Job Listings

Note: Job listings are free. To post a job listing, please submit it to the SMB Digest. The listings here are typically pulled from each Digest. Please contact the webmaster for further details.

Listings shown below were posted in the following Digests:


(Click on job title for additional information.)
  • PhD Position: Bioinformatics/Computational Biology, UNSW, Australia
    • SMB Digest Vol 16, Issue 23 - June 8, 2016

      The Viral Immunology Systems Program (VISP) at the Kirby Institute for Infection and Immunity at the University of New South Wales, Sydney Australia is looking for PhD students to work on research projects in the area of bioinformatics / computational biology as well as statistical analyses that are aimed at understanding viral evolution and the role of host immune response. These projects and will involve high- throughput data, such as next-generation sequencing, as well as immunological data (flow- cytometry, single cell sorting and sequencing of T and B cell repertoire). The group has recently established single cell genomics laboratory assays to study antigen specific T cell responses and their subtype evolution during an infection.

      Computational projects are suited to students with a strong background in quantitative disciplines such as Bioinformatics, Computer Science, Physics, Statistics, Mathematics or similar. Successful applicants will join a team of researchers at the Kirby Institute and The School of Medical Sciences, which hosts > 140 PhD and Masters students and researchers in various field of Medical Sciences. There is also a great opportunity to interact with researchers involved in wet-lab activities.

      We have recently established the VISP program and the web page is under construction. Additional information on the Computational Biology Group's research interests is available at:

      Please include a cover letter and CV that provide details about research interests, education, employment history (if any), skills.

      Post-graduate scholarships are available to support tuition and living expenses for domestic (Australian Postgraduate Award APA)

      and overseas PhD students to study in Australia. More information on the postgraduate research scholarships is available at:

      Top-up scholarships are available in our group for USD5-10K.

      Interested applicants should contact Dr Fabio Luciani:

  • PhD Position: Cardiac Modelling, Maastricht University, Netherlands
    • SMB Digest Vol 16, Issue 23 - June 8, 2016

      We have a PhD position in Maastricht with a closing date coming very soon. In this project, computer simulation of the failing heart will be combined with data from patients and animal experiments to determine how pacemaker therapy can be optimally delivered in the individual patient.

      This would be a great opportunity for an applied mathematics / engineering masters student with an interest in cardiac research who's interested in working in a different country. The student will be based in Maastricht and collaborate closely with Bordeaux and Graz.

      For further details, visit:

      Interested candidates will need to send a cover letter and your CV to Joost Lumens, PhD ( before June 10, 2016.

  • PhD: Evolutionary transitions, University of Adelaide, Australia
      SMB Digest Vol 16, Issue 21 - May 25, 2016

      PhD Scholarship: Mathematical modelling of evolutionary transitions. School of Mathematical Sciences, University of Adelaide, Australia.

      The scholarship is open to all international students, so this would be a great opportunity for someone to come and study in Australia for a few years.

      Details at:

  • M2 Systems & Synthetic Biology, U Paris-Saclay & U. Evry, France
    • SMB Digest Vol 16, Issue 20 - May 18, 2016 Dear colleagues,

      Applications for the Master 2 in Systems & Synthetic Biology (mSSB) - proposed by the University of Evry-Val-d'Essonne and the University Paris-Saclay - are open until 15 July, 2016 on the website of U. Paris Saclay.

      This Master 2 is highly trans-disciplinary; Applicants may come from Universities or from Engineering schools after a first year of master (M1), or an equivalent qualification, in Life Sciences, Computer Sciences, Mathematics, Engineering, Chemistry and Physical Sciences. So we would appreciate your help in transmitting these informations to potentially interested students.

      Following this Master, several PhD programs are possible on site. Research trainings are also proposed in Europe (England, Germany, Switzerland, Spain, ...) and in the US.

  • PhDs & Postdocs: Hepatic Cell Differentiation..., UCLouvain, Belgium
    • SMB Digest Vol 16, Issue 20 - May 18, 2016 Experts in development and cancer biology are teaming up with modellers to build a network of experimentalists and theoretically-oriented scientists at UCLouvain and de Duve Institute (Louvain-la-Neuve and Brussels, Belgium). The goal of the network is to unravel fundamental mechanisms of organ development and growth by combining mathematical modelling with experimental approaches in cell, molecular and mouse transgenic technology.

      Our specific goals are to identify and predict the dynamics of signalling pathways and transcriptional networks which drive thyroid and pancreas morphogenesis, and which regulate hepatic cell differentiation and liver cancer development. We are seeking PhD students and post-doctoral fellows who will develop mathematical models, in collaboration with experimentalists. We offer the opportunity to interact with experts in experimental biology and applied mathematics, and to acquire transversal skills via participation to national and international workshops.

      The research will be performed in the laboratories of Emmanuel Hanert (, Frederic Lemaigre ( and Christophe Pierreux (

      PhD candidates must hold a Master degree in mathematics, (bio-)engineering, physics or in an equivalent quantitative discipline. Post-doctoral candidates must have a strong track record of conducting interdisciplinary research in computational biology. They must have published the results of his/her PhD in international peer-reviewed journals. Candidates are expected to be fluent in English, written and spoken. They should not have resided or have carried out their main activity (work, studies, etc.) in Belgium for more than 12 months in the 3 years immediately prior to the start of the fellowship.

      Interested candidates should send their CV, a motivation letter and the names of three references to

  • PhD Position: Modeling Global Change & Animal Movements, SLU, Sweden
    • SMB Digest Vol 16, Issue 20 - May 18, 2016 Global change and animal movements - Towards a socio-ecological predictive framework

      *Project Background*
      Global change encompasses environmental, social, economic and demographic changes on planet earth. Animals are an important component of the natural world due to their crucial ecological, social, and economic role in ecosystems. Global changes driven by resource extraction, energy and infrastructure development, climate change and urbanization are dramatically affecting animal populations and their movements resulting in challenges for management, driving human wildlife conflicts as well as hindering the sustainable development and use of natural resources. In such transformed landscapes, the vital questions are, 'how', 'where', 'when' and 'why' do animals move and how do these altered movements transform the landscapes as well as human societies (ecologically, socially and economically) that depend upon these animals? Moreover, how can we better predict animal movements under 'multiuse-landscape' and 'climate change' scenarios? Using case studies of two large mammal species (reindeer and moose) that are ecologically, socially and economically important in the northern/arctic ecosystem, the project aims to answer these questions. The goal is to develop a socio-ecological movement modelling approach that goes beyond correlative or species distribution models and provides a predictive tool that can be used in developing diverse future land use scenarios, developed with and for community users and geared toward adaptation strategies in a changing world.

      This NORDFORSK funded project seeks a candidate with a strong quantitative and modelling background in ecology, advanced skills in statistics and data analyses are almost essential as vast amount of data is already collected. A master degree in quantitative ecology or biology is desirable, or otherwise, those with a master in general ecology or biology may also apply and demonstrate their quantitative abilities. The candidate should be able to work in a multicultural and multidisciplinary environment, and have a good level of autonomy and creativity. A good knowledge of spoken English and writing skills are essential. Knowledge of Swedish and/or Sami is a plus. The expected start of the position is 1st October 2016. The place of work will be the Department of Wildlife, Fish and Environmental Studies at the Swedish University of Agricultural Sciences, Umeå, with occasional trips to the field site in northern Sweden.

      Use this APPLICATION FORM:

      Further information:
      Navinder Singh,, +46(0)706760103
      Göran Ericsson, +46(0)706765012

      Applications, marked with ref no SLU ua 1265/2016, must have arrived at the Registrar of SLU, P.O. Box 7070, S- 750 07 Uppsala or no later than 2016-08-31.

  • PhD Position: Modelling of infectious diseases, UNSW, Australia
    • SMB Digest Vol 16, Issue 20 - May 18, 2016 Applying mathematical models to estimate the impact and cost-effectiveness of vaccination programs

      We have a potential PhD research project in the area of infectious disease modelling, which will allow a candidate to develop and apply statistical, economic and mathematical modelling approaches. These skills are becoming increasing sought after in healthcare, both within academia and industry, and should help to build a strong foundation for a future career. The PhD candidate will have opportunities to work with leading experts at UNSW and with collaborators internationally. It will also present an excellent opportunity for an independent and self-motivated person to submit a number of peer-reviewed publications.

      Mathematical modelling is an important tool to estimate the impact of vaccination programs before they are implemented. These models can be used to predict future changes in disease both in those vaccinated and in the wider population via herd protection. The projections of program impact can then be used in cost-effectiveness models to assess the value for money that vaccination strategies offer in comparison to other potential health spending options. Estimates of cost-effectiveness are becoming a vital part of decision making process for many governments when considering the funding of new pharmaceutical interventions.

      UNSW Australia (The University of New South Wales) is one of Australia's leading research universities and is ranked in the top 50 universities internationally by the QS World University Rankings (2015). Based in Sydney, the infectious disease group at The School of Public Health and Community Medicine are a multidisciplinary research team that includes mathematicians, health economists, epidemiologists, clinicians and policy experts. We have extensive expertise in the evaluation of vaccine preventable diseases and have research collaborations with key international institutions such as the World Health Organization (WHO) and the US Centers for Disease Control (CDC).



