EID Project Descriptions (For potential medical and research students)


PI: Manoj Krishnan, PhD 

My laboratory studies the mechanisms by which cellular anti-viral innate immune pathways neutralize infection of RNA viruses such as dengue, influenza and chikunguniya. We anticipate to integrating the identification of new concepts in the regulatory mechanisms of anti-viral response with the discovery of novel candidate molecules that can be potentially used as immunomodulators. Three broader questions that we investigate are given below. 

Examples of current projects in our laboratory: 

1. Understand the global regulation and integration of innate immune antiviral pathways leading to effective infection clearance

The collective action of several cell intrinsic pathways that together constitute the innate immune antiviral defense is critical for combating viral infection. Although several key upstream viral pathogen sensors (e.g., TLRs and RIG-I), and the pivotal downstream molecules that drive the antiviral response (e.g., NFkB, MAP kinase, Interferons) are well characterized, a comprehensive understanding of the cellular proteins and pathways that regulate and integrate these pathways is currently lacking. Using the transcriptional activation of Interferons as a paradigm, we are investigating how different antiviral pathways are regulated and integrated, during both infection clearance and diseases. 

2. Understand how dendritic cells undergo maturation after viral infection, leading to effective adaptive Immune response

The dendritic cells of the immune system play a pivotal role in shaping the long-term immune response against infection as well as vaccines. After pathogen stimulation, the dendritic cells undergo a process called “maturation”, a central process by which they acquire the capacity to induce adaptive immune response against infection and vaccine. However, the mechanism underlying dendritic cell maturation is poorly defined. We are investigating the genes and signaling processes that regulate dendritic cell maturation. 

3. Discovery of novel molecules to modulate immune pathways and processes

Modulators of immune responses will have immense prophylactic and therapeutic applications. One of the best examples is adjuvant, a component of most vaccines that serve the purpose facilitating the development of an optimal immune response. We explore the possibility of discovering novel small molecular weight compounds that can modulate the immune signaling pathways, through high-throughput drug discovery screening. Subsequent to their discovery and validation, these compounds will be tested for their efficacy using ex vivo and in vivo models.



PI: Gavin Smith, PhD

Co-PI: Vijaykrishna Dhanasekaran, PhD 


Our research integrates ideas from a number of different fields including evolutionary genetics, virology, ecology, and infectious disease epidemiology. We conduct human and animal disease surveillance, virus isolation and characterization (genetic and phenotypic), then conduct large-scale analyses to generate hypotheses that we test in the lab using tissue culture and animal models. We are primarily interested in the roles played by mutation, natural selection, recombination/reassortment and host immune response on virus diversity within an individual, during transmission within a population and during inter-species transmission between hosts. We work mostly on influenza but also have projects on Astro-, Corona-, Paramyxo-, and Flavi-viruses. 

Examples of current projects in our laboratory: 

1. Viral diversity within hosts and populations

Investigation of the viral diversity within an individual or a population of different animal species including humans and small mammals such as bats and rodents. 

2. Evolutionary dynamics and molecular epidemiology of human and animal viruses

Largely sequencing and/or computational studies to investigate the population behavior of viruses in a variety of human and animal viruses on different spatio-temporal scales.

3. Anti-viral resistance

Using phenotypic tests to determine the rate of antiviral resistance in influenza A viruses from Singapore, the Philippines and India. 

4. Evolutionary consequences of reassortment in influenza A viruses

Reverse genetics and ferret infection experiments of influenza A viruses to determine the implications of reassortment on influenza virus evolution. 



PI: Ashley St. John, PhD

The research program in the lab is currently focused on studying how the initial inflammatory events of infection shape downstream immune protection or pathology, particularly in the context of viral pathogens such as dengue virus. 

This lab employs approaches including the use of animal models and techniques in cellular immunology to functionally test the impact of immune mediators on immunosurveillance for viral pathogens, cellular activation and trafficking within lymph nodes, and protective immunological memory and immune pathology. Studying primary immune processes and immunosurveillance events for pathogens that impact adaptive immunity is a key aim of my work and one that has implications for vaccine design and the development of novel immunotherapeutics. 

Current potential projects for students include:

1. exploring the mechanism underlying dengue vascular pathogenesis

2. describing the innate immune response generated by dengue virus in the skin and draining lymph nodes

3. Investigating the association between asthma and respiratory syncytial virus infection



PI: Prof Mariano Garcia-Blanco, MD, PhD 

Project 1 : Influence of dengue virus genetics on infection in mosquito vectors (under the supervision of Dr. Julien Pompon) 

Dengue is a debilitating disease caused by a virus transmitted by mosquitoes, from the species Aedes aegypti. Mechanisms leading to dengue epidemics are not well understood. Here, we will study the impact of virus genetics on epidemic potential by identifying the genetic factors that affect virus replication in mosquitoes.

The student will have to infect mosquitoes through oral blood feeding, extract RNA and quantify the virus load using bio-molecular and cell biology tools.

The project should help Singapore better control dengue epidemics.The project will take place in the renowned Duke-NUS graduate medical school in the molecular virology laboratory of Prof. Garcia-Blanco.  

Project start date: October 2015

Project 2: The impact of insecticide resistance on mosquito vector competence for dengue virus

Dengue is a debilitating disease caused by a virus transmitted by mosquitoes, from the species Aedes aegypti. Given the absence of licensed vaccine or medication to cure the disease, the only efficient method to curb the epidemics is to reduce the mosquito population using insecticide, mainly pyrethroids. However, the use of insecticide resulted in the selection of insecticide resistance in mosquitoes.

