Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

Mean Arterial Blood Pressure Management of Acute Traumatic Spinal Cord Injured Patients during the Pre-Hospital and Early Admission Period

(2017) Jin W. Tee et al.   JOURNAL OF NEUROTRAUMA

A Targeted Proteomics Analysis of Cerebrospinal Fluid after Acute Human Spinal Cord Injury

(2017) Femke Streijger et al.   JOURNAL OF NEUROTRAUMA

Cerebrospinal Fluid Biomarkers To Stratify Injury Severity and Predict Outcome in Human Traumatic Spinal Cord Injury

(2017) Brian K. Kwon et al.   JOURNAL OF NEUROTRAUMA

Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes

(2017) Kevin Drew et al.   Molecular Systems Biology

Can we predict protein from mRNA levels?

(2017) Nikolaus Fortelny et al.   NATURE

Differential analysis of RNA-seq incorporating quantification uncertainty

(2017) Harold Pimentel et al.   NATURE METHODS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Database resources of the National Center for Biotechnology Information

(2017) et al.   NUCLEIC ACIDS RESEARCH

Integrating GWAS and Co-expression Network Data Identifies Bone Mineral Density Genes SPTBN1 and MARK3 and an Osteoblast Functional Module

(2017) Gina M. Calabrese et al.   Cell Systems

Differential Neuroproteomic and Systems Biology Analysis of Spinal Cord Injury

(2016) Ahmed Moghieb et al.   MOLECULAR & CELLULAR PROTEOMICS

Astrocyte scar formation aids central nervous system axon regeneration

(2016) Mark A. Anderson et al.   NATURE

A scored human protein–protein interaction network to catalyze genomic interpretation

(2016) Taibo Li et al.   NATURE METHODS

Integrated genomics and proteomics define huntingtin CAG length–dependent networks in mice

(2016) Peter Langfelder et al.   NATURE NEUROSCIENCE

Gene expression elucidates functional impact of polygenic risk for schizophrenia

(2016) Menachem Fromer et al.   NATURE NEUROSCIENCE

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

(2016) Evgeny M. Zdobnov et al.   NUCLEIC ACIDS RESEARCH

Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system

(2016) Alexis Vandenbon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput proteomics reveal alarmins as amplifiers of tissue pathology and inflammation after spinal cord injury

(2016) Athanasios Didangelos et al.   Scientific Reports

Mean Arterial Blood Pressure Correlates with Neurological Recovery after Human Spinal Cord Injury: Analysis of High Frequency Physiologic Data

(2015) Gregory Hawryluk et al.   JOURNAL OF NEUROTRAUMA

Integrative network analysis reveals molecular mechanisms of blood pressure regulation

(2015) T. Huan et al.   Molecular Systems Biology

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease

(2015) Michael R Johnson et al.   NATURE NEUROSCIENCE

Cell type– and brain region–resolved mouse brain proteome

(2015) Kirti Sharma et al.   NATURE NEUROSCIENCE

Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders

(2015) Neelroop N. Parikshak et al.   NATURE REVIEWS GENETICS

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Transcriptome analyses reveal molecular mechanisms underlying functional recovery after spinal cord injury

(2015) Hongmei Duan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NT3-chitosan elicits robust endogenous neurogenesis to enable functional recovery after spinal cord injury

(2015) Zhaoyang Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Uncovering disease-disease relationships through the incomplete interactome

(2015) J. Menche et al.   SCIENCE

Systems genetics identifies Sestrin 3 as a regulator of a proconvulsant gene network in human epileptic hippocampus

(2015) Michael R. Johnson et al.   Nature Communications

A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome

(2015) Susan Dina Ghiassian et al.   PLoS Computational Biology

FastRFunctions for Robust Correlations and Hierarchical Clustering

(2015) Peter Langfelder et al.   Journal of Statistical Software

An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

(2014) Y. Zhang et al.   JOURNAL OF NEUROSCIENCE

Restoring function after spinal cord injury: towards clinical translation of experimental strategies

(2014) Leanne M Ramer et al.   LANCET NEUROLOGY

Integrated systems analysis reveals a molecular network underlying autism spectrum disorders

(2014) J. Li et al.   Molecular Systems Biology

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

(2014) Erik L.L. Sonnhammer et al.   NUCLEIC ACIDS RESEARCH

Gene: a gene-centered information resource at NCBI

(2014) Garth R. Brown et al.   NUCLEIC ACIDS RESEARCH

Integrative Functional Genomic Analyses Implicate Specific Molecular Pathways and Circuits in Autism

(2013) Neelroop N. Parikshak et al.   CELL

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

(2013) Bin Zhang et al.   CELL

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

HINT: High-quality protein interactomes and their applications in understanding human disease

(2012) Jishnu Das et al.   BMC Systems Biology

Two gene co-expression modules differentiate psychotics and controls

(2012) C Chen et al.   MOLECULAR PSYCHIATRY

Early versus Delayed Decompression for Traumatic Cervical Spinal Cord Injury: Results of the Surgical Timing in Acute Spinal Cord Injury Study (STASCIS)

(2012) Michael G. Fehlings et al.   PLoS One

HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens

(2011) X. Wang et al.   BIOINFORMATICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Transcriptomic analysis of autistic brain reveals convergent molecular pathology

(2011) Irina Voineagu et al.   NATURE

The UniProt-GO Annotation database in 2011

(2011) E. C. Dimmer et al.   NUCLEIC ACIDS RESEARCH

Ensembl BioMarts: a hub for data retrieval across taxonomic space

(2011) R. J. Kinsella et al.   Database-The Journal of Biological Databases and Curation

Is My Network Module Preserved and Reproducible?

(2011) Peter Langfelder et al.   PLoS Computational Biology

Annexin A1: A Central Player in the Anti-Inflammatory and Neuroprotective Role of Microglia

(2010) S. McArthur et al.   JOURNAL OF IMMUNOLOGY

Analytical approaches to RNA profiling data for the identification of genes enriched in specific cells

(2010) Joseph D. Dougherty et al.   NUCLEIC ACIDS RESEARCH

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

Identification of Two Distinct Macrophage Subsets with Divergent Effects Causing either Neurotoxicity or Regeneration in the Injured Mouse Spinal Cord

(2009) K. A. Kigerl et al.   JOURNAL OF NEUROSCIENCE

Chemotropic guidance facilitates axonal regeneration and synapse formation after spinal cord injury

(2009) Laura Taylor Alto et al.   NATURE NEUROSCIENCE

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function

(2008) J. D. Cahoy et al.   JOURNAL OF NEUROSCIENCE

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Geometric Interpretation of Gene Coexpression Network Analysis

(2008) Steve Horvath et al.   PLoS Computational Biology