Protein Sequence Analysis

Sebastian Maurer-Stroh
Deputy Executive Director (Research)

Vachiranee Limviphuvadh
Research Scientist

Gunalan Vithiagaran, Kenanov Dimitar
Senior Post-Doctoral Research Fellows

Lee Tze Chuen
Senior Research Officer

Miyajima Jhoann Margarette Tristeza
Research Officer

Chong Cheng Shoong Ken, Han Xiaochuan Alvin
PhD Students

Sebastian Maurer-Stroh
Deputy Executive Director (Research)

GROUP MEMBERS:

Vachiranee Limviphuvadh
Research Scientist

Gunalan Vithiagaran, Kenanov Dimitar
Senior Post-Doctoral Reseach Fellows

Lee Tze Chuen
Senior Research Officer

Miyajima Jhoann Margarette Tristeza
Research Officer

Chong Cheng Shoong Ken, Han Xiaochuan Alvin
PhD Students

Our group's expertise is in computational protein sequence and structure analysis to predict various aspects of molecular and cellular functions (enzymatic activities, posttranslational modifications, cleavage, translocation signals, 3D structures, effects of mutations, phylogenetic relationships, cellular pathways etc.) for discovering the molecular mechanisms of biological and clinical phenotypes and experimental validation together with collaborators. Our repertoire of computational analysis methods is applicable and useful in multiple research areas but our main focus currently is on infectious diseases, human mutations, allergy and enzyme function prediction.

Infectious Diseases

One of our traditional strongholds since the swine flu in 2009 is infectious disease research. Our FluSurver (http://flusurver.bii.a-star.edu.sg/) is the most complete one-stop influenza mutation analysis tool being used by researchers and surveillance experts globally. We have several published and ongoing projects with the WHO CC in Australia and National Influenza Centres relating to influenza drug resistance, viral fitness, host specificity and antigenic changes. The FluSurver is also a primary analysis tool for GISAID, the most complete influenza database also known for always hosting the latest outbreak sequences.

Because we can quickly go from genomes to protein structures through modelling in our computers often only requiring the new sequences as input, our group offers powerful support in infectious disease surveillance and rapid outbreak investigations to get a quick handle on bugs here and around the world. Besides Influenza, we also helped characterizing MERS, Ebola, HIV, Noro, Adeno, Hepatitis C, West Nile, Dengue and Zika viruses. Through close collaboration with the National Public Health Laboratory at the National Centre for Infectious Diseases of the Ministry of Health we contribute our knowledge and computational expertise at the national frontline for infectious disease surveillance.

Human Mutations and Protein Sequence Analysis

We aim at bridging the gap from nucleotide variation to protein structures to interpret effects of human mutations. For example, we have helped clinical collaborators to analyze variants found in patients and tried to mechanistically explain their possible role in a range of diseases like cancer, myopia, leprosy or atopic dermatitis. We are participating in the National Precision Medicine Programme to help mapping mutations into 3D protein structures relative to drug binding sites.

In our ongoing flagship industry project, large multinational Procter & Gamble and BII are jointly developing animal-testing-free Bioinformatics techniques for assessing the allergy potential of proteins using their amino acid sequence and tertiary structure. Often including industry collaborations, we are applying our sequence function and pathway analysis capabilities to support BII’s Natural Product Library and the A*STAR Biotransformation Innovation Platform as well as the Pharma Innovation Programme Singapore. A new direction is to support A*STAR’s Innovations in Food and Chemical Safety programme at the academia-industry interface. In this collaboration with many different groups, our role includes in silico protein allergy prediction, protein binding target identification, pathway analysis and to highlight common SNPs in the local population that may alter the response to toxic compounds.

Figure 1
Figure 1 - Mutations with protein structural consequences unique in the local Zika virus genomes overlayed on Singapore map and phylogenetic tree.

