Bioinformatics Institute

Publication date Article title Author(s)
7 May 2021 Riemannian Similarity Learning Cheng Li
11 Jan 2021 Identification of pathways modulating vemurafenib resistance in melanoma cells via a genome-wide CRISPR/Cas9 screen Corinna Jie Hui Goh, Jin Huei Wong, Chadi El Farran, Ban Xiong Tan, Cynthia R. Coffill, Yuin-Hain Loh, David Lane, Prakash Arumugam
29 Sep 2020 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 Tran-To Su Su, Swati Sinha, Birgit Eisenhaber, Frank Eisenhaber
12 Sep 2020 Disorder driven allosteric control of protein activity Wei-Ven Tee, Enrico Guarnera, Igor N Berezovsky
9 Sep 2020 Virtual screening of potentially endocrine‑disrupting chemicals against nuclear receptors and its application to identify PPARγ‑bound fatty acids Chaitanya K Jaladanki, Yang He, Li Na Zhao, Sebastian Maurer-Stroh, Lit-Hsin Loo, Haiwei Song, Hao Fan
3 Sep 2020 Augmented Reality in scientific visualization and communications: A new dawn of looking at antibody interactions Samuel Ken-En Gan, Kwok-Fong Chan, Jun-Jie Poh, Wei-Ling Wu
1 Sep 2020 Critical role for cold shock protein YB-1 in cytokinesis Antony Braithwaite, Sunali Mehta, Michael Algie, Tariq Al-Jabry, Cushla McKinney, Srinivasaraghavan Kannan, Chandra S Verma, Weini Ma, Jessie Zhang, Tara K Bartolec, V. Pragathi Masamsetti, Kim Parker, Luke Henderson, Maree L Gould, Puja Bhatia, Rhodri Harfoot, Megan Chircop, Torsten Kleffmann, Scott B Cohen, Adele G Woolley, Anthony J Cesare
18 Aug 2020 Straightforward incorporation of multiple ligand types into molecular dynamics simulations for efficient binding site detection and characterization Yaw Sing Tan, Chandra S Verma
13 Aug 2020 Accelerated spin dynamics using deep learning corrections Sojeong Park, Wooseop Kwak, Hwee Kuan Lee
29 Jun 2020 Optimum concentration-response curve metrics for supervised selection of discriminative cellular phenotypic endpoints for chemical hazard assessment James A Miller
11 May 2020 Macrocyclization of an all-D linear α-helical peptide imparts cellular permeability Srinivasaraghavan Kannan, Pietro G. A. Aronica, Simon Ng, Dawn Thean Gek Lian, Yuri Frosi, Sharon Chee, Shimin Jiang, Tsz Ying Yuen, Ahmad Sadruddin, Hung Yi Kristal Kaan, Arun Chandramohan, Yi Han, Jin Huei Wong, Yaw Sing Tan, Zi Wei Chang, Fernando Jose Ferrer-Gago, Prakash Arumugam, Shiying Chen, Laurent Claude Stephane Renia, Christopher J. Brown, Charles W. Johannes, Brian Henry, David P. Lane, Tomi K Sawyer, Chandra S. Verma, Anthony William Patridge
11 May 2020 AlloSigMA 2: paving the way to designing allosteric effectors and to exploring allosteric effects of mutations Zhen Wah Tan, Enrico Guarnera, Wei-Ven Tan, Igor N. Berezovsky
10 May 2020 Extending the Martini coarse-grained forcefield to N-glycans Aishwary T. Shivgan, Jan K. Marzinek, Roland G. Huber, Alexander Krah, Richard H. Henchman, Paul Matsudaira, Chandra S. Verma, Peter J. Bond
5 May 2020 De-risking Drug Discovery of Intracellular Targeting Peptides: Screening Strategies to Eliminate False-Positive Hits Simon Ng, Yu-Chi Juang, Arun Chandramohan, Hung Yi Kristal Kaan, Ahmad Sadruddin, Tsz Ying Yuen, Fernando J. Ferrer-Gago, Xue'Er Cheryl Lee, Liew Xi, Charles W. Johanes, Christopher J. Brown, Srinivasaraghavan Kanan, Pietro G. Aronica, Nils A. Berglund, Chandra S. Verma, Lijuan Liu, Alexander Stoeck, Tomi K. Sawyer, Anthony W. Partridge, David P. Lane
29 Apr 2020 Targeting codon 158 p53-mutant cancers via the induction of p53 acetylation Li Ren Kong, Richard Weijie Ong, Tua Zea Tan, Nur Afiqah Binte Mohamed Salleh, Matan Thangavelu, Jane Vin Chan, Lie Yong Judice Koh, Giridharan Periyasamy, Jieying Amelia Lau, Thi Bich Uyen Le, Lingzhi Wang, Miyoung Lee, Srinivasaraghavan Kannan, Chandra S. Verma, Chwee Ming Lim, Wee Joo Chng, David P. Lane, Ashok Venkitaraman, Huynh The Hung, Chit Fang Cheok, Boon Cher Goh
24 Apr 2020 Mechanism of polyamine induced colistin resistance through electrostatic networks on bacterial outer membranes Jianguo Li, Roger Beuerman, Chandra S. Verma
24 Apr 2020 Increased Protein S-Glutathionylation in Leber’s Hereditary Optic Neuropathy (LHON) James Chun Yip Chan, Stephanie Chupin, Lei Zhou, Naïg Gueguen, Valérie Desquiret-Dumas, Siew Kwan Koh, Jianguo Li, Yao Gan, Lu Deng, Chandra Verma, Roger W. Beuerman, Dan Milea, Eric Chun Yong Chan Chan, Pascal Reynier
23 Apr 2020 New ideas for non-animal approaches to predict repeated-dose systemic toxicity: Report from an EPAA Blue Sky Workshop Ruth A. Roberts, Thomas Steger-Hartmann, Evita Vanenbossche, Mark R. Viant, Matthieu Vinken, Maurice Whelan, Zvonar Zvonimir, Mark T. D. Cronin, Catherine Mahony, Randolph S. Ashton, Barbara Birk, Alan R. Boobis, Tom Cull, George P. Daston, Lorna Ewart, Thomas B. Knudsen, Irene Manou, Sebastian Maurer-Stroh, Luigi Margiotta-Casaluci, Boris P. Muller, Pär Nordlund
21 Apr 2020 Directed Computational Evolution of Quorum-Quenching Lactonases from the Amidohydrolase Superfamily Maybelle Kho Kho, Lin Na Zhao, Bo Xue, Shreyas Supekar, Robert C. Robinson, Hao Fan, Wen Shan Yew
18 Apr 2020 Sagacity in antibody humanization for therapeutics, diagnostics and research purposes: considerations of antibody elements and their roles Wei-Li Ling, Wai-Heng Lua, Samuel Ken-En Gan
5 Apr 2020 A benzene-mapping approach for uncovering cryptic pockets in membrane-bound proteins Lorena Zuzic, Jan K. Marzinek, Jim Warwicker, Peter J. Bond
4 Apr 2020 Probability of change in life: Amino acid changes in single nucleotide substitutions Kwok-Fong Chan, Stelios Koukouravas, Joshua Yi Yeo, Darius Wen-Shuo Koh, Ken-En Samuel Gan
25 Mar 2020 A common MET polymorphism harnesses HER2 signaling to drive aggressive squamous cell carcinoma Nur Afiqah Binte Mohamed Salleh, Richard Weijie Ong, Li Ren Kong, Tuan Zea Tan, Nicholas L. Syn, Robby Miguel Goh, Chee Wai Fhu, Daniel S W Tan, Gopalakrishna Iyer, Srinivasaraghavan Kannan, Chandra S. Verma, Yaw Chyn Lim, Ross Soo, Jingshan Ho, Yiqing Huang, Joline S. J. Lim, Benedict Junrong Yan, Min En Nga, Seng Gee Lim, H. Philip Koeffler, Soo Chin Lee, Dennis Kappei, Huyhn The Hung, Boon Cher Goh
19 Mar 2020 Identification and engineering of 32 membered antifungal macrolactone notonesomycins Falicia Goh, Mingzi M. Zhang, Tian Ru Lim, Kia Ngee Low, Choy Eng Nge, Elena Heng, Wan Lin Yeo, Fernanda L. Sirota, Sharon Crasta, Zann Tan, Veronica Ng, Chung Yan Leong, Hubin Zhang, Alexander Lezhava, Swaine L. Chen, Shawn S. Hoon, Frank Eisenhaber, Birgit Eisenhaber, Yoganathan Kanagasundaram, Fong T. Wong, Siew Bee Ng
