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• Post-doctoral position in mathematical and/or computational biology: Multiscale modeling of single cell-based dynamics of ovarian development

  • When
    15 Sep 2024
  • Location
    Paris

  A call is open for an 18 month postdoc at Inria Saclay center, entitled "Post-doctoral position in mathematical and/or computational biology: Multiscale modeling of single cell-based dynamics of ovarian development" :
  https://recrutement.inria.fr/public/classic/fr/offres/2024-07738

  The postdoc position is open in the framework of the AI4scMED ("MultiScale AI for SingleCell-Based Precision Medicine") consortium (https://ai4scmed.github.io) of PEPR Santé Numérique (project no. 22-PESN-0002). The postdoc will be supervised by Frédérique Clément (Inria), Chloe Audebert (Sorbonne Université) and Fabien Crauste (CNRS & Université Paris Cité).

  The contract is expected to start between October, 1st and December, 1st 2024.

  For any additional information, you can contact Frédérique Clément (frederique.clement@inria.fr), Chloe Audebert (chloe.audebert@sorbonne-universite.fr) and Fabien Crauste (fabien.crauste@math.cnrs.fr).

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• Fully Funded Fellowship

  • When
    19 Sep 2024
  • Location
    Dresden, Germany

  More info here: https://www.csbdresden.de/join-us/as-a-postdoc

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• Two exciting PhD opportunities at Cardiff University in Math Bio!

  • When
    14 Oct 2024
  • Location
    Cardiff

  Two PhD opportunities at Cardiff University to student Mathematical Biology:

  1) Are you ready to make a real impact in healthcare? We're offering a fully funded PhD project that could change the way neonatal sepsis is detected in intensive care units worldwide. Using cutting-edge machine learning and data analysis, you'll develop an automated system capable of identifying sepsis up to 72 hours earlier than current methods, potentially saving countless infant lives. With access to high-resolution NICU data from India, and the chance to work at the intersection of mathematics, bioinformatics, and medical research, this is a unique opportunity to make a difference. Click here to learn more and apply:
  https://www.findaphd.com/phds/project/gw4biomed2-mrc-dtp-phd-studentship-neonatal-sepsis-detection-automation-for-neonatal-intensive-care-units/?p174172
  
  2) Discover the groundbreaking PhD opportunity in "Healing and Harm: Modelling the Relation Between Cell Motion and Environmental Topography." This research project will revolutionise our understanding of cellular motion and its impact on health by merging cutting-edge mathematics with innovative biology. In collaboration with experimentalists at the University of Reading, you will develop a sophisticated mechanical model to decode how cells move during muscle healing and cancer metastasis. Unlike traditional models that simplify environmental complexity, this project will incorporate real tissue data to better understand and influence cellular behaviour, with the ultimate goal of accelerating healing and inhibiting cancer spread. For more information follow the link:
  https://www.findaphd.com/phds/project/epsrc-dtp-phd-studentship-in-healing-and-harm-modelling-the-relation-between-cell-motion-and-environmental-topography/?p174119

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• Post-doc Position in population dynamics, PDE/PBPK models

  • When
    31 Oct 2024
  • Location
    INRIA Saclay

  The postdoc position is open in the framework of two projects led by MUSCA, the OVOPAUSE ANR project and the OVOTOX FC3R project, gathering researchers from different institutions and scientific background (applied mathematics, developmental and reproductive biology, ecotoxicology).

  The position is an opportunity to be involved in a strongly interdisciplinary consortium, and to strengthen experience in mathematical and computational biology by working on the coupling of population dynamics models with compartmental pharmacokinetic models. The contract is expected to start in the beginning of year 2025, from January to March.