Protein Sequence Analysis Group Members

Dr. MAURER-STROH Sebastian
Deputy Executive Director (Research)
 
  Biography Details
NameTitle
Dr. MAURER-STROH SebastianPrincipal Investigator
Dr. LIMVIPHUVADH VachiraneeResearch Scientist
Dr. KENANOV Dimitar Senior Post-Doctoral Research Fellow
Dr. VITHIAGARAN GunalanSenior Post-Doctoral Research Fellow
Mr. LEE Tze ChuenSenior Research Officer
Ms. MIYAJIMA Jhoann Margarette TristezaResearch Officer
Dr. TAN Soon Heng, ChrisCollaborator
Mr. HAN Xiaochuan Alvin PhD student
Mr. CHONG Cheng Shoong, Ken PhD student
No Publications

Our group's expertise is in computational protein sequence and structure analysis to predict various aspects of molecular and cellular functions (enzymatic activities, posttranslational modifications, cleavage, translocation signals, 3D structures, effects of mutations, phylogenetic relationships, cellular pathways etc.) for discovering the molecular mechanisms of biological and clinical phenotypes and experimental validation together with collaborators. Our repertoire of computational analysis methods is applicable and useful in multiple research areas but our main focus currently is on infectious diseases, human mutations, allergy and enzyme function prediction.

Infectious Diseases

One of our traditional strongholds since the swine flu in 2009 is infectious disease research. Our FluSurver (http://flusurver.bii.a-star.edu.sg/) is the most complete one-stop influenza mutation analysis tool being used by researchers and surveillance experts globally. We have several published and ongoing projects with the WHO CC in Australia and National Influenza Centres relating to influenza drug resistance, viral fitness, host specificity and antigenic changes. The FluSurver is also a primary analysis tool for GISAID, the most complete influenza database also known for always hosting the latest outbreak sequences.

Because we can quickly go from genomes to protein structures through modelling in our computers often only requiring the new sequences as input, our group offers powerful support in infectious disease surveillance and rapid outbreak investigations to get a quick handle on bugs here and around the world. Besides Influenza, we also helped characterizing MERS, Ebola, HIV, Noro, Adeno, Hepatitis C, West Nile, Dengue and Zika viruses. Through close collaboration with the National Public Health Laboratory at the National Centre for Infectious Diseases of the Ministry of Health we contribute our knowledge and computational expertise at the national frontline for infectious disease surveillance.

Human Mutations and Protein Sequence Analysis

We aim at bridging the gap from nucleotide variation to protein structures to interpret effects of human mutations. For example, we have helped clinical collaborators to analyze variants found in patients and tried to mechanistically explain their possible role in a range of diseases like cancer, myopia, leprosy or atopic dermatitis. We are participating in the National Precision Medicine Programme to help mapping mutations into 3D protein structures relative to drug binding sites.

In our ongoing flagship industry project, large multinational Procter & Gamble and BII are jointly developing animal-testing-free Bioinformatics techniques for assessing the allergy potential of proteins using their amino acid sequence and tertiary structure. Often including industry collaborations, we are applying our sequence function and pathway analysis capabilities to support BII’s Natural Product Library and the A*STAR Biotransformation Innovation Platform as well as the Pharma Innovation Programme Singapore. A new direction is to support A*STAR’s Innovations in Food and Chemical Safety programme at the academia-industry interface. In this collaboration with many different groups, our role includes in silico protein allergy prediction, protein binding target identification, pathway analysis and to highlight common SNPs in the local population that may alter the response to toxic compounds.

Figure 1
Figure 1 - Mutations with protein structural consequences unique in the local Zika virus genomes overlayed on Singapore map and phylogenetic tree.

Protein Sequence Analysis Group Members

Dr. MAURER-STROH Sebastian
Deputy Executive Director (Research)
 
  Biography Details
NameTitle
Dr. MAURER-STROH SebastianPrincipal Investigator
Dr. LIMVIPHUVADH VachiraneeResearch Scientist
Dr. KENANOV Dimitar Senior Post-Doctoral Research Fellow
Dr. VITHIAGARAN GunalanSenior Post-Doctoral Research Fellow
Mr. LEE Tze ChuenSenior Research Officer
Ms. MIYAJIMA Jhoann Margarette TristezaResearch Officer
Dr. TAN Soon Heng, ChrisCollaborator
Mr. HAN Xiaochuan Alvin PhD student
Mr. CHONG Cheng Shoong, Ken PhD student
No Publications