16 Mar 2020 Investigation of three clusters of COVID-19 in Singapore: implications for surveillance and response measures Rachel Pung, Calvin J. Chiew, Barnaby E. Young, Sarah Chin, Mark I-C Chen, Hannah E. Clapham, Alex R. Cook, Sebastian Maurer-Stroh, Matthias P. H. S Toh, Cuiqin Poh, Mabel Low, Joshua Lum, Valerie T. J. Koh, Tze M. Mak, Lin Cui, Raymond V. T. P Lin, Derrick Heng, Yee-Sin Leo, David C. Lye, Vernon J. M. Lee
9 Mar 2020 The Determination of HIV-1 RT Mutation Rate, Its Possible Allosteric Effects, and Its Implications on Drug Resistance Joshua Yi Yeo, Ghin-Ray Goh, Chinh Tran-To Su, Samuel Ken-En Gan
3 Mar 2020 How Ligand Binding Affects the Dynamical Transition Temperature in Proteins Alexander Krah, Roland G. Huber, Peter J. Bond
28 Feb 2020 Viruses go modular Ariel Shepley-McTaggart, Hao Fan, Marius Sudol, Ronald N. Harty
27 Feb 2020 Early transmission patterns of coronavirus disease 2019 (COVID-19) in travellers from Wuhan to Thailand, January 2020 Noppavan Janejai, Pilailuk Okada, Rome Buathong, Siripaporn Phuygun, Thanutsapa Thanadachakul, Sittiporn Parnmen, Warawan Wongboot, Sunthareeya Waicharoen, Supaporn Wacharapluesadee, Sumonmal Uttayamakul, Apichart Vachiraphan, Malinee Chittaganpitch, Nanthawan Mekha, Sopon Iamsirithaworn, Raphael T. C. Lee, Sebastian Maurer-Stroh
14 Feb 2020 Structure of formylpeptide receptor 2-Gi complex reveals insights into ligand recognition and signaling Youwen Zhuang, Heng Liu, X Edward Zhou, Ravi Kumar Verma, Parker W. de Waal, Wonjo Jang, Ting-Hai Xu, Lei Wang, Xing Meng, Gongpu Zhao, Yanyong Kang, Karsten Melcher, Hao Fan, Nevin A. Lambert, H. Eric Xu, Cheng Zhang
12 Feb 2020 Allosteric drugs and mutations: chances, challenges, and necessity Enrico Guarnera, Igor N. Berezovsky
12 Feb 2020 Not all therapeutic antibody isotypes are equal: the case of IgM versus IgG in Pertuzumab and Trastuzumab Firdaus Samsudin, Joshua Yi Yeo, Samuel Ken-En Gan, Peter J. Bond
11 Feb 2020 A Case Study with Triazole Fungicides to Explore Practical Application of Next-Generation Hazard Assessment Methods for Human Health Leo T. M. van der Ven, Emiel Rorije, R. Connie Sprong, Daniele Zink, Remco Derr, Giel Hendriks, Lit-Hsin Loo, Mirjam Luijten
7 Feb 2020 Thrombin-derived C-terminal fragments aggregate and scavenge bacteria and their proinflammatory products Jitka Petrolova, Ganna Petruk, Roland G. Huber, Eilish W. McBurnie, Mariena J. A. van der Plas, Peter J. Bond, Manoj Puthia, Artur Schmidtchen
7 Feb 2020 Machine-Learning Studies on Spin Models Kenta Shiina, Hiroyuki Mori, Yutaka Okabe, Hwee-Kuan Lee
25 Jan 2020 Multiscale modelling and simulation of viruses Jan K. Marzinek, Roland G. Huber, Peter J. Bond
6 Jan 2020 Modular mimicry and engagement of the Hippo pathway by Marburg virus VP40: Implications for filovirus biology and budding Hao Fan, Sachdev S. Sidhu, Ziying Han, Shantoshini Dash, Cari A. Sagum, Gordon Ruthel, Chaitanya K. Jaladanki, Corbett T. Berry, Michael P. Schwoerer, Nina M. Harty, Bruce D. Freedman, Mark T. Bedford, Marius Sudol, Olena Shtanko, Ronald N. Harty
24 Dec 2019 Flavivirus Cross-Reactivity to Dengue Nonstructural Protein 1 Antigen Detection Assays Li Kiang Tan, Wing Yan Wong, Hui Ting Yang, Roland G. Huber, Peter J. Bond, Lee Ching Ng, Sebastian Maurer-Stroh, Hapuarachchige Chanditha Hapuarachchi