  Apply for this position at https://recrutement.inria.fr/public/classic/fr/offres/2024-08077

  The impact of micropollutants on living organisms is a major concern, whether at the individual or population level. Due to their living environment and their physiology, fish are particularly exposed to these micro-pollutants and in particular to endocrine disruptors (ED). They therefore constitute sentinel species for detecting and  understanding the multiscale reprotoxic effects of EDs and their adverse outcomes on the reproductive fitness from the individual up to the population levels. The field of toxicology, and more generally eco-toxicology, has recently acquired methodological tools, such as qAOP (quantitative Adverse Outcome Pathways), based on dynamic models with quantitative outputs to rigorously assess the effects of EDs from available experimental data and knowledge (Conolly et al. 2017). qAOP models can predict ED effects in silico and be used both for basic research and regulatory purposes, while limiting the use of laboratory animals.

  The postdoc work will be dedicated to enriching a qAOP model developed by the hosting team and collaborators. The first task will consist in coupling a size-structured (PDE-based) mechanistic model of oogenesis (the developmental process leading to the release of a fertilizable femate gamete), considering all maturation stages and their control (Bonnet et al. 2020, Ballif et al. 2024), with a physiologically-based pharmacokinetic (compartmental ODE-based) model representing the hormonal dynamics within the reproductive (hypothalamo-pituitary-gonadal) axis (Pery et al. 2014, Ly et al. 2023). The coupling will be based on careful mapping of functions involved in the different models, addition of missing variables when needed, and timescale separation when possible to enforce model parcimony. The second task will be to design appropriate numerical schemes to simulate the model in both physiological and toxicological situations (exposure to EDs) and perform an extensive parameter estimation and sensitivity/identifiability analysis. The calibrated coupled models will enable a detailed assessment of reprotoxic effects, in particular long-term effects and rebound/compensation mechanisms affecting the oocyte population and hormonal feedback loops. If time allows, and according to the interest of the post-doctoral candidate, we will tackle a qualitative analysis of the coupled model to shed light onto the structural influence of parameters on the model behavior and the related impact on the reproductive function.

  References
  G. Ballif, F. Clément and R. Yvinec, Nonlinear compartmental modeling to monitor ovarian follicle population dynamics on the whole lifespan, J. Math. Biol., 89:9, 2024.
  C. Bonnet, K. Chahour, F. Clément, M. Postel, R. Yvinec. Multiscale population dynamics in reproductive biology: singular perturbation reduction in deterministic and stochastic models. ESAIM Proc. Surveys, 67: 72-99, 2020.
  R.B. Conolly, G.T. Ankley, W.Y. Cheng, M.L. Mayo, D.H. Miller, E.J. Perkins, D.L. Villeneuve, K.H. Watanabe. Quantitative adverse outcome pathways and their application to predictive toxicology. Environ. Sci. Technol., 51(8):4661–4672, 2017.
  T.-K. Ly, J. De Oliveira, E. Chadili, K. Le Menach, H. Budzinski, A. James, N. Hinfray, R. Beaudouin. Imazalil and prochloraz toxicokinetics in fish probed by a physiologically based kinetic (PBK) model, 04 December 2023 (preprint available at 10.21203/rs.3.rs-3580808)
  A. Pery, J. Devillers, C. Brochot, E. Mombelli, O. Palluel , B. Piccini , F. Brion, R. Beaudouin. A Physiologically - Based Toxicokinetic Model for the Zebrafish Danio rerio. Environ. Sci. Technol., 55848: 781-790, 2014.

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• Postdoc position in Machine learning for genomics annotations in plants

  • When
    1 Nov 2024
  • Location
    Instituto de Biologia Molecular y Celular de Plantas Primo Yufera (IBMCP), Valencia, Spain.

  We are looking for a two years postdoctoral to investigate the genome annotations in non-model plants by means of machine learning approaches.

  Genome annotations is one of the major bottlenecks to obtain high quality genomes, especially in non-model species. Efficient tools to evaluate the quality of a genome annotation are needed. The goal for this position is to develop a toolkit with several applications to evaluate genome annotations using K-mers and AI. This is a project developed in collaboration with Dr. Ian Morilla (UMA, Spain).

  Qualifications
  Applicants should have demonstrated experience in the field of bioinformatics and/or computational biology. They should be proficient in at least one programming language (preferably Python). The candidate should have proficiency on data science, with focus machine learning. Deep learning apsproaches will be a plus. Good English communication skills are essential. The applicants should have a PhD degree in the fields of Biology or Computational Science.

  The applicant should meet the requirements needed to apply to CSIC work system (https://sede.csic.gob.es/servicios/formacion-y-empleo/bolsa-de-trabajo).

  If you are interested in this position or have any questions, please contact Prof. Aureliano Bombarely or Prof. Ian Morilla
  (abombarely@ibmcp.upv.es, ian.morilla@ihsm.uma-csic.es)

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• Postdoc position in mathematical biology

  • When
    1 Nov 2024
  • Location
    University of Jena

  Postdoc position

  Your tasks:
  o Research in the fields of Bioinformatics and Systems Biology
  o Cooperation with experimentalists
  o Teaching bioinformatics courses (tutorials, introductory courses etc.)
  o Supervising Bachelor and Master theses (Bioinformatics)
  o Literature and patent search
  o Working on an academic qualification project, usually Habilitation.

  Prerequisites:
  o PhD degree or its analogue (e.g., Dr. rer. nat., Dr. Ing. Or PhD), or at least submitted dissertation, in Bioinformatics, Computer Science, Biology, or another field of the Life Sciences
  o Interest in mathematical modelling of biological processes
  o Programming skills

  Salary according to 90 % of TVL-13 in Germany. Please send applications to Stefan Schuster (stefan.schu@uni-jena.de)

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• PhD position, Mathematical Modeling - Women's Health

  • When
    1 Nov 2024
  • Location
    Bern, University of Bern, Switzerland

  Call: https://ohws.prospective.ch/public/v1/jobs/079255fa-c36a-4ba0-acd6-088cb81d8f44

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• Call for a director at the Computational and Quantitative Biology Unit at Sorbonne University

  • When
    1 Dec 2024
  • Location
    Paris, Sorbonne University

  The Department of Computational and Quantitative Biology (LCQB) at the
  prestigious Sorbonne University, located in the heart of Paris, France, is on the
  lookout for a new director set to start January 1, 2025. This position is for a five-
  year term, with the possibility of renewal.

  Full details are available here:
  https://dropsu.sorbonne-universite.fr/s/iegn9ftgTb6EmbS

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• Open PhD position in Theoretical Ecology

  • When
    31 Dec 2024
  • Location
    Potsdam, Potsdam University, Germany

  4-years position (75%) | E13 TV-L | Potsdam close to Berlin

  Project Title: Modelling context-dependent shifts in the forms of symbioses

  Project Description: Symbiotic interactions - representing prolonged physical associations of several species - are common in natural systems and can determine population dynamics, species persistence and ecosystem functioning, as demonstrated for example in coral reefs and plantpollinator networks. Symbiotic interactions can take different forms including parasitism, mutualism and competition.
  Depending on the underlying costs and benefits of the symbiotic interaction, the form of symbiosis may shift between different types of species interactions, e.g. mutualism and predator-prey interaction (see figure). While recent work has shown that the costs and benefits of symbioses depend on the densities of the symbiosis partners, we currently lack an understanding of how the form of symbioses depends on species traits and the overall food web context. This is particularly important as individuals and populations may adapt their traits to altered environmental conditions and as the food web structure may strongly vary across time and space. Hence, we want to improve general theory in community ecology by accounting for context-dependent changes in the form of symbiosis including the species’ potential to adapt to altering conditions in a food web context.

  The project is embedded into a network of experimental and theoretical working groups across Germany, conducting regular workshops and meetings promoting international networking. The prospective PhD student will join the working group of Prof. Dr. Ursula Gaedke, jointly supervised by Dr. Toni Klauschies. The prospective PhD candidate has the opportunity to closely interact with an experimental PhD student addressing the same overarching topic in our working group and related research groups on Campus. They can join the Potsdam Graduate School (PoGS) allowing for a broad interdisciplinary training of soft skills and early career development. The unique location of our campus in Park Sanssouci is part of a historical place in Potsdam
  providing a fruitful scientific environment and good working atmosphere.

