Integrative Meta-Analysis of Huntington’s Disease Transcriptome Landscape

A selective inhibitor of the NLRP3 inflammasome as a potential therapeutic approach for neuroprotection in a transgenic mouse model of Huntington’s disease

(2022) Kai-Po Chen et al.   Journal of Neuroinflammation

The absence of the aryl hydrocarbon receptor in the R6/1 transgenic mouse model of Huntington´s disease improves the neurological phenotype

(2021) Quetzalli D. Angeles-López et al.   BEHAVIOURAL BRAIN RESEARCH

Ensembl 2022

(2021) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Single-nucleus RNA-seq identifies Huntington disease astrocyte states

(2020) Osama Al-Dalahmah et al.   Acta Neuropathologica Communications

Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation

(2020) Hyeseung Lee et al.   NEURON

Unbiased Profiling of Isogenic Huntington Disease hPSC-Derived CNS and Peripheral Cells Reveals Strong Cell-Type Specificity of CAG Length Effects

(2019) Jolene Ooi et al.   Cell Reports

miRDB: an online database for prediction of functional microRNA targets

(2019) Yuhao Chen et al.   NUCLEIC ACIDS RESEARCH

QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes

(2019) Zhanye Zheng et al.   NUCLEIC ACIDS RESEARCH

Early epigenomic and transcriptional changes reveal Elk-1 transcription factor as a therapeutic target in Huntington’s disease

(2019) Ferah Yildirim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Role of Microglia and Astrocytes in Huntington’s Disease

(2019) Thulani H. Palpagama et al.   Frontiers in Molecular Neuroscience

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk

(2018) Jian Zhou et al.   NATURE GENETICS

Genome-wide Analyses Identify KIF5A as a Novel ALS Gene

(2018) Aude Nicolas et al.   NEURON

COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference

(2018) Takeshi Obayashi et al.   NUCLEIC ACIDS RESEARCH

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease

(2017) Kuan-lin Huang et al.   NATURE NEUROSCIENCE

Developmental alterations in Huntington's disease neural cells and pharmacological rescue in cells and mice

(2017) Ryan G Lim et al.   NATURE NEUROSCIENCE

Huntington’s Disease iPSC-Derived Brain Microvascular Endothelial Cells Reveal WNT-Mediated Angiogenic and Blood-Brain Barrier Deficits

(2017) Ryan G. Lim et al.   Cell Reports

A spectral approach integrating functional genomic annotations for coding and noncoding variants

(2016) Iuliana Ionita-Laza et al.   NATURE GENETICS

SNP2TFBS – a database of regulatory SNPs affecting predicted transcription factor binding site affinity

(2016) Sunil Kumar et al.   NUCLEIC ACIDS RESEARCH

Correction: RNA Sequence Analysis of Human Huntington Disease Brain Reveals an Extensive Increase in Inflammatory and Developmental Gene Expression

(2016) Adam Labadorf et al.   PLoS One

A method for calculating probabilities of fitness consequences for point mutations across the human genome

(2015) Brad Gulko et al.   NATURE GENETICS

A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants

(2015) Lars G Fritsche et al.   NATURE GENETICS

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Functional annotation of noncoding sequence variants

(2014) Graham R S Ritchie et al.   NATURE METHODS

PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways

(2013) Anindya Bhattacharya et al.   NUCLEIC ACIDS RESEARCH

Extensive changes in DNA methylation are associated with expression of mutant huntingtin

(2013) C. W. Ng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeting H3K4 trimethylation in Huntington disease

(2013) M. Vashishtha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data

(2012) Richard N. Smith et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

(2012) Hashem A. Shihab et al.   HUMAN MUTATION

SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update)

(2012) A. Z. Dayem Ullah et al.   NUCLEIC ACIDS RESEARCH

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

A novel target for Huntington's disease: ERK at the crossroads of signaling

(2011) László Bodai et al.   BIOESSAYS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Protein aggregates in Huntington's disease

(2011) Montserrat Arrasate et al.   EXPERIMENTAL NEUROLOGY

What have we learned from gene expression profiles in Huntington's disease?

(2011) Tamara Seredenina et al.   NEUROBIOLOGY OF DISEASE

Inferring causative variants in microRNA target sites

(2011) Laurent F. Thomas et al.   NUCLEIC ACIDS RESEARCH

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

(2011) L. D. Ward et al.   NUCLEIC ACIDS RESEARCH

Manipulation of FASTQ data with Galaxy

(2010) D. Blankenberg et al.   BIOINFORMATICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

InterPro: the integrative protein signature database

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