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1.

Recombination of repeat elements generates somatic complexity in human genomes.

Pascarella, Giovanni; Hon, Chung Chau; Hashimoto, Kosuke; Busch, Annika; Luginbühl, Joachim; Parr, Callum; Hin Yip, Wing; Abe, Kazumi; Kratz, Anton; Bonetti, Alessandro; Agostini, Federico; Severin, Jessica; Murayama, Shigeo; Suzuki, Yutaka; Gustincich, Stefano; Frith, Martin; Carninci, Piero.

Cell ; 185(16): 3025-3040.e6, 2022 08 04.

Article in English | MEDLINE | ID: mdl-35882231

2.

Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs.

de Hoon, Michiel; Bonetti, Alessandro; Plessy, Charles; Ando, Yoshinari; Hon, Chung-Chau; Ishizu, Yuri; Itoh, Masayoshi; Kato, Sachi; Lin, Dongyan; Maekawa, Sho; Murata, Mitsuyoshi; Nishiyori, Hiromi; Shin, Jay W; Stolte, Jens; Suzuki, Ana Maria; Tagami, Michihira; Takahashi, Hazuki; Thongjuea, Supat; Forrest, Alistair R R; Hayashizaki, Yoshihide; Kere, Juha; Carninci, Piero.

Genome Res ; 2022 Aug 12.

Article in English | MEDLINE | ID: mdl-35961773

3.

Defining super-enhancers by highly ranked histone H4 multi-acetylation levels identifies transcription factors associated with glioblastoma stem-like properties.

Das, Nando D; Chang, Jen-Chien; Hon, Chung-Chau; Kelly, S Thomas; Ito, Shinsuke; Lizio, Marina; Kaczkowski, Bogumil; Watanabe, Hisami; Katsushima, Keisuke; Natsume, Atsushi; Koseki, Haruhiko; Kondo, Yutaka; Minoda, Aki; Umehara, Takashi.

BMC Genomics ; 24(1): 574, 2023 Sep 27.

Article in English | MEDLINE | ID: mdl-37759202

4.

Recounting the FANTOM CAGE-Associated Transcriptome.

Imada, Eddie Luidy; Sanchez, Diego Fernando; Collado-Torres, Leonardo; Wilks, Christopher; Matam, Tejasvi; Dinalankara, Wikum; Stupnikov, Aleksey; Lobo-Pereira, Francisco; Yip, Chi-Wai; Yasuzawa, Kayoko; Kondo, Naoto; Itoh, Masayoshi; Suzuki, Harukazu; Kasukawa, Takeya; Hon, Chung-Chau; de Hoon, Michiel J L; Shin, Jay W; Carninci, Piero; Jaffe, Andrew E; Leek, Jeffrey T; Favorov, Alexander; Franco, Gloria R; Langmead, Ben; Marchionni, Luigi.

Genome Res ; 30(7): 1073-1081, 2020 07.

Article in English | MEDLINE | ID: mdl-32079618

5.

SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells.

Moody, Jonathan; Kouno, Tsukasa; Chang, Jen-Chien; Ando, Yoshinari; Carninci, Piero; Shin, Jay W; Hon, Chung-Chau.

Bioinformatics ; 38(22): 5126-5128, 2022 11 15.

Article in English | MEDLINE | ID: mdl-36173306

6.

Enhancer target prediction: state-of-the-art approaches and future prospects.

Umarov, Ramzan; Hon, Chung-Chau.

Biochem Soc Trans ; 51(5): 1975-1988, 2023 10 31.

Article in English | MEDLINE | ID: mdl-37830459

7.

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

Hon, Chung-Chau; Ramilowski, Jordan A; Harshbarger, Jayson; Bertin, Nicolas; Rackham, Owen J L; Gough, Julian; Denisenko, Elena; Schmeier, Sebastian; Poulsen, Thomas M; Severin, Jessica; Lizio, Marina; Kawaji, Hideya; Kasukawa, Takeya; Itoh, Masayoshi; Burroughs, A Maxwell; Noma, Shohei; Djebali, Sarah; Alam, Tanvir; Medvedeva, Yulia A; Testa, Alison C; Lipovich, Leonard; Yip, Chi-Wai; Abugessaisa, Imad; Mendez, Mickaël; Hasegawa, Akira; Tang, Dave; Lassmann, Timo; Heutink, Peter; Babina, Magda; Wells, Christine A; Kojima, Soichi; Nakamura, Yukio; Suzuki, Harukazu; Daub, Carsten O; de Hoon, Michiel J L; Arner, Erik; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R.

Nature ; 543(7644): 199-204, 2017 03 09.

Article in English | MEDLINE | ID: mdl-28241135

8.

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

Abugessaisa, Imad; Ramilowski, Jordan A; Lizio, Marina; Severin, Jesicca; Hasegawa, Akira; Harshbarger, Jayson; Kondo, Atsushi; Noguchi, Shuhei; Yip, Chi Wai; Ooi, Jasmine Li Ching; Tagami, Michihira; Hori, Fumi; Agrawal, Saumya; Hon, Chung Chau; Cardon, Melissa; Ikeda, Shuya; Ono, Hiromasa; Bono, Hidemasa; Kato, Masaki; Hashimoto, Kosuke; Bonetti, Alessandro; Kato, Masaki; Kobayashi, Norio; Shin, Jay; de Hoon, Michiel; Hayashizaki, Yoshihide; Carninci, Piero; Kawaji, Hideya; Kasukawa, Takeya.

Nucleic Acids Res ; 49(D1): D892-D898, 2021 01 08.

Article in English | MEDLINE | ID: mdl-33211864

9.

Expanded ENCODE delivers invaluable genomic encyclopedia.

Hon, Chung-Chau; Carninci, Piero.

