Imad Abugessaisa

Profile Information

Affiliation: Senior research scientist (Senior research scientist), RIKEN Center for Integrative Medical Sciences, RIKEN

Degree: Ph.D.(Linköping University)
M.Sc.(Linköping University)

Researcher number: 10749906
ORCID ID: https://orcid.org/0000-0001-7458-801X
J-GLOBAL ID: 201701012849904395
researchmap Member ID: B000284209

External link: http://www.ims.riken.jp/labo/64/people.html

Senior research scientist

Research Interests

Research Areas

Life sciences / Genomics /

Research History

May, 2020 - Present

(Senior research scientist), RIKEN IMS Center for Integrative Medical Sciences
Mar, 2014 - May, 2020

Associated, Department of Medicine, Solna, Karolinska Institutet
Apr, 2018 - Apr, 2020

Research scientist, RIKEN Center for Integrative Medical Sciences,
Mar, 2014 - Mar, 2018

Research scientist, RIKEN Center for Life Science Technologies, RIKEN
Mar, 2012 - Feb, 2014

Assistant prof(FOASS), Department of Medicine, Solna, Karolinska Institutet
Mar, 2010 - Feb, 2012

Postdoctoral, Department of Medicine, Solna, Karolinska Institutet
Oct, 2008 - Feb, 2010

R&D specialist, Future position X, SWEDEN
Jan, 2008 - Oct, 2008

Researcher, SICS East Swedish ICT AB

Education

Jul, 2015 - Jul, 2015

Systems Biology of Disease, Institute for Systems Biology, Seattle, USA
Mar, 2015 - Mar, 2015

Protégé, School of Medicine, Stanford University
Mar, 2010 - Feb, 2012

Postdoc, Department of Medicine, Solna, Karolinska Institutet
2012 - 2012

High performance computing for next generation sequencing, Principe Felipe Research Center, Spain
2011 - 2012

Effective leadership program, Leadership management Institute
Sep, 2003 - Jun, 2008

Ph.D., Department of Computer and Information Science, Linköpings universitet
Jan, 2004 - Oct, 2005

M.Sc., Department of Computer and Information Science, Linköpings universitet
Jan, 2000 - Dec, 2002

M.Sc., Faculty of Engineering & Technology, Gazera university, Sudan
2002 - 2002

Project/ Resource Capacity management in contract R&D Research, UNESCO
2001 - 2001

Basic Web Technology Skills for courseware Development, American University of Beirut
Apr, 1994 - Jul, 1999

B.Sc., Computer science, Future University Sudan

Papers

OVCH1 Antisense RNA 1 is differentially expressed between non-frail and frail old adults.

Imad Abugessaisa, Ri-Ichiroh Manabe, Tsugumi Kawashima, Michihira Tagami, Chitose Takahashi, Yasushi Okazaki, Stefania Bandinelli, Takeya Kasukawa, Luigi Ferrucci

GeroScience, 46(2) 2063-2081, Apr, 2024
Computational approach to evaluate scRNA-seq data quality and gene body coverage with SkewC.

Imad Abugessaisa, Akira Hasegawa, Shintaro Katayama, Juha Kere, Takeya Kasukawa

STAR protocols, 4(1) 102038-102038, Mar 17, 2023
Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7)

Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli, Jordan A. Ramilowski, Jessica Severin, Yoshihide Hayashizaki, Masayoshi Itoh, Michihira Tagami, Mitsuyoshi Murata …

Nature Communications, 13(1), Dec 1, 2022
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, Kayoko Yasuzawa, Divya M. Sivaraman, Jordan A. Ramilowski, Youtaro Shibayama, Saumya Agrawal, Anika V. Prabhu, Callum Parr, Jessica Severin …

Cell Reports, 41(13) 111893-111893, Dec, 2022
43

SkewC: Identifying cells with skewed gene body coverage in single-cell RNA sequencing data.

Imad Abugessaisa, Akira Hasegawa, Shuhei Noguchi, Melissa Cardon, Kazuhide Watanabe, Masataka Takahashi, Harukazu Suzuki, Shintaro Katayama, Juha Kere, Takeya Kasukawa

iScience, 25(2) 103777-103777, Feb 18, 2022 Peer-reviewedLead author
36

Inducing human retinal pigment epithelium-like cells from somatic tissue.

Ivo Ngundu Woogeng, Bogumil Kaczkowski, Imad Abugessaisa, Haiming Hu, Akihiro Tachibana, Yoshiki Sahara, Chung-Chau Hon, Akira Hasegawa, Noriko Sakai, Mitsuhiro Nishida …

Stem cell reports, 17(2) 289-306, Feb 8, 2022 Peer-reviewed
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli, Jordan A. Ramilowski, Jessica Severin, Yoshihide Hayashizaki, Masayoshi Itoh, Michihira Tagami, Mitsuyoshi Murata …

Nature Communications, 12(1), Dec, 2021
The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background.

Luca Ducoli, Saumya Agrawal, Chung-Chau Hon, Jordan A Ramilowski, Eliane Sibler, Michihira Tagami, Masayoshi Itoh, Naoto Kondo, Imad Abugessaisa, Akira Hasegawa …

BMC genomic data, 22(1) 33-33, Sep 14, 2021 Peer-reviewed
159

A robust machine learning framework to identify signatures for frailty: a nested case-control study in four aging European cohorts

David Gomez-Cabrero, Stefan Walter, Imad Abugessaisa, Rebeca Miñambres-Herraiz, Lucia Bernad Palomares, Lee Butcher, Jorge D. Erusalimsky, Francisco Jose Garcia-Garcia, José Carnicero, Timothy C. Hardman …

GeroScience, 43(3) 1317-1329, Feb 18, 2021 Peer-reviewed
Functional annotation of human long noncoding RNAs using chromatin conformation data

Saumya Agrawal, Tanvir Alam, Masaru Koido, Ivan V. Kulakovskiy, Jessica Severin, Imad Abugessaisa, Andrey Buyan, Josee Dostie, Masayoshi Itoh, Naoto Kondo …

Jan 14, 2021
15

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs.

