Works by Benoukraf, Touati

Results: 31

Second-order threat conditioning in the amygdala-posterior piriform cortex network.

Published in:

Communications Biology, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42003-025-08287-2

By:

Sepahvand, Tayebeh;
Qin, Tian;
Hasan, Zia;
Power, Kyron D.;
Carew, Samantha J.;
Nazari, Negar;
Janes, Alyssa M.;
Salman, Ali;
Xia, Yue;
Benoukraf, Touati;
Yuan, Qi

Publication type:

Article

Pasha: a versatile R package for piling chromatin HTS data.

Published in:

Bioinformatics, 2016, v. 32, n. 16, p. 2528, doi. 10.1093/bioinformatics/btw206

By:

Fenouil, Romain;
Descostes, Nicolas;
Spinelli, Lionel;
Koch, Frederic;
Maqbool, Muhammad Ahmad;
Benoukraf, Touati;
Cauchy, Pierre;
Innocenti, Charlène;
Ferrier, Pierre;
Andrau, Jean-Christophe

Publication type:

Article

CoCAS: a ChIP-on-chip analysis suite.

Published in:

Bioinformatics, 2009, v. 25, n. 7, p. 954, doi. 10.1093/bioinformatics/btp075

By:

Benoukraf, Touati;
Cauchy, Pierre;
Fenouil, Romain;
Jeanniard, Adrien;
Koch, Frederic;
Jaeger, Sébastien;
Thieffry, Denis;
Imbert, Jean;
Andrau, Jean-Christophe;
Spicuglia, Salvatore;
Ferrier, Pierre

Publication type:

Article

Leveraging the MethMotif Toolkit to Characterize Context‐Specific Features and Roles of Methylation Sensitive Transcription Factors.

Published in:

Current Protocols, 2025, v. 5, n. 4, p. 1, doi. 10.1002/cpz1.70129

By:

Dyer, Matthew;
Siu, Gastongay;
Thieffry, Denis;
Benoukraf, Touati

Publication type:

Article

NanoVar: accurate characterization of patients' genomic structural variants using low-depth nanopore sequencing.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-01968-7

By:

Tham, Cheng Yong;
Tirado-Magallanes, Roberto;
Goh, Yufen;
Fullwood, Melissa J.;
Koh, Bryan T.H.;
Wang, Wilson;
Ng, Chin Hin;
Chng, Wee Joo;
Thiery, Alexandre;
Tenen, Daniel G.;
Benoukraf, Touati

Publication type:

Article

Transposon mutagenesis identifies genes driving hepatocellular carcinoma in a chronic hepatitis B mouse model.

Published in:

Nature Genetics, 2014, v. 46, n. 1, p. 24, doi. 10.1038/ng.2847

By:

Bard-Chapeau, Emilie A;
Nguyen, Anh-Tuan;
Rust, Alistair G;
Sayadi, Ahmed;
Lee, Philip;
Chua, Belinda Q;
New, Lee-Sun;
de Jong, Johann;
Ward, Jerrold M;
Chin, Christopher K Y;
Chew, Valerie;
Toh, Han Chong;
Abastado, Jean-Pierre;
Benoukraf, Touati;
Soong, Richie;
Bard, Frederic A;
Dupuy, Adam J;
Johnson, Randy L;
Radda, George K;
Chan, Eric Chun Yong

Publication type:

Article

Correspondence on NanoVar's performance outlined by Jiang T. et al. in "Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation".

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05484-w

By:

Tham, Cheng Yong;
Benoukraf, Touati

Publication type:

Article

Additional Cover.

Published in:

Aging Cell, 2025, v. 24, n. 3, p. 1, doi. 10.1111/acel.70046

By:

Singh, Akash Kumar;
Joshi, Ila;
Reddy, Neeharika M. N.;
Purushotham, Sushmitha S.;
Eswaramoorthy, M.;
Vasudevan, Madavan;
Banerjee, Sourav;
Clement, James P.;
Kundu, Tapas K.;
Omoluabi, Tamunotonye;
Hasan, Zia;
Piche, Jessie E.;
Flynn, Abeni R. S.;
Doré, Jules J. E.;
Walling, Susan G.;
Weeks, Andrew C. W.;
Benoukraf, Touati;
Yuan, Qi

Publication type:

Article

Locus coeruleus vulnerability to tau hyperphosphorylation in a rat model.

