Works matching AU Abugessaisa, Imad

Results: 22

Iron regulatory pathways differentially expressed during Madurella mycetomatis grain development in Galleria mellonella.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-60875-2

By:

Abugessaisa, Imad;
Konings, Mickey;
Manabe, Ri-Ichiroh;
Murphy, Cathal M.;
Kawashima, Tsugumi;
Hasegawa, Akira;
Takahashi, Chitose;
Tagami, Michihira;
Okazaki, Yasushi;
Eadie, Kimberly;
Lim, Wilson;
Doyle, Sean;
Verbon, Annelies;
Fahal, Ahmed H.;
Kasukawa, Takeya;
van de Sande, Wendy W. J.

Publication type:

Article

The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background.

Published in:

BMC Genomic Data, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12863-021-00992-1

By:

Ducoli, Luca;
Agrawal, Saumya;
Hon, Chung-Chau;
Ramilowski, Jordan A.;
Sibler, Eliane;
Tagami, Michihira;
Itoh, Masayoshi;
Kondo, Naoto;
Abugessaisa, Imad;
Hasegawa, Akira;
Kasukawa, Takeya;
Suzuki, Harukazu;
Carninci, Piero;
Shin, Jay W.;
de Hoon, Michiel J. L.;
Detmar, Michael

Publication type:

Article

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

Published in:

GeroScience, 2024, v. 46, n. 2, p. 2063, doi. 10.1007/s11357-023-00961-9

By:

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

Publication type:

Article

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

Published in:

GeroScience, 2021, v. 43, n. 3, p. 1317, doi. 10.1007/s11357-021-00334-0

By:

Gomez-Cabrero, David;
Walter, Stefan;
Abugessaisa, Imad;
Miñambres-Herraiz, Rebeca;
Palomares, Lucia Bernad;
Butcher, Lee;
Erusalimsky, Jorge D.;
Garcia-Garcia, Francisco Jose;
Carnicero, José;
Hardman, Timothy C.;
Mischak, Harald;
Zürbig, Petra;
Hackl, Matthias;
Grillari, Johannes;
Fiorillo, Edoardo;
Cucca, Francesco;
Cesari, Matteo;
Carrie, Isabelle;
Colpo, Marco;
Bandinelli, Stefania

Publication type:

Article

Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

Published in:

2022

By:

Grapotte, Mathys;
Saraswat, Manu;
Bessière, Chloé;
Menichelli, Christophe;
Ramilowski, Jordan A.;
Severin, Jessica;
Hayashizaki, Yoshihide;
Itoh, Masayoshi;
Tagami, Michihira;
Murata, Mitsuyoshi;
Kojima-Ishiyama, Miki;
Noma, Shohei;
Noguchi, Shuhei;
Kasukawa, Takeya;
Hasegawa, Akira;
Suzuki, Harukazu;
Nishiyori-Sueki, Hiromi;
Frith, Martin C.;
FANTOM consortium;
Abugessaisa, Imad

Publication type:

Correction Notice

Accelerating Translational Research by Clinically Driven Development of an Informatics Platform–A Case Study.

Published in:

PLoS ONE, 2014, v. 9, n. 9, p. 1, doi. 10.1371/journal.pone.0104382

By:

Abugessaisa, Imad;
Saevarsdottir, Saedis;
Tsipras, Giorgos;
Lindblad, Staffan;
Sandin, Charlotta;
Nikamo, Pernilla;
Ståhle, Mona;
Malmström, Vivianne;
Klareskog, Lars;
Tegnér, Jesper

Publication type:

Article

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

Published in:

Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-018-08126-5

By:

Kouno, Tsukasa;
Moody, Jonathan;
Kwon, Andrew Tae-Jun;
Shibayama, Youtaro;
Kato, Sachi;
Huang, Yi;
Böttcher, Michael;
Motakis, Efthymios;
Mendez, Mickaël;
Severin, Jessica;
Luginbühl, Joachim;
Abugessaisa, Imad;
Hasegawa, Akira;
Takizawa, Satoshi;
Arakawa, Takahiro;
Furuno, Masaaki;
Ramalingam, Naveen;
West, Jay;
Suzuki, Harukazu;
Kasukawa, Takeya

Publication type:

Article

STATegra EMS: an Experiment Management System for complex next-generation omics experiments.

