February 2014: We have published a couple of studies into protein solubility and aggregation, both computational, one dealing largely with protein solubility in over-expression and one with protein solubility subsequent to expression:
Soluble expression of proteins correlates with a lack of positively-charged surface.
Lysine and arginine content of proteins: computational analysis suggests a new tool for solubility design.
Both of these publications are open access, the first through BBSRC support of Pedro Chan's PhD, and the second owing to the contribution of Spyros Charonis, undertaking an EPSRC-funded PhD via a Doctoral Training Centre at UCL. This is hopefully just a start in the area of linked computational and experimental protein solubility studies, that several members in the Curtis, Warwicker, and other collaborating academic and industrial groups, are pursuing.
February 2014: Our PhD students continue to benefit from the various interleaved schemes that their studentships involve. Thus, Rose Keeling is currently on an extended visit to our Industrial collaborator, MedImmune, Cambridge, in the formulation group, with Shahid Uddin and Malgorzata Tracka. Spyros Charonis has a training course, delivered by the UCL hub of the CDT scheduled for later in February.
January 2014: Ivan Sazanavets has left the lab for 'omics data processing employment. We are preparing work for publication based on Ivan's PhD. Stefan Ivanov enjoyed (so we are led to believe) the CCPBioSim multiscale modelling conference in Manchester (well next door to us at the MIB really, we're cheap).
December 2013: Spyros attended the 10th Annual BioProcess UK conference in London. The 2014 version is due to be in LIverpool.
November 2013: We currently have two specific PhD projects being advertised under separate University of Manchester schemes. The A*STAR project is joint with with Frank and Birgit Eisenhaber at BII, Singapore. The Manchester project is joint between our School of Life Sciences group and those of Sam De Visser (Chemical Engineering) and Chris Blanford (Materials Science). Three different Schools, but actually our offices are next to eachother in the MIB! Deadline for the DTP project is 6 December. More information from the FLS PhD study web pages or from me.
November 2013: Spyros Charonis attended a couple of events outside of Manchester recently, a training meeting at the UCL hub of the EPSRC CDT that funds the PhD, and a Biotechnology YES workshop at BioCity Scotland. Rose Keeling has been part of a BBSRC/BRIC Skills School at Eden Biodesign.
September 2013: Well, that's something of a gap. Our group along with that of Robin Curtis, has been preparing work for submission/publication in a key area for us, protein solubility and aggregation. In the meantime several collaborations (with the groups of Steve High and David Leys) in other areas have been published:
With the changeover of academic years, we have said goodbye to undergraduate project students, Nurul Borhan, Andrej Gnip and Esther Fagnano. We have also said goodbye to Dorota Roberts, moving on from a joint BBSRC project with the groups of Robin Curtis and Jeremy Derrick. We welcome incoming PhD students Stefav Ivanov and Max Hebditch, both in collaborations, Stefan in the area of specific protein-protein interactions and Max generally in non-specific protein-protein interactions.
January 2013: We received the news of Andrew Grant's passing away over the holiday period. Andrew, who worked at AstraZeneca, Alderley Park, was a very good friend to the group over the years, and was (current PhD student) Ivan Sazanavets co-supervisor. We will miss him very much, for his science and for his personality and friendship. Andrew's long time collaborator, Anthony Nicholls of OpenEye software has written an appreciation. Andrew was External Examiner for Salim Bougouffa's PhD; Salim writes, "I knew he was a really nice man from the genuine smile he had throughout the viva". That's not usual Examiner behaviour!
December 2012: December graduation was fun again, with the MSc Bioinformatics and Systems Biology class graduating, and often a PhD student well known to our group. This December Andrew Cawley graduated, himself a graduate of the Bioinformatics MSc, some years ago.
November 2012: We currently (deadline early December 2012) have two specific PhD projects being advertised under separate University of Manchester schemes (one joint with with Chandra Verma at BII, Singapore). More information from the FLS PhD study web pages or, of course, from me.
October 2012: We have two undergraduate project students for the coming year. Andrej Gnip wiill be looking at potassium channel bioinformatics, in the mould of Binbin Liu's paper but more widely in the superfamily. Nurul Borhan will be helping us to test our solubility prediction software, with computational work translated to testing in Alan Dickson's lab, working with PhD student Alejandro Carballo.
