PI-seminar-day 2021

Title: From sequence to structure and function
Abstract: This talk shows how expertise in sequence analysis bridging quickly to 3D structure and protein function can have impact in applications areas from viruses to shampoo, novel food, flavors, drugs and human diseases.

Abstract: The Gene Function Discovery group uses sophisticated formal methods for discovery of biomolecular mechanisms from biological/medical data (primarily biomolecular sequences, expression profiles and 3D structures as well as experimental life science data and clinical records). Examples of success stories are provided as well as ongoing projects with PhD students, academic and industrial collaborators. The digitalization of A*STAR's Natural Organism Library (NOL), the omics characterization of samples and the in silico screening of the resulting iNOL for diverse applications including natural product research is a major effort for the team in the future.

Abstract: Our lab investigates structure and function of RNA. RNA plays many roles in biological systems spanning genetic, enzymatic and regulatory functions. Many of these roles depend on spatial structure or specific RNA-RNA interactions. We follow an integrative approach to analyze data obtained by sequencing, NMR, X-ray crystallography, chemical probing and crosslinking experiments as well as molecular simulations. Relating structure, dynamics and function allows us to identify RNA elements that are crucial for the life cycle of viruses. In this overview, we show recent results of our research into RNA interactions and structure in Dengue, Zika, SARS-CoV-2, Chikungunya and Influenza viruses.

Abstract: The research focus of Fan Lab is to develop computational techniques to study protein-ligand interactions. The developed methods are used in basic research, to help understand and regulate biological processes, in particular, structure-function mechanisms of GPCRs, transporters, and kinases. Meanwhile, these methods were also employed in applied research, to help engineer industrial enzymes, evaluate toxicity of chemicals including food ingredients, and discover new drug leads.

Abstract: In this video, I share how my group uses computational tools to complement experimental efforts in chemical biology. One of the main themes of our research is the application of fragment-based concepts to computer-aided ligand/drug design.

Title: From Theoretical Models to Simulations and Design: Protein Function, Allostery and Chromatin
Abstract: Recent advances in our work on evolution-based protein design, studies of protein allostery, and theoretical models of chromatin are briefly discussed.

Title: Multiscale Simulation, Modelling & Design: Infectious Diseases and the Host Response
Abstract: This short talk gives a brief overview of our recent progress in computational approaches to modelling viral and bacterial envelopes and their interactions with host immunity, along with novel peptide- and antibody-based therapeutic developments.

Abstract: Translating molecular simulations to the clinic - This video outlines how careful applications of advanced biomolecular simulations combined with experiments are opening new windows into clinical applications for diseases ranging from cancer to bacterial infections

Title: AI Applications in Clinical Research
Abstract: In this video, we share a spectrum of AI work that are relevant in clinical research. We also place emphasis on the development of theoretical AI methodologies that are inspired by real world clinical applications

Abstract: The Complex Cellular Phenotype Analysis Group develops and uses novel phenotypic and molecular profiling methods to elucidate the mode of actions (MoAs) of xenobiotics, and build computational models that can predict in vivo effects based on these MoAs. Our current research focuses on building bioimage databases and visualization tools, assessing chemical/drug safety and efficacy, and digital medicine for cancer.

Abstract: I will briefly introduce the biophysical modeling capabilities of the group in the context of cultured meat. I will highlight the role of microtubules and microtubule associated proteins in nuclear positioning in myotube formation, as well as the mechanisms of how these proteins can come together to generate forces to position nuclei. I will describe simulations to study these biophysical processes. I will also describe optimization algorithms for culture media formulation.

Abstract: It is becoming apparent that changes in human exposures and behaviors are shaping the health adversities of future. Also, the availability of big data and multi-omics technologies are providing deeper insights into human variation and disease susceptibility. Our multidisciplinary team specializes in building multi-omics roadmaps and using systems approaches to identify biomarkers and interventions linked with health adversities (eg. Metabolic disorders and mental health) and suboptimal lifestyle that are currently plaguing the global health and economy. During our research journey we have established distinguished collaborations and delivered tangible scientific advances to multiple consortia, cohort studies, intervention trials, national platforms and nutrition industries.

Abstract: Innovations in Antibody Therapeutics and Viral Epitope Prediction Experimental Platform with Non-A*STAR areas of Scientific Phone Apps and Device Prototyping and Psychology. More information can be seen from publications in https://scholar.google.com.sg/citations?user=3zUyNmYAAAAJ&hl=en and https://www.researchgate.net/profile/Samuel_Ken_En_Gan as well as videos in fb.com/APDLab/.

Abstract: Modern data derived from living systems are large and often time-series based. The proper interpretation of the complex data requires techniques borrowed from other disciplines such as mathematics, physics, computer science and statistics. In this talk, I highlight selected works from our lab using systems biology approaches to tackle immune, cancer and microbial biofilm complexities and their regulation.

Abstract: BioMed DAR is a SSSO (Standard Systems Support Office) to support clinical research data management for A*STAR BMRC funded programmes

Abstract: This presentation will share some bioimage analysis and AI-based digital pathology diagnosis capabilities of CDP teams. We focus on cellular level digital image analysis, including cell/nuclei segmentation, cell tracking to under the migrating cell behaviors, collagen image quantification for the organ fibrosis, and cancer progression, etc. Our recent developments on the structural annotation of digital pathology image databased, digital pathology image quality control, and AI-model learning for the diagnosis, etc., are also demonstrated.

Abstract: Cancer diagnosis and treatment often require tissue biopsies and resections that are sent for microscopic assessment (known as ‘histopathology’), which is a time-consuming and labour-intensive process. For organs requiring complex access such as endoscopy, difficulties in adequate tissue sampling are compounded. Real-time visualization of tissue before and after excision that approaches the diagnostic quality and surpasses the coverage of resection histopathology may expedite disease detection and intervention.