Published in:

BMC Systems Biology, 2014, v. 8, n. Suppl 2, p. 1, doi. 10.1186/1752-0509-8-S2-S9

By:

Hernández de Diego, Rafael;
Boix-Chova, Noemi;
Gómez-Cabrero, David;
Tegner, Jesper;
Abugessaisa, Imad;
Conesa, Ana

Publication type:

Article

Data integration in the era of omics: current and future challenges.

Published in:

BMC Systems Biology, 2014, v. 8, n. Suppl 2, p. 1, doi. 10.1186/1752-0509-8-S2-I1

By:

Gomez-Cabrero, David;
Abugessaisa, Imad;
Maier, Dieter;
Teschendorff, Andrew;
Merkenschlager, Matthias;
Gisel, Andreas;
Ballestar, Esteban;
Bongcam-Rudloff, Erik;
Conesa, Ana;
Tegnér, Jesper

Publication type:

Article

Systems Medicine: from molecular features and models to the clinic in COPD.

Published in:

2014

By:

Gomez-Cabrero, David;
Menche, Jörg;
Cano, Isaac;
Abugessaisa, Imad;
Huertas-Migueláñez, Mercedes;
Tenyi, Akos;
de Mas, Igor;
Kiani, Narsis A;
Marabita, Francesco;
Falciani, Francesco;
Burrowes, Kelly;
Maier, Dieter;
Wagner, Peter;
Selivanov, Vitaly;
Cascante, Marta;
Roca, Josep;
Barabási, Albert-László;
Tegnér, Jesper

Publication type:

Journal Article

Implementation of the CDC translational informatics platform - from genetic variants to the national Swedish Rheumatology Quality Register.

Published in:

Journal of Translational Medicine, 2013, v. 11, n. 1, p. 1, doi. 10.1186/1479-5876-11-85

By:

Abugessaisa, Imad;
Gomez-Cabrero, David;
Snir, Omri;
Lindblad, Staffan;
Klareskog, Lars;
Malmström, Vivianne;
Tegnér, Jesper

Publication type:

Article

Implementation of the CDC translational informatics platform--from genetic variants to the national Swedish Rheumatology Quality Register.

Published in:

2013

By:

Abugessaisa, Imad;
Gomez-Cabrero, David;
Snir, Omri;
Lindblad, Staffan;
Klareskog, Lars;
Malmström, Vivianne;
Tegnér, Jesper

Publication type:

journal article

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

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-23143-7

By:

Grapotte, Mathys;
Saraswat, Manu;
Bessière, Chloé;
Menichelli, Christophe;
Ramilowski, Jordan A.;
Severin, Jessica;
Hayashizaki, Yoshihide;
Itoh, Masayoshi;
Tagami, Michihira;
Murata, Mitsuyoshi;
Kojima-Ishiyama, Miki;
Noma, Shohei;
Noguchi, Shuhei;
Kasukawa, Takeya;
Hasegawa, Akira;
Suzuki, Harukazu;
Nishiyori-Sueki, Hiromi;
Frith, Martin C.;
FANTOM consortium;
Abugessaisa, Imad

Publication type:

Article

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki.

Published in:

Database: The Journal of Biological Databases & Curation, 2016, v. 2016, p. 1, doi. 10.1093/database/baw105

By:

Abugessaisa, Imad;
Hisashi Shimoji;
Serkan Sahin;
Atsushi Kondo;
Harshbarger, Jayson;
Lizio, Marina;
Yoshihide Hayashizaki;
Carninci, Piero;
Forrest, Alistair;
Takeya Kasukawa;
Hideya Kawaji

Publication type:

Article

Annotation of nuclear lncRNAs based on chromatin interactions.

Published in:

PLoS ONE, 2024, v. 19, n. 5, p. 1, doi. 10.1371/journal.pone.0295971

By:

Agrawal, Saumya;
Buyan, Andrey;
Severin, Jessica;
Koido, Masaru;
Alam, Tanvir;
Abugessaisa, Imad;
Chang, Howard Y.;
Dostie, Josée;
Itoh, Masayoshi;
Kere, Juha;
Kondo, Naoto;
Li, Yunjing;
Makeev, Vsevolod J.;
Mendez, Mickaël;
Okazaki, Yasushi;
Ramilowski, Jordan A.;
Sigorskikh, Andrey I.;
Strug, Lisa J.;
Yagi, Ken;
Yasuzawa, Kayoko

Publication type:

Article

Update of the FANTOM web resource: enhancement for studying noncoding genomes.

