We are seeking applicants for two fully-funded PhD positions as part of an exciting research project in evolutionary biology in the School of Biological Sciences at the University of Auckland. 

The project is supported by a prestigious Marsden Fund grant from the Royal Society
of New Zealand (Royal Society Te Aparangi) to Drs. Nobuto Takeuchi, Austen Ganley, and Profs. Anthony Poole & Timothy Cooper.

One PhD position is in computational modelling (Takeuchi lab), and the other is in laboratory-based experimental bacterial evolution (Poole lab). Each position provides a stipend of NZD 33,825 per annum (tax exempt) for the full three-year PhD program as well as full university fees (for both national and international candidates).

The overall goal of the project is to understand what drives the evolution of reproductive divisions of labour (RDL), where sterile 'helpers' assist specialised 'reproducers' in transmitting genetic information. RDL has evolved repeatedly at vastly different biological scales. Examples include eusocial insects with queens and workers,
multicellular organisms with germline and soma cells, and cells with genomes and enzymes (enzymes provide catalysis, 'helping' genomes transmit genetic information). What drives the repeated evolution of RDL across different scales? Traditionally, it has been hypothesised that RDL increases group-level production efficiency because investment in a particular task brings accelerating returns - we call this the 'efficiency' hypothesis. However, our recent modelling work suggests that efficiency gains are not necessary for RDL to evolve [1]. Based on this, we propose an alternative hypothesis: that RDL evolves because of its ability to inhibit the evolution of 'cheaters' – individuals that avoid cooperation and replicate uncontrollably. We call this the cheater hypothesis. While the traditional efficiency hypothesis relies on system-specific explanations for how RDL increases production efficiency, the new cheater hypothesis is simple: it predicts RDL is beneficial under any conditions where cheaters can prosper and is, thus, independent of idiosyncrasies in different systems because cheating is known to occur across many systems and biological scales.

The goal of the two PhD projects is to test both efficiency and cheater hypotheses using complementary computational modelling and lab-based experimental evolution approaches. Specifically, the computational PhD student will use individual-based modelling to determine general conditions under which queen-worker RDL evolves to
inhibit cheater evolution. The experimental PhD student will undertake experimental evolution using E. coli to test both the cheater and efficiency hypotheses by quantitatively assessing the effects of RDL in a molecular-level system involving helper and reproducer plasmids.

Your role:
PhD position 1 (computational modelling):
Your role will be to implement individual-based models using a fast programming language, such as C++ and Java, run the models using Linux clusters, and analyse data generated by the models, with the goal of determining the general conditions under which queen-worker RDL evolves. You will also collaborate with experimental team members to identify parameters relevant to their experiments. You will obtain world-class training in modelling, designing research, writing papers, presenting your research at scientific conferences, and collaborating with team members. You will have ample opportunities to interact with multiple academics, including your main supervisor, Nobuto Takeuchi, and your co-supervisor, Austen Ganley, and other PhD students through regular meetings and retreats.

Post-graduate research experience in one of evolutionary theory, theoretical ecology, theoretical/mathematical biology, statistical physics, mathematical modelling, and/or any relevant fields is necessary, but project-specific training will be provided. Programming skills, a keen interest in quantitative and abstract thinking, and excellent academic communication skills are essential.

PhD position 2 (laboratory evolution):
Your role will be to first use molecular and synthetic biology approaches to build a plasmid-based RDL system and then use laboratory evolution approaches to examine whether the evolutionary dynamics of these systems are consistent with the efficiency hypothesis or the cheater hypothesis. You will obtain world-class training in synthetic biology, performing experimental tests of theoretical predictions, designing research, performing laboratory evolution experiments, writing papers, presenting your research at international scientific conferences, and collaborating with team members. You will have ample opportunities to interact with multiple academics, including your main supervisor, Anthony Poole, and your co-supervisor, Nobuto Takeuchi, and other PhD students through regular meetings and retreats.

Research experience in at least one of synthetic biology, laboratory evolution experiments, microbiology, and/or molecular genetics is necessary, but project-specific training will also be provided. Enthusiasm for working in an interdisciplinary team, strong troubleshooting skills, and excellent academic communication skills are also essential.

About us:
Dr. Takeuchi is a theoretical biologist interested in the evolution of biological complexity. His research group uses modelling and bioinformatics to study how biological systems accumulate information through evolution.

Prof. Poole has expertise in experimental evolution. His research group uses both experimental and computational methods study the early evolution of life. His lab is actively using experimental evolution coupled to genome sequencing, with the bacterium E. coli as the main model system, to test questions that relate to the first emergence of modern biological systems.

Our labs are based in the School of Biological Sciences situated on the University of Auckland's city campus in downtown Auckland. Auckland is the largest city in New Zealand. Sitting astride two stunning harbours, with parks, beaches, rainforests and mild winters, it is a vibrant, multicultural and multilingual city. The annual Global Liveability Index ranked Auckland in the world's top 10 liveable cities in 2024.

How to apply:
Please send applications
for PhD Position 1 (computational modelling) to Dr. Nobuto Takeuchi (nobuto.takeuchi@auckland.ac.nz)
for PhD Position 2 (experimental evolution) to Prof. Anthony Poole (a.poole@auckland.ac.nz)
by Sunday, September 8, 2024, in the following format:
1. A Curriculum Vitae,
2. A personal statement (750 words maximum) outlining (i) your interest in the position, (ii) what you hope to achieve from the PhD and (iii) your research experience to date,
3. Academic transcripts for all university course grades to date,
4. Contact details for two academic or professional referees (at least one academic).

