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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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• PhD position in Theoretical Biology

  • When
    31 Dec 2024
  • Location
    Plön

  I am looking for a PhD student to join my research group at the Max Planck Institute for Evolutionary Biology. The position is part of the Collaborative Research Unit 'Density dependent symbiosis in planktonic systems – DynaSym', which brings together several research groups across Germany to test and develop basic concepts of density dependence of the symbiosis form (e.g., shift from predator-prey to mutualistic interaction and back).

  Modeling parasite epidemics in host populations with symbiont-mediated immunity

  Protective symbionts can provide hosts with immunity against virulent parasites. Yet, symbionts themselves may also be costly for the host. The form of symbiosis is thus context dependent: mutualistic upon exposure (or infection) with the virulent parasite but parasitic in its absence. Classical theory on host-parasite systems only considers two players -- the host and the parasite. The possibility of protective symbiosis clearly demonstrates the need for theory that goes beyond two-species systems. In this project, we will develop theoretical models to study the joint changes in the densities of hosts, symbionts, and parasites and the associated changes in the form of symbiosis. Initially, we will mostly develop general theory, but we will later also explore models that match the biology of Daphnia and its parasites. In collaboration with other members of the Research Unit, models can moreover be tailored to other systems of protective symbiosis that are studied empirically within DynaSym.

  The ideal student is interested in applying mathematical modeling to gain insights into biological problems, enthusiastic about math as well as about biology, and excited about engaging in the research unit DynaSym. The student will learn how to set up and analyse theoretical models to describe biological processes and profit from close interactions with empirical researchers. Applicants should have a background in mathematics, physics, biology, computer science, or a related field. Good quantitative skills are essential. Prior experience in mathematical modeling and knowledge of a programming language (C, C++, Java, Python, Julia...) is an advantage.

  The Research Unit DynaSym has recently been funded by the German Research Foundation DFG (www.uni-konstanz.de/en/university/news-and-media/current-announcements/news-in-detail/mal-freund-mal-feind) and is a collaborative initiative bringing together research groups from across Germany and international collaborators. 8 projects will collaborate within the research unit and cover experimental work with plankton systems, modeling, theory development, and synthesis work. Workshops, retreats, and research visits to other research groups are planned for all participants to facilitate exchange and additional training.

  Working environment
  The student will join the research group 'Stochastic Evolutionary Dynamics' at the Max Planck Institute for Evolutionary Biology. The group is part of the Department of Theoretical Biology. The student will hence be part of a community of researchers working at the intersection of mathematics and biology with many opportunities to take part in journal clubs, reading groups etc.
  The Max Planck Institute is a lively institute with around 180 employees from more than 30 nations. There are currently two departments (Theoretical Biology and Microbial Population Biology) and several additional research groups. It hosts several workshops per year and continuously welcomes international short-term and long-term visitors, creating a stimulating and positive research environment. We maintain close interactions with Kiel University and belong to the Kiel Evolution Center. The area is a center of evolutionary biology in Germany.

  Plön
  Plön is a small town, embedded into a beautiful landscape with numerous lakes and close to the Baltic Sea. The area provides ample opportunity for free time activities such as swimming, canoeing, or biking in a stunning environment. At the same time, the cities of Kiel and Lübeck (≥200,000 inhabitants) are only half an hour train ride away. Hamburg (Germany’s second largest city) can be reached within 1.5h by train.

  Application
  Interested students should send their application (motivation letter, CV, copies of certificates, contact details of two references) in a single pdf by email to uecker@evolbio.mpg.de and to bewerbung@evolbio.mpg.de. Please use the code PhD2024 in the subject line. We ask you to refrain from including a photo on your CV.

  The Max Planck Society strives for gender and diversity equality. We welcome applications from all backgrounds. The Max Planck Society is committed to employing more disabled individuals and especially encourages them to apply. The Max Planck Society seeks to increase the number of women in those areas where they are underrepresented and therefore explicitly encourages women to apply.

  For further questions, please get in contact with Dr. Hildegard Uecker.
  Review of applications will begin immediately and will continue until the position is filled.

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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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• PhD positions in Precision Medicine

  • When
    13 Jan 2025
  • Location
    Edinburgh, UK

  Interested in using your quantitative, computational, and theoretical skills to research better ways to treat human diseases?
  Apply for a Precision Medicine PhD in Edinburgh!

  There are up to 3 projects with me:
  https://usher.ed.ac.uk/precision-medicine-doctoral-training-programme/mathematical-modeling-of-pancreatic-islet-behaviour
  https://usher.ed.ac.uk/precision-medicine-doctoral-training-programme/dissecting-macrophage-fibroblast-cell-circuits-in
  https://usher.ed.ac.uk/precision-medicine-doctoral-training-programme/using-synthetic-biology-and-quantitative-analysis-to

  Linus Schumacher

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• PhD position: Modelling antibiotic resistance

  • When
    15 Jan 2025
  • Location
    University of Edinburgh

  We are aiming to recruit a PhD student to start in October 2025 on the proposed project "Modelling stochastic emergence of antibiotic resistance in bacterial populations".

  The PhD will be based in the research group of Helen Alexander in the School of Biological Sciences, with good links to the local mathematical biology community. The ideal candidate would have (or be completing) a first degree in Mathematics, Physics, or another scientific discipline with strong mathematical and computational skills, and a keen interest in answering biological questions. Funding opportunities are available for both UK and international students, with application deadlines between early to mid-January.

