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• Post-Doc Position: Mathematical Modelling to optimise IVF Outcome with a Personalised Medicine Approach

  • When
    31 Aug 2022
  • Location
    Basel, ETH Zurich

  This is an interdisciplinary Post-Doc position funded by a 3-year grant from the Personalised Health and Related Technologies (PHRT) program. You will work in the group of Prof Iber (ETH, computational biology), and collaborate with Prof Ulbrich (ETH, animal physiology), and Prof De Geyter (University Hospital Basel, reproductive medicine). 

  Project background

  The goal of the project is to develop computational personalized medicine approaches to improve the success rate of in vitro fertilization (IVF) using human and farm animal data. Given our detailed understanding of ovarian follicle maturation, personalized medicine approaches can go beyond statistical correlation and can be based on a mechanistic understanding of the hormonal control of ovarian follicle maturation.

   Job description

  You will focus on the development of predictive mathematical models that integrate literature data and newly generated data from farm animals and patients (3D images, hormone levels, gene expression time series) into a consistent framework that will allow us to provide data- and model-driven guidance regarding the best IVF treatment schedule. In collaboration with a PHRT-funded PhD student, the mathematical model will be carefully tested in clinical settings and then integrated into software for clinical use.

  Your profile

  • You are experienced in building mechanistic, predictive mathematical models based on biological data.
  • It is a plus if you have previous experience with image processing, finite element methods, and software engineering, as well as expertise regarding the female endocrine and reproductive system.
  • You are self-motivated and enthusiastic about leveraging mechanistic modelling for personalised medicine, advancing FemTech, and contributing to the establishment of a strong personalised medicine/personalised health research community in Switzerland, for the eventual benefit of patients and citizens.

  We offer

  • an internationally highly competitive salary and further benefits
  • excellent working conditions, with the possibility to work partly in the home office
  • a friendly and collaborative working environment
  • the opportunity to translate science to the clinic
  • support for career development after the PHRT-funded Post-Doc via suitable academic fellowships such as SNF Ambizione, or an ETH Pioneer Fellowship to commercialise the results

  The preferred starting date is October 2022; the exact starting date can be negotiated. 

   Application:

  Please apply via our online application portal: https://www.jobs.ethz.ch/job/view/JOPG_ethz_iU0C4kQJU5gfL69FCh. 

   Further information about the group can be found on our website: https://bsse.ethz.ch/cobi. Questions regarding the position should be directed to Prof Iber by e-mail: iberd@ethz.ch (no applications).

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• Graduate (PhD) position: Gene networks and the evolution of organismic complexity

  • When
    1 Sep 2022
  • Location
    Autonomous University of Barcelona (UAB), Spain

   1.Basic job and project description:
  The position is the Autonomous University of Barcelona (UAB), Spain
  
  -The main project questions are:
  How gene networks evolved to lead to the evolution of complex and robust phenotypes?
  
  Can be uncover some principles on how gene networks wired over evolution to reach such complexity?
  
  How these principles affect the tempo and mode of evolution.
  
  Any other question of the applicants interest that are related to the previous questions.
  
  We will use computational models of gene networks during development and computational models of evolution by natural selection to study such questions for the case of organismic complexity (e.g. anatomy). The models we develop are genotype-phenotype maps, relating genetic changes to phenotypic variation. These models are based on realistic gene network models of pattern formation and morphogenesis that lead to realistic 3D multicellular (animal) phenotypes. So actual embryonic and adult morphologies arise from our models, either of specific organs (e.g. teeth, wings, limbs) or generic embryo-like morphologies.
  
  The position is in Salazar-Ciudad’s group and it entails obtaining a PhD degree.
  
  2. Background of the project:
  There is no consensus definition of complexity, yet it is evident that organisms are complex and explaining such complexity is one of the most fundamental questions of biology. Morphological complexity has not increased in the evolution of all lineages and, in general, it is unclear whether there is a general trend of increasing complexity in evolution. Yet, one may ask about the mechanisms by which such complexity has increased in the lineages where it has increased. How complexity increases during evolution is necessarily related to development: any evolutionary change in morphology is first a change in the development that produces such morphology.
  
  It has been argued that, in spite of the remarkable morphological complexity of organisms, their development is achieved through a limited number of cell behaviors and types of cell interactions. These cell behaviors would be cell division, cell adhesion, cell death, cell growth, cell contraction, extracellular signal and matrix secretion, extracellular signal reception and cell differentiation. In addition to cell behaviors, development involves interactions between cells, either mechanical or through extracellular signalling.
  
