2020
Tham CY, Tirado-Magallanes R, Goh Y, Fullwood MJ, Koh BTH, Wang W, Ng CH, Chng WJ, Thiery A, Tenen DG, Benoukraf T. NanoVar: Accurate Characterization of Patients’ Genomic Structural Variants Using Low-Depth Nanopore Sequencing. . Genome Biol 21, 56 (2020). https://doi.org/10.1186/s13059-020-01968-7
2019
Rao VK, Swarnaseetha A, Tham GH, Lin WQ , Han BB , Benoukraf T , Xu GL, Ong CT. Phosphorylation of Tet3 by cdk5 is critical for robust activation of BRN2 during neuronal differentiation. Nucleic Acids Res. 2019 Dec. doi: 10.1093/nar/gkz1144. PMID: 31807777
Lin QXX, Thieffry D, Jha S, Benoukraf T. TFregulomeR reveals transcription factors’ context-specific features and functions. Nucleic Acids Res. 2019 Nov. doi: 10.1093/nar/gkz1088. PMID: 31754708
Tham CY, Tirado-Magallanes R, Goh Y, Fullwood MJ, Koh BTH, Wang W, Ng CH, Chng WJ, Thiery A, Tenen DG, Benoukraf T. NanoVar: Accurate Characterization of Patients’ Genomic Structural Variants Using Low-Depth Nanopore Sequencing. bioRxiv 662940; doi: 10.1101/662940 (Preprint).
Lin QXX, Rebbani K, Jha S, Benoukraf T. ZBTB33 (Kaiso) methylated binding sites are associated with primed heterochromatin. bioRxiv 585653; doi: 10.1101/585653 (Preprint).
Adusumalli S, Ngian ZK, Lin WQ, Benoukraf T#, Ong CT#. Increased intron retention is a post-transcriptional signature associated with progressive aging and Alzheimer’s disease. Aging Cell. 2019 Mar 13:e12928. doi: 10.1111/acel.12928. PMID: 30868713.
Lin QXX, Sian S, An O, Thieffry D, Jha S, Benoukraf T. MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles. Nucleic Acids Res. 2019 Jan 8;47(D1):D145-D154. doi: 10.1093/nar/gky1005. PMID: 30380113.
2018
Abdul Hadi LH, Lin QXX, Minh TT, Loh M, Ng HK, Salim A, Soong R, Benoukraf T. miREM: an expectation-maximization approach for prioritizing miRNAs associated with gene-set. BMC Bioinformatics. 2018 Aug 10;19(1):299. doi:10.1186/s12859-018-2292-1.PMID: 30097004.
Rajagopalan D, Tirado-Magallanes R, Bhatia SS, Teo WS, Sian S, Hora S, Lee KK, Zhang Y, Jadhav SP, Wu Y, Gan YH, Karnani N, Benoukraf T, Jha S. TIP60 represses activation of endogenous retroviral elements. Nucleic Acids Res. 2018 Jul 24. doi: 10.1093/nar/gky659. PMID: 30053221.
Fong ELS, Toh TB, Lin QXX, Liu Z, Hooi L, Rashid MBMA, Benoukraf T, Chow EK, Huynh TH, Yu H. Datasets describing the growth and molecular features of hepatocellular carcinoma patient-derived xenograft cells grown in a three-dimensional macroporous hydrogel. Data Brief. 2018 Mar 17;18:594-606. doi: 10.1016/j.dib.2018.03.045. eCollection 2018 Jun. PMID: 29900213.
Saei A, Palafox M, Benoukraf T, Kumari N, Jaynes PW, Iyengar PV, Muñoz-Couselo E, Nuciforo P, Cortés J, Nötzel C, Kumarakulasinghe NB, Richard JLC, Bin Adam Isa ZF, Pang B, Guzman M, Siqin Z, Yang H, Tam WL, Serra V, Eichhorn PJA. Loss of USP28-mediated BRAF degradation drives resistance to RAF cancer therapies. J Exp Med. 2018 Jul 2;215(7):1913-1928. doi: 10.1084/jem.20171960. Epub 2018 Jun 7. PMID: 29880484.
Numata A, Kwok HS, Kawasaki A, Li J, Zhou QL, Kerry J, Benoukraf T, Bararia D, Li F, Ballabio E, Tapia M, Deshpande AJ, Welner RS, Delwel R, Yang H, Milne TA, Taneja R, Tenen DG. The basic helix-loop-helix transcription factor SHARP1 is an oncogenic driver in MLL-AF6 acute myelogenous leukemia . Nat Commun. 2018 Apr
24;9(1):1622. doi: 10.1038/s41467-018-03854-0. PMID: 29692408.