  For a full project description and further information on how to apply, please see: https://biology.ed.ac.uk/alexander/join

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• PhD position in Infectious Disease Modelling

  • When
    27 Jan 2025
  • Location
    Bristol, UK

  The aim of this PhD is to use data analytics, data linkage and mathematical models to inform the use and necessary test characteristics of saliva-based tests for vaccination evaluation.

  The aims of the project are to:

  • Develop transmission models for vaccine-preventable respiratory pathogens (Streptococcus pneumoniae and Respiratory Syncytial Virus) and emerging threats (Group A Streptococcus) in the UK
  • Identify opportunities for early identification of changes in population immunity that would provide a rapid assessment of vaccine effectiveness and coverage.
  • Explore the trade-offs involved in detecting population protection.

  More information here: https://www.findaphd.com/phds/project/modelling-salivo-surveillance-for-detecting-population-immunity-transmission-dynamics-and-changes-in-vaccine-effectiveness/?p179939 

  Please contact us if you wish to discuss the project, our (wonderful) team or your suitability.

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• Postdoctoral position in Biostatistics for Clinical Cancer Research

  • When
    31 Jan 2025
  • Location
    Institut Curie, France

  A postdoctoral position of up to 3 years is available in the “Cancer Systems Pharmacology” team (Ballesta Lab) within the "Bioinformatics and Computational Systems Biology of Cancer" Unit (U900 INSERM, Mines ParisTech, Institut Curie) at Institut Curie.

  The hosting structure
  Institut Curie is a major player in the research and fight against cancer. It consists of a Hospital group and a Research Center of more than 1000 employees with a strong international representativeness. The objective of the Research Center is to develop fundamental research and use the produced knowledge to improve the diagnosis, prognosis, and therapeutics of cancers as part of the continuum between basic research and innovation serving the patient.

  Laboratory
  The "Bioinformatics and Computational Systems Biology of Cancer" research unit is a very active and growing interdisciplinary department gathering bioinformaticians, biologists, physicians, mathematicians, statisticians, physicists, and computer scientists. This postdoctoral project will be hosted in the “Cancer Systems Pharmacology” team which designs mathematical and statistical approaches for optimizing and personalizing anticancer treatments integrating multi-type preclinical and clinical data. The project is a collaboration with the “Statistical Methods for Precision Medicine” team (Latouche Lab) of the unit, the Cancer chronotherapy Paris-Saclay research unit (Hôpital Paul Brousse, Villejuif), and also involves several additional teams of clinicians.

  The project
  The postdoctorate candidate will focus on investigating the impact of the administration timing over the 24h span of cancer immunotherapy on treatment outcomes in patients. He/She will work in the framework of a collaborative project funded by INSERM through the “Mathématiques et Informatique contre le Cancer” call (MIC, 2024-2028) that aims to enhance the efficacy of Immune Checkpoint Inhibitors (ICI) through personalized administration timing. The circadian timing system has significant influence on the immune system1 and recent preclinical and retrospective cohort studies, including one of our group2, have highlighted an association between ICI timing of administration and treatment outcomes.

  The candidate will perform analysis of cohorts of patients with cancers treated with ICI in order to decipher optimal ICI timing in terms of survival, antitumor response and toxicities, accounting for the patient characteristics (e.g. sex, age, performance status, …). In addition, he/she will develop novel statistical methods for analyzing the association of drug timing with patient survival and evaluate them on both synthetic and real-world data3,4. The candidate will further investigate the optimal design of prospective clinical trials addressing the relevance of personalized administration timing regarding patient outcomes. In connection with applied mathematicians of the team, he/she may further investigate the molecular determinants of such timing dependencies using mechanistic models based on ordinary differential equations.

  Key responsibilities
  o Conduct original research in the area of chrono-immunotherapy
  o Develop and implement biostatistics methods using synthetic or real-world clinical data
  o Interact with biologists and clinicians
  o Publish scientific articles at international peer-review journals
  o Present results internally and at international conferences
  Skills/qualifications
  o PhD degree in the area of biostatistics, or applied mathematics
  o Significant computational/programming skills (e.g. R, MatLab, Python)
  o Experience in working with survival analysis and clinical data.
  o Strong interest in biological sciences and clinical research
  o Strong communication and writing skills
  Contract Information
  The position is available immediately and opened until filled. The salary will be set according to the Institut Curie salary grids which include a bonus for bioinformaticians. Benefits include collective catering, reimbursement of transportation fees up to 70%, and supplementary health insurance. Institut Curie also offers numerous opportunities for training in both scientific and soft skills. The location of the position is on the site of Saint-Cloud (92) of Institut Curie.
  
  Selection process
  For initial consideration and more details about the scientific areas of research, send an e-mail including your CV, a brief statement of interest and contact information for two academic references to annabelle.ballesta@inserm.fr.

  Institut Curie is an inclusive, equal opportunity employer and is dedicated to the highest standards of research integrity.

  References
  1. A Lévi, F., Okyar, A., Hadadi, E., F Innominato, P. & Ballesta, A. Circadian Regulation of Drug Responses: Toward Sex-Specific and Personalized Chronotherapy. Annu Rev Pharmacol Toxicol (2023) doi:10.1146/annurev-pharmtox-051920-095416.
  2. Catozzi, S. et al. Early morning immune checkpoint blockade and overall survival of patients with metastatic cancer: An In-depth chronotherapeutic study. European Journal of Cancer 199, 113571 (2024).
  3. Efird, J. T. Sinusoidal Cox Regression—A Rare Cancer Example. Cancer Inform 9, CIN.S6202 (2010).
  4. Ramanathan, K. et al. Assessing Seasonality Variation with Harmonic Regression: Accommodations for Sharp Peaks. IJERPH 17, 1318 (2020).

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