Computational approach to evaluate scRNA-seq data quality and gene body coverage with SkewC

por Abugessaisa, Imad, Hasegawa, Akira, Katayama, Shintaro, Kere, Juha, Kasukawa, Takeya
Publicado 2023

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

por Abugessaisa, Imad, Gomez-Cabrero, David, Snir, Omri, Lindblad, Staffan, Klareskog, Lars, Malmström, Vivianne, Tegnér, Jesper
Publicado 2013

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

por Hernández-de-Diego, Rafael, Boix-Chova, Noemi, Gómez-Cabrero, David, Tegner, Jesper, Abugessaisa, Imad, Conesa, Ana
Publicado 2014

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

por Abugessaisa, Imad, Saevarsdottir, Saedis, Tsipras, Giorgos, Lindblad, Staffan, Sandin, Charlotta, Nikamo, Pernilla, Ståhle, Mona, Malmström, Vivianne, Klareskog, Lars, Tegnér, Jesper
Publicado 2014

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

por Abugessaisa, Imad, Noguchi, Shuhei, Hasegawa, Akira, Harshbarger, Jayson, Kondo, Atsushi, Lizio, Marina, Severin, Jessica, Carninci, Piero, Kawaji, Hideya, Kasukawa, Takeya
Publicado 2017

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

por Abugessaisa, Imad, Hasegawa, Akira, Noguchi, Shuhei, Cardon, Melissa, Watanabe, Kazuhide, Takahashi, Masataka, Suzuki, Harukazu, Katayama, Shintaro, Kere, Juha, Kasukawa, Takeya
Publicado 2022

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

por Gomez-Cabrero, David, Abugessaisa, Imad, Maier, Dieter, Teschendorff, Andrew, Merkenschlager, Matthias, Gisel, Andreas, Ballestar, Esteban, Bongcam-Rudloff, Erik, Conesa, Ana, Tegnér, Jesper
Publicado 2014

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki

por Abugessaisa, Imad, Shimoji, Hisashi, Sahin, Serkan, Kondo, Atsushi, Harshbarger, Jayson, Lizio, Marina, Hayashizaki, Yoshihide, Carninci, Piero, Forrest, Alistair, Kasukawa, Takeya, Kawaji, Hideya
Publicado 2016

SCPortalen: human and mouse single-cell centric database

por Abugessaisa, Imad, Noguchi, Shuhei, Böttcher, Michael, Hasegawa, Akira, Kouno, Tsukasa, Kato, Sachi, Tada, Yuhki, Ura, Hiroki, Abe, Kuniya, Shin, Jay W, Plessy, Charles, Carninci, Piero, Kasukawa, Takeya
Publicado 2018

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

por 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
Publicado 2019

Linking FANTOM5 CAGE peaks to annotations with CAGEscan

por Bertin, Nicolas, Mendez, Mickaël, Hasegawa, Akira, Lizio, Marina, Abugessaisa, Imad, Severin, Jessica, Sakai-Ohno, Mizuho, Lassmann, Timo, Kasukawa, Takeya, Kawaji, Hideya, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Carninci, Piero, Plessy, Charles
Publicado 2017

Monitoring transcription initiation activities in rat and dog

por Lizio, Marina, Mukarram, Abdul Kadir, Ohno, Mizuho, Watanabe, Shoko, Itoh, Masayoshi, Hasegawa, Akira, Lassmann, Timo, Severin, Jessica, Harshbarger, Jayson, Abugessaisa, Imad, Kasukawa, Takeya, Hon, Chung Chau, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R.R., Kawaji, Hideya
Publicado 2017

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

por 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
Publicado 2021

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

por Gomez-Cabrero, David, Menche, Jörg, Cano, Isaac, Abugessaisa, Imad, Huertas-Migueláñez, Mercedes, Tenyi, Akos, de Mas, Igor Marin, Kiani, Narsis A, Marabita, Francesco, Falciani, Francesco, Burrowes, Kelly, Maier, Dieter, Wagner, Peter, Selivanov, Vitaly, Cascante, Marta, Roca, Josep, Barabási, Albert-László, Tegnér, Jesper
Publicado 2014

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

por Francescatto, Margherita, Lizio, Marina, Philippens, Ingrid, Pardo, Luba M., Bontrop, Ronald, Sakai, Mizuho, Watanabe, Shoko, Itoh, Masayoshi, Hasegawa, Akira, Lassmann, Timo, Severin, Jessica, Harshbarger, Jayson, Abugessaisa, Imad, Kasukawa, Takeya, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Kawaji, Hideya, Rizzu, Patrizia, Heutink, Peter
Publicado 2017

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

por Francescatto, Margherita, Lizio, Marina, Philippens, Ingrid, Pardo, Luba M., Bontrop, Ronald, Sakai, Mizuho, Watanabe, Shoko, Itoh, Masayoshi, Hasegawa, Akira, Lassmann, Timo, Severin, Jessica, Harshbarger, Jayson, Abugessaisa, Imad, Kasukawa, Takeya, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Kawaji, Hideya, Rizzu, Patrizia, Heutink, Peter
Publicado 2018

Inducing human retinal pigment epithelium-like cells from somatic tissue

por Woogeng, Ivo Ngundu, Kaczkowski, Bogumil, Abugessaisa, Imad, Hu, Haiming, Tachibana, Akihiro, Sahara, Yoshiki, Hon, Chung-Chau, Hasegawa, Akira, Sakai, Noriko, Nishida, Mitsuhiro, Sanyal, Hashimita, Sho, Junki, Kajita, Keisuke, Kasukawa, Takeya, Takasato, Minoru, Carninci, Piero, Maeda, Akiko, Mandai, Michiko, Arner, Erik, Takahashi, Masayo, Kime, Cody
Publicado 2022

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

por Lizio, Marina, Harshbarger, Jayson, Abugessaisa, Imad, Noguchi, Shuei, Kondo, Atsushi, 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, Ono, Hiromasa, Bono, Hidemasa, Hayashizaki, Yoshihide, Carninci, Piero, Forrest, Alistair R.R., Kasukawa, Takeya, Kawaji, Hideya
Publicado 2017

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

por 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, Lassmann, Timo, Hon, Chung-Chau, Arner, Erik, Carninci, Piero, Plessy, Charles, Shin, Jay W.
Publicado 2019

Comparative transcriptomics of primary cells in vertebrates

por Alam, Tanvir, Agrawal, Saumya, Severin, Jessica, Young, Robert S., Andersson, Robin, Arner, Erik, Hasegawa, Akira, Lizio, Marina, Ramilowski, Jordan A., Abugessaisa, Imad, Ishizu, Yuri, Noma, Shohei, Tarui, Hiroshi, Taylor, Martin S., Lassmann, Timo, Itoh, Masayoshi, Kasukawa, Takeya, Kawaji, Hideya, Marchionni, Luigi, Sheng, Guojun, R.R. Forrest, Alistair, Khachigian, Levon M., Hayashizaki, Yoshihide, Carninci, Piero, de Hoon, Michiel J.L.
Publicado 2020