Studying and modelling dynamic biological processes using time-series gene expression data

An integrative clustering and modeling algorithm for dynamical gene expression data

(2011) J. Sivriver et al.   BIOINFORMATICS

GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods

(2011) Thomas Schaffter et al.   BIOINFORMATICS

Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions

(2011) Christoph Hafemeister et al.   BIOINFORMATICS

A Platform for Processing Expression of Short Time Series (PESTS)

(2011) Anshu Sinha et al.   BMC BIOINFORMATICS

Impulse Control: Temporal Dynamics in Gene Transcription

(2011) Nir Yosef et al.   CELL

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics

(2011) M. A. Mendoza-Parra et al.   Molecular Systems Biology

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Microbial environments confound antibiotic efficacy

(2011) Henry H Lee et al.   Nature Chemical Biology

Large Scale Comparison of Innate Responses to Viral and Bacterial Pathogens in Mouse and Macaque

(2011) Guy Zinman et al.   PLoS One

A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction

(2011) A. Vinayagam et al.   Science Signaling

Temporal Dynamics of Host Molecular Responses Differentiate Symptomatic and Asymptomatic Influenza A Infection

(2011) Yongsheng Huang et al.   PLoS Genetics

Dissecting Inflammatory Complications in Critically Injured Patients by Within-Patient Gene Expression Changes: A Longitudinal Clinical Genomics Study

(2011) Keyur H. Desai et al.   PLOS MEDICINE

A computationally efficient modular optimal discovery procedure

(2010) Sangsoon Woo et al.   BIOINFORMATICS

Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes

(2010) Michael Klutstein et al.   BMC GENOMICS

Deconvolution of Chromatin Immunoprecipitation-Microarray (ChIP-chip) Analysis of MBF Occupancies Reveals the Temporal Recruitment of Rep2 at the MBF Target Genes

(2010) Majid Eshaghi et al.   EUKARYOTIC CELL

New insights into the blood-stage transcriptome ofPlasmodium falciparumusing RNA-Seq

(2010) Thomas D. Otto et al.   MOLECULAR MICROBIOLOGY

Emerging properties of animal gene regulatory networks

(2010) Eric H. Davidson   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Signalling ballet in space and time

(2010) Boris N. Kholodenko et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Characterizing Dynamic Changes in the Human Blood Transcriptional Network

(2010) Jun Zhu et al.   PLoS Computational Biology

Detection and correction of false segmental duplications caused by genome mis-assembly

(2010) David R Kelley et al.   GENOME BIOLOGY

Constrained mixture estimation for analysis and robust classification of clinical time series

(2009) Ivan G. Costa et al.   BIOINFORMATICS

An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation)

(2009) Martin J Aryee et al.   BMC BIOINFORMATICS

A dynamic network of transcription in LPS-treated human subjects

(2009) Junhee Seok et al.   BMC Systems Biology

An Epigenetic Switch Involving NF-κB, Lin28, Let-7 MicroRNA, and IL6 Links Inflammation to Cell Transformation

(2009) Dimitrios Iliopoulos et al.   CELL

A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection

(2009) Sagi D. Shapira et al.   CELL

A Systematic Analysis of Tinman Function Reveals Eya and JAK-STAT Signaling as Essential Regulators of Muscle Development

(2009) Ya-Hsin Liu et al.   DEVELOPMENTAL CELL

Timing of Gene Expression Responses to Environmental Changes

(2009) Gal Chechik et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Systems-level dynamic analyses of fate change in murine embryonic stem cells

(2009) Rong Lu et al.   NATURE

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS

Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity

(2009) Esti Yeger-Lotem et al.   NATURE GENETICS

Function of C/EBPδ in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals

(2009) Vladimir Litvak et al.   NATURE IMMUNOLOGY

Using movies to analyse gene circuit dynamics in single cells

(2009) James C. W. Locke et al.   NATURE REVIEWS MICROBIOLOGY

Identification of microRNAs with regulatory potential using a matched microRNA-mRNA time-course data

(2009) V. Jayaswal et al.   NUCLEIC ACIDS RESEARCH

IL-3 and Oncogenic Abl Regulate the Myeloblast Transcriptome by Altering mRNA Stability

(2009) Jason Ernst et al.   PLoS One

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

(2009) I. Amit et al.   SCIENCE

Integrating Proteomic, Transcriptional, and Interactome Data Reveals Hidden Components of Signaling and Regulatory Networks

(2009) S.-s. C. Huang et al.   Science Signaling

Model-Based Deconvolution of Cell Cycle Time-Series Data Reveals Gene Expression Details at High Resolution

(2009) Dan Siegal-Gaskins et al.   PLoS Computational Biology

Alignment and classification of time series gene expression in clinical studies

(2008) T.-h. Lin et al.   BIOINFORMATICS

Quantitative phosphoproteomic analysis of signaling network dynamics

(2008) Forest M White   CURRENT OPINION IN BIOTECHNOLOGY

Differentiation and Transplantation of Human Embryonic Stem Cell–Derived Hepatocytes

(2008) Hesham Basma et al.   GASTROENTEROLOGY

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses

(2008) Denis Gaucher et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors

(2008) Fabio Mohn et al.   MOLECULAR CELL

Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation

(2008) Ophir Shalem et al.   Molecular Systems Biology

Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network

(2008) Gal Chechik et al.   NATURE BIOTECHNOLOGY

Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation

(2008) Luis López-Maury et al.   NATURE REVIEWS GENETICS

Global regulatory logic for specification of an embryonic cell lineage

(2008) P. Oliveri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells

(2008) Z. Bar-Joseph et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Similarity Queries for Temporal Toxicogenomic Expression Profiles

(2008) Adam A. Smith et al.   PLoS Computational Biology

Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics

(2008) Stephen A. Ramsey et al.   PLoS Computational Biology