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A. Forrest · SciRah

Researcher profile · Semantic Scholar

A. Forrest

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A. Forrest — researcher profile on SciRah

h-index: 58
Works: 191
Citations: 23K

Most-cited papers

An atlas of human long non-coding RNAs with accurate 5′ ends
C. Hon, Jordan A. Ramilowski, J. Harshbarger, N. Bertin +35 more
2017Nature951 citations Open access
Semantic Scholar
Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows
E. Denisenko, Belinda B. Guo, Matthew G. Jones, Rui Hou +7 more
2020Genome Biology590 citations Open access
Semantic Scholar
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells
E. Arner, Carsten O. Daub, K. Vitting-Seerup, Robin Andersson +105 more
2015Science588 citations Open access
Semantic Scholar
An integrated expression atlas of miRNAs and their promoters in human and mouse
Derek de Rie, I. Abugessaisa, T. Alam, E. Arner +66 more
2017Nature Biotechnology492 citations Open access
Semantic Scholar
Stromal cell diversity associated with immune evasion in human triple‐negative breast cancer
Sunny Z. Wu, D. Roden, Chenfei Wang, Holly Holliday +28 more
2020EMBO Journal372 citations Open access
Semantic Scholar
Predicting cell-to-cell communication networks using NATMI
Rui Hou, E. Denisenko, Ting-Ong Huan, Jordan A. Ramilowski +1 more
2020Nature Communications281 citations Open access
Semantic Scholar
A predictive computational framework for direct reprogramming between human cell types
O. Rackham, J. Firas, Hai Fang, M. Oates +11 more
2016Nature Genetics276 citations Open access
Semantic Scholar
Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution.
Charles A. Herring, Rebecca K. Simmons, S. Freytag, Daniel Poppe +17 more
2022Cell198 citations Open access
Semantic Scholar
Sensitization to immune checkpoint blockade through activation of a STAT1/NK axis in the tumor microenvironment
Rachael M. Zemek, Emma de Jong, W. Chin, I. Schuster +17 more
2019Science Translational Medicine190 citations Open access
Semantic Scholar
Functional annotation of human long noncoding RNAs via molecular phenotyping
Jordan A. Ramilowski, Chi-Wai Yip, Saumya Agrawal, Jen-Chien Chang +112 more
2019bioRxiv150 citations Open access
Semantic Scholar
Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease
J. K. Baillie, E. Arner, Carsten O. Daub, Michiel J. L. de Hoon +12 more
2017PLoS Genetics121 citations Open access
Semantic Scholar
FANTOM5 CAGE profiles of human and mouse samples
Shuhei Noguchi, T. Arakawa, S. Fukuda, M. Furuno +174 more
2017Scientific Data119 citations Open access
Semantic Scholar
scMatch: a single-cell gene expression profile annotation tool using reference datasets
Rui Hou, E. Denisenko, A. Forrest
2019Bioinform.108 citations Open access
Semantic Scholar
Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals
M. Lizio, J. Harshbarger, I. Abugessaisa, S. Noguchi +21 more
2016Nucleic Acids Res.97 citations Open access
Semantic Scholar
Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages
Sugata Roy, S. Schmeier, B. Kaczkowski, E. Arner +14 more
2018Scientific Reports87 citations Open access
Semantic Scholar
Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers.
B. Kaczkowski, Yujiro Tanaka, H. Kawaji, A. Sandelin +6 more
2016Cancer Research87 citations Open access
Semantic Scholar
The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types
H. Kawaji, T. Kasukawa, A. Forrest, Piero Carninci +1 more
2017Scientific Data75 citations Open access
Semantic Scholar
FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki
I. Abugessaisa, H. Shimoji, S. Şahin, A. Kondo +7 more
2016Database J. Biol. Databases Curation71 citations Open access
Semantic Scholar
DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium.
L. Dieterich, Sarah Klein, Anthony Mathelier, Adriana Śliwa-Primorac +15 more
2015Cell Reports48 citations Open access
Semantic Scholar
Single-nucleus RNA sequencing of pre-malignant liver reveals disease-associated hepatocyte state with HCC prognostic potential
R. Carlessi, E. Denisenko, Ebru Boslem, Julia Köhn-Gaone +21 more
2022bioRxiv45 citations Open access
Semantic Scholar
Temporally restricted activation of IFNβ signaling underlies response to immune checkpoint therapy in mice
Rachael M. Zemek, W. Chin, Vanessa S. Fear, Ben Wylie +12 more
2022Nature Communications45 citations Open access
Semantic Scholar
Bi‐allelic mutations in MYL1 cause a severe congenital myopathy
G. Ravenscroft, I. Zaharieva, C. Bortolotti, M. Lambrughi +16 more
2018Human Molecular Genetics43 citations Open access
Semantic Scholar
Systematic analysis of transcription start sites in avian development
M. Lizio, Ruslan M. Deviatiiarov, Hiroki Nagai, Laura Galán +12 more
2017PLoS Biology40 citations Open access
Semantic Scholar
Comparative transcriptomics of primary cells in vertebrates
Tanvir Alam, Saumya Agrawal, Jessica Severin, Robert S. Young +21 more
2020Genome Research39 citations Open access
Semantic Scholar
Integration of genetics and miRNA–target gene network identified disease biology implicated in tissue specificity
S. Sakaue, Jun Hirata, Y. Maeda, Eiryo Kawakami +31 more
2018Nucleic Acids Research39 citations Open access
Semantic Scholar
YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses
Chih-Yu Chen, Wenqiang Shi, Bradley P. Balaton, A. Matthews +11 more
2016Scientific Reports39 citations Open access
Semantic Scholar
Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution
Anna Ehrlund, N. Mejhert, C. Björk, Robin Andersson +15 more
2016Diabetes34 citations Open access
Semantic Scholar
On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase
Hans Ienasescu, Kang Li, Robin Andersson, Morana Vitezic +14 more
2016Database J. Biol. Databases Curation32 citations Open access
Semantic Scholar
Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes
Xian-Yang Qin, Mitsuko Hara, E. Arner, Y. Kawaguchi +18 more
2017EBioMedicine31 citations Open access
Semantic Scholar
Brain-Enriched Coding and Long Non-coding RNA Genes Are Overrepresented in Recurrent Neurodevelopmental Disorder CNVs.
H. Alinejad-Rokny, J. Heng, A. Forrest
2020Cell Reports30 citations Open access
Semantic Scholar
Unravelling the molecular basis for regulatory T‐cell plasticity and loss of function in disease
Timothy J. Sadlon, Cheryl Y. Brown, V. Bandara, C. Hope +7 more
2018Clinical & Translational Immunology30 citations Open access
Semantic Scholar
Functional annotation of the vlinc class of non-coding RNAs using systems biology approach
G. S. St Laurent, Yuri Vyatkin, D. Antonets, Maxim T. Ri +15 more
2016Nucleic Acids Research30 citations Open access
Semantic Scholar
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
Isabel A. Hemming, A. Forrest, P. Shipman, K. Woodward +3 more
2016American Journal of Medical Genetics Part B: Neuropsychiatric Genetics29 citations
Semantic Scholar
CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes
M. Bayati, H. Rabiee, M. Mehrbod, F. Vafaee +3 more
2018Scientific Reports26 citations Open access
Semantic Scholar
Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis
Masafumi Horie, Y. Yamaguchi, Akira Saito, T. Nagase +11 more
2016Scientific Reports26 citations Open access
Semantic Scholar
Intra- and intertumoral heterogeneity of liver metastases in a patient with uveal melanoma revealed by single-cell RNA sequencing
Wei-Tao Lin, A. Beasley, N. Ardakani, E. Denisenko +6 more
2021Cold Spring Harbor molecular case studies25 citations Open access
Semantic Scholar
Biallelic loss-of-function OBSCN variants predispose individuals to severe, recurrent rhabdomyolysis
M. Cabrera-Serrano, L. Caccavelli, M. Savarese, A. Vihola +32 more
2021bioRxiv25 citations Open access
Semantic Scholar
New era in genetics of early-onset muscle disease: Breakthroughs and challenges.
G. Ravenscroft, Mark R. Davis, P. Lamont, A. Forrest +1 more
2017Seminars in Cell and Developmental Biology25 citations
Semantic Scholar
Integrative CAGE and DNA Methylation Profiling Identify Epigenetically Regulated Genes in NSCLC
Masafumi Horie, B. Kaczkowski, M. Ohshima, H. Matsuzaki +14 more
2017Molecular Cancer Research25 citations Open access
Semantic Scholar
Human genome meeting 2016
A. K. Srivastava, Y. Wang, R. Huang, C. Skinner +496 more
2016Human Genomics23 citations Open access
Semantic Scholar
Expression Levels of Therapeutic Targets as Indicators of Sensitivity to Targeted Therapeutics
Riti Roy, Louise N. Winteringham, T. Lassmann, A. Forrest
2019Molecular Cancer Therapeutics22 citations Open access
Semantic Scholar
Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases
Silvia Zucchelli, Stefania Fedele, P. Vatta, R. Calligaris +11 more
2019Molecular Neurobiology21 citations Open access
Semantic Scholar
Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease
J. Baillie, Andrew Bretherick, C. Haley, S. Clohisey +30 more
2016bioRxiv21 citations Open access
Semantic Scholar
Molecular Insights Into Regulatory T-Cell Adaptation to Self, Environment, and Host Tissues: Plasticity or Loss of Function in Autoimmune Disease
Cheryl Y. Brown, Timothy J. Sadlon, C. Hope, Ying Y. Wong +12 more
2020Frontiers in Immunology20 citations Open access
Semantic Scholar
Myoglobinopathy is an adult-onset autosomal dominant myopathy with characteristic sarcoplasmic inclusions
M. Olivé, M. Engvall, G. Ravenscroft, M. Cabrera-Serrano +40 more
2019Nature Communications19 citations Open access
Semantic Scholar
Linking FANTOM5 CAGE peaks to annotations with CAGEscan
N. Bertin, Mickaël Mendez, A. Hasegawa, M. Lizio +10 more
2017Scientific Data19 citations Open access
Semantic Scholar
DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C
Sarah Klein, L. Dieterich, Anthony Mathelier, C. Chong +14 more
2016Journal of Cell Science19 citations Open access
Semantic Scholar
Corrigendum: A draft network of ligand-receptor-mediated multicellular signalling in human
Jordan A. Ramilowski, T. Goldberg, J. Harshbarger, Edda Kloppmann +7 more
2016Nature Communications19 citations Open access
Semantic Scholar
Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line
M. Lizio, Y. Ishizu, M. Itoh, T. Lassmann +9 more
2015Frontiers in Genetics18 citations Open access
Semantic Scholar
Characterization of the humanized FRG mouse model and development of an AAV-LK03 variant with improved liver lobular biodistribution
Marti Cabanes-Creus, R. G. Navarro, S. H. Liao, S. Scott +11 more
2023Molecular Therapy: Methods & Clinical Development15 citations Open access
Semantic Scholar

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