Biological Sciences (PhD / MPhil) - 2013/2014 entry

As a PhD student in the Department of Biological Sciences, you will become part of a rich research environment at Birkbeck and University College London. The department is part of a multidisciplinary centre for world-class research, the Institute of Structural and Molecular Biology (ISMB), which seeks to integrate techniques from the chemical and physical sciences to provide insight into the molecular basis of biological processes. 85% of our research was recognised as having international impact in the 2008 Research Assessment Exercise, with 15% receiving the highest possible rating of world‐leading.

Our academic staff have many years' experience in teaching both part-time and full-time research students, and offer internationally recognised expertise in the following key areas of research:

• structural biology
• microbiology
• computational biology 
• chemical biology
• cell biology
• biophysics
• biology (organismal).

We also co-supervise PhD students based at the nearby Institute for Hepatology.

We have state-of-the-art laboratories equipped for protein crystallography, cryo-electron microscopy and tomography, confocal microscopy, biophysics, spectroscopy, molecular biology, synthetic and analytical chemistry and microbiology. We have excellent computing facilities and infrastructure, including two large clusters supported by three full-time computer management staff. Through the ISMB staff, students are able to access a still wider range of equipment on the UCL campus, including protein nanoelectrospray, mass spectrometry and protein NMR. Further information about departmental resources, and resources at the ISMB, are available on the departmental web pages.

How will I be taught?

Studying for a PhD will provide you with opportunities to make your own research discoveries within the research-intensive environment of the ISMB. You will receive guidance from your project supervisor, from the PhD Graduate Committee, and from other members of the academic staff as you carry out your research and your progress is assessed.

We provide a wide range of courses catering specifically for the training needs of research students. This training includes a formal programme of lectures on graduate studies (Science in the Real World), transferable skills, and modern techniques.

We run lecture courses which are especially relevant to PhD students in particular research areas (including a series on the Principles and Practice of Structural Biology and an advanced lecture series). PhD students are also encouraged to attend any appropriate lectures from our departmental MSc programmes and distance learning courses, subject to approval by their supervisor. Depending on your chosen supervisor and research project you may have the opportunity to attend and contribute to research laboratory group meetings, or to attend external conferences.

Activities that will further enhance your scientific experience include: a biennial retreat; a biennial symposium; an annual graduate symposium; weekly ‘Friday Wrap’ meetings where postdocs and senior PhD students present their latest work; and a series of joint ISMB seminars that take place throughout term-time. There are other seminar opportunities in the numerous surrounding research institutes.

ISMB Joint PhD Programmes

Students on the ISMB joint PhD programmes attend courses during their first year, which provide the opportunity for them to broaden theoretical and practical knowledge in structural, computational and chemical biology. They also carry out interdisciplinary laboratory rotations in structural, computational and chemical biology, and gain expertise of research in participating departments outside Birkbeck.

PhD students are assessed throughout their studies and are required to meet specific assessment milestones which include: written reports, oral and poster presentations, essays and vivas. The assessment process ensures that you will have the opportunity to develop your eventual thesis, and that guidance and improvement can be provided to you throughout your studies. Further details of PhD assessment procedures are available on the departmental website.

What can I go on to do?

PhD/MPhil research degrees open up rich and varied career opportunities. Our graduates have found posts in industry and the public sector, and are on the academic staffs of major universities throughout the world.

The rigorous nature of research degree training also provides valuable skills that will enhance your career possibilities outside academia, including careers in science publishing, business, research management and teaching.

Structural biology

• Dr Tracey Barrett, BSc, DPhil: Protein crystallography; eukaryotic and bacterial DNA repair mechanisms; eukaryotic homologous recombination targets; NK-kB signalling.
• Dr Ajit K Basak, BSc, MSc, PhD: Protein crystallography; structure and functions of bacterial proteins with special interest in toxins, pore-forming toxins and regulatory proteins (from gram +ve and gram –ve bacterial system), yeast proteins.
• Dr John Christodoulou, BSc, PhD: Structural biology of protein folding and misfolding on the ribosome; NMR spectroscopy.
• Dr Bibek Gooptu, BSc, PhD, MB BChir, MRCP: Molecular mechanisms of disease; conformational disorders; serpin polymerisation.
• Professor Nicholas Keep, BA, MA, PhD: Protein crystallography; proteins implicated in muscular dystrophy; bacterial resuscitation, particularly Tuberculosis.
• Professor Neil Q McDonald, BSc, PhD: Molecular mechanisms controlling growth factor-mediated signalling pathways.
• Dr Carolyn A Moores, BA, PhD: Structure and function of the cytoskeleton; electron microscopy.
• Professor David S Moss, BSc, PhD:  Bacterial toxins; immunoinformatics; computational biology.
• Professor Elena Orlova, BSc, MRes, PhD: Structural electron microscopy; portal proteins; ion channels; proteins involved in control of chromosomal replication.
• Dr Jim E Pitts, BSc, PhD: Protein engineering of the proteins involved in the bacterial biphenyl pathway.
• Professor Helen R Saibil, BSc, PhD, FMedSci, FRS: Molecular chaperones and protein folding; protein misfolding in amyloid fibrils; membrane pore-forming proteins.
• Dr Renos Savva, BSc, PhD: Virus–host interactions: protein–protein and protein–nucleic acid. Recombinant methods development and structural molecular biology.
• Professor Christine Slingsby, BSc, DPhil: Eye lens, cataract and stress proteins.
• Dr Konstantinos Thalassinos, BSc, MRes, PhD: Biological mass spectrometry; ion mobility mass spectrometry; protein folding; mass spectrometry-based proteomics; proteomics software development.
• Dr Cara Vaughan, PhD: Structural Biology of Hsp90 and its co-chaperones; Hsp90 role in kinetochore assembly; protein crystallography and single particle electron microscopy.
• Professor Gabriel Waksman, PhD, FMedSci, FRS: structural and functional biology of bacterial secretion systems.
• Professor Bonnie A Wallace, BS, MPhil, PhD, DSc: Membrane proteins; protein crystallography; circular dichroism spectroscopy and bioinformatics.

Microbiology

• Dr Sanjib Bhakta, BSc, MSc, PhD, DPhil: Characterising structure, function, inhibition and regulation of key enzymes in cell wall biosynthetic pathways to identify novel therapeutic targets in mycobacteria; understanding molecular mechanisms of persistence and drug resistance in M. tuberculosis; developing high throughput models for evaluating antimycobacterials.
• Dr Richard D Hayward, BSc, PhD:  Bacterial pathogenesis; cellular microbiology; protein secretion systems; chlamydia; infertility.
• Professor Nicholas Keep, BA, MA, PhD: Protein crystallography; proteins implicated in muscular dystrophy; bacterial resuscitation, particularly Tuberculosis.
• Dr Philip Lowden, BA, PhD: Chemistry, genetics and enzymology of natural product biosynthesis in bacteria and fungi; medicinal chemistry of Huntington's Disease; chemical studies of post-translational protein modifications.
• Dr Jane L Nicklin, BSc, PhD: Biochemical activities of fungi, including natural products with biomedical applications, biological control of plant pests, weeds and diseases.
• Dr Andrew Osborne, BSc, PhD: The molecular mechanism of protein export by the malaria parasite.
• Dr Renos Savva, BSc, PhD: Virus–host interactions: protein–protein and protein–nucleic acid; recombinant methods development and structural molecular biology.
• Professor Gabriel Waksman, PhD, FMedSci, FRS: structural and functional biology of bacterial secretion systems.

Computational Biology

• Dr Paul M King, BA, DPhil: Computer simulation; computer-aided drug design.
• Professor David S Moss, BSc, PhD:  Bacterial toxins; immunoinformatics; computational biology.
• Dr Irilenia Nobeli, BSc, MSc, PhD: Bioinformatics, chemoinformatics and molecular simulations applied to molecular recognition, metabolome analysis, inhibitor discovery and protein function, non-coding RNA.
• Dr Adrian Shepherd, BA, MSc, PhD: Immunoinformatics (wirus-host interactions, immune responses to protein theraputics); biomedical text mining.
• Dr Alona Sosinsky, MSc, PhD: Annotation of eukaryotyc genomes; discovery of regulatory regions and regulatory mechanisms for eukaryotic genes; understanding determinants of specificity in protein-DNA recognition.
• Dr Katherine C Thompson, MA, DPhil: Spectroscopy, kinetics and computational biological chemistry.
• Dr Maya Topf, BSc, MSc, DPhil: Structure and function characterisation of macromolecular assemblies by a combination of experimental data, bioinformatics and modelling techniques.
• Professor Bonnie A Wallace, BS, MPhil, PhD, DSc: Membrane proteins; protein crystallography; circular dichroism spectroscopy and bioinformatics.
• Dr Mark A Williams, BSc, PhD: Molecular simulation approaches to biomolecular thermodynamics; empirical structure-thermodynamic relationships; structure-based inhibitor design.

