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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.

Research Programmer – CCGI Canada’s Michael Smith Genome Sciences Centre (GSC)   Today’s Research. Tomorrow’s Medicine. The GSC is a department of the BC Cancer Research Institute and a high-throughput genome sequencing facility. We are leaders in genomics, proteomics and bioinformatics in pursuit of novel treatment strategies for cancers and other diseases. Among the world’s first genome centres to be established within a cancer clinic, for more than two decades our scientists and innovators have been designing and deploying cutting-edge technologies to benefit health and advance clinical research. Among the GSC’s most significant accomplishments are the first publication to demonstrate the use of whole-genome sequencing to inform cancer treatment planning, the first published sequence of the SARS coronavirus genome and major contributions to the first physical map of the human genome as part of the Human Genome Project. By joining the GSC you will become part of an exceptional and diverse team of scientists, clinicians, experts and professionals operating at the leading edge of clinical research. We look for people who share our core values—science, timeliness, respect—to join us on our mission to use genome science for the betterment of health and society. Job Reference No: RP_R00008_CCGI_2024_07_12 Summary Canada’s Michael Smith Genome Sciences Centre (GSC) of the BC Cancer Research Institute is a state-of-the-art, large scale, high throughput, clinically accredited genomics and bioinformatics facility in one of the most beautiful, diverse and eclectic cities in the world. As a Research Programmer within the Centre for Clinical Genomics Informatics team at the GSC, you will be responsible for technical support for clinical programs through development, testing and validation of clinical bioinformatics processes. The Research Programmer will report to the Process Development Coordinator and is anchored within a team of exceptional computational scientists and programmers, who collaborate directly on the development and maintenance of robust, cost efficient, and competitive clinical genomics pipelines. By working within the GSCs bioinformatics facility, you will collaborate with clinical and research computational biologists and programmers across bioinformatics groups, clinical lab staff and the quality assurance group to deliver clinical diagnostic genomic testing for patients in BC. This is an opportunity to work with highly motivated colleagues in a science-oriented, creative and dynamic environment. We offer a competitive salary, excellent benefits and significant career development opportunities. So, what are you waiting for? Apply now!  

Project description: When a tumor cell dies, its contents are dispersed into the bloodstream and can serve as a biomarker for cancer. Liquid biopsies thus offer a new alternative for cancer diagnosis by detecting cancer markers in the blood. In this context, our lab is developing cutting-edge molecular and computational methods to improve on the sensitivity and specificity of circulating tumor DNA (ctDNA). Our team has access to the CRCHUM’s institutional biobanks and thus has opportunities to create ctDNA assays for many different cancer types, including ovarian, head & neck, lung, skin and bladder cancer. This research project will enable graduate students to develop an expertise in next generation sequencing, bioinformatics, machine learning, oncology and genomics. Description générale du projet : Lorsqu’une cellule tumorale meurt, son contenu est versé dans la circulation et peut servir en tant que biomarqueur pour le cancer. Les biopsies liquides ouvrent donc une nouvelle ère dans le diagnostic du cancer, en rendant possible la détection de tumeurs à partir d’un simple prélèvement sanguin. Dans ce contexte, notre laboratoire développe des technologies moléculaires et informatiques pour améliorer la sensibilité et la spécificité de la détection de l’ADN tumoral (ctDNA). Via les biobanques institutionnelles du CRCHUM, notre équipe a accès à une large cohorte de patients atteints de divers cancers (ovaire, tête et cou, vessie, poumon, mélanome). Ainsi, ce projet de recherche permettra à l’étudiant.e sélectioné.e de développer une expertise en next generation sequencing, bioinformatique, apprentissage machine, oncologie et en génomique.

Laboratory: Bioinformatics and Proteomics Laboratory (ADLab) – Prof. Arnaud Droit. The laboratory specializes in the development of advanced computational methods and artificial intelligence and statistical approaches for the analysis of massive datasets. ADLab collaborates with academic and industrial partners internationally and has high-performance computing infrastructure. Institution: Faculty of Medicine, Université Laval, Quebec City, Canada Job Description: Prof. Arnaud Droit’s laboratory (ADLab) is recruiting a bioinformatics student to work on the analysis of proteomics data generated by latest-generation mass spectrometers. This research will be conducted as part of the fight against antibiotic resistance, which represents a major threat to public health. This issue is a consequence of the overuse of antibiotics, which promotes the emergence of resistant bacteria, making many infections difficult to treat. It is therefore crucial to develop new approaches to detect and counter these resistances. The candidate will contribute to the development of computational tools for the analysis and validation of proteomics data, as well as the application of machine learning methods for identifying diagnostic biomarkers in biological fluids (detection of bacteria, treatment resistance, etc.).

