2021
Yoon J, Grinchuk OV, Kannan S, Ang MJY, Li Z, Tay EXY, Lok KZ, Lee BWL, Chuah YH, Chia K, Tirado Magallanes R, Liu C, Zhao H, Hor JH, Lim JJ, Benoukraf T, Toh TB, Chow EK, Kovalik JP, Ching J, Ng SY, Koh MJ, Liu X, Verma CS, Ong DST. A chemical biology approach reveals a dependency of glioblastoma on biotin distribution. Sci Adv. 2021 Sep 3;7(36):eabf6033.
Zhou Q, Yu M, Tirado-Magallanes R, Li B, Kong L, Guo M, Tan ZH, Lee S, Chai L, Numata A, Benoukraf T, Fullwood MJ, Osato M, Ren B, Tenen DG. ZNF143 mediates CTCF-bound promoter-enhancer loops required for murine hematopoietic stem and progenitor cell function. Nat Commun. 2021 Jan 4;12(1):43.
2020
Luo X, Fong ELS, Zhu C, Lin QXX, Xiong M, Li A, Li T, Benoukraf T, Yu H, Liu S. Hydrogel-based colorectal cancer organoid co-culture models. Acta Biomater. 2020 Dec 31:S1742-7061(20)30751-0.
Chong YC, Toh TB, Chan Z, Lin QXX, Thng DKH, Hooi L, Ding Z, Shuen T, Toh HC, Dan YY, Bonney GK, Zhou L, Chow P, Wang Y, Benoukraf T, Chow EK, Han W. Targeted Inhibition of Purine Metabolism Is Effective in Suppressing Hepatocellular Carcinoma Progression. Hepatol Commun. 2020 Jul 27;4(9):1362-1381. doi: 10.1002/hep4.1559.
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
2013
2011
2010
2009
#: Corresponding authors
*: Co-first authors