  Your qualification: MSc degree in Ecology or other relevant subjects such as Physics, Mathematics or Environmental Science. We are seeking enthusiastic and committed candidates who enjoy ecology and applied mathematics with a solid background in ecology and ecological modelling. The successful candidate is expected to implement and analyze numerically differential equation models with a modern programming language such as Python, MatLab or Mathematica. Very good English writing and communication skills are expected, German is an asset but not essential.

  Application: To apply, please send the following documents as a single PDF to gaedke@uni-potsdam.de (the position is open until it is filled)

  · Cover letter, including a statement of motivation and from when on you would be available
  · Detailed curriculum vitae including a description of your pre-knowledge in (theoretical) ecology,
  programming and former research activities
  · Certifications of education
  · If possible, provide letters of recommendation from previous supervisors

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• Open PhD position in Experimental Plankton Ecology

  • When
    31 Dec 2024
  • Location
    Potsdam, Potsdam University, Germany

   4-years position (75%) | E13 TV-L | Potsdam close to Berlin

  Project Title: Context dependent effects on protective symbiosis driven by predation, competition and parasitism

  Project Description:
  Symbiosis is a biological interaction which refers to the physical association of individuals from different species that can be positive, negative or neutral to either species. In planktonic systems several symbiotic interactions can occur simultaneously and can interact with each other. We want to study the symbiosis between Daphnia and the rotifer Brachionus rubens within a multi-species interaction web. B. rubens can attach to Daphnia which reduces the fitness of Daphnia. At the same time both species compete for resources (algae). The
  attachment becomes more relevant, when a predator of B. rubens, A. brighwelli (another rotifer) is present because attached B. rubens are protected from predation. The aim is to quantify the costs and benefits for Brachionus and Daphnia under varying conditions and to better understand symbioses in a community context. Thus, the present project will contribute to a new food web theory which includes density dependence of symbioses. In addition, video analyses will be performed to study the attachment process in more detail.

  In the case of final approval, the project is embedded into a network of several experimental and theoretical working groups across Germany conducting regular workshops and meetings.

  The prospective PhD student will join the working group of apl. Prof. Dr. Guntram Weithoff at the University of Potsdam. We provide an active research  environment covering a broad range in ecological research. Beyond that, the Potsdam Graduate School (PoGS) offers a broad program on interdisciplinary training in soft skills and early career development.

  Your qualification: MSc degree in Ecology preferably in Aquatic Ecology or a related field. We are looking for a motivated candidate with good experimental skills. Further relevant skills are: sound knowledge in conceptional ecology, statistics and very good English in writing and communication.
  

  Application: To apply, please send the following documents as a single PDF to weithoff@uni-potsdam.de (the position is open until it is filled):
  • Cover letter, including a statement of motivation and from when on you would be available
  • Curriculum vitae including information on relevant skills
  • Certificates of education
  • If possible, provide letters of recommendation from previous supervisors

  
  

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• ERC-funded postdoc and PhD positions in mathematical biology / biophysics / theoretical developmental biology

  • When
    1 Jan 2025
  • Location
    University of Aberdeen

  The Hiscock lab is hiring! Funded by an ERC Starting Grant, we are looking to recruit people with a strong quantitative background to work on some of the most fundamental problems in developmental biology.

  We welcome applications from theoretical/computational biologists, but also from applied mathematicians, (bio)physicists, and computer programmers. We develop dynamical models (mainly PDEs) to understand the remarkable ways in which biological systems, especially embryos, self-organize into complex structures. We combine analytical theory with large-scale simulations – developing new theory and computational methods where required – and also collaborate closely with experimentalists from around the world.

  Positions are available at both PhD and postdoctoral levels with significant flexibility on start date; we will also provide in-depth mentorship for applications to independent fellowships. We are a curious, friendly and collaborative team based in the beautiful and affordable Northeast of Scotland, come join us!

  If you are interested to know more, please get in touch with Tom directly: thomas.hiscock@abdn.ac.uk

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