J. Severin

发表

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Colin N. Dewey, Paul E. Boardman, David D. Shteynberg, 2004, Nature.

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.

Albert J. Vilella, R. Durbin, E. Birney, 2009, Genome research.

Automatic matrix determination in four dye fluorescence‐based DNA sequencing

M. Westphall, L. M. Smith, J. Severin, 1996, Electrophoresis.

Gateways to the FANTOM5 promoter level mammalian expression atlas

Derek W Wright, T. Meehan, A. Diehl, 2015, Genome Biology.

An atlas of human long non-coding RNAs with accurate 5′ ends

Jordan A. Ramilowski, J. Gough, C. Hon, 2017, Nature.

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Jordan A. Ramilowski, Piero Carninci, Y. Hayashizaki, 2020, Nature Communications.

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Thomas J. Ha, Kelly J. Morris, Louise N. Winteringham, 2015, Science.

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

Martin S. Taylor, Denis C. Bauer, Andrew M. Waterhouse, 2009, Nature Genetics.

A conditional knockout resource for the genome-wide study of mouse gene function

J. Harrow, A. Bradley, B. Rosen, 2011, Nature.

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

Jay W. Shin, C. Hon, Piero Carninci, 2018, Nature Communications.

A Whole-Genome Shotgun Optical Map of Yersinia pestis Strain KIM

E. Dimalanta, F. Blattner, N. Perna, 2002, Applied and Environmental Microbiology.

An integrated expression atlas of miRNAs and their promoters in human and mouse

Jay W. Shin, Thomas J. Ha, Louise N. Winteringham, 2017, Nature Biotechnology.

A software system for data analysis in automated DNA sequencing.

M. Westphall, L. M. Smith, J. Severin, 1998, Genome research.

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

Andrew M. Waterhouse, Piero Carninci, Y. Hayashizaki, 2009, Genome Biology.

Additional data file 5

Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji, 2003 .

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

Carsten O. Daub, Philipp Kapranov, Thomas R. Gingeras, 2010, Nature Methods.

Functional annotation of human long noncoding RNAs using chromatin conformation data

Jay W. Shin, Jordan A. Ramilowski, C. Hon, 2021 .

Evidence of transcription at polyT short tandem repeats

Jordan A. Ramilowski, Piero Carninci, Y. Hayashizaki, 2019, bioRxiv.

Sequence-level instructions direct transcription at polyT short tandem repeats

Jordan A. Ramilowski, Piero Carninci, Y. Hayashizaki, 2019 .

Linking FANTOM5 CAGE peaks to annotations with CAGEscan

Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji, 2017, bioRxiv.

Functional annotation of human long noncoding RNAs via molecular phenotyping.

Boris Lenhard, Lusy Handoko, Piero Carninci, 2020, Genome research.

Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping

Howard Y. Chang, Martin S. Taylor, Jay W. Shin, 2020 .

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

Jay W. Shin, C. Hon, Piero Carninci, 2018, bioRxiv.

Functional annotation of human long noncoding RNAs via molecular phenotyping

Howard Y. Chang, Martin S. Taylor, Jay W. Shin, 2019, bioRxiv.

Single-Molecule Approach to Bacterial Genomic Comparisons via Optical Mapping

David C. Schwartz, Christopher Churas, Eileen T. Dimalanta, 2004, Journal of bacteriology.

Reconstruction of Monocyte Transcriptional Regulatory Network Accompanies Monocytic Functions in Human Fibroblasts

Jay W. Shin, Christophe Simon, Y. Hayashizaki, 2012, PloS one.

Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells

Piero Carninci, Y. Hayashizaki, D. Hume, 2015, Journal of leukocyte biology.

Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line

Piero Carninci, Y. Hayashizaki, Harukazu Suzuki, 2015, Front. Genet..

FANTOM5 CAGE profiles of human and mouse samples

Jay W. Shin, Thomas J. Ha, Kelly J. Morris, 2017, Scientific Data.

Comparative transcriptomics of primary cells in vertebrates

Martin S. Taylor, Jordan A. Ramilowski, Robert S. Young, 2020, Genome research.

Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions

A. Sandelin, N. Bertin, A. Forrest, 2014, Molecular genetics and metabolism.

Promoter architecture of mouse olfactory receptor genes.

J. Kawai, Piero Carninci, Y. Hayashizaki, 2012, Genome research.

Systematic identification of cis-interacting lncRNAs and their targets

Howard Y. Chang, Jay W. Shin, Jordan A. Ramilowski, 2022, bioRxiv.

Non-allelic homologous recombination of Alu and LINE-1 elements generates somatic complexity in human genomes

C. Hon, Piero Carninci, M. Frith, 2020 .

Antisense oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types

Jay W. Shin, Jordan A. Ramilowski, C. Hon, 2022, bioRxiv.

DNA Sequencing A Software System for Data Analysis in Automated

Lloyd M. Smith, M. Westphall, J. Severin, 1998 .