      We seek an outstanding prospective PhD candidate with strong applied mathematics skills and a keen interest in applying these to important scientific and policy questions. Potential candidates should have a first class Honours degree or Masters degree with a high distinction average. Prior study can be from a variety disciplines, including mathematics, statistics, economics, computer science, engineering, physics, medical science, etc. It is not essential that the applicant have experience in the specific research area as our team has specialists who can offer training to candidates with applied mathematics skills as part of the PhD research.

      The supervisors will support the selected prospective candidate to apply for competitive PhD scholarship via UNSW, with options for domestic or international students. Those meeting the initial criteria who wish to discuss further should email A/Prof Anthony Newall ( with a CV and copies of academic transcripts for all degrees.

  • PhD: Energy variability & genetic decision making..., Birmingham, UK
    • SMB Digest Vol 16, Issue 19 - May 11, 2016

      Title: Energy variability and genetic decision making in stochastic cells
      Supervisors: (Dr Iain Johnston) and Prof George Bassel

      FindAPhD entry:


      Why do some cancer cells die immediately in response to chemotherapy, while others remain in a growing tumour? How do stem cells decide which tissue to form, and when to do so? Understanding cellular decision making is crucial in our attempts to predict how diseases will progress and to understand how cell-to-cell differences arise in biology. These decisions are often made by networks of interacting genes acting as biological "processors", with genes modulating each others' expression and governing cell behaviour [1]. A vital feature of these networks, often neglected in their analysis, is that they are embedded in a world subject to physical constraints: the processes involved in gene interactions require a source of energy, and take place in the chaotic and noisy environment that is the biological cell.

      Energy and noise are of central importance in cellular decisions: research from IGJ and others has shown that variability in mitochondria (fundamental energy sources in the cell) modulates stem cell fate choices, and that random influences (including collisions between molecules, and partitioning at cell divisions) have profound effects on cellular decisions [2]. Descriptions of gene regulation often omit these important dependences and so are only of limited use in predictive biomedical modelling, particularly in personalised medicine where biological heterogeneity is a key focus. Our ability to unify and harness biological "big data", particularly large-scale omics measurements of noisy transcript and protein populations, also suffers from this lack of a physical framework to quantify uncertainty and distinguish functional and spurious connections between genes. Clearly, appropriate physical models for the energy dependence and stochastic dynamics of gene regulation are required.

      This transformative project will develop, in concert, new modelling approaches to provide a bottom-up physical description of these important features, and new statistical tools forging a connection between these models and a wealth of currently available, large-scale, heterogeneous data. The researcher will use tools from stochastic processes [2, 3], dynamical systems [2, 4], and statistical inference (including likelihood-free approaches) [3, 5] to develop a unified descriptive and predictive theory linking regulation of energy-dependent and stochastic gene expression with noisy data. Some experience with these fields, and/or with biophysics/systems biology, will be helpful, but prior experience with biological topics is not essential. Through this research we aim to understand physical features governing variability in cellular decision making, to improve the reliability of in silico predictions of the behaviour of regulatory motifs and biological pathways (including stem cell fate decisions and cell death triggers), and to increase the statistical and interpretative power of omics data for understanding biology and disease.

      Funding Notes: Funding available for three years from the EPSRC, for UK or EU students only.

      [1] Karleback & Shamir, Nat Rev Mol Cell Biol 9 770 (2008)
      [2] Johnston et al., PLoS Comput Biol 8 e1002416 (2012)
      [3] Johnston et al., eLife 4 e07464 (2015)
      [4] Wang et al., Biophys J 99 29 (2010)
      [5] Johnston, Stat App Genet Mol Biol 13 379 (2014)

  • PhD Positions: Mathematical Biology / Medicine, QUT, Australia
    • SMB Digest Vol 16, Issue 18 - May 4, 2016

      Scholarships are available for several PhD students to join my research group. Projects that cover mathematical biology and mathematical medicine are available, and scholarships are suitable for both domestic and international students.

      A more complete description of the projects and application procedure can be found at and more details about my research group are available at

  • PhD: T cell-mediated immune regulation, Imperial, UK
    • SMB Digest Vol 16, Issue 16 - April 20, 2016

      We have an opening for 4-year PhD studentship for a UK/EU student (3-year residency rule applies).

      To reveal the mechanism of T cell-mediated immune regulation using molecular and systems approaches
      Supervisors: Masahiro Ono (Life Sciences) and Reiko Tanaka (Bioengineering), Imperial College London

      This project will investigate dynamic mechanisms of T cell-mediated immune regulation using molecular and systems approaches. We are especially interested in how the T cell regulation mechanism develops or evolves during development and ageing. T cells are conventionally classified into regulatory (suppressive) T cells and memory T cells. It is, however, obscure how these cells develop and exhibit their functions in vivo, and such dynamic activities can be measured only by appropriately combining new molecular tools and mathematical modelling.

      During this 4-year BBSRC funded project, we aim to reveal positive and negative feedback mechanisms of the T cell system, using a combination of our newly developed transgenic technology that measures the time-dependent dynamics of T cells in vivo and computational/mathematical modelling and simulation.


      Closing date: 29 April 2016
      Initial applications should include a full CV, names and addresses and contact details of two academic referees, a personal statement (500 words max) and a covering letter.
      Contact: Masahiro Ono (; Reiko Tanaka (

  • PhD: Modelling visuomotor coordination..., Exeter, UK
    • SMB Digest Vol 16, Issue 16 - April 20, 2016

      I have an open PhD Positions in my group at the University of Exeter. I am looking for PhD students with quantitative background (mathematics, physics, computer science or engineering) who are interested in applying their skills in solving biomedical and/or healthcare problems.

      Carlota Palmer Studentships:

      2. Modelling visuomotor coordination in People with Parkinson's Disease

      For further details and how to apply see:

      Please feel free to contact me if you have any questions regarding these positions.

      Krasimira Tsaneva-Atanasova

      ALTEREGO - Enhancing Social Interaction with an AlterEgo artificial agent

  • PhD: Math Modeling in Animal/Vet. Science, U. of Newcastle, UK
    • SMB Digest Vol 16, Issue 13 - March 30, 2016

      PhD studentship: Mathematical modeling in Animal/Veterinary Science, University of Newcastle, UK

      School of Agriculture, Food and Rural Development, University of Newcastle
      Funding per year: £16,557 (with Industrial Enhancement) + tuition fees
      Start and duration: 1 October 2016 for 4 years
      Closing date for applications: 14 May 2016
      Sponsors: BBSRC, KTN, AB Vista

      This project will use a range of mathematical and statistical modeling techniques to predict the digestion and metabolism of two macro-minerals essential in livestock feeding: Calcium and Phosphorus. The ultimate goal is to incorporate the model into a user-targeted tool. The project has both theoretical and applied training components and focuses on learning quantitative skills as well as the relevant context of nutrition and metabolism, offering a practical perspective of modeling and opportunities for gaining research experience linked to the agri-food industry.

      For further details see: or contact Professor Ilias Kyriazakis at

  • PhD Position: Mathematical Ecology, Osnabrück Univ, Germany
    • SMB Digest Vol 16, Issue 12 - March 23, 2016

      PhD Position: Mathematical Ecology, Osnabrück Univ, Germany

      A PhD scholarship is available at Osnabrück University (Germany) for work on a project in mathematical ecology. The project aims to combine mathematical models of resource exploitation (e.g. harvesting, grazing, fisheries) with ideas from human decision making and behavioral complexity in the face of uncertainty and/or impending regime shifts.

      The scholarship is part of start-up funding for a nucleus of a Research Training Group at the interface of ecological and socio-economic systems. The position is available for three years and should be started between June and October 2016. The yearly gross salary is from approx. EUR 21,500-31,000 depending on experience. More details are available at

      For further information and inquiries, please contact Prof. Frank Hilker (

      Closing date for applications: 24th March, 2016.

  • NCI Graduate Student Recruiting Program
    • SMB Digest Vol 16, Issue 11 - March 16, 2016

      Dear Colleagues,

      The National Cancer Institute (NCI) is actively seeking Ph.D. students to participate in the NCI Graduate Student Recruiting Program, to be held June22-24 at the National Institutes of Health (NIH) Bethesda, Maryland campus.

      The deadline to submit applications is April, 4th 2016 and the online application can be found at: Selected candidates will spend two days discussing their research through poster sessions, meeting current trainees at the National Cancer Institute (NCI), and learning about the research at NCI. The NCI-GSRP will support all travel costs for invited applicants to attend the event.

