Job Listings

Subject area description Miscarriage is the most common pregnancy complication, with over 23 million pregnancies ending in miscarriage every year.  This project aims to identify fetal genetic factors (SNP and de novo copy number variants) behind miscarriage, particularly among fetuses with normal chromosome counts. The postdoc fellow will lead a project using large-scale genotyping array data from miscarried fetuses and their mothers (including calling of aneuploidies and copy number variants) and contribute to ongoing efforts in this field (GWAS, meta-analyses, etc).

Job Summary The Centre for Molecular Medicine and Therapeutics at the University of British Columbia seeks applications for a Research Associate in the Wasserman Lab working on the Silent Genomes Project.  The Wasserman laboratory partners with a strong genetics community to develop and apply computational (bioinformatics) methods to improve diagnosis for individuals with rare genetic disorders caused by variations in genome sequences.  The Silent Genomes Project is a national collaboration focused on the establishment of an Indigenous Background Variant Library under Indigenous governance and oversight.   Based on the campus of BC Children’s Hospital, the Wasserman laboratory is the lead laboratory for the technical implementation of the Indigenous Background Variant Library, including the implementation of software pipelines for processing whole genome sequence data generated at an approved genome centre, the implementation of quality control analyses, the construction of the database to host the generated genetic data and the implementation of the interface via which the data can be accessed by approved users.  The work, while computational in focus, requires close interaction with an Indigenous governance committee, collaborators and trainees.  The ideal candidate will apply computational skills to develop computationally efficient and reproducible results for the detection of genetic variants across whole genome sequences from hundreds to thousands of individual samples, establish and document standard operating procedures for such analyses, incorporate new innovative methods for detection of genetic variants (either for new classes of variants or using data from different sequencing techniques (e.g. long-read)), and contribute to the development of scientific manuscripts, reports and funding applications.  Central to the work, is extraordinary attention to the sensitivity of the data being processed, with particular emphasis on the rights of Indigenous peoples and the central importance of adhering to the Indigenous governance procedures within the project. Experience with whole genome sequence processing and analysis, pipeline management software (e.g. Nextflow or SnakeMake) and working with highly sensitive genetic data are strong advantages.   Organizational Status This is a leadership role, requiring a high degree of independence, initiative and professional judgement.  The successful candidate reports to and receives guidance from Dr. W. Wasserman (Professor, Medical Genetics, Project Leader), with input and advice from Dr. L. Arbour (Medical Geneticist, Co-Project Leader) and Dr. Nadine Caron (Co-Project Leader) as needed.  The successful candidate supervises staff members and possibly University students or volunteers working on Silent Genomes.     Consequence of Error/Judgement Lack of careful attention to protocols and regulatory and ethical guidelines could suspend the Investigator’s laboratory and/or the University as a site for further research and/or funding. Performance must strictly conform to research protocols, Tri-Council policy statement, and standard Canadian guidelines for health research involving Indigenous People.   A high level of cultural competency and sensitivity is necessary in this position, as any insensitive actions could jeopardize our longstanding research relationship with the Indigenous communities we work with.   Errors in the dissemination of DNA sequence data or any breach of confidentiality could jeopardize this research study and Dr. Wasserman’s research program. A confidentiality agreement must be signed, stating that any identifying and/or personal information will be held in the strictest confidence.  Inaccuracies or incompleteness of data collection, or errors in the collection and handling of biological samples could result in erroneous data analysis and study results; therefore, it is imperative that the successful candidate is detail- oriented and very careful with their work.   Supervision Received The incumbent works with wide latitude and demonstrates a high degree of independence.  They report to and receive guidance from Dr. W. Wasserman (Professor, Medical Genetics, Project Leader).   Supervision Given The incumbent provides direction and expertise to project team members, including research assistants, overseeing the daily activities of trainees, and directing a scientific computer programmer participating on the Silent Genomes project.