Imad Abugessaisa, Jordan A Ramilowski, Marina Lizio, Jesicca Severin, Akira Hasegawa, Jayson Harshbarger, Atsushi Kondo, Shuhei Noguchi, Chi Wai Yip, Jasmine Li Ching Ooi …

Nucleic acids research, 49(D1) D892-D898, Nov 19, 2020 Peer-reviewedLead author
Single-cell transcriptomics, scRNA-Seq and C1 CAGE discovered distinct phases of pluripotency during naïve-to-primed conversion in mice

Michael Böttcher, Yuhki Tada, Jonathan Moody, Masayo Kondo, Hiroki Ura, Imad Abugessaisa, Takeya Kasukawa, Chung-Chau Hon, Koji Nagao, Piero Carninci …

Sep 25, 2020
Comparative transcriptomics of primary cells in vertebrates.

Tanvir Alam, Saumya Agrawal, Jessica Severin, Robert S Young, Robin Andersson, Erik Arner, Akira Hasegawa, Marina Lizio, Jordan A Ramilowski, Imad Abugessaisa …

Genome research, 30(7) 951-961, Jul, 2020 Peer-reviewed
Functional annotation of human long noncoding RNAs via molecular phenotyping.

Jordan A Ramilowski, Chi Wai Yip, Saumya Agrawal, Jen-Chien Chang, Yari Ciani, Ivan V Kulakovskiy, Mickaël Mendez, Jasmine Li Ching Ooi, John F Ouyang, Nick Parkinson …

Genome research, 30(7) 1060-1072, Jul, 2020 Peer-reviewed
428

refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites

Abugessaisa, I, Noguchi S, Hasegawa A, Kondo A, Kawaji H, Carninci P, Kasukawa T

Journal of Molecular Biology, 431(13) 2407-2422, Jun, 2019 Peer-reviewedLead author
376

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

Tsukasa Kouno, Jonathan Moody, Andrew Tae-Jun Kwon, Youtaro Shibayama, Sachi Kato, Yi Huang, Michael Böttcher, Efthymios Motakis, Mickaël Mendez, Jessica Severin …

Nature communications, 10(1) 360-360, Jan 21, 2019 Peer-reviewed
280

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

Marina Lizio, Imad Abugessaisa, Shuhei Noguchi, Atsushi Kondo, Akira Hasegawa, Chung Chau Hon, Michiel de Hoon, Jessica Severin, Shinya Oki, Yoshihide Hayashizaki …

Nucleic Acids Research, 47(D1) D752-D758, Nov, 2018 Peer-reviewed
Incidence and risk factors for adalimumab and infliximab anti-drug antibodies in rheumatoid arthritis: a European retrospective multicohort analysis

Jocelyn Quistrebert, Signe Hässler, Delphine Bachelet, Cyprien Mbogning, Anne Musters, Paul Peter Tak, Carla Ann Wijbrandts, Marieke Herenius, Sytske Anne Bergstra, Gülşah Akdemir …

Seminars in Arthritis and Rheumatism, 48(6) 967-975, Oct, 2018 Peer-reviewed
Transcription start site profiling of 15 anatomical regions of the Macaca mulatto central nervous system (vol 4, 170163, 2017)

Francescatto Margherita, Lizio Marina, Philippens Ingrid, Pardo Luba M, Bontrop Ronald, Sakai Mizuho, Watanabe Shoko, Itoh Masayoshi, Hasegawa Akira, Lassmann Timo …

Scientific Data, 5(1) 2-2, 2018 Peer-reviewed
Monitoring transcription initiation activities in rat and dog

Marina Lizio, Abdul Kadir Mukarram, Mizuho Ohno, Shoko Watanabe, Masayoshi Itoh, Akira Hasegawa, Timo Lassmann, Jessica Severin, Jayson Harshbarger, Imad Abugessaisa …

SCIENTIFIC DATA, 4 170173-170173, Nov, 2017 Peer-reviewed

Books and Other Publications

Single Cell Databases: An Emerging and Essential Tool

(Role: Contributor)

Jan, 2022 (ISBN: 9789811658129)
Practical Guide to Life Science Databases

(Role: Editor)

SPringer Nature, Jan, 2022 (ISBN: 9789811658129)
The FANTOM5 Computation Ecosystem: Genomic Information Hub for Promoters and Active Enhancers

Abugessaisa, Imad, Noguchi, Shuhei, Carninci, Piero, Kasukawa, Takeya (Role: Contributor, 199-217)

Springer, 2017
Genome annotation

Abugessaisa, Imad, Kasukawa, Takeya, Kawaji, Hideya, Abugessaisa, Imad, T (Role: Contributor, 107-121)

Springer, Nov, 2016
Molecular foundation of computational bioscience

Imad (Role: Contributor, 6-32)

Oxford University Press, 2014

Research Projects

Mapping the Madurella mycetomatis pathogen and host responses during and after antifungal treatment to identify prognostic therapeutic markers for mycetoma

科学研究費助成事業基盤研究(C), 基盤研究(C), 日本学術振興会, Apr, 2020 - Mar, 2023

アブケセーサイマド
MycEXomics:Development of field-friendly POC diagnostic test for the four most common causative agents of mycetoma

Global Health Innovative Technology Fund, Apr, 2020 - Sep, 2022

Profile Information

Research Interests

Research Areas

Research History

Education

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