      The NCI is committed to excellence in science and to fostering diversity and inclusion. The purpose of this event is to invite qualified individuals to get acquainted with the science and resources at the National Cancer Institute and interview with our Principal Investigators seeking to

Postdoctoral positions

(Click on job title for additional information.)
  • Postdoc: Modeling viral dynamics and evolution, UPMC, France
    • SMB Digest Vol 16, Issue 24 - June 15, 2016

      Dr. Igor Rouzine at LQCB, Institut de Biologie Paris-Seine, Université Pierre et Marie Curie, Paris, seeks to fill two postdoctoral positions to model dynamics and evolution of viruses on multiple scales of biological organization. The Laboratory of Quantitative and Computational Biology offers a unique environment of four experimental and five theoretical teams working on different biological topics. The topics of this project, conducted in collaboration with data analysts and experimental teams at UPMC and elsewhere, include applied virus evolution (virulence, evasion of immune response), general mathematical methods and numeric tools, and HIV pathogenesis. Clinically, the project is connected to the development of new types of therapy and personalized medicine. The candidate should possess solid numeric and analytic skills and have some experience in modeling biological systems. A successful candidate will be intellectually independent but flexible and able to thrive in an interdisciplinary environment. Ph.D. degree in physical sciences is preferred but not required. Results will be published in leading journals and used to guide experiments of collaborating teams. The positions will start in the Fall of 2016, October 1, and will remain open until filled. Interested individuals are requested to send their CV, publication list, and names and electronic addresses of two references to

  • Postdocs: Modeling to develop new types of antiviral therapy, UCSF, USA
    • SMB Digest Vol 16, Issue 24 - June 15, 2016

      Prof. Andino at the Department of Molecular Biology and Immunology, University of California, San Francisco, anticipates a strong possibility of one or several postdoctoral openings starting in October 1 to model dynamics and evolution of viruses at multiple levels of biological organization. The successful candidate will participate in a large interdisciplinary project to develop new types of antiviral therapy with the participation of leading virologists, modelers, and data analysts from IBM, Boston University, University of Haifa, Université Pierre et Marie Curie, and other organizations. The candidate should possess excellent numeric skills and have previous experience in modeling biological systems. We seek individuals who are intellectually independent but open and flexible and can communicate with an interdisciplinary team. Ph.D. in physical sciences is preferred but not required. The results will be published in leading journals and used to guide experiments of collaborating groups. The anticipated positions, subject to funding approval, will start in the Fall of 2016, October 1, and remain open until filled. Interested individuals are requested to send their CV, publication list, and names and electronic addresses of two references to Dr. Rouzine,

  • Postdoc: Disease Ecology, University of Minnesota, USA
    • SMB Digest Vol 16, Issue 22 - June 1, 2016

      Department of Ecology, Evolution, and Behavior; University of Minnesota

      Our research group seeks to hire 2-3 motivated and conceptually driven post-doctoral associates to work collaboratively using empirical and/or theoretical approaches to test community ecology and behavioral ecology theory in pathogen communities. This work will focus on, but not necessarily be limited to
      (i) investigating the role of vector behavior on pathogen dynamics,
      (ii) testing the relevance of resource competition and metacommunity theory to pathogen communities, and
      (iii) investigating the interactions between disease and movement broadly.

      The successful applicant will work within a collaborative research team of faculty, postdoctoral researchers, and graduate students that includes expertise in using mathematical, statistical, and empirical approaches in behavioral, community, and disease ecology. We are particularly interested in applicants with strong skills in mathematics, statistical and analytical techniques, or molecular techniques relevant to the detection of phytoviruses using qPCR or metagenomics techniques. Demonstration of excellent writing skills are is an essential qualification for these positions. The appointment is initially for one year, but may be renewed annually. Starting date is negotiable and may begin as soon as possible.

      Questions about this position should be addressed to Drs. Allison Shaw (, Elizabeth Borer (, or Eric Seabloom (

      Review of applications will begin 15 June 2016 and positions will remain open until filled.

      Apply for this position (Job Opening ID: 310245) via the University of Minnesota Office of Human Resources website:

  • Postdoc: Mathematical Epidemiology, University of Utah, USA
      SMB Digest Vol 16, Issue 21 - May 25, 2016

      This position provides research support for mathematical and computer modeling projects in support of public health decision making for healthcare epidemiology, within the University of Utah Health Sciences Center. The postdoctoral fellow will work on one or more funded projects aimed at modeling interventions to reduce the incidence of healthcare associated infections in a regional network of hospitals and nursing homes. Within this scope, the postdoctoral fellow will have the opportunity to focus on theoretical and applied modeling topics of interest, including network epidemiology, antibiotic resistance and stewardship, strain competition, vaccine immunology, modes of transmission, and optimal intervention strategy.

      Essential Functions:
      1. Provides support for scientific literature search and synthesis of reviewed literature
      2. Assists in planning and executing models and computer simulations according to project needs
      3. Prepares and communicates research results in written and oral summary
      4. Works collaboratively with supervisor and other project team members in supporting project needs

      Minimum Qualifications:
      This position requires expertise in mathematical modeling and computer programming with a minimum of a PhD degree, computer programming skills, an ability to manage deadlines, good writing and communication skills, and an ability to effectively work within a multi-disciplinary collaborative environment.

      Interested candidates should apply online at

  • Postdoc: Biomechanics, University of Manchester, UK
      SMB Digest Vol 16, Issue 21 - May 25, 2016

      Applications are invited for a 2.5-year position focused on the biological physics and mechanics of the human placenta. The post is supported by a recently-awarded MRC Grant "Blood flow (dys)regulation and transfer function in the human placenta: an integrated in silico and ex vivo approach to fetal growth restriction".

      You will join a rapidly expanding effort in biomechanics within the School of Mathematics, working directly with Dr I. L. Chernyavsky and Professor O. E. Jensen, in close collaboration with physiologists and clinicians from the Institute of Human Development and the University of Southampton. This position forms a part of a wider recruitment that will involve employment of a Research Associate in experimental placental physiology to support the mathematical modelling effort.

      The theoretical part of the project lies at the interface between applied mathematics, continuum mechanics, multi-scale physics, spatial statistics and image analysis. The main aim of this project is in development of integrated analytical and computational techniques, informed by experimental data, for the study of flow and transport processes in the human placenta, a unique and critically important interface between the maternal and fetal circulations.

      You will hold (or be about to complete) a PhD in Applied Mathematics, Physics, Bioengineering, or a closely related field. You will have a solid track record of publications relevant to the project area, and a strong aptitude for interdisciplinary research. For further information and details of how to apply, please visit our web site or contact Dr Chernyavsky (

      The closing date for applications is 16 June 2016

  • Postdoc: Bacterial growth..., INRIA Grenoble - Rhâne-Alpes, France
      SMB Digest Vol 16, Issue 21 - May 25, 2016

      The IBIS group at INRIA Grenoble ­ Rhône­Alpes, in collaboration with the Laboratoire Interdisciplinaire de Physique of the Université Grenoble Alpes, is looking for a post­doctoral researcher to work on the mechanistic basis of growth rate control in bacteria. In particular, in the framework of the RESET project (, we are studying the relation between RNA polymerase expression and growth rate variability, under a variety of conditions, using single­cell time­series reporter gene data, image analysis, and mathematical modeling (Izard, Gomez Balderas et al., Mol. Syst. Biol., 11:840, 2015).

      Applicants are expected to have a background in biophysics, mathematical biology, or bioinformatics, with a strong interest in the application of quantitative methods to the study of biological systems. We offer a one­-year contract in an interdisciplinary and international environment in our research centre located in the French Alps (

      For more information on the position and for applications, please contact Hidde de Jong ( Applications should be accompanied by a CV and a motivation letter.

  • Postdoc: Plant modelling, INRA Avignon, France
      SMB Digest Vol 16, Issue 21 - May 25, 2016

      The INRA GAFL and PSH units are seeking a highly-qualified post-doctoral researcher to work on a project on genotype-phenotype kinetic modelling, in France. The successful candidate should hold a PhD with a background in modelling, and also have experience in parameter estimation, optimization and sensitivity analysis. The appointment is for 2 years, with a start date by the end 2016 or early 2017.

      The objective of this project is to integrate the genetic control of sugar metabolism in an existing kinetic model (Desnoues et al, in preparation) and to use it for ideotype design. At term, an improved optimisation strategy together with the mechanistic nature of the model have the potential to facilitate the discovery of new genes of interest for the modification of sugar metabolism.

      The position depends on the success of the project proposed to AgreenSkills/ AgreenSkills+.

      For details and application, candidates can contact Dr. QUILOT-TURION Bénédicte at

  • Postdoctoral Fellow: Quantitative Systems Pharmacology, Pfizer, USA
      SMB Digest Vol 16, Issue 21 - May 25, 2016

      Job Title: Postdoctoral Fellow - Cardiovascular and Metabolic Diseases
      Research Unit, Quantitative Systems Pharmacology, 1026494
      Location: United States-Massachusetts-Cambridge

      The Quantitative Systems Pharmacology (QSP) Lab in Pfizer's Cardiovascular and Metabolic Diseases (CVMET) Research Unit is responsible for developing insights to help advance CVMET clinical candidates and identifying and evaluating promising new therapeutic targets through physiologically-based modeling and simulation, and analysis and interpretation of preclinical and clinical data. We seek a highly motivated postdoctoral candidate to develop and analyze mechanistic, mathematical models of cardiomyocyte biophysics to enable the in silico testing of mechanistic hypotheses and improve the identification and evaluation of therapeutic targets for the treatment of heart failure (HF).

      The successful candidate will apply quantitative systems modeling and simulation methods to develop a validated mathematical model that couples cellular electrophysiology and ion transients to cellular metabolism, mitochondrial function, and contractile force generation in human cardiomyocytes. In addition to enabling in silico identification and assessment of HF drug targets, the successful candidate will pursue new avenues for scientific development in areas of QSP modeling, cellular biophysics, data analysis, and uncertainty quantification. The mechanistic insights gained from detailed analyses of the in silico model will generate physiological hypotheses that may be tested experimentally and/or in the clinic. The expectation is that the resulting findings will lead to improved confidence in rationale for the pursuit of novel agents for the treatment of heart failure.

      To be considered for this position, please apply at by searching Job ID 1026494.

