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Author Details

Carsten O Daub
International Institute of Molecular and Cell Biology in Warsaw
2002
90
42
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36631751xcore: an R package for inference of gene expression regulators.BMC Bioinformatics2023
35190730Sequence determinants of human gene regulatory elements.Nat Genet2022
34078885Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.Nat Commun2021
33863803Human White Adipose Tissue Displays Selective Insulin Resistance in the Obese State.Diabetes2021
34950881Generation of RNA sequencing libraries for transcriptome analysis of globin-rich tissues of the domestic dog.STAR Protoc2021
32170312*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments.Gigascience2020
31931856Identification and transfer of spatial transcriptomics signatures for cancer diagnosis.Breast Cancer Res2020
32718981Comparative transcriptomics of primary cells in vertebrates.Genome Res2020
32718981Comparative transcriptomics of primary cells in vertebrates.Genome Res2020
33017400Ten simple rules for annotating sequencing experiments.PLoS Comput Biol2020
32150541A putative silencer variant in a spontaneous canine model of retinitis pigmentosa.PLoS Genet2020
29325522Correction to: Relatively frequent switching of transcription start sites during cerebellar development.BMC Genomics2018
30177712Promoter Usage and Dynamics in Vascular Smooth Muscle Cells Exposed to Fibroblast Growth Factor-2 or Interleukin-1β.Sci Rep2018
30089658Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli.Open Biol2018
29494619Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.PLoS Comput Biol2018
29510665Characterization of the human RFX transcription factor family by regulatory and target gene analysis.BMC Genomics2018
29307116Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection.Cerebellum2018
29177471Long-Term Improvement in Aortic Pulse Wave Velocity After Weight Loss Can Be Predicted by White Adipose Tissue Factors.Am J Hypertens2018
27803022Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution.Diabetes2017
28241135An atlas of human long non-coding RNAs with accurate 5' ends.Nature2017
28263993Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease.PLoS Genet2017
29087374Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system.Sci Data2017
28904364Acute doses of caffeine shift nervous system cell expression profiles toward promotion of neuronal projection growth.Sci Rep2017
28829439An integrated expression atlas of miRNAs and their promoters in human and mouse.Nat Biotechnol2017
28850106FANTOM5 CAGE profiles of human and mouse samples.Sci Data2017
28927749Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes.EBioMedicine2017
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
27545890The Adipose Transcriptional Response to Insulin Is Determined by Obesity, Not Insulin Sensitivity.Cell Rep2016
25569094Telomerase reverse transcriptase regulates microRNAs.Int J Mol Sci2015
26658111Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage.PLoS One2015
26549461DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium.Cell Rep2015
26179713Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells.Sci Rep2015
26117540Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium.Nucleic Acids Res2015
25863981Transcriptome analysis of controlled and therapy-resistant childhood asthma reveals distinct gene expression profiles.J Allergy Clin Immunol2015
25885578Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response.PLoS Comput Biol2015
25655563System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions.Sci Rep2015
25678556Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.Science2015
25723102Gateways to the FANTOM5 promoter level mammalian expression atlas.Genome Biol2015
24379347Additive effects of microRNAs and transcription factors on CCL2 production in human white adipose tissue.Diabetes2014
25079787A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators.Genome Biol2014
24856929Early B cell factor 1 regulates adipocyte morphology and lipolysis in white adipose tissue.Cell Metab2014
24884663MOIRAI: a compact workflow system for CAGE analysis.BMC Bioinformatics2014
24600346NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements.Front Cell Neurosci2014
24670763An atlas of active enhancers across human cell types and tissues.Nature2014
24670764A promoter-level mammalian expression atlas.Nature2014
24669905Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines.BMC Genomics2014
24727769Interactive visualization and analysis of large-scale sequencing datasets using ZENBU.Nat Biotechnol2014
24671951High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis.Blood2014
23036959Molecular networks of DYX1C1 gene show connection to neuronal migration genes and cytoskeletal proteins.Biol Psychiatry2013
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Collaborators

Yoshihide Hayashizaki
Center for Integrative Medical Sciences
Co-authored papers 60
Piero Carninci
RIKEN Center for Integrative Medical Sciences
Co-authored papers 46
Alistair R R Forrest
RIKEN Center for Integrative Medical Sciences
Co-authored papers 37
Hideya Kawaji
RIKEN Center for Integrative Medical Sciences
Co-authored papers 36
Timo Lassmann
Telethon Kids Institute, University of Western Australia
Co-authored papers 35
Erik Arner
RIKEN Center for Integrative Medical Sciences (IMS)
Co-authored papers 29
Harukazu Suzuki
RIKEN Center for Integrative Medical Sciences
Co-authored papers 25
Masayoshi Itoh
RIKEN Center for Integrative Medical Sciences
Co-authored papers 24
Jun Kawai
RIKEN Center for Integrative Medical Sciences
Co-authored papers 20
Dave S B Hoon
Saint John's Cancer Institute at Saint John's Health Center
Co-authored papers 18
Jessica Severin
Center for Integrative Medical Sciences
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Marina Lizio
Cerevance Ltd
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David A Hume
Mater Research Institute-UQ, Translational Research Institute
Co-authored papers 13
Nicolas Bertin
University Bordeaux, CNRS
Co-authored papers 13
Geoffrey J Faulkner
Mater Research Institute - University of Queensland
Co-authored papers 13
Albin Sandelin
University of Copenhagen
Co-authored papers 11
Peter Arner
Karolinska Institutet at Karolinska Hospital-Huddinge
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Takeya Kasukawa
RIKEN Center for Integrative Medical Sciences
Co-authored papers 9
Takahiro Arakawa
Tokyo University of Technology
Co-authored papers 9
Michael Rehli
University Hospital Regensburg
Co-authored papers 9
Niklas Mejhert
Karolinska Institutet
Co-authored papers 9
Christine A Wells
The University of Melbourne
Co-authored papers 9
Peter Heutink
German Center for Neurodegenerative Diseases (DZNE).
Co-authored papers 8
Mariko Okada-Hatakeyama
Institute for Protein Research, Osaka University
Co-authored papers 8
Alexander Maxwell Burroughs
National Center for Biotechnology Information, National Institutes of Health
Co-authored papers 8
Shintaro Katayama
Folkhalsan Research Center
Co-authored papers 8
Juha Kere
Folkhalsan Research Center, University of Helsinki
Co-authored papers 8
Morana Vitezic
University of Copenhagen
Co-authored papers 8
Jayson Harshbarger
RIKEN Center for Integrative Medical Sciences
Co-authored papers 8
Miki Kojima
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Release 1.2