB Signaling Pathways in Human Gingival Fibroblasts

(2019) Wenyan Kang et al.   Oxidative Medicine and Cellular Longevity

Integrative approaches to reconstruct regulatory networks from multi-omics data: A review of state-of-the-art methods

(2019) Nisar Wani et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

(2018) MacIntosh Cornwell et al.   BMC BIOINFORMATICS

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors

(2018) Hui Hu et al.   NUCLEIC ACIDS RESEARCH

A guide to gene regulatory network inference for obtaining predictive solutions: Underlying assumptions and fundamental biological and data constraints

(2018) Sara Barbosa et al.   BIOSYSTEMS

iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data

(2018) Steven Xijin Ge et al.   BMC BIOINFORMATICS

Circadian clocks and insulin resistance

(2018) Dirk Jan Stenvers et al.   Nature Reviews Endocrinology

BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud

(2018) Denis Torre et al.   Cell Systems

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

A new promoter element associated with daily time keeping in Drosophila

(2017) Brandi Sharp et al.   NUCLEIC ACIDS RESEARCH

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

(2017) Sayed Mohammad Ebrahim Sahraeian et al.   Nature Communications

Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets

(2016) Yalchin Oytam et al.   BMC BIOINFORMATICS

Natural Cubic Spline Regression Modeling Followed by Dynamic Network Reconstruction for the Identification of Radiation-Sensitivity Gene Association Networks from Time-Course Transcriptome Data

(2016) Agata Michna et al.   PLoS One

Discovery of RNA splicing and genes in pieces

(2016) Arnold J. Berk   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circadian System and Glucose Metabolism: Implications for Physiology and Disease

(2016) Jingyi Qian et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Past Roadblocks and New Opportunities in Transcription Factor Network Mapping

(2016) Michael R. Brent   TRENDS IN GENETICS

CLOCKWORK ORANGE Enhances PERIOD Mediated Rhythms in Transcriptional Repression by Antagonizing E-box Binding by CLOCK-CYCLE

(2016) Jian Zhou et al.   PLoS Genetics

The Drosophila HNF4 nuclear receptor promotes glucose-stimulated insulin secretion and mitochondrial function in adults

(2016) William E Barry et al.   eLife

Polyester: simulating RNA-seq datasets with differential transcript expression

(2015) Alyssa C. Frazee et al.   BIOINFORMATICS

T-REx: Transcriptome analysis webserver for RNA-seq Expression data

(2015) Anne de Jong et al.   BMC GENOMICS

Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis

(2015) Daniel Spies et al.   Computational and Structural Biotechnology Journal

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series

(2014) M. J. Nueda et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A review on the computational approaches for gene regulatory network construction

(2014) Lian En Chai et al.   COMPUTERS IN BIOLOGY AND MEDICINE

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

(2014) Rekin's Janky et al.   PLoS Computational Biology

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

(2013) Weijun Luo et al.   BIOINFORMATICS

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

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

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Dynamics of the Drosophila Circadian Clock: Theoretical Anti-Jitter Network and Controlled Chaos

(2010) Hassan M. Fathallah-Shaykh   PLoS One

The Centrality of RNA

(2009) Phillip A. Sharp   CELL

Reduction of Lobe leads to TORC1 hypoactivation that induces ectopic Jak/STAT signaling to impair Drosophila eye development

(2009) Ying-Hsuan Wang et al.   MECHANISMS OF DEVELOPMENT

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

FlyBase: enhancing Drosophila Gene Ontology annotations

(2008) S. Tweedie et al.   NUCLEIC ACIDS RESEARCH