  • Postdoc: HIV Modeling, University of British Columbia, Canada
    • SMB Digest Vol 16, Issue 20 - May 18, 2016 We are seeking a postdoctoral fellow to work on detailed modelling of HIV spread among gay, bisexual and other men who have sex with men (MSM) in Canada. The primary objective for our modelling research is to examine the real and potential impact of an innovative internet-based testing program for MSM, establishing a foundation which can then be extended by the postdoc in this position to a range of other testing and prevention interventions for this population. This postdoc position offers an excellent opportunity to gain experience in the translation of model results into real world public health policies and practice.

      The successful candidate will join a public health modelling team headed by Dr. Mark Gilbert (BC Centre for Disease Control, University of British Columbia (UBC), Ontario HIV Treatment Network) and Dr. Daniel Coombs (Department of Mathematics, UBC), working with provincial, national and international collaborators. The position will be based in Vancouver, working alongside the research team as well as public health staff, community agencies, and policy-makers involved with the implementation of these interventions.

      The ideal candidate will have the following skills:
      (A) excellent interpersonal skills, being able to communicate effectively with a wide range of stakeholders, including public health professionals, health care economists, and staff working in community-based organizations in the area of HIV prevention for MSM;
      (B) be a creative modeller, and able to compute from very simple ODEs to fairly complex simulation/network models;
      (C) be able to work independently to assimilate data from epidemiologic and sociological studies into the model framework (as well as primary analysis of data from cohorts of HIV negative and positive men in Vancouver and a large online survey of MSM across Canada);
      (D) be familiar with epidemic (or similar) modelling, analysis and computation, including stochastic models.

      Prior experience working on public health modelling projects is an asset. This is primarily a research position but there may be opportunities to gain teaching experience, depending on the candidate. Competitive salary and benefits. This is a two-year position.

      For additional information or enquiries please contact Mark Gilbert ( or Daniel Coombs ( Applications (with CV, research statement and names of two references) should be sent to Kim Thomson by June 1, 2016. Email:

  • Postdoc: Disturbance Ecology, Penn State, USA
    • SMB Digest Vol 16, Issue 18 - May 4, 2016

      A UK-US NSF-NERC joint-funded postdoctoral position is available to study the interplay between diversity, disturbance and invasion, using experimental microcosms to illuminate ecological theory.

      Invasion by alien species represents a major threat to the maintenance of the world's biodiversity. Biological invasions also have significant economic and environmental impacts on agriculture, epidemiology and conservation. Unfortunately, our current understanding of the processes involved, and hence our ability to manage disturbed systems, is hampered by the large number of interacting factors that can affect invasion. This project will examine how biological diversity and environmental perturbations interact to affect invasion, using a mix of experiments and theoretical research. The project will focus on experimental populations of microbes, combined with a related modeling agenda, to study: 1) the effect of independent, and combined, manipulation of disturbance and diversity on invasion success; and 2) the role of pre-adaptation to disturbance regimes in mediating invasion resistance. The postdoc will additionally assess the hypothesized importance of pre-adaptation to disturbance regimes by assessing invasion success following changes to previously established regimes. The project will involve successive iterations between these large bacterial community experiments and system-specific and general theory.

      Research will be based in the laboratory of Dr. Katriona Shea ( in the Department of Biology at The Pennsylvania State University, USA, with experimental work conducted in the laboratory of Dr. Angus Buckling ( at the University of Exeter Cornwall campus, UK. Please contact Katriona Shea (; +1 814-321-4809) for more information.

      We seek a postdoctoral researcher who has expertise in ecological/ evolutionary modeling with a clear interest in applications to community ecology and a strong desire to integrate theory with empirical research. A Ph.D. in Quantitative Ecology, Population Biology, Applied Mathematics or an equivalent area is required. Expertise in theory for microbial systems dynamics, using stochastic analytical and/or simulation population models, and empirical expertise in such systems, is highly desirable. Candidates should demonstrate a track record of publication; have strong organizational, written, and oral communication skills; and be able to work both independently and as part of a collaborative team.

      Interested applicants should apply online at with an application, a CV, a 1-2 page statement of research interests that explicitly describes professional qualifications for this position, and contact information for three referees. This is a fixed term position funded for one year from date of hire with possibility of refunding. Review of applications will immediately and continue until a suitable candidate is found.

  • Postdoc: Biological Modelling, Grenoble, France
    • SMB Digest Vol 16, Issue 18 - May 4, 2016

      A post-doctoral position for one year is available and starts in October 2016 (deadline for applications is before the end of August 2016) in the DyCTiM team of the TIMC-IMAG laboratory, UGA - CNRS (UMR5525) in Grenoble, France.

      The postdoctoral fellow will be involved in an interdisciplinary research that associates computer scientists and applied mathematicians of TIMC-IMAG, and biologists of IAB and TIMC-IMAG.

      *Project*. The project concerns the mechanisms of cytoskeleton reorganizations and crosstalks that drive blood platelet activation. Its precise regulation ensures hemostasis and prevents thrombosis. The flat shaped disc formed by quiescent platelets is maintained by the marginal band (MB), a peripheral ring of microtubules. We have shown recently that the initial shape change during platelet activation is due to cytoskeleton (microtubules and actin) and motor-driven MB extension inducing MB's coiling and consequently its change from a disc to a spherical shape. The postdoctoral fellow will develop a biomechanical multi-scale and individual- based model of microtubules, actin filaments and motors to understand the manner the MB forms and reorganizes as the levels of platelet activation change (due to microtubule acetylation, molecular motor expression levels...).

      *Qualification*. This is an interdisciplinary project in the field of complex systems in biology. The fellow will work closely with biologists, microscopists and computer scientists.

      Only highly motivated candidates with strong skills in computer programming (mainly in C++) and a good background in biological (or physical) modelling techniques will be considered. The candidate should have proven creativity and scientific activity by publications in peer-reviewed journals. Good written and oral communication skills are required. A first experience as a post-doctoral researcher is qualifying.

      Applicants may send a detailed CV (including a publication list and oral communications, detailed skills, contact information), a cover letter, and two reference letters to Nicolas GLADE (

  • Postdoc: Computational Biology, Ryerson University, Canada
    • SMB Digest Vol 16, Issue 17 - April 27, 2016

      A postdoctoral position is available in Computational Biology in the Department of Mathematics, Ryerson University ( The research will be led jointly by Dr. Silvana Ilie and Dr. Katrin Rohlf. This position provides an opportunity to engage in research in Applied Mathematics, with a limited amount of teaching. The salary is competitive, with funding provided for one year.

      We are seeking qualified and motivated applicants in Applied Mathematics, to work on interdisciplinary projects aimed at developing stochastic modelling and simulation tools for studying biological systems. The ideal candidate would have a strong background in Applied Mathematics (Numerical Analysis and Probability) and/or Computer Science. Strong programming skills in Matlab are mandatory. In addition, experience with dynamical systems (ODEs and PDEs) is expected. Knowledge of biological/chemical reaction modeling and stochastic simulation (temporal and spatio-temporal) is considered an asset.

      The fellowship is open to candidates of any nationality and selection will be based upon the candidate's research potential and teaching ability. Ideally the job will begin on September 1, 2016, however there is some flexibility in the starting date.

      The screening process will start on May 19, 2016, and continue until the position is filled. Please note the position is advertised pending budgetary approval. Applicants should submit a curriculum vitae and three letters of recommendation. At least one of these letters should report on the candidate's teaching abilities. Application material and reference letters should be sent directly by e-mail to

      We appreciate all replies to this advertisement, but only applicants under consideration will be contacted. Ryerson University has an Employment Equity Program and encourages applications from all qualified candidates, including aboriginal peoples, persons with disabilities, members of visible minorities, and women.

  • Postdoc: Mathematical Immunology, Imperial College London, UK
    • SMB Digest Vol 16, Issue 17 - April 27, 2016

      I am looking for a postdoc with an interest in Mathematical Immunology to join my team. The attached job ad, job description and application form can be found at with the following reference: HM2016080. The closing date for applications is 8th May, the start date for the post is flexible.

  • Postdocs: Epigenomics & Multi-scale Modelling, U. North Dakota, USA
    • SMB Digest Vol 16, Issue 17 - April 27, 2016

      The Rhen Lab seeks two highly motivated postdocs. Our overarching goal is to understand mechanisms underlying organism-environment interactions and genotype-environment interactions, which are ubiquitous in nature. Such interactions have implications for problems as diverse as predicting the impact of climate change on individual species and understanding individual differences in susceptibility to environmental causes of disease.

      Postdoctoral Fellow in Epigenomics -- This position focuses on epigenetic regulation of genes required for testis and ovary development in a species with temperature-dependent sex determination. The successful candidate will conduct and analyze ChIP-qPCR and ChIP-Seq studies. Proficiency with standard bioinformatics methods is required. Prior experience with genome assembly, annotation, or genome-wide ChIP analysis is preferred. Excellent opportunity for individuals with bioinformatics training to expand their understanding of biology and develop practical expertise with wet lab techniques.

      Postdoctoral Fellow in Multi-scale Modeling -- This position focuses on development of multi-scale models to link "inside-the-skin" biological systems with "outside-the-skin" environmental factors. The successful candidate will develop multi-scale models that integrate genetic, epigenetic, and gene expression data for temperature-dependent sex determination with data on the spatial and temporal pattern of variation in temperature across North America. Expertise in computational and/or mathematical modeling is required. Familiarity with multi-scale modeling is preferred. Excellent chance for individuals with quantitative background to enter the life sciences.

      Interested candidates should send their CV, a letter that describes their scientific interests and research experience, and the names of three references to Dr. Turk Rhen at

  • Postdoc: 2016 Complex Systems Postdoctoral Fellowship
    • SMB Digest Vol 16, Issue 16 - April 20, 2016

      The James S. McDonnell Foundation (JSMF) has posted updated guidelines for the 2016 Postdoctoral Fellowship Award program in Studying Complex Systems.

      *The Fellowship*
      -The JSMF Fellowship is designed to provide students with an opportunity to seek potential postdoctoral research opportunities on the basis of the student's interest and desire to obtain additional skills and experience that will further their pursuit of careers in complex systems science. Award details
      -200,000 USD to be expended in 2-3 years
      -JSMF could support up to 10 Fellowships each year

      *Eligibility* -This fellowship is intended for Ph.D. students with theoretical and/or experimental training in Complex Systems Science that anticipate completing their graduate training in late 2016 or in 2017.
      -Applicants should not have already identified a postdoctoral position and a postdoctoral research mentor.
      -Candidates from any country are eligible to apply.
      -JSMF Fellowships can only be used to support postdoctoral training at a qualified institution.

      -Applications and letters of support will be accepted online beginning May 1, 2016.
      -The deadline to submit all application materials is June 30, 2016, 15:59 CDT (20:59 UTC).

      For complete program details and application guidelines visit: or

  • Postdoc/PhD: Modeling Infectious Diseases, Zurich, Switzerland
    • SMB Digest Vol 16, Issue 16 - April 20, 2016

      We are looking for a highly motivated Postdoc or PhD-Student interested in the Mathematical Modeling of Infectious Disease transmission. The project combines mathematical modeling with molecular epidemiology approaches and clinical data in order to investigate epidemiological trends and prevention strategies in HIV/HCV. Accordingly, the candidate should have in addition to a strong mathematical background, skills to deal with complex and diverse data, and a strong interest in infectious-disease epidemiology.

      The Project will be carried out in the context of the Swiss HIV Cohort Study (SHCS) and the Zurich Primary HIV Infection Study (ZPHI). Those studies are the ideal setting for these projects as they are highly representative for the HIV population in Switzerland and combine sequence and clinical data of extraordinary quality. The student/postdoc will work on a range of specified research projects, but will be also highly encouraged and expected to develop and investigate his own research questions. In case of a PhD-student, the PhD will take place within the PhD-Program Epidemiology and Biostatistics of the Life Science Zurich Graduate School (run jointly by the University of Zurich and the ETH Zurich).

      Research will be conducted at the Division of Infectious Diseases at the University Hospital of Zurich; University of Zurich (supervision: Roger Kouyos,, The Division of Infectious Diseases provides a highly interdisciplinary and translational research environment with links both to clinical practice and basic science. Moreover, we are strongly interconnected with a variety of other research institutes in Zurich and beyond. In particular, we maintain strong collaborations with the Institute of Medical Virology at the University of Zurich, and the Institutes of Theoretical Biology and Computational Biology at the ETH Zurich.

      Applicants should send a cover letter, a detailed CV, and contact information for two or three academic references to:

  • Postdoc: Dynamic Modelling in Systems Biology, Netherlands
  • Postdoctoral Fellow in Mathematical Oncology, Moffitt Cancer Center, Tampa FL
    • SMB Digest Vol 16, Issue 14 - April 6, 2016

      Applications are sought for the position of post-doctoral research fellow to work under the supervision of Dr. Heiko Enderling on inter-disciplinary research projects on quantitative personalized medicine, with focus on cancer radiotherapy and immunotherapy. We seek a talented individual with a PhD and background in applied mathematics, physics or a computational discipline to work in the unique research environment of the Integrated Mathematical Oncology (IMO) department at Moffitt Cancer Center on the University of South Florida campus. IMO integrates mathematicians, computer scientists, and physicists together with imaging specialists as well as clinical and experimental oncologists to develop novel approaches for the understanding, treatment and prevention of cancer.

      The successful candidate will have a desire to work closely with experimentalists and clinicians and experience in modeling biological systems, with a preference for those with knowledge of immunology, radiation, and/or cancer. Desired are demonstrated creativity, high motivation, good communication skills and experience in developing/ writing publications in quality peer reviewed scientific journals. Preference will be given to candidates with the ability to program (C/C++/Java/Matlab), visualize and analyze numerical/experimental data.

      Interested applicants should send a cover letter and C.V. directly to, and formally apply through the Moffitt online recruitment system at requisition #19288.

  • Postdoc in York: Developing novel numerical methods for fish population dynamics
    • SMB Digest Vol 16, Issue 14 - April 6, 2016

      You are invited to apply for an EU-funded two-year postdoctoral research position at the University of York to develop and implement novel numerical modelling techniques, and to apply them in the field of fish population dynamics as part of the MINOUW project (

      This research position is suitable for you if you have a strong background in continuous dynamical systems (PDEs), numerical analysis and scientific computing, and are ready to bring your expertise to a new field of application where your work can have the greatest impact. Fisheries policy is strongly driven by predictions from mathematical models, more so than most areas of public policy, but as yet only very basic numerical analysis techniques are applied to the scientific models. Improvements are urgently needed. Your mathematical work will help science to make better recommendations for actions to maintain the health of marine ecosystems while at the same time exploiting them sustainably to provide high-quality food, employment for fishers and a prosperous fishing industry. In addition to benefiting nature and society, this post will open a potential career path for you, because fisheries science needs researchers with a strong mathematical background.

      At the University of York we have developed partial integro-differential equations to model marine ecosystems. Your first task will be to develop and implement efficient numerical schemes for these equations. Beyond that, the position offers you much scope to influence the further direction of the research. Because you will be working as part of the MINOUW project, you have immediate contact to 14 partner institutions across Europe, which will help you to bring your work to have real-world impact. If you have prior experience in large-scale modelling of continuous systems (weather, climate, currents, fluids, fields, etc.) this will be useful, as it will be transferable.

      Ideally you will begin the post before August 2016. However the precise start date is subject to negotiation.

      For further information consult the candidate brief and for enquiries please contact:

      Gustav Delius ( or Richard Law (

      The closing date for receipt of applications is 12:00 midnight on Monday 2 May 2016.

      Interviews are likely to be held the week commencing 23 May 2016.

  • Postdoc position in Computational Neuroscience, Lancaster, PA (USA)
    • SMB Digest Vol 16, Issue 14 - April 6, 2016

      POSTDOCTORAL FELLOW in Computational Neuroscience

      Job Description

      The interdisciplinary research team of Drs Christina Weaver (Mathematics, Franklin & Marshall College, Lancaster PA) and Jennifer Luebke (Anatomy & Neurobiology, Boston University School of Medicine, Boston MA) is launching a project to explore structural and functional abnormalities of neurons in two different mouse models of Huntington's Disease, and how these abnormalities might contribute to system-level dysfunction. Computational modeling of cortical and striatal neurons (both spatially extended compartmental models and point neuron models) will be conducted in tandem with empirical studies of these same neurons using in vitro slice electrophysiology and confocal laser scanning microscopy. The neuron models developed in this project will be incorporated into models of local microcircuits and larger cortico-striatal networks, likely in collaboration with other research teams, and will be used to inform future experiments. As part of this project, one postdoctoral position in computational neuroscience is available. Computational modeling of the empirically characterized neurons will use parameter optimization algorithms developed in the Weaver lab. For an overview of our interdisciplinary approach, see our joint publications including Luebke et al., Cerebral Cortex (2015), PMID 24323499 and Coskren et al., J. Comput. Neuro. (2015), PMID 25527184. The Weaver lab will have close, ongoing collaborations with the Luebke lab, including several visits to Boston where the empirical studies will take place. Initial appointment is for one year, and may be extended to a total of three years. The candidate will be hired by Franklin & Marshall College, though a remote employment arrangement may be possible.

      Applicants should have a strong background or interest in computational neuroscience, and have a keen interest in interdisciplinary approaches to neuroscience that integrate modeling, imaging, and physiological experiments. Review of applications will begin immediately, and will continue until the position is filled. Interested applicants should send their CV, a brief statement of current and future research interests, and the contact information of three references to

      Required Skills
      Ph.D. or equivalent in computational neuroscience, computational mathematics, or a related field from an accredited institution

      Excellent written and verbal communication skills

      Experience with automated parameter optimization, conductance-based modeling of single neurons, and/or NEURON compartmental modeling software is preferred.

      The fellow will have funds to support conference travel and professional development, and full access to campus services including F&M's Faculty Center. Lancaster, PA is a thriving small city, about an hour's train ride from Philadelphia, PA and 1.5 hour drive to Baltimore, MD. Applicants can learn more about working at F&M and living in the Lancaster community at

      Franklin & Marshall College is committed to having an inclusive campus community where all members are treated with dignity and respect. As an Equal Opportunity Employer, the College does not discriminate in its hiring or employment practices on the basis of gender, sex, race, ethnicity, color, national origin, religion, age, disability, family or marital status, sexual orientation, or any protected characteristic.

