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List of works by Alistair Forrest

14-3-3 acts as an intramolecular bridge to regulate cdc25B localization and activity

scientific article

A Transcriptional Switch Point During Hematopoietic Stem and Progenitor Cell Ontogeny

scientific article published on 16 November 2016

A draft network of ligand-receptor-mediated multicellular signalling in human

scientific article published on 22 July 2015

A novel corepressor, BCoR-L1, represses transcription through an interaction with CtBP.

scientific article published on 22 March 2007

A promoter-level mammalian expression atlas

scientific article

A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE.

scientific article

A role for YY1 in sex-biased transcription revealed through X-linked promoter activity and allelic binding analyses

article

A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators

scientific article

Abstract 2897: Recurrent transcriptome alterations across multiple cancer types

Alternate transcription of the Toll-like receptor signaling cascade

scientific article published on 17 February 2006

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

An atlas of active enhancers across human cell types and tissues

scientific article

An atlas of combinatorial transcriptional regulation in mouse and man

scientific article

An atlas of human long non-coding RNAs with accurate 5' ends.

scientific article

An integrated expression atlas of miRNAs and their promoters in human and mouse.

scientific article

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease.

scientific article

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

scientific article (publication date: 5 December 2002)

Anlaysis of complementary expression profiles following WT1 induction versus repression reveals the cholesterol/fatty acid synthetic pathways as a possible major target of WT1.

scientific article published on April 2004

Annotating non-coding transcription using functional genomics strategies.

scientific article

Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases

scientific article published on 04 January 2019

Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage

scientific article published on 14 December 2015

Author Correction: Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

scholarly article published in Scientific Data

Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer

scientific article

Bi-allelic mutations in MYL1 cause a severe congenital myopathy

scientific article published on 01 December 2018

Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE.

scientific article

CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors.

scientific article

CAGE-defined promoter regions of the genes implicated in Rett Syndrome.

scientific article published on 24 December 2014

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs

scientific article published on 9 June 2016

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

scientific article

CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments.

scientific article

CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes

scientific article published on 28 January 2020

CC Chemokine Ligand 2 and Leukemia Inhibitory Factor Cooperatively Promote Pluripotency in Mouse Induced Pluripotent Cells ⬇️

scientific article published on August 1, 2011

CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes

scientific article

Cdc25B activity is regulated by 14-3-3.

scientific article published in July 2001

Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells

scientific article

Characterizing embryonic gene expression patterns in the mouse using nonredundant sequence-based selection

scientific article

Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines

scientific article

Comparative transcriptomics of primary cells in vertebrates

scientific article published on 27 July 2020

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium

scientific article

Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli

scientific article published on 01 August 2018

Corrigendum: Genome-wide analysis of mammalian promoter architecture and evolution

scholarly article published in Nature Genetics

Corrigendum: Tiny RNAs associated with transcription start sites in animals

scholarly article published in Nature Genetics

Deep sequencing blood transcriptomes

scientific article published on 01 April 2014

DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium

scientific article published on 4 November 2015

DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C.

scientific article published on 19 May 2016

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation

scientific article published on 27 March 2014

Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection

scientific article published on 6 January 2018

Effects of cytosine methylation on transcription factor binding sites

scientific article

Exploration of the cell-cycle genes found within the RIKEN FANTOM2 data set.

scientific article

Expression Levels of Therapeutic Targets as Indicators of Sensitivity to Targeted Therapeutics

scientific article published on 29 August 2019

Expression analysis of the long non-coding RNA antisense to Uchl1 (AS Uchl1) during dopaminergic cells' differentiation in vitro and in neurochemical models of Parkinson's disease

scientific article

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions

scientific article published on 19 April 2009

FANTOM5 CAGE profiles of human and mouse samples

scientific article published on 29 August 2017

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki

scientific article

Functional annotation of human long noncoding RNAs via molecular phenotyping

scientific article published on 27 July 2020

Gateways to the FANTOM5 promoter level mammalian expression atlas

scientific article

Genome-wide analysis of mammalian promoter architecture and evolution

scientific article (publication date: June 2006)

Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases.

scientific article

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation.

scientific article published on 23 December 2015

High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis.

scientific article published on 26 March 2014

Identification of gourmet meat using FINS (forensically informative nucleotide sequencing)

scientific article published on 01 July 1994

Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis

scientific article published on 18 September 2019

Integration of genetics and miRNA-target gene network identified disease biology implicated in tissue specificity

article

Integrative CAGE and DNA Methylation Profiling Identify Epigenetically Regulated Genes in NSCLC.

scientific article published on 11 July 2017

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU.

scientific article published in March 2014

LRRN4 and UPK3B Are Markers of Primary Mesothelial Cells ⬇️

scientific article published on October 3, 2011

Linking FANTOM5 CAGE Peaks To Annotations With CAGEscan

Linking FANTOM5 CAGE peaks to annotations with CAGEscan

scientific article published on 3 October 2017

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat.

scientific article

Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line

scientific article

MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments

scientific article published on 24 June 2022

Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules

scientific article

MiR-107 and MiR-185 can induce cell cycle arrest in human non small cell lung cancer cell lines.

scientific article

Monitoring transcription initiation activities in rat and dog.

scientific article

Myoglobinopathy is an adult-onset autosomal dominant myopathy with characteristic sarcoplasmic inclusions

scientific article published on 27 March 2019

New era in genetics of early-onset muscle disease: Breakthroughs and challenges

scientific article published on 9 August 2016

Novel genes regulated by Sonic Hedgehog in pluripotent mesenchymal cells

scientific article

Pax9 and Jagged1 act downstream of Gli3 in vertebrate limb development

scientific article published on August 2005

Phosphoregulators: protein kinases and protein phosphatases of mouse.

scientific article

Predicting cell-to-cell communication networks using NATMI

scientific article published on 06 October 2020

Pseudo-messenger RNA: phantoms of the transcriptome

scientific article

Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics.

scientific article

Redefinition of the human mast cell transcriptome by deep-CAGE sequencing

scientific article

Reinforcing the association between distal 1q CNVs and structural brain disorder: A case of a complex 1q43-q44 CNV and a review of the literature

scientific article published on 7 February 2016

Retinoic acid potentiates inflammatory cytokines in human mast cells: identification of mast cells as prominent constituents of the skin retinoid network

scientific article

Sensitization to immune checkpoint blockade through activation of a STAT1/NK axis in the tumor microenvironment

scientific article published on 01 July 2019

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

scientific article published in March 2018

Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer.

scientific article

Subcellular Localization of Mammalian Type II Membrane Proteins

scientific article published on 01 May 2006

Systematic analysis of transcription start sites in avian development

scientific article published on 5 September 2017

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

scientific article published on 02 June 2020

Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome

scientific article

Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells

scientific article published on 25 February 2015

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

scientific article published on 19 April 2009

The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types

scientific article published on 29 August 2017

The abundance of short proteins in the mammalian proteome

scientific article

The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells

scientific article published on 22 June 2010

The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations

scientific article published on 26 March 2014

The frequent evolutionary birth and death of functional promoters in mouse and human

scientific article published on 30 July 2015

The regulated retrotransposon transcriptome of mammalian cells

scientific article (publication date: May 2009)

The statistical geometry of transcriptome divergence in cell-type evolution and cancer.

scientific article published on 14 January 2015

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

scientific article

Tiny RNAs associated with transcription start sites in animals

scientific article published on 19 April 2009

Tissue-specific gene expression in soybean (Glycine max) detected by cDNA microarray analysis

article

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

scientific article

Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs

scientific article

Transcription Factor NKX6.3 Sheds Light on Gastric Cancer Progression.

scientific article published on 16 June 2016

Transcription and enhancer profiling in human monocyte subsets

scientific article published on 26 March 2014

Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

scientific article

Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution.

scientific article

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages.

scientific article

Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions.

scientific article

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers

scientific article published on 9 November 2015

Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis

scientific article published on 20 September 2016

Unamplified cap analysis of gene expression on a single-molecule sequencer.

scientific article

Unravelling the molecular basis for regulatory T-cell plasticity and loss of function in disease

scientific article published on 27 February 2018

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

scientific article published on 12 November 2010

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

scientific article published on 27 October 2016

YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses

scientific article

scMatch: a single-cell gene expression profile annotation tool using reference datasets

scientific article published on 01 November 2019

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