We welcome informal enquiries about either project (please contact us at the email addresses listed above).

Reference
[1] Takeuchi & Kaneko. 2019 The origin of the central dogma through
conflicting multilevel selection. Proc. R. Soc. B. 286:20191359.
https://doi.org/10.1098/rspb.2019.1359

At the Multiscale Mathematical Biology group of Leiden University (www.mathbioleiden.nl) led by Prof. Roeland Merks, we have two upcoming vacancies, one for a PhD student and a second one for a postdoc within the NWO Gravitation project Green Tissue Engineering (GreenTE).

GreenTE is a multidisciplinary consortium of 7 Dutch universities. Together, GreenTE will unravel how plants sense and respond to mechanical stimuli. These fundamental insights will be the basis to develop engineering interventions to improve plant regeneration, seed longevity and defenses against disease. The successful applicants will be an integral member of the GreenTE community, which offers an open, diverse and inspiring environment to engage in multidisciplinary mechanobiology research at the intersection of biology, chemistry and physics, and is expected to participate in GreenTE events, training and collaborations.

In Leiden, we are looking for a PhD student on the mathematical and computational modeling of the mechanical regulation of plant development and regeneration using our existing two-dimensional plant simulation code VirtualLeaf, and for a postdoc whose primary responsibility will be to extend our plant tissue simulation codes (VirtualLeaf) and models of plant tissue growth to three dimensions.

Both projects’ key aim is to help answer the biological and biophysical questions coming up in the consortium, and they will therefore contain a substantial degree of theoretical biology. They will be carried out in close collaboration with experimental and theoretical scientists in the GreenTE consortium. Specifically, the PhD student will be co-supervised by Prof. Dolf Weijers, of Wageningen University and the postdoc will be co-supervised by Prof. Jasper van der Gucht of Wageningen University. The PhD student and postdoc will be based at the Faculty of Science of Leiden University with the Multiscale Mathematical Biology group (www.mathbioleiden.nl).

For more information and application (deadline September 9th, 2024), see:
1. PhD student: https://www.universiteitleiden.nl/en/vacancies/2024/q3/24-43915049phd-modeling-the-mechanical-regulation-of-plant-development-and-regeneration-1.0-fte
2. Postdoc: https://www.universiteitleiden.nl/en/vacancies/2024/q3/24-43815050postdoc-three-dimensional-simulation-models-of-plant-tissue-mechanobiology-1.0-fte-for-three-years

For questions, contact Roeland Merks (merksrmh@math.leidenuniv.nl); please note that applications by e-mail cannot be considered.

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).

I wanted to draw your attention to the workshop that Tamas Insperger and I organized for Udine, Italy for Oct 14-18, 2024. 

It will have distinctly DDE and modeling perspective and likely will be near the last times that many of the speakers will give live teaching-style lectures (e.g.me, Stepan and Morasso). I suspect it may be expensive to travel to the meeting; however, it is possible to attend online. I think that the lectures given by Insperger and Stepan plus others would be of interest to mathematical biology students working on DDEs as well as those interested in falls in the elderly, etc.

We are pleased to announce the workshop "The Numerical Brain: forward and inverse problems in neuroscience applications", which will be held on the 21st-23rd of October 2024, organised within the Amsterdam Centre for Dynamics and Computation, at VU Amsterdam.

The workshop is at the intersection between numerical analysis, computational and experimental neuroscience. It aims to form a community working on numerical methods for simulating brain processes and inferring parameters or states. The workshop will bring together scientists who specialize in data assimilation and uncertainty quantification methods, both within and outside the field of neuroscience.

A list of participants can be found on our website
amsterdam-dynamics.nl/the-numerical-brain

The event is supported by funding from our Centre, NWO, the NDNS+ and STAR clusters. Registration will be open in due course: we anticipate attendance will be free, with an optional fee for a social dinner.

We would be grateful if you helped us spreading the word, and we look forward to hosting you in Amsterdam in October.
The organisers
Daniele Avitabile and Svetlana Dubinkina

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)

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)

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

We are pleased to announce about the fourth in the series the conference"On the Trails of Mathematics" which is one of the main activities of the association Polish Women in Mathematics will be held from 8th to 11th November 2024 in Będlewo, Poland.

The purpose of our conferences is to help promote the scientific achievements and merits of women whose research, professional activity and publications have made significant contribution to the development of science, mainly in mathematics and related fields. Of course, we are not limiting the conference to women participants only, as we have gender equality in mind and we would like to promote equal opportunity and equal treatment of women in the mathematical sciences.

This conference will be intended to honour the Polish mathematician – Cecylia Krieger-Dunaj and her successors in particular two women from Poland: Izabella Łaba and Nicole Tomczak-Jaegermann. All three are among the top scientists in the world in their fields of research, honoured with numerous awards by international scientific organizations. These women, through their achievements and outstanding contributions to the development of world science, can serve as so-called "Role Models" for all young scientists – not only for women, but also for men.

In particular, we invite to participate in special session "Mathematical modeling in biology and medicine" organized by Urszula Foryś, Agnieszka Bartłomiejczyk and Zuzanna Szymańska.

The registration deadline is September 15, 2024.

For further details on the conference and the registration procedure, please visit:
https://sites.google.com/impan.pl/otowim24

We are looking forward to welcoming in Będlewo you soon!

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

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

 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