Job Description:
Responsibilities: Students will be expected to contribute to the objectives in either of the following research areas: Evolution of HIV-1 within hosts. Despite the availability of highly effective drug treatments, HIV-1 establishes a life-long chronic infection for which we have yet to develop a cure. When HIV-1 infects a cell, it integrates itself into the host genome and, in some cases, enters a dormant state where it becomes invisible to the immune system. This creates a long-lived reservoir of “latently” infected cells that is the main barrier to a cure. We are combining techniques in pattern analysis and phylogenetics (github.com/PoonLab/Kaphi) to reconstruct how this rapidly-evolving virus spreads through the body, and to identify potential targets to eradicate the virus reservoir. Detecting transmission outbreaks. For infectious diseases, a genetic cluster is a subset of infections that have barely accumulated any genetic differences since their recent descent from a common ancestor. Clustering has become a popular method for rapidly screening clinical databases for potential transmission outbreaks. Based on recent work, we now know that clustering methods can be badly confounded by when the infections were sampled from the population. We are developing and validating a new approach inspired by speciation models to detect lineage-specific shifts in branching rates, and working with global partners to develop open-source monitoring systems to support public health efforts in real time while protecting individual privacy. Qualifications: • An undergraduate (bachelor’s) and/or master’s (MSc) degree in biology, microbiology, bioinformatics, mathematics, statistics, computer science, or a related field. • An avid, demonstrable interest in evolutionary biology and infectious disease research. • Previous training or experience in any programming or scripting language from course work, workshops, or online/self-directed learning. Applicants without prior programming experience may be considered if they have a strong background in quantitative methods (e.g., statistics, linear algebra, probability, discrete math). • Proficiency in communicating and writing in the English language. • An ability to work effectively in a collaborative environment. • All applicants must also meet the admission requirements of the university (http://grad.uwo.ca/prospective_students/applying/index.html) as well as the specific department (I hold appointments at the Departments of Pathology, Microbiology, and Applied Mathematics).
Additional Info:
The Poon lab is an entirely “dry” research computing and open-source software development group (http://github.com/PoonLab). The lab is housed in a newly renovated space in the Department of Pathology, and equipped with custom-built Linux workstations, a small high-performance computing cluster and an espresso machine. My lab mostly runs on Python, R and LaTeX – my objective is to enable all my trainees develop a working knowledge of all three languages. Western University is one of Canada’s top research-intensive universities, and home to the Western HIV Investigators Group (WHIG), a highly collaborative team of 8 principal investigators with diverse and complementary research programs, including evolution and pathogenesis (Dr. Eric Arts), natural resistance and host microbiomes (Dr. Jessica Prodger), and bioinformatics and phylogenetics (Dr. Poon). The adjacent London Regional Genomics Centre provides state-of-the-art next-generation sequencing services on Illumina MiSeq and NextSeq systems. Known as “Forest City”, the city of London, Ontario, features river valleys, abundant parks, tree-lined streets, bicycle paths, frequent city festivals, an international airport and a reasonable cost of living. [Click Here to Access the Original Job Post]
Responsibilities: Students will be expected to contribute to the objectives in either of the following research areas: Evolution of HIV-1 within hosts. Despite the availability of highly effective drug treatments, HIV-1 establishes a life-long chronic infection for which we have yet to develop a cure. When HIV-1 infects a cell, it integrates itself into the host genome and, in some cases, enters a dormant state where it becomes invisible to the immune system. This creates a long-lived reservoir of “latently” infected cells that is the main barrier to a cure. We are combining techniques in pattern analysis and phylogenetics (github.com/PoonLab/Kaphi) to reconstruct how this rapidly-evolving virus spreads through the body, and to identify potential targets to eradicate the virus reservoir. Detecting transmission outbreaks. For infectious diseases, a genetic cluster is a subset of infections that have barely accumulated any genetic differences since their recent descent from a common ancestor. Clustering has become a popular method for rapidly screening clinical databases for potential transmission outbreaks. Based on recent work, we now know that clustering methods can be badly confounded by when the infections were sampled from the population. We are developing and validating a new approach inspired by speciation models to detect lineage-specific shifts in branching rates, and working with global partners to develop open-source monitoring systems to support public health efforts in real time while protecting individual privacy. Qualifications: • An undergraduate (bachelor’s) and/or master’s (MSc) degree in biology, microbiology, bioinformatics, mathematics, statistics, computer science, or a related field. • An avid, demonstrable interest in evolutionary biology and infectious disease research. • Previous training or experience in any programming or scripting language from course work, workshops, or online/self-directed learning. Applicants without prior programming experience may be considered if they have a strong background in quantitative methods (e.g., statistics, linear algebra, probability, discrete math). • Proficiency in communicating and writing in the English language. • An ability to work effectively in a collaborative environment. • All applicants must also meet the admission requirements of the university (http://grad.uwo.ca/prospective_students/applying/index.html) as well as the specific department (I hold appointments at the Departments of Pathology, Microbiology, and Applied Mathematics).
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Additional Info:
The Poon lab is an entirely “dry” research computing and open-source software development group (http://github.com/PoonLab). The lab is housed in a newly renovated space in the Department of Pathology, and equipped with custom-built Linux workstations, a small high-performance computing cluster and an espresso machine. My lab mostly runs on Python, R and LaTeX – my objective is to enable all my trainees develop a working knowledge of all three languages. Western University is one of Canada’s top research-intensive universities, and home to the Western HIV Investigators Group (WHIG), a highly collaborative team of 8 principal investigators with diverse and complementary research programs, including evolution and pathogenesis (Dr. Eric Arts), natural resistance and host microbiomes (Dr. Jessica Prodger), and bioinformatics and phylogenetics (Dr. Poon). The adjacent London Regional Genomics Centre provides state-of-the-art next-generation sequencing services on Illumina MiSeq and NextSeq systems. Known as “Forest City”, the city of London, Ontario, features river valleys, abundant parks, tree-lined streets, bicycle paths, frequent city festivals, an international airport and a reasonable cost of living. [Click Here to Access the Original Job Post]