Published in:

Aging Cell, 2025, v. 24, n. 3, p. 1, doi. 10.1111/acel.14405

By:

Omoluabi, Tamunotonye;
Hasan, Zia;
Piche, Jessie E.;
Flynn, Abeni R. S.;
Doré, Jules J. E.;
Walling, Susan G.;
Weeks, Andrew C. W.;
Benoukraf, Touati;
Yuan, Qi

Publication type:

Article

Characterisation of Genome-Wide PLZF/RARA Target Genes.

Published in:

PLoS ONE, 2011, v. 6, n. 9, p. 1, doi. 10.1371/journal.pone.0024176

By:

Spicuglia, Salvatore;
Vincent-Fabert, Christelle;
Benoukraf, Touati;
Tibéri, Guillaume;
Saurin, Andrew J.;
Zacarias-Cabeza, Joaquin;
Grimwade, David;
Mills, Ken;
Calmels, Boris;
Bertucci, François;
Sieweke, Michael;
Ferrier, Pierre;
Duprez, Estelle

Publication type:

Article

Initiation of V(D)J Recombination by Dβ-Associated Recombination Signal Sequences: A Critical Control Point in TCRβ Gene Assembly.

Published in:

PLoS ONE, 2009, v. 4, n. 2, p. 1, doi. 10.1371/journal.pone.0004575

By:

Franchini, Don-Marc;
Benoukraf, Touati;
Jaeger, Sébastien;
Ferrier, Pierre;
Payet-Bornet, Dominique

Publication type:

Article

Wanted DEAD/H or Alive: Helicases Winding Up in Cancers.

Published in:

2017

By:

Wanpei Cai;
Zhi Xiong Chen;
Rane, Grishma;
Singh, Shikha Satendra;
Zhang'e Choo;
Chao Wang;
Yi Yuan;
Tuan Zea Tan;
Arfuso, Frank;
Yap, Celestial T.;
Pongor, Lorinc S.;
Henry Yang;
Lee, Martin B.;
Boon Cher Goh;
Sethi, Gautam;
Benoukraf, Touati;
Tergaonkar, Vinay;
Kumar, Alan Prem;
Cai, Wanpei;
Xiong Chen, Zhi

Publication type:

journal article

LPS independent activation of the pro-inflammatory receptor Trem1 by C/EBPε in granulocytes.

Published in:

Scientific Reports, 2017, p. 46440, doi. 10.1038/srep46440

By:

Suh, Hyung C.;
Benoukraf, Touati;
Shyamsunder, Pavithra;
Yin, Tong;
Cao, Qi;
Said, Jonathan;
Lee, Stephen;
Lim, Ricky;
Yang, Henry;
Salotti, Jacqueline;
Johnson, Peter F.;
Madan, Vikas;
Koeffler, H. Phillip

Publication type:

Article

The basic helix-loop-helix transcription factor SHARP1 is an oncogenic driver in MLL-AF6 acute myelogenous leukemia.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-03854-0

By:

Akihiko Numata;
Hui Si Kwok;
Akira Kawasaki;
Jia Li;
Qi-Ling Zhou;
Kerry, Jon;
Touati Benoukraf;
Bararia, Deepak;
Feng Li;
Ballabio, Erica;
Tapia, Marta;
Deshpande, Aniruddha J.;
Welner, Robert S.;
Delwel, Ruud;
Yang, Henry;
Milne, Thomas A.;
Taneja, Reshma;
Tenen, Daniel G.

Publication type:

Article

Methodological aspects of whole-genome bisulfite sequencing analysis.