  • Postdoc: Cancer Multiscale Computational Systems Biology
    • SMB Digest Vol 16, Issue 13 - March 30, 2016

      Postdoctoral Position in Cancer Multiscale Computational Systems Biology
      Departments of Biomedical Engineering and Oncology
      Johns Hopkins University

      Seeking an independent and motivated Postdoctoral Researcher in Dr. Aleksander Popel's laboratory in the Departments of Biomedical Engineering and Oncology, The Johns Hopkins School of Medicine.

      The successful candidate will join a team that combines computational and experimental researchers using computational modeling and computational systems biology tools to discover and elucidate mechanisms of tumor angiogenesis and metastasis, immuno-oncology, tumor microenvironment, and perform drug discovery research.

      Specific skills include strong computational modeling of signaling pathways and multiscale modeling from signaling pathways to tumor scales.

      Applicant must have a doctoral degree with a demonstrated record of innovative scientific accomplishments as evidenced by first-author papers published or accepted in premier journals.

      Qualified candidates must be able to work independently, demonstrate outstanding communication skills, have a strong commitment to science, and work well within a group.

      US citizens, permanent residents or holders of an F1/OPT visa with at least six months of work authorization left.

      Johns Hopkins University is an Equal Opportunity Employer with a commitment to diversity. All individuals are encouraged to apply.

      How to apply: Email curriculum vitae and names of three references to: Dr. A.S. Popel, Dept. of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205. E-mail

  • Postdoc: Applied Math, U. of Waterloo, Canada
    • SMB Digest Vol 16, Issue 13 - March 30, 2016

      Department of Applied Mathematics, University of Waterloo
      Postdoctoral Fellowship in Applied Mathematics

      Applications are invited for a postdoctoral fellowship in the Department of Applied Mathematics at the University of Waterloo, with an anticipated start date of September 1, 2016. This is a one-year fellowship with the possibility of renewal for another year.

      In addition to engaging in research close collaboration with a faculty member or members in the department, the successful candidate will be responsible for teaching two, one-term courses. Candidates should indicate in their cover letter the names of faculty member(s) they propose to work with. Selection will be based on the candidate's research potential, availability of a supervisor, fit with a research area in the department and teaching ability. All interested recent PhDs are encouraged to apply.

      The Department of Applied Mathematics has 22 regular faculty and two lecturers. Research interests include scientific computing, control theory, differential equations and dynamical systems, fluid dynamics, mathematical biology and medicine, and mathematical physics. The department has a substantial graduate program with over 80 graduate students pursuing Masters or PhD degrees, and strong undergraduate programs in applied mathematics and mathematical physics. More information about the department can be found at

      Application for this fellowship is through the website Candidates should submit a cover letter, curriculum vitae and a one-page research statement to Applicants should also arrange for three letters of recommendation, with at least one letter addressing the candidate's teaching abilities, to be submitted through website.

      The application deadline is April 1, 2016.

      We appreciate all replies to this advertisement, but only applicants under consideration will be contacted.

      The University of Waterloo is strongly committed to employment equity within its community, and to recruiting a diverse faculty and staff. The University encourages applications from all qualified candidates, including women, members of visible minorities, Aboriginal persons, members of sexual minorities, and persons with disabilities.

      This position is contingent upon funding.

      Chris Bauch, PhD
      Professor and University Research Chair

  • Postdoc: Plant Modeling, INRA Avignon, France
    • SMB Digest Vol 16, Issue 13 - March 30, 2016

      Two-years Postdoc on plant modeling at INRA Avignon in France

      The INRA GAFL and PSH units are seeking a highly-qualified post-doctoral researcher to work on a project on genotype-phenotype kinetic modeling, in France. The successful candidate should hold a PhD with a background in modeling, and also have experience in optimization paradigm is needed moving from the optimization of individual parameters to the optimization of the combination of alleles involved in the control of the genotype- dependent parameters of the model. For this purpose, the optimization algorithm has to be adapted to explore a discrete, binary, solution space describing the presence or absence of each QTL effect on the value of each model parameter. In a second step, genetic constraints describing linkage and interactions between genes (pleiotropy and epistasis) among QTLs could be added to the algorithm, further reducing the allowable search space.

      At term, an improved optimization strategy together with the mechanistic nature of the model have the potential to facilitate the discovery of new genes of interest for the modification of sugar metabolism.

      Valentina Baldazzi

  • Postdoc Positions at the Center For Quantitative Medicine
    • SMB Digest Vol 16, Issue 12 - March 23, 2016

      The Computational Systems Medicine research group led by Professor Vera-Licona and the Systems Biology group led by Prof. Reinhard Laubenbacher at the Center for Quantitative Medicine at UConn Health have openings for talented and highly motivated postdoctoral fellows who wish to work on exciting research problems that are both computationally challenging and biologically important.

      Our research groups work within the fields of computational systems medicine, computational systems biology, mathematical biology and bioinformatics. We focus on the design and software development of mathematical algorithms for the modeling, simulation and control of biological networks, making use of high throughput sequencing and pharmacological data.

      The postdoctoral fellow in Prof. Vera-Licona?s group will be working on the development of algorithms and software tools for the analysis and targeted control of signal transduction networks geared towards the identification and prioritization of combinatorial network interventions. The openings in the Laubenbacher group are focused on the development of multi-scale models of disease processes, with particular emphasis on the use of agent-based modeling.

      Qualifications: Ideal candidate should have a PhD degree in mathematics, computer science, computational biology or bioinformatics. A strong computational background is required (background in graph and network algorithms, search algorithms is especially beneficial, as is substantial programming experience, preferentially Java, C++, Python for the Vera-Licona group). For exceptional computational candidates, it is not essential to have extensive knowledge of biology up front. Previous experience programming in Cytoscape or experience in molecular biology would be a plus.

      Starting date: July 15, 2016 or later for the Vera-Licona group, at the earliest possible time for the Laubenbacher group.

      How to apply: Send the following materials to
      1. A current CV with research background and publications list,
      2. A 1-2 page research statement with the specific areas you want to work on, how they fit with our research group, and how they build upon your previous work
      3. Two recommendation letters from your previous research supervisors and collaborators to be sent directly to

      UConn Health is an affirmative action employer in addition to an EEO and M/F/V/PwD employer.

Faculty and other positions

(Click on job title for additional information.)
  • Associate Director..., Dana Farber Cancer Institute, USA
    • SMB Digest Vol 16, Issue 24 - June 15, 2016

      Position Title: Associate Director for Scientific Operations, Center for Cancer Evolution - Sr Scientist
      Company Name: Dana Farber Cancer Institute
      Location: Boston, Massachusetts, United States, 02101

      For details and to apply, see

  • Selected NIH Intramural Research and other job openings - June 2016
    • SMB Digest Vol 16, Issue 23 - June 8, 2016

      Staff Scientist
      Section on Development and Affective Neuroscience, NIMH
      (Review of applications begins: July 1)

      The Section on Development and Affective Neuroscience (SDAN) in the Intramural Research Program (IRP), National Institute on Mental Health (NIMH), seeks a Staff Scientist.

      Research in SDAN is designed to achieve an integrated understanding of brain system perturbations that occur in pediatric emotional disorders, particularly anxiety disorders. SDAN then attempts to use this understanding to identify children at particularly high risk, to improve current treatments, and to develop new ones. Current projects in SDAN examine the predictive utility of functional magnetic imaging (fMRI) profiles for diverse clinical outcomes, applied in research on children and adolescents at temperamental risk for anxiety or receiving treatment for anxiety.

      The NIMH IRP brings together a highly interactive and dynamic group of collaboratively focused scientists. These individuals are at the forefront of research on mental disorders. SDAN is housed on the main NIH campus in Bethesda, Maryland.

      The SDAN Staff Scientist serves as a laboratory leader who contributes to mentoring of postdoctoral fellows and other laboratory staff and trainees. The position requires specific expertise in the analysis of fMRI data, as reflected in training and publication record. The successful candidate should have a doctoral degree, postdoctoral research experience, and an outstanding publication record. Requisite expertise includes basic analysis of fMRI data using the general linear model as well as expertise in more advanced approaches to fMRI data. The main job of the Staff Scientist will be to be the leader of data analytic approaches in SDAN and to apply advanced analytic approaches in particular, with a focus on computational neuroscience, multivoxal pattern analysis (MVPA), and machine learning. Salary is commensurate with experience.

      Applicants should submit their curriculum vitae with bibliography, statement of interest, and names and contact information for three references to Daniel Pine at Applications will be reviewed starting July 1, 2016, and accepted until the position is filled. HHS, NIH, and NIMH are equal opportunity employers.

      The NIH Intramural Research Program

      Link to Fellowships and Positions of Interest to fellows

      Link to NIH Jobs

  • Quantitative Systems Pharmacologist, Merck, USA
      SMB Digest Vol 16, Issue 21 - May 25, 2016

      The Quantitative Pharmacology and Pharmacometrics (QP2) group at Merck is now hiring at 3 levels: Senior Scientist, Associate Principal Scientist, and Principal Scientist. Qualified candidates will be hired at the level commensurate with their experience. We sponsor work visas for qualified candidates. Please see below for job description and forward to potential candidates. Thank you for your consideration.

      Location: West Point, PA; Upper Gwynedd, PA; Kenilworth, NJ; Rahway, NJ; Boston, MA.

