Publications

2024

December

Gupta M, Lei M, Cham TJ, Lee HK. D-LORD for motion Stylization. IEEE Transactions on Systems, Man, and Cybernetics: Systems 2024 Nov;1–14, doi: 10.48550/arXiv.2412.04097

Baskaran L, Leng S, Dutta U, Teo L, Yew MS, Sia H, Chew N, Huang W, Lee HK, Vaughan R, Ngiam KY, Lu Z, Wang X, Tan EWP, Cheng NZY, Tan SY, Chan M, Zhong L. Cohort profile: AI-driven national Platform for CCTA for clinicaL and industriaL applicatiOns (APOLLO). BMJ Open. 2024 Dec 2;14(12):e089047. doi: 10.1136/bmjopen-2024-089047

November

Yusof Z, Tong YW, Selvarajoo K, Parakh SK, Foo SC. Overcoming challenges in microalgal bioprocessing through data-driven and computational approaches. Current Opinion in Food Science, Vol. 61, Feb 2025, 101253

Kedir WM, Li L, Tan YS, Bajalovic N, Loke DK. Nanomaterials and methods for cancer therapy: 2D materials, biomolecules, and molecular dynamics simulations. Journal of Materials Chemistry B, 2024, 12, 12141-12173, doi: 10.1039/D4TB01667J

October

Yeo HC, Varsheni V, Selvarajoo K. Identifying effective evolutionary strategies-based protocol for uncovering reaction kinetic parameters under the effect of measurement noises. BMC Biology, 22, 235 (2024). https://doi.org/10.1186/s12915-024-02019-4

Badowski C, Benny P, Verma CS, Lane EB. Desmoplakin CSM models unravel mechanisms regulating the binding to intermediate filaments and putative therapeutics for cardiocutaneous diseases. Scientific Reports, 2024 Oct 5;14(1):23206. doi: 10.1038/s41598-024-73705-0

Khanijou JK, Hee YT, Scipion CPM, Chen X, Selvarajoo K. Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli. npj Systems Biology and Applications, 10, 109 (2024). https://doi.org/10.1038/s41540-024-00440-7

September

Tee WV, Berezovsky IN. Toward the Design of Allosteric Effectors: Gaining Comprehensive Control of Drug Properties and Actions. Journal of Medicinal Chemistry, 2024 Sep 26. doi: 10.1021/acs.jmedchem.4c01043.

Pabis K, Barardo D, Gruber J, Sirbu O, Malavolta M, Selvarajoo K, Kaeberlein M, Kennedy BK. The impact of short-lived controls on the interpretation of lifespan experiments and progress in geroscience - Through the lens of the "900-day rule". Ageing Research Reviews, 2024 Sep 26;101:102512. doi: 10.1016/j.arr.2024.102512

Lee HK. The First Adventures on Differential Geometry. Book: World Scientific Publishing, Pg 224, doi: 10.1142/13930

August

Li M, Li J, Lu X, Schroder R, Chandramohan A, Wuelfing WP, Templeton AC, Xu W, Gindy M, Kesisoglou F, Ling J, Sawyer T, Verma CS, Partridge AW, Su Y. Molecular Mechanism of P53 Peptide Permeation through Lipid Membranes from Solid-State NMR Spectroscopy and Molecular Dynamics Simulations. Journal of the American Chemical Society, 2024, 146, 33, 23075–23091, doi: 10.1021/jacs.4c04230

July

Lee YF, Phua CZJ, Yuan J, Zhang B, Lee MY, Kannan S, Chiu YHJ, Koh CWQ, Yap CK, Lim EKH, Chen J, Lim Y, Lee JJH, Skanderup AJ, Wang Z, Zhai W, Tan NS, Verma CS, Tay Y, Tan DSW, Tam WL. PARP4 interacts with hnRNPM to regulate splicing during lung cancer progression. Genome Medicine 2024 Jul 22;16(1):91. doi: 10.1186/s13073-024-01328-1

Karnaneedi S, Johnston EB, Bose U, Juhász A, Broadbent JA, Ruethers T, Jerry EM, Kamath SD, Limviphuvadh V, Stockwell S, Byrne K, Clarke D, Colgrave ML, Maurer-Stroh S, Lopata AL. The Allergen Profile of Two Edible Insect Species—Acheta domesticus and Hermetia illucens. Molecular Nutrition & Food Research, 2024 Aug;68(16):e2300811. doi: 10.1002/mnfr.202300811

Sethi R, Ang KS, Li M, Long Y, Ling J, Chen J. ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists. Nature Communications, 2024 Jul 3;15(1):5600, doi: 10.1038/s41467-024-48188-2

June

Ng NHJ, Ghosh S, Bok CM, Ching C, Low BSJ, Chen JT, Lim E, Miserendino MC, Tan YS, Hoon S, Teo AKK. HNF4A and HNF1A exhibit tissue specific target gene regulation in pancreatic beta cells and hepatocytes. Nature Communications, 2024 Jun 22;15(1):4288. doi: 10.1038/s41467-024-48647-w

Rashid MM, Selvarajoo K. Advancing drug-response prediction using multi-modal and -omics machine learning integration (MOMLIN): a case study on breast cancer clinical data. Briefings in Bioinformatics, Volume 25, Issue 4, July 2024, bbae300, https://doi.org/10.1093/bib/bbae300

Long Y, Ang KS, Sethi R, Liao S, Heng Y, van Olst L, Ye S, Zhong C, Xu H, Zhang D, Kwok I, Husna N, Jian M, Ng LG, Chen A, Gascoigne NRJ, Gate D, Fan R, Xu X, Chen J. Deciphering spatial domains from spatial multi-omics with SpatialGlue. Nature Methods 2024, doi: 10.1038/s41592-024-02316-4

Chen BK, Hu TY, Jin H, Lee HK,Kawaguchi K. Exact Conversion of In-Context Learning to Model Weights in Linearized-Attention Transformers. Forty-first International Conference on Machine Learning, 2024, doi:10.48550/arXiv.2406.02847

May

Shiina K, Lee HK, Okabe Y, Hiroyuki M. Weakly-supervised learning of Schrodinger equation. Journal of the Physical Society of Japan, Vol 93, No.6

Huo X, Ong KH, Lau KW, Gole L, Tan CL, Zhang C, Zhang Y, Zhu X, Li L, Han H, Young D, Lu H, Xu J, Chen W, Sanders SJ, Lee HK, Hue SSS, Yu W, Tan SY. A comprehensive AI model development framework for consistent Gleason grading. Communications Medicine 4, 84 (2024). https://doi.org/10.1038/s43856-024-00502-1

Selvarajoo K, Maurer-Stroh S. Towards multi-omics synthetic data integration. Briefings in Bioinformatics, Vol. 25, Issue 3, May 2024, doi: 10.1093/bib/bbae213

Young R, Huang T, Luo Z, Tan YS, Kaur A, Lau YH. Development of stapled NONO-associated peptides reveals unexpected cell permeability and nuclear localisation. Journal of Peptide Science, Vol. 30, Issue 5, May 2024, doi: 10.1002/psc.3562

April

Berezovsky IN, Seeliger MA. Editorial overview: Molecular determinants, mechanisms, and state-of-the-art approaches in allostery. Current Opinion in Structural Biology, Vol. 86, June 2024:102810. doi: 10.1016/j.sbi.2024.102810

Pabis K, Barardo D, Sirbu O, Selvarajoo K, Gruber J, Kennedy BK. A concerted increase in readthrough and intron retention drives transposon expression during aging and senescence. Elife. 2024 Apr 3;12:RP87811. doi: 10.7554/eLife.87811

Tang Z, Feng J, Challa M, Rowthu SR, Xiong S, Zou C, Li J, Verma CS, Peng H, He X, Huang C, He Y. Discovery of novel Thymol-TPP antibiotics that eradicate MRSA persisters. European Journal of Medicinal Chemistry, Vol. 270, 15 Apr 24, doi: 10.1016/j.ejmech.2024.116381

March

Helmy M, Elhalis H, Rashid MM, Selvarajoo K. Can digital twin efforts shape microorganism-based alternative food?”. Current Opinion in Biotechnology, Vol. 87, Jun 2024, 103115, doi: 10.1016/j.copbio.2024.103115

Zhang Y, Lee RY, Tan CW, Guo X, Yim WW, Lim JC, Wee FY, Yang WU, Kharbanda M, Lee JJ, Ngo NT, Leow WQ, Loo LH, Lim TK, Sobota RM, Lau MC, Davis MJ, Yeong J. Spatial omics techniques and data analysis for cancer immunotherapy applications. Current Opinion in Biotechnology, Vol. 87, Jun 2024, 103111, doi: 10.1016/j.copbio.2024.103111

February

Singhal V, Chou N, Lee J, Yue Y, Liu J, Chock WK, Lin L, Chang YC, Teo EML, Aow J, Lee HK, Chen KH, Prabhakar S. BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis. Nature Genetics, Vol 56, March 2024, Pg 431-441, doi: 10.1038/s41588-024-01664-3

Narmada BC, Khakpoor A, Shirgaonkar N, Narayanan S, Kim Aw PP, Singh M, Ong KH, Owino CO, Ting Ng JW, Yew HC, Binte Mohamed Nasir NS, Au VB, Sng R, Kaliaperumal N, Toe Wai Khine HH, Casuscelli di Tocco F, Masayuki O, Naikar S, Ng HX, Chia SL, Yi Seah CX, Alnawaz MH, Lee Yoon Wai C, Ling Tay AY, Singh MK, Chew V, Yu W, Connolly JE, Periyasamy G, Plissonnier ML, Levrero M, Lim SG, DasGupta R. Single cell landscape of functionally cured chronic hepatitis B patients reveals activation of innate and altered CD4-CTL-driven adaptive immunity. Journal of Hepatology, Volume 81, Issue 1, 42 – 61.

Nelson CB, Rogers S, Roychoudhury K, Tan YS, Atkinson CJ, Sobinoff AP, Tomlinson CG, Hsu A, Lu R, Dray E, Haber M, Fletcher JI, Cesare AJ, Hegde RS, Pickett HA. The Eyes Absent family members EYA4 and EYA1 promote PLK1 activation and successful mitosis through tyrosine dephosphorylation. Nature Communications 15, 1385 (2024), doi: 10.1038/s41467-024-45683-4

Shivgan AT, Marzinek JK, Krah A, Matsudaira P, Verma CS, Bond PJ. Coarse-Grained Model of Glycosaminoglycans for Biomolecular Simulations. Journal of Chemical Theory and Computation, Vol. 20, Issue 8, Pg 3308-3321, doi: 10.1021/acs.jctc.3c01088

Khanijou JK, Yeoh HC, Selvarajoo K. Digital Twin approach to aid cultured meat research and development. Metabolic Engineering Communications

Yeo HC, Varsheni V, Selvarajoo K. Exploring evolutionary strategies for uncovering the kinetic parameters of an artificial biological pathway under the effect of measurement noises . Briefing in Bioinformatics

Jayakody T, Inoue A, Kannan S, Nakamura G, Kawakami K, Mendis K, Nguyen TB, Li J, Herr DR, Verma CS, Dawe GS. Mechanisms of biased agonism by Gαi/o-biased stapled peptide agonists of the relaxin-3 receptor. Science Signaling, Feb 13, Vol. 17, No. 823, doi: 10.1126/scisignal.abl5880

January

Krutz NL, Kimber I, Winget J, Nguyen MN, Limviphuvadh V, Maurer-Stroh S, Mahony C, Gerberick GF. Identification and semi-quantification of protein allergens in complex mixtures using proteomic and AllerCatPro 2.0 bioinformatic analyses: a proof-of-concept investigation. Journal of Immunotoxicology, Vol. 21, 2024, Issue 1, doi: 10.1080/1547691X.2024.2305452

Alfatah M, Zhang Y, Naaz A, Cheng TYN, Eisenhaber F. PICLS with human cells is the first high throughput screening method for identifying novel compounds that extend lifespan. Biology Direct, 19, Article no 8, 2024, doi:10.1186/s13062-024-00455-4

Chandramohan A, Josien H, Yuen TY, Duggal R, Spiegelberg D, Yan L, Juang YA, Ge L, Aronica PG, Kaan HYK, Lim YH, Peier A, Sherborne B, Hochman J, Lin S, Biswas K, Nestor M, Verma CS, Lane DP, Sawyer TK, Garbaccio R, Henry B, Kannan S, Brown CJ, Johannes CW, Partridge AW. Design-Rules for Stapled Alpha-Helical Peptides with On-Target In Vivo Activity: Application to Mdm2/X dual antagonists. Nature Communications 2024 Jan 12;15(1):489. doi: 10.1038/s41467-023-43346-4

Tee WV, Berezovsky IN. Allosteric drugs: New principles and design approaches. Current Opinion Opinion in Structural Biology, Vol. 84, Feb 2024.

2023

December

Samsudin F, Zuzic L, Marzinek JK, Bond PJ. Mechanisms of allostery at the viral surface through the eyes of molecular simulation. Current Opinion in Structural Biology, Vol 84, Feb 2024, 102761, doi: 10.1016/j.sbi.2023.102761

Puthia M, Petrlova J, Petruk G, Butrym M, Samsudin F, Andersson MÅ, Strömdahl AC, Wasserstrom S, Hartman E, Kjellström S, Caselli L, Klementieva O, Bond PJ, Malmsten M, Raina DB, Schmidtchen A. Bioactive Suture with Added Innate Defense Functionality for the Reduction of Bacterial Infection and Inflammation. Advanced Healthcare Materials 2023 Sep 9:e2300987. doi: 10.1002/adhm.202300987. Epub ahead of print.

Khanijou JK, Hee YT, Selvarajoo K. Identifying Key In Silico Knockout for Enhancement of Limonene Yield Through Dynamic Metabolic Modelling. Book Chapter: Systems Biology - Methods in Molecular Biology, Vol 2745, doi: 10.1007/978-1-0716-3577-3_1

Guilvout I, Samsudin F, Huber H, Bond PJ, Bardiaux B, Francetic O. Membrane platform protein PulF of the Klebsiella type II secretion system forms a trimeric ion channel essential for endopilus assembly and protein secretion. Molecular and Cellular Biology, 2023 Dec 8:e0142323. doi: 10.1128/mbio.01423-23

Channarayapatna Srinivasa A, Bhanu Prakash,KN, Sherin MS, Dikendra B, Sim ZTJ, Chew LH Justin, Chen WX, Yeo JPA, Lim WS, Tan CHT. Multimodal Large Language Models for Comprehensive Cardiometabolic Health Risk Analysis: An Interdisciplinary Explorative Study. Journal of the American Medical Informatics Information.

Feng C, Ong K, Young DM, Chen B, Li L, Huo X, Lu H, Gu W, Liu F, Tang H, Zhao M, Yang M, Zhu K, Huang L, Wang Q, Marini GPL, Gui K, Han H, Sanders SJ, Li L, Yu W, Mao J. Artificial intelligence-assisted quantification and assessment of whole slide images for pediatric kidney disease diagnosis. Bioinformatics 2024 Jan 2;40(1):btad740. doi: 10.1093/bioinformatics/btad740\

Liao KC, Xie X, Sundstrom AKB, Lim XN, Tan KK, Zhang Y, Zou J, Bifani AM, Poh HX, Chen JJ, Ng WC, Lim SY, Ooi EE, Sessions OM, Tay Y, Shi PY, Huber RG, Wan Y. Dengue and Zika RNA-RNA interactomes reveal pro- and anti-viral RNA in human cells. Genome Biology, 2023 Dec 5;24(1):279. doi: 10.1186/s13059-023-03110-9

Gole L, Liu F, Ong KH, Li L, Han H, Young D, Marini GPL, Wee A, Zhao J, Rao H, Yu W, Wei L. Quantitative image-based collagen structural features predict the reversibility of hepatitis C virus-induced liver fibrosis post antiviral therapies. Scientific Reports, 2023 Apr 19;13(1):6384, doi: 10.1038/s41598-023-33567-4

November

Yu Chung Chooi, Qinze Arthur Zhang, Faidon Magkos, Maisie Ng, Navin Michael, Xiaorong Wu, Vera Sergeyevna Brok Volchanskaya, Xianning Lai, Elvy Riani Wanjaya, Untzizu Elejalde, Chew Chan Goh, Clara Poh Lian Yap, Long Hui Wong, Kevin Junliang Lim, S Sendhil Velan, Jadegoud Yaligar, Mark Dhinesh Muthiah, Yap Seng Chong, Evelyn Xiu Ling Loo, Johan G. Eriksson, Kezlyn Li Ming Lim, Mabel Shu Fung Kouk, Evelyn Wai Mei Chong, Munirah Abd Gani, Lisha Li, Vicky Hwee Kee Tay, Yeshe Manuel Kway, Mukkesh Kumar, Suresh Anand Sadananthan, Kaijie Khoo, Danyu Koh, Rebecca Lim, Chin Wei Kang, Kwang Li Sin, Jun Wei Lim. Effect of an Asian-adapted Mediterranean diet and pentadecanoic acid on fatty liver disease: the TANGO randomized controlled trial. The American Journal of Clinical Nutrition, 2023 Nov 29:S0002-9165(23)66285-9. doi: 10.1016/j.ajcnut.2023.11.013

Hong JH, Yong CH, Heng HL, Chan JY, Lau MC, Chen J, Lee JY, Lim AH, Li Z, Guan P, Chu PL, Boot A, Ng SR, Yao X, Wee FYT, Lim JCT, Liu W, Wang P, Xiao R, Zeng X, Sun Y, Koh J, Kwek XY, Ng CCY, Klanrit P, Zhang Y, Lai J, Tai DWM, Pairojkul C, Dima S, Popescu I, Hsieh SY, Yu MC, Yeong J, Kongpetch S, Jusakul A, Loilome W, Tan P, Tan J, Teh BT. Integrative multiomics enhancer activity profiling identifies therapeutic vulnerabilities in cholangiocarcinoma of different etiologies. Gut. 4 November 2023. doi: 10.1136/gutjnl-2023-330483

Stamatis D, Verma CS, Essex J. Benchmarking RNA all-atom force fields using hairpin motifs. ChemRxiv, Theoretical and Computational Chemistry.