  The questions we want to approach in this study are: how should these interactions and cell behaviors be coordinated to produce complex and robust morphologies in evolution? The question is, then, whether there are some logical requirements that developmental mechanisms should fulfill in order to lead to complex robust morphologies. Are there, for example, some requirements at the level of gene network topology or at the level of cell behaviors and their coordination during development? How do these requirements arise in evolution?
  
  If, as suggested above, pattern transformations in development involve a limited set of cell behaviors and cell interactions, then any mathematical model implementing those and intracellular gene networks should be able to reproduce, to a large extent, the range of pattern transformations possible in animal development. In this project we will use one such model, EmbryoMaker (Marin-Riera et al, 2015)⁠, to simulate a large number of possible developmental mechanisms and try to discover what, if anything, do the mechanisms leading to robust complex morphologies have in common.
  
  3. Job description
  The main tasks of the student include using existing models of embryonic development (e.g. EmbryoMaker) in order to simulate the development of complex morphologies. These models will be combined with models of evolution, in a population context with mutation, genetic drift and natural selection on morphology (see for example Salazar-Ciudad and Marin-Riera, 2013). The gene networks found to lead to the development of complex and robust phenotypes in evolution would be analyzed to extract general regularities, if any, these gene networks need to fulfill. The main tasks, thus, consist in simulation, theorizing, data analysis, coding, literature searching, writing and presenting results in conferences. We seek candidates highly motivated for theoretical work and data analysis with a broad understanding of the evolutionary theory and/or developmental biology and/or modeling.
  
  4. Requirements:
  - Candidates should have a University Degree and a Master’s Degree in biology, or similar, within the European Higher Education System (minimum 300 ECTS) or equivalent by September 2021.
  
  -Scientific programming skills or a willingness to acquire them is required.
  
  -The most important requirement is a strong interest and motivation on science and evolution. A capacity for creative and critical thinking is also required.
  
  5. Salary and conditions:
  -The salary would be the standard one graduate students in Spain. Full-time employment
  
  6. The application must include:
  -Application letter including a statement of interests and motivation.
  
  -CV (including publications, the contribution of the applicant in each publication, degrees obtained, subjects included in degree and grades, average grade)
  
  Foreign applicants, especially non-EU applicants, should attach an explanation of their University's grading system. All documents should be in English, no official translation is required in the initial application but may be requested afterwards. Applications should be sent to Isaac Salazar-Ciudad by email:
  isaac.salazar@uab.cat
  
  7. Starting:
  The start date is negotiable after September of  2022.
  
  8. Application deadline:
  1st of September 2022
  
  9. Work environment:
  Salazar-Ciudad group is between the Genetics deparment in the UAB (www.uab.cat) and the mathematics research center, CRM: www.crm.cat
  
  Both the CRM and Genetics department are very international and, thus, not being able to speak Catalan or Spanish is not a problem. Nearly half of the PIs in the CRM are foreigners. The everyday working language is English, and most administrative tasks, training and seminars arranged by the department and CRM are conducted in English.
  
  The UAB is one of the largest and best Universities in Spain.
  
  10. References:
  Salazar-Ciudad I, Marín-Riera M.Adaptive dynamics under development-based genotype-phenotype maps. Nature. 2013 May 16;497(7449):361-4.
  
  Hagolani PF, Zimm R, Marin-Riera M, Salazar-Ciudad I. Cell signaling stabilizes morphogenesis against noise. Development. 2019 Oct 18;146(20):dev179309. doi: 10.1242/dev.179309. PMID: 31628213
  
  Hagolani PF, Zimm R, Vroomans R, Salazar-Ciudad I. On the evolution and development of morphological complexity: A view from gene regulatory networks. PLoS Comput Biol. 2021 Feb 24;17(2):e1008570.
  

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• PhD position on Computational methods for analyzing the dynamics of certain diseases

  • When
    2 Sep 2022
  • Location
    University of Udine, Italy

  Open call for PhD position on “Computational methods for analyzing the dynamics of certain diseases” in the PhD programme in Mathematical and Physical Sciences at the University of Udine under the funding of the National Recovery and Resilience Plan (PNRR).

  The successful candidate will join the research group at CDLab ( http://cdlab.uniud.it/ ). 

  You can find more details at

  https://www.uniud.it/en/research/do-research/doctorate-res/ammissione/active-notice/call-for-applications-for-the-admission-to-the-phd-programmes-of-the-university-of-udine-in-the-academic-year-2022-2023-38th-cycle-under-the-funding-of-the-national-recovery-and-resilience-plan-pnrr-with-reference-to-the-following-misures-ministry2019s
  

  (section Mathematical and Physical Sciences​)

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• Two PhD positions in Biophysics

  • When
    8 Sep 2022
  • Location
    Krakow, Poland

  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 PhD studies will take place at the Faculty of Physics, Astronomy and Applied Computer Science of Jagiellonian University, Kraków, Poland. 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.