Fong ELS, Toh TB, Lin QXX, Liu Z, Hooi L, Mohd Abdul Rashid MB, Benoukraf T, Chow EK, Huynh TH, Yu H. Generation of matched patient-derived xenograft in vitro-in vivo models using 3D macroporous hydrogels for the study of liver cancer. Biomaterials. 2018 Mar;159:229-240. doi: 10.1016/j.biomaterials.2017.12.026. Epub 2018 Jan 4. PMID: 29353739.
2017
Wurm AA, Zjablovskaja P, Kardosova M, Gerloff D, Bräuer-Hartmann D, Katzerke C, Hartmann JU, Benoukraf T, Fricke S, Hilger N, Müller AM, Bill M, Schwind S, Tenen DG, Niederwieser D, Alberich-Jorda M, Behre G. Disruption of the C/EBPα-miR-182 balance impairs granulocytic differentiation. Nat Commun. 2017 Jun 29;8(1):46. doi: 10.1038/s41467-017-00032-6. PMID: 28663557
Ponnaluri VKC, Zhang G, Estève PO, Spracklin G, Sian S, Xu SY, Benoukraf T, Pradhan S. NicE-seq: high-resolution open chromatin profiling. Genome Biol. 2017 Jun 28;18(1):122. doi: 10.1186/s13059-017-1247-6. PMID: 28655330
Suh HC, Benoukraf T, Shyamsunder P, Yin T, Cao Q, Said J, Lee S, Lim R, Yang H, Salotti J, Johnson PF, Madan V, Koeffler HP. LPS independent activation of the pro-inflammatory receptor Trem1 by C/EBPε in granulocytes. Sci Rep. 2017 Apr 25;7:46440. doi: 10.1038/srep46440. PMID: 28440307
Zjablovskaja P, Kardosova M, Danek P, Angelisova P, Benoukraf T, Wurm AA, Kalina T, Sian S, Balastik M, Delwel R, Brdicka T, Tenen DG, Behre G, Fiore F, Malissen B, Horejsi V, Alberich-Jorda M. EVI2B is a C/EBPα target gene required for granulocytic differentiation and functionality of hematopoietic progenitors. Cell Death Differ. 2017 Apr;24(4):705-716. doi: 10.1038/cdd.2017.6. Epub 2017 Feb 10. PMID: 28186500
Cai W, Chen ZX, Rane G, Singh SS, Choo Z, Wang C, Yuan Y, Tan TZ, Arfuso F, Yap CT, Pongor LS, Yang H, Lee MB, Goh BC, Sethi G, Benoukraf T, Tergaonkar V, Kumar AP. Wanted DEAD/H or Alive: Helicases Winding Up in Cancers. J Natl Cancer Inst. 2017 Jan 25;109(6). pii: djw278. doi: 10.1093/jnci/djw278. Print 2017 Jan. PMID: 28122908.
Tirado-Magallanes R, Rebbani K, Lim R, Pradhan S, Benoukraf T. Whole genome DNA methylation: beyond genes silencing. Oncotarget. 2017 Jan 17;8(3):5629-5637. doi: 10.18632/oncotarget.13562. PMID: 27895318 
2016
Fenouil R, Descostes N, Spinelli L, Koch F, Maqbool MA, Benoukraf T, Cauchy P, Innocenti C, Ferrier P, Andrau JC. Pasha : a versatile R package for piling chromatin HTS data. Bioinformatics. 2016; 32 (16): 2528-2530. doi: 10.1093/bioinformatics/btw206. PMID: 27153642.
Bhattacharya B, Hui Low SH, Chong ML, Chia D, Koh KX, Sapari NS, Kaye S, Hung H, Benoukraf T, Soong R. Acquired resistance to combination treatment through loss of synergy with MEK and PI3K inhibitors in colorectal cancer. Oncotarget. 2016 Apr 11. doi: 10.18632/oncotarget.8692. PMID: 27081080.
2015
Adusumalli S, Mohd Omar MF, Soong R, Benoukraf T. Methodological aspects of whole-genome bisulfite sequencing analysis. Brief Bioinform. 2015 May;16(3):369-79. PMID: 24867940.
2014
Sapari NS1, Elahi E1, Wu M1, Loh M2, Ng HK1, Han X1, Yap HL3, Klemm TP4, Pang B5, Benoukraf T1, Teo YY6, Iacopetta B7, Lee SC3, Soong R8.
