Publications

2025

Fan, Y., De Silva, S., Tabassum N., Peng X., Lim V., Cheng X., Datta K., Lowe R., Johns T., Mattson M., Mathivanan S., Sobey C., Okun E., Liu Y., Chen G., Lai M., Jo D., Gunaratne J., Arumugam Thiruma V (2025) Uncovering Shared and Tissue-Specific Molecular Adaptations to Intermittent Fasting in Liver, Brain, and Muscle. eLife 14:RP107332. doi: 10.7554/eLife.107332.1

Lou, X., Lim, J., Li, B., Yu, D., & Gunaratne, J. (2025). Mass spectrometry-based proteomics pipeline for screening hazardous proteins in alternative protein-based foods. Food Chemistry, 145395. doi: 10.1016/j.foodchem.2025.145395 PMID: 40623337

Wu, J. Y., Wee, S., Ler, S. G., Henry, C. J., & Gunaratne, J. (2025). Unraveling the impact of tempeh fermentation on protein nutrients: An in vitro proteomics and peptidomics approach. Food Chemistry, 143154. doi: 10.1016/j.foodchem.2025.143154 PMID: 39914355

Fan Y, Peng X, Tabassum NI, Cheng X, Selvaraji S, Tran V, Hughes TAG, Wickramasinghe B, Jamal A, Dinh QN, Gelderblom M, Drummond GR, Sobey CG, Penman J, Johns TG, Vemuganti R, Gunaratne J, Mattson MP, Jo DG, Jelinic M, Arumugam TV. Impact of Parental Time-Restricted Feeding on Offspring Metabolic Phenotypic Traits. Int J Biol Sci. 2025 Feb 10;21(5):1852-1862. doi: 10.7150/ijbs.107469. PMID: 40083700

2024

Tan, W. X., Lim, L. Y., Afsha, N., Chan, G. M. E., Ching, C., Oguz, G., Neo, S.P., Mohamed Ali, S., Ramasamy, A., Gunaratne, J. and Hunziker, W., Chin M. K., Teo, A. K. K. (2024). ZHX3 interacts with CEBPB to repress hepatic gluconeogenic gene expression and uric acid secretion. PNAS Nexus, pgae568. doi:10.1093/pnasnexus/pgae568 PMID: 39990763

An H, Hong Y, Goh YT, Koh CWQ, Kanwal S, Zhang Y, Lu Z, Yap PML, Neo SP, Wong CM, Wong AST, Yu Y, Ho JSY, Gunaratne J, Goh WSS. m6Am sequesters PCF11 to suppress premature termination and drive neuroblastoma differentiation. Mol Cell. 2024 Nov 7;84(21):4142-4157.e14. doi: 10.1016/j.molcel.2024.10.004. Epub 2024 Oct 30. PMID: 39481383.

Cs Seet R, Ml Quek A, Teng O, Krishnan S, Jl Ng G, Yen Ng M, Mahadevan A, Wj Chioh F, Pin Yeo K, Ying Lim H, Kim J, Lf Swa C, Mq Pek N, Arumugam TV, Angeli V, Gunaratne J, Cheung C. Plasma NOTCH3 and the risk of cardiovascular recurrence in patients with ischemic stroke. QJM. 2024 Jul 16:hcae136. doi: 10.1093/qjmed/hcae136. PMID: 39012624.

De Silva S, Alli-Shaik A, Gunaratne J. Machine Learning-Enhanced Extraction of Biomarkers for High-Grade Serous Ovarian Cancer from Proteomics Data. Sci Data. 2024 Jun 25;11(1):685. doi: 10.1038/s41597-024-03536-1. PMID: 38918474; PMCID: PMC11199488.

De Silva S, Alli-Shaik A, Gunaratne J. FlexStat: combinatory differentially expressed protein extraction. Bioinform Adv. 2024 Apr 11;4(1):vbae056. doi:10.1093/bioadv/vbae056. PMID: 38681522; PMCID: PMC11055397.

Vankadara S, Ke Z, Wang S, Foo SY, Gunaratne J, Lee MA, Koh X, Chia CSB. Cytotoxic activity and cell specificity of a novel LHRH peptide drug conjugate, D-Cys6-LHRH vedotin, against ovarian cancer cell lines. Chem Biol Drug Des. 2024 Apr;103(4):e14516. doi: 10.1111/cbdd.14516. PMID: 38618710.

2023

Ong JWJ, Tan KS, Lee JJX, Seet JE, Choi HW, Ler SG, Gunaratne J, Narasaraju T, Sham LT, Patzel V, Chow VT. Differential effects of microRNAs miR-21, miR-99 and miR-145 on lung regeneration and inflammation during recovery from influenza pneumonia. J Med Virol. 2023 Dec;95(12):e29286. doi: 10.1002/jmv.29286. PMID:38087452.

Tan YW, Teo FMS, Ler SG, Alli-Shaik A, Nyo M, Chong CY, Tan NWH, Wang RYL, Gunaratne J*, Chu JJH. Potential relevance of salivary legumain for the clinical diagnostic of hand, foot, and mouth disease. J Med Virol. 2023 Nov;95(11):e29243. doi: 10.1002/jmv.29243. PMID: 38009231.

Arumugam TV, Alli-Shaik A, Liehn EA, Selvaraji S, Poh L, Rajeev V, Cho Y, Cho Y, Kim J, Kim J, Swa HLF, Hao DTZ, Rattanasopa C, Fann DY, Mayan DC, Ng GY, Baik SH, Mallilankaraman K, Gelderblom M, Drummond GR, Sobey CG, Kennedy BK, Singaraja RR, Mattson MP, Jo DG, Gunaratne J. Multiomics analyses reveal dynamic bioenergetic pathways and functional remodeling of the heart during intermittent fasting. Elife. 2023 Sep 28;12:RP89214. doi: 10.7554/eLife.89214. PMID:37769126; PMCID: PMC10538958.

Li D, Neo SP, Gunaratne J, Sabapathy K. EPLIN-β is a novel substrate of ornithine decarboxylase antizyme 1 and mediates cellular migration. J Cell Sci. 2023 Jun 15;136(12):jcs260427. doi: 10.1242/jcs.260427. Epub 2023 Jun 16. PMID:37325974; PMCID: PMC10281260.

Ludi Z, Sule AA, Samy RP, Putera I, Schrijver B, Hutchinson PE, Gunaratne J, Verma I, Singhal A, Nora RD, van Hagen PM, Dik WA, Gupta V, Agrawal R. Diagnosis and biomarkers for ocular tuberculosis: From the present into the future. Theranostics. 2023 Apr 1;13(7):2088-2113. doi: 10.7150/thno.81488. PMID:37153734; PMCID: PMC10157737.

2022

Badurdeen Z, Alli-Shaik A, Ratnatunga NVI, Abeysekera TDJ, Wijetunge S, Hemage RKD, Fernando BNTW, Hettiarachchi TW, Gunaratne J, Nanayakkara N. Serum Transforming Growth Factor-Beta 1 and Creatinine for Early Diagnosis of CKD of Unknown or Uncertain Etiology Phenotypes. Kidney Int Rep. 2022 Nov 16;8(2):368-372. doi: 10.1016/j.ekir.2022.11.004. PMID: 36815118; PMCID: PMC9939351.

Zeng G, Neo SP, Pang LM, Gao J, Chong SC, Gunaratne J, Wang Y. Comprehensive Interactome Analysis for the Sole Adenylyl Cyclase Cyr1 of Candida albicans. Microbiol Spectr. 2022 Dec 21;10(6):e0393422. doi: 10.1128/spectrum.03934-22. Epub 2022 Oct 31. PMID: 36314909; PMCID: PMC9769623.

Atherton P, Konstantinou R, Neo SP, Wang E, Balloi E, Ptushkina M, Bennett H, Clark K, Gunaratne J, Critchley D, Barsukov I, Manser E, Ballestrem C. Tensin3 interaction with talin drives the formation of fibronectin-associated fibrillar adhesions. J Cell Biol. 2022 Oct 3;221(10):e202107022. doi: 10.1083/jcb.202107022. Epub 2022 Sep 8. PMID: 36074065; PMCID: PMC9462884.

Alli-Shaik A, Qiu B, Lai SL, Cheung N, Tan G, Neo SP, Tan A, Cheung CMG, Hong W, Wong TY, Wang X, Gunaratne J. System-wide vitreous proteome dissection reveals impaired sheddase activity in diabetic retinopathy. Theranostics. 2022 Sep 11;12(15):6682-6704. doi: 10.7150/thno.72947. PMID: 36185601; PMCID: PMC9516227.

Neo SP, Alli-Shaik A, Wee S, Lim Z, Gunaratne J. Englerin A Rewires Phosphosignaling via Hsp27 Hyperphosphorylation to Induce Cytotoxicity in Renal Cancer Cells. J Proteome Res. 2022 Aug 5;21(8):1948-1960. doi: 10.1021/acs.jproteome.2c00248. Epub 2022 Jul 15. PMID: 35838755.

Ng GY, Sheng DPLK, Bae HG, Kang SW, Fann DY, Park J, Kim J, Alli-Shaik A, Lee J, Kim E, Park S, Han JW, Karamyan V, Okun E, Dheen T, Hande MP, Vemuganti R, Mallilankaraman K, Lim LHK, Kennedy BK, Drummond GR, Sobey CG, Gunaratne J, Mattson MP, Foo RS, Jo DG, Arumugam TV. Integrative epigenomic and transcriptomic analyses reveal metabolic switching by intermittent fasting in brain. Geroscience. 2022 Aug;44(4):2171-2194. doi: 10.1007/s11357-022-00537-z. Epub 2022 Mar 31. PMID: 35357643; PMCID: PMC9617005.

Lim Z, Mohd-Ismail NKB, Png E, Sze CW, Lin Q, Hong W, Lim SG, Tan YJ, Gunaratne J. Phosphoproteomics Unravel HBV Triggered Rewiring of Host Phosphosignaling Events. Int J Mol Sci. 2022 May 4;23(9):5127. doi: 10.3390/ijms23095127. PMID: 35563518; PMCID: PMC9104152.

Chu Yuan Kee MJ, Bharath SR, Wee S, Bowler MW, Gunaratne J, Pan S, Zhang L, Song H. Structural insights into the substrate-bound condensation domains of non-ribosomal peptide synthetase AmbB. Sci Rep. 2022 Mar 30;12(1):5353. doi: 10.1038/s41598-022-09188-8. PMID: 35354859; PMCID: PMC8968710.

Chang C, Rajasekaran M, Qiao Y, Dong H, Wang Y, Xia H, Deivasigamani A, Wu M, Sekar K, Gao H, Sun M, Niu Y, Li Q, Tao L, Yan Z, Wang M, Chen S, Zhao S, Chen D, Li L, Yang F, Gao H, Chen B, Su L, Xu L, Chen Y, Seshachalam VP, Chen G, Gunaratne J, Hong W, Shi J, Chen G, Grierson DS, Chabot B, Xie T, Hui KM, Chen J. The aberrant upregulation of exon 10-inclusive SREK1 through SRSF10 acts as an oncogenic driver in human hepatocellular carcinoma. Nat Commun. 2022 Mar 16;13(1):1363. doi: 10.1038/s41467-022-29016-x. PMID: 35296659; PMCID: PMC8927159.

2021

Liu Y, Castano D, Girolamo F, Trigueros-Motos L, Bae HG, Neo SP, Oh J, Narayanaswamy P, Torta F, Rye KA, Jo DG, Gunaratne J, Jung S, Virgintino D, Singaraja RR. Loss of ABCA8B decreases myelination by reducing oligodendrocyte precursor cells in mice. J Lipid Res. 2022 Jan;63(1):100147. doi: 10.1016/j.jlr.2021.100147. Epub 2021 Nov 6. PMID: 34752805; PMCID: PMC8953628.

Chia J, Wang SC, Wee S, Gill DJ, Tay F, Kannan S, Verma CS, Gunaratne J, Bard FA. Src activates retrograde membrane traffic through phosphorylation of GBF1. Elife. 2021 Dec 6;10:e68678. doi: 10.7554/eLife.68678. PMID: 34870592; PMCID: PMC8727025.

Baskaran Y, Tay FP, Ng EYW, Swa CLF, Wee S, Gunaratne J, Manser E. Proximity proteomics identifies PAK4 as a component of Afadin-Nectin junctions. Nat Commun. 2021 Sep 7;12(1):5315. doi: 10.1038/s41467-021-25011-w. PMID: 34493720; PMCID: PMC8423818.

Tan HYA, Sim MFM, Tan SX, Ng Y, Gan SY, Li H, Neo SP, Gunaratne J, Xu F, Han W. HOXC10 Suppresses Browning to Maintain White Adipocyte Identity. Diabetes. 2021 Aug;70(8):1654-1663. doi: 10.2337/db21-0114. Epub 2021 May 14. PMID: 33990396; PMCID: PMC8385616.

Shin EM, Huynh VT, Neja SA, Liu CY, Raju A, Tan K, Tan NS, Gunaratne J, Bi X, Iyer LM, Aravind L, Tergaonkar V. GREB1: An evolutionarily conserved protein with a glycosyltransferase domain links ERα glycosylation and stability to cancer. Sci Adv. 2021 Mar 17;7(12):eabe2470. doi: 10.1126/sciadv.abe2470. PMID: 33731348; PMCID: PMC7968844.

2020

Tan B, Peng S, Yatim SMJM, Gunaratne J, Hunziker W, Ludwig A. An Optimized Protocol for Proximity Biotinylation in Confluent Epithelial Cell Cultures Using the Peroxidase APEX2. STAR Protoc. 2020 Jul 31;1(2):100074. doi: 10.1016/j.xpro.2020.100074. PMID: 33111110; PMCID: PMC7580243.

Tan B, Yatim SMJM, Peng S, Gunaratne J, Hunziker W, Ludwig A. The Mammalian Crumbs Complex Defines a Distinct Polarity Domain Apical of Epithelial Tight Junctions. Curr Biol. 2020 Jul 20;30(14):2791-2804.e6. doi: 10.1016/j.cub.2020.05.032. Epub 2020 Jun 11. PMID: 32531288.

Kosok M, Alli-Shaik A, Bay BH, Gunaratne J. Comprehensive Proteomic Characterization Reveals Subclass-Specific Molecular Aberrations within Triple- negative Breast Cancer. iScience. 2020 Feb 21;23(2):100868. doi: 10.1016/j.isci.2020.100868. Epub 2020 Jan 28. PMID: 32058975; PMCID: PMC7015993.

2019

Khattar E, Maung KZY, Chew CL, Ghosh A, Mok MMH, Lee P, Zhang J, Chor WHJ, Cildir G, Wang CQ, Mohd-Ismail NK, Chin DWL, Lee SC, Yang H, Shin YJ, Nam DH, Chen L, Kumar AP, Deng LW, Ikawa M, Gunaratne J, Osato M, Tergaonkar V. Rap1 regulates hematopoietic stem cell survival and affects oncogenesis and response to chemotherapy. Nat Commun. 2019 Dec 13;10(1):5349. doi: 10.1038/s41467-019-13082-9. PMID: 31836706; PMCID: PMC6911077.
Bai B, Yang W, Fu Y, Foon HL, Tay WT, Yang K, Luo C, Gunaratne J, Lee P, Zile MR, Xu A, Chin CWL, Lam CSP, Han W, Wang Y. Seipin Knockout Mice Develop Heart Failure With Preserved Ejection Fraction. JACC Basic Transl Sci. 2019 Nov 20;4(8):924-937. doi: 10.1016/j.jacbts.2019.07.008. PMID: 31909301; PMCID: PMC6939002.
Lin Q, Low LWL, Lau A, Chua EWL, Matsuoka Y, Lian Y, Monteiro A, Tate S, Gunaratne J, Carney TJ. Tracking genome-editing and associated molecular perturbations by SWATH mass spectrometry. Sci Rep. 2019 Oct 23;9(1):15240. doi: 10.1038/s41598-019-51612-z. PMID: 31645615; PMCID: PMC6811567.
Fernando BNTW, Alli-Shaik A, Hemage RKD, Badurdeen Z, Hettiarachchi TW, Abeysundara HTK, Abeysekara TDJ, Wazil A, Rathnayake S, Gunaratne J, Nanayakkara N. Pilot Study of Renal Urinary Biomarkers for Diagnosis of CKD of Uncertain Etiology. Kidney Int Rep. 2019 Jul 24;4(10):1401-1411. doi: 10.1016/j.ekir.2019.07.009. PMID: 31701049; PMCID: PMC6829189.
Ng GY, Kang SW, Kim J, Alli-Shaik A, Baik SH, Jo DG, Hande MP, Sobey CG, Gunaratne J, Fann DY, Arumugam TV. Genome-Wide Transcriptome Analysis Reveals Intermittent Fasting-Induced Metabolic Rewiring in the Liver. Dose Response. 2019 Sep 25;17(3):1559325819876780. doi: 10.1177/1559325819876780. PMID: 31598117; PMCID: PMC6764061.
Palmer N, Talib SZA, Ratnacaram CK, Low D, Bisteau X, Lee JHS, Pfeiffenberger E, Wollmann H, Tan JHL, Wee S, Sobota R, Gunaratne J, Messerschmidt DM, Guccione E, Kaldis P. CDK2 regulates the NRF1/Ehmt1 axis during meiotic prophase I. J Cell Biol. 2019 Sep 2;218(9):2896-2918. doi:10.1083/jcb.201903125. Epub 2019 Jul 26. PMID: 31350280; PMCID: PMC6719441.
Mohd-Ismail NK, Lim Z, Gunaratne J, Tan YJ. Mapping the Interactions of HBV cccDNA with Host Factors. Int J Mol Sci. 2019 Sep 1;20(17):4276. doi: 10.3390/ijms20174276. PMID: 31480501; PMCID: PMC6747236.
Ong JWJ, Tan KS, Ler SG, Gunaratne J, Choi H, Seet JE, Chow VT. Insights into Early Recovery from Influenza Pneumonia by Spatial and Temporal Quantification of Putative Lung Regenerating Cells and by Lung Proteomics. Cells. 2019 Aug 26;8(9):975. doi: 10.3390/cells8090975. PMID: 31455003; PMCID: PMC6769472.
Liu Z, Liow SS, Lai SL, Alli-Shaik A, Holder GE, Parikh BH, Krishnakumar S, Li Z, Tan MJ, Gunaratne J, Barathi VA, Hunziker W, Lakshminarayanan R, Tan CWT, Chee CK, Zhao P, Lingam G, Loh XJ, Su X. Retinal-detachment repair and vitreous- like-body reformation via a thermogelling polymer endotamponade. Nat Biomed Eng. 2019 Aug;3(8):598-610. doi: 10.1038/s41551-019-0382-7. Epub 2019 Apr 8. PMID: 30962587.
Lim JP, Nair S, Shyamasundar S, Chua PJ, Muniasamy U, Matsumoto K, Gunaratne J*, Bay BH. Silencing Y-box binding protein-1 inhibits triple-negative breast cancer cell invasiveness via regulation of MMP1 and beta-catenin expression. Cancer Lett. 2019 Jun 28;452:119-131. doi: 10.1016/j.canlet.2019.03.014. Epub 2019 Mar 21. PMID: 30905819.
Wee S, Alli-Shaik A, Kek R, Swa HLF, Tien WP, Lim VW, Leo YS, Ng LC, Hapuarachchi HC, Gunaratne J. Multiplex targeted mass spectrometry assay for one-shot flavivirus diagnosis. Proc Natl Acad Sci U S A. 2019 Apr 2;116(14):6754-6759. doi: 10.1073/pnas.1817867116. Epub 2019 Mar 18. PMID: 30886083; PMCID: PMC6452653.

Wee S, Alli-Shaik A, Kek R, Swa HLF, Tien WP, Lim VW, Leo YS, Ng LC, Hapuarachchi HC, Gunaratne J. Multiplex targeted mass spectrometry assay for one-shot flavivirus diagnosis. Proc Natl Acad Sci U S A. 2019 Apr 2;116(14):6754-6759. doi: 10.1073/pnas.1817867116. Epub 2019 Mar 18. PMID: 30886083; PMCID: PMC6452653.

2018

Chong PSY, Zhou J, Chooi JY, Chan ZL, Toh SHM, Tan TZ, Wee S, Gunaratne J, Zeng Q, Chng WJ. Non-canonical activation of β-catenin by PRL-3 phosphatase in acute myeloid leukemia. Oncogene. 2019 Feb;38(9):1508-1519. doi: 10.1038/s41388-018-0526-3. Epub 2018 Oct 10. PMID: 30305722.
Koh CWQ, Goh YT, Toh JDW, Neo SP, Ng SB, Gunaratne J, Gao YG, Quake SR, Burkholder WF, Goh WSS. Single-nucleotide-resolution sequencing of human N6-methyldeoxyadenosine reveals strand-asymmetric clusters associated with SSBP1 on the mitochondrial genome. Nucleic Acids Res. 2018 Dec 14;46(22):11659-11670. doi: 10.1093/nar/gky1104. PMID: 30412255; PMCID: PMC6294517.
Jakhar R, Luijten MNH, Wong AXF, Cheng B, Guo K, Neo SP, Au B, Kulkarni M, Lim KJ, Maimaiti J, Chong HC, Lim EH, Tan TBK, Ong KW, Sim Y, Wong JSL, Khoo JBK, Ho JTS, Chua BT, Sinha I, Wang X, Connolly JE, Gunaratne J, Crasta KC. Autophagy Governs Protumorigenic Effects of Mitotic Slippage-induced Senescence. Mol Cancer Res. 2018 Nov;16(11):1625-1640. doi: 10.1158/1541-7786.MCR-18-0024. Epub 2018 Jul 23. PMID: 30037855.
Chen J, Rajasekaran M, Xia H, Kong SN, Deivasigamani A, Sekar K, Gao H, Swa HL, Gunaratne J, Ooi LL, Xie T, Hong W, Hui KM. CDK1-mediated BCL9 phosphorylation inhibits clathrin to promote mitotic Wnt signalling. EMBO J. 2018 Oct 15;37(20):e99395. doi: 10.15252/embj.201899395. Epub 2018 Sep 14. PMID: 30217955; PMCID: PMC6187222.
Liao KC, Chuo V, Ng WC, Neo SP, Pompon J, Gunaratne J, Ooi EE, Garcia-Blanco MA. Identification and characterization of host proteins bound to dengue virus 3' UTR reveal an antiviral role for quaking proteins. RNA. 2018 Jun;24(6):803-814. doi: 10.1261/rna.064006.117. Epub 2018 Mar 23. PMID: 29572260; PMCID: PMC5959249.

2017

Boopathy GTK, Lynn JLS, Wee S, Gunaratne J, Hong W. Phosphorylation of Mig6 negatively regulates the ubiquitination and degradation of EGFR mutants in lung adenocarcinoma cell lines. Cell Signal. 2018 Mar;43:21-31. doi: 10.1016/j.cellsig.2017.11.006. Epub 2017 Dec 2. PMID: 29196224.
Alli-Shaik A, Wee S, Lim LHK, Gunaratne J. Phosphoproteomics reveals network rewiring to a pro-adhesion state in annexin-1-deficient mammary epithelial cells. Breast Cancer Res. 2017 Dec 12;19(1):132. doi: 10.1186/s13058-017-0924-4. PMID: 29233185; PMCID: PMC5727667.
Tan KK, Ler SG, Gunaratne J, Bay BH, Ponnampalam G. In vitro cytotoxicity of L-amino acid oxidase from the venom of Crotalus mitchellii pyrrhus. Toxicon. 2017 Dec 1;139:20-30. doi: 10.1016/j.toxicon.2017.09.012. Epub 2017 Sep 22. PMID: 28943466.
Toloczko A, Guo F, Yuen HF, Wen Q, Wood SA, Ong YS, Chan PY, Shaik AA, Gunaratne J, Dunne MJ, Hong W, Chan SW. Deubiquitinating Enzyme USP9X Suppresses Tumor Growth via LATS Kinase and Core Components of the Hippo Pathway. Cancer Res. 2017 Sep 15;77(18):4921-4933. doi: 10.1158/0008-5472.CAN-16-3413. Epub 2017 Jul 18. PMID: 28720576; PMCID: PMC6047736.
Singaravelu P, Lee WL, Wee S, Ghoshdastider U, Ding K, Gunaratne J, Grimes JM, Swaminathan K, Robinson RC. <i>Yersinia</i> effector protein (YopO)-mediated phosphorylation of host gelsolin causes calcium-independent activation leading to disruption of actin dynamics. J Biol Chem. 2017 May 12;292(19):8092-8100. doi: 10.1074/jbc.M116.757971. Epub 2017 Mar 9. PMID: 28280241; PMCID: PMC5427284.
Lim JP, Shyamasundar S, Gunaratne J, Scully OJ, Matsumoto K, Bay BH. YBX1 gene silencing inhibits migratory and invasive potential via CORO1C in breast cancer in vitro. BMC Cancer. 2017 Mar 16;17(1):201. doi:10.1186/s12885-017-3187-7. PMID: 28302118; PMCID: PMC5356414.
Lee WL, Singaravelu P, Wee S, Xue B, Ang KC, Gunaratne J, Grimes JM, Swaminathan K, Robinson RC. Mechanisms of Yersinia YopO kinase substrate specificity. Sci Rep. 2017 Jan 4;7:39998. doi: 10.1038/srep39998. PMID: 28051168; PMCID: PMC5209680.

2016

Brichkina A, Nguyen NT, Baskar R, Wee S, Gunaratne J, Robinson RC, Bulavin DV. Proline isomerisation as a novel regulatory mechanism for p38MAPK activation and functions. Cell Death Differ. 2016 Oct;23(10):1592-601. doi: 10.1038/cdd.2016.45. Epub 2016 May 27. PMID: 27233083; PMCID: PMC5041188.
Ward AM, Calvert ME, Read LR, Kang S, Levitt BE, Dimopoulos G, Bradrick SS, Gunaratne J, Garcia-Blanco MA. The Golgi associated ERI3 is a Flavivirus host factor. Sci Rep. 2016 Sep 29;6:34379. doi: 10.1038/srep34379. PMID: 27682269; PMCID: PMC5041148.
Diril MK, Bisteau X, Kitagawa M, Caldez MJ, Wee S, Gunaratne J, Lee SH, Kaldis P. Loss of the Greatwall Kinase Weakens the Spindle Assembly Checkpoint. PLoS Genet. 2016 Sep 15;12(9):e1006310. doi: 10.1371/journal.pgen.1006310. PMID: 27631493; PMCID: PMC5025047.
Dong JM, Tay FP, Swa HL, Gunaratne J, Leung T, Burke B, Manser E. Proximity biotinylation provides insight into the molecular composition of focal adhesions at the nanometer scale. Sci Signal. 2016 Jun 14;9(432):rs4. doi: 10.1126/scisignal.aaf3572. PMID: 27303058.
Alli Shaik A, Qiu B, Wee S, Choi H, Gunaratne J, Tergaonkar V. Erratum: Phosphoprotein network analysis of white adipose tissues unveils deregulated pathways in response to high-fat diet. Sci Rep. 2016 Jun 10;6:27230. doi: 10.1038/srep27230. Erratum for: Sci Rep. 2016 May 16;6:25844. doi: 10.1038/srep25844. PMID: 27282927; PMCID: PMC4901533.
Shaik AA, Qiu B, Wee S, Choi H, Gunaratne J*, Tergaonkar V. Phosphoprotein network analysis of white adipose tissues unveils deregulated pathways in response to high-fat diet. Sci Rep. 2016 May 16;6:25844. doi: 10.1038/srep25844. Erratum in: Sci Rep. 2016 Jun 10;6:27230. doi: 10.1038/srep27230. PMID: 27180971; PMCID: PMC4867603.
Bararia D, Kwok HS, Welner RS, Numata A, Sárosi MB, Yang H, Wee S, Tschuri S, Ray D, Weigert O, Levantini E, Ebralidze AK, Gunaratne J, Tenen DG. Acetylation of C/EBPα inhibits its granulopoietic function. Nat Commun. 2016 Mar 23;7:10968. doi: 10.1038/ncomms10968. PMID: 27005833; PMCID: PMC4814574.

2015

Lee J, Wee S, Gunaratne J, Chua RJ, Smith RA, Ling L, Fernig DG, Swaminathan K, Nurcombe V, Cool SM. Structural determinants of heparin-transforming growth factor-β1 interactions and their effects on signaling. Glycobiology. 2015 Dec;25(12):1491-504. doi: 10.1093/glycob/cwv064. Epub 2015 Aug 24. PMID: 26306634.
Manokaran G, Finol E, Wang C, Gunaratne J, Bahl J, Ong EZ, Tan HC, Sessions OM, Ward AM, Gubler DJ, Harris E, Garcia-Blanco MA, Ooi EE. Dengue subgenomic RNA binds TRIM25 to inhibit interferon expression for epidemiological fitness. Science. 2015 Oct 9;350(6257):217-21. doi: 10.1126/science.aab3369. Epub 2015 Jul 2. PMID: 26138103; PMCID: PMC4824004.
Ho L, Tan SY, Wee S, Wu Y, Tan SJ, Ramakrishna NB, Chng SC, Nama S, Szczerbinska I, Chan YS, Avery S, Tsuneyoshi N, Ng HH, Gunaratne J, Dunn NR, Reversade B. ELABELA Is an Endogenous Growth Factor that Sustains hESC Self- Renewal via the PI3K/AKT Pathway. Cell Stem Cell. 2015 Oct 1;17(4):435-47. doi:10.1016/j.stem.2015.08.010. Epub 2015 Sep 17. Erratum in: Cell Stem Cell. 2015 Nov 5;17(5):635. Sczerbinska, Iwona [corrected to Szczerbinska, Iwona]. PMID: 26387754.
Yang BX, El Farran CA, Guo HC, Yu T, Fang HT, Wang HF, Schlesinger S, Seah YF, Goh GY, Neo SP, Li Y, Lorincz MC, Tergaonkar V, Lim TM, Chen L, Gunaratne J, Collins JJ, Goff SP, Daley GQ, Li H, Bard FA, Loh YH. Systematic identification of factors for provirus silencing in embryonic stem cells. Cell. 2015 Sep 24;163(1):230-45. doi: 10.1016/j.cell.2015.08.037. Epub 2015 Sep 10. PMID: 26365490; PMCID: PMC4686136.
Koh HW, Swa HL, Fermin D, Ler SG, Gunaratne J, Choi H. EBprot: Statistical analysis of labeling-based quantitative proteomics data. Proteomics. 2015 Aug;15(15):2580-91. doi: 10.1002/pmic.201400620. Epub 2015 May 28. PMID: 25913743.
Pfister NT, Fomin V, Regunath K, Zhou JY, Zhou W, Silwal-Pandit L, Freed- Pastor WA, Laptenko O, Neo SP, Bargonetti J, Hoque M, Tian B, Gunaratne J, Engebraaten O, Manley JL, Børresen-Dale AL, Neilsen PM, Prives C. Mutant p53 cooperates with the SWI/SNF chromatin remodeling complex to regulate VEGFR2 in breast cancer cells. Genes Dev. 2015 Jun 15;29(12):1298-315. doi: 10.1101/gad.263202.115. Epub 2015 Jun 16. PMID: 26080815; PMCID: PMC4495400.
Kumar P, Nandi S, Tan TZ, Ler SG, Chia KS, Lim WY, Bütow Z, Vordos D, De la Taille A, Al-Haddawi M, Raida M, Beyer B, Ricci E, Colombel M, Chong TW, Chiong E, Soo R, Park MK, Ha HK, Gunaratne J*, Thiery JP. Highly sensitive and specific novel biomarkers for the diagnosis of transitional bladder carcinoma. Oncotarget. 2015 May 30;6(15):13539-49. doi: 10.18632/oncotarget.3841. PMID: 25915536; PMCID: PMC4537032.

2014

Zhang W, Neo SP, Gunaratne J, Poulsen A, Boping L, Ong EH, Sangthongpitag K, Pendharkar V, Hill J, Cohen SM. Feedback regulation on PTEN/AKT pathway by the ER stress kinase PERK mediated by interaction with the Vault complex. Cell Signal. 2015 Mar;27(3):436-42. doi: 10.1016/j.cellsig.2014.12.010. Epub 2014 Dec 19. PMID: 25530215.
Chakraborty S, Lakshmanan M, Swa HL, Chen J, Zhang X, Ong YS, Loo LS, Akıncılar SC, Gunaratne J, Tergaonkar V, Hui KM, Hong W. An oncogenic role of Agrin in regulating focal adhesion integrity in hepatocellular carcinoma. Nat Commun. 2015 Jan 29;6:6184. doi: 10.1038/ncomms7184. PMID: 25630468; PMCID: PMC4317502.
Tan CL, Teissier S, Gunaratne J, Quek LS, Bellanger S. Stranglehold on the spindle assembly checkpoint: the human papillomavirus E2 protein provokes BUBR1-dependent aneuploidy. Cell Cycle. 2015;14(9):1459-70. doi:10.1080/15384101.2015.1021519. PMID: 25789401; PMCID: PMC4614697.
Ng CT, Yung LY, Swa HL, Poh RW, Gunaratne J*, Bay BH. Altered protein expression profile associated with phenotypic changes in lung fibroblasts co- cultured with gold nanoparticle-treated small airway epithelial cells. Biomaterials. 2015 Jan;39:31-8. doi: 10.1016/j.biomaterials.2014.10.063. Epub 2014 Nov 13. PMID: 25477169.
Swa HL, Shaik AA, Lim LH, Gunaratne J. Mass spectrometry based quantitative proteomics and integrative network analysis accentuates modulating roles of annexin-1 in mammary tumorigenesis. Proteomics. 2015 Jan;15(2-3):408-18. doi: 10.1002/pmic.201400175. Epub 2014 Sep 30. PMID: 25124533.
Alli Shaik A, Wee S, Li RH, Li Z, Carney TJ, Mathavan S, Gunaratne J. Functional mapping of the zebrafish early embryo proteome and transcriptome. J Proteome Res. 2014 Dec 5;13(12):5536-50. doi: 10.1021/pr5005136. Epub 2014 Sep 26. PMID: 25230361.
Qiu B, Shi X, Wong ET, Lim J, Bezzi M, Low D, Zhou Q, Akıncılar SC, Lakshmanan M, Swa HL, Tham JM, Gunaratne J, Cheng KK, Hong W, Lam KS, Ikawa M, Guccione E, Xu A, Han W, Tergaonkar V. NUCKS is a positive transcriptional regulator of insulin signaling. Cell Rep. 2014 Jun 26;7(6):1876-86. doi: 10.1016/j.celrep.2014.05.030. Epub 2014 Jun 12. PMID: 24931609.
Huang YF, Wee S, Gunaratne J, Lane DP, Bulavin DV. Isg15 controls p53 stability and functions. Cell Cycle. 2014;13(14):2200-10. doi: 10.4161/cc.29209. Epub 2014 May 20. PMID: 24844324; PMCID: PMC4111675.
Ward AM, Gunaratne J, Garcia-Blanco MA. Identification of dengue RNA binding proteins using RNA chromatography and quantitative mass spectrometry. Methods Mol Biol. 2014;1138:253-70. doi: 10.1007/978-1-4939-0348-1_16. PMID: 24696342.

2013

Lai D, Tan CL, Gunaratne J, Quek LS, Nei W, Thierry F, Bellanger S. Localization of HPV-18 E2 at mitochondrial membranes induces ROS release and modulates host cell metabolism. PLoS One. 2013 Sep 24;8(9):e75625. doi: 10.1371/journal.pone.0075625. PMID: 24086592; PMCID: PMC3782431.
Bard-Chapeau EA, Gunaratne J, Kumar P, Chua BQ, Muller J, Bard FA, Blackstock W, Copeland NG, Jenkins NA. EVI1 oncoprotein interacts with a large and complex network of proteins and integrates signals through protein phosphorylation. Proc Natl Acad Sci U S A. 2013 Jul 30;110(31):E2885-94. doi: 10.1073/pnas.1309310110. Epub 2013 Jul 15. PMID: 23858473; PMCID: PMC3732971.
Xie Z, Gunaratne J, Cheong LL, Liu SC, Koh TL, Huang G, Blackstock WP, Chng WJ. Plasma membrane proteomics identifies biomarkers associated with MMSET overexpression in T(4;14) multiple myeloma. Oncotarget. 2013 Jul;4(7):1008-18. doi: 10.18632/oncotarget.1049. PMID: 23900284; PMCID: PMC3759662.
Gunaratne J, Schmidt A, Quandt A, Neo SP, Saraç OS, Gracia T, Loguercio S, Ahrné E, Xia RL, Tan KH, Lössner C, Bähler J, Beyer A, Blackstock W, Aebersold R. Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas. Mol Cell Proteomics. 2013 Jun;12(6):1741-51. doi: 10.1074/mcp.M112.023754. Epub 2013 Mar 5. PMID: 23462206; PMCID: PMC3675828.
Zhang W, Hietakangas V, Wee S, Lim SC, Gunaratne J, Cohen SM. ER stress potentiates insulin resistance through PERK-mediated FOXO phosphorylation. Genes Dev. 2013 Feb 15;27(4):441-9. doi: 10.1101/gad.201731.112. PMID: 23431056; PMCID: PMC3589560.

2012

Khong JH, Zhang T, Gunaratne J, Blackstock W, Surana U. "Reductional anaphase" in replication-defective cells is caused by ubiquitin-conjugating enzyme Cdc34-mediated deregulation of the spindle. Cell Cycle. 2012 Aug 1;11(15):2896-910. doi: 10.4161/cc.21303. Epub 2012 Aug 1. PMID: 22805765.
Swa HL, Blackstock WP, Lim LH, Gunaratne J. Quantitative proteomics profiling of murine mammary gland cells unravels impact of annexin-1 on DNA damage response, cell adhesion, and migration. Mol Cell Proteomics. 2012 Aug;11(8):381-93. doi: 10.1074/mcp.M111.011205. Epub 2012 Apr 16. PMID: 22511458; PMCID: PMC3412969.
Tan CL, Gunaratne J, Lai D, Carthagena L, Wang Q, Xue YZ, Quek LS, Doorbar J, Bachelerie F, Thierry F, Bellanger S. HPV-18 E2^E4 chimera: 2 new spliced transcripts and proteins induced by keratinocyte differentiation. Virology. 2012 Jul 20;429(1):47-56. doi: 10.1016/j.virol.2012.03.023. Epub 2012 Apr 27. PMID: 22541938.
Coffill CR, Muller PA, Oh HK, Neo SP, Hogue KA, Cheok CF, Vousden KH, Lane DP, Blackstock WP, Gunaratne J. Mutant p53 interactome identifies nardilysin as a p53R273H-specific binding partner that promotes invasion. EMBO Rep. 2012 Jun 29;13(7):638-44. doi: 10.1038/embor.2012.74. PMID: 22653443; PMCID: PMC3388785.
Lößner C, Wee S, Ler SG, Li RH, Carney T, Blackstock W, Gunaratne J. Expanding the zebrafish embryo proteome using multiple fractionation approaches and tandem mass spectrometry. Proteomics. 2012 Jun;12(11):1879-82. doi: 10.1002/pmic.201100576. PMID: 22653788.
Chuang LS, Lai SK, Murata-Hori M, Yamada A, Li HY, Gunaratne J, Ito Y. RUNX3 interactome reveals novel centrosomal targeting of RUNX family of transcription factors. Cell Cycle. 2012 May 15;11(10):1938-47. doi: 10.4161/cc.20278. Epub 2012 May 15. PMID: 22544322.
Bard-Chapeau EA, Jeyakani J, Kok CH, Muller J, Chua BQ, Gunaratne J, Batagov A, Jenjaroenpun P, Kuznetsov VA, Wei CL, D'Andrea RJ, Bourque G, Jenkins NA, Copeland NG. Ecotopic viral integration site 1 (EVI1) regulates multiple cellular processes important for cancer and is a synergistic partner for FOS protein in invasive tumors. Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):2168-73. doi: 10.1073/pnas.1119229109. Epub 2012 Jan 19. PMID: 22308434; PMCID: PMC3277513.
Migliori V, Müller J, Phalke S, Low D, Bezzi M, Mok WC, Sahu SK, Gunaratne J, Capasso P, Bassi C, Cecatiello V, De Marco A, Blackstock W, Kuznetsov V, Amati B, Mapelli M, Guccione E. Symmetric dimethylation of H3R2 is a newly identified histone mark that supports euchromatin maintenance. Nat Struct Mol Biol. 2012 Jan 8;19(2):136-44. doi: 10.1038/nsmb.2209. PMID: 22231400.

2011

Lössner C, Blackstock W, Gunaratne J. Enhanced performance of pulsed Q collision induced dissociation-based peptide identification on a dual-pressure linear ion trap. J Am Soc Mass Spectrom. 2012 Jan;23(1):186-9. doi: 10.1007/s13361-011-0256-z. Epub 2011 Oct 27. PMID: 22033888.
Ward AM, Bidet K, Yinglin A, Ler SG, Hogue K, Blackstock W, Gunaratne J, Garcia-Blanco MA. Quantitative mass spectrometry of DENV-2 RNA-interacting proteins reveals that the DEAD-box RNA helicase DDX6 binds the DB1 and DB2 3' UTR structures. RNA Biol. 2011 Nov Dec;8(6):1173-86. doi: 10.4161/rna.8.6.17836. Epub 2011 Nov 1. PMID: 21957497; PMCID: PMC3256426.
Gunaratne J, Goh MX, Swa HL, Lee FY, Sanford E, Wong LM, Hogue KA, Blackstock WP, Okumura K. Protein interactions of phosphatase and tensin homologue (PTEN) and its cancer-associated G20E mutant compared by using stable isotope labeling by amino acids in cell culture-based parallel affinity purification. J Biol Chem. 2011 May 20;286(20):18093-103. doi: 10.1074/jbc.M111.221184. Epub 2011 Mar 17. PMID: 21454687; PMCID: PMC3093882.

*Co-correspondence

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