      Fo further details and to apply online, please visit

      * Senior Scientist, R3 (QUA004740)
      * Associate Principal Scientist, R4 (QUA004739)
      * Principal Scientist, R5 (QUA004336)

  • Quantitative Systems Pharmacologist / Modeler, Pfizer, USA
    • SMB Digest Vol 16, Issue 20 - May 18, 2016 Job Title: Quantitative Systems Pharmacologist / Modeler Job ID 1031636

      About Pfizer:
      A career at Pfizer offers opportunity, ownership and impact. All over the world, Pfizer colleagues work together to positively impact health for everyone, everywhere. Our colleagues have the opportunity to grow and develop a career that offers both individual and company success; be part of an ownership culture that values diversity and where all colleagues are energized and engaged; and the ability to impact the health and lives of millions of people. Pfizer, a global leader in the biopharmaceutical industry, is continuously seeking top talent who are inspired by our purpose to innovate to bring therapies to patients that significantly improve their lives.

      Role Description:
      The Quantitative Systems Pharmacology (QSP) Lab in Pfizer?s Cardiovascular and Metabolic Diseases (CVMet) Research Unit is responsible for identifying and evaluating promising therapeutic targets and drug candidates through the application of systems modeling and simulation approaches. We seek a highly motivated candidate with experience in cardiomyocyte/cardiac function to lead the development of mechanistic, mathematical models to enable the in silico testing of novel targets and compounds for the treatment of heart failure (HF). The successful applicant will be responsible for providing QSP support to CVMet programs from target ideation through Phase 2 clinical development.

      * Develop and execute strategy for the application of QSP approaches to identify and evaluate novel pathways, targets and drug candidates for the treatment of HF
      * Work in close collaboration with CVMet biologists and clinicians to advance our HF programs and improve our understanding of disease mechanisms
      * Serve as QSP modeling & simulation expert in multidisciplinary project teams to solve challenging problems in drug discovery and development; contribute to preclinical and clinical study design
      * Develop and/or utilize state-of-the-art mathematical and statistical tools to gain insight into causal relationships between individual components within metabolic pathways and systems
      * Analyze and interpret complex data sets in the context of disease mechanisms and pathways; develop a deep disease knowledgebase

      * Ph.D. in Applied Mathematics, Engineering, Physics or a related discipline with strong numerical components focusing on modeling and simulation in the area of cardiomyocyte/cardiac function and 5+ years of experience in applying quantitative systems pharmacology approaches in drug discovery and development.
      * Deep understanding of theory, principles, and statistical aspects of mathematical modeling and simulation, including numerical methods, parameter estimation/optimization, ordinary differential equations (ODEs), and how these can be applied in the development of complex models of biological pathways and systems
      * Extensive, hands-on experience with modeling and simulation software (e.g., MATLAB, SimBiology, C/C++)
      * Self-directed, independent researcher who excels in a collaborative, multi-disciplinary environment
      * Excellent communication and writing skills
      * Primary authorship on relevant publications in peer-reviewed scientific journals

  • Research Scientist: Computational Bioinformatician, BHSAI, USA
    • SMB Digest Vol 16, Issue 19 - May 11, 2016

      The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF) is seeking a Computational Bioinformatician to support the U.S. Army Medical Research and Materiel Command's Biotechnology High Performance Computing Software Applications Institute (BHSAI) []. HJF provides scientific, technical, and programmatic support services to the BHSAI. This opening is for dynamic bioinformatics research scientists interested in working in multiple cross-disciplinary research projects.


      The Bioinformatics Research Scientist is responsible for advancing scientific knowledge by developing and applying their knowledge to original research problems in Military Medicine. The Research Scientist will apply their experiences in the analysis, collection, mining, and integration of multiple high-throughput datasets using computational bioinformatics and systems biology methods to understand chemical and biological interactions at the cellular and organism level.

      Foreign nationals are welcome to apply. U.S. citizenship or permanent resident status is not required. This position is located in Frederick, Maryland.

      The candidate is expected to simultaneously work on multiple projects, involving a diverse and interdisciplinary team of scientists across multiple laboratories.

      For further details, see:

  • Lecturer/Senior Lecturer/Assoc. Prof. (3 positions), Melbourne, Australia
    • SMB Digest Vol 16, Issue 18 - May 4, 2016

      Lecturer/Senior Lecturer/Associate Professor in Pure Mathematics;
      Applied Mathematics; Statistics (3 positions)

      School of Mathematics and Statistics, Faculty of Science, The University of Melbourne, Australia

      Salary: Level B AUD$92,654 - AUD$110,022 p.a.; Level C AUD$113,496 - AUD$130,866 p.a.; Level D AUD$136,658 - AUD$150,555 p.a.; PLUS 17% superannuation.

      The University plan seeks to increase the diversity of the workforce and the representation of women in areas they have been traditionally under- represented. Consistent with this, the School of Mathematics and Statistics is seeking to increase the representation of women in the academic workforce across mathematical disciplines. Pursuant to a Special Measure under Section 12 (1) of the Equal Opportunity Act 2010 (Vic), the School is seeking to lift the representation of women and therefore *will only consider applications from suitably qualified female candidates for these three positions.*

      The University of Melbourne's School of Mathematics and Statistics is one of Australia's leading mathematics and statistics schools. It has achieved this status through the high quality of its research and teaching programs. The School offers a wide range of subjects to undergraduate and postgraduate students and is involved in aspects of community life that impact on the interests of the School and the discipline.

      The School is seeking to further enhance its expertise in applied mathematics, pure mathematics and statistics, and seeks to appoint suitably qualified female candidates in three full-time continuing positions:
      * 1 position in Applied Mathematics
      * 1 position in Pure Mathematics
      * 1 position in Statistics

      The School maintains activity in all areas of the mathematical sciences. It has research foci in many areas of algebra, analysis, geometry and topology, number theory, continuum modelling, mathematical biology, mathematical physics, discrete mathematics, operations research mathematical and applied statistics including statistical genomics, stochastic modelling and probability theory. Applications are invited across these and, moreover, in any area of the mathematical sciences.

      The successful applicants are expected to:
      * lead a vigorous research program in their relevant discipline;
      * demonstrate a strong commitment to teaching (teaching will occur within the School of Mathematics and Statistics' undergraduate and MSc programs);
      * demonstrate a strong commitment to the supervision of research students (at undergraduate, MSc and PhD levels);
      * undertake administrative tasks for the School.

      The three successful candidates will be appointed at either Academic Level B, C or D, dependent upon the Selection Panel's assessment of the individual's application.

      Applicants are asked to please nominate (in the cover letter) which discipline they would prefer to be aligned with (Applied Mathematics, Pure Mathematics or Statistics). Please note the Selection Panel may exercise its discretion to recommend a different alignment.

      Clink on this link to watch Professor Aleks Owczarek (Head of School) and colleagues discuss these exciting opportunities for suitably qualified women:

      The University of Melbourne provides a wide range of opportunities for exciting research collaborations within the School, wider University, as well as externally. Learn more about Research at The University of Melbourne:

      The University of Melbourne has been accepted as a pilot institution in the Science in Australia Gender Equality (SAGE) pilot of Athena Swan in Australia. To learn more about this program, click on the links below:

      Enquiries only to: Professor Aleks Owczarek, Tel +61 3 8344 7887,
      Close date: 31 July 2016
      For position information and to apply online go to

  • Associate Director.., Dana Farber Cancer Institute, USA
    • SMB Digest Vol 16, Issue 18 - May 4, 2016

      Job Title: Associate Director for Scientific Operations, Center for Cancer
      Evolution - Sr Scientist
      Company Name: Dana Farber Cancer Institute
      Location: Boston, Massachusetts, United States, 02101

      *About Dana-Farber*
      Located in Boston, Dana-Farber Cancer Institute brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people with the best technologies in a genuinely positive environment, we provide compassionate and comprehensive care to patients of all ages; we conduct research that advances treatment; we educate tomorrow's physician/researchers; we reach out to underserved members of our community; and we work with amazing partners, including other Harvard Medical School-affiliated hospitals.

      The mission of Dana-Farber Cancer Institute is to provide expert, compassionate care to children and adults with cancer while advancing the understanding, diagnosis, treatment, cure, and prevention of cancer and related diseases.
      Our Core Values are:
      * Impact - Above all else, we make a difference by relieving the burden of disease now and for the future through our research, clinical care, education, outreach and advocacy.
      * Excellence - We pursue excellence relentlessly and with integrity in all that we do, adhering always to the highest standards of conduct.
      * Compassion and respect - For those in our care and for one another.
      * Discovery - We foster the spirit of inquiry, promoting collaboration and innovation across traditional boundaries while celebrating individual creativity.

      Reports to: Director of Scientific Operations
      Role and Responsibilities: The Associate Director for Scientific Operations will work closely with the Director to fulfill the scientific mission of the CCE. The principal mission of the CCE is to develop and validate mathematical modeling strategies of tumor evolution and treatment response, and eventually utilize these strategies to identify best therapeutic intervention. We will investigate the treatment response of cancer cells and their microenvironment, develop novel mathematical frameworks describing the evolutionary dynamics of tumor progression and treatment response that are parameterized using the experimental systems, and predict and validate optimum intervention strategies that will ultimately be implemented as prospective clinical trials. The Associate Director for Scientific Operations will have responsibility for furthering the daily research operations of the Center. In addition, the Associate Director for Scientific Operations will have oversight responsibilities for the CCE's scientific mission and will, jointly with Center Leadership, supervise the Postdoctoral Fellows. More specifically, he/she will have the following responsibilities:
      * Support the Director in setting the scientific direction and the operational priorities for the Center.
      * Create mathematical models and statistical/bioinformatic analysis platforms in a variety of contexts such as evolutionary dynamics of cancer and cancer progression, treatment responses and treatment optimization and implement them in the scope of the Center's research.
      * Direct and facilitate collaborative projects
      * Assist in grant and manuscript preparation and develop fundraising material for the Center.
      * Prepare reports and give presentations as needed.
      * Attend at least one conference/meeting per year related to the activities of the Center.