Feasibility of low-throughput next generation sequencing for germline DNA screening. Clin Chem. 2014 Dec;60(12):1549-57. PMID:
25338684.
[PubMed] [Read by QxMD]
Next generation sequencing (NGS) promises many benefits for clinical diagnostics. However, current barriers to its adoption include suboptimal amenability for low clinical throughputs and uncertainty over data accuracy and analytical procedures. We assessed the feasibility and performance of low-throughput NGS for detecting germline mutations for Lynch syndrome (LS). [...]
Bard-Chapeau EA1, Nguyen AT1, Rust AG2, Sayadi A1, Lee P3, Chua BQ1, New LS4, de Jong J5, Ward JM1, Chin CK1, Chew V6, Toh HC7, Abastado JP6, Benoukraf T8, Soong R8, Bard FA1, Dupuy AJ9, Johnson RL10, Radda GK3, Chan EC4, Wessels LF5, Adams DJ2, Jenkins NA#1, Copeland NG#1.
Transposon mutagenesis identifies genes driving hepatocellular carcinoma in a chronic hepatitis B mouse model. Nat Genet. 2014 Jan;46(1):24-32. PMID:
24316982.
[PubMed] [Read by QxMD]
The most common risk factor for developing hepatocellular carcinoma (HCC) is chronic infection with hepatitis B virus (HBV). To better understand the evolutionary forces driving HCC, we performed a near-saturating transposon mutagenesis screen in a mouse HBV model of HCC. This screen identified 21 candidate early stage drivers and a very large number (2,860) of candidate later stage drivers that were enriched for genes that are mutated, deregulat [...]
Liss A1, Ooi CH, Zjablovskaja P, Benoukraf T, Radomska HS, Ju C, Wu M, Balastik M, Delwel R, Brdicka T, Tan P, Tenen DG, Alberich-Jorda M.
The gene signature in CCAAT-enhancer-binding protein α dysfunctional acute myeloid leukemia predicts responsiveness to histone deacetylase inhibitors. Haematologica. 2014 Apr;99(4):697-705. PMID:
24162792.
[PubMed] [Read by QxMD]
C/EPBα proteins, encoded by the CCAAT-enhancer-binding protein α gene, play a crucial role in granulocytic development, and defects in this transcription factor have been reported in acute myeloid leukemia. Here, we defined the C/EBPα signature characterized by a set of genes up-regulated upon C/EBPα activation. We analyzed expression of the C/EBPα signature in a cohort of 525 patients with acute myeloid leukemia and identified a subset char [...]
2013
Di Ruscio A1, Ebralidze AK, Benoukraf T, Amabile G, Goff LA, Terragni J, Figueroa ME, De Figueiredo Pontes LL, Alberich-Jorda M, Zhang P, Wu M, D'Alò F, Melnick A, Leone G, Ebralidze KK, Pradhan S, Rinn JL, Tenen DG.
DNMT1-interacting RNAs block gene-specific DNA methylation. Nature. 2013 Nov 21;503(7476):371-6. PMID:
24107992.
[PubMed] [Read by QxMD]
DNA methylation was first described almost a century ago; however, the rules governing its establishment and maintenance remain elusive. Here we present data demonstrating that active transcription regulates levels of genomic methylation. We identify a novel RNA arising from the CEBPA gene locus that is critical in regulating the local DNA methylation profile. This RNA binds to DNMT1 and prevents CEBPA gene locus methylation. Deep sequencing of t [...]
Welner RS1, Bararia D, Amabile G, Czibere A, Benoukraf T, Bach C, Wansa KD, Ye M, Zhang H, Iino T, Hetherington CJ, Akashi K, Tenen DG.
C/EBPα is required for development of dendritic cell progenitors. Blood. 2013 May 16;121(20):4073-81. PMID:
23547051.
[PubMed] [Read by QxMD]
Dendritic cells (DCs) are master regulators of the immune system, but molecular regulation of early DC differentiation has been poorly understood. Here, we report that the transcription factor C/EBPα coordinates the development of progenitor cells required for production of multiple categories of DCs. C/EBPα was needed for differentiation from stem/progenitor cells to common DC progenitors (CDPs), but not for transition of CDP to mature DCs. C/ [...]
Benoukraf T1, Wongphayak S, Hadi LH, Wu M, Soong R.
GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data. Nucleic Acids Res. 2013 Feb 1;41(4):e55. PMID:
23268441.
[PubMed] [Read by QxMD]
High-throughput sequencing is increasingly being used in combination with bisulfite (BS) assays to study DNA methylation at nucleotide resolution. Although several programmes provide genome-wide alignment of BS-treated reads, the resulting information is not readily interpretable and often requires further bioinformatic steps for meaningful analysis. Current post-alignment BS-sequencing programmes are generally focused on the gene-specific level, [...]