The goal of the project is to understand what is the impact on dengue transmission of insecticide resistance in mosquitoes. The result of the research will have broad impact on the current anti-vector approach. 

The student will have to isolate an insecticide resistant mosquito colony using molecular and biomolecular tools. The  project will take place both in Duke-NUS graduate medical school and in the Environment Health Institute, National Environment Agency in Singapore.

Project start date: October 2015

Please contact Dr. Julien Pompon at Julien.pompon@duke-nus.edu.sg



We have a particular interest in the mechanisms affecting the pathogenic potential of viruses.  The laboratory frequently utilises high-throughput sequencing as a tool to elucidate these mechanisms.  Recently, we have explored the human transcriptome in response to a pathogenic and vaccine derivative dengue virus infection and have analysed the changes in dengue virus quasi-species during human to mosquito transmission to characterise the genetic constraints its human and mosquito hosts place on the viral genome. The tools developed for these studies readily translate to the mechanistic analysis of other pathogens as well.  In collaboration with clinical partners both local and international, we are applying these tools to study the emergence of both novel pathogens as well as known pathogens with novel clinical manifestations/associations.

Examples of current projects in our laboratory:

1) The molecular basis for EV71 pathogenesis and epidemic potential

Enterovirus 71 (EV71) is known to cause a spectrum of clinical syndromes that range from hand, foot and mouth disease (HFMD) to CNS infections that result in long-term sequelae or death, most frequently in children under the age of four. Currently, there is neither vaccine nor specific antiviral treatment to ameliorate the course of infection. There has been a change in clinical presentation, pathogenicity and epidemic potential of EV71 in Asia over the last 15 years that may be the result of viral evolution. Where these genetic changes occur and how they are mechanistically responsible for the emergence of more virulent strains of EV71 is unknown. The lack of such understanding prevents an evidence-based approach to surveillance and disease prevention. To address this, we will utilise a unique collection of clinically relevant strains from Singapore and the ongoing EV71 epidemic in Vietnam to characterise the mechanisms of pathogenesis and epidemic potential. Using the full genome sequence of these viruses we will test the functional relevance of distinguishing mutations by assessing their effect on the virus and the effect they have on the ability of the virus to suppress the host’s innate antiviral response.

2) A Hybridization-Based Enrichment Strategy to Increase the Accuracy of Next Generation Sequencing in Clinical Samples

The principle problem encountered when employing NGS directly on patient samples is the high ratio of host to viral RNA.  To compensate for this, we developed a hybridisation-based enrichment strategy consisting of virus-specific probes to capture viral genomic material from an NGS library prepared directly from patient sample. This strategy has allowed us to significantly enrich viral genomic material relative to unenriched material.  The resulting genome data not only serve to identify the pathogen, but also for phylogenetic analyses to describe the most likely origin of the identified pathogens. Implementation of this platform will help to identify pathogens in clinical and environmental samples that would otherwise go undetected by conventional methodologies.  We are currently utilising this platform to investigate several cohorts:

a) Central nervous system (CNS) Infections result in significant morbidity and mortality worldwide.  However, the vast majority of CNS infections remain without an identified aetiology. In order to better understand the causes of meningitis, encephalitis, and infectious acute flaccid paralysis in Singapore eligible patients are currently being recruited from 6 major public hospitals in Singapore which cover approximately 90% of all acute CNS infection cases in the country. 

b) A hospital-based surveillance programme that is collecting 3000 cases of respiratory, CNS, enteric and hepatic disease for detailed clinical and epidemiological investigation. In addition, this study also includes a longitudinal collection of 1000 individuals at occupational risk of zoonotic infections, plus records of risk behaviours. This latter collection includes a linked sampling programme for putative animal reservoirs of zoonotic infections generating >1000 specimens.

c) Fever is one of the most common causes of hospitalisation and death in sub-Saharan Africa, but the infections causing these deaths are poorly understood. As part of this study, we will utilise our pathogen enrichment platform to help identify the causes of death among persons with fever. Overall, successful completion of these studies will enable the development of targeted treatment and prevention interventions to reduce deaths due to infectious diseases in low-resource settings.

3) Metagenomic analysis of irritable bowel syndrome

In Singapore, IBS affects 9% of the total population. While seldom fatal, the morbidity associated with IBS and the burden it places on the healthcare system is enormous.  In a local population survey, more than 3 quarters of the respondents have used TCM in the preceding year and 40% have used it for a GI related symptom.  To study the efficacy of common TCM formulations for the treatment of IBS, we are conducting a randomized controlled trial of traditional Chinese medicine for treatment of irritable bowel syndrome.  As part of this study, the effect of TCM on GI transit and gut microbiome associated with TCM treatment will also be studied, which could provide new mechanistic insights into the pathogenesis of TCM.

4) Genetic analysis of a dengue epidemic

Sri Lanka has experienced confirmed dengue outbreaks since the 1960s although severe dengue disease (DHF/DSS) didn’t appear until 1989. Since then, cyclical outbreaks associated with severe disease have occurred throughout the island. The most recent epidemic began in 2009 with the apparent introduction of a new genotype of DENV-1. To better understand the mechanisms underlying the persistence of this ongoing epidemic, a longitudinal study was conducted in hospitals in the Colombo district from April 2012 to March 2014. In order to glean as much information as possible about the viral genetics from this large cohort, we developed a novel Next Generation Sequencing (NGS) platform that can function without any a priori knowledge of the target dengue genome.    

October Sessions, PhD
Assistant Professor