      The Associate Director will be designated a Senior or Principal Research Scientist and as such must fulfill the Dana-Farber requirements for this title. In addition, the Associate Director must fulfill the following requirements:
      * PhD level education with proven work experience in his/her respective field of endeavor.
      * Background in applied or pure mathematics, statistics, bioinformatics or computational biology; an interest in cancer biology and a work experience in probability theory and statistics are necessary.
      * Ability to work with senior level academic track scientists both within and outside his/her lab.
      * Ability to manage research databases.
      * Extensive knowledge of mathematical modeling and evolutionary theory as related to cancer, biostatistics methods and bioinformatics software, and the ability to create novel analysis platforms
      * Strong management and supervisory skills.
      * Excellent computer, analytical and writing skills.

      *How to Apply*
      Please apply directly online at Click Search Job Openings and use the Job ID number to quickly locate the appropriate job listing. Once you have located the desired job, click on the checkbox in the 'Select' column, and then click the 'Apply Now' button, located at the bottom of the screen.
      DFCI Employees please apply directly through PeopleSoft Self Service. Sign on to PeopleSoft and navigate to Main Menu > DFCI Careers.

      *Equal Employment Opportunity*
      Dana-Farber Cancer Institute is an equal opportunity employer and affirms the right of every qualified applicant to receive consideration for employment without regard to race, color, religion, sex, gender identity or expression, national origin, sexual orientation, genetic information, disability, age, ancestry, military service, protected veteran status, or other groups as protected by law.

      Apply Here:

  • Senior Lecturer: Mathematical Modelling and Analysis, Umeå, Sweden
    • SMB Digest Vol 16, Issue 16 - April 20, 2016

      The Department of Mathematics and Mathematical Statistics at Umeå University, Sweden, invites applicants for a research-oriented permanent position as senior lecturer in mathematical modelling and analysis (e.g., mathematical ecology).

      The successful applicant is expected to sustain active research within mathematical modelling and analysis with connections to the department's current activities in this area and to neighboring departments and units. Examples of relevant research areas are population dynamics, frequency-dependent evolution, structured population models, and optimal switching. The holder of the position will primarily be based at Umeå University's creative research environment IceLab (, which currently houses about 20 young scientists conducting interdisciplinary research, training, and education at the intersection of physics, mathematics, social sciences, and the life sciences.

      For full application details, please see

      Applications must be submitted through Umeå University's web-based recruitment system linked above. Last application date is 2016-05-30.

  • Selected NIH Intramural Research and other openings - April 2016
    • SMB Digest Vol 16, Issue 14 - April 6, 2016

      Staff Scientist DCEG-NCI (deadline: April 29)

      The National Cancer Institute (NCI), Intramural Research Program (IRP), a major research component of the National Institutes of Health (NIH) in the Department of Health and Human Services (DHHS), is recruiting a Staff Scientist within the Division of Cancer Epidemiology and Genetics (DCEG). This Staff Scientist will support a research program in molecular epidemiology of cancer and work under the direction of the DCEG Deputy Director. The overall aim of the research program is to identify biomarkers of cancer risk and progression in combination with other sources of exposure information collected from large epidemiological studies. Specific areas of research include: 1) molecular characterization of tumors to identify exposure signatures and subtype-specific causes of cancer, 2) identification of biomarkers of risk, including genetic and epigenetic changes, 3) integration of biomarkers and other risk factors into cancer risk prediction models, and 4) evaluation of their utility in risk stratification to inform personal and public health decisions.

      The successful candidate will be responsible for the coordination of research activities and the management of large epidemiological studies including acquiring, manipulating and integrating data from a variety of sources, quality control, statistical data analyses and manuscript preparation. He/she will be involved in collaborative research with intramural and extramural researchers and several international consortia, with opportunities for a lead role in publications. Qualifications include a Ph.D. or equivalent doctoral degree in epidemiology, biostatistics or related field. Prior postdoctoral training experience in epidemiological research with a history of publications that reflect experience in the methodological and analytical requirements of this position is highly desirable. Excellent written and oral (English) communication, interpersonal and teamwork skills are also required. US citizenship is not a requirement.

      Salary is commensurate with research experience and accomplishments. Full Federal benefits including salary, leave, health and life insurance, long-term care insurance, retirement, and savings plan (401k equivalent) will be provided. All employees of the Federal Government are subject to the conflict of interest statutes and regulations, including the Standards of Ethical Conduct. Additional information regarding the NCI/DCEG IRP is available at the following website: To apply: Please send a cover letter, curriculum vitae, bibliography, statement of research interests, and supply the names of three references to: Catherine McClave, Special Advisor for Division Operations; National Institute of Cancer, Division of Cancer Epidemiology & Genetics, 9609 Medical Center Drive, Rm. 7E-440, Bethesda, MD 20892-9774. Or email: Applications must be received on or before April 29, 2016 for consideration.

      The NIH Intramural Research Program

      Link to Fellowships and Positions of Interest to fellows

  • Assistant Director for Mathematical and Physical Sciences (AD/MPS)
    • SMB Digest Vol 16, Issue 13 - March 30, 2016

      Dear Colleague:

      We are initiating a national search for the National Science Foundation's Assistant Director for Mathematical and Physical Sciences (MPS) and seek your assistance in the identification of candidates. Dr. Fleming Crim has served in this position, with distinction, since January 2013.

      The Assistant Director, MPS, leads a directorate comprised of five divisions ? Astronomical Sciences (AST), Chemistry (CHE), Materials Research (DMR), Mathematical Sciences (DMS), Physics (PHY) ? and the Office of Multidisciplinary Activities (OMA). Enclosed is an information sheet that summarizes the directorate's activities and the responsibilities of the position, together with the criteria that will be used in the search.

      We are very pleased to announce that Dr. Saul Perlmutter, Franklin W. and Karen Weber Dabby Professor at the University of California, Berkeley, will head the search committee. We seek your help in identifying candidates with the following qualifications: outstanding leadership; a deep sense of scholarship; a grasp of the issues facing the mathematical and physical sciences in the areas of research and education; experience developing and overseeing complex scientific facilities; and the ability to serve effectively as a key member of the NSF management team. Recommendations of individuals from any sector ? academic, industry, or government ? are welcome. The National Science Foundation is an equal opportunity employer committed to employing a highly qualified staff that reflects the diversity of our nation.

      Please send your recommendations, including any supporting information that you can provide, to the AD/MPS Search Committee via e-mail ( or at the following address: National Science Foundation, Office of the Director, Suite 1205, 4201 Wilson Boulevard, Arlington, VA 22230. We would appreciate receiving your recommendations by May 13, 2016.

      Your assistance in this very important task is appreciated.

      /// signed ///
      France A. Córdova
      National Science Foundation

      The full letter can be accessed here:

  • Senior Lecturer in Mathematical Biology at The U. of Chicago
    • SMB Digest Vol 16, Issue 11 - March 16, 2016

      Senior Lecturer in Mathematical Biology at The University of Chicago, Biological Sciences Collegiate Division job posting 02952.

      The Biological Sciences Collegiate Division at the University of Chicago invites applications for a position at the rank of Senior Lecturer in mathematical biology beginning in the Autumn of 2016. The Senior Lecturer will be responsible for working with the faculty to develop and deploy a mathematical and computational curriculum directly within existing course sequences for undergraduate biology majors. The goal of this embedded curriculum is to enable deeper exploration of dynamic and stochastic biological processes at all stages of students? education in biology. Opportunities for teaching separate courses in the applicant?s area of specialty are available. The Senior Lecturer will be expected to assist faculty in applying for extramural support for program development, as needed, and to pursue academic activities publishable in the appropriate scientific and education literature.

      Applicants must have a Ph.D. in mathematics or a related field and preferably postdoctoral experience studying biological phenomena. Strong interest and demonstrated proficiency in undergraduate teaching and curriculum development is required. A record of collaborative work with biologists is important. The appointment will be for three years and is renewable.

      To apply for this position, visit our Web site at job posting 02952. Please complete your application and submit supporting materials by April 11, 2016. Applicants are required to submit the following materials: 1) a cover letter, 2) a curriculum vitae, 3) a sample course syllabus, 4) course evaluations or evidence of past teaching performance, and 5) three letters of reference. The review of applications will begin April 1, 2016, and will continue until the position is filled. Early application is strongly recommended.

      The University of Chicago is an Affirmative Action/Equal Opportunity/Disabled/Veterans Employer and does not discriminate on the basis of race, color, religion, sex, sexual orientation, gender identity, national or ethnic origin, age, status as an individual with a disability, protected veteran status, genetic information, or other protected classes under the law. For additional information please see the University's Notice of Nondiscrimination at Job seekers in need of a reasonable accommodation to complete the application process should call 773-702-5671 or email with their request.

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