Chemical Biology

• Dr Sanjib Bhakta, BSc, MSc, PhD, DPhil: Characterising structure, function, inhibition and regulation of key enzymes in cell wall biosynthetic pathways to identify novel therapeutic targets in mycobacteria; understanding molecular mechanisms of persistence and drug resistance inM. tuberculosis; developing high throughput models for evaluating antimycobacterials.
• Dr Paul M King, BA, DPhil: Computer simulation; computer-aided drug design.
• Dr Philip Lowden, BA, PhD: Chemistry, genetics and enzymology of natural product biosynthesis in bacteria and fungi; medicinal chemistry of Huntington's Disease; chemical studies of post-translational protein modifications.
• Professor Neil Q McDonald, BSc, PhD: Growth factor-mediated signalling pathways and interstrand crosslink repair.
• Dr Marianne Odlyha, BA, BSc, MSc, PhD: Environmental research for assessment of indoor conditions surrounding cultural materials and damage assessment of (macro to nanoscale) biomaterials.
• Dr Jonathan M Slater, BSc, PhD, CChem, MRSC: Electrochemistry, including sensors and sensor arrays; microfabrication and capillary electrophoresis.
• Dr Katherine C Thompson, MA, DPhil: Spectroscopy, kinetics and computational biological chemistry.
• Dr Salvador Tomas, BSc, PhD: Study of intermolecular interactions and applications towards molecular nano-engineering; molecular phenomena at lipid bilayers and implications in cellular regulation.

Cell Biology

• Dr Emmanuel Boucrot, BSc, PhD: Dissecting molecular mechanisms of intracellular membrane trafficking during cell regeneration, cell migration and bacterial infection and understanding their perturbations during ageing and some cancers.
• Dr Richard D Hayward, BSc, PhD:  Bacterial pathogenesis; cellular microbiology; protein secretion systems; chlamydia; infertility.
• Dr Andrew Osborne, BSc, PhD: The molecular mechanism of protein export by the malaria parasite.
• Dr Richard C Rayne, BSc, PhD: Physiology of insects: neurobiology (peptidergic signalling) and immunology (cell-mediated defences).
• Professor Helen R Saibil, BSc, PhD, FMedSci, FRS: Molecular chaperones and protein folding; protein misfolding in amyloid fibrils; membrane pore-forming proteins.

• Dr Tracey Barrett, BSc, DPhil: Protein crystallography; eukaryotic and bacterial DNA repair mechanisms; eukaryotic homologous recombination targets; NK-kB signalling.
• Dr Ajit K Basak, BSc, MSc, PhD: Structure and function studies of bacterial toxins and their different complexes.
• Dr Carolyn A Moores, BA, PhD: Structure and function of the cytoskeleton; electron microscopy.
• Dr Marianne Odlyha, BA, BSc, MSc, PhD: Environmental research for assessment of indoor conditions surrounding cultural materials and damage assessment of (macro to nanoscale) biomaterials.
• Professor Elena Orlova, BSc, MRes, PhD: Structural electron microscopy; portal proteins; ion channels; proteins involved in control of chromosomal replication.
• Dr Konstantinos Thalassinos, BSc, MRes, PhD: Biological mass spectrometry; ion mobility mass spectrometry; protein folding; mass spectrometry-based proteomics; proteomics software development.
• Dr Salvador Tomas, BSc, PhD: Study of intermolecular interactions and applications towards molecular nano-engineering; molecular phenomena at lipid bilayers and implications in cellular regulation.
• Dr Mark A Williams, BSc, PhD: Thermodynamics of protein complex formation; protein design and engineering; protein NMR; structure-based inhibitor design; structural biology of anti-microbial targets.

Biology (Organismal)

• Dr Glenn K Baggott, BSc, PhD: Avian embryonic physiology; water economy of, and ion movements within, the egg; natural incubation; microbial modification and penetration of the egg shell.
• Dr Bibek Gooptu, BSc, PhD, MB BChir, MRCP: Molecular mechanisms of disease; conformational disorders; serpin polymerisation.
• Dr David C Havill, BSc, PhD: Ecophysiological studies on potential effects of climate change on plant distribution and physiological processes; ecophysiology of salt marsh plants.
• Dr Martin J Ingrouille, BSc, PhD: Evolution of plants; taxonomy of complex plant groups; molecular systematics; speciation; breeding systems; population and geographical patterns of variation. All research is carried out in collaboration with colleagues at the Royal Botanic Gardens, Kew.
• Dr Jane L Nicklin, BSc, PhD: Biochemical activities of fungi, including natural products with biomedical applications, biological control of plant pests, weeds and diseases.
• Dr Richard C Rayne, BSc, PhD: Physiology of insects: neurobiology (peptidergic signalling) and immunology (cell-mediated defences).

• If you have secured your own PhD funding, you can apply at any time during the year. PhD students usually begin their studies at the beginning of the academic year (October), but with special permission you may commence at the beginning of the spring term.
• Applications for the interdisciplinary Institute of Structural and Molecular Biology (ISMB) PhD studentships must be received by the deadlines specified each year (see the ISMB website for more information).
• The closing dates for any additional PhD studentships available will be stated along with the details advertised.