The Cumming School of Medicine and Faculty of Science at the University of Calgary are accepting applications for a Postdoctoral Scholar in Bioinformatics and its application to Wastewater-Based Surveillance (WBS) of antimicrobial resistance and emerging pathogens. The postdoc will be part of an interdisciplinary research team that uses wastewater to track the dynamics of infectious agents. We have developed an integrated surveillance network monitoring 43 municipalities, as well as several sentinel surveillance hubs including a large number of tertiary care hospitals and populations of special interest from which we collect samples 1-3x per week.  Wastewater data can be compared with population-level data and hospital-specific data drawing from a single provincial health provider – and the potential of this unique network is exceptional. To date we have amassed >2000 samples that have been processed as raw wastewater and culture enriched raw wastewater (for specific pathogens).  A parallel agriculture and agri-food network is being developed which will be further leveraged.  The postdoc will work directly with a transdisciplinary team of clinicians and researchers at the University of Calgary (Cumming School of Medicine and Faculties of Science, Engineering, and Veterinary Medicine, and Advancing Canadian Water Assets (ACWA)) and their collaborators including those at the Universities of Alberta, Athabasca and Lethbridge. The Postdoc will also have the opportunity to collaborate with public health, pharmacy, infection control, and antimicrobial stewardship experts at Alberta Health Services. The successful applicant will join a productive transdisciplinary team with supporting research funding from NSERC, CIHR, Genome Alberta, and Alberta Health. Working with the Primary Investigators Michael Parkins and John Conly (Cumming School of Medicine, Departments of Medicine and Microbiology, Immunology & Infectious Diseases) and Casey Hubert (UCalgary Research Chair, Faculty of Science). The Postdoc will work as part of a large team that includes several HQP staff and trainees including those in graduate, undergraduate and post graduate training programs.  There will be abundant opportunities for collaboration with others interested in bioinformatics and mentorship of junior trainees.

AbCellera is breaking the barriers of conventional drug development to propel antibody-based medicines from target to clinic. We are a team of scientists, engineers, creatives, and business professionals who believe that advancing science enhances lives. We have developed technologies to unlock high-value drug targets, including antibody-drug conjugates and T-cell engagers for cancer, and complex transmembrane proteins for indications such as metabolic and endocrine conditions, pain, and autoimmunity. We are looking for a motivated and talented individual currently pursuing a PhD in Bioinformatics, Computational Biology, or Structural Biology to join our Protein Engineering team as an intern for an 8 month term. You will execute and implement workflows that will inform therapeutic development in two areas: (1) genomics surveillance of viral pathogens, and (2) protein and antibody engineering. In this role, you will interact with a diverse team in a fast-paced environment, liaising between wet-lab scientists, protein engineers, data scientists, and software engineers. While in this position, based in beautiful Vancouver, you will receive guidance and supervision from experienced team members within the Protein Engineering team. The internship is designed to offer exposure to real-world projects and the opportunity to contribute to the advancement of antibody-based medicines from target to clinic within Canada. How you might spend your days Develop bioinformatic tools and processes to monitor viral evolution of emerging pathogens, with the purpose of enabling the rapid identification of potential escape variants that may impact antibody therapeutics. This will involve identifying publicly available viral genome sequences, calling variants, classifying strains, and examining how genomic changes relate to viral pathogenicity, immune evasion, or drug resistance Develop, execute, and optimize antibody bioinformatics and in-silico protein engineering tools and workflows to accelerate therapeutic development. This will involve evaluation of antibody sequence diversity and sequence risks to help identify drug candidates, as well as implementation of strategies for sequence optimization and liability remediation Develop data visualizations and summary reports of complex data sets to help drive key scientific insights Prepare and present materials to educate internal and external partner teams, and communicate strategies, key findings, and implications We’d love to hear from you if You are currently pursuing a PhD in Bioinformatics, Computational Biology, Structural Biology, or a related field You are excited about the opportunity to develop and execute computational workflows to solve real-world drug discovery problems You have solid experience with bioinformatics tools for genome and evolutionary analyses, including sequence alignment, variant calling, phylogenetics, and data visualization, ideally in the context of viruses You have experience working with protein sequences and probing sequence-structure relationships to understand and optimize protein function You have working knowledge of antibody structure and function, and awareness of tools and techniques applicable to sequence optimization of antibodies (desirable) You have excellent programming skills in Python or another programming language, and experience collaborating on a shared codebase You are strongly self-motivated and work independently to identify project needs and follow that up with building and implementing solutions You are a collaborative team player who enjoys working with multidisciplinary teams to meet project deliverables and timelines You have experience preparing scientific reports and presentations to communicate research findings and drive decision-making What we offer AbCellera’s hiring range for this role is CAD $4,600 – $5,200 per month, commensurate with your education and job-related knowledge, skills, and experience. In addition to base pay, we offer a number of ways to support AbCellerites in maximizing their work-life synergy. You will have a vacation allowance as well as additional days off as part of our company-wide office closures (a real value to all!), and sick leave time while on your internship. Scientific and technical mentorship is a priority. And you’ll find we prioritize teams and social groups to build community and connections across AbCellera. About AbCellera AbCellera is a global company that discovers and develops antibody-based medicines that help people live longer, happier, and more productive lives. We are focused on bringing innovative medicines to patients, both by advancing our internal pipeline of programs and partnering with companies that have novel science or innovative technology. And it all starts with our team. We’ve built a place where people feel they are part of something bigger than themselves. A place that exists to push the limits of science and technology, and aims to bring better therapies to patients. We look for people with drive and energy. Idealists. People we love and people we trust. This may be unconventional, but it is the key to our success. To apply Please submit your application through our website and refer to Job ID 23278 in your cover letter. We apologize in advance, but we receive a large volume of applications and are only able to contact those who are selected for an interview. Start date: ASAP Duration: 8 months Location: Vancouver, BC Workplace arrangement: On-site