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• Postdoc in Interdisciplinary and Industrial Mathematics

  • When
    4 Jun 2023
  • Location
    Birmingham, UK

  We are looking for a postdoc who is excited to collaborate closely with experimental and industrial partners to develop mathematical and machine learning models to advance biomedical problems.
  https://www.jobs.ac.uk/job/CZV036/research-fellow

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• 2-year Postdoc position in Theoretical Evolutionary Ecology

  • When
    9 Jun 2023
  • Location
    Bielefeld University, Department of Evolutionary Biology

  The Faculty of Biology offers a full-time research position in Theoretical Evolutionary Ecology

  The position can start on January 1, 2024 and is funded until the end of the year 2025 by the German Research Foundation (DFG) within the collaborative research centre (SFB/TRR 212) entitled: A Novel Synthesis of Individualisation across Behaviour, Ecology and Evolution: Niche Choice, Niche Conformance, Niche Construction (NC3). The aim of the Postdoc project is to develop ecological and evolutionary theory to contribute towards a better understanding of individual niche variation.

  For further information, please use this link: https://uni-bielefeld.hr4you.org/job/view/2395/research-position-postdoc?page_lang=en
  

  For informal inquiries on the projects and the involved departments, please contact Klaus Reinhold (klaus.reinhold@uni-bielefeld.de)

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• Computational postdoctoral position in the design of synthetic pathways and regulatory proteins

  • When
    15 Jun 2023
  • Location
    Vrije Universiteit Brussel

  As part of a VUB strategic research project for ‘Synthetic biology for the development of microbial cell factories’, we are offering a postdoctoral position where the (re-)design of regulatory proteins is combined with modelling their impact on regulation in dynamic biological systems. The position is associated with two computational groups at the VUB: i) the Bio2Byte group led by Prof. Dr. Wim Vranken, with focus on predicting biophysical protein characteristics and interpreting these predictions in relation to life science problems such as molecular causes of human diseases or protein design (see https://bio2byte.be/) and ii) the group of Prof. Dr. Sophie de Buyl (see https://aphy.research.vub.be/prof-dr-sophie-de-buyl), with interest in gaining a fundamental understanding of the physical principles that control the emergent properties of biological systems.
  
  The project will assist in designing synthetic circuits to regulate E. coli metabolism, especially fatty acid production pathways. The computational work will be closely linked to experimental validation in the laboratory of Prof. Dr. Eveline Peeters (https://micr.research.vub.be/), with expertise in developing dynamical pathway regulation through biosensors. Approaches relying on both transcriptional (DNA) and post-transcriptional (RNA) levels will be developed and intertwined in iterative computation/experiment cycles. The project relies both on developing approaches in bioinformatics, where regulatory protein data is collected and analysed in relation to DNA/RNA binding, and in mathematical modelling, where the combined effect of introducing such regulatory proteins is studied. The end goal is to create general strategies for the efficient production and regulation of metabolites in E. coli.
  The three groups have an extensive international network of collaborations within and outside of Europe. We offer an open, dynamic and rewarding research environment, focused on teamwork and collaborations, that stimulates initiative taking, discussion and originality.
  
  Profile
  You have a Ph.D. degree in sciences or engineering, with further postdoctoral training a bonus. You are analytical, structured, pragmatic problem solver with attention to detail, and have excellent interpersonal and communication skills, as well as many as possible of the following competences:
  ● Experience in dynamical modelling of biological systems;
  ● Experience using protein structure and sequence information, including protein structure prediction methods such as AlphaFold2;
  ● Experience in modelling stochastic processes;
  ● Experience with handling and integrating large datasets, building bioinformatic tools such as automated analysis pipelines, dashboards and databases;
  ● Experience with machine learning and/or protein modelling and/or assessing the impact of amino acid mutations and/or structure prediction of proteins complexed with DNA/RNA is desirable;
  
  What we offer
  The position is immediately available, for initially 1 year but with possibility to extend. You will be mainly located at the (IB)2 Interuniversity Institute of Bioinformatics in Brussels (http://ibsquare.be/), Etterbeek VUB/ULB campus, which provides an interdisciplinary environment across sciences and (bio-)engineering.
  
  Applications and further information
  Please contact Wim.Vranken@vub.be and Sophie.de.Buyl@vub.be for additional information. To apply, please fill in and submit this online form: https://bit.ly/dynProtDesign, before the deadline of the 1st of June 2023. You have to include 1) a motivation letter detailing your interest and suitability for this position and 2) a CV including at least 2 contacts for references. Additional information can be uploaded via the application form.

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• Postdoc position in Theoretical Biology

  • When
    30 Jun 2023
  • Location
    Würzburg, Germany

  We offer a Research Scientist (Postdoc) position at the Center for Computational and Theoretical Biology, University of Würzburg, Germany for a maximum duration of four years.

  We are seeking an independent and communicative postdoctoral researcher to join our team in theoretical biology. The ideal candidate will be interested in interdisciplinary collaborative research, have a strong record of originality, and be able to generate their own project ideas. The position will be available for four years and include some teaching duties. In addition, we will support candidates who wish to write grants and applications for starting their own research group. This is a unique opportunity for a highly motivated researcher to develop their own research program and gain valuable experience in teaching and mentoring.

  The research agenda of our group focuses on the origins and dynamics of eco- evolutionary processes and patterns across scales of organisation, from sub-cellular to societal. We are interested in understanding the fundamental properties of living systems and develop translational applications such as in agriculture, conservation, and medicine when possible. To get an idea of the interests of our group please visit our publications.

  The successful candidate therefore gets a wide berth in exploring systems from microbial to social and will have the freedom to develop an ambitious project to develop their independent research profile.
  Details: https://tecoevo.github.io/positions/#postdocs

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• PhD position in Theoretical Immunology

  • When
    7 Jul 2023
  • Location
    University College London

  The immune system keeps a record of past infections. Can we learn to ‘read’ this record?

  The Qimmuno Lab at University College London (https://qimmuno.com/) is looking for a PhD student for a 3 year studentship entitled 'Physics-guided machine learning of the immune receptor code'.

  The adaptive immune system protects against infections and cancers by detecting them through hypervariable surface receptors on T cells. Each receptor binds to specific molecular targets, giving T cells the ability to sensitively detect fragments of viral or cancer-associated proteins. Individuals rarely have the exact same receptors as stochastic genetic recombination creates enormous receptor diversity. To crack the ‘code’ that links the immune record to an individual’s past, an important open problem is to identify common patterns in specific receptors. The aim of this project is to develop novel machine learning approaches to predict which immune receptors confer specificity to the same ligand.

  For detailed information, please see https://www.findaphd.com/phds/project/physics-guided-machine-learning-of-the-immune-receptor-code/?p158629

  Application Deadline: July 7
  The project is available for students eligible for UK home student fees

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• PhD offer: Stochastic process, random walks and predator-prey dynamics

  • When
    1 Sep 2023
  • Location
    Ecole Polytechnique (France)

  To describe the dynamics of an ecological system with several interacting species, at least three ingredients must be simultaneously considered: 1) how the number and distribution of consumers (or predators) and resources (or prey) vary in the environment, 2) how interactions between individuals take place, 3) how interactions between individuals translate into births and deaths.

  The classical model describing such a system is the deterministic Lotka-Volterra system (and its numerous derivations) where these three ingredients are generally implicitly assumed to occur at the same time scales. The aim of this PhD thesis is to study the properties of such systems using a stochastic approach, seeking in particular to highlight different regimes depending on the assumptions made about these three ingredients.

  The PhD student will build on the work already carried out by the supervisors: a stochastic model of the interaction rates between prey and predators under the assumption that resources are instantaneously regenerated once consumed (Billiard et al. 2018), or on the contrary that resources are never regenerated during the random walk in space of the predator (Bansaye et al., in prep.), or indeed a multiscale approximation of population dynamics but in a non-spatial model with general interaction times (Bansaye and Cloez, 2021).

  The aim of this thesis will be to study some relevant intermediate models where the time scales involved in the rates of interaction and population size variation are explicitly controlled. In particular, we will be interested in the lifetime of a predator whose survival depends on the amount of prey actually consumed as a function of the rate of prey regeneration. We will also want to determine under which hypotheses of the relationship of scales between consumption and reproduction speed, prey and predators can coexist over a long time. The thesis project is in the mathematical fields of space covering by a random walk (Le Gall, 1986), branching random walks, stochastic processes in random environments, and birth and death processes with interaction.