Krah A, Ragunathan P, Bond PJ, Grüber G. Variations of the Mycobacterium abscessus F-ATP synthase subunit a-c interface alter binding and potency of the anti-TB drug bedaquiline. Biochemical and Biophysical Research Communications, Vol 690, 1 Jan 2024, 690:149249. doi: 10.1016/j.bbrc.2023.149249.

Tang Z, Jiang W, Li S, Huang X, Yang Y, Chen X, Qiu J, Xiao C, Xie Y, Zhang X, Li J, Verma CS, He Y, Yang A. Design and evaluation of tadpole-like conformational antimicrobial peptides. Communications Biology, 2023 Nov 18;6(1):1177. doi: 10.1038/s42003-023-05560-0

Sim JZT, Bhanu Prakash KN, Huang WM, Tan CH. Harnessing artificial intelligence in radiology to augment population health. Frontiers in Medical Technology, Vol 5, 2023, doi:10.3389/fmedt.2023.1281500

Goh, Y.S. Fong, S.-W. Tay, M.Z. Rouers, A. Chang, Z.W. Chavatte, J.-M. Hor, P.X. Loh, C.Y. Huang, Y. Tan, Y.J. Wang, B. Ngoh, E.Z.X. Mohd Salleh, S.N. Lee, R.T.C. Lim, G. Yu, J.J. Soh, Z.K. Chin, Y.Q. Lim, J.J. Ongko, J. Libau, E.A. Abdullah, M.R.B. Diong, S.H. Teo, J. Yeo, H.P. Chua, A.C.Y. Torres-Ruesta, A. Amrun, S.N. Yeo, N.K.-W. Neo, V.K. Chen, W.Y. Kam, I.K.J. Ong, A.S.M. Goh, E.Y.W. Wong, N. Lim, Z.F.S. Maurer-Stroh, S. Wang, C.-I. Leo, Y.‐S. Lin, R.T.P. Lam, M.C. Lye, D.C. Young, B.E. Ng, L.F.P. Renia, L. Higher Delta variant-specific neutralizing antibodies prevented infection in close contacts vaccinated with ancestral mRNA vaccines during the SARS-CoV-2 Delta wave. Scientific Reports 13, Article no 19331 (2023), doi: 10.1038/s41598-023-46800-x

Tulsian NK, Palur RV, Qian X, Gu Y, D/O Shunmuganathan B, Samsudin F, Wong YH, Lin J, Purushotorman K, Kozma MM, Wang B, Lescar J, Wang CI, Gupta RK, Bond PJ, MacAry PA. Defining neutralization and allostery by antibodies against COVID-19 variants. Nature Communications 2023 Nov 1;14(1):6967. doi: 10.1038/s41467-023-42408-x.

October

Wang Z, Wang Y, Fan H. Simulation Study on Route Selection and Efficiency of Subway Passenger Emergency Evacuation. 2023 IEEE International Smart Cities Conference (ISC2), Bucharest, Romania, 24-27 Sep 2023, pp. 1-7, doi: 10.1109/ISC257844.2023.10293589

Li Yen Chong, Felicia Wee, Jeffrey Lim, Craig Joseph, Zhen Wei Neo, Jia Ying Joey Lee, Lit-Hsin Loo and Joe Yeong. 222-D Automated hyperplex staining and imaging system on various cancer tissues using off the shelf antibodies. Journal for ImmunoTherapy of Cancer, Volume 11, Issue Suppl 2:A1687-1817

Chin WX, Kong HY, Zhu IXY, Teo ZY, Faruk R, Lee RCH, Ho SX, Aw ZQ, Yi B, Hou XJ, Tan AKY, Yogarajah T, Huber RG, Cai Y, Wan Y, Chu JJH. Flavivirus genome recoding by codon optimisation confers genetically stable in vivo attenuation in both mice and mosquitoes. PLoS Pathogens,2023 Oct 26;19(10):e1011753. doi: 10.1371/journal.ppat.1011753

Lau MS, Hu Z, Zhao X, Tan YS, Liu J, Huang H, Yeo CJ, Leong HF, Grinchuk OV, Chan JK, Yan J, Tee WW. Transcriptional repression by a secondary DNA binding surface of DNA topoisomerase I safeguards against hypertranscription. Nature Communications, 14, 6464 (2023), doi:10.1038/s41467-023-42078-9

Jelinska C, Kannan S, Frosi Y, Ramlan SR, Winnerdy F, Lakshminarayanan R, Johannes CW, Brown CJ, Phan AT, Rhodes D, Verma CS. Stitched peptides as potential cell permeable inhibitors of oncogenic DAXX protein. RSC Chemical Biology, 2023, doi: 10.1039/D3CB00149K

Meivita MP, Go SX, Mozar FS, Li L, Tan YS, Bajalovic N, Loke DK. Shape complementarity processes for ultrashort-burst sensitive M13-PEG-WS2-powered MCF-7 cancer cell sensors. Nanoscale. 2023 Oct 26;15(41):16658-16668. doi: 10.1039/d3nr03573e

September

Alfatah M, Cui L, Goh CJH, Cheng TYN, Zhang Y, Naaz A, Wong JH, Lewis J, Poh WJ, Arumugam P. Metabolism of glucose activates TORC1 through multiple mechanisms in Saccharomyces cerevisiae. Cell Reports 2023 Oct 31;42(10):113205. doi: 10.1016/j.celrep.2023.113205

Petruk G, Puthia M, Samsudin F, Petrlova J, Olm F, Mittendorfer M, Hyllén S, Edström D, Strömdahl AC, Diehl C, Ekström S, Walse B, Kjellström S, Bond PJ, Lindstedt S, Schmidtchen A. Targeting Toll-like receptor-driven systemic inflammation by engineering an innate structural fold into drugs. Nature Communications 2023 Sep 29;14(1):6097. doi: 10.1038/s41467-023-41702-y. PMID: 37773180; PMCID: PMC10541425

Zhang X, Wang Y, Supekar S, Cao X, Zhou J, Dang J, Chen S, Jenkins L, Marsango S, Li, X, Liu G, Milligan G, Feng M, Fan H, Gong W, Zhang C. Pro-phagocytic function and structural basis of GPR84 signaling. Nature Communications, 14, 5706 (2023). https://doi.org/10.1038/s41467-023-41201-0

Lena, J., Gonçalves, R.A., Kharel, S., Kannan, S., Verma, C.S., Pinchi, K.M., Lim, S., & Lam, Y.M. Elucidating the effect of poly(ethylene terephthalate) chain structure on its enzymatic degradation behaviour. ACS Sustainable Chemistry & Engineering, 2023, 11, 38, 13974–13987, doi:10.1021/acssuschemeng.3c02695

Cserző M, Eisenhaber B, Eisenhaber F, Magyar C, Simon I. The First Quarter Century of the Dense Alignment Surface Transmembrane Prediction Method. International Journal of Molecular Sciences. 2023; 24(18):14016. doi:10.3390/ijms241814016

Jun M, Lee YL, Zhou T, Maric M, Burke B, Park S, Low BC, Chiam KH. Subcellular Force Imbalance in Actin Bundles Induces Nuclear Repositioning and Durotaxis. ACS Applied Materials and Interfaces 2023 Sep 20;15(37):43387-43402. doi: 10.1021/acsami.3c07546

August

Wang Z, Lu H, Wu Y, Ren S, Diaty DM, Fu Y, Zou Y, Zhang L, Wang Z, Wang F, Li S, Huo X, Yu W, Xu J. Predicting recurrence in osteosarcoma via a quantitative histological image classifier derived from tumour nuclear morphological features. CAAI Transactions on Intelligence Technology, Vol 8, Issue 3, Sep 2023, Pg 836-848, doi: 10.1049/cit2.12175

Awate S, Mubarka S, Huber RG. Whole Genomic Characterization of Streptococcus iniae Isolates from Barramundi (Lates calcarifer) and Preliminary Evidence of Cross-Protective Immunization. Vaccines 2023, 11(9), 1443; doi:10.3390/vaccines11091443

Zhou T, Cheah CCH, Chin EWM, Chen J, Farm HJ, Goh ELK, Chiam KH. ContrastivePose: A contrastive learning approach for self-supervised feature engineering for pose estimation and behavorial classification of interacting animals. Computers in Biology and Medicine, Vol 165, Oct 2023, 107416, doi: 10.1016/j.compbiomed.2023.107416

Lena JB, Goncalves RA, Kharel S, Kannan S, Verma CS, Pinchi KM, Lim S, Lam YM. Elucidating the Effect of Polyethylene Terephthalate Chain Structure on Its Enzymatic Degradation Behavior. ACS Sustainable Chemistry and Engineering, 2023, 11, 38, 13974–13987, doi: 10.1021/acssuschemeng.3c02695

Kaya NA, Tai D, Lim X, Lim JQ, Lau MC, Goh D, Phua CZJ, Wee FYT, Joseph CR, Lim JCT, Neo ZW, Ye J, Cheung L, Lee J, Loke KSH, Gogna A, Yao F, Lee MY, Shuen TWH, Toh HC, Hilmer A, Chan YS, Lim TK, Tam WL, Choo SP, Yeong J, Zhai W. Multimodal molecular landscape of response to Y90-resin microsphere radioembolization followed by nivolumab for advanced hepatocellular carcinoma. Journal for Immunotherapy of Cances, 2023 Aug;11(8):e007106. doi: 10.1136/jitc-2023-007106

Dutta C, Krishnamurthy P, Su D, Yoo SH, Collie GW, Pasco M, Marzinek JK, Bond PJ, Verma C, Grélard A, Loquet A, Li J, Luo M, Barboiu M, Guichard G, Kini RM, Kumar PP. Nature-inspired synthetic oligourea foldamer channels allow water transport with high salt rejection. Chem. Vol 9, Issue 8, P2237-22542023 Aug 10;9:2237-54, doi: 10.1016/j.chempr.2023.04.007

July

Querdasi FR, Enders C, Karnani N, Broekman B, Yap Seng C, Gluckman PD, Mary Daniel L, Yap F, Eriksson JG, Cai S, Chong MF, Toh JY, Godfrey K, Meaney MJ, Callaghan BL. Multigenerational adversity impacts on human gut microbiome composition and socioemotional functioning in early childhood. PNAS: Proceedings of the National Academy of Sciences of the United States of America, 2023 Jul 25;120(30):e2213768120. doi: 10.1073/pnas.2213768120

Teo YX, Lee KY, Goh CJH, Wang LC, Sobota RM, Chiam KH, Du C, Wan ACA. Fungus-derived protein particles as cell-adhesive matrices for cell-cultivated food. npj Science of Food, 7, 34 (2023), doi: 10.1038/s41538-023-00209-y

Krutz NL, Kimber I, Winget J, Nguyen MN, Limviphuvadh V, Maurer-Stroh S, Mahony C, Gerberick GF. Application of AllerCatPro 2.0 for protein safety assessments of consumer products. Frontiers in Allergy, 11 Jul 23, Vol. 4, doi:10.3389/falgy.2023.1209495

June

Selvarajoo K, Giuliani A. Systems Biology and Omics Approaches for Complex Human Diseases. Biomolecules. 2023; 13(7):1080. https://doi.org/10.3390/biom13071080

Sirbu O, Helmy M, Giuliani A, Selvarajoo K. Globally invariant behavior of oncogenes and random genes at population but not at single cell level. npj Systems Biology and Application, 2023 Jun 24;9(1):28. doi: 10.1038/s41540-023-00290-9

Loh JT, Teo JKH, Kannan S, Verma CS, Lim HH, Lam KP. Disrupting the Dok3–Card9 Interaction with Synthetic Peptides Enhances Antifungal Effector Functions of Human Neutrophils. Pharmaceutics 2023, 15(7), 1780; doi: doi/10.3390/pharmaceutics15071780

Li E, Yaochai MY, Ng JM, Huber RG, Bond PJ, Krah A. Observation of multiple protein temperature transitions dependent upon the chemical environment. Journal of Molecular Liquids, Vol 385, 1 Sept 2023, doi: org/10.1016/j.molliq.2023.122348

Waller C, Marzinek JK, McBurnie E, Bond PJ, Williamson PTF, Khalid S. Impact on S. aureus and E. coli Membranes of Treatment with Chlorhexidine and Alcohol Solutions: Insights from Molecular Simulations and Nuclear Magnetic Resonance. Journal of Molecular Biology, Vol. 435, Issue 11, 1 Jun 2023, 435(11):167953. doi: 10.1016/j.jmb.2023.167953

Mah MG, Linster M, Low DHW, Zhuang Y, Jayakumar J, Samsudin F, Wong FY, Bond PJ, Mendenhall IH, Su YCF, Smith GJD. Spike-Independent Infection of Human Coronavirus 229E in Bat Cells. Microbiol Spectr. 2023 Jun 15;11(3):e0348322. doi: 10.1128/spectrum.03483-22.

Patel A, Patel P, Mandlik D, Patel K, Malaviya P, Johar K, Swamy KBS, Patel S, Tanavde V. A novel 3-miRNA network regulates tumour progression in oral squamous cell carcinoma. Biomarker Research 2023 Jun 14;11(1):64. doi: 10.1186/s40364-023-00505-5. PMID: 37316916

Chua BN, Guo WM, Wong HT, Ow DSW, Ho PL, Koh W, Koay A, Wong FT. A sweeter future: Using protein language models for exploring sweeter brazzein homologs. Food Chemistry, Vol 426, 15 Nov 2023, doi: 10.1016/j.foodchem.2023.136580

May

Fleischmann J, Schwaighofer S, De Falco L, Enzler F, Feichtner A, Kugler V, Tschaikner P, Huber RG, Stefan E. Tracking and blocking interdependencies of cellular BRAF-MEK oncokinase activities. PNAS Nexus, 2023, 2, 1-4, doi: 10.1093/pnasnexus/pgad185

Tan KML, Chee J, Lim KLM, Ng M, Gong M, Xu J, Tin F, Natarajan P, Lee BL, Ong CN, Tint MT, Kee MZL, Müller-Riemenschneider F, Gluckman PD, Meaney MJ, Kumar M, Karnani N, Eriksson JG, Nandanan B, Wyss A, Cameron-Smith D. Safety, Tolerability, and Pharmacokinetics of β-Cryptoxanthin Supplementation in Healthy Women: A Double-Blind, Randomized, Placebo-Controlled Clinical Trial. Nutrients, 2023 May 16;15(10):2325. doi: 10.3390/nu15102325

Kasper SH, Otten S, Squadroni B, Orr-Terry C, Kuang Y, Musallem L, Ge L, Yan L, Srinivasaraghavan K, Verma CS, Brown CJ, Johannes CW, Lane DP, Chandramohan A, Patridge AW, Roberts LR, Josien H, Therien AG, Hett EC, Howell BJ, Peier A, Ai X, Cassaday J. A high-throughput microfluidic mechanoporation platform to enable intracellular delivery of cyclic peptides in cell-based assays. Bioengineering & Translational Medicine, 13 May 2023, doi: 10.1002/btm2.10542

Zhou T, Reji R, Kairon RS and Chiam KH. A review of algorithmic approaches for cell culture media optimization. Frontiers in Bioengineering and Biotechnology, 11:1195294, doi: 10.3389/fbioe.2023.1195294

Dutta C, Krishnamurthy P, Su D, Sung HY, Collie GW, Pasco M, Marzinek JK, Bond PJ, Verma CS, Grelard A, Loquet A, Li J, Luo M, Barboiu M, Guichard G, Kini RM, Kumar PP. Nature-inspired synthetic oligourea foldamer channels allow water transport with high salt rejection. Chem, 11 May 23, Vol. 9, Issue 5, doi.org/10.1016/j.chempr.2023.04.007

Zuzic L, Marzinek JK, Anand GS, Warwicker J, Bond PJ. A pH-dependent cluster of charges in a conserved cryptic pocket on flaviviral envelopes. Elife. 2023 May 5;12:e82447. doi: 10.7554/eLife.82447.