A promoter-level mammalian expression atlas

Cesare Furlanello, Finn Drabløs, Carsten O. Daub, 2015 .

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Martin S. Taylor, Jay W. Shin, Thomas J. Ha, 2021, Nature Communications.

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

Jay W. Shin, C. Hon, Piero Carninci, 2018, bioRxiv.

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

Robert S. Young, J. Blake, T. Meehan, 2015, PLoS biology.

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

Finn Drabløs, David J. Arenillas, Piero Carninci, 2016, Nucleic Acids Res..

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU

Yoshihide Hayashizaki, Hideya Kawaji, Marina Lizio, 2014, Nature Biotechnology.

Ensembl 2006

Andreas Prlic, Damian Smedley, Daniel Rios, 2005, Nucleic Acids Res..

Ensembl 2005

Damian Smedley, Ewan Birney, Javier Herrero, 2004, Nucleic Acids Res..

FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies

Piero Carninci, Hideya Kawaji, Shuhei Noguchi, 2017, Scientific Data.

Combined inhibition of XIAP and BCL2 drives maximal therapeutic efficacy in genetically diverse aggressive acute myeloid leukemia

Jordan A. Ramilowski, Y. Okazaki, P. Vyas, 2021, Nature Cancer.

Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji, 2017, Scientific Data.

Ensembl 2007

Andreas Prlic, Damian Smedley, Ewan Birney, 2006, Nucleic Acids Res..

eHive: An Artificial Intelligence workflow system for genomic analysis

Paul Flicek, Albert J. Vilella, Leo Gordon, 2010, BMC Bioinformatics.

The Transcriptional Network That Controls Growth Arrest and Macrophage Differentiation in the Human Myeloid Leukemia Cell Line THP-1

D. Hume, J. Severin, A. Lengeling, 2020, Frontiers in Cell and Developmental Biology.

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

Carsten O. Daub, Piero Carninci, Yoshihide Hayashizaki, 2010, Nucleic Acids Res..

Monitoring transcription initiation activities in rat and dog

Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji, 2017, Scientific Data.

Whole-genome shotgun optical mapping of Rhodobacter sphaeroides strain 2.4.1 and its use for whole-genome shotgun sequence assembly.

Jessica Severin, Samuel Kaplan, Shiguo Zhou, 2003, Genome research.

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

Akira Hasegawa, Piero Carninci, Yoshihide Hayashizaki, 2018, Nucleic Acids Res..

Explorer Promoter architecture of mouse olfactory receptor genes

J. Kawai, Piero Carninci, Y. Hayashizaki, 2017 .

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

Akira R. Kinjo, Fumikazu Konishi, Kiyoko F. Aoki-Kinoshita, 2011, J. Biomed. Semant..

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

T. Gingeras, P. Kapranov, I. Bell, 2010, Nature Methods.

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU

Y. Hayashizaki, N. Bertin, A. Forrest, 2014 .

Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping 1

Howard Y. Chang, Martin S. Taylor, Jay W. Shin, 2019 .

FANTOM5 CAGE profiles of human and mouse samples.

Jay W. Shin, Thomas J. Ha, Kelly J. Morris, 2017, Scientific data.

Linking FANTOM5 CAGE peaks to annotations with CAGEscan

Piero Carninci, Y. Hayashizaki, T. Lassmann, 2017, Scientific Data.

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

Piero Carninci, Y. Hayashizaki, K. Schroder, 2009, Genome Biology.

Edinburgh Explorer The Transcriptional Network that Controls Growth Arrest and Macrophage Differentiation in the Human Myeloid Leukemia Cell Line THP-1

D. Hume, J. Severin, A. Lengeling, 2020 .

Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line

Piero Carninci, Y. Hayashizaki, Harukazu Suzuki, 2015, Front. Genet..

Shotgun optical mapping of the entire Leishmania major Friedlin genome.

Jessica Severin, Shiguo Zhou, Kenneth Stuart, 2004, Molecular and biochemical parasitology.

Functional annotation of human long noncoding RNAs using chromatin conformation data

Jay W. Shin, Jordan A. Ramilowski, C. Hon, 2021 .

ZENBU-Reports: a graphical web-portal builder for interactive visualization and dissemination of genome-scale data

Jay W. Shin, Jordan A. Ramilowski, J. Severin, 2023, NAR genomics and bioinformatics.

Comparative transcriptomics of primary cells in vertebrates

Martin S. Taylor, Jordan A. Ramilowski, Robert S. Young, 2020, Genome Research.

Edinburgh Research Explorer The FANTOM web resource

Y. Hayashizaki, A. Forrest, H. Kawaji, 2022 .

Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types.

Jay W. Shin, Jordan A. Ramilowski, C. Hon, 2022, Cell reports.

Edinburgh Research Explorer Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions

A. Sandelin, A. Forrest, H. Kawaji, 2022 .

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

Martin S. Taylor, Denis C. Bauer, Ariel S. Schwartz, 2009, Nature Genetics.