2011
Spicuglia S1, Vincent-Fabert C, Benoukraf T, Tibéri G, Saurin AJ, Zacarias-Cabeza J, Grimwade D, Mills K, Calmels B, Bertucci F, Sieweke M, Ferrier P, Duprez E.
Characterisation of genome-wide PLZF/RARA target genes. PLoS One. 2011;6(9):e24176. PMID:
21949697.
[PubMed] [Read by QxMD]
The PLZF/RARA fusion protein generated by the t(11;17)(q23;q21) translocation in acute promyelocytic leukaemia (APL) is believed to act as an oncogenic transcriptional regulator recruiting epigenetic factors to genes important for its transforming potential. However, molecular mechanisms associated with PLZF/RARA-dependent leukaemogenesis still remain unclear.We searched for specific PLZF/RARA target genes by ChIP-on-chip in the haematopoietic ce [...]
Pekowska A1, Benoukraf T, Zacarias-Cabeza J, Belhocine M, Koch F, Holota H, Imbert J, Andrau JC, Ferrier P, Spicuglia S.
H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J. 2011 Aug 16;30(20):4198-210. PMID:
21847099.
[PubMed] [Read by QxMD]
Combinations of post-translational histone modifications shape the chromatin landscape during cell development in eukaryotes. However, little is known about the modifications exactly delineating functionally engaged regulatory elements. For example, although histone H3 lysine 4 mono-methylation (H3K4me1) indicates the presence of transcriptional gene enhancers, it does not provide clearcut information about their actual position and stage-specifi [...]
Cauchy P1, Benoukraf T, Ferrier P.
Processing ChIP-chip data: from the scanner to the browser. Methods Mol Biol. 2011;719:251-68. PMID:
21370088.
[PubMed] [Read by QxMD]
High-density tiling microarrays are increasingly used in combination with chromatin immunoprecipitation (ChIP) assays to delineate the regulation of gene expression. Besides the technical challenges inherent to such complex biological assays, a critical, often daunting issue is the correct interpretation of the sheer amount of raw data generated by utilizing computational methods. Here, we go through the main steps of this intricate process, incl [...]
2010
Pekowska A1, Benoukraf T, Ferrier P, Spicuglia S.
A unique H3K4me2 profile marks tissue-specific gene regulation. Genome Res. 2010 Nov;20(11):1493-502. PMID:
20841431.
[PubMed] [Read by QxMD]
Characterization of the epigenetic landscape fundamentally contributes toward deciphering the regulatory mechanisms that govern gene expression. However, despite an increasing flow of newly generated data, no clear pattern of chromatin modifications has so far been linked to specific modes of transcriptional regulation. Here, we used high-throughput genomic data from CD4(+) T lymphocytes to provide a comprehensive analysis of histone H3 lysine 4 [...]
2009
Bonnet M1, Huang F, Benoukraf T, Cabaud O, Verthuy C, Boucher A, Jaeger S, Ferrier P, Spicuglia S.
Duality of enhancer functioning mode revealed in a reduced TCR beta gene enhancer knockin mouse model. J Immunol. 2009 Dec 15;183(12):7939-48. PMID:
19923469.
[PubMed] [Read by QxMD]
The TCRbeta gene enhancer (Ebeta) commands TCRbeta gene expression through the lifespan of T lymphocytes. Genetic and molecular studies have implied that in early thymocytes, Ebeta directs chromatin opening over the Dbeta-Jbeta-Cbeta domains and triggers initial Dbeta-Jbeta recombination. In mature T cells, Ebeta is required for expression of the assembled TCRbeta gene. Whether these separate activities rely on distinct Ebeta regulatory sequences [...]
Benoukraf T1, Cauchy P, Fenouil R, Jeanniard A, Koch F, Jaeger S, Thieffry D, Imbert J, Andrau JC, Spicuglia S, Ferrier P.
CoCAS: a ChIP-on-chip analysis suite. Bioinformatics. 2009 Apr 1;25(7):954-5. PMID:
19193731.
[PubMed] [Read by QxMD]
High-density tiling microarrays are increasingly used in combination with ChIP assays to study transcriptional regulation. To ease the analysis of the large amounts of data generated by this approach, we have developed ChIP-on-chip Analysis Suite (CoCAS), a standalone software suite which implements optimized ChIP-on-chip data normalization, improved peak detection, as well as quality control reports. Our software allows dye swap, replicate corre [...]
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