Group

Previous members

Post docs

Antonio Cavallo was a Wellcome Trust funded post doc working on an automated database of single amino acid polymorphisms and their structural effects. (2002-4)

Jacob Hurst took over the SAAP project (2005-2006) and worked on the antibody database (2006-2009)

Craig Porter worked on the SAAP project for 6 months (2006) and rejoined the group in March 2008 to work on enhancements to ProFit. (2008-2009)

Dave Gregory worked on a voluntary part-time basis to tidy up various code in the group and ensure that our databases and servers can be updated and maintained easily. (2010)

Walter Eaves worked on the Abysis database for 4 months (2013)

PhD rotation students

Luke Goodsell worked on modelling of antibodies (Autumn 2008)

Irene Farabella worked on prediction of metal binding sites at protein interfaces (Autumn 2008)

Chris Fu worked on modelling the mTOR protein (Spring 2010)

Stuart Tetchner was a Wellcome Trust rotation student jointly supervised by Steve Perkins working on predicting zinc binding sites in complement proteins (Autumn 2011)

Heledd Davies was a Wellcome Trust rotation student working on conformational changes in antibodies on forming a complex with an antigen (2012)

PhD students

Helen Fooks was a Ph.D. student co-supervised by me and Gail Hutchinson. She was working on pairing preferences in parallel beta-sheets with a view to developing potentials for modelling and threading. (1999-2003)

Gabby Reeves was a Ph.D. student at UCL co-supervised by me and Christine Orengo at UCL. She was working on the CATH database and its application to comparative modelling. (1999-2003)

Alison Cuff was a Ph.D. student working on the p53 database and automated analysis of mutations. (2000-2003)

Martin Blythe was a Ph.D. student based at the Jenner Institute working with Darren Flower and me on prediction of linear B-cell epitopes from primary sequence of protein antigens. He was co-supervised by me while I was at Reading, but was then supervised by Gail Hutchinson (2002-2003)

Danielle Talbot improving alignment for comparative modelling (2001-2006) [Thesis]

Sri Vishnu Vardhan Deevi automated annotation of proteins in the MEP pathway and those targetted to the apicoplast. (2003-2008) He is now working at the Sanger Centre. [Thesis]

Abhinandan Raghavan analysis of antibody sequence and structure. (2004-2008) He has now taken a Presidential Fellowship at Novartis. [Thesis]

Lisa McMillan prediction of the effects of mutations at a local structual level and extrapolating to predict whether a mutation will be disease-causing. (2005-2009) Now working at the Department of Computer Science, University of Glasgow. [Thesis as submitted]

Irena Sani was working on interactions of RNA (2008-2010)

Anja Baresic is examining the structural effects of mutations in 'compensated pathogenic deviations' and developing methods to prediction residues involved in protein-protein interactions and therefore sensitive to mutations. (2007-2011) [Thesis]

Undergraduate project students

Abigail Collis was a Nuffield Summer Student Bursary holder working on analysing the amino acid distribution in antibody combining sites. (Summer 2000)

Lee Allcorn was an undergraduate project student working on an automatically updated web page of information about antibody structures. (2000-2001)

Adam Brouwer was an undergraduate project student working on analysis of CDR lengths in antibodies. (2000-2001)

Paul Carrodus was an undergraduate project student working on analysis of the p53 data. (2001-2002)

Adam Gregory was an undergraduate project student working on prediction of antigen type from antibody sequence data. (2001-2002)

James Shimmen was an undergraduate project student working on prediction of antigen type from antibody sequence data. (2002-2003)

Gemma Yarham was an undergraduate project student working on analysis of patents in antibody humanization. (2002-2003)

Elliot Brown was an undergraduate project student working with Gail Hutchinson and me on analysis of the SARS genome. (2003-4)

Ken Cheung Analysis of repeated sequences in proteins (2004-5)

Sang Tae Kim Analysis of mutations in OTC (2004-5)

Kenric Leung Looking at mutations in Protein C (2005-6)

Hubert Rogers Looking at compensated mutations (2006-7)

Chok SingWei Analysis of mutant proteins (2006-7)

Michael Eckett Humanness of antibody sequences using IMGT data (2007-8)

Nick Sicard-Askey Glycosylation sites in antibodies (2007-8)

Ashley Brownlow was looking at antibody humanization patents. (2009)

Oliver Huish has been comparing early and late response antibodies using Abysis. (2009)

Alex Stones was looking at the TGN1412 drug trail. (2009/10)

Jamie Gregory did a literature project looking at alternative scaffold for creating drugs. (2010/11)

Ross Kruger examined variation in packing quality in protein structures to investigate whether there is any link with function, or evolution.

Joseph Replogle is looking at clustering of mutations in protein structures (2011-2012)

Tarit Puvanuttrai is working on GroEL-dependent proteins (2011-2012)

Catherine Orr and Jennifer Dhingra are doing literature projects on the TGN1412 drug trial (2011-2012)

Oliver King performed a literature review on Effects of mutation on protein structure and function (2012/13)

Rashmi Rajasabhai looked at occurrence of indirect repeated amino acid motifs (2012/13)

Daniel Usvyat looked at the performance of transcription factor binding site prediction programs (2012/13)

Jake Chambers performed a literature review of alternative scaffolds (2012/13)

MSc/MRes project students

Luke Kontogiannis was an M.Res. student from York who developed an automated web site summarizing information on serine protease enzyme structures. (2003)

James Allen Analysis of sequence fragments which distinguish human and mouse antibodies (2005)

Adebola Fakoredi Analysis of mutations in phenylalanine hydroxylase. (2006)

Birunthini Yogashangary Antibody sequence database. (2004-6)

Ayodele Babatunde Antibody sequence database. (2004-6)

Kerry White was an M.Res. student from York who worked on an improved method for automatic application of antibody numbering schemes (2007).

Stephen Clayton was an M.Res. student from York who developed a facility for the SAAPdb project to allow users to add their own mutations and examined void sizes (2007).

Brian Kelly was an M.Sc. student from Birkbeck analyzing correlations between CDR-H3 in antibodies and the type of antigen (2007).

Amina Satour is an M.Res. student from Birkbeck who is developing methods to predict destabilizