Publications


2020

Danek P,  Adamcova MK, Janeckova L,  Karkoulia E, Vanickova K, Fabisik M, Asencio CL, Korinek V, Benoukraf T, Tirado-Magallanes R, Zhou Q, Rahmatova7, Pytlik SR, Brdicka T,  Tenen DG, Alberich-Jorda M. Beta-catenin-TCF/LEF signaling promotes steady-state and emergency granulopoiesis via G-CSF receptor upregulation. Blood. 2020. Accepted.

Chong YC, Tan BT, Chan Z, Lin QQX, Hooi L, Ding Z, Shuen WH, Toh HC, Chow P, Wang Y, Benoukraf T, Chow EKH, Han W. Targeted Inhibition of Purine Metabolism is Effective in Suppressing Hepatocellular Carcinoma Progression. Hepatology Communications. 2020. doi:10.1002/hep4.1559.

Matsumura T, Muddineni SSNA, Nakamura-Ishizu A., Tan DQ, Wang CQ, Tirado-Magallanes R., Sian S, Benoukraf T, Okuda T, Asou N, Matsuoka M, Osato M, Suda T. Hematopoietic stem cells acquire survival advantage by loss of RUNX1 methylation identified in familial leukemia. Blood. 2020 Jun 23:blood.2019004292. doi: 10.1182/blood.2019004292.

Numata A, Kwok HS, Zhou QL, Li J, Tirado-Magallanes R, Espinosa Angarcia V, Hannah R, Park J, Wang CQ, Krishnan V, Rajagopalan D, Zhang Y, Zhou S, Welner RS, Osato M, Jha S, Bohlander SK, Göttgens B, Yang H, Benoukraf T, Lough J, Bararia D, Tenen DG. Lysine acetyltransferase Tip60 is required for hematopoietic stem cell maintenance. 2020, Blood. 2020 Jun 15:blood.2019001279. doi: 10.1182/blood.2019001279.

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 Classified as: Good for Teaching & Review / Commentary.

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]

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]

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]

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]

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]

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]

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]

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]

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]

2010

Jia J1, Pekowska A, Jaeger S, Benoukraf T, Ferrier P, Spicuglia S. Assessing the efficiency and significance of Methylated DNA Immunoprecipitation (MeDIP) assays in using in vitro methylated genomic DNA. BMC Res Notes. 2010 Sep 16;3:240. PMID: 20846371. [PubMed] [Read by QxMD]

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]

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]

Franchini DM1, Benoukraf T, Jaeger S, Ferrier P, Payet-Bornet D. Initiation of V(D)J recombination by Dbeta-associated recombination signal sequences: a critical control point in TCRbeta gene assembly. PLoS One. 2009;4(2):e4575. PMID: 19238214. [PubMed] [Read by QxMD]

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]

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