Alistair Forrest
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Australian computer scientist
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Computer Science
Alistair Forrest's Degrees
- Masters Computer Science University of Melbourne
- PhD Computer Science Australian National University
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Why Is Alistair Forrest Influential?
(Suggest an Edit or Addition)According to Wikipedia, Alistair Forrest is an Australian molecular biologist who uses bioinformatics and DNA sequencing to study transcriptional regulation in mammals. He is based in Yokohama, Japan and is head of the Genome Information Analysis Team. He is also a co-author of over 50 peer-reviewed articles with The Transcriptional Landscape of the Mammalian Genome one being cited over 1,000 times and brings him an h-index of 31.
Alistair Forrest's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- The Transcriptional Landscape of the Mammalian Genome (2005) (3394)
- An atlas of active enhancers across human cell types and tissues (2014) (2106)
- A promoter-level mammalian expression atlas (2014) (1664)
- Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs (2002) (1543)
- Genome-wide analysis of mammalian promoter architecture and evolution (2006) (1317)
- Stem cell transcriptome profiling via massive-scale mRNA sequencing (2008) (1116)
- Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat (2012) (827)
- An atlas of human long non-coding RNAs with accurate 5′ ends (2017) (783)
- The regulated retrotransposon transcriptome of mammalian cells (2009) (735)
- Gateways to the FANTOM5 promoter level mammalian expression atlas (2015) (611)
- An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man (2010) (592)
- A draft network of ligand–receptor-mediated multicellular signalling in human (2015) (580)
- Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells (2015) (502)
- The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line (2009) (441)
- Tiny RNAs associated with transcription start sites in animals (2009) (370)
- An integrated expression atlas of miRNAs and their promoters in human and mouse (2017) (361)
- The miR-17-5p microRNA is a key regulator of the G1/S phase cell cycle transition (2008) (292)
- Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation (2015) (289)
- Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance (2014) (258)
- Induction of microRNAs, mir-155, mir-222, mir-424 and mir-503, promotes monocytic differentiation through combinatorial regulation (2010) (245)
- A predictive computational framework for direct reprogramming between human cell types (2016) (234)
- Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows (2019) (226)
- MiR-107 and MiR-185 Can Induce Cell Cycle Arrest in Human Non Small Cell Lung Cancer Cell Lines (2009) (218)
- The Abundance of Short Proteins in the Mammalian Proteome (2006) (213)
- Effects of cytosine methylation on transcription factor binding sites (2014) (211)
- CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses (2015) (191)
- Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006) (189)
- Unamplified cap analysis of gene expression on a single-molecule sequencer. (2011) (186)
- Redefinition of the human mast cell transcriptome by deep-CAGE sequencing. (2014) (166)
- An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man (2010) (165)
- FANTOM5 CAGE profiles of human and mouse samples (2017) (153)
- Interactive visualization and analysis of large-scale sequencing datasets using ZENBU (2014) (151)
- Novel genes regulated by Sonic Hedgehog in pluripotent mesenchymal cells (2002) (140)
- Transcription and enhancer profiling in human monocyte subsets. (2014) (136)
- Stromal cell diversity associated with immune evasion in human triple‐negative breast cancer (2020) (128)
- Regulation of CDC25B phosphatases subcellular localization (2000) (119)
- Sensitization to immune checkpoint blockade through activation of a STAT1/NK axis in the tumor microenvironment (2019) (119)
- Cdc25B activity is regulated by 14-3-3 (2001) (117)
- 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 (2015) (109)
- Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation (2014) (107)
- A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. (2008) (104)
- Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome. (2003) (104)
- Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing (2014) (97)
- Pax9 and Jagged1 act downstream of Gli3 in vertebrate limb development (2005) (96)
- Cdc25-dependent activation of cyclin A/cdk2 is blocked in G2 phase arrested cells independently of ATM/ATR (2001) (92)
- Functional annotation of human long noncoding RNAs via molecular phenotyping (2019) (91)
- Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals (2016) (91)
- Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium (2015) (90)
- The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation (2009) (89)
- 14-3-3 Acts as an Intramolecular Bridge to Regulate cdc25B Localization and Activity* (2003) (89)
- Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease (2017) (88)
- Alternate transcription of the Toll-like receptor signaling cascade (2006) (82)
- Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response (2015) (81)
- Predicting cell-to-cell communication networks using NATMI (2020) (80)
- Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation. (2014) (79)
- The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations. (2014) (72)
- FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions (2009) (71)
- Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers. (2016) (70)
- A Novel Corepressor, BCoR-L1, Represses Transcription through an Interaction with CtBP* (2007) (69)
- Pseudo–Messenger RNA: Phantoms of the Transcriptome (2006) (69)
- Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages (2018) (69)
- LRRN4 and UPK3B Are Markers of Primary Mesothelial Cells (2011) (69)
- scMatch: a single-cell gene expression profile annotation tool using reference datasets (2019) (65)
- Multiple splicing variants of cdc25B regulate G2/M progression. (1999) (65)
- FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki (2016) (64)
- Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation (2010) (61)
- RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE) (2014) (55)
- Whole genome transcriptome analysis (2009) (52)
- Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics (2015) (52)
- Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases (2006) (51)
- Phosphoregulators: protein kinases and protein phosphatases of mouse. (2003) (51)
- Ceruloplasmin Is a Novel Adipokine Which Is Overexpressed in Adipose Tissue of Obese Subjects and in Obesity-Associated Cancer Cells (2014) (50)
- CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors (2015) (49)
- Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules (2014) (48)
- The frequent evolutionary birth and death of functional promoters in mouse and human (2015) (48)
- Tissue-specific gene expression in soybean (Glycine max) detected by cDNA microarray analysis (2002) (46)
- The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types (2017) (45)
- The statistical geometry of transcriptome divergence in cell-type evolution and cancer (2015) (37)
- Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions (2014) (36)
- DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium. (2015) (35)
- A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation (2014) (33)
- The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells. (2010) (33)
- Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells (2015) (31)
- On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase (2016) (30)
- Anlaysis of complementary expression profiles following WT1 induction versus repression reveals the cholesterol/fatty acid synthetic pathways as a possible major target of WT1 (2004) (29)
- Automated Workflow for Preparation of cDNA for Cap Analysis of Gene Expression on a Single Molecule Sequencer (2012) (28)
- High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis. (2014) (28)
- Systematic analysis of transcription start sites in avian development (2017) (27)
- A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators (2014) (27)
- Characterizing embryonic gene expression patterns in the mouse using nonredundant sequence-based selection. (2003) (27)
- Functional annotation of the vlinc class of non-coding RNAs using systems biology approach (2016) (27)
- New era in genetics of early-onset muscle disease: Breakthroughs and challenges. (2017) (25)
- The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome (2015) (25)
- Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution (2016) (25)
- Bi‐allelic mutations in MYL1 cause a severe congenital myopathy (2018) (25)
- 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 (2016) (24)
- Comparative transcriptomics of primary cells in vertebrates (2020) (24)
- Subcellular Localization of Mammalian Type II Membrane Proteins (2006) (24)
- Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage (2015) (23)
- Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes (2017) (21)
- Retinoic acid potentiates inflammatory cytokines in human mast cells: Identification of mast cells as prominent constituents of the skin retinoid network (2015) (21)
- CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes (2018) (21)
- YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses (2016) (21)
- Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE (2010) (19)
- CC Chemokine Ligand 2 and Leukemia Inhibitory Factor Cooperatively Promote Pluripotency in Mouse Induced Pluripotent Cells (2011) (19)
- Integrative CAGE and DNA Methylation Profiling Identify Epigenetically Regulated Genes in NSCLC (2017) (19)
- Unravelling the molecular basis for regulatory T‐cell plasticity and loss of function in disease (2018) (18)
- Brain-Enriched Coding and Long Non-coding RNA Genes Are Overrepresented in Recurrent Neurodevelopmental Disorder CNVs. (2020) (18)
- Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis (2016) (17)
- Specific Mesothelial Signature Marks the Heterogeneity of Mesenchymal Stem Cells From High‐Grade Serous Ovarian Cancer (2014) (17)
- PhosphoregDB: The tissue and sub-cellular distribution of mammalian protein kinases and phosphatases (2006) (17)
- CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes (2014) (17)
- Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells (2015) (17)
- Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines (2014) (17)
- Exploration of the cell-cycle genes found within the RIKEN FANTOM2 data set. (2003) (16)
- Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis (2009) (16)
- Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases (2019) (16)
- The Evolution of Human Cells in Terms of Protein Innovation (2014) (16)
- DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C (2016) (15)
- Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease (2018) (14)
- CAGE-defined promoter regions of the genes implicated in Rett Syndrome (2014) (13)
- Corrigendum: A draft network of ligand-receptor-mediated multicellular signalling in human (2016) (12)
- Linking FANTOM5 CAGE peaks to annotations with CAGEscan (2017) (12)
- Systematic bias assessment in solid tissue 10x scRNA-seq workflows (2019) (11)
- Molecular Insights Into Regulatory T-Cell Adaptation to Self, Environment, and Host Tissues: Plasticity or Loss of Function in Autoimmune Disease (2020) (10)
- CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs (2016) (10)
- Annotating non-coding transcription using functional genomics strategies. (2009) (10)
- Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line (2015) (10)
- Myoglobinopathy is an adult-onset autosomal dominant myopathy with characteristic sarcoplasmic inclusions (2019) (9)
- Expression Levels of Therapeutic Targets as Indicators of Sensitivity to Targeted Therapeutics (2019) (9)
- Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution (2022) (8)
- Human genetics and genomics meetings going virtual: practical lessons learned from two international meetings in early 2020 (2020) (8)
- MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments (2022) (8)
- Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows (2020) (8)
- MaxHiC: robust estimation of chromatin interaction frequency in Hi-C and capture Hi-C experiments (2020) (7)
- CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments (2014) (7)
- Comprehensive Characterization of Transcriptional Activity during Influenza A Virus Infection Reveals Biases in Cap-Snatching of Host RNA Sequences (2020) (6)
- Correction: Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response (2017) (6)
- Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli (2018) (6)
- Monitoring transcription initiation activities in rat and dog (2017) (6)
- Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis (2019) (6)
- Intra- and intertumoral heterogeneity of liver metastases in a patient with uveal melanoma revealed by single-cell RNA sequencing (2021) (5)
- Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease (2016) (4)
- Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system (2017) (4)
- CORRIGENDUM: CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes (2014) (4)
- Temporally restricted activation of IFNβ signaling underlies response to immune checkpoint therapy in mice (2022) (4)
- Corrigendum: Genome-wide analysis of mammalian promoter architecture and evolution (2007) (4)
- Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection (2018) (3)
- Human genome meeting 2016 (2016) (3)
- Probability of Individual Inducible Genes from Gene-Autonomous Transcriptional System : Macrophage Heterogeneity Arises Generation of Diversity in the Innate Immune (2001) (3)
- Biallelic loss-of-function OBSCN variants predispose individuals to severe, recurrent rhabdomyolysis (2021) (3)
- A Transcriptional Switch Point During Hematopoietic Stem and Progenitor Cell Ontogeny. (2017) (3)
- Brain-enriched coding and long non-coding RNA genes are overrepresented in recurrent autism spectrum disorder CNVs (2019) (2)
- Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (2021) (2)
- Transcription Factor NKX6.3 Sheds Light on Gastric Cancer Progression (2016) (2)
- Corrigendum: Tiny RNAs associated with transcription start sites in animals (2009) (2)
- Single-cell analysis reveals diverse stromal subsets associated with immune evasion in triple-negative breast cancer (2020) (2)
- Improved CRISPR/Cas9 gene editing in primary human myoblasts using low confluency cultures on Matrigel (2021) (2)
- Single Nucleus RNA Sequencing of Pre-Malignant Liver Reveals Disease-Associated Hepatocyte State with HCC Prognostic Potential (2022) (2)
- Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs (2022) (1)
- Circulating MDSC modulate IPF progression by orchestrating immunosuppressive and pro-fibrotic networks (2018) (1)
- RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE) (2014) (1)
- Long non-coding antisense RNA to UCHL1 identifies a new class of natural and synthetic activator of translation (SINEUPs) (2012) (1)
- Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules (2014) (1)
- CAGE-defined promoter regions of the genes implicated in Rett Syndrome (2014) (1)
- Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages (2018) (1)
- Spatial transcriptomics reveals ovarian cancer subclones with distinct tumour microenvironments (2022) (1)
- Genome-wide analysis of mammalian promoter architecture and evolution (vol 38, pg 626, 2006) (2007) (1)
- CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes (2020) (1)
- Comprehensive characterisation of molecular host-pathogen interactions in influenza A virus-infected human macrophages (2019) (1)
- Myoglobinopathy is an adult-onset autosomal dominant myopathy with characteristic sarcoplasmic inclusions (2019) (0)
- Correction to: Relatively frequent switching of transcription start sites during cerebellar development (2018) (0)
- expression table of the human CAGE peaks (2017) (0)
- Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (2022) (0)
- Assessing inflammatory patterns in asthma endotypes : new diagnostic and therapeutic perspectives (2018) (0)
- Human genome meeting 2016 (2016) (0)
- Improved CRISPR/Cas9 gene editing in primary human myoblasts using low confluency cultures on Matrigel (2021) (0)
- Community Detection in a Weighted Directed Hypergraph Representation of Cell-to-cell Communication Networks (2020) (0)
- Erratum: Generation of diversity in the innate immune system: Macrophage heterogeneity arises from gene-autonomous transcriptional probability of individual inducible genes (The Journal of Immunology (2002) 168 (44-50)) (2002) (0)
- FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells (2016) (0)
- Data from: Monitoring transcription initiation activities in rat and dog (2017) (0)
- Gateways to the FANTOM5 promoter level mammalian expression atlas (2015) (0)
- human.primary_cell.hCAGE.hg19.tpm.refgene.osc (2015) (0)
- Functional genomics of the protein kinases and phosphatases of mouse (2006) (0)
- A role for YY1 in sex-biased transcription revealed through X-linked promoter activity and allelic binding analyses (2016) (0)
- Genome-wide analysis of mammalian promoter architecture and evolution based upon human and mouse CAGE data, Supplementary Data (2006) (0)
- A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators (2014) (0)
- Characterization of the humanized FRG mouse model and development of an AAV-LK03 variant with improved liver lobular biodistribution (2023) (0)
- Correction: MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments (2022) (0)
- Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection (2018) (0)
- Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases (2019) (0)
- Abstract 2897: Recurrent transcriptome alterations across multiple cancer types (2016) (0)
- Author Correction: Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system (2018) (0)
- Evidence for enhancer noncoding RNAs (enhancer-ncRNAs) with gene regulatory functions relevant to neurodevelopmental disorders (2020) (0)
- Temporally restricted activation of IFNβ signaling determines response to immune checkpoint therapy (2021) (0)
- Correction to: Relatively frequent switching of transcription start sites during cerebellar development (2018) (0)
- Deep sequencing blood transcriptomes. (2014) (0)
- Functional characterization of long non-coding RNAs in FANTOM6 (2016) (0)
- Transcriptional landscape of Mycobacterium tuberculosis-infected macrophages (2017) (0)
- Effects of cytosine methylation on transcription factor binding sites (2014) (0)
- Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis (2019) (0)
- sample information of the human samples (2017) (0)
- regulators of hematopoiesis High-throughput transcription profiling identifies putative epigenetic (2014) (0)
- reveal timed changes and dynamic enhancer methylation Analysis of the DNA methylome and transcriptome in granulopoiesis (2014) (0)
- Unrevealing biological functions of thousands of long non-coding RNAs in human (2017) (0)
- Quantitative Proteomics Reveals Novel Fibrotic Networks Of Myeloid-Derived Suppressor Cell And Monocytes In Ipf (2017) (0)
- Human genetics and genomics meetings going virtual: practical lessons learned from two international meetings in early 2020 (2020) (0)
- CDNA microarray analysis of soybean: monitoring expression profiles of 4,100 genes (2002) (0)
- Author Correction: Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system (2018) (0)
- Analysis of E-cadherin trafficking by reverse transfection: Rac1 and Cdc42 regulate cell surface delivery (2002) (0)
- Stranded RNA‐Seq: Strand‐Specific Shotgun Sequencing of RNA (2012) (0)
- genomic coordinates of the human CAGE peaks (2017) (0)
- genomic coordinates of the mouse CAGE peaks (2017) (0)
- Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines (2014) (0)
- assay information of the mouse qualitycontrol samples for HeliScopeCAGE (2017) (0)
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Alistair Forrest is affiliated with the following schools:
