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Author Details

Jay W Shin
Genome Institute of Singapore (GIS)
2004
60
26
Emma Lundberg (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37592035Single-nucleotide variant calling in single-cell sequencing data with Monopogen.Nat Biotechnol2024
37263619Single-Cell RNA-Seq Reveals LRRC75A-Expressing Cell Population Involved in VEGF Secretion of Multipotent Mesenchymal Stromal/Stem Cells Under Ischemia.Stem Cells Transl Med2023
37608799ZENBU-Reports: a graphical web-portal builder for interactive visualization and dissemination of genome-scale data.NAR Genom Bioinform2023
37442134Expression of the readthrough transcript CiDRE in alveolar macrophages boosts SARS-CoV-2 susceptibility and promotes COVID-19 severity.Immunity2023
35262217Microglia integration into human midbrain organoids leads to increased neuronal maturation and functionality.Glia2022
35486244Complete Transcriptome Analysis by 5'-End Single-Cell RNA-Seq with Random Priming.Methods Mol Biol2022
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
33568674LETR1 is a lymphatic endothelial-specific lncRNA governing cell proliferation and migration through KLF4 and SEMA3C.Nat Commun2021
33711266Decoding Neuronal Diversification by Multiplexed Single-cell RNA-Seq.Stem Cell Reports2021
33835127Functional annotation of lncRNA in high-throughput screening.Essays Biochem2021
34521352The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background.BMC Genom Data2021
33373636Piperidine-4-carboxamide as a new scaffold for designing secretory glutaminyl cyclase inhibitors.Int J Biol Macromol2021
32670003Brainstem Organoids From Human Pluripotent Stem Cells.Front Neurosci2020
32032507Widely Distributed Neurotensinergic Neurons in the Brainstem Regulate NREM Sleep in Mice.Curr Biol2020
32079618Recounting the FANTOM CAGE-Associated Transcriptome.Genome Res2020
31838097Inhibition of the transcription factor ROR-γ reduces pathogenic Th17 cells in acetylcholine receptor antibody positive myasthenia gravis.Exp Neurol2020
32737576Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids.Cell Tissue Res2020
32929222An era of single-cell genomics consortia.Exp Mol Med2020
30664627C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution.Nat Commun2019
31719197Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians.Proc Natl Acad Sci U S A2019
29092000The Human Cell Atlas: Technical approaches and challenges.Brief Funct Genomics2018
29467494Alternative transcription of a shorter, non-anti-angiogenic thrombospondin-2 variant in cancer-associated blood vessels.Oncogene2018
29045713SCPortalen: human and mouse single-cell centric database.Nucleic Acids Res2018
28850106FANTOM5 CAGE profiles of human and mouse samples.Sci Data2017
30159423The essentiality of non-coding RNAs in cell reprogramming.Noncoding RNA Res2017
29206104The Human Cell Atlas.Elife2017
28829439An integrated expression atlas of miRNAs and their promoters in human and mouse.Nat Biotechnol2017
28850122Distinct transcriptional responses of lymphatic endothelial cells to VEGFR-3 and VEGFR-2 stimulation.Sci Data2017
26780608A predictive computational framework for direct reprogramming between human cell types.Nat Genet2016
27199372DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C.J Cell Sci2016
25957166Batf2/Irf1 induces inflammatory responses in classically activated macrophages, lipopolysaccharides, and mycobacterial infection.J Immunol2015
26253466Paradigm shifts in genomics through the FANTOM projects.Mamm Genome2015
26549461DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium.Cell Rep2015
24676093Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing.Genome Res2014
25013174A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation.Nucleic Acids Res2014
25049417PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease.Proc Natl Acad Sci U S A2014
24927846Repositioning monocyte TFRN into fibroblasts.Methods Mol Biol2014
24670764A promoter-level mammalian expression atlas.Nature2014
23142027Identification of ZNF395 as a novel modulator of adipogenesis.Exp Cell Res2013
24156252Temporal dynamics and transcriptional control using single-cell gene expression analysis.Genome Biol2013
22428058Reconstruction of monocyte transcriptional regulatory network accompanies monocytic functions in human fibroblasts.PLoS One2012
22797548Analysis of a novel highly metastatic melanoma cell line identifies osteopontin as a new lymphangiogenic factor.Int J Oncol2012
22879381Establishment of single-cell screening system for the rapid identification of transcriptional modulators involved in direct cell reprogramming.Nucleic Acids Res2012
22925887CpG site-specific alteration of hydroxymethylcytosine to methylcytosine beyond DNA replication.Biochem Biophys Res Commun2012
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Collaborators

Piero Carninci
RIKEN Center for Integrative Medical Sciences
Co-authored papers 21
Yoshihide Hayashizaki
Center for Integrative Medical Sciences
Co-authored papers 21
Michael Detmar
Institute of Pharmaceutical Sciences, ETH Zurich
Co-authored papers 20
Harukazu Suzuki
RIKEN Center for Integrative Medical Sciences
Co-authored papers 19
Dave S B Hoon
Saint John's Cancer Institute at Saint John's Health Center
Co-authored papers 15
Chung-Chau Hon
RIKEN center for Integrative Medical Sciences, Hiroshima University
Co-authored papers 13
Alistair R R Forrest
RIKEN Center for Integrative Medical Sciences
Co-authored papers 10
Masayoshi Itoh
RIKEN Center for Integrative Medical Sciences
Co-authored papers 10
Takeya Kasukawa
RIKEN Center for Integrative Medical Sciences
Co-authored papers 10
Hideya Kawaji
RIKEN Center for Integrative Medical Sciences
Co-authored papers 9
Akira Hasegawa
RIKEN Center for Integrative Medical Sciences
Co-authored papers 9
Marina Lizio
Cerevance Ltd
Co-authored papers 8
Imad Abugessaisa
RIKEN Center for Integrative Medical Sciences
Co-authored papers 7
Jessica Severin
Center for Integrative Medical Sciences
Co-authored papers 7
Atsutaka Kubosaki
National Institute of Health Sciences.
Co-authored papers 7
Carsten O Daub
International Institute of Molecular and Cell Biology in Warsaw
Co-authored papers 6
Erik Arner
RIKEN Center for Integrative Medical Sciences (IMS)
Co-authored papers 6
Takahiro Suzuki
RIKEN Center for Integrated Medical Science (IMS) Yokohama City Kanagawa Japan.
Co-authored papers 6
Timo Lassmann
Telethon Kids Institute, University of Western Australia
Co-authored papers 6
Michihira Tagami
RIKEN Center for Integrative Medical Sciences
Co-authored papers 6
Yuri Ishizu
RIKEN Center for Life Science Technologies
Co-authored papers 5
Jordan A Ramilowski
Advanced Medical Research Center, Yokohama City University
Co-authored papers 5
Charles Plessy
Okinawa Institute of Science and Technology
Co-authored papers 5
Mitsuyoshi Murata
Center for Integrative Medical Sciences
Co-authored papers 5
Yuki Hasegawa
Shinshu University
Co-authored papers 5
Hiromi Nishiyori
Center for Integrative Medical Sciences
Co-authored papers 5
Sachi Kato
RIKEN Center for Life Science Technologies
Co-authored papers 5
Noriko Ninomiya
Japan Tobacco Inc.
Co-authored papers 4
Alessandro Bonetti
RIKEN Center for Integrative Medical Sciences
Co-authored papers 4
Christophe Simon
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Release 1.2