12 Dec 2019 In Memory of Vladimir B. Bajic (1952–2019) Zhang Zhang, Jun Yu, Frank Eisenhaber, Xin Gao, Takashi Gojobori
10 Dec 2019 Quantum scale biomimicry of low dimensional growth: An unusual complex amorphous precursor route to TiO2 band confinement by shape adaptive biopolymer-like flexibility for energy applications Dahyun Choi, Sanjiv Sonkaria, Stephen J. Fox, Shivraj Poudel, Sung-yong Kim, Suhee Kang, Seheon Kim, Chandra S. Verma, Sung Hoon Ahn, Caroline Sunyong Lee, Varsha Khare
6 Dec 2019 Deciphering the mechanistic effects of eIF4E phosphorylation on mRNA‐cap recognition Dilraj Lama, Chandra S. Verma
1 Dec 2019 New High-Throughput Screening Identifies Compounds That Reduce Viability Specifically in Liver Cancer Cells That Express High Levels of SALL4 by Inhibiting Oxidative Phosphorylation Justin L. Tan, Feng Li, Joanna Z. Yeo, Kol Jia Yong, Mahmoud A. Bassal, Guo Hao Ng, May Yin Lee, Chung Yan Leong, Hong Kee Tan, Chan-shuo Wu, Bee Hui Liu, Tim H. Chan, Zi Hui Tan, Yun Shen Chan, Siyu Wang, Zhi Han Lim, Tan Boon Toh, Lissa Hooi, Kia Ngee Low, Siming Ma, Nikki R. Kong, Alicia J. Stein, Yue Wu, Matan T. Thangavelu, Atsushi Suzuki, Giridharan Periyasamy, John M. Asara, Yock Young Dan, Glenn K. Bonney, Edward K. Chow, Guo-Dong Lu, Huck Hui Ng, Yoganathan Kanagasundaram, Siew Bee Ng, Wai Leong Tam, Daniel G. Tenen, Li Chai
28 Nov 2019 The Dual Interactions of p53 with MDM2 and p300: Implications for the Design of MDM2 Inhibitors Srinivasaraghavan Kannan, Anthony W. Partridge, David P. Lane, Chandra S. Verma
28 Nov 2019 On the ion coupling mechanism of the MATE transporter ClbM Alexander Krah, Roland G. Huber, Ulrich Zachariae, Peter J. Bond
25 Nov 2019 G Protein–Coupled Receptors in Asthma Therapy: Pharmacology and Drug Action Stacy Gelhaus Wendell, Hao Fan, Cheng Zhang
13 Nov 2019 Knockout of the non-essential gene SUGCT creates diet-linked, age-related microbiome disbalance with a diabetes-like metabolic syndrome phenotype Joanna Niska-Blakie, Lakshmi Gopinathan, Kia Ngee Low, Yang Lay Kien, Christine M. F. Goh, Matias J. Caldez, Elisabeth Pfeiffenberger, Oliver S. Jones, Chee Bing Ong, Igor V. Kurochkin, Vincenzo Coppola, Lino Tessarollo, Hyungwon Choi, Yoganathan Kanagasundaram, Frank Eisenhaber, Sebastian Maurer-Stroh, Philipp Kaldis
11 Nov 2019 Insights into the Effects of Cancer Associated Mutations at the UPF2 and ATP-Binding Sites of NMD Master Regulator: UPF1 Umesh Kalathiya, Monikaben Padariya, Kamila Pawlicka, Chandra S. Verma, Douglas Houston, Ted R. Hupp, Javier Antonio Alfaro
1 Nov 2019 The quantification of antibody elements and receptors subunit expression using qPCR: The design of VH, VL, CH, CL, FcR subunits primers for a more holistic view of the immune system Wei-Li Ling, Yuen-Ling Ng, Anil Wipat, David Philip Lane, Samuel Ken-En Gan
10 Oct 2019 Linker length affects photostability of protein-targeted sensor of cellular microviscosity Markéta Kubánková, Joseph E. Chambers, Roland G. Huber, Peter J. Bond, Stefan J. Marciniak, Marina K. Kuimova
9 Oct 2019 Inferring putative transmission clusters with Phydelity Alvin X. Han, Edyth Parker, Sebastian Maurer-Stroh, Colin A. Russell