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title: About - Biocompute Lab
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    <h1>Join us</h1>

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      <p>If you would like to join the lab, internal positions we are advertising are listed below. It is recommended to contact <a href="mailto:thomas.gorochowski@bristol.ac.uk">Thomas Gorochowski</a> directly to discuss any applications. We are also always happy to support applications for externally funded scholarship or fellowships if your research interests align with ours. If this is something you'd like to pursue then <a href="mailto:thomas.gorochowski@bristol.ac.uk">contact us</a> with details of your plans.</p>
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      <p class="bcl-box">No internal open positions available at present</p>
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    <h2 class="border-bottom">Avaiable Positions (Funded)</h2>

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        <h4 class="bclcol1">PhD: Engineering unconventional gene regulation</h4>
        <p><b>Primary supervisor:</b> Thomas Gorochowski (Bristol, UK)<br>
        <b>Secondary supervisor:</b> Michiel Stock (Ghent, Belgium)<br>
        The ability to control when and where genes are expressed in living cells is a central pillar of synthetic biology and underpins the engineering of biology for diverse applications. Historically, gene regulation has mostly been considered at the level of DNA-binding proteins (e.g., transcription factors), however, we are beginning to realise the important role that other biophysical factors can have at all levels – a phenomena called polycomputing. In this project, the student will explore how induced DNA supercoiling and spatial interactions between distant sections of DNA can be used to engineer complex gene regulatory patterns that would be difficult or impossible to implement using traditional synthetic biology approaches. The project will combine a mix of biophysical and graph-based modelling, genome engineering, and genetic circuit design. It is an opportunity for a creative and ambitious student to take steps towards reimaging how to build genetic systems that better harness diverse biological processes. The project will be carried out in close collaboration with Dr. Stock at the University of Ghent in Belgium. It is expected that the student will spend time across both labs to build the underlying models describing these processes and develop the experiments needed to test new ideas and genetic designs. Both labs value diverse perspectives on science and aim to support an engaging and supportive environment that is required to tackle challenging scientific questions. <a href="https://www.findaphd.com/phds/project/funded-phd-engineering-unconventional-gene-regulation/?p162387">More information...</a></p>
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        <h4 class="bclcol1">PhD: Tracing and shaping the evolutionary paths of engineered biology</h4>
        <p><b>Primary supervisor:</b> Thomas Gorochowski (Bristol, UK)<br>
        <b>Secondary supervisors:</b> Tiffany Taylor (Bath, UK), Jordi Paps (Bristol, UK)<br>
        No biological system can avoid evolution, yet most engineered biology to date completely overlooks its impact. This project aims to address this failing by helping us better understand how design choices when implementing synthetic genetic circuits affect the routes that evolution takes once the system is deployed. To do this, the project will develop a mixture of experimental and modelling approaches to recover the evolutionary paths of an engineered population of cells and use this data to guide future circuit designs that lessen or exploit the impact of evolutionary change. The project will consist of two major parts. First, we will develop new nanopore sequencing methods that allow for the accurate reconstruction of evolutionary trajectories by sampling long-term evolutionary experiments. Then, building on this capability, we will employ experimental evolution techniques using a wide range of cells transformed with different synthetic genetic circuits. By assessing how these circuits evolve under a range of environmental conditions, we aim to elucidate principles for creating more robust genetic systems and potentially exploiting predictable patterns in evolution to engineer robustness and adaptation into our systems. This project will be supported by Professor Taylor at the University of Bath who brings a wealth of experience in experimental evolution. <a href="https://www.swbio.ac.uk/programme/projects-available/">More information...</a></p>
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        <h4 class="bclcol1">PhD: Rewiring ant communications to control behaviour using engineered bacteria</h4>
        <p><b>Primary supervisor:</b> Thomas Gorochowski (Bristol, UK)<br>
        <b>Secondary supervisors:</b> Nathalie Stroeymeyt (Bristol, UK), John Love (Exeter, UK)<br>
        Social insects such as ants make extensive use of chemical signals deposited into their environment as a means to coordinate collective colony-level behaviours that go far beyond the capabilities of each individual. This indirect communication process, known as stigmergy, has been shown to underpin the ability for ants to efficiently forage for food, build and repair complex nests, and assess the suitability of new nest sites. Over the past few decades our understanding of the biochemical composition of these signals has substantially increased. However, difficulties in producing these molecules using standard approaches with chemistry has hindered the ability to effectively study their role and function. The aim of this project is to give researchers the ability to “talk” to ants using their own chemical signals using new, synthetic biology approaches for bio-compound production. This will allow for a better understanding of the rules ants use to generate emergent collective behaviours by allowing the communications within these systems to be perturbed in precise and controllable ways. Such knowledge would not only offer new insight into how our own societies might be better organised (e.g. to reduce the spread of disease), but also offers a means to develop interventions that can disrupt the functioning of a colony as an avenue towards novel, non-destructive pest control methods. <a href="https://www.bristol.ac.uk/biology/courses/postgraduate/phdstudentships/">More information...</a></p>
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        <h4 class="bclcol1">PhD: Harnessing the power of synthetic biology to engineer novel lytic bacteriophages</h4>
        <p><b>Primary supervisor:</b> Tobias Bergmiller (Exeter, UK)<br>
        <b>Secondary supervisors:</b> Thomas Gorochowski (Bristol, UK), Ben Temperton (Exeter, UK)<br>
        The ongoing antimicrobial resistance crisis that is going to leave mankind devoid of high-efficacy drugs against bacterial infections has led to a new renaissance of bacteriophage (phage) research. Phages are viruses that predate and kill bacteria. Their narrow-range specificity towards target bacteria, including the critical multi-drug resistant ESKAPE pathogens Acinetobacter baumannii and Klebsiella pneumoniae, makes them much thought-after future therapeutics. Their exceptionally high natural abundance creates a source of new phage variants to tackle emerging bacterial pathogens and phage “building blocks” that can be used to design functionally enhanced synthetic bacteriophages. We are interested in obligatory lytic phages that have very short life cycles, small genomes, and that destroy their bacterial hosts within minutes. They are commonly self-sufficient and self-dependent and likely to be effective across a broad number of hosts. Our aim is to enhance their functionality using synthetic biology tools. Nevertheless, lytic phages are notoriously difficult to work with: genome engineering to construct synthetic phages, and technologies for “rebooting” lytic phages from their in-vitro assembled DNA genomes currently lacks sufficient speed and efficiency. While progress has been made using CRISPR-based genome engineering, phage engineering and rebooting are a serious bottle neck in the endeavour to use phage to tackle the AMR crisis, and more broadly in agriculture and the food industry. In this interdisciplinary PhD studentship, you will use a range of methods spanning molecular and bacterial genetics, synthetic biology and bioinformatics to devise new phage engineering and rebooting techniques. You will leverage the Exeter-based Citizen Phage Library (https://citizenphage.com) and create an inventory of modularised phage parts. By using a combination of CRISPR technologies and other DNA “scissors” you will develop new avenues of phage rebooting and breeding, and a suite of novel synthetic bacteriophages that target Gram-negative ESKAPE pathogens.  <a href="https://www.exeter.ac.uk/study/funding/award/?id=4933">More information...</a></p>
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        <h4 class="bclcol1">PhD: The evolution of eukaryotic gene order: following the birth, life and death of a eukaryotic gene cluster</h4>
        <p><b>Primary supervisor:</b> Hans-Wilhelm Nuetzmann (Exeter, UK)<br>
        <b>Secondary supervisors:</b> Daniel Henk (Bath, UK), Thomas Gorochowski (Bristol, UK)<br>
        How are eukaryotic genomes organised? How are they evolving? How are genes ordered along chromosomes? Does gene order matter for sustainable applications? These are the questions at the heart of this PhD project that combines experimental evolution, genomics, chromatin genetics and biotechnology to improve our fundamental understanding of eukaryotic genome evolution and to expand the design principles in synthetic biology. In this project, you will study the real-time evolution of metabolic pathway genes in yeasts. Fungi and yeast produce a vast variety of metabolites (or natural products). These complex molecules have important ecological functions in the interaction between microbes and the environment. In addition to their ecological functions, natural products are major sources of pharmaceuticals and other high-value compounds. The repertoire of natural products found in fungi and yeasts is highly diverse, each species and even strain having its own pool of molecules to cope with the demands of its environmental niche. The genes for the synthesis of large numbers of natural products are rapidly evolving and physically co-localised in so called ‘gene clusters’. But how these clusters come about and evolve so rapidly is entirely unknown. Here, we propose to follow the real-time evolution of the pulcherriminic acid gene cluster as model system to study the evolution of gene order in eukaryotes. This cluster is present in distantly related yeasts and provides host species with growth advantages under iron-limiting conditions and in competition with other microbes. Pulcherriminic acid has recently become of interest to the biotech industry as a biocontrol agent. Altogether, the proposed project will provide an interdisciplinary research experience to the student and contribute to our fundamental understanding of genome evolution. <a href="https://www.findaphd.com/phds/project/nerc-gw4-dtp-phd-studentship-for-2024-entry-the-evolution-of-eukaryotic-gene-order-following-the-birth-life-and-death-of-a-eukaryotic-gene-cluster/?p162725">More information...</a></p>
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        <h4 class="bclcol1">3-year Postdoc: A next-generation computational biodesign platform</h4>
        <p><b>Primary supervisor:</b> Thomas Gorochowski (Bristol, UK)<br>
        <b>Secondary supervisor:</b> Tom Ouldridge (Imerpial College London, UK)<br>
        More details to follow soon, but contact <a href="mailto:thomas.gorochowski@bristol.ac.uk">Dr Gorochowski</a> if you would like to learn more early. Position expected to start early 2024 with possible further 3-year extension and hope is for this role to support the development of an aligned independant fellowship. The project will also involve close collaboration across with the University of Oxford and Imperial College London. Brilliant chance to establish an academic research career in the growing field of synthetic and engineering biology.</p>
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    <h2 class="border-bottom">Postdocs</h2>
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      <h4 class="bclcol1">Bristol Vice-Chancellor's Fellowships</h4>
      <p>This scheme offers an exciting opportunity for exceptional early-career researchers to advance their research careers, setup their own group at the University of Bristol. Fellowships are available across the strategic priorities of university. <a href="https://www.bristol.ac.uk/vc-fellows/">More details...</a></p>

      <h4 class="bclcol1">EU Marie Skłodowska-Curie Fellowship</h4>
      <p>The objective of these fellowships is to support researchers’ careers and foster excellence in research. The Postdoctoral Fellowships action targets researchers holding a PhD who wish to carry out their research activities abroad, acquire new skills and develop their careers. Suitable for EU citizens that would like to work in the UK. <a href="https://marie-sklodowska-curie-actions.ec.europa.eu/actions/postdoctoral-fellowships">More details...</a></p>
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    <h2 class="border-bottom">PhD</h2>
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      <p>For students looking for PhD studentship, we recommend applying to one of the doctoral training centres based at Bristol or associated EU training networks. Any internally funded opportunities will be posted as openings above.</p>

      <h4 class="bclcol1">SynBioCDT</h4>
      <p>The EPSRC and BBSRC Synthetic Biology Centre for Doctoral Training (SynBioCDT) is a 4-year doctoral programme that offers training in the new field of Synthetic Biology, the "Engineering of Biology". This centre is a collaboration between the Universities of Oxford, Bristol and Warwick. <a href="https://www.bristol.ac.uk/vc-fellows/">More details...</a></p>
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    <h2 class="border-bottom">Other</h2>
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      <h4 class="bclcol1">DAAD RISE Worldwide</h4>
      <p>RISE stands for Research Internships in Science and Engineering. RISE Worldwide offers summer research internships across the world to German undergraduate students with academic training in biology, chemistry, physics, earth sciences, engineering, or a closely related field. RISE Worldwide is funded by the German Federal Ministry of Education and Research. <a href="https://www.daad.de/rise/en/">More details...</a></p>

      <h4 class="bclcol1">Biochemical Society Summer Studentships</h4>
      <p>The Biochemical Society offers grants for stipends of £200 per week for 6–8 weeks, and up to £1,600 in total, to support an undergraduate student to carry out a summer lab placement. The student does not need to be a member of the Society, but when ranking proposals preference will be given to student members. <a href="https://www.daad.de/rise/en/">More details...</a></p>
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