  The candidate is expected to have:

  •       MSc (or equivalent) in biophysics, physics, mathematics, computer science or similar, allowing application to the Doctoral School,
  

  •       excellent academic track record,

  •       interest in the interdisciplinary aspect of the project,

  •       experience with numerical solvers (C++, Python, Mathematica),

  •       proficiency in written and spoken English.

  We offer:

  • interdisciplinary research on interface of physics and biology,
  • research projects jointly with experimental labs (Austria, Poland),
  • opportunities of research visits in collaborating labs and participation in international conferences.

  The exact requirements, dates and details on application procedure are available at the webpage of Doctoral School of Exact and Natural Sciences https://science.phd.uj.edu.pl/en_GB/rekrutacja/konkursy_otwarte/.

  I encourage interested candidates to contact me in advance at marcin.zagorski@uj.edu.pl and provide CV, list of publications, and at least one recommendation letter. Further information on group activity is available at https://zagorskigroup.com/.

  The application deadline is September 8, 2022.

   Marcin Zagórski

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• Postdoc position: The role of compartmentalization within signaling pathways

  • When
    9 Sep 2022
  • Location
    INRIA Saclay - Île-de-France

  Recent biological imaging have shown that membrane receptors involved in intracellular signaling pathways are capable of inducing cascades of biochemical reactions from extremely dynamic pools of intracellular compartments. The subcellular trafficking of receptors generates spatio-temporal heterogeneous cellular compartments with a critical role on physiological functions, and profound consequences on the search for new therapeutic strategies.

  The candidate will develop new modeling formalism, combining biochemical reaction networks and coagulation-fragmentation dynamics to fully represent the diversity and complexity of signaling pathways. By comparing the models with data from confocal microscopy imaging with super spatio-temporal resolution, the candidate will reveal how the spatio-temporal heterogeneity of intracellular compartments conditions the response of cells to extracellular signals.

  The candidate will design efficient numerical schemes for partial differential equation (PDE) of coagulation type to explore the role of endocytosis, recycling and coagulation-fragmentation dynamics in receptor trafficking, as well the importance of highly dynamics phase transition and coarsening phenomena in downstream second messenger activation.

  Using ideas from chemical reaction network theory, the candidate will analyse the long-time behavior of the developed models, according to the underlying reaction network topology and coagulation-fragmentation dynamics, and its consequence for cellular response.

  Please contact Romain Yvinec (romain.yvinec@inrae.fr) for more information and before applying.

  Detailed annoucement and application procedure: https://recrutement.inria.fr/public/classic/en/offres/2022-05220

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• Open positions at The @Mathematical and Theoretical Biology Group at BCAM

  • When
    15 Sep 2022
  • Location
    Spain

  The @Mathematical and Theoretical Biology Group at BCAM is hiring promising researchers!!! 2 positions to be filled.

  Please see information below:

  - 1+ 1 years Postdoctoral Researcher on "Modeling spatial dynamics of disease spreading". Within the BMTF project, the research project will be focused on the development of spatio-temporal models variations on infectious diseases transmission and control and its impact on the Basque surveillance system; Modeling different social contact structures to understand disease spreading; Modeling the role of social behavioral changes, lock downs and other control measures affecting the dynamics of seasonal respiratory disease.

  Applicants must have a relevant curriculum in the scientific area of biomathematics applied to infectious disease, stochastic processes and network theory. We look for applicants with PhD degree in applied mathematics, mathematical biology, physics or related disciplines on quantitative life sciences field.

  Apply here:

  http://www.bcamath.org/en/research/job/ic2022-05-postdoctoral-fellow-in-biomathematics-at-the-mathematical-and-theoretical-biology-group

  Deadline: September 15th 2022, 14:00 CET (UTC+1) .

  - 1 year Research Technician position to work on "Modeling infectious disease dynamics"

  We seek promising young researchers, eventually interested to develop a PhD project on infectious disease dynamics.

  Note that a PhD position is to be financed by a national or international call. Candidates must apply for the PhD grant individually, with the support of the host institution and supervisor.

  The preferred candidate will have: 
  • Strong background in statistics
  • Information Technology Background
  • Knowledge of bio-statistics and experience in advanced programming are essential.

  Applicants must have their Bachelor’s or Master degree preferable in computer science, mathematics or quantitative life sciences field.

  Apply here:

  http://www.bcamath.org/en/research/job/ic2022-05-research-technician-in-biomathematics-at-the-mathematical-and-theoretical-biology-group

  Deadline: September 15th 2022, 14:00 CET (UTC+1) .

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