4.7 Article

Gene regulatory network inference in long-lived C. elegans reveals modular properties that are predictive of novel aging genes

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

Gene regulatory network inference from sparsely sampled noisy data

Atte Aalto et al.

NATURE COMMUNICATIONS (2020)

Article Biochemistry & Molecular Biology

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

Emily R. Miraldi et al.

GENOME RESEARCH (2019)

Article Biochemistry & Molecular Biology

Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During C. elegans Aging

Janna Hastings et al.

FRONTIERS IN MOLECULAR BIOSCIENCES (2019)

Article Biochemistry & Molecular Biology

Human Ageing Genomic Resources: new and updated databases

Robi Tacutu et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Multidisciplinary Sciences

Systematic analysis of complex genetic interactions

Elena Kuzmin et al.

SCIENCE (2018)

Article Multidisciplinary Sciences

Reprogramming of regulatory network using expression uncovers sex-specific gene regulation in Drosophila

Yijie Wang et al.

NATURE COMMUNICATIONS (2018)

Article Biochemical Research Methods

Time-lagged Ordered Lasso for network inference

Phan Nguyen et al.

BMC BIOINFORMATICS (2018)

Article Physics, Fluids & Plasmas

Consistencies and inconsistencies between model selection and link prediction in networks

Toni Valles-Catala et al.

PHYSICAL REVIEW E (2018)

Article Biochemistry & Molecular Biology

Ensembl 2017

Bronwen L. Aken et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans

Aaron C. Daugherty et al.

GENOME RESEARCH (2017)

Article Biochemical Research Methods

RTFBSDB: an integrated framework for transcription factor binding site analysis

Zhong Wang et al.

BIOINFORMATICS (2016)

Article Biochemical Research Methods

Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains

Joshua Starmer et al.

BMC BIOINFORMATICS (2016)

Review Biochemistry & Molecular Biology

Metabolic Control of Longevity

Carlos Lopez-Otin et al.

Article Biochemistry & Molecular Biology

A gene-centered C.elegans protein-DNA interaction network provides a framework for functional predictions

Juan I. Fuxman Bass et al.

MOLECULAR SYSTEMS BIOLOGY (2016)

Article Biochemical Research Methods

Inferring causal molecular networks: empirical assessment through a community-based effort

Steven M. Hill et al.

NATURE METHODS (2016)

Article Multidisciplinary Sciences

A global genetic interaction network maps a wiring diagram of cellular function

Michael Costanzo et al.

SCIENCE (2016)

Review Endocrinology & Metabolism

Investigating Connections between Metabolism, Longevity, and Behavior in Caenorhabditis elegans

George A. Lemieux et al.

TRENDS IN ENDOCRINOLOGY AND METABOLISM (2016)

Article Biochemistry & Molecular Biology

Identification of lipid droplet structure-like/resident proteins in Caenorhabditis elegans

Huimin Na et al.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH (2015)

Article Biochemistry & Molecular Biology

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

Mario L. Arrieta-Ortiz et al.

MOLECULAR SYSTEMS BIOLOGY (2015)

Article Biochemical Research Methods

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim et al.

NATURE METHODS (2015)

Article Oncology

Ovariectomy shortens the life span of female mice

Valeria Benedusi et al.

ONCOTARGET (2015)

Article Biochemical Research Methods

Evolution of Bow-Tie Architectures in Biology

Tamar Friedlander et al.

PLOS COMPUTATIONAL BIOLOGY (2015)

Article Biochemical Research Methods

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

Maria Jose Nueda et al.

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

Matthew T. Weirauch et al.

Article Physics, Fluids & Plasmas

Efficient Monte Carlo and greedy heuristic for the inference of stochastic block models

Tiago P. Peixoto

PHYSICAL REVIEW E (2014)

Article Geriatrics & Gerontology

The Scientific Quest for Lasting Youth: Prospects for Curing Aging

Joao Pedro de Magalhaes

REJUVENATION RESEARCH (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

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

Alex Greenfield et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

NCBI GEO: archive for functional genomics data sets-update

Tanya Barrett et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

The TFEB orthologue HLH-30 regulates autophagy and modulates longevity in Caenorhabditis elegans

Louis R. Lapierre et al.

NATURE COMMUNICATIONS (2013)

Article Biochemical Research Methods

Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks

Sushmita Roy et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Differential Function of the Two Atg4 Homologues in the Aggrephagy Pathway in Caenorhabditis elegans

Fan Wu et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2012)

Article Biochemical Research Methods

Wisdom of crowds for robust gene network inference

Daniel Marbach et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

Autophagy and Lipid Metabolism Coordinately Modulate Life Span in Germline-less C. elegans

Louis R. Lapierre et al.

CURRENT BIOLOGY (2011)

Review Cell Biology

Networks in Caenorhabditis elegans

Kristin C. Gunsalus et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2011)

Article Biochemistry & Molecular Biology

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

Roger Pique-Regi et al.

GENOME RESEARCH (2011)

Review Biology

The first long-lived mutants: discovery of the insulin/IGF-1 pathway for ageing

Cynthia Kenyon

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2011)

Article Genetics & Heredity

DAF-12 Regulates a Connected Network of Genes to Ensure Robust Developmental Decisions

Daniel Hochbaum et al.

PLOS GENETICS (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Review Multidisciplinary Sciences

The genetics of ageing

Cynthia J. Kenyon

NATURE (2010)

Article Biochemical Research Methods

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

Eran Eden et al.

BMC BIOINFORMATICS (2009)

Article Biochemical Research Methods

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

Steffen Durinck et al.

NATURE PROTOCOLS (2009)

Review Genetics & Heredity

The evolution of hierarchical gene regulatory networks

Douglas H. Erwin et al.

NATURE REVIEWS GENETICS (2009)

Article Multidisciplinary Sciences

Missing and spurious interactions and the reconstruction of complex networks

Roger Guimera et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Review Multidisciplinary Sciences

Is Genetic Evolution Predictable?

David L. Stern et al.

SCIENCE (2009)

Article Multidisciplinary Sciences

Drosophila, germ-line modulation of insulin signaling and lifespan

Thomas Flatt et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biochemistry & Molecular Biology

Brain IGF-1 Receptors Control Mammalian Growth and Lifespan through a Neuroendocrine Mechanism

Laurent Kappeler et al.

PLOS BIOLOGY (2008)

Article Multidisciplinary Sciences

Genomic analysis of the hierarchical structure of regulatory networks

Haiyuan Yu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biochemical Research Methods

Hierarchical modularity of nested bow-ties in metabolic networks

Jing Zhao et al.

BMC BIOINFORMATICS (2006)

Article Cell Biology

Highly optimised global organisation of metabolic networks

R Tanaka et al.

IEE PROCEEDINGS SYSTEMS BIOLOGY (2005)

Article Biochemical Research Methods

Genorne-wide RNAi screening in Caenorhabditis elegans

RS Kamath et al.

METHODS (2003)

Article Biochemical Research Methods

The connectivity structure, giant strong component and centrality of metabolic networks

HW Ma et al.

BIOINFORMATICS (2003)

Article Biochemistry & Molecular Biology

Cytoscape: A software environment for integrated models of biomolecular interaction networks

P Shannon et al.

GENOME RESEARCH (2003)

Review Cell Biology

Molecular mechanisms of selector gene function and evolution

RS Mann et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2002)

Review Multidisciplinary Sciences

Reverse engineering of biological complexity

ME Csete et al.

SCIENCE (2002)

Article Biotechnology & Applied Microbiology

Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans

Ravi S. Kamath et al.

GENOME BIOLOGY (2001)