October 2012: Spyros Charonis has submitted his Masters thesis and commenced a PhD with Robin Curtis and Jim Warwicker, on computational modelling of protein solubility. This PhD is funded by EPSRC and is part of a UCL centre in emerging macromolecular therapies.
October 2012: Two PhD students from Professor Srinivasan's group in Bangalore have arrived for a 2 month visit to our group (Raksha) and those of Simon Lovell and David Robertson (Sudha). This almost closes out the UKIERI funded exchanges that have been so useful over the last 4 years.
October 2012: Jim has finished enjoyable stints as External Examiner for Masters degrees in Applied Bioinformatics at Cranfield, and in Molecular Biophysics at KCL. Thanks to Mark Sanderson, Roberto Steiner and Brian Sutton for hosting me at KCL. I've seen this next door neighbour spring up in the last few years.
September 2012: Another year of our MSc in Bioinformatics and Systems Biology has passed, fun as usual, with 4 of our students undertaking summer projects in the Cambridge area (EBI and Sanger). In other project work, my group had the pleasure of working with Muxin Gu (now a PhD student in Catherine Millar's group), and Madikay Senghore.
September 2012: Andrew Cawley's article on protein-mRNA interactions, with a genomic perspective, is out in NAR. We managed to get "polyelectrostatic" in the title!
July 2012: Andrew Cawley's PhD viva (successful) coincided with Pedro Chan's graduation day (enjoyable).
May 2012: Jim attended the Prague Protein Spring meeting, an excellent few days of 'protein discussions'.
April 2012: Jim spoke at the 5th Annual Proteins Congress in London, presenting our work on protein solubility prediction.
March 2012: A contigent from Manchester attended and presented at the Spring BBSRC/BRIC dissemination meeting in Leeds.
February 2012: It was a pleasure to host Nagasuma Chandra's visit through Manchester, part of our UKIERI exchange programme.
January 2012: Rose Keeling is spending some months at MedImmune, Cambridge (the Industrial partner for Rose's project in the BBSRC/BRIC scheme), learning the ropes in their Formulation group.
November 2011: A BBSRC/BRIC funded project to Robin Curtis, Jeremy Derrick, Alan Dickson and JW, "Understanding and predicting aggregation in biopharmaceuticals", is just starting.
October 2011: A BBSRC/BRIC funded PhD student, Rose Keeling, is commencing a industrial-linked project, supervised at the Manchester end by JW and Robin Curtis.
September 2011: Allied to the efforts of the (not necessarily only protein) pKa coop, various of the groups involved are now publishing their results of predictions of pKas in SNase mutants (Bertrand Garcia Moreno group). Our own is here, and there is also a 'combo' article.
July 2011: Pedro Chan has been PhD viva-ed, assessed for minor corrections, and subsequently approved. Congratulations!
July 2011: Andrew Cawley and Ivana Sazanavets attended the Vienna ISMB meeting, with many Manchester colleagues and also with members of the partner groups on our UKIERI funded award for joint work in the area of protein complexes.
June 2011: Joint work with Pawel Leznicki and Steve High implies a perhaps surprising ability of tail anchor segments to drag PEGylated chains partially into a membrane.
June 2011: As part of our move to add protein solubility prediction to the various charge-related algorithms that we have helped develop, Jim spoke at Informa Life Sciences conference on Non-Antibody Protein Production, in Berlin.
April 2011: Jim Warwicker has able to put faces to names for many colleagues in the 'protein electrostatics and pKa prediction' field after a meeting organised by Emil Alexov at Clemson University.
January 2011: Alejandro (Alex) Carballo has joined us as a PhD student, jointly with Alan Dickson's group, helping us to look at structural bioinformatics and protein solubility, testing predictions.
December 2010: The December Graduation ceremony is always a good time, with our MSc Bioinformatics 2009/10 class, and PhD students. This year Salim Bougouffa and Tracey Bray received their PhDs.
October 2010: Tracey Bray's PhD viva came in at a hefty 5 hours, but the Examiners's recommendation went the other way - no corrections!
October 2010: Collaborative work on eIF4E / 4E-BP appears in this paper from John McCarthy's group.
September 2010: Welcome to the new MSc Bioinformatics group, the last under that course name, from 2011 the course reflects the changing landscape: MSc Bioinformatics and Systems Biology.