The Centre for Molecular Medicine and Therapeutics at the University of British Columbia seeks applications for a Post-Doctoral Scientist in the Wasserman Lab working on the Silent Genomes Project.  The Wasserman laboratory partners with a strong genetics community to develop and apply computational (bioinformatics) methods to improve diagnosis for individuals with rare genetic disorders caused by variations in genome sequences. The Silent Genomes Project is a national collaboration focused on the establishment of an Indigenous Background Variant Library under Indigenous governance and oversight.   Based on the campus of BC Children’s Hospital, the Wasserman laboratory is the lead laboratory for the technical implementation of the Indigenous Background Variant Library, including the implementation of software pipelines for processing whole genome sequence data generated at an approved genome centre, the implementation of quality control analyses, the construction of the database to host the generated genetic data and the implementation of the interface via which the data can be accessed by approved users.  The work, while computational in focus, requires close interaction with an Indigenous governance committee, collaborators and trainees.  In addition to engineering, the Wasserman laboratory seeks to develop innovative bioinformatics methods for assessing the quality of and improving the library.  The candidate will apply computational skills to develop computationally efficient and reproducible results for the detection of genetic variants across whole genome sequences, create methods to separate shared from not shared genetic variation data from related individuals, create methods to predict the number of novel genetic variants (compared to an existing background variation database), and develop procedures for assessing the presence of structural variants, initially detected in long-read sequencing data, in short-read whole genome sequence data, and contribute to the development of scientific manuscripts, reports and funding applications.  Central to the work, is extraordinary attention to the sensitivity of the data being processed, with particular emphasis on the rights of Indigenous peoples and the central importance of adhering to the Indigenous governance procedures within the project. Experience with whole genome sequence processing and analysis, pipeline management software (e.g. Nextflow) and working with highly sensitive genetic data are strong advantages.   Organizational Status This is a leadership role, requiring a high degree of independence, initiative and professional judgement.  The successful candidate reports to and receives guidance from Dr. W. Wasserman (Professor, Medical Genetics, Project Leader).  The successful candidate supervises staff members and possibly University students or volunteers working on Silent Genomes.  They will contribute to development of reports for oversight bodies and funding organizations.   Supervision Received The incumbent works with wide latitude and demonstrates a high degree of independence.  They report to and receive guidance from Dr. W. Wasserman (Professor, Medical Genetics, Project Leader)   Supervision Given The incumbent provides expertise to project team members, including  University students and other trainees participating on the Silent Genomes project.   Consequence of Error/Judgement Lack of careful attention to protocols and regulatory and ethical guidelines could suspend the Investigator and/or University as a site for further research and/or funding. Performance must strictly conform to research protocols, Tri-Council policy statement, and standard Canadian guidelines for health research involving Indigenous People. A high level of cultural competency and sensitivity is necessary in this position, as any insensitive actions could jeopardize our longstanding research relationship with the Indigenous communities we work with. Errors in the dissemination of DNA sequence data or any breach of confidentiality could jeopardize this research study and Dr. Wasserman’s research program. A confidentiality agreement must be signed, stating that any identifying and/or personal information will be held in the strictest confidence.

University College Dublin is recruiting fifty early-career faculty through the Ad Astra Fellowship programme. Within the School of Medicine there are two posts within the broad area of AI in medicine. The application of artificial intelligence in clinical medicine and biomedical research and practice is a key strategic priority of the School. In this post, the successful applicant will be involved in state-of-the-art research and teaching in the application of AI to medicine and medical research. This will cover areas including, but not limited to the role of AI in diagnostics, data analysis and clinical intervention decisions.

The PI will be expected to mentor trainees and early career investigators, to build collaborations both within and outside the OICR community, and to work with FACIT, OICR’s commercialization partner, to translate research findings into real-world products and services. In addition to base funds provided by the Institute to support the PI’s salary and core personnel, the PI is expected to raise additional research funds from external competitive granting agencies. OICR will assist the PI in obtaining a faculty appointment at the University of Toronto or another affiliated academic institution.   In the case of a successful senior candidate, OICR will provide opportunities to take on leadership responsibilities within the Computational Biology program. The incumbent will work with other senior leaders at OICR and make significant contributions to develop strategic research priorities and operational tactics.   Housed within OICR’s Adaptive Oncology theme, the Computational Biology Program provides a robust intellectual environment with multiple investigators working with technologies ranging from spatial ‘omics to large language models of clinical records. An institutional cluster comprising ~9,000 CPU threads, and 18 GPU servers with a total of 36 NVIDIA CUDA cards as well as a large OpenStack virtualization environment, is available to support analysis by members of the Program. In addition, extensive compute resources, including large GPU clusters, are available to OICR faculty via Canada’s Digital Research Alliance.   OICR is a multi-disciplinary, team-science-driven translational research institute with PIs working in the areas of medical imaging instrumentation, robotics, drug design and development, biomarker discovery and assay development, spatial biology, and genomics. In addition to the facilities provided by the Computational Biology Program, the candidate will have access to a series of technology platforms for large-scale molecular data generation ranging from whole genome sequencing of challenging clinical specimens, to spatial transcriptomics and proteomics, cell-free DNA analysis, long-read sequencing, and digital histopathology. OICR develops and hosts multiple biobanks comprising hundreds of thousands of tissue and blood specimens, including the Ontario Health Study and the Ontario Tumour Bank. In addition, OICR develops and operates multiple data-rich biological databases including the international ICGC-ARGO Cancer Genome data platform, the Ontario Hereditary Cancer Research Network, and the Ontario node of the TFRI Marathon of Hope Comprehensive Cancer Centre Network. We are the host institution for the Global Alliance for Genomics in Health and a co-developer of the Pan-Canadian Genome Library. Finally, we believe in open-source and community development and are a signatory to the San Francisco Declaration on Research Assessment (DORA).   Please visit https://oicr.on.ca/research-portfolio/ for details on our research portfolio.

