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Author Details

Chung-Chau Hon
RIKEN center for Integrative Medical Sciences, Hiroshima University
2003
75
32
PMIDPaper TitleJournal TitlePublished Year
37592035Single-nucleotide variant calling in single-cell sequencing data with Monopogen.Nat Biotechnol2024
36411359Prediction of the cell-type-specific transcription of non-coding RNAs from genome sequences via machine learning.Nat Biomed Eng2023
37759202Defining super-enhancers by highly ranked histone H4 multi-acetylation levels identifies transcription factors associated with glioblastoma stem-like properties.BMC Genomics2023
37945584CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data.Nat Commun2023
37830459Enhancer target prediction: state-of-the-art approaches and future prospects.Biochem Soc Trans2023
35208849RNA Sequencing Reveals Widespread Transcription of Natural Antisense RNAs in <i>Entamoeba</i> Species.Microorganisms2022
35620640Critical roles of FGF, RA, and WNT signalling in the development of the human otic placode and subsequent lineages in a dish.Regen Ther2022
35777499Mediators of Capillary-to-Venule Conversion in the Chronic Inflammatory Skin Disease Psoriasis.J Invest Dermatol2022
36577377Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types.Cell Rep2022
36173306SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells.Bioinformatics2022
35961773Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs.Genome Res2022
36353619Single-cell transcriptomics of human gut T cells identifies cytotoxic CD4<sup>+</sup>CD8A<sup>+</sup> T cells related to mouse CD4 cytotoxic T cells.Front Immunol2022
33211864FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs.Nucleic Acids Res2021
34521352The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background.BMC Genom Data2021
34425866Systematic functional interrogation of human pseudogenes using CRISPRi.Genome Biol2021
34414426Heterogeneity among enhancer RNAs: origins, consequences and perspectives.Essays Biochem2021
32149610The single-cell eQTLGen consortium.Elife2020
32079618Recounting the FANTOM CAGE-Associated Transcriptome.Genome Res2020
33214622Genomic determinants for initiation and length of natural antisense transcripts in Entamoeba histolytica.Sci Rep2020
33148170Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene.BMC Genomics2020
32728235Expanded ENCODE delivers invaluable genomic encyclopedia.Nature2020
30407557Update of the FANTOM web resource: expansion to provide additional transcriptome atlases.Nucleic Acids Res2019
30664627C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution.Nat Commun2019
29092000The Human Cell Atlas: Technical approaches and challenges.Brief Funct Genomics2018
30080437JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states.Epigenetics2018
30341348Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis.Sci Rep2018
29580841Long Non-Coding RNAs Associated with Metabolic Traits in Human White Adipose Tissue.EBioMedicine2018
28829439An integrated expression atlas of miRNAs and their promoters in human and mouse.Nat Biotechnol2017
28241135An atlas of human long non-coding RNAs with accurate 5' ends.Nature2017
29182598Monitoring transcription initiation activities in rat and dog.Sci Data2017
27577684Intron retention-dependent gene regulation in Cryptococcus neoformans.Sci Rep2016
27767091Extensive transcriptome analysis correlates the plasticity of Entamoeba histolytica pathogenesis to rapid phenotype changes depending on the environment.Sci Rep2016
24442674Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages.Nucleic Acids Res2014
25210888Gene expression profiling in Entamoeba histolytica identifies key components in iron uptake and metabolism.PLoS One2014
25043062Exonuclease-mediated degradation of nascent RNA silences genes linked to severe malaria.Nature2014
25104019Regulation of transcription termination by glucosylated hydroxymethyluracil, base J, in Leishmania major and Trypanosoma brucei.Nucleic Acids Res2014