Stephenson MC, Ho JXM, Migliavacca E, Kalimeri M, Karnani N, Banerji S, Totman JJ, Feige JN, Merchant RA, Tay SKH. Evidence for inefficient contraction and abnormal mitochondrial activity in sarcopenia using magnetic resonance spectroscopy. Journal of Cachexia, Sarcopenia and Muscle 2023;14: 1482–1494, doi: 10.1002/jcsm.13220

Zhou T, Chiam KH. Synthetic data generation method for data-free knowledge distillation in regression neural networks. Expert Systems with Applications, Vol 227, 1 Oct 2023, 120327, doi: 10.1016/j.eswa.2023.120327

Boon PLS, Martins AS, Lim XN, Enguita FJ, Santos NC, Bond PJ, Wan Y, Martins IC, Huber RG. Dengue Virus Capsid Protein Facilitates Genome Compaction and Packaging. International Journal of Molecular Sciences. 2023; 24(9):8158, doi: 10.3390/ijms24098158

April

Frittoli E, Palamidessi A, Iannelli F, Zanardi F, Villa S, Barzaghi L, Abdo H, Cancila V, Beznoussenko GV, Della Chiara G, Pagani M, Malinverno C, Bhattacharya D, Pisati F, Yu W, Galimberti V, Bonizzi G, Martini E, Mironov AA, Gioia U, Ascione F, Li Q, Havas K, Magni S, Lavagnino Z, Pennacchio FA, Maiuri P, Caponi S, Mattarelli M, Martino S, d'Adda di Fagagna F, Rossi C, Lucioni M, Tancredi R, Pedrazzoli P, Vecchione A, Petrini C, Ferrari F, Lanzuolo C, Bertalot G, Nader G, Foiani M, Piel M, Cerbino R, Giavazzi F, Tripodo C, Scita G. Tissue fluidification promotes a cGAS–STING cytosolic DNA response in invasive breast cancer. Nature Materials, 22, 644–655 (2023), doi: 10.1038/s41563-022-01431-x

Teo Z.L, Kwee A, Lim J.C.W, Lam C.S.P, Ho D, Maurer-Stroh S, Su Y, Chesterman S, Chen T, Tan C.C, Wong T.Y, Ngiam K.Y, Tan C.H, Soon D, Choong M.L, Chua R, Wong S, Lim C, Cheong W.Y, Ting D.S.W. Artificial intelligence innovation in healthcare: Relevance of reporting guidelines for clinical translation from bench to bedside. Annals of the Academy of Medicine Singapore, Vol. 52, No 4, 199-212, doi: 10.47102/annals-acadmedsg.2022452

Koh WLC, Poh SE, Lee CK, Chan THM, Yan G, Kong KW, Lau L, Lee WYT, Cheng C, Hoon S, Seow Y. Towards a Rapid-Turnaround Low-Depth Unbiased Metagenomics Sequencing Workflow on the Illumina Platforms. Bioengineering 2023, 10(5), 520, doi: 10.3390/bioengineering10050520

Oner MU, Kye-Jet JMS, Lee HK, Sung WK. Distribution based MIL pooling filters: Experiments on a lymph node metastases dataset. Medical Image Analysis, 2023, Vol. 87, July 2023, Article 102813, doi: 10.1016/j.media.2023.102813

Lee RY, Ng CW, Rajapakse MP, Ang N, Yeong JPS, Lau MC. The promise and challenge of spatial omics in dissecting tumour microenvironment and the role of AI. Frontiers in Oncology, 2023, 1 May, Vol 13, doi: 10.3389/fonc.2023.1172314

Lee RY, Wu Y, Goh D, Tan V, Ng CW, Lim JCT, Lau MC, Yeong JPS. Application of Artificial Intelligence to In Vitro Tumor Modeling and Characterization of the Tumor Microenvironment. Advanced Healthcare Materials, 2023 Apr 15, doi: 10.1002/adhm.202202457

Tan ZW, Toong PJ, Guarnera E, Berezovsky IN. Disrupted chromatin architecture in olfactory sensory neurons: looking for the link from COVID-19 infection to anosmia. Scientific Reports 2023 Apr 11;13(1):5906, doi: 10.1038/s41598-023-32896-8

Guarnera E, Berezovsky IN. Sequence-dependent model of allosteric communication. The Journal of Chemical Physics, 158, Issue 13, 7 Apr 23, doi: 10.1063/5.0139848

March

Paknezhad, M. Rengarajan, H. Yuan, C. Suresh, S. Gupta, M. Ramasamy, S. Lee, H.K. Improving transparency and representational generalizability through parallel continual learning. Neural Networks, Volume 161, April 2023, Pages 449-465, doi: 10.1016/j.neunet.2023.02.007

Shih CC, Chen J, Lee AS, Bertin N, Hebrard M, Khor CC, Li Z, Juan Tan JH, Meah WY, Peh SQ, Mok SQ, Sim KS, Liu J, Wang L, Wong E, Li J, Tin A, Cheng CY, Heng CK, Yuan JM, Koh WP, Saw SM, Friedlander Y, Sim X, Chai JF, Chong YS, Davila S, Goh LL, Lee ES, Wong TY, Karnani N, Leong KP, Yeo KK, Chambers JC, Lim SC, Goh RSM, Tan P, Dorajoo R. A five-safes approach to a secure and scalable genomics data repository. iScience. 2023 Mar 31;26(4):106546. doi: 10.1016/j.isci.2023.106546

Batagov A, Dalan R, Wu A, Lai W, Tan CS, Eisenhaber F. Generalized metabolic flux analysis framework provides mechanism-based predictions of ophthalmic complications in type 2 diabetes patients. Health Inormation Science and Systems 2023 Mar 29;11(1):18. doi: 10.1007/s13755-023-00218-x

Tay MZ, Goh YS, Fong SW, Chang ZW, Rouers A, Wong N, Torres-Ruesta A, Huang Y, Selvam SK, Hor PX, Loh CY, Wang B, Mohd Salleh SN, Ngoh EZX, Lee RTC, Neo V, Kam IKJ, Poh XY, Rao S, Chia PY, Ong SWX, Lee TH, Lim C, Teo J; NCID Study Group; PRIBIVAC Cohort Study Group; Maurer-Stroh S, Wang CI, Leo YS, Lin RTP, Lye DC, Young BE, Ng LFP, Renia L. Heterologous mRNA vaccine boosters induce a stronger and longer-lasting antibody response against Omicron XBB variant. The Lancet Regional Health - Western Pacific, 2023 Apr;33:100732. doi: 10.1016/j.lanwpc.2023.100732

February

Ta LDH, Chan JCY, Yap GC, Huang CH, Tham EH, Loo EXL, Suani NHA, Shek LP, Karnani N, Goh AEN, Van Bever HPS, Teoh OH, Chan YH, Lay C, Knol J, Yap F, Tan KH, Chong YS, Chong MFF, Chan SY, Eriksson JG, Godfrey KM, Chan ECY, Lee BW. Prenatal diet, plasma micronutrients/metabolome and inflammatory status influence the development of atopic eczema in early childhood. Allergy: European Journal of Allergy and Clinical Immunology, Vol 78, Issue 3, March 2023, Pg 867-871, doi: 10.1111/all.15573

Tantoso E, Eisenhaber B, Sinha S, Jensen LJ, Eisenhaber F. About the dark corners in the gene function space of Escherichia coli remaining without illumination by scientific literature. Biology Direct, 2023 Feb 28;18(1):7. doi: 10.1186/s13062-023-00362-0

Krah A, Vogelaar T, de Jong SI, Claridge JK, Bond PJ, McMillan DGG. ATP binding by an F1Fo ATP synthase ε subunit is pH dependent, suggesting a diversity of ε subunit functional regulation in bacteria. Frontiers in Molecular Biosciences, 2023 Feb 27;10:1059673. doi: 10.3389/fmolb.2023.1059673

Koh LCW, Seow Y, Kong KW, Lau MLL, Kumar SK, Yan G, Lee CK, Yan B, Tambyah PA, Hoon S. Sub genomic analysis of SARS-CoV-2 using short read amplicon-based sequencing. Frontiers in Genetics, Volume 14 - 2023, doi: 10.3389/fgene.2023.1086865

Gangavarapu K, Latif AA, Mullen JL, Alkuzweny M, Hufbauer E, Tsueng G, Haag E, Zeller M, Aceves CM, Zaiets K, Cano M, Zhou X, Qian Z, Sattler R, Matteson NL, Levy JI, Lee RTC, Freitas L, Maurer-Stroh S; GISAID Core and Curation Team; Suchard MA, Wu C, Su AI, Andersen KG, Hughes LD. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. Nature Methods 2023 Apr;20(4):512-522. doi: 10.1038/s41592-023-01769-3

Chen L, Mir SA, Bendt AK, Chua EWL, Narasimhan K, Tan KM, Loy SL, Tan KH, Shek LP, Chan J, Yap F, Meaney MJ, Chan SY, Chong YS, Gluckman PD, Eriksson JG, Karnani N, Wenk MR. Plasma lipidomic profiling reveals metabolic adaptations to pregnancy and signatures of cardiometabolic risk: a preconception and longitudinal cohort study. BMC Med. 2023 Feb 13;21(1):53. doi: 10.1186/s12916-023-02740-x

Samsudin F, Raghuvamsi P, Petruk G, Puthia M, Petrlova J, MacAry P, Anand GS, Bond PJ, Schmidtchen A. SARS-CoV-2 spike protein as a bacterial lipopolysaccharide delivery system in an overzealous inflammatory cascade. Journal of Molecular Cell Biology, 2023 Feb 7;14(9):mjac058. doi: 10.1093/jmcb/mjac058

Chan SY, Barton SJ, Loy SL, Chang HF, Titcombe P, Wong JT, Ebreo M, Ong J, Tan KM, Nield H, El-Heis S, Kenealy T, Chong YS, Baker PN, Cutfield WS, Godfrey KM; NiPPeR Study Group. Time-to-conception and clinical pregnancy rate with a myo-inositol, probiotics, and micronutrient supplement: secondary outcomes of the NiPPeR randomized trial. Fertility and Sterility, Vol 119, Issue 6, Jun 2023, Pg 1031-1042. doi: 10.1016/j.fertnstert.2023.01.047

Toh MR, Wong EYT, Wong SH, Ng AWT, Loo LH, Chow PK, Ngeow J. Global Epidemiology and Genetics of Hepatocellular Carcinoma. Gastroenterology. 2023 Apr;164(5):766-782. doi: 10.1053/j.gastro.2023.01.033

January

Huber RG, Pandey S, Chhangani D, Rincon-Limas DE, Staff NP, Yeo CJJ. Identification of potential pathways and biomarkers linked to progression in ALS. Annals of Clinical and Translational Neurology, 2023 Feb;10(2):150-165. doi: 10.1002/acn3.51697

Cable J, Denison MR, Kielian M, Jackson WT, Bartenschlager R, Ahola T, Mukhopadhyay S, Fremont DH, Kuhn RJ, Shannon A, Frazier MN, Yuen KY, Coyne CB, Wolthers KC, Ming GL, Guenther CS, Moshiri J, Best SM, Schoggins JW, Jurado KA, Ebel GD, Schäfer A, Ng LFP, Kikkert M, Sette A, Harris E, Wing PAC, Eggenberger J, Krishnamurthy SR, Mah MG, Meganck RM, Chung D, Maurer-Stroh S, Andino R, Korber B, Perlman S, Shi PY, Bárcena M, Aicher SM, Vu MN, Kenney DJ, Lindenbach BD, Nishida Y, Rénia L, Williams EP. Positive-strand RNA viruses—a Keystone Symposia report. Annals of the New York Academy of Sciences, 2023 Mar;1521(1):46-66. doi: 10.1111/nyas.14957

Dung NT, Hung LM, Hoa HTT, Nga LH, Hong NTT, Thuong TC, Ngoc NM, Ny NTH, Quy VT, Thoa VTK, Thanh NT, Tho PV, Toan LM, Quang VM, Man DNH, Phat NT, Phuong TTL, Tam TTT, Thoa PTN, Tam NH, Lan TTT, Thanh TT, Maurer-Stroh S, Khanh LTT, Yen LM, Hung NH, Thwaites G, Tung NLN, Thwaites L, Chau NVV, Anh NT, Van Tan L. Monkeypox Virus Infection in 2 Female Travelers Returning to Vietnam from Dubai, United Arab Emirates, 2022. Emerging Infectious Diseases, Vol. 29, No. 4, April 2023, 778-781. doi: 10.3201/eid2904.221835

Wong E, Bertin N, Hebrard M, Tirado-Magallanes R, Bellis C, Lim WK, Chua CY, Tong PML, Chua R, Mak K, Lim TM, Cheong WY, Thien KE, Goh KT, Chai JF, Lee J, Sung JJ, Wong TY, Chin CWL, Gluckman PD, Goh LL, Ban KHK, Tan TW; SG10K_Health Consortium; Sim X, Cheng CY, Davila S, Karnani N, Leong KP, Liu J, Prabhakar S, Maurer-Stroh S, Verma CS, Krishnaswamy P, Goh RSM, Chia I, Ho C, Low D, Virabhak S, Yong J, Zheng W, Seow SW, Seck YK, Koh M, Chambers JC, Tai ES, Tan P. The Singapore National Precision Medicine Strategy. Nature Genetics, 2023 Feb;55(2):178-186. doi: 10.1038/s41588-022-01274-x

Zhang S, Chong LH, Woon JYX, Chua TX, Cheruba E, Yip AK, Li HY, Chiam KH, Koh CG. Zyxin regulates embryonic stem cell fate by modulating mechanical and biochemical signaling interface. Communications Biology 2023 Jan 18;6(1):62. doi: 10.1038/s42003-023-04421-0

Si Z, Li J, Ruan L, Reghu S, Ooi YJ, Li P, Zhu Y, Hammond PT, Verma CS, Bazan GC, Pethe K, Chan-Park MB. Designer co-beta-peptide copolymer selectively targets resistant and biofilm Gram-negative bacteria. Biomaterials 2023 Mar;294:122004. doi: 10.1016/j.biomaterials.2023.122004

Kimoto M, Tan HP, Tan YS, Mislan NABM, Hirao I. Success probability of high-affinity DNA aptamer generation by genetic alphabet expansion. Philosophical Transactions of the Royal Society B, Biological Sciences, 2023 Feb 27;378(1871) doi: 10.1098/rstb.2022.0031

KN BP, CS A, Mohammed A, Chitta KK, To XV, Srour H, Nasrallah F. An end-end deep learning framework for lesion segmentation on multi-contrast MR images—an exploratory study in a rat model of traumatic brain injury. Medical and Biological Engineering and Computing, Vol 61, pg 847-865 (2023) doi: 10.1007/s11517-022-02752-4

Cheng L, Deepak RNVK, Wang G, Meng Z, Tao L, Xie M, Chi W, Zhang Y, Yang M, Liao Y, Chen R, Liang Y, Zhang J, Huang Y, Wang W, Guo Z, Wang Y, Lin JD, Fan H, Chen L. Hepatic mitochondrial NAD+ transporter SLC25A47 activates AMPKα mediating lipid metabolism and tumorigenesis. Hepatology. 2023 Feb 21. doi: 10.1097/HEP.0000000000000314

Go MK, Zhu T, Lim KJH, Hartono YD, Xue B, Fan H, Yew WS. Cannabinoid Biosynthesis Using Noncanonical Cannabinoid Synthases. International Journal of Molecular Sciences, 2023 Jan 9;24(2):1259. doi: 10.3390/ijms24021259

Ong SS, Xu J, Sim CK, Khng AJ, Ho PJ, Kwan PKW, Ravikrishnan A, Tan KB, Tan QT, Tan EY, Tan SM, Putti TC, Lim SH, Tang ELS, Nagarajan N, Karnani N, Li J, Hartman M. Profiling Microbial Communities in Idiopathic Granulomatous Mastitis. International Journal of Molecular Sciences. 2023; 24(2):1042. doi: 10.3390/ijms24021042

Loh JT, Teo JKH, Kannan S, Verma CS, Andiappan AK, Lim HH, Lam KP. DOK3 promotes atopic dermatitis by enabling the phosphatase PP4C to inhibit the T cell signaling mediator CARD11. Science Signaling, 2023 Oct 31; 16(809):eadg5171. doi: 10.1126/scisignal.adg5171

Pabis K, Barardo D, Selvarajoo K, Gruber J, Kennedy BK. A concerted increase in readthrough and intron retention drives transposon expression during aging and senescence. eLife 12: RP87811 doi: 10.7554/eLife.87811.1

Ong YY, Pang WW, Michael N, Aris IM, Sadananthan SA, Tint MT, Liang Choo JT, Ling LH, Karnani N, Velan SS, Fortier MV, Tan KH, Gluckman PD, Yap F, Chong YS, Godfrey KM, Chan SY, Eriksson JG, Chong MF, Wlodek ME, Lee YS. Timing of introduction of complementary foods, breastfeeding, and child cardiometabolic risk: a prospective multiethnic Asian cohort study. The American Journal of Clinical Nutrition, 2023 Jan;117(1):83-92, doi: 10.1016/j.ajcnut.2022.10.021

2022

December

Meivita MP, Lee D, Naikar JS, Go SX, Teoh WC, Tan YS, Bajalovic N, Loke DK. An Efficient, Short Stimulus PANC-1 Cancer Cell Ablation and Electrothermal Therapy Driven by Hydrophobic Interactions. Pharmaceutics. 2022 Dec 28;15(1):106. doi: 10.3390/pharmaceutics15010106

Helmy M, Elhalis H, Liu Y, Chow Y, Selvarajoo K . Perspective: Multiomics and Machine Learning Help Unleash the Alternative Food Potential of Microalgae. Advances in Nutrition, 2022 Dec 23, doi: 10.1016/j.advnut.2022.11.002

November

Oner MU, Ng MY, Giron DM, Xi CEC, Xiang LAY, Singh M, Yu W, Sung W, Wong CF, Lee HK. An AI-assisted tool for efficient prostate cancer diagnosis in low-grade and low-volume cases. Patterns, (2022), doi: 10.1016/j.patter.2022.100642

Wei S, Behn J, Poore CP, Low SW, Nilius B, Fan H, Liao P. Binding epitope for recognition of human TRPM4 channel by monoclonal antibody M4M. Scientific Reports, 2022 Nov 15;12(1):19562. doi: 10.1038/s41598-022-22077-4

October

Khanijou JK, Kulyk H, Berges C, Khoo LW, Ng P, Yeo HC, Helmy M, Bellvert F, Wee C, Selvarajoo K.Metabolomics and modelling approaches for systems metabolic engineering. Metabolic Engineering Communications, Vol. 15, Dec 2022, doi: doi.org/10.1016/j.mec.2022.e00209

Selvarajoo K. Computational Biology and Machine Learning for Metabolic Engineering and Synthetic Biology. Book Chapter : Methods in Molecular Biology, Vol : 2553, doi: 10.1007/978-1-0716-2617-7, ISBN: 978-1-0716-2616-0

Helmy M, Selvarajoo K. Application of GeneCloudOmics: Transcriptomic Data Analytics for Synthetic Biology. Book Chapter : Computational Biology and Machine Learning for Metabolic Engineering and Synthetic Biology, 2022, pp 221-263, doi:10.1007/978-1-0716-2617-7_12, ISBN: 978-1-0716-2617-7

Samsudin F, Raghuvamsi P, Petruk G, Puthia M, Petrlova J, MacAry P, Anand GS, Bond PJ, Schmidtchen A. SARS-CoV-2 spike protein as a bacterial lipopolysaccharide delivery system in an overzealous inflammatory cascade. Journal of Molecular Cell Biology, 2022 Oct 14, mjac058, doi: 10.1093/jmcb/mjac058

September

Yeo HC, Selvarajoo K. Machine learning alternative to systems biology should not solely depend on data. Briefings in Bioinformatics, 2022, doi: 10.1093/bib/bbac436

Tan ZW, Tee WV, Guarnera E, Berezovsky IN. AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design. Nucleic Acids Res. 2022 Sep 28:gkac828. doi: 10.1093/nar/gkac828

Patel A, Patel S, Patel P, Mandlik D, Patel K, Tanavde V. Salivary Exosomal miRNA-1307-5p Predicts Disease Aggressiveness and Poor Prognosis in Oral Squamous Cell Carcinoma Patients. International Journal of Molecular Sciences. 2022; 23(18):10639, doi: 10.3390/ijms231810639

Michael N, Gupta V, Fogel A, Huang J, Chen L, Sadananthan SA, Ong YY, Aris IM, Pang WW, Yuan WL, Loy SL, Thway Tint M, Tan KH, Chan JK, Chan SY, Shek LP, Yap F, Godfrey K, Chong YS, Gluckman P, Velan SS, Forde CG, Lee YS, Eriksson JG, Karnani N. Longitudinal characterization of determinants associated with obesogenic growth patterns in early childhood. International Journal of Epidemiology, 2022 Sep 10;dyac177. doi: 10.1093/ije/dyac177

Bose U, Broadbent JA, Juhász A, Karnaneedi S, Johnston EB, Stockwell S, Byrne K, Limviphuvadh V, Maurer-Stroh S, Lopata AL, Colgrave ML. Comparison of protein extraction protocols and allergen mapping from black soldier fly Hermetia illucens. Journal of Proteomics, 2022 Oct 30;269:104724. doi: 10.1016/j.jprot.2022.104724. Epub 2022 Sep 10

Krah A, Gruber G, Bond PJ. Binding properties of the anti-TB drugs bedaquiline and TBAJ-876 to a mycobacterial F-ATP synthase. Current Research in Structural Biology, Vol. 4, 2022, Pg 278-284, doi : 10.1016/j.crstbi.2022.09.001

Palafox M, Monserrat L, Bellet M, Villacampa G, Gonzalez-Perez A, Oliveira M, Brasó-Maristany F, Ibrahimi N, Kannan S, Mina L, Herrera-Abreu MT, Òdena A, Sánchez-Guixé M, Capelán M, Azaro A, Bruna A, Rodríguez O, Guzmán M, Grueso J, Viaplana C, Hernández J, Su F, Lin K, Clarke RB, Caldas C, Arribas J, Michiels S, García-Sanz A, Turner NC, Prat A, Nuciforo P, Dienstmann R, Verma CS, Lopez-Bigas N, Scaltriti M, Arnedos M, Saura C, Serra V. High p16 expression and heterozygous RB1 loss are biomarkers for CDK4/6 inhibitor resistance in ER+ breast cancer. Nature Communications 2022 Sep 7;13(1):5258. doi: 10.1038/s41467-022-32828-6

August

Chew QH, Prakash KNB, Koh LY, Chilla G, Yeow LY, Sim K. Neuroanatomical subtypes of schizophrenia and relationship with illness duration and deficit status. Schizophrenia Research, Vol. 248, Oct 22, Pg 107-113, doi: 10.1016/j.schres.2022.08.004,

Frosi Y, Lin YC, Shimin J, Ramlan SR, Hew K, Engman AH, Pillai A, Yeung K, Cheng YX, Cornvik T, Nordlund P, Goh M, Lama D, Gates ZP, Verma CS, Thean D, Lane DP, Asial I, Brown CJ. Engineering an Autonomous VH Domain to modulate intracellular pathways and to Interrogate the eIF4F Complex. Nature Communications 2022 Aug 18;13(1):4854. doi: 10.1038/s41467-022-32463-1

July

Mir SA, Chen L, Burugupalli S, Burla B, Ji S, Smith AAT, Narasimhan K, Ramasamy A, Tan KM, Huynh K, Giles C, Mei D, Wong G, Yap F, Tan KH, Collier F, Saffery R, Vuillermin P, Bendt AK, Burgner D, Ponsonby AL, Lee YS, Chong YS, Gluckman PD, Eriksson JG, Meikle PJ, Wenk MR, Karnani N. Population-based plasma lipidomics reveals developmental changes in metabolism and signatures of obesity risk: a mother-offspring cohort study. BMC Medicine 2022 Jul 25;20(1):242. doi: 10.1186/s12916-022-02432-y

Berezovsky IN, Nussinov R. Multiscale Allostery: Basic Mechanisms and Versatility in Diagnostics and Drug Design. Journal of Molecular Biology, Volume 434, Issue 17, 15 September 2022, 167751, doi: 10.1016/j.jmb.2022.167751

Nicolaou ST, Kannan S, Warwicker J, Verma CS. Activation of p53: How phosphorylated Ser15 triggers sequential phosphorylation of p53 at Thr18 by CK1δ. Proteins. 2022 Dec;90(12):2009-2022. doi: 10.1002/prot.26393. Epub 2022 Jul 14

June

Iyengar PV, Marvin DL, Lama D, Tan TZ, Suriyamurthy S, Xie F, van Dinther M, Mei H, Verma CS, Zhang L, Ritsma L, Ten Dijke P. TRAF4 inhibits bladder cancer progression by promoting BMP/SMAD signalling pathway. Molecular Cancer Research, 2022 Jun 22, doi: 10.1158/1541-7786.MCR-20-1029

Goh CJH, Cui L, Wong JH, Lewis J, Goh M, Kong KW, Yang LK, Alfatah M, Kanagasundaram Y, Hoon S, Arumugam P. Diethyl phthalate (DEP) perturbs nitrogen metabolism in Saccharomyces cerevisiae. Scientific Reports, 2022 Jun 17;12(1):10237. doi: 10.1038/s41598-022-14284-w

Puthia M, Marzinek JK, Petruk G, Ertürk Bergdahl G, Bond PJ, Petrlova J. Antibacterial and Anti-Inflammatory Effects of Apolipoprotein E. Biomedicines 2022, 10, 1430, doi: 10.3390/biomedicines10061430

Tantoso E, Eisenhaber B, Kirsch M, Shitov V, Zhao Z, Eisenhaber F. To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131. BMC Biology 2022 Jun 16;20(1):146. doi: 10.1186/s12915-022-01347-7

Alfatah M, Eisenhaber F . The PICLS high-throughput screening method for agents extending cellular longevity identifies 2,5-anhydro-D-mannitol as novel anti-aging compound. Geroscience. 2022 Jun 15. doi: 10.1007/s11357-022-00598-0. Epub ahead of print

Chen H, Wang J, Liu Y, Ling IQE, Shih CC, Wu D, Fu Z, Lee RTC, Xu M, Chow VT, Maurer-Stroh S, Zhou D, Liu J, Zhai W. MADE: A Computational Tool for Predicting Vaccine Effectiveness for the Influenza A(H3N2) Virus Adapted to Embryonated Egg.Vaccines. 2022; 10(6):907. doi: 10.3390/vaccines10060907

Yeong J, Lum HYJ, Teo CB, Tan BKJ, Chan YH, Tay RYK, Choo JRE, Jeyasekharan AD, Miow QH, Loo LH, Yong WP, Sundar R. Choice of PD-L1 immunohistochemistry assay influences clinical eligibility for gastric cancer immunotherapy. Gastric Cancer 2022, doi : 10.1007/s10120-022-01301-0

Zuzic L, Samsudin F, Shivgan AT, Raghuvamsi PV, Marzinek JK, Boags A, Pedebos C, Tulsian NK, Warwicker J, MacAry P, Crispin M, Khalid S, Anand GS, Bond PJ. Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein. Structure 30, Pg 1062-1074, Aug 4 2022, doi: 10.1016/j.str.2022.05.006

Kumar M, Ang LT, Png H, Ng M, Tan K, Loy SL, Tan KH, Chan JKY, Godfrey KM, Chan SY, Chong YS, Eriksson JG, Feng M, Karnani N. Automated Machine Learning (AutoML)-Derived Preconception Predictive Risk Model to Guide Early Intervention for Gestational Diabetes Mellitus. International Journal of Environmental Research and Public Health, 2022, 19(11), 6792, doi: 10.3390/ijerph19116792

May

Nguyen MN, Krutz NL, Limviphuvadh V, Lopata AL, Gerberick GF, Maurer-Stroh S. AllerCatPro 2.0: a web server for predicting protein allergenicity potential.Nucleic Acids Research, 2022 May 30, Vol. 50 doi: 10.1093/nar/gkac446

ElSawy KM, Alminderej FM, Verma CS, Caves LSD. Activating the p53 anti-cancer pathway by targeting the MDM2/MDMX dimer interface with short peptide segments: a computational peptide design experiment. Molecular Systems Design & Engineering, 2022, 2022,7, 996-1006 doi: 10.1039/D2ME00042C

Parikh BH, Liu Z, Blakeley P, Lin Q, Singh M, Ong JY, Ho KH, Lai JW, Bogireddi H, Tran KC, Lim JYC, Xue K, Al-Mubaarak A, Yang B, R S, Regha K, Wong DSL, Tan QSW, Zhang Z, Jeyasekharan AD, Barathi VA, Yu W, Cheong KH, Blenkinsop TA, Hunziker W, Lingam G, Loh XJ, Su X. A bio-functional polymer that prevents retinal scarring through modulation of NRF2 signalling pathway. Nature Communications, 2022 May 19; 13(1):2796. doi: 10.1038/s41467-022-30474-6

April

Smith DJ, Helmy M, Lindley ND, Selvarajoo K. The transformation of our food system using cellular agriculture: What lies ahead and who will lead it? Trends in Food Science & Technology 127, (2022): 368-376. doi: 10.1016/j.tifs.2022.04.015

Liu Y, Chi W, Tao L, Wang G, Deepak RNVK, Sheng L, Chen T, Feng Y, Cao X, Cheng L, Zhao X, Liu X, Deng H, Fan H, Jiang P, Chen L. Ablation of H+/glucose Exporter SLC45A2 Enhances Melanosomal Glycolysis to Inhibit Melanin Biosynthesis and Promote Melanoma Metastasis. Journal of Investigative Dermatology, 2022 Apr 22, doi: 10.1016/j.jid.2022.04.008

Pan H, Tan PF, Lim IY, Huan J, Teh AL, Chen L, Gong M, Tin F, Mir SA, Narasimhan K, Chan JKY, Tan KH, Kobor MS, Meikle PJ, Wenk MR, Chong YS, Eriksson JG, Gluckman PD, Karnani N. Integrative Multi-Omics database (iMOMdb) of Asian Pregnant Women. Human Molecular Genetics, 2022, Apr 21:ddac079. doi: 10.1093/hmg/ddac079

Lim KJH, Hartono YD, Xue B, Go MK, Fan H, Yew WS. Structure-Guided Engineering of Prenyltransferase NphB for High-Yield and Regioselective Cannabinoid Production. ACS Catalysis, 2022, 12, 4628−4639, doi:10.1021/acscatal.2c00786

March

Nemoto W, Yamanishi Y, Limviphuvadh V, Fujishiro S, Shimamura S, Fukushima A and Toh H. A Web Server for GPCR-GPCR Interaction Pair Prediction.Frontiers in Endocrinology, 24 Mar 22, doi: 10.3389/fendo.2022.825195

Kolloff C, Mazur A, Marzinek JK, Bond PJ, Olsson S, Hiller S. Motional clustering in supra-τ c conformational exchange influences NOE cross-relaxation rate. Journal of Magnetic Resonance, Vol. 338, May 2022, doi : 10.1016/j.jmr.2022.107196

Teh YC, Chooi MY, Liu D, Kwok I, Lai GC, Ayub Ow Yong L, Ng M, Li JLY, Tan Y, Evrard M, Tan L, Liong KH, Leong K, Goh CC, Chan AYJ, Shadan NB, Mantri CK, Hwang YY, Cheng H, Cheng T, Yu W, Tey HL, Larbi A, St John A, Angeli V, Ruedl C, Lee B, Ginhoux F, Chen SL, Ng LG, Ding JL, Chong SZ. Transitional premonocytes emerge in the periphery for host defense against bacterial infections. Science Advances, 2022 Mar 4; 8(9): eabj4641. doi: 10.1126/sciadv.abj4641

Jing JL, Ning TCY, Natali F, Eisenhaber F, Alfatah M. Iron Supplementation Delays Aging and Extends Cellular Lifespan through Potentiation of Mitochondrial Function. Cells, 2022; 11(5):862, doi: 10.3390/cells11050862

February

Ng TYJ, Tan YS.Accelerated Ligand-Mapping Molecular Dynamics Simulations for the Detection of Recalcitrant Cryptic Pockets and Occluded Binding Sites. Journal of Chemical Theory and Computation, 2022 18 (3), 1969-1981. doi: 10.1021/acs.jctc.1c01177 "

Tang LWT, Wei W, Verma RK, Koh SK, Zhou L, Fan H, Chan ECY. Direct and Sequential Bioactivation of Pemigatinib to Reactive Iminium Ion Intermediates Culminate in Mechanism-Based Inactivation of Cytochrome P450 3A. Drug Metabolism and Disposition, 13 Feb 22, doi: 10.1124/dmd.121.000804

Li J, Kannan S, Aronica P, Brown C, Patridge A, Verma C. Molecular descriptors suggest stapling as a strategy for optimizing membrane permeability of cyclic peptides. The Journal of Chemical Physics, 2022 Feb 14; Vol. 156, Issue 6, doi: 10.1063/5.0078025

January

Paknezhad M, Cuong PN, Winarto AA, Cheong A, Beh CY, Wu J. Explaining adversarial vulnerabiity with a data sparisty hypothesis. Neurocomputing, 2022, doi: 10.1016/j.neucom.2022.01.062

Chen L, Ling KTM, Gong M, Chong MFF, Tan KH, Chong YS, Meaney MJ, Gluckman PD, Eriksson JG, Karnani N.Variability in newborn telomere length is explained by inheritance and intrauterine environment. BMC Medicine, 2022 Jan 25;20(1):20. doi: 10.1186/s12916-021-02217-9

Tan ZW, Tee WV, Samsudin F, Guarnera E, Bond PJ, Berezovsky IN. Allosteric perspective on the mutability and druggability of the SARS-CoV-2 Spike protein. Structure, 20 Jan 2022, doi: 10.1016/j.str.2021.12.011

Reid LM, Guzzetti I, Svensson T, Carlsson AC, Su W, Leek T, Von Sydow L, Czechtizky W, Miljak M, Verma C, De Maria L, Essex JW.How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP, TP2 and ONEG? Chemical Science, 2022, 13, 1957-1971, doi: 10.1039/d1sc03496k

2021

December

Krishna Deepak RNV, Verma RK, Hartono YD, Yew WS, Fan H. Recent Advances in Structure, Function, and Pharmacology of Class A Lipid GPCRs: Opportunities and Challenges for Drug Discovery. Pharmaceuticals 2022, 15(1), 12, doi: 10.3390/ph15010012

Ankrah NYD, Bernstein DB, Biggs M, Carey M, Engevik M, García-Jiménez B, Lakshmanan M, Pacheco AR, Sulheim S, Medlock GL. Enhancing Microbiome Research through Genome-Scale Metabolic Modeling. mSystems. 2021 Dec 21;6(6):e0059921. doi: 10.1128/mSystems.00599-21. Epub 2021 Dec 14

Szenker-Ravi E, Ott T, Khatoo M, de Bellaing AM, Goh WX, Chong YL, Beckers A, Kannesan D, Louvel G, Anujan P, Ravi V, Bonnard C, Moutton S, Schoen P, Fradin M, Colin E, Megarbane A, Daou L, Chehab G, Di Filippo S, Rooryck C, Deleuze JF, Boland A, Arribard N, Eker R, Tohari S, Ng AY, Rio M, Lim CT, Eisenhaber B, Eisenhaber F, Venkatesh B, Amiel J, Crollius HR, Gordon CT, Gossler A, Roy S, Attie-Bitach T, Blum M, Bouvagnet P, Reversade B. Discovery of a genetic module essential for assigning left–right asymmetry in humans and ancestral vertebrates Nature. Genetics 2021 Dec 13. doi: 10.1038/s41588-021-00970-4

Oner MU, Chen J, Revkov E, James A, Seow YH, Kaya AN, Alvarez JJS, Takano A, Cheng XM, Lim TKH, Tan DSW, Zhai W, Skanderup AJ, Sung WK, Lee HK. Obtaining spatially resolved tumor purity maps using deep multiple instance learning in a pan-cancer study. Patterns, Feb 11 2022, doi: 10.1016/j.patter.2021.100399

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.

Tan K, Tint MT, Michael N, Yap F, Chong YS, Tan KH, Godfrey KM, Larbi A, Lee YS, Chan SY, Fortier MV, Eriksson JG, Karnani N. Determinants of cord blood adipokines and association withneonatal abdominal adipose tissue distribution. International Journal of Obesity, 2021 Dec 4, doi: 10.1038/s41366-021-00975-3

Khare S, Gurry C, Freitas L, Schultz MB, Bach G, Diallo A, Akite N, Ho J, Lee TCR, Yeo W, Team GCC, Maurer-Stroh S. GISAID's Role in Pandemic Response. China CDC Weekly, 2021, 3(49): 1049-1051, doi: 10.46234/ccdcw2021.255

Tromp J, Seekings PJ, Hung CL, Iversen MB, Frost MJ, Ouwerkerk W, Jiang Z, Eisenhaber F, Goh RSM, Zhao H, Huang W, Ling LH, Sim D, Cozzone P, Richards AM, Lee HK, Solomon SD, Lam CSP, Ezekowitz JA. Automated Interpretation of Systolic and Diastolic Function on the Echocardiogram: A Multicohort Study. The Lancet Digital Health, Vol 4, Issue 1, E46-E54, Jan 1 2022, doi: 10.1016/S2589-7500(21)00235-1

Arvind CS, Totla A,Tanisha J, Nandini S, Jyothi R, Aditya K, Keerthan, M Farhan, Sumukh G Guruprasad AK. Deep Learning Based Plant Disease Classification With Explainable AI and Mitigation Recommendation. Proceedings: 2021 IEEE Symposium Series on Computational Intelligence (SSCI), 2021, 5-7 Dec 2021, pp. 01-08, doi: 10.1109/SSCI50451.2021.9659869

November

Giuliani A, Thuy TB, Helmy M, Selvarajoo K. Identifying toggle genes from transcriptome-wide scatter: A new perspective for biological regulation. Genomics, Vol. 114, Issue 1, Jan 2022, Pg 215-228, doi :10.1016/j.ygeno.2021.11.027

Helmy M, Agrawal R, Ali Javed, Soudy M, Thuy TB, Selvarajoo K. GeneCloudOmics: A Data Analytic Cloud Platform for High-Throughput Gene Expression Analysis. Frontiers in Bioinformatics, Nov 21, Vol. 1, Article 693836, doi : 10.3389/fbinf.2021.693836

Eisenhaber F, Verma C, Blundell T. In memoriam of Narayanaswamy Srinivasan (1962-2021). Proteins, 2021, Nov 25, doi: 10.1002/prot.26287

Barbieri A, Thonghin N, Shafi T, Prince SM, Collins RF, Ford RC. Structure of ABCB1/P-Glycoprotein in the Presence of the CFTR Potentiator Ivacaftor. Membranes 2021, 11, 923, doi: 10.3390/membranes11120923

Trovato F, Trylska J, Bond PJ and Wolynes PG. Editorial: Combining Simulations, Theory, and Experiments into Multiscale Models of Biological Events. Frontiers in Molecular Biosciences, 19 Nov 21, 8:797754. doi: 10.3389/fmolb.2021.797754

Yip AK, Zhang S, Chong LH, Cheruba E, Woon JYX, Chua TX, Goh CJH, Yang H, Tay CY, Koh CG, Chiam KH. Zyxin Is Involved in Fibroblast Rigidity Sensing and Durotaxis. Frontiers in Cell and Developmental Biology, Nov 2021, Vol 9, Article 735298, doi: 10.3389/fcell.2021.735298

Helmy M, Selvarajoo K. Systems Biology to Understand and Regulate Human Retroviral Proinflammatory Response. Frontiers in Immunology, Nov 2021, Vol. 12, Article 736349, doi: 10.3389/fimmu.2021.736349

Ng OT, Koh V, Chiew CJ, Marimuthu K, Thevasagayam NM, Mak TM, Chua JK, Ong SSH, Lim YK, Ferdous Z, Johari AKB, Chen MI, Maurer-Stroh S, Cui L, Lin RTP, Tan KB, Cook AR, Leo PY, Lee PVJ. Impact of Delta Variant and Vaccination on SARS-CoV-2 Secondary Attack Rate Among Household Close Contacts. The Lancet Regional Health - Western Pacific, 2021 Dec;17:100299, doi:10.1016/j.lanwpc.2021.100299

October

Chawla H, Jossi SE, Faustini SE, Samsudin F, Allen JD, Watanabe Y, Newby ML, Marcial-Juarez E, Lamerton RE, McLellan JS, Bond PJ, Richter AG, Cunningham AF, Crispin M. Glycosylation and Serological Reactivity of an Expression-enhanced SARS-CoV-2 Viral Spike Mimetic. Journal of Molecular Biology, Vol. 434, Issue 2, 2022, doi : 10.1016/j.jmb.2021.167332

Chan SSY, Lee D, Meivita MP, Li L, Tan YS, Bajalovic N, Loke DK. Ultrasensitive two-dimensional material-based MCF-7 cancer cell sensor driven by perturbation processes. Nanoscale Advances, 2021, 3, 6974-6983, doi : 10.1039/D1NA00614B

Kong JW, Lam Z, Chan KH, Ganguly R, Lee JYJ, Loo LH, Webster RD, Wong ZX, Leong WK. Group VIII Metal Carbonyl Cluster-Boronic Acid Conjugates: Cytotoxicity and Mode of Action Studies. ACS Omega, 22 Oct 2021, 6(43):29045-29053, doi: 10.1021/acsomega.1c04116

Wang J, Zhang T, Yu Z, Tan WT, Wen M, Shan Y, Lambert FRP, Huber RG, Wan Y. Genome-wide RNA structure changes during human neurogenesis modulate gene regulatory networks. Molecular Cell, Vol. 81, Issue 23, 2 Dec 2021, Pg 4942-4953, doi: 10.1016/j.molcel.2021.09.027

Lim IY, Lin X, Teh AL, Wu Y, Chen L, He M, Chan SY, MacIsaac JL, Chan JKY, Tan KH, Chong MFF, Kobor MS, Godfrey KM, Meaney MJ, Lee YS, Eriksson JG, Gluckman PD, Chong YS, Karnani N. Dichotomy in the Impact of Elevated Maternal Glucose Levels on Neonatal Epigenome. The Journal of Clinical Endocrinology & Metabolism, 2021, doi: 10.1210/clinem/dgab710

Ting DSJ, Li J, Verma CS, Goh ETL, Nubile M, Mastropasqua L, Said DG, Beuerman RW, Lakshminarayanan R, Mohammed I and Dua HS. Evaluation of Host Defense Peptide (CaD23)-Antibiotic Interaction and Mechanism of Action: Insights From Experimental and Molecular Dynamics Simulations Studies. Frontiers in Pharmacology, Oct 2021, Vol. 12, Article 731499, doi: 10.3389/fphar.2021.731499

Zhang J, Tann WJW, Chang ECC, Lee HK. Common Component in Black-Boxes Is Prone to Attacks. Proceedings : Computer Security – ESORICS 2021 26th European Symposium on Research in Computer Security, Darmstadt, Germany, October 4–8, 2021, Proceedings, Part I

September

Nowak J, Lau MC, Borowsky J, Vayrynen J, Haruki K, Zhao M, Costa AD, Gu S, Da Silva A, Arima K, Yeong J, Felt K, Hamada T, Nishihara R, Lennerz J, Fuchs C, Wu C, Meyerhardt J, Ogino S. Tumor-Immune Partitioning and Clustering (TIPC): an algorithm for identifying tumor-immune cell spatial interaction signatures within the tumor microenvironment. Science Translational Medicine, doi: https://doi.org/10.1101/2020.05.29.111542

Deacy AM, Gan SK, Derrick JP. Superantigen Recognition and Interactions: Functions, Mechanisms and Applications. Frontiers in Immunology 2021 Sep 20;12:731845. doi: 10.3389/fimmu.2021.731845

Hiew SH, Wang JK, Koh K, Yang H, Bacha A, Lin J, Yip YS, Vos MIG, Chen L, Sobota RM, Tan NS, Tay CY, Miserez A. Bioinspired short peptide hydrogel for versatile encapsulation and controlled release of growth factor therapeutics. Acta Biomaterialia, Vol. 136, Dec 21, Pg 111-123, doi: 10.1016/j.actbio.2021.09.023

Wang B, Goh YS, Fong SW, Young BE, Ngoh EZX, Chavatte JM, Salleh SNM, Yeo NK, Amrun SN, Hor PX, Loh CY, Lee CY, Chan YH, Chang ZW, Tay MZ, Rouers A, Torres-Ruesta A, Carissimo G, Soh MK, Lee RTC, Xu Y, Pada S, Lin RTP, Leo YS, Lye DC, Maurer-Stroh S, Ng LFP, Renia L, Wang CI. Resistance of SARS-CoV-2 Delta variant to neutralization by BNT162b2-elicited antibodies in Asians. The Lancet Regional Health Western Pacific, 2021 Oct;15:100276doi:, 10.1016/j.lanwpc.2021.100276

Xu W, Kannan S, Verma CS, Nacro K. Update on the Development of MNK Inhibitors as Therapeutic Agents. Journal of Medicinal Chemistry, 2021 Sep 17. doi: 10.1021/acs.jmedchem.1c00368

Tram NDT, Selvarajan V, Boags A, Mukherjee D, Marzinek JK, Cheng B, Jiang ZC, Goh P, Koh JJ, Teo JWP, Bond PJ, Ee PLR. Manipulating turn residues on de novo designed β-hairpin peptides for selectivity against drug-resistant bacteria. Acta Biomater. 2021 Sep 8:S1742-7061(21)00592-4. doi: 10.1016/j.actbio.2021.09.004

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. Science Advances 2021 Sep; 7(36): eabf6033. doi: 10.1126/sciadv.abf6033. Epub 2021 Sep 3

Leong TKM, Shern LW, Lee WEZ, Tan B, Zhao LX, Wen LL, Nadia J, Lee JYJ, Suresh N, Loo LH, Szu E, Yeong J. Leveraging advances in immunopathology and artificial intelligence to analyze in vitro tumor models in composition and space. Advanced Drug Delivery Reviews, 1 Sept 21, doi: 10.1016/j.addr.2021.113959

August

Amirruddin NS, Tan WX, Tan YS, Gardner DS, Bee YM, Verma CS, Hoon S, Lee KO, Teo AKK. Progressive endoplasmic reticulum stress over time due to human insulin gene mutation contributes to pancreatic beta cell dysfunction. Diabetologia. 2021 Nov;64(11):2534-2549. doi: 10.1007/s00125-021-05530-3. Epub 2021 Aug 27

Yang SL, DeFalco L, Anderson DE, Zhang Y, Aw JGA, Lim SY, Lim XN, Tan KY, Zhang T, Chawla T, Su Y, Lezhava A, Merits A, Wang LF, Huber RG, Wan Y. Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions. Nature Communications, 2021 Aug 25 ;12(1):5113, doi: 10.1038/s41467-021-25357-1

Tan KP, Kanitkar TR, Kwoh CK, Madhusudhan MS. Packpred: Predicting the Functional Effect of Missense Mutations. Frontiers in Molecular Biosciences, 20 Aug 21, doi :10.3389/fmolb.2021.646288

Tan S, Kermasson L, Hilcenko C, Kargas V, Traynor D, Boukerrou AZ, Escudero-Urquijo N, Faille A, Bertrand A, Rossmann M, Goyenechea B, Jin L, Moreil J, Alibeu O, Beaupain B, Bôle-Feysot C, Fumagalli S, Kaltenbach S, Martignoles JA, Masson C, Nitschké P, Parisot M, Pouliet A, Radford-Weiss I, Tores F, de Villartay JP, Zarhrate M, Koh AL, Phua KB, Reversade B, Bond PJ, Bellanné-Chantelot C, Callebaut I, Delhommeau F, Donadieu J, Warren AJ, Revy P. Somatic genetic rescue of a germline ribosome assembly defect. Nature Communications 2021 Aug 19;12(1):5044. doi: 10.1038/s41467-021-24999-5

McGill MG, Pokhvisneva I, Clappison AS, McEwen LM, Beijers R, Tollenaar MS, Pham H, Kee MZL, Garg E, de Mendonça Filho EJ, Karnani N, Silveira PP, Kobor MS, de Weerth C, Meaney MJ, O'Donnell KJ. Maternal Prenatal Anxiety and the Fetal Origins of Epigenetic Aging. Biological Psychiatry 2022 Feb 1;91(3):303-312. doi: 10.1016/j.biopsych.2021.07.025. Epub 2021 Aug 19

Selvarajoo K. The need for integrated systems biology approaches for biotechnological applications. Biotechnology Notes 2, 2021, Pg 39-43, doi: 10.1016/j.biotno.2021.08.002

Liu H, Deepak RNVK, Shiriaeva A, Gati C, Batyuk A, Hu H, Weierstall U, Liu W, Wang L, Cherezo V, Fan H, Zhang C. Molecular basis for lipid recognition by the prostaglandin D2 receptor CRTH2. Proceedings of the National Academy of Sciences of the United States of America (PNAS), August 10, 2021 118 (32) e2102813118; https://doi.org/10.1073/pnas.2102813118

Sirota FL, Maurer-Stroh S, Li Z, Eisenhaber F, Eisenhaber B. Functional Classification of Super-Large Families of Enzymes Based on Substrate Binding Pocket Residues for Biocatalysis and Enzyme Engineering Applications. Frontiers in Bioengineering and Biotechnology, 2 Aug 2021, doi: 10.3389/fbioe.2021.701120

Bhanu PK, Arvind CS, Yeow LY, Chen WX, Lim WS, Tan CH. CAFT: a deep learning‑based comprehensive abdominal fat analysis tool for large cohort studies. Magnetic Resonance Materials in Physics, Biology and Medicine, 2021 Aug 2. doi: 10.1007/s10334-021-00946-9. Epub ahead of print. Erratum in: MAGMA. 2021 Sep 4

July

Ong SWX, Chiew CJ, Ang LW, Mak TM, Cui L, Toh MPHS, Lim YD, Lee PH, Lee TH, Chia PY, Maurer-Stroh S, Lin RTP, Leo YS, Lee VJ, Lye DC, Young BE. Clinical and virological features of SARS-CoV-2 variants of concern: a retrospective cohort study comparing B.1.1.7 (Alpha), B.1.315 (Beta), and B.1.617.2 (Delta) Clinical Infectious Diseases, 2021 Aug 23; doi: 10.1093/cid/ciab721

Liu W, Kou CKL, Park KH, Lee HK. Solving the inverse problem of time independent Fokker–Planck equation with a self supervised neural network method. Scientific Reports, 2021 Jul 30;11(1):15540, PMID: 34330934, doi: 10.1038/s41598-021-94712-5

Tang LWT, Teng JW, Koh SK, Zhou L, Go ML, Chan ECY, Verma RK, Fan H. Infigratinib is a Reversible Inhibitor and Mechanism-based Inactivator of Cytochrome P450 3A4. Drug Metabolism and Disposition, 2 Aug 21, PMID : 34326139, doi : 10.1124/dmd.121.000508.

Pung R, Lin B, Maurer-Stroh S, Sirota FL, Mak TM, Octavia S, Pang J, Tan IB, Tan C, Ong BC, Cook AR. Factors influencing SARS-CoV-2 transmission and outbreak control measures in densely populated settings. Scientific Reports, 2021 Jul 27;11(1):15297, doi: 10.1038/s41598-021-94463-3. PMID: 34315928

Malleret B, El Sahili A, Tay MZ, Carissimo G, Ong ASM, Novera W, Lin J, Suwanarusk R, Kosaisavee V, Chu TTT, Sinha A, Howland SW, Fan Y, Gruszczyk J, Tham WH, Colin Y, Maurer-Stroh S, Snounou G, Ng LFP, Chan JKY, Chacko AM, Lescar J, Chandramohanadas R, Nosten F, Russell B, Rénia L. Plasmodium vivax binds host CD98hc (SLC3A2) to enter immature red blood cells. Scientific Reports, 2021 Jul 27;11(1):15297, doi: 10.1038/s41598-021-94463-3. PMID: 34315928

Nguyen TB, Lane DP, Verma CS.Can Glycosylation Mask the Detection of MHC Expressing p53 Peptides by T-cell Receptors. Biomolecules 2021, 11(7), 1056. doi: 10.3390/biom11071056

Sana B, Ho T, Kannan S, Ke D, Li EHY, Seayad J, Verma CS, Duong HA, Ghadessy FJ.Engineered RebH Halogenase Variants Demonstrating a Specificity Switch from Tryptophan towards Novel Indole Compounds. ChemBioChem, 2021, PMID: 34240527, 10.1002/cbic.202100210

Holdbrook DA, Marzinek JK, Boncel S, Boags A, Tan YS, Huber RG, Verma CS, Bond PJ.The nanotube express: Delivering a stapled peptide to the cell surface. Journal of Colloid and Interface Science, 2021, PMID: 34280765, doi: 10.1016/j.jcis.2021.07.023

Tang LWT, Verma RK, Yong RP,Li X, Wang L, Lin Q, Fan H, Chan ECY. Differential Reversible and Irreversible Interactions between Benzbromarone and Human Cytochrome P450s 3A4 and 3A5. Molecular Pharmacology July 1, 2021, PMID: 34210765, doi : 10.1124/molpharm.121.000256

Wong HH, Seet SH, Maier M, Gurel A, Traspas RM, Lee C, Zhang S, Talim B, Loh AYT, Chia CY, Teoh TS, Sng D, Rensvold J, Unal S, Shishkova E, Cepni E, Nathan FM, Sirota FL, Liang C, Yarali N, Simsek-Kiper PO, Mitani T, Ceylaner S, Arman-Bilir O, Mbarek H, Gumruk F, Efthymiou S, Çïmen DU, Georgiadou D, Sotiropoulou K, Houlden H, Paul F, Pehlivan D, Lainé C, Chai G, Ali NA, Choo SC, Keng SS, Boisson B, Yılmaz E, Xue S, Coon JJ, Nguyen Ly TT, Gilani N, Hasbini D, Kayserili H, Zaki MS, Isfort RJ, Ordonez N, Tripolszki K, Bauer P, Rezaei N, Seyedpour S, Khotaei GT, Bascom CC, Maroofian R, Chaabouni M, Alsubhi A, Eyaid W, Işıkay S, Gleeson JG, Lupski JR, Casanova JL, Pagliarini DJ, Akarsu NA, Maurer-Stroh S, Cetinkaya A, Bertoli-Avella A, Mathuru AS, Ho L, Bard FA, Reversade B. Loss of C2orf69 defines a fatal autoinflammatory syndrome in humans and zebrafish that evokes a glycogen-storage-associated mitochondriopathy. The American Journal of Human Genetics, July 1, 2021, Vol. 108, No. 7, p1301-1317, PMID: 34038740, doi: 10.1016/j.ajhg.2021.06.009 (Correction/Published Erratum)

June

Goh JJN, Behn J, Chong CS, Zhong G, Maurer-Stroh S, Fan H, Loo LH. Structure-based virtual screening of CYP1A1 inhibitors: towards rapid tier-one assessment of potential developmental toxicants. Archives of Toxicology, 2021, doi : 10.1007/s00204-021-03111-2

Aronica PGA, Reid LM, Desai N, Li J, Fox SJ, Yadahalli S, Essex JW, Verma CS. Computational Methods and Tools in Antimicrobial Peptide Research. Journal of Chemical Information and Modeling 2021 Jul 26;61(7):3172-3196. doi: 10.1021/acs.jcim.1c00175, PMID: 34165973

Chong CS, Limviphuvadh V, Maurer-Stroh S. Global spectrum of population-specific common missense variation in cytochrome P450 pharmacogenes. Human Mutation 2021, PMID: 34153149, doi: 10.1002/humu.24243

Zhu X, Li X, Ong K, Zhang W, Li W, Li L, Young D, Su Y, Shang B, Peng L, Xiong W, Liu Y, Liao W, Xu J, Wang F, Liao Q, Li S, Liao M, Li Y, Rao L, Lin J, Shi J, You Z, Zhong W, Liang X, Han H, Zhang Y, Tang N, Hu A, Gao H, Cheng Z, Liang L, Yu W, Ding Y. Hybrid AI assistive diagnostic model permits rapid TBS classification of cervical liquid-based thin-layer cell smears. Nature Communications 2021 Jun 10;12(1):3541. doi: 10.1038/s41467-021-23913-3, PMID: 34112790

Yap J, Deepak RNVK, Tian Z, Ng WH, Goh KC, Foo A, Tee ZH, Mohanam MP, Sim YR, Degirmenci U, Lam P, Chen ZZ, Fan H, Hu J. The Stability of R-spine Defines RAF Inhibitor Resistance: A Comprehensive Analysis of Oncogenic BRAF Mutants with In-frame Insertion of αC-β4 loop. Science Advances, 9 Jun 21, Vol. 7, No. 24, doi : 10.1126/sciadv.abg0390, PMID: 34108213

Lim J, Kumar A, Low K, Verma CS, Mu Y, Miserez A, Pervushin K. Liquid-Liquid Phase Separation of Short Histidine- and Tyrosine-Rich Peptides: Sequence Specificity and Molecular Topology. The Journal of Physical chemistry. B, 09 Jun 2021, 125(25):6776-6790, doi: 10.1021/acs.jpcb.0c11476 PMID: 34106723

Konings F, Perkins MD, Kuhn JH, Pallen MJ, Alm EJ, Archer BN, Barakat A, Bedford T, Bhiman JN, Caly L, Carter LL, Cullinane A, de Oliveira T, Druce J, El Masry I, Evans R, Gao GF, Gorbalenya AE, Hamblion E, Herring BL, Hodcroft E, Holmes EC, Kakkar M, Khare S, Koopmans MPG, Korber B, Leite J, MacCannell D, Marklewitz M, Maurer-Stroh S, Rico JAM, Munster VJ, Neher R, Munnink BO, Pavlin BI, Peiris M, Poon L, Pybus O, Rambaut A, Resende P, Subissi L, Thiel V, Tong S, van der Werf S, von Gottberg A, Ziebuhr J, Van Kerkhove MD. SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse. Nature Microbiology, Vol. 6, July 2021, pg 821–823 (2021) PMID: 34108654, doi: 10.1038/s41564-021-00932-w

Su TTC, Lua WH, Poh JJ, Ling WL, Yeo YJ, Gan SKE. Molecular insights of nickel binding to therapeutic antibodies as a possible new antibody superantigen. Frontiers in Immunology, 2021, doi: 10.3389/fimmu.2021.676048

May

Park S, Saw SN, Li X, Paknezhad M, Coppola D, Dinish U, Attia A, Yew YW, Tien GTS, Lee HK, Olivo M. Model Learning Analysis of 3D Optoacoustic Mesoscopic Images for the Classification of Atopic Dermatitis. Biomedical Optics Express, Vol. 12, No. 6, pg 3671-3683 (2021), doi: 10.1364/BOE.415105

Wong HH, Seet SH, Maier M, Gurel A, Traspas RM, Lee C, Zhang S, Talim B, Loh AYT, Chia CY, Teoh TS, Sng D, Rensvold J, Unal S, Shishkova E, Cepni E, Nathan FM, Sirota FL, Liang C, Yarali N, Simsek-Kiper PO, Mitani T, Ceylaner S, Arman-Bilir O, Mbarek H, Gumruk F, Efthymiou S, Uğurlu Çi Men D, Georgiadou D, Sotiropoulou K, Houlden H, Paul F, Pehlivan D, Lainé C, Chai G, Ali NA, Choo SC, Keng SS, Boisson B, Yılmaz E, Xue S, Coon JJ, Ly TTN, Gilani N, Hasbini D, Kayserili H, Zaki MS, Isfort RJ, Ordonez N, Tripolszki K, Bauer P, Rezaei N, Seyedpour S, Khotaei GT, Bascom CC, Maroofian R, Chaabouni M, Alsubhi A, Eyaid W, Işıkay S, Gleeson JG, Lupski JR, Casanova JL, Pagliarini DJ, Akarsu NA, Maurer-Stroh S, Cetinkaya A, Bertoli-Avella A, Mathuru AS, Ho L, Bard FA, Reversade B. Loss of C2orf69 defines a fatal autoinflammatory syndrome in humans and zebrafish that evokes a glycogen-storage-associated mitochondriopathy. The American Journal of Human Genetics, July 1, 2021, Vol. 108, No. 7, p1167-1356, PMID: 34038740, doi: 10.1016/j.ajhg.2021.05.003. 5

Low BSJ, Lim CS, Ding SSL, Tan YS, Ng NHJ, Krishnan VG, Ang SF, Neo CWY, Verma CS, Hoon S, Lim SC, Tai ES, Teo AKK. Decreased GLUT2 and glucose uptake contribute to insulin secretion defects in MODY3/HNF1A hiPSC-derived mutant β cells. Nature Communications 2021, May 25;12(1):3133, PMID: 34035238, doi: 10.1038/s41467-021-22843-45

Leow JWH, Verma RK, Lim ABH, Fan H, Chan ECY. Atypical kinetics of cytochrome P450 2J2: epoxidation of arachidonic acid and reversible inhibition by xenobiotic inhibitors. European Journal of Pharmaceutical Sciences 2021, 10.1016/j.ejps.2021.105889

Low JL, Du W, Gocha T, Oguz G, Zhang X, Chen MW, Masirevic S, Yim DGR, Tan IB, Ramasamy A, Fan H, DasGupta R. Molecular docking-aided identification of novel small molecule inhibitors targeting the β-catenin-TCF4 interaction. iScience 2021, doi: 0.1016/j.isci.2021.102544

Nicolaou ST, Hebditch M, Jonathan OJ, Verma CS, Warwicker J.PhosIDP: a web tool to visualize the location of phosphorylation sites in disordered regions. Scientific Reports, 2021 May 11;11(1):9930, PMID: 33976270, doi: 10.1038/s41598-021-88992-0

Alfatah M, Wong JH, Krishnan VG, Lee YC, Sin QF, Goh CJH, Kong KW, Lee WT, Lewis J, Hoon S, Arumugam P. TORC1 regulates the transcriptional response to glucose and developmental cycle via the Tap42-Sit4-Rrd1/2 pathway in Saccharomyces cerevisiae. BMC Biology, 19, 95 (2021), doi: 10.1186/s12915-021-01030-3

Shiina K, Mori H, Tomita Y, Lee HK, Okabe Y. Inverse renormalization group based on image super-resolution using deep convolutional networks. Scientific Reports, 2021 May 5;11(1):9617, PMID: 33953229, doi: 10.1038/s41598-021-88605-w

April

Vu QN, Young R, Sudhakar HK, Gao T, Huang T, Tan YS, Lau YH. Cyclisation strategies for stabilising peptides with irregular conformations. RSC Medicinal Chemistry, 2021 Apr 28;12(6):887-901, PMID: 34263169, doi: 10.1039/d1md00098e.

Asarnow D, Wang B, Lee WH, Hu Y, Huang CW, Faust B, Ng PML, Ngoh EZX, Bohn M, Bulkley D, Pizzorno A, Ary B, Tan HC, Lee CY, Minhat RA, Terrier O, Soh MK, Teo FJ, Yeap YYC, Seah SGK, Chan CEZ, Connelly E, Young NJ, Maurer-Stroh S, Renia L, Hanson BJ, Rosa-Calatrava M, Manglik A, Cheng Y, Craik CS, Wang CI. Structural insight into SARS-CoV-2 neutralizing antibodies and modulation of syncytia. Cell, 2021. Oct 17, Vol. 184, Issue 12, Pg 1392-3204, doi: 10.1016/j.cell.2021.04.033, PMID: 33974910

Kuang W, Zhang J, Lan Z, RNV Krisna Deepak, Liu Chao, Ma Zhilong, Cheng L, Zhao X, Meng X, Wang W, Wang X, Xu L, Jiao Y, Luo Q, Meng Z, Kee K, Liu X, Deng H, Li W, Fan H, Chen L. SLC22A14 is a mitochondrial riboflavin transporter required for sperm oxidative phosphorylation and male fertility. Cell Report, Vol 35, Issue 3, 109025, April 20, 2021, doi: 10.1016/j.celrep.2021.109025

Kaur H, Jakob RP, Marzinek JK, Green R, Imai Y, Bolla JR, Agustoni E, Robinson CV, Bond PJ, Maier T, Hiller S. The antibiotic darobactin mimics a β-strand to inhibit outer membrane insertase. Nature 2021, doi: 10.1038/s41586-021-03455-w

Yin M, Goncearenco A, Berezovsky IN. Deriving and Using Descriptors of Elementary Functions in Rational Protein Design. Frontiers in Bioinformatics, 13 Apr 21, doi: 10.3389/fbinf.2021.657529

Tee WV, Tan ZW, Lee K, Guarnera E, Berezovsky IN. Exploring the Allosteric Territory of Protein Function. The Journal of Physical Chemistry B, 2021, 125, 15, 3763–3780, PMID: 33844527, doi: 10.1021/acs.jpcb.1c00540

TYoung BE, Wei WE, Fong SW, Mak TM, Anderson DE, Chan YH, Pung R, Heng CS, Ang LW, Zheng AKE, Lee B, Kalimuddin S, Pada S, Tambyah PA, Parthasarathy P, Tan SY, Sun L, Smith GJ, Lin RTP, Leo YS, Renia L, Wang LF, Ng LF, Maurer-Stroh S, Lye DC, Lee VJ. Association of SARS-CoV-2 clades with clinical, inflammatory and virologic outcomes: An observational study. Cell, 2021. Oct 17, Vol. 184, Issue 12, Pg 1392-3204, doi: 10.1016/j.cell.2021.04.033, PMID: 33974910 0

Selvarajoo K. Searching for unifying laws of general adaptation syndrome: Comment on “Dynamic and thermodynamic models of adaptation” by Gorban et al. Physics of Life Reviews, Vol. 37, Jul 21, Pg 97-99

March

Poh JJ, Wu, WL, Goh NWJ, Tan SMX, Gan SKE. Spectrophotometer on-the-go: The development of a 2-in-1 UV–Visportable Arduino-based spectrophotometer. Sensors and Actuators A: Physical, Volume 325, 1 July 2021, 112698 doi: 10.1016/j.sna.2021.112698

Ooi KH, Liu MM, Tay JWD, Teo SY, Kaewsapsak P, Jin S, Lee CK, Hou J, Maurer-Stroh S, Lin W, Yan B, Yan G, Gao YG, Tan MH.An engineered CRISPR-Cas12a variant and DNA-RNA hybrid guides enable robust and rapid COVID-19 testing. Nature Communications, 2021 Mar 19;12(1):1739, PMID: 33741959, doi: 10.1038/s41467-021-21996-6

Heymann D, Mohanram H, Kumar A, Verma CS, Lescar J, Miserez A. Structure of a consensus chitin-binding domain revealed by solution NMR. Journal of Structural Biology, Vol. 213, Issue 2, Jun 21, doi: 10.1016/j.jsb.2021.107725

Chew ZY, Wu WL, Gan SKE. Application Notes - APD LAMP Diagnostic App: Automated Colorimetric Analysis and Documentation. Scientific Phone Apps and Mobile Devices (2021), Vol. 7, Article 1, 10.30943/2021/17032021

De Falco L, Silva NM, Huber RG, Martins IC. The Pseudo-Circular Genomes of Flaviviruses: Structures, Mechanisms, and Functions of Circularization. Cells 2021, 10(3), 642. doi: 10.3390/cells10030642

Chua AQ, Al Knawy B, Grant B, Legido-Quigley H, Lee WC, Leung GM, Looi MK, Maurer-Stroh S. How the lessons of previous epidemics helped successful countries fight covid-19. BMJ. 2021 Mar 11;372:n486. doi: 10.1136/bmj.n486. PMID: 33707174.

February

Fibriansah G, Lim EXY, Marzinek JK, Ng TS, Tan JL, Huber RG, Lim XN, Chew VSY, Kostyuchenko VA, Shi J, Anand GS, Bond PJ, Crowe JE Jr, Lok SM. Antibody affinity versus dengue morphology influences neutralization. PLOS Pathogens, 2021, 17(2): e1009331. PMID: 33621239, doi: 10.1371/journal.ppat.1009331

Lee CY, Amrun SN, Chee RS, Goh YS, Mak TM, Octavia S, Yeo NK, Chang ZW, Tay MZ, Torres-Ruesta A, Carissimo G, Poh CM, Fong SW, Bei W, Lee S, Young BE, Tan SY, Leo YS, Lye DC, Lin RT, Maurer-Stroh S, Lee B, Wang CI, Renia L, Ng LF. Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. Clinical & Translational Immunology 2021 Feb 22;10(2):e1241. doi: 10.1002/cti2.1241, PMID: 33628442

Zhang C, Chen X, Lee RTC, T R, Maurer-Stroh S, Rühl M. Bioinformatics-aided identification, characterization and applications of mushroom linalool synthases. Communications Biology 2021 Feb 17;4(1):223. doi: 10.1038/s42003-021-01715-z. PMID: 33597725

Shepley-McTaggart A, Schwoerer MP, Sagum CA, Bedford MT, Jaladanki CK, Fan H, Cassel J, Harty RN.Ubiquitin Ligase SMURF2 Interacts with Filovirus VP40 and Promotes Egress of VP40 VLPs. Viruses 2021, 13(2), 288, doi: 10.3390/v13020288

Min N, Ong YHB, Han AX, Ho SX, Yen EWP, Ban KHK, Maurer-Stroh S, Chong CY, Chu JJH.An epidemiological surveillance of hand foot and mouth disease in paediatric patients and in community: A Singapore retrospective cohort study, 2013-2018. PLOS Neglected Tropical Diseases, 2021 Feb 10;15(2):e0008885. doi: 10.1371/journal.pntd.0008885. PMID: 33566802

Guarnera E, Tan ZW, Berezovsky IN. Three-dimensional Chromatin Ensemble Reconstruction via Stochastic Embedding. Structure 2021

Raghuvamsi PV, Tulsian NK, Samsudin F, Qian X, Purushotorman K, Yue G, Kozma MM, Hwa WY, Lescar J, Bond PJ, MacAry PA, Anan GS. SARS-CoV-2 S protein:ACE2 interaction reveals novel allosteric targets. Elife, 2021 Feb 8;10:e63646. doi: 10.7554/eLife.63646, PMID: 33554856, doi: 10.7554/eLife.63646

Liang JJ, Ruthel G, Sagum CA, Bedford MT, Sidhu SS, Sudol M, Jaladanki CK, Fan H, Freedman BD, Harty RN. Angiomotin Counteracts the Negative Regulatory Effect of Host WWOX on Viral PPxY-Mediated Egress. Journal of Virology Feb 2021, JVI.00121-21; DOI: 10.1128/JVI.00121-21

January

Srinivasaraghavan K, Aronica PGA, Binh NT, Li J, Verma CS. Computational design of macrocyclic binders of S100B(ββ) : A novel peptide theranostic. Molecules 2021, 26(3), 721; doi: 10.3390/molecules26030721, PMID: 33573254

Khong NZ, Zeng Y, Lai SK, Koh CG, Liang ZX, Chiam KH, Li HY. Dynamic swimming pattern of Pseudomonas aeruginosa near a vertical wall during initial attachment stages of biofilm formation. Scientific Reports, 2021 Jan 21;11(1):1952, PMID: 33479476, doi: 10.1038/s41598-021-81621-w

Bose U, Broadbent JA, Juhasz A, Karnaneedi S, Johnston EB, Stockwell S, Bryne K, Limviphuvadh V, Maurer-Stroh S, Lopata AL, Colgrave ML. Protein extraction protocols for optimal proteome measurement and arginine kinase quantitation from cricket Acheta domesticus for food safety assessment. Food Chemistry Vol. 348, 30 Jun 2021, doi: 10.1016/j.foodchem.2021.129110

Budharaj A, Pandey S, Kannan S, Verma CS, Venkatraman P. The Polybasic Insert of the SARS CoV-2 Spike Protein, the RBD and the feline SARS – Evolved or Yet to Evolve. Biochemistry and Biophysics Reports, Vol. 25, Mar 21, doi: 10.1016/j.bbrep.2021.1009071

Eisenhaber B, Sinha S, Jadalanki CK, Shitov VA, Tan QW, Sirota FL, Eisenhaber F. Conserved sequence motifs in human TMTC1, TMTC2, TMTC3, and TMTC4, new Omannosyltransferases from the GT-C/PMT clan, are rationalized as ligand binding sites. Biology Direct 16, Article no 4, 2021, doi: 10.1186/s13062-021-00291-w

Tang LWT, Verma RK, Fan H, Chan ECY. Mechanism-based Inactivation of Cytochrome P450 3A4 by Benzbromarone. Molecular Pharmacology, Vol. 99, Issue 2, 1 Feb 21,PMID : 33436520, doi: 10.1124/molpharm.120.000086

Goh CJH, Wong JH, El Farran C, Tan BX, Coffill CR, Loh YH, Lane D, Arumugam P. Identification of pathways modulating vemurafenib resistance in melanoma cells via a genome-wide CRISPR/Cas9 screen. G3 Genes|Genomes|Genetics, Volume 11, Issue 2, February 2021, doi: 10.1093/g3journal/jkaa069, PMID: 33604667

2020

December

Samsudin F, Gan SKE, Bond PJ. The Impact of Gag Non-Cleavage Site Mutations on HIV-1 Viral Fitness from Integrative Modelling and Simulations. Computational and Structural Biotechnology Journal, 2020

Dumitru AC, Krishna DRNV, Liu H, Koehler M, Zhang C*, Fan H*, Alsteens D*. Submolecular probing of the complement C5a receptor–ligand binding reveals a cooperative two-site binding mechanism. Communications Biology volume 3, Article number: 786 (2020)

Chan KF, Su TTC, Krah A, Phua SX, Yeo YJ, Ling WL, Bond PJ, Gan SKE. An Alternative HIV-1 Non-Nucleoside Reverse Transcriptase Inhibition Mechanism: Targeting the p51 Subunit. Molecules, 2020, Vol: 25, Pg: 5902, doi: 10.3390/molecules25245902

Petruk G, Puthia M, Petrlova J, Samsudin F, Stromdahl AC, Cerps S, Uller L, Kjellstrom S, Bond PJ, Schmidtchen A. SARS-CoV-2 Spike protein binds to bacterial lipopolysaccharide and boosts proinflammatory activity. Journal of Molecular Cell Biology, 2020, doi: 10.1093/jmcb/mjaa067

Ling WL, Su TTC, Lua WH, Poh JJ, Ng YL, Wipat A, Gan SKE. Essentially Leading Antibody Production: An Investigation of Amino Acids, Myeloma, and Natural V-Region Signal Peptides in Producing Pertuzumab and Trastuzumab Variants. Frontiers in Immunology, 2020, Vol. 11, Pg 3175, doi: 10.3389/fimmu.2020.604318

Koel BF, Vigeveno RM, Pater M, Koekkoek SM, Han AX, Tuan HM, Anh TTN, Hung NT, Thinh LQ, Hai LT, Ngoc HTB, Chau NVV, Ngoc NM, Chokephaibulkit K, Puthavathana P, Kinh NV, Trinh T, Lee RTC, Maurer-Stroh S, Eggink D, Thanh TT, Tan LV, van Doorn HR, de Jong MD. Longitudinal sampling is required to maximize detection of intrahost A/H3N2 virus variants. Virus Evolution, Volume 6, Issue 2, July 2020, veaa088, PMID: 33343927, https://doi.org/10.1093/ve/veaa088

November

Mayrhofer JE, Enzler F, Feichtner A, Röck R, Fleischmann J, Raffeiner A, Tschaikner P, Ogris E, Huber RG, Hartl M, Schneider R, Troppmair J, Torres-Quesada O, Stefan E. Mutation-oriented profiling of autoinhibitory kinase conformations predicts RAF inhibitor efficacies. Proceedings of the National Academy of Sciences of the United States of America (PNAS), Nov 23;202012150. doi: 10.1073/pnas.2012150117, PMID: 33229534

Petruk G, Petrlova J, Samsudin F, Giudice RD, Bond PJ, Schmidtchen A. Concentration- and pH-dependent oligomerization of the thrombin-derived C-terminal peptide TCP-25. Biomolecules 2020, 10(11), 1572; doi: 10.3390/biom10111572

Krah A, Huber RG, McMillan DGG, Bond PJ. The Molecular Basis for Purine Binding Selectivity in the Bacterial ATP Synthase ϵ Subunit. ChemBioChem, 2020, 10.1002/cbic.202000291

Theappeta KRV, Zhao LN, Nge CE, Crasta S, Leong CY, Ng V, Kanagasundaram Y*, Fan H*, Ng SB*. In-Silico Identified New Natural Sortase A Inhibitors Disrupt S. aureus Biofilm Formation. Int. J. Mol. Sci. 2020, 21(22), 8601; https://doi.org/10.3390/ijms21228601

October

Hochreiter B, Chong CS, Hartig A, Maurer-Stroh S, Berger J, Schmid JA, Kunze M. A Novel FRET Approach Quantifies the Interaction Strength of Peroxisomal Targeting Signals and Their Receptor in Living Cells. Cells 2020, 9(11), 2381; doi: 10.3390/cells9112381

Xiao QP, Wang L, Supekar S, She T, Liu H, Ye F, Huang JZ, Fan H, Wei ZY, Zhang C. Structure of human steroid 5α-reductase 2 with the anti-androgen drug finasteride. Nat Commun 11, 5430 (2020). https://doi.org/10.1038/s41467-020-19249-z

Brown CJ, Verma CS, Lane DP, Lama D. Conformational ordering of intrinsically disordered peptides for targeting translation initiation. Biochimica et Biophysica Acta (BBA), Vol 1865, Issue 1, Jan 2021, doi: 10.1016/j.bbagen.2020.129775

Bauer DC, Metke-Jimenez A, Maurer-Stroh S, Tiruvayipati S, Wilson LOW, Jain Y, Perrin A, Ebrill K, Hansen DP, Vasan SS. Interoperable medical data: the missing link for understanding COVID-19. Transboundary and Emerging Diseases, 2020 Oct 23. doi: 10.1111/tbed.13892, PMID: 33095970

Krah A, van der Hoeven B, Mestrom L, Tonin F, Knobel KCC, Bond PJ, McMillan DGG. A second shell residue modulates a conserved ATP-binding site with radically different affinities for ATP. Biochimica et Biophysica Acta (BBA), Vol 1865, Issue 1, Jan 2021, doi: 10.1016/j.bbagen.2020.129766

Faulkner M, Szabó I, Weetman SL, Sicard F, Huber RG, Bond PJ, Rosta E, Liu LN.Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein. Scientific Reports, 10, Article 17501, 2020, doi: 10.1038/s41598-020-74536-5

Kumar A, Mohanram H, Li J, Le Ferrand H, Verma C, Miserez A. Disorder-Order Interplay of a Barnacle Cement Protein Triggered by Interactions with Calcium and Carbonate Ions: A Molecular Dynamics Study. Chemistry of Materials 2020, 32, Pg 8845-8859, doi: 10.1021/acs.chemmater.0c02319

Young TL, Whisenhunt KN, Jin J, LaMartina SM, Martin SM, Souma T, Limviphuvadh V, Suri F, Souzeau E, Zhang X, Dan Y, Anagnos E, Carmona S, Jody NM, Stangel N, Higuchi EC, Huang SJ, Siggs OM, Simões MJ, Lawson BM, Martin JS, Elahi E, Narooie-Nejad M, Motlagh BF, Quaggin SE, Potter HD, Silva ED, Craig JE, Egas C, Maroofian R, Maurer-Stroh S, Bradfield YS, Tompson SW. SVEP1 as a Genetic Modifier of TEK-Related Primary Congenital Glaucoma. Investigative Ophthalmology & Visual Science, October 2020, Vol. 61, 6, doi: 10.1167/iovs.61.12.6

Li J, Beuerman R, Verma CS. Dissecting the Molecular Mechanism of Colistin Resistance in mcr-1 Bacteria. Journal of Chemical Information and Modeling, 2020 Oct 26;60(10):4975-4984. doi: 10.1021/acs.jcim.0c01051, PMID: 33017152 0

Akram F, Koh PE, Wang F, Zhou S, Tan SH, Paknezhad M, Park S, Hennedige T, Thng CH, Lee HK, Sommat K. Exploring MRI based radiomics analysis of intratumoral spatial heterogeneity in locally advanced nasopharyngeal carcinoma treated with intensity modulated radiotherapy. PLOS ONE, 2020; 15(10), doi: 10.1371/journal.pone.0240043, PMID: 33017440

Cocco E, Lee JE, Kannan S, Schram AM, Won HH, Shifman S, Kulick A, Baldino L, Toska E, Arruabarrena-Aristorena A, Kittane S, Wu F, Cai Y, Arena S, Mussolin B, Kannan R, Vasan N, Gorelick AN, Berger MF, Novoplansky O, Jagadeeshan S, Liao Y, Rix U, Misale S, Taylor BS, Bardelli A, Hechtman JF, Hyman DM, Elkabets M, de Stanchina E, Verma CS, Ventura A, Drilon A, Scaltriti M. TRK xDFG mutations trigger a sensitivity switch from type I to II kinase inhibitors. Cancer Discovery, 2020 Oct 1;CD-20-0571. doi: 10.1158/2159-8290.CD-20-0571, PMID: 33004339

September

Su TTC, Sinha S, Eisenhaber B, Eisenhaber F. Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site. Biology Direct, 15, Article number: 14 (2020), doi: 10.1186/s13062-020-00266-3

Ghode A, Gross LZF, Tee WF, Guarnera E, Berezovsky IN, Biondi RM, Anan GS. Synergistic Allostery in Multiligand-Protein Interactions. Biophysical Journal, Vol. 119, Issue 9, 3 Nov 20, Pg 1833-1848, doi: 10.1016/j.bpj.2020.09.019

Chao W, Kannan S, Verma CS, Swaminathan K, Wong SK. Molecular modeling and interaction between Arabidopsis sulfite oxidase and the GW motif of Turnip crinkle virus coat protein. Virology Vol. 551, Dec 2020, Pg 64-74, doi: 10.1016/j.virol.2020.08.013, PMID: 33038689

Atkuru S, Muniraj G, Sudhaharan T, Chiam KH, Wright GD, Sriram G.Cellular ageing of oral fibroblasts differentially modulates extracellular matrix organization. Journal of Periodontal Research, doi: 10.1111/jre.12799

Chakraborty A, Jenjaroenpun P, Li J, El Hilali S, McCulley A, Haarer B, Hoffman EA, Belak A, Thorland A, Hehnly H, Schildkraut C, Chen CL, Kuznetsov VA, Feng W. Replication Stress Induces Global Chromosome Breakage in the Fragile X Genome. Cell Reports, Vol. 32, Issue 12, 22 Sep 2020. 109178, doi: 10.1016/j.celrep.2020.108179, PMID: 32966779

Tee WV, Guarnera E, Berezovsky IN. Disorder driven allosteric control of protein activity. Current Research in Structural Biology, Volume 2, 2020, Pages 191-203

Jaladanki CK, He Y, Zhao LN, Maurer-Stroh S, Loo LH, Song HW, Fan H.Virtual screening of potentially endocrine-disrupting chemicals against nuclear receptors and its application to identify PPARγ-bound fatty acids. Arch Toxicol (2020). https://doi.org/10.1007/s00204-020-02897-x

Ladds MJGW, Popova G, Pastor-Fernandez A, Kannan S, Van Leeuwen IMM, Hakansson M, Walse B, Tholander F, Bhatia R, Verma CS, Lane DP, Lain S. Exploitation of DHODH and p53 activation as therapeutic targets - a case study in polypharmacology. Journal of Biological Chemistry, 2020, doi: 10.1074/jbc.RA119.012056

Arruabarrena-Arestorena A, Maag JLV, Kittane S, Cai Y, Karthaus WR, Ladewig E, Park J, Kannan S, Ferrando L, Cocco E, Ho SY, Tan DS, Sallaku M, Wu F, Acevedo B, Selenica P, Ross DS, Witkin M, Sawyers C, Reis-Filho JS, Verma CS, Jauch R, Koche R, Baselga J, Razavi P. Toska E, Scalltriti M.FOXA1 mutations reveal distinct chromatin profiles and influence therapeutic response in breast cancer. Cancer Research, 2020, Volume 80, Issue 16 Supplement, pp. 3439, DOI: 10.1158/1538-7445.AM2020-3439

Chan KF, Poh JJ, Wo WL, Gan SKE.Augmented Reality in scientific visualization and communications: A new dawn of looking at antibody interactions. Antibody Therapeutics, tbaa021, https://doi.org/10.1093/abt/tbaa021

Mahta S, Algie M, Al-jabry T, Mckinney C, Kannan S, Verma CS, Ma WN, Zhang J, Bartolec TK. Masamsetti VP, Parker K, Henderson L, Gould ML, Bhatia P, Harfoot R, Chrcop M, Kleffmann T, Cohen SB, Woolley AG, Cesare AJ, Braithwaite A.Critical role for cold shock protein YB-1 in cytokinesis. Cancers 2020, 12(9), 2473; https://doi.org/10.3390/cancers12092473

August

Saskői E, Hujber Z, Nyírő G, Likó I, Mátyási B, Petővári G, Mészáros K, Kovács AL, Patthy L, Supekar S, Fan H, Sváb G, Tretter L, Sarkar A, Nazir A, Sebestyén A, Patócs A, Mehta A, Takács-Vellai K. The SDHB Arg230His mutation causing familial paraganglioma alters glycolysis in a new Caenorhabditis elegans model. Dis Model Mech 2020 Aug 28; dmm.044925. doi: 10.1242/dmm.044925. Online ahead of print.

Krah A, Marzinek JK, Bond PJ. Characterizing the Hydration Properties of Proton Binding Sites in the ATP Synthase c-Rings of Bacillus Species. The Journal of Physical Chemistry B, 2020, 124, 33, Pg 7176-7183. PMID: 32687713

Young BE, Fong SW, Chan YH, Mak TM, Ang LW, Anderson DE, Lee CY, Amrun SN, Lee B, Goh YS, Su YCF, Wei WE, Kalimuddin S, Chai LYA, Pada S, Tan SY, Sun L, Parthasarathy P, Chen YYC, Barkham T, Lin RTP, Maurer-Stroh S, Leo YS, Wang LF, Renia L, Lee VJ, Smith GJD, Lye DC, Ng LFP. Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study. Lancet. 2020 29 August-4 September; 396(10251): 603–611. Published online 2020 Aug 18. doi: 10.1016/S0140-6736(20)31757-8, PMID: 32822564

Tan YS, Verma CS. Straightforward incorporation of multiple ligand types into molecular dynamics simulations for efficient binding site detection and characterization. J Chem Theory Comput. 2020 Sep 10. doi: 10.1021/acs.jctc.0c00405. PMID: 32810406

Park SJ, Kwak WS, Lee HK.Accelerated spin dynamics using deep learning corrections. Sci Rep 10, 13772 (2020). https://doi.org/10.1038/s41598-020-70558-1.

Alm E, Broberg EK, Connor T, Hodcroft EB, Komissarov AB, Maurer-Stroh S, Melidou A, Neher RA, O'Toole Á, Pereyaslov D; WHO European Region sequencing laboratories and GISAID EpiCoV group; WHO European Region sequencing laboratories and GISAID EpiCoV group. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. Euro Surveillance. 2020 Aug;25(32):2001410. doi: 10.2807/1560-7917.ES.2020.25.32.2001410, PMID: 32794443

Tomita Y, Shiina K, Okabe Y, Lee HK. Machine-learning study using improved correlation configuration and application to quantum Monte Carlo simulation. Physical Reivew E, Vol. 102, Issue 2, Aug 2020, doi: 10.1103/PhysRevE.102.021302.

Malik A, Aronica PGA, Verma CS. DStabilize: A web resource to generate mirror images of biomolecules. Structure 28, 1-3, Nov 3 2020, doi: 10.1016/j.str.2020.07.014

July

Krutz NL, Kimber I, Maurer-Stroh S, Gerberick GF. Determination of the relative allergenic potency of proteins: hurdles and opportunities. Critical Reviews in Toxicology. 2020 Jul;50(6):521-530. doi: 10.1080/10408444.2020.1793895, PMID: 32729356

Watanabe H, Ng CH, Limviphuvadh V, Suzuki S, Yamada T.Gluconobacter dominates the gut microbiome of the Asian palm civet Paradoxurus hermaphroditus that produces kopi luwak. PeerJ 8:e9579 https://doi.org/10.7717/peerj.9579 .

Zuzic L, Marzinek JK, Warwicker J, Bond PJ. A benzene-mapping approach for uncovering cryptic pockets in membrane-bound proteins. . bioRxiv, 5 Apr 2020, doi: 10.1101/2020.04.04.0251631

Shearer J, Marzinek JK, Bond PJ, Khalid S. Molecular dynamics simulations of bacterial outer membrane lipid extraction: Adequate sampling? The Journal of Chemical Physics, Vol. 153, Issue 4, 2020, doi: 10.1063/5.0017734

Su YCF, Anderson DE, Young BE, Linster M, Zhu F, Jayakumar J, Zhuang Y, Kalimuddin S, Low JGH, Tan CW, Chia WN, Mak TM, Octavia S, Chavatte JM, Lee RTC, Pada S, Tan SY, Sun L, Yan GZ, Maurer-Stroh S, Mendenhall IH, Leo YS, Lye DC, Wang LF, Smith GJD. Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2. mBio. 2020 Jul 21;11(4):e01610-20. doi: 10.1128/mBio.01610-20, PMID: 32694143

Zheng Z, Monteil VM, Maurer-Stroh S, Yew CW, Leong C, Mohd-Ismail NK, Cheyyatraivendran Arularasu S, Chow VTK, Lin RTP, Mirazimi A, Hong W, Tan YJ. Monoclonal antibodies for the S2 subunit of spike of SARS-CoV-1 cross-react with the newly-emerged SARS-CoV-2. Euro Surveillance. 2020 Jul;25(28):2000291. doi: 10.2807/1560-7917.ES.2020.25.28.2000291, PMID: 32700671

Shivgan AT, Marzinek JK, Huber RG, Krah A, Henchman RH, Matsudaira P, Verma CS, Bond PJ. Extending the Martini coarse-grained forcefield to N-glycans. Journal of Chemical Information and Modeling, 23 Jul 2020, 60(8):3864-3883, DOI: 10.1021/acs.jcim.0c00495 PMID: 32702979

June

Miller JA, Loo LH. Optimum concentration-response curve metrics for supervised selection of discriminative cellular phenotypic endpoints for chemical hazard assessment. Archives of Toxicology 2020, doi: 10.1007/s00204-020-02813-3.

Kamariah N, Huber RG, Bond PJ, Muller Volker, Gruber G. 3D reconstruction and flexibility of the hybrid engine Acetobacterium woodii F-ATP synthase. Biochemical and Biophysical Research Communications, Vol. 527, Issue 2, 25 June 2020, Pg 518-524

Scalla M, Chua GL, Chin CF, Alsaif H, Borovikov A, Riazuddin S, Riazuddin S, Manzini MC, Severino M, Kuk A, Fan H, Jamshidi Y, Toosi MB, Doosti M, Karimiani EG, Salpietro V, Dadali E, Baydakova G, Konovalov F, Lozier E, O'Connor E, Sabr Y, Alfaifi A, Ashrafzadeh F, Striano P, Zara F, Alkuraya FS, Houlden H, Maroofian R, Silver DL. Biallelic MFSD2A variants associated with congenital microcephaly, developmental delay, and recognizable neuroimaging features. European Journal of Human Genetics 2020, doi: 10.1038/s41431-020-0669-x

Farrukee R, Tai CM, Oh DY, Anderson DE, Gunalan V, Hibberd M, Lau GY, Barr IG, Messling VV, Maurer-Stroh S, Hurt AC. Utilising animal models to evaluate oseltamivir efficacy against influenza A and B viruses with reduced in vitro susceptibility. PLoS Pathogens 2020 Jun 18;16(6):e1008592. doi: 10.1371/journal.ppat.1008592, PMID: 32555740

Cheong EJY, Nai PC, Neo RWY, Lin F, Chiong E, Esuvaranathan K, Fan H, Szmulewitz R, Peer CJ, Figg WD, Chai CLL, Miners JO, Chan ECY. Slow tight binding inhibition of CYP17A1 by abiraterone redefines its kinetic selectivity and dosing regimen. Journal of Pharmacology and Experimental Therapeutics, Vol. 374, Issue 1, 1 July 2020, doi:10.1124/jpet.120.265868

Hussain F, Basu S, Jun HHH, Loo LH, Zink D. Predicting direct hepatocyte toxicity in humans by combining high-throughput imaging of HepaRG cells and machine learning-based phenotypic profiling. Archives of Toxicology 2020, doi: 10.1007/s00204-020-02778-3

Huber RG, Marzinek JK, Boon PLS, Yue W, Bond PJ.Computational modelling of flavivirus dynamics: The ins and outs. Methods, 2020 Jun 8, doi: 10.1016/j.ymeth.2020.06.004, PMID: 32526282

Cheok TS, Quek YS, Choo BJK, Gan SKE. What makes one civil?: The associations between civility scores, gender, rational-experiential processing styles, self-consciousness and socioeconomic factors in Singapore. APD Trove 2020, Vol: 3, Pg1-17, doi: 10.30943/2020/03062020

May

Srinivasaraghavan K, Aronica P, Ng S, Lian DTG, Frosi Y, Chee S, Jiang SM, Tsz YY, Sadruddind A, Kaand HYK, Chandramohand A, Wong JH, Tan YS, Chang ZW, Ferrer-Gagob FJ, Arumugam P, Han Y, Chen SY, Réniai L, Brown CJ, Johannes CW, Henry B, Lane DP,Sawyer TK, Verma CS, Partridge AW. Macrocyclization of an all-D linear α-helical peptide imparts cellular permeability. DOI: 10.1039/C9SC06383H (Edge Article) Chem. Sci., 2020, Advance Article.

Ng S, Juang YC, Chandramohan A, Kaan HYK, Sadruddin A, Tsz YY, Ferrer FJ, Lee XEC, Johannes CW, Brown CJ, Kannan S, Aronica PG, Berglund N, Verma CS, Liu L, Stoeck A, Sawyer TK, Partridge AW, Lane DP. De-risking drug discovery of intracellular targeting peptides: screening strategies to eliminate false-positive hits. Structure. 2020 Apr 6. pii: S0969-2126(20)30093-9. doi: 10.1016/j.str.2020.03.011.

Tan ZW, Guarnera E, Tee WV, Berezovsky IN. AlloSigMA 2: paving the way to designing allosteric effectors and to exploring allosteric effects of mutations. Nuclei Acids Research, 2020, doi: 10.1093/nar/gkaa338

Choo BJK, Cheok TS, Gunasegaran D, Wan KS, Quek YS, Tan CSL, Quek BK, Gan SKE. The Sound of Music on the Pocket: A Study of Background Music in Retail. SocArXiv. May 24. doi:10.31235/osf.io/7a45h.

April

Kong LR, Ong RW, Tan TZ, Mohamed Salleh NA, Thangavelu M, Chan JV, Koh J, Periyasamy G, Lau A, Thi Bul. Wang L. Lee MY, Kannan S, Verma CS, Lim CM, Joo CW, Lane D, Venkitaraman A, Hung H, Cheok CF, Goh BC. Targeting codon 158 p53-mutant cancers via the induction of p53 acetylation. Nature Communications 11, Article no: 2086, 2020, doi: 10.1038/s41467-020-15608-y

Li JG, Beuerman R, Verma CS. Mechanism of Polyamine Induced Colistin Resistance through Electrostatic Networks on Bacterial Outer Membranes. BBA - Biomembrane, Volume 1862, Issue 9, 1 September 2020, doi: 10.1016/j.bbamem.2020.183297

Zhou L, Chan JCY, Chupin S, Gueguen N, Desquiret-Dumas V, Koh SK, Li J, Gao Y, Deng L, Verma CS, Beuerman RW, Chan ECY, Milea D, Reynier P. Increased Protein S-Glutathionylation in Leber’s Hereditary Optic Neuropathy (LHON).. International Journal of Molecular Sciences, 2020 Apr 24;21(8), doi: 10.3390/ijms21083027, PMID: 32344771

Mahony C, Ashton RS, Birk B, Boobis AR, Cull T, Dashton GP, Ewart L, Knudsen TB, Manou I, Maurer-Stroh S, Margiotta-Casaluci L, Müller BP, Nordlund P, Roberts RA, Steger-Hartmann T, Vandenbossche E, Viant MR, Vinken M, Whelan M, Zvonimir Z, Cronin MTD. New ideas for non-animal approaches to predict repeated-dose systemic toxicity: Report from an EPAA Blue Sky Workshop. Regulatory Toxicology and Pharmacology, Vol. 114, Jul 2020, doi: 10.1016/j.yrtph.2020.104668. PMID: 32335207

Li J, Beuerman R, Verma CS. Mechanism of Polyamine Induced Colistin Resistance through Electrostatic Networks on Bacterial Outer Membranes. BBA - Biomembrane, Volume 1862, Issue 9, 1 September 2020, doi: 10.1016/j.bbamem.2020.183297

Mahoney C, Ashton RS, Birk B, Boobis AR, Cull T, Daston GP, Ewart L, Knudsen TB, Manou I, Maurer-Stroh S, Margiotta-Casaluci L, Muller BP, Nordlund Par, Roberts RA, Steger-Hartmann T, Vandenbossche E, Viant Mark R, Vinken M, Whelan M, Zvonimir Z, Cronin MTD. New ideas for non-animal approaches to predict repeated-dose systemic toxicity: Report from an EPAA Blue Sky Workshop. Regulatory Toxicology and Pharmacology, Vol. 114, Jul 2020, doi: 10.1016/j.yrtph.2020.104668. PMID: 32335207

Go MK, Zhao LN, Xue B, Supekar S, Robinson RC, Fan H*, Yew WS*. Directed Computational Evolution of Quorum-Quenching Lactonases from the Amidohydrolase Superfamily. Structure. 2020 Apr 6. pii: S0969-2126(20)30093-9. doi: 10.1016/j.str.2020.03.011. [Epub ahead of print]

Ling WL, Lua WH, Gan SKE. Sagacity in Antibody humanization for therapeutics, diagnostics and research purposes: Considerations of antibody elements and their roles. Antibody Therapeutics, 2020, Vol. 3, Issue 2, April 2020, Pg 71-79, doi: 10.1093/abt/tbaa005

Chan KF, Koukouravas S, Yeo YJ, Koh DWS, Gan SKE. Probability of change in life: Amino acid changes in single nucleotide substitutions. BioSystems, 2020 April 4, doi: 10.1016/j.biosystems.2020.104135

March

Lim ZV, Akram F, Ngo CP, Winarto AA, Lee WQ, Liang K, Oon HH, Thng STG, Lee HK. Automated grading of acne vulgaris by deep learning with convolutional neural networks. Skin Research & Technology, Vol 26, Issue 2, March 2020, Pg 187-192, doi: 10.1111/srt.12794, PMID: 31565821

Kong LR, Mohmed Salleh NA, Ong RW, Tan TZ, Syn NL, Goh RM, Fhu CW,Tan DSW, Iyer NG, Kannan S, Verma CS, Lim YC, Soo R, Ho J, Huang Y, Lim JSJ, Yan BJ, Nga ME, Lim SG, Koeffler HP, Lee SC, Kappei D, Hung HT, Goh BC. A common MET polymorphism harnesses HER2 signaling to drive aggressive squamous cell carcinoma. Microbial Cell Factories, 2020 Mar 19;19(1):71. doi: 10.1186/s12934-020-01328-x, PMID: 32192516

Goh F, Zhang MM, Lim TR, Low KN, Nge CE, Heng E, Yeo WL, Sirota FL, Crasta S, Tan Z, Ng V, Leong CY, Zhang H, Lezhava A, Chen SL, Hoon SS, Eisenhaber F, Eisenhaber B, Kanagasundaram Y, Wong FT, Ng SB. Identification and engineering of 32 membered antifungal macrolactone notonesomycins. Microbial Cell Factories, 2020 Mar 19;19(1):71. doi: 10.1186/s12934-020-01328-x, PMID: 32192516

Petrlova J, Petruk G, Huber RG, McBurnie EW, van der Plas MJA, Bond PJ, Puthia M, Schmidtchen A. Thrombin-derived C-terminal fragments aggregate and scavenge bacteria and their proinflammatory products. Journal of Biological Chemistry, 2020 Mar 13;295(11):3417-3430. doi: 10.1074/jbc.RA120.012741, PMID: 32034093

Pung R, Chiew CJ, Young BE, Chin S, Chen MI, Clapham HE, Cook AR, Maurer-Stroh S, Toh MPHS, Poh C, Low M, Lum J, Koh VTJ, Mak TM, Cui L, Lin RVTP, Heng D, Leo YS, Lye DC, Lee VJM. Investigation of three clusters of COVID-19 in Singapore: implications for surveillance and response measures - Singapore 2019 Novel Coronavirus Outbreak Research Team. Lancet 2020, Vol. 395, Issue 10229, Pg 1039-1046, March 28, 2020, doi: 10.1016/S0140-6736(20)30528-6, PMID: 32192580

Yeo YJ, Goh GR, Su TTC, Gan SKE. The Determination of HIV-1 RT Mutation Rate, Its Possible Allosteric Effects, and Its Implications on Drug Resistance. Viruses 2020, 12, 297; doi:10.3390/v12030297

Krah A, Huber RG, Bond PJ. How ligand binding affects the dynamical transition temperature in proteins. ChemPhysChem 2020, doi:10.1002/cphc.201901221

February

Shepley-McTaggart A, Fan H, Sudol M, Harty RN. Viruses go modular. Journal of Biological Chemistry, 2020, PMID: 32111739, doi: 10.1074/jbc.REV119.012414

Okada P, Buathong R, Phuygun S, Thanadachakul T, Parnmen S, Wongboot W, Waicharoen S, Wacharapluesadee S, Uttayamakul S, Vachiraphan A, Chittaganpitch M, Mekha N, Janejai N, Iamsirithaworn S, Lee RT, Maurer-Stroh S. Early transmission patterns of coronavirus disease 2019 (COVID-19) in travellers from Wuhan to Thailand. Eurosurveillance, Vol. 25, Issue 8, 27 Feb 2020, doi: 10.2807/1560-7917.ES.2020.25.8.2000097, PMID: 32127124

Zhuang Y, Liu H, Zhou XE, Verma RK, de Waal P, Jang W, Xu TH, Wang L, Meng X, Zhao G, Kang Y, Melcher K, Fan H, Lambert N, Xu E, Zhang C. Structure of formylpeptide receptor 2-Gi complex reveals insights into ligand recognition and signaling. Nature Communications, 2020 Feb 14;11(1):885. doi: 10.1038/s41467-020-14728-9, PMID: 32060286

Guarnera E, Berezovsky IN. Allosteric drugs and mutations: chances, challenges, and necessity. Current Opinion in Structural Biology, 2020 Feb 12;62:149-157. doi: 10.1016/j.sbi.2020.01.010, PMID : 32062398

Samsudin F, Yeo YJ, Gan KES, Bond PJ. Not all therapeutic antibody isotypes are equal: The case of IgM versus IgG in Pertuzumab and Trastuzumab. Chemical Science 2020, doi: 10.1039/C9SC04722K

Van der Ven LT, Rorije E, Sprong RC, Zink D, Derr R, Hendriks G, Loo LH, Luijten M. A Case Study with Triazole Fungicides to Explore Practical Application of Next-Generation Hazard Assessment Methods for Human Health. Chemical Research in Toxicology, 2020, 33, 3, Pg. 834-848, doi: 10.1021/acs.chemrestox.9b00484

Shiina K, Mori H, Okabe Y, Lee HK. Machine-Learning Studies on Spin Models. Scientific Reports 10, Article no. 2177, 2020, doi: 10.1038/s41598-020-58263-5, PMID: 32034178

Martin ER, Barbieri A, Ford RC, Robinson RC. In vivo crystals reveal critical features of the interaction between cystic fibrosis transmembrane conductance regulator (CFTR) and the PDZ2 domain of Na+/H+ exchange cofactor NHERF1. Journal of Biological Chemistry, 295, 2020, Pg 4464-4476, PMID: 32014995, doi: 10.1074/jbc.RA119.012015

January

Mehta S, McKinney C, Algie M, Verma CS, Kannan S, Harfoot R, Bartolec TK, Bhatia P, Fisher AJ, Gould M, Parker K, Cesare AJ, Cunliffe HE, Cohen SB, Kleffmann T, Braithwaite AW, Woolley AG. Dephosphorylation of YB-1 is Required for Nuclear Localisation During G2 Phase of the Cell Cycle. Cancers 2020, Feb 12(2), 315, doi: 10.3390/cancers12020315, PMID: 32013098

Kim PR, Koon YL, Lee TCR, Azizan F, Koh HZD, Chiam KH, Koh CG. Phosphatase POPX2 interferes with cell cycle by interacting with Chk1. Cell Cycle, Vol. 19, 2020, Issue 4, doi: 10.1080/15384101.2020.1711577

Marzinek JK, Huber RG, Bond PJ. Multiscale modelling and simulation of viruses. Current Opinion in Structural Biology 2020, 61:146-152, doi: 10.1016/j.sbi.2019.12.019, PMID: 31991326

Kumar AP, Verma CS, Lukman S. Structural dynamics and allostery of Rab proteins: strategies for drug discovery and design. Briefings in Bioinformatics, 2020. Jan 17, doi: 10.1093/bib/bbz161, PMID: 31950981

Han Z, Dash S, Sagum CA, Ruthel G, Jaladanki CK, Berry CT, Schwoerer MP, Harty NM, Freedman BD, Bedford MT, Fan H, Sidhu SS, Sudol M, Shtanko O, Harty RN. Modular Mimicry and Engagement of the Hippo Pathway by Marburg Virus VP40: Implications for Filovirus Biology and Budding. PLOS Panthogens, 2020 Jan 6;16(1):e1008231. doi: 10.1371/journal.ppat.1008231, PMID: 31905227

Past Publications (2004-2019)

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