Graduate Research Opportunities

One of BII's missions is to nurture a pool of young talent in the area of Bioinformatics and equip them with the necessary skills to push the frontiers of modern science. Under the supervision of renowned scientists, graduates who pursue a PhD under the programmes affiliated to BII can look forward to a conducive learning environment, a culture of active collaborations and a network of strong international linkages. The experiences include participation in journal publications as well as poster presentations in international conferences.

The scholarships and awards that are available for PhD are as follows:

More details on SINGA can be found via this link.

List of BII Supervisors and Projects (SINGA)

 

Principal Investigators (PIs)/ Supervisors

Potential PhD Project Title/Area

Degree Awarded by

Biomolecular Function Discovery Division

Dr. Birgit Eisenhaber
Dr. Frank Eisenhaber

Gene Function Prediction / Annotator Group

Discovery of biomolecular mechanisms with sequence analysis and data mapped onto genomes, analysis of omics clinical data, prediction of gene function from sequence.

 NUS/NTU

Dr. Sebastian Maurer-Stroh

Computational sequence and structure analysis to combat viral infectious diseases.

 NUS
Biomolecular Modeling and Design Division

Dr. Chandra Verma

Atomistic Simulations & Design in Biology Group

Molecular modelling & simulations of biomolecular mechanisms; design of drugs, peptides, proteins, enzymes, antibodies in oncology; inflammation, antimicrobials. Machine learning/AI in drug design.

NUS/NTU

Dr. Fan Hao

Structure-based Ligand Discovery & Design Group

Ligand discovery for GPCRs, transporters, and kinases to help develop chemical probes and drugs for related diseases (e.g. cancer); Enzyme function annotation and redesign for synthetic biology; In-silico chemical toxicity prediction.

 NUS

Dr. Peter J. Bond

Multiscale Simulation, Modelling & Design Group

Multiscale modelling and simulation of biomolecules, towards novel therapeutic development. Focus on innate immune receptors, inflammatory pathways, and hostpathogen interactions.

  Group website
NUS

Dr. Igor N. Berezovsky

Physics & Evolution of Biological Macromolecules Group

Allosteric regulation of protein function, evolution of protein function, chromatin structural dynamics and epigenetic regulation, protein thermostability.

 NUS
Imaging Informatics Division

Dr. Chiam Keng Hwee

Biophysical Modelling Group

Biophysical modelling of durotaxis and metastasis of cancer cells.

NUS/NTU

Dr. Lee Hwee Kuan

Computer Vision & Pattern Discovery Group

Artificial Intelligence for healthcare: theory and applications Project involves close collaborations with hospitals.

Group website
NUS

Dr. Loo Lit Hsin

Complex Cellular Phenotype Analysis Group

In vitro cell-based models for predicting the toxicity of chemicals and drugs, highthroughput phenotypic profiling, and systems biology.

Group website
NUS
Translational Research Division

Dr. Samuel K.E. Gan

Antibody and Product Development Group

Antibody Engineering; Viral drug design and resistance (Computational + Experimental); Smartphone biomedical lab; Psychobiology)

SUSS, various UK and Thai Universities

Dr. Ng Siew Bee

Natural Product Biology Group

Discovery and mode-of-action study of bioactive compounds, biosynthesis of secondary metabolites.

NTU/NUS

Dr. Yoganathan Kanagasundaram

Natural Product Chemistry Group

Metabolomics, Purification and structure elucidation of bioactive and novel compounds.

NTU/NUS

Dr. Prakash Arumugam

Chemical Genomics Group
  1. Chemogenomic profiling in mammalian cells using Genomewide CRISPR/Cas9-based Knockout(GeCKO).
  2. Mechanism of Target of Rapamycin Complex 1 ( TORC1) Signalling. These projectswill be jointly supervised by Dr Prakash Arumugam and Prof. Chandra Varma
  Group website
NTU/NUS

For more details of each project, please email your queries to the PI/supervisor-in-charge.