Étudiant de doctorat en Informatique ou en Bioinformatique à l’Université du Québec à Montréal (Montréal, Canada) Contexte du projet La comparaison de séquences génétiques et génomiques est essentielle pour comprendre la diversité du vivant. Les arbres et réseaux phylogénétiques ont grandement contribué à notre compréhension de l’histoire du vivant. Cependant, l’augmentation exponentielle des séquences génétiques disponibles nécessite de nouvelles méthodes pour explorer la diversité des données évolutives. Le projet est mené par une équipe multidisciplinaire de l’Université du Québec à Montréal (UQAM) (Prof. Vladimir Makarenkov), de l’Université de Sherbrooke (Prof. Guillaume Blanchet et Prof. Nadia Tahiri) et de l’Université de Montréal (Prof. Pierre Legendre). Objectif du projet Le projet utilisera des réseaux de similarité (ou graphe de similarité) où chaque nœud représente une séquence génétique. Les nœuds de ces réseaux sont connectés par des arêtes si leurs séquences montrent une similarité significative. Ce type de structures en réseau doit permettre une analyse plus souple et complète des données génomiques et métagénomiques, surpassant les limitations des méthodes actuelles basées sur les arbres et réseaux phylogénétiques. L’objectif principal de notre projet est de développer des méthodes informatiques et mathématiques pour analyser de grands jeux de données biologiques et bioinformatiques via des réseaux de similarité. Le candidat doit posséder un diplôme de maîtrise en Bioinformatique, en Informatique ou en Mathématiques avec une bonne moyenne générale. Rémunération: bourse non imposable de 29 000 CAD par année.

Project Background. We are seeking a motivated PhD student to join our research team in developing advanced methods for phylogenetic network analysis, with a specific focus on network consensus algorithms. Significant progress has been made in consensus tree methodologies. A consensus tree is a phylogenetic tree that synthesizes multiple phylogenetic trees, each with the same leaf labels but possibly differing topologies. These trees are often generated through bootstrapping or other sampling techniques. Traditional approaches to consensus tree construction focus primarily on topological aspects, often overlooking the importance of branch length, which captures the temporal progression of genetic mutations. However, in the context of consensus networks, very few studies have introduced relevant concepts. Project Objective. Our project addresses this limitation by integrating branch-length data not only into the construction of consensus trees but also into network consensus construction. This more comprehensive approach aims to provide a richer and more accurate representation of evolutionary relationships by combining topological structure, branch frequency, clade frequency, and branch length. The candidate must hold a Master’s degree in Mathematics, Computer Science, or Bioinformatics with a strong overall GPA. Compensation: non-taxable scholarship of +20,000 CAD per year. To apply, please send your CV, list of peer-reviewed articles (optional), and a cover letter to: Prof. Nadia Tahiri

The laboratory of Dr. Arielle Elkrief, co-Director of the CHUM Microbiome Centre is searching for a talented and self-driven Computational Biologist or Bioinformatician to join our computational team as a post-doctoral fellow. The candidate will focus on establishing computational infrastructure for analysing complex and multimodal microbiome data. The candidate will be working closely with other computational biologists, basic scientists, students, and researchers including members of the Dr. Bertrand Routy laboratory, co-Director of the CHUM Microbiome Centre. The Elkrief lab will provide both computational support with a senior computational biologist on-staff. The candidate will be responsible for designing a data architecture to leverage and integrate in house microbiome-oncology datasets, processing, visualizing and interpreting data for multiple projects. The lab focuses on developing novel microbiome-based therapies for people with lung cancer and melanoma treated with immunotherapy. This includes investigating the role of fecal microbial transplantation, probiotics, prebiotics, and diet in prospective clinical patient trials, with a focus on integrating multi-omic translational correlative approaches using biospecimens from patients enrolled on these trials. The specific role of the candidate will be to perform primary computational biology analyses on samples from multiple clinical trials with high potential for impact.

The Business Development (BD) Officer will create and maintain strategic relationships with the life science research community to build business and technological innovation opportunities for the Canadian Centre for Computational Genomics (C3G) at McGill University. The candidate will develop a strong understanding of our genomics analysis, software, and cloud computing infrastructure capabilities to promote the corresponding service offer at a provincial, national and international level. The BD Officer will spearhead business relations planning and initiatives, including outreach communications, campaigns, follow-ups, event promotion, and engagement. In collaboration with C3G Managers, the incumbent will oversee the strategic alignment and timely execution of all BD activities.

The Neural Circuit Development Research Unit headed by Dr. Artur Kania is seeking candidates to fill in the position of Bioinformatician. It is a temporary full time position (2 years), that may be extended for a longer period of time.