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269 days ago

PhD

PhD position: Modeling biological knowledge with large language models

Centre de Recherche du CHU de Québec - Université Laval -

Within this project funded by the ADlab laboratory (Arnaud Droit Lab, compbio.ca), the main goal will be to transform the access and analysis of biological knowledge databases (BKDs) through the integration of these databases into a knowledge graph and the use of large language models (LLMs). This initiative aims to facilitate natural querying of biological data, making research more accessible to biologists without specific expertise in programming or data analysis. The main objectives include:

  • Building a biological knowledge graph that integrates multiple BKDs to improve their cohesion and extract valuable information.
  • Developing and training specific LLMs capable of interpreting and querying this graph in natural language.
  • Creating and evaluating a conversational agent based on these LLMs, to allow intuitive querying of BKDs using natural language requests.

318 days ago

PhD

PhD position in bioinformatics – Fully funded

United Arab Emirates University -

A fully funded PhD position is available at United Arab Emirates University. The project involves integrating mathematical models of the date palm tree with Omics data to explore the impact of both biotic and abiotic stresses.

REQUIRED QUALIFICATIONS
– Proficiency in programming languages, particularly R/MATLAB/PYTHON.
– IELTS score of > 6.5 (mandatory)
– Basic knowledge in plant molecular biology, metabolism, and growth.
– Experience in RNA extractions and NGS analysis.

ADDITIONAL QUALIFICATIONS
– Understanding of biological networks.
– Deep knowledge in the field of Mathematical modeling.
– Experience in plant growth experiments.
– Strong academic background.

If interested, please forward your CV and a compelling statement of intent to tauqeer.uaeu@gmail.com

only shortlisted candidate will be contacted.

All the best

320 days ago

PhD

Computational biologist / Bioinformatician (m/f/d) / (PhD), Oldenburg, Germany

Carl von Ossietzky University of Oldenburg -

The Faculty VI Medicine and Health Sciences includes the areas of human medicine, medical physics and acoustics, neuroscience, psychology and health services research. Together with the four regional hospitals the Faculty VI forms the Oldenburg University Medical Center. We also have a close cooperation with the University Medical Center at the University of Groningen.
In the division for Medical Genetics of the Department of human medicine there is a vacancy for a
Computational biologist / Bioinformatician (m/f/d) / (PhD)
(salary according to E13 TV-L, 75 %)
to be filled as soon as possible for a limited period of 3 years (potential extension). There is the possibility of personal scientific qualification (doctorate thesis).
The position will be hosted at the Institute of Medical Genetics, University of Oldenburg. Our group uses multi-omic approaches (genomic, transcriptomic and epigenetic) to elucidate the molecular basis of several human pathologies, including cancer, congenital heart diseases (CHD) and rare diseases.
We implement different short read-based next-generation sequencing (NGS) and long read-based nanopore sequencing to identify pathogenic genetic variants. In addition, we apply single-cell RNA sequencing and emerging methods of spatial biology to study normal cell development as well as disease progression. Our group collaborates with European Consortia and international teams from the UK, US, Canada, Belgium, the Netherlands and Denmark.
The PhD candidate will work in a research project directed to the identification of pathogenic gene variants associated to hereditary cancer predisposition using long read-based nanopore sequencing. As part of the project the candidate will assess the added diagnostic value of nanopore sequencing in unresolved cases of cancer predisposition previously tested with gene panels and/or exome/genome sequencing using NGS. The position holder is expected to perform NGS and nanopore sequencing data analysis, develop computational pipelines for pathogenic variant filtering, and to identify genetic alterations associated to hereditary cancer.
We offer:
  • An interdisciplinary and collaborative environment that supports innovation and professional development of team members.
  • Participation in the development of a young university team with creative freedom.
  • The possibility of independent scientific project work.
  • Collaboration with national and international teams and consortia.
  • Payment in accordance with collective bargaining law (special annual payment, public service pension scheme, asset-related benefits) incl. 30 days annual leave
  • Support and guidance during your onboarding phase
  • Remuneration at the TV-L E13 (75%) salary level,  with annual nonus.
  • A family-friendly environment with flexible working hours (flexitime) and the possibility of pro-rata mobile work
  • Benefits from the university’s health promotion program
  • An extensive and free further education program as well as programs geared toward the promotion of early career researchers (https://uol.de/en/school6/early-career)

328 days ago

PhD

PhD in Phage for Salmonella control in the Poultry Industry

University of Guelph -

Department: Pathobiology
Description of the Area/Topic of Research:

The Ricker lab at the University of Guelph is currently recruiting 1 PhD student and 1 post-doctoral fellow or research associate, in collaboration with Dr. Hany Anany (AAFC), for projects recently funded through the Canadian Poultry Research Council (CPRC) and Agriculture-AgriFood Canada (AAFC).

Antimicrobial resistance (AMR) is one of the largest human health concerns of this generation, as the continued emergence of resistance threatens to interfere with our ability to treat and prevent human infectious diseases. Combating AMR requires a One Health approach, combining efforts at limiting resistance emergence and spread within human, animal and environmental reservoirs.

We are currently seeking two candidates (a PhD student and a postdoctoral fellow) for a 4-year project investigating the use of phage to control Salmonella within the poultry industry. The successful candidates will meet or exceed the minimum academic requirements for entry to a PhD program, have a relevant publication record appropriate to their current career stage, and have previous experience working with phage. An interest in the combination of microbiology techniques and bioinformatic approaches is essential. Experience in metagenomics, phage biology, phage-host interactions, designing and performing bacterial challenge studies and/or viromics are all considered strong assets. Work will be performed at both the University of Guelph and AAFC in Guelph under joint supervision of Drs. Ricker and Anany.

Funding for this project is pending final confirmation and a start date of May 1, 2024 is preferred but is negotiable.

Description of Lab/Group/Area: Dr Ricker is an early career researcher recruited to the University of Guelph through the Food from Thought program for her expertise in microbial community analysis and antimicrobial resistance (AMR) in agriculture.  Her developing research program focuses on AMR prevalence in bacterial communities, horizontal gene transfer mechanisms, promotion of healthy gut microbial communities, and the impact of mitigation strategies on the emergence, persistence, and dissemination of AMR and pathogens in a One Health framework.

Dr. Anany is a Bacteriophage Research Scientist at the Guelph Research and Development Center (GRDC), Agriculture and Agri-Food Canada. In addition, he serves as an Adjunct Professor at the Food Science Department, University of Guelph. His research program focuses on understanding phage biology and its interaction with bacterial hosts for taxonomical and application purposes throughout the food supply chain. Dr. Anany’s research program also extends to exploring the composition and dynamics of the phageome /virome throughout the food supply chain, aiming to deepen our understanding of these complex viral communities and their role in food safety.

472 days ago

PhD

Associate Director for Training – Research Associate

Harvard Chan School of Public Health -

The Harvard Chan Bioinformatics Core (HBC) invites applications for the position of Research Associate / Associate Training Director. This position combines applied bioinformatics research with teaching and program management. We are a leading center for bioinformatics research, services, and training at the Harvard T.H. Chan School of Public Health, collaborating closely with biomedical scientists across Harvard to implement approaches for analysis, interpretation, visualization, and dissemination of scientific discoveries using high-throughput omics data.

We are seeking a skilled and motivated bioinformatician or computational biologist to co-direct our training program. The ideal candidate should possess a strong background in high-throughput sequencing data analysis and a genuine passion for sharing bioinformatics knowledge and best practices. Team management experience is vital, as this role involves leading and collaborating with others. Moreover, we value excellent communication and teaching abilities, along with strong quantitative and analytical skills.