Nature ; 583(7818): 685-686, 2020 07.

Article in English | MEDLINE | ID: mdl-32728235

10.

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

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.

Nucleic Acids Res ; 47(D1): D752-D758, 2019 01 08.

Article in English | MEDLINE | ID: mdl-30407557

11.

Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene.

Kajihara, Daniela; Hon, Chung-Chau; Abdullah, Aimi Naim; Wosniak, João; Moretti, Ana Iochabel S; Poloni, Joice F; Bonatto, Diego; Hashimoto, Kosuke; Carninci, Piero; Laurindo, Francisco R M.

BMC Genomics ; 21(1): 766, 2020 Nov 04.

Article in English | MEDLINE | ID: mdl-33148170

12.

Exonuclease-mediated degradation of nascent RNA silences genes linked to severe malaria.

Zhang, Qingfeng; Siegel, T Nicolai; Martins, Rafael M; Wang, Fei; Cao, Jun; Gao, Qi; Cheng, Xiu; Jiang, Lubin; Hon, Chung-Chau; Scheidig-Benatar, Christine; Sakamoto, Hiroshi; Turner, Louise; Jensen, Anja T R; Claes, Aurelie; Guizetti, Julien; Malmquist, Nicholas A; Scherf, Artur.

Nature ; 513(7518): 431-5, 2014 Sep 18.

Article in English | MEDLINE | ID: mdl-25043062

13.

Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.

Janbon, Guilhem; Ormerod, Kate L; Paulet, Damien; Byrnes, Edmond J; Yadav, Vikas; Chatterjee, Gautam; Mullapudi, Nandita; Hon, Chung-Chau; Billmyre, R Blake; Brunel, François; Bahn, Yong-Sun; Chen, Weidong; Chen, Yuan; Chow, Eve W L; Coppée, Jean-Yves; Floyd-Averette, Anna; Gaillardin, Claude; Gerik, Kimberly J; Goldberg, Jonathan; Gonzalez-Hilarion, Sara; Gujja, Sharvari; Hamlin, Joyce L; Hsueh, Yen-Ping; Ianiri, Giuseppe; Jones, Steven; Kodira, Chinnappa D; Kozubowski, Lukasz; Lam, Woei; Marra, Marco; Mesner, Larry D; Mieczkowski, Piotr A; Moyrand, Frédérique; Nielsen, Kirsten; Proux, Caroline; Rossignol, Tristan; Schein, Jacqueline E; Sun, Sheng; Wollschlaeger, Carolin; Wood, Ian A; Zeng, Qiandong; Neuvéglise, Cécile; Newlon, Carol S; Perfect, John R; Lodge, Jennifer K; Idnurm, Alexander; Stajich, Jason E; Kronstad, James W; Sanyal, Kaustuv; Heitman, Joseph; Fraser, James A.

PLoS Genet ; 10(4): e1004261, 2014 Apr.

Article in English | MEDLINE | ID: mdl-24743168

14.

Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages.

Vasquez, Juan-José; Hon, Chung-Chau; Vanselow, Jens T; Schlosser, Andreas; Siegel, T Nicolai.

Nucleic Acids Res ; 42(6): 3623-37, 2014 Apr.

Article in English | MEDLINE | ID: mdl-24442674

15.

Regulation of transcription termination by glucosylated hydroxymethyluracil, base J, in Leishmania major and Trypanosoma brucei.

Reynolds, David; Cliffe, Laura; Förstner, Konrad U; Hon, Chung-Chau; Siegel, T Nicolai; Sabatini, Robert.

Nucleic Acids Res ; 42(15): 9717-29, 2014 Sep.

Article in English | MEDLINE | ID: mdl-25104019

16.

Identification of the virulence landscape essential for Entamoeba histolytica invasion of the human colon.

Thibeaux, Roman; Weber, Christian; Hon, Chung-Chau; Dillies, Marie-Agnès; Avé, Patrick; Coppée, Jean-Yves; Labruyère, Elisabeth; Guillén, Nancy.

PLoS Pathog ; 9(12): e1003824, 2013.

Article in English | MEDLINE | ID: mdl-24385905

17.

Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytica.

Hon, Chung-Chau; Weber, Christian; Sismeiro, Odile; Proux, Caroline; Koutero, Mikael; Deloger, Marc; Das, Sarbashis; Agrahari, Mridula; Dillies, Marie-Agnes; Jagla, Bernd; Coppee, Jean-Yves; Bhattacharya, Alok; Guillen, Nancy.

Nucleic Acids Res ; 41(3): 1936-52, 2013 Feb 01.

Article in English | MEDLINE | ID: mdl-23258700

18.

Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum.

Siegel, T Nicolai; Hon, Chung-Chau; Zhang, Qinfeng; Lopez-Rubio, Jose-Juan; Scheidig-Benatar, Christine; Martins, Rafael M; Sismeiro, Odile; Coppée, Jean-Yves; Scherf, Artur.

BMC Genomics ; 15: 150, 2014 Feb 22.

Article in English | MEDLINE | ID: mdl-24559473

19.

Annotation of nuclear lncRNAs based on chromatin interactions.

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; Yip, Chi Wai; Hon, Chung Chau; Hoffman, Michael M; Terao, Chikashi; Kulakovskiy, Ivan V; Kasukawa, Takeya; Shin, Jay W; Carninci, Piero; de Hoon, Michiel J L.

PLoS One ; 19(5): e0295971, 2024.

Article in English | MEDLINE | ID: mdl-38709794

20.

CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data.

Hou, Ruiyan; Hon, Chung-Chau; Huang, Yuanhua.

Nat Commun ; 14(1): 7240, 2023 11 09.

Article in English | MEDLINE | ID: mdl-37945584

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