TFregulomeR reveals transcription factors' context-specific features and functions

by Lin, Q.X.X., Thieffry, D., Jha, S., Benoukraf, T.
Published 2021

Whole genome DNA methylation: Beyond genes silencing

by Tirado-Magallanes, R, Rebbani, K, Lim, R, Pradhan, S, Benoukraf, T
Published 2020

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

by Jia, J, Pekowska, A, Jaeger, S, Benoukraf, T, Ferrier, P, Spicuglia, S
Published 2020

Initiation of V(D)J recombination by D?-associated recombination signal sequences: A critical control point in TCR? gene assembly

by Franchini D.-M., Benoukraf T., Jaegar S., Ferrier P., Payet-Bornet D.
Published 2019

Increased intron retention is a post-transcriptional signature associated with progressive aging and Alzheimer’s disease

by Adusumalli, S., Ngian, Z.-K., Lin, W.-Q., Benoukraf, T., Ong, C.-T.
Published 2022

GBSA: A comprehensive software for analysing whole genome bisulfite sequencing data

by Benoukraf, T., Wongphayak, S., Hadi, L.H.A., Wu, M., Soong, R.
Published 2014

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

by Lin, Quy Xiao Xuan, Sian, Stephanie, An, Omer, Thieffry, Denis, Jha, Sudhakar, Benoukraf, Touati
Published 2019

NicE-seq: high resolution open chromatin profiling

by PONNALURI, VK CHAITHANYA, ZHANG, GUOQIANG, ESTEVE, PIERRE-OLIVIER, SPRACKLIN, GEORGE, SIAN, STEPHANIE, XU, SHUANG-YONG, BENOUKRAF, TOUATI, PRADHAN, SRIHARSA
Published 2019

H3K4 tri-methylation provides an epigenetic signature of active enhancers

by Pekowska, A., Benoukraf, T., Zacarias-Cabeza, J., Belhocine, M., Koch, F., Holota, H., Imbert, J., Andrau, J.-C., Ferrier, P., Spicuglia, S.
Published 2014

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

by Abdul Hadi L.H., Xuan Lin Q.X., Minh T.T., Loh M., Ng H.K., Salim A., Soong R., Benoukraf T.
Published 2020

Acquired resistance to combination treatment through loss of synergy with MEK and PI3K inhibitors in colorectal cancer

by Bhattacharya B., Low S.H.H., Chong M.L., Chia D., Koh K.X., Sapari N.S., Kaye S., Hung H., Benoukraf T., Soong R.
Published 2020

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

by Rao, Vinay Kumar, Swarnaseetha, Adusumalli, Tham, Guo-Hong, Lin, Wei-Qi, Han, Bin-Bin, Benoukraf, Touati, Xu, Guo-Liang, Ong, Chin-Tong
Published 2022

LPS independent activation of the pro-inflammatory receptor Trem1 by C/EBP? in granulocytes

by Suh, H.C, Benoukraf, T, Shyamsunder, P, Yin, T, Cao, Q, Said, J, Lee, S, Lim, R, Yang, H, Salotti, J, Johnson, P.F, Madan, V, Koeffler, H.P
Published 2020

The gene signature in CCAAT-enhancer-binding protein α dysfunctional acute myeloid leukemia predicts responsiveness to histone deacetylase inhibitors

by Liss, A., Ooi, C.-H., Zjablovskaja, P., Benoukraf, T., Radomska, H.S., Ju, C., Wu, M., Balastik, M., Delwel, R., Brdicka, T., Tan, P., Tenen, D.G., Alberich-Jorda, M.
Published 2014

Characterisation of genome-wide PLZF/RARA target genes

by Spicuglia, S., Vincent-Fabert, C., Benoukraf, T., Tibéri, G., Saurin, A.J., Zacarias-Cabeza, J., Grimwade, D., Mills, K., Calmels, B., Bertucci, F., Sieweke, M., Ferrier, P., Duprez, E.
Published 2014

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

by Tham, C.Y., Tirado-Magallanes, R., Goh, Y., Fullwood, M.J., Koh, B.T.H., Wang, W., Ng, C.H., Chng, W.J., Thiery, A., Tenen, D.G., Benoukraf, T.
Published 2021

TIP60 represses activation of endogenous retroviral elements

by Rajagopalan, D., Tirado-Magallanes, R., Bhatia, S.S., Teo, W.S., Sian, S., Hora, S., Lee, K.K., Zhang, Y., Jadhav, S.P., Wu, Y., Gan, Y.-H., Karnani, N., Benoukraf, T., Jha, S.
Published 2021

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

by Tham, Cheng Yong, Tirado-Magallanes, Roberto, Goh, Yufen, Fullwood, Melissa Jane, Koh, Bryan T. H., Wang, Wilson, Ng, Chin Hin, Chng, Wee Joo, Thiery, Alexandre, Tenen, Daniel G., Benoukraf, Touati
Published 2021

Datasets describing the growth and molecular features of hepatocellular carcinoma patient-derived xenograft cells grown in a three-dimensional macroporous hydrogel

by Fong, E.L.S., Toh, T.B., Lin, Q.X.X., Liu, Z., Hooi, L., Rashid, M.B.M.A., Benoukraf, T., Chow, E.K.-H., Huynh, T.H., Yu, H.
Published 2021

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

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.
Published 2022