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Jessica Severin · SciRah

Researcher profile · Semantic Scholar

Jessica Severin

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Jessica Severin — researcher profile on SciRah

h-index: 30
Works: 76
Citations: 13K

Most-cited papers

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
L. Hillier, W. Miller, E. Birney, W. Warren +171 more
2004Nature2,815 citations Open access
Semantic Scholar
A promoter-level mammalian expression atlas
A. Forrest, H. Kawaji, M. Rehli, J. Baillie +256 more
2014Nature1,977 citations Open access
Semantic Scholar
A conditional knockout resource for the genome–wide study of mouse gene function
W. Skarnes, B. Rosen, A. West, M. Koutsourakis +14 more
2011Nature1,743 citations Open access
Semantic Scholar
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.
A. Vilella, Jessica Severin, A. Ureta-Vidal, L. Heng +2 more
2009Genome Research1,254 citations Open access
Semantic Scholar
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
Gateways to the FANTOM5 promoter level mammalian expression atlas
M. Lizio, J. Harshbarger, H. Shimoji, Jessica Severin +38 more
2015Genome Biology840 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
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
Harukazu Suzuki, A. Forrest, E. van Nimwegen, Carsten O. Daub +156 more
2009Nature Genetics470 citations Open access
Semantic Scholar
Update of the FANTOM web resource: expansion to provide additional transcriptome atlases
M. Lizio, I. Abugessaisa, Shuhei Noguchi, A. Kondo +9 more
2018Nucleic Acids Res.228 citations Open access
Semantic Scholar
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan
C. Plessy, Nicolas Bertin, Hazuki Takahashi, Roberto Simone +20 more
2010Nature Methods170 citations Open access
Semantic Scholar
Interactive visualization and analysis of large-scale sequencing datasets using ZENBU
Jessica Severin, M. Lizio, J. Harshbarger, H. Kawaji +4 more
2014Nature Biotechnology168 citations
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
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
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
C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution
Tsukasa Kouno, Jonathan Moody, A. T. Kwon, Youtaro Shibayama +22 more
2018Nature Communications85 citations Open access
Semantic Scholar
FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies
I. Abugessaisa, Shuhei Noguchi, A. Hasegawa, J. Harshbarger +6 more
2017Scientific Data82 citations Open access
Semantic Scholar
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
H. Kawaji, Jessica Severin, M. Lizio, A. Forrest +8 more
2010Nucleic Acids Res.78 citations Open access
Semantic Scholar
The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
H. Kawaji, Jessica Severin, M. Lizio, Andrew M. Waterhouse +8 more
2009Genome Biology78 citations Open access
Semantic Scholar
Single-Molecule Approach to Bacterial Genomic Comparisons via Optical Mapping
Shi-Guo Zhou, Andrew C. Kile, Michael Bechner, Michael Place +12 more
2004Journal of Bacteriology71 citations Open access
Semantic Scholar
A Whole-Genome Shotgun Optical Map of Yersinia pestis Strain KIM
Shi-Guo Zhou, W. Deng, T. Anantharaman, A. Lim +20 more
2002Applied and Environmental Microbiology69 citations Open access
Semantic Scholar
Promoter architecture of mouse olfactory receptor genes.
C. Plessy, G. Pascarella, N. Bertin, A. Akalin +15 more
2012Genome Research60 citations Open access
Semantic Scholar
Whole-genome shotgun optical mapping of Rhodobacter sphaeroides strain 2.4.1 and its use for whole-genome shotgun sequence assembly.
Shi-Guo Zhou, E. Kvikstad, Andrew C. Kile, Jessica Severin +9 more
2003Genome Research53 citations Open access
Semantic Scholar
Shotgun optical mapping of the entire Leishmania major Friedlin genome.
Shi-Guo Zhou, Andrew C. Kile, E. Kvikstad, Michael Bechner +10 more
2004Molecular and biochemical parasitology (Print)46 citations
Semantic Scholar
Recombination of repeat elements generates somatic complexity in human genomes.
G. Pascarella, C. Hon, Kosuke Hashimoto, Annika Busch +13 more
2022Cell45 citations Open access
Semantic Scholar
Reconstruction of Monocyte Transcriptional Regulatory Network Accompanies Monocytic Functions in Human Fibroblasts
Takahiro Suzuki, Mika Nakano-Ikegaya, Haruka Yabukami-Okuda, M. D. de Hoon +8 more
2012PLoS ONE44 citations Open access
Semantic Scholar
eHive: An Artificial Intelligence workflow system for genomic analysis
Jessica Severin, K. Beal, A. Vilella, S. Fitzgerald +5 more
2010BMC Bioinformatics44 citations Open access
Semantic Scholar
The Transcriptional Network That Controls Growth Arrest and Macrophage Differentiation in the Human Myeloid Leukemia Cell Line THP-1
Iveta Gazova, L. Lefevre, S. Bush, S. Clohisey +8 more
2020Frontiers in Cell and Developmental 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
Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions
Margaret R. Davis, Robin Andersson, Jessica Severin, M. D. de Hoon +6 more
2014Molecular Genetics and Metabolism39 citations Open access
Semantic Scholar
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli +20 more
2020Nature Communications31 citations Open access
Semantic Scholar
Automatic matrix determination in four dye fluorescence‐based DNA sequencing
Z. Yin, Jessica Severin, Michael C. Giddings, Weian Huang +2 more
1996Electrophoresis28 citations
Semantic Scholar
Combined inhibition of XIAP and BCL2 drives maximal therapeutic efficacy in genetically diverse aggressive acute myeloid leukemia
Mari Hashimoto, Y. Saito, R. Nakagawa, Ikuko Ogahara +26 more
2021Nature Cancer24 citations
Semantic Scholar
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions
Jessica Severin, Andrew M. Waterhouse, H. Kawaji, T. Lassmann +9 more
2009Genome Biology22 citations Open access
Semantic Scholar
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications
Toshiaki Katayama, Mark D. Wilkinson, Rutger A. Vos, T. Kawashima +53 more
2011Journal of Biomedical Semantics21 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
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
Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells
A. Joshi, C. Pooley, Tom C. Freeman, A. Lennartsson +13 more
2015Journal of Leukocyte Biology18 citations Open access
Semantic Scholar
Update of the FANTOM web resource: enhancement for studying noncoding genomes
Tomoe Nobusada, Chi-Wai Yip, Saumya Agrawal, Jessica Severin +19 more
2024Nucleic Acids Research17 citations Open access
Semantic Scholar
Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types.
Chi-Wai Yip, C. Hon, K. Yasuzawa, D. Sivaraman +30 more
2022Cell Reports16 citations Open access
Semantic Scholar
Antisense oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types
Chi-Wai Yip, Chung-Chau Hon, K. Yasuzawa, D. Sivaraman +30 more
2022bioRxiv11 citations Open access
Semantic Scholar
Systematic identification of cis-interacting lncRNAs and their targets
Saumya Agrawal, I. Kulakovskiy, Jessica Severin, M. Koido +25 more
2021bioRxiv9 citations Open access
Semantic Scholar
Profiling of transcribed cis-regulatory elements in single cells
Jonathan Moody, Tsukasa Kouno, A. Suzuki, Youtaro Shibayama +11 more
2021bioRxiv9 citations Open access
Semantic Scholar
ZENBU-Reports: a graphical web-portal builder for interactive visualization and dissemination of genome-scale data
Jessica Severin, Saumya Agrawal, Jordan A. Ramilowski, Ruslan Deviatiiarov +3 more
2023NAR Genomics and Bioinformatics8 citations Open access
Semantic Scholar
Monitoring transcription initiation activities in rat and dog
M. Lizio, A. K. Mukarram, Mizuho Ohno, Shoko Watanabe +12 more
2017Scientific Data7 citations Open access
Semantic Scholar
Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system
Margherita Francescatto, M. Lizio, I. Philippens, L. Pardo +16 more
2017Scientific Data5 citations Open access
Semantic Scholar
Evidence of transcription at polyT short tandem repeats
Chloé Bessière, Manu Saraswat, Mathys Grapotte, Christophe Menichelli +11 more
2019bioRxiv4 citations Open access
Semantic Scholar
Annotation of nuclear lncRNAs based on chromatin interactions
Saumya Agrawal, A. Buyan, Jessica Severin, M. Koido +25 more
2024PLoS ONE3 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 +24 more
2 citations
Semantic Scholar
The human RNA-DNA interactome is cell type-specific and dynamic
A. Lambolez, P. Sahlén, Wenjing Kang, Xu-Feng Shu +127 more
2026bioRxiv1 citations Open access
Semantic Scholar

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