  Profile sought: This project is open to any student of mathematics or theoretical physics with strong skills in probability and stochastic processes. The student should also have a strong interest in interdisciplinary interaction (in ecology) since the co-supervision will be ensured by two mathematicians and a biologist.

  Supervisors: Vincent Bansaye (CMAP, Ecole Polytechnique), Sylvain Billiard (Evo-Eco-Paléo, Université de Lille), Jean-René Chazottes (CPHT, CNRS, Ecole Polytechnique)
  

  Laboratory of affiliation: Ecole Polytechnique

  Contacts: sylvain.billiard@univ-lille.fr ; vincent.bansaye@polytechnique.edu ;
  Jean-Rene.Chazottes@cpht.polytechnique.fr

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• Two 4-year research scholarships for PhD students

  • When
    2 Oct 2023
  • Location
    Kraków, Jagiellonian University

  *** Job description ***
  I am looking for two students interested in pursuing their PhD in Biophysics focused on understanding the biophysical limiting factors of patterning precision in developing tissues. The positions are fully funded by the National Science Center Poland (NCN).
  The project goal is to understand to what extent growth, cellular dynamics, biomechanical feedbacks and global mechanical constraints limit patterning precision in the growing tissue. The successful candidate is expected to actively take part in the project by proposing and analyzing models in the framework of theoretical and computational biophysics. The proposed models will be informed with high resolution experimental data provided by external collaborators.
  Both scholarships (#1 and #2) are aimed for applicants with computational background. The applicant should have MSc in biophysics, physics, mathematics, computer science or similar. The applicant should successfully apply to PhD school in Polish research institution or university.

  The applicants should have:
  - interest in the interdisciplinary aspect of the project,
  - experience with numerical solvers (C++, Python), (scholarship #1)
  - experience with image segmentation algorithms, (scholarship #2)
  - proficiency in written and spoken English.

  The project goal is to understand to what extent growth, cellular dynamics, biomechanical feedbacks and global mechanical constraints limit patterning precision in the growing tissue. The successful candidate is expected to actively take part in the project by proposing and analyzing models in the framework of theoretical and computational biophysics. The proposed models will be informed with high resolution experimental data provided by external collaborators.

  *** Scope of work ***
  scholarship #1: The PhD student will develop a vertex model of growing tissue. The model will include novel methods to simulate cellular and bio-mechanical processes taking place in biological tissues. The simulation results will be informed with high resolution experimental data provided by external collaborators. The PhD student will estimate level of patterning precision as a function of growth, cellular and mechanical factors. The PhD student will actively take part in group research activities, including dissemination of project results through publications, scientific conferences, research seminars and general audience talks.
  scholarship #2: The PhD student will identify possible cellular mechanisms and biomechanical feedbacks affecting patterning precision in vertebrate tissues. The PhD student will derive estimates of bio-mechanical tissue properties from high resolution experimental data provided by external collaborators. The estimates will be used to inform computational models of biomechanical feedbacks. The PhD student will actively take part in group research activities, including dissemination of project results through publications, scientific conferences, research seminars and general audience talks.

  *** Important dates ***
  Call opening: 28 April 2023
  Doctoral School recruitment at Jagiellonian University: June and September 2023
  Application deadline: 2 October 2023
  Results: by 17 October 2023.

  *** Additional information ***
  The NCN funded scholarship for PhD students is provided for 4-years.
  The group webpage: https://zagorskigroup.com/
  Selected candidates will be invited for an interview. Successful candidate will be selected by a committee chaired by the project leader. The condition of successful application to Doctoral School in Polish research institution or university needs to be fulfilled to be considered in this opening. Please consult details at https://science.phd.uj.edu.pl/en_GB/start. Please contact me in advance at marcin.zagorski@uj.edu.pl to prepare application to Doctoral School at Jagiellonian University.
  The official announcement can be found at https://fais.uj.edu.pl/wydzial/zatrudnienie/. 

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