24743168Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.PLoS Genet2014
24559473Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum.BMC Genomics2014
24416462Bioassay-guided fractionation of extracts from Codiaeum variegatum against Entamoeba histolytica discovers compounds that modify expression of ceramide biosynthesis related genes.PLoS Negl Trop Dis2014
23258700Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytica.Nucleic Acids Res2013
24385905Identification of the virulence landscape essential for Entamoeba histolytica invasion of the human colon.PLoS Pathog2013
23548803Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments.Infect Genet Evol2013
22384074Endoplasmic reticulum stress-sensing mechanism is activated in Entamoeba histolytica upon treatment with nitric oxide.PLoS One2012
22865222Characterisation of animal angiotensin-converting enzyme 2 receptors and use of pseudotyped virus to correlate receptor binding with susceptibility of SARS-CoV infection.Hong Kong Med J2012
22574738Phylodynamics of H5N1 avian influenza virus in Indonesia.Mol Ecol2012
22230315Cell culture-adapted IBDV uses endocytosis for entry in DF-1 chicken embryonic fibroblasts.Virus Res2012
21483708A proteomic and cellular analysis of uropods in the pathogen Entamoeba histolytica.PLoS Negl Trop Dis2011
20016037Intraspecies diversity of SARS-like coronaviruses in Rhinolophus sinicus and its implications for the origin of SARS coronaviruses in humans.J Gen Virol2010
20837072Molecular epidemiology of PRRSV: a phylogenetic perspective.Virus Res2010
20554771Phylogeny-based evolutionary, demographical, and geographical dissection of North American type 2 porcine reproductive and respiratory syndrome viruses.J Virol2010
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Collaborators

Jay W Shin
Genome Institute of Singapore (GIS)
Co-authored papers 13
Piero Carninci
RIKEN Center for Integrative Medical Sciences
Co-authored papers 13
Takeya Kasukawa
RIKEN Center for Integrative Medical Sciences
Co-authored papers 9
Akira Hasegawa
RIKEN Center for Integrative Medical Sciences
Co-authored papers 8
Yoshihide Hayashizaki
Center for Integrative Medical Sciences
Co-authored papers 8
Dave S B Hoon
Saint John's Cancer Institute at Saint John's Health Center
Co-authored papers 8
Imad Abugessaisa
RIKEN Center for Integrative Medical Sciences
Co-authored papers 8
Marina Lizio
Cerevance Ltd
Co-authored papers 7
Hideya Kawaji
RIKEN Center for Integrative Medical Sciences
Co-authored papers 6
Masayoshi Itoh
RIKEN Center for Integrative Medical Sciences
Co-authored papers 6
Jessica Severin
Center for Integrative Medical Sciences
Co-authored papers 6
Harukazu Suzuki
RIKEN Center for Integrative Medical Sciences
Co-authored papers 5
Michihira Tagami
RIKEN Center for Integrative Medical Sciences
Co-authored papers 4
Jordan A Ramilowski
Advanced Medical Research Center, Yokohama City University
Co-authored papers 4
Timo Lassmann
Telethon Kids Institute, University of Western Australia
Co-authored papers 4
Jayson Harshbarger
RIKEN Center for Integrative Medical Sciences
Co-authored papers 4
Alistair R R Forrest
RIKEN Center for Integrative Medical Sciences
Co-authored papers 4
Michael Detmar
Institute of Pharmaceutical Sciences, ETH Zurich
Co-authored papers 3
Kosuke Hashimoto
Kwansei Gakuin University
Co-authored papers 3
Erik Arner
RIKEN Center for Integrative Medical Sciences (IMS)
Co-authored papers 3
Kayoko Yasuzawa
RIKEN Center for Integrative Medical Sciences
Co-authored papers 3
Aki Minoda
Co-authored papers 3
Edward C Holmes
Sydney Institute for Infectious Diseases, The University of Sydney
Co-authored papers 2
Yuri Ishizu
RIKEN Center for Life Science Technologies
Co-authored papers 2
Bogumil Kaczkowski
RIKEN Center for Integrative Medical Sciences
Co-authored papers 2
Yulia A Medvedeva
Research Center of Biotechnology RAS, Russian Academy of Sciences
Co-authored papers 2
Alessandro Bonetti
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Co-authored papers 2
Shuhei Noguchi
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