More details on ARAP can be found via this link

BII Supervisors and their Projects

Structure-based ligand discovery for overcoming multi-drug resistance

  • Principal Supervisor (Manchester) - Professor Bob Ford
  • BII Supervisor - Dr. Fan Hao

ABCB1 - P-glycoprotein is an ATP-binding cassette (ABC) transporter. ABCB1 - along with a few other ABC proteins, is responsible for cancer chemotherapy failure in a high proportion of cases. It is able to transport xenobiotics and drugs out of cells - rendering them resistant to said compounds. At the blood-brain barrier, ABCB1 performs a vital role in maintaining the integrity of the brain. It performs a similar gatekeeper role in stem cells. The structure of ABCB1 has been studied for several years in the Ford laboratory, with 2 people in his group currently working on this. Good inhibitors or activators of ABCB1 are actively being sought. The Ford lab published the first structure of ABCB1 and has produced the only structure for the outward-facing conformation of the protein (ie with ATP bound). This project will combine the strengths in protein chemistry and structural biology of the Ford lab with the strengths in protein structure modelling, structure-based ligand discovery, and molecular dynamics simulation of biomolecules in the Fan laboratory at the BII, A*STAR in Singapore. In Manchester, the student will participate in the generation structural data for ABCB1 which is currently being expressed and purified in the Ford lab. The student will specifically carry out crystal trials and cryo-EM studies with known ABCB1 substrates and inhibitors with the aim of identifying likely binding sites. The work will then extend to protein structure modelling and structure-based ligand discovery. The candidate ligands from these efforts will be tested in a biochemical assay based on the purified protein.

More details on AGS can be found via this link.

List of BII Supervisors and Projects (AGS)
 
Principal Investigators (PIs)/ Supervisors Research Area / Theme Overseas Partner Universities Collaborators
Dr. FAN Hao A multidisciplinary approach to understanding the influence of HDAC9 variants on STROKE, and developing therapeutics based on HDAC9 inhibition. University of Cambridge Prof. Hugh Markus
Dr. BOND Peter
Integrated Multiscale Approaches of Theory and Experiments to Characterise Amyloid Formation at Membrane Surfaces Imperial College London Dr. Alfonso De Simone
A computational and experimental platform for modulation of innate immunity University of Cambridge Prof. Clare Bryant
Identifying druggable protein-protein interactions by computational sampling of cryptic binding pockets University of Cambridge Dr. David Huggins
Computational approaches supporting diversity-oriented synthesis (DOS) for disrupting bacterial quorum sensing University of Cambridge Prof. David Spring
Dr. Andreas Bender
Development of long-timescale simulation methods to neuroreceptors University of Oxford Dr. Phil Biggin
Dr. Chandra Verma
The interaction of metastasis-associated MAGE-A proteins with components of the p53 tumour suppressor network as novel anti-cancer therapeutic targets University of Dundee Dr. David Meed
Studies of p53 interactions with DNA Karolinska Institutet Prof Lennart Nilsson
Trp metabolim by the enzyme Indoleamine 2,3-dioxygenase Imperial College London Prof Andrew George
Drug design from the inhibition of growth factor signalling to translation University of Dundee Dr. Ruth Brenk
Dr. Lee Hwee Kuan
Dr. Cheng Li
Dr. Loo Lit Hsin
Computer Vision and Machine Learning for Pattern Discovery in Microscopy Images University of Illinois at Urbana-Champaign  
Computer Vision and Machine Learning for Pattern Discovery in Microscopy Images Imperial College London  
Computer Vision and Machine Learning for Pattern Discovery in Microscopy Images University of Dundee  
Dr. Sebastian
Maurer-Stroh
Computational prediction and experimental verification of novel functional aspects of ATM and ATR kinases The University of Dundee Dr. John Rouse
Development of a computer algorithm for the prediction of O-GlcNAc modifications followed by experimental verification of predicted substrates and cell biological consequences The University of Dundee Dr. Daan Van Aalten
Computational prediction and experimental verification of novel functional aspects of SMC proteins involved in DNA damage repair Karolinska Institutet Dr. Camilla Sjogren
Dr. Vladimir Kuznetsov Computational and mathematical approaches to analysis of critical macro-molecular and cellular events associated with tumor dormancy, cellular dynamics and cancer progression. The University of Dundee Dr. Mark Chaplain


For more details of each project, please email your queries to the PI/supervisor-in-charge.