August 2010: All change for the group, as Tracey Bray puts the finishing touches to her PhD thesis, Mitra and Harish complete their studies, and Pedro Chan is also writing up his PhD. And we move from the Michael Smith building to the Manchester Interdisciplinary Biocentre, 71 to 16 on this map.
July 2010: The lab hosted a 1 month placement for local student Lucy Hall, funded by the Nuffield Foundation Science Bursaries.
June 2010: Jim Warwicker enjoyed a visit to Graham Kemp's group at Chalmers University in Gothenburg, for a Licentiate review.
May 2010: MSc Bioinformatics students Mitra Kabir and Harish Prabhaharan will be joining the the lab for their long (summer) projects.
April 2010: Tracey Bray and Jim Warwicker attended a meeting at King's College, London on Biological Interfaces, organised by the Thomas Young Centre. An excellent day and a half of talks and discussions.
April 2010: Pedro Chan's attendance at RECOMB-2010 has been disrupted by the volcanic ash cloud. This organisers have rescheduled this conference for August 2010..
April 2010: Ivan Sazanavets will be joining us in Autumn 2010, to take up the CASE PhD studentship (with Andrew Grant of AstraZeneca). Rather than coming to the Michael Smith building, Ivan will be joining us in our new environment, the MIB, following a planned Summer 2010 move.
March 2010: An application for WT VIP funding has been awarded, allowing Pedro to work over the summer on the bioinformatics of specificity in the recognition of transmembrane helices, in collaboration with the labs of Steve High and Blanche Schwappach.
March 2010: Jim took part in Andrey Karshikoff's Graduate student course, at the Karolinska Institute in Stockholm. Andrey hosted impeccably, and included a free tour of his snow-induced roof collapse.
February-April 2010: MSc Bioinformatics students, Dave Lee and Mike Nelson were welcomed in our lab, for their short projects. Dave has been comparing DNA-protein and protein-protein interactions, and Mike studying complementarity and hetero-oligomerisation in a family mitochondrial chaperones, in collaboration with Hui Lu.
November 2009: Tracey Bray's paper comparing site prediction tools is published. Here is our SitesIdentify tool.
October 2009: Pedro Chan's paper on protein adaptation to subcellular pH is published in BMC Biol. Pedro also has a nice colour PDB by conservation tool, currently under test.
James Kitchen's PhD is now finished and hard-bound, sitting in the lab as a shining example ...
September 2009: Both James Kitchen and Salim Bougouffa have been PhD viva-ed
September 2009: Jim attended Andrey Karshikoff's 2009 "Sofia Protein Science Workshop", a 'charged' event, with such luminaries as Andrey himself, Bertrand Garcia-Moreno and Emil Alexov.
July 2009: Tracey Bray attended the 2009 ISMB and 3DSIG meetings in Stockholm.
June 2009: A CASE PhD studentship is available in our laboratory, joint with Andrew Grant at the Alderley Park site of AstraZeneca. More details are available.
June 2009: James Kitchen and Salim Bougouffa have submitted their PhD theses for examination. James is now in Robin Allaby's group at Warwick HRI.
May 2009: Nidhi and Swapna are giving talks to the Manchester Bioinformaticians today (Thurs 21). We eagerly await the talks and the cake, made by Tracey Bray. Do we dare eat it?
March 2009: PhD students Ms Seshadri Swapna and Ms Nidhi Tyagi start a 2 month visit to the Warwicker and Lovell laboratories in Manchester, from Professor Srinivasan's group, and funded by UKIERI.
March 2009: James Kitchen visits Professor Srinivasan's Lab at the Indian Institute of Science, Bangalore, funded by a 3 year award from UKIERI.
March 2009: Publication of Tracey Bray's first paper, in J Mol Biol:
Sequence and Structural Features of Enzymes and their Active Sites by EC Class. PubMed
March 2009: Publication of work with Richard Greaves on possible stabilising sugar binding sites in extremophile proteins:
Stability and solubility of proteins from extremophiles. PubMed
October 2008: Andrew Cawley starts his PhD in the group, combining the work of writing up PhD students James Kitchen and Salim Bougouffa.
October 2008: Publication of Salim Bougouffa's first paper, in BMC Bioinformatics:
Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces. PubMed
March 2008: Publication of James Kitchen's first paper, in BMC Structural Biology:
Charge environments around phosphorylation sites in proteins. PubMed