Published in:

Briefings in Bioinformatics, 2015, v. 16, n. 3, p. 369, doi. 10.1093/bib/bbu016

By:

Adusumalli, Swarnaseetha;
Omar, Mohd Feroz Mohd;
Soong, Richie;
Benoukraf, Touati

Publication type:

Article

ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-020-20282-1

By:

Zhou, Qiling;
Yu, Miao;
Tirado-Magallanes, Roberto;
Li, Bin;
Kong, Lingshi;
Guo, Mingrui;
Tan, Zi Hui;
Lee, Sanghoon;
Chai, Li;
Numata, Akihiko;
Benoukraf, Touati;
Fullwood, Melissa Jane;
Osato, Motomi;
Ren, Bing;
Tenen, Daniel G.

Publication type:

Article

miREM: an expectation-maximization approach for prioritizing miRNAs associated with gene-set.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2292-1

By:

Abdul Hadi, Luqman Hakim;
Quy Xiao Xuan Lin;
Tri Tran Minh;
Loh, Marie;
Ng, Hong Kiat;
Salim, Agus;
Soong, Richie;
Benoukraf, Touati

Publication type:

Article

Assessing the efficiency and significance of Methylated DNA Immunoprecipitation (MeDIP) assays in using in vitro methylated genomic DNA.

Published in:

BMC Research Notes, 2010, v. 3, p. 240, doi. 10.1186/1756-0500-3-240

By:

Jia, Jinsong;
Pekowska, Aleksandra;
Jaeger, Sebastien;
Benoukraf, Touati;
Ferrier, Pierre;
Spicuglia, Salvatore

Publication type:

Article

Feasibility of Low-Throughput Next Generation Sequencing for Germline DNA Screening.

Published in:

Clinical Chemistry, 2014, v. 60, n. 12, p. 1549, doi. 10.1373/clinchem.2014.227728

By:

Sapari, Nur Sabrina;
Elahi, Eiram;
Mengchu Wu;
Loh, Marie;
Hong Kiat Ng;
Xiao Han;
Hui Ling Yap;
Klemm, Thomas P.;
Pang, Brendan;
Benoukraf, Touati;
Yik Ying Teo;
Iacopetta, Barry;
Soo Chin Lee;
Soong, Richie

Publication type:

Article

PU.1-c-Jun interaction is crucial for PU.1 function in myeloid development.

Published in:

Communications Biology, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s42003-022-03888-7

By:

Zhao, Xinhui;
Bartholdy, Boris;
Yamamoto, Yukiya;
Evans, Erica K.;
Alberich-Jordà, Meritxell;
Staber, Philipp B.;
Benoukraf, Touati;
Zhang, Pu;
Zhang, Junyan;
Trinh, Bon Q.;
Crispino, John D.;
Hoang, Trang;
Bassal, Mahmoud A.;
Tenen, Daniel G.

Publication type:

Article

MethMotif.Org 2024: a database integrating context-specific transcription factor-binding motifs with DNA methylation patterns.

Published in:

Nucleic Acids Research, 2024, v. 52, n. D1, p. D222, doi. 10.1093/nar/gkad894

By:

Dyer, Matthew;
Lin, Quy Xiao Xuan;
Shapoval, Sofiia;
Thieffry, Denis;
Benoukraf, Touati

Publication type:

Article

Phosphorylation of Tet3 by cdk5 is critical for robust activation of BRN2 during neuronal differentiation.

Published in:

Nucleic Acids Research, 2020, v. 48, n. 3, p. 1225, doi. 10.1093/nar/gkz1144

By:

Rao, Vinay Kumar;
Swarnaseetha, Adusumalli;
Tham, Guo-Hong;
Lin, Wei-Qi;
Han, Bin-Bin;
Benoukraf, Touati;
Xu, Guo-Liang;
Ong, Chin-Tong

Publication type:

Article

TFregulomeR reveals transcription factors' context-specific features and functions.

Published in:

Nucleic Acids Research, 2020, v. 48, n. 2, p. e10, doi. 10.1093/nar/gkz1088

By:

Lin, Quy Xiao Xuan;
Thieffry, Denis;
Jha, Sudhakar;
Benoukraf, Touati

Publication type:

Article

MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles.