Published in:

Nucleic Acids Research, 2025, v. 53, n. D1, p. D419, doi. 10.1093/nar/gkae1047

By:

Nobusada, Tomoe;
Yip, Chi Wai;
Agrawal, Saumya;
Severin, Jessica;
Abugessaisa, Imad;
Hasegawa, Akira;
Hon, Chung Chau;
Ide, Satoru;
Koido, Masaru;
Kondo, Atsushi;
Masuya, Hiroshi;
Oki, Shinya;
Tagami, Michihira;
Takada, Toyoyuki;
Terao, Chikashi;
Thalhath, Nishad;
Walker, Scott;
Yasuzawa, Kayoko;
Shin, Jay W;
de Hoon, Michiel J L

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2019, v. 47, n. D1, p. D752, doi. 10.1093/nar/gky1099

By:

Lizio, Marina;
Abugessaisa, Imad;
Noguchi, Shuhei;
Kondo, Atsushi;
Hasegawa, Akira;
Hon, Chung Chau;
de Hoon, Michiel;
Severin, Jessica;
Oki, Shinya;
Hayashizaki, Yoshihide;
Carninci, Piero;
Kasukawa, Takeya;
Kawaji, Hideya

Publication type:

Article

SCPortalen: human and mouse single-cell centric database.

Published in:

Nucleic Acids Research, 2018, v. 46, n. D1, p. D781, doi. 10.1093/nar/gkx949

By:

Abugessaisa, Imad;
Noguchi, Shuhei;
Böttcher, Michael;
Hasegawa, Akira;
Kouno, Tsukasa;
Kato, Sachi;
Tada, Yuhki;
Ura, Hiroki;
Abe, Kuniya;
Shin, Jay W

Publication type:

Article

Laboratory biomarkers and frailty: presentation of the FRAILOMIC initiative.

Published in:

Clinical Chemistry & Laboratory Medicine, 2015, v. 53, n. 10, p. e253, doi. 10.1515/cclm-2015-0147

By:

Lippi, Giuseppe;
Jansen-Duerr, Pidder;
Viña, Jose;
Durrance-Bagale, Anna;
Abugessaisa, Imad;
Gomez-Cabrero, David;
Tegnér, Jesper;
Grillari, Johannes;
Erusalimsky, Jorge;
Sinclair, Alan;
Rodriguez-Manãs, Leocadio

Publication type:

Article

Gateways to the FANTOM5 promoter level mammalian expression atlas.

Published in:

Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s13059-014-0560-6

By:

Lizio, Marina;
Harshbarger, Jayson;
Hisashi Shimoji;
Severin, Jessica;
Takeya Kasukawa;
Sahin, Serkan;
Abugessaisa, Imad;
Shiro Fukuda;
Fumi Hori;
Sachi Ishikawa-Kato;
Mungall, Christopher J.;
Arner, Erik;
Baillie, J. Kenneth;
Bertin, Nicolas;
Hidemasa Bono;
de Hoon, Michiel;
Diehl, Alexander D.;
Dimont, Emmanuel;
Freeman, Tom C.;
Kaori Fujieda

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2017, v. 45, n. D1, p. D737, doi. 10.1093/nar/gkw995

By:

Lizio, Marina;
Harshbarger, Jayson;
Abugessaisa, Imad;
Shuei Noguchi;
Atsushi Kondo;
Severin, Jessica;
Mungall, Chris;
Arenillas, David;
Mathelier, Anthony;
Medvedeva, Yulia A.;
Lennartsson, Andreas;
Drabløs, Finn;
Ramilowski, Jordan A.;
Rackham, Owen;
Gough, Julian;
Andersson, Robin;
Sandelin, Albin;
Ienasescu, Hans;
Hiromasa Ono;
Hidemasa Bono

Publication type:

Article

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

Published in:

Nature Biotechnology, 2017, v. 35, n. 9, p. 872, doi. 10.1038/nbt.3947

By:

de Rie, Derek;
Abugessaisa, Imad;
Alam, Tanvir;
Arner, Erik;
Arner, Peter;
Ashoor, Haitham;
Åström, Gaby;
Babina, Magda;
Bertin, Nicolas;
Burroughs, A Maxwell;
Carlisle, Ailsa J;
Daub, Carsten O;
Detmar, Michael;
Deviatiiarov, Ruslan;
Fort, Alexandre;
Gebhard, Claudia;
Goldowitz, Daniel;
Guhl, Sven;
Ha, Thomas J;
Harshbarger, Jayson

Publication type:

Article