Published in:

Nucleic Acids Research, 2019, v. 47, n. D1, p. D145, doi. 10.1093/nar/gky1005

By:

Xuan Lin, Quy Xiao;
Sian, Stephanie;
An, Omer;
Thieffry, Denis;
Jha, Sudhakar;
Benoukraf, Touati

Publication type:

Article

Disruption of the C/EBPα-miR-182 Balance Impairs Granulocytic Differentiation.

Published in:

Nature Communications, 2017, v. 8, n. 6, p. 1, doi. 10.1038/s41467-017-00032-6

By:

Wurm, Alexander Arthur;
Zjablovskaja, Polina;
Kardosova, Miroslava;
Gerloff, Dennis;
Bräuer-Hartmann, Daniela;
Katzerke, Christiane;
Hartmann, Jens-Uwe;
Benoukraf, Touati;
Fricke, Stephan;
Hilger, Nadja;
Müller, Anne-Marie;
Bill, Marius;
Schwind, Sebastian;
Tenen, Daniel G.;
Niederwieser, Dietger;
Alberich-Jorda, Meritxell;
Behre, Gerhard

Publication type:

Article

ColocZStats: a z-stack signal colocalization extension tool for 3D slicer.

Published in:

Frontiers in Physiology, 2024, p. 1, doi. 10.3389/fphys.2024.1440099

By:

Xiang Chen;
Thakur, Teena;
Jeyasekharan, Anand D.;
Benoukraf, Touati;
Meruvia-Pastor, Oscar

Publication type:

Article

NicE-seq: high resolution open chromatin profiling.

Published in:

Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1247-6

By:

Ponnaluri, V. K. Chaithanya;
Guoqiang Zhang;
Estève, Pierre-Olivier;
Spracklin, George;
Sian, Stephanie;
Shuang-yong Xu;
Benoukraf, Touati;
Pradhan, Sriharsa

Publication type:

Article

DNMT1-interacting RNAs block gene-specific DNA methylation.

Published in:

Nature, 2013, v. 503, n. 7476, p. 371, doi. 10.1038/nature12598

By:

Di Ruscio, Annalisa;
Ebralidze, Alexander K.;
Benoukraf, Touati;
Amabile, Giovanni;
Goff, Loyal A.;
Terragni, Jolyon;
Figueroa, Maria Eugenia;
De Figueiredo Pontes, Lorena Lobo;
Alberich-Jorda, Meritxell;
Zhang, Pu;
Wu, Mengchu;
D'Alò, Francesco;
Melnick, Ari;
Leone, Giuseppe;
Ebralidze, Konstantin K.;
Pradhan, Sriharsa;
Rinn, John L.;
Tenen, Daniel G.

Publication type:

Article

Increased intron retention is a post‐transcriptional signature associated with progressive aging and Alzheimer's disease.

Published in:

Aging Cell, 2019, v. 18, n. 3, p. 1, doi. 10.1111/acel.12928

By:

Adusumalli, Swarnaseetha;
Ngian, Zhen‐Kai;
Lin, Wei‐Qi;
Benoukraf, Touati;
Ong, Chin‐Tong

Publication type:

Article

GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data.

Published in:

Nucleic Acids Research, 2013, v. 41, n. 4, p. e55, doi. 10.1093/nar/gks1281

By:

Benoukraf, Touati;
Wongphayak, Sarawut;
Hadi, Luqman Hakim Abdul;
Wu, Mengchu;
Soong, Richie

Publication type:

Article

H3K4 tri-methylation provides an epigenetic signature of active enhancers.

Published in:

EMBO Journal, 2011, v. 30, n. 20, p. 4198, doi. 10.1038/emboj.2011.295

By:

Pekowska, Aleksandra;
Benoukraf, Touati;
Zacarias-Cabeza, Joaquin;
Belhocine, Mohamed;
Koch, Frederic;
Holota, Hélène;
Imbert, Jean;
Andrau, Jean-Christophe;
Ferrier, Pierre;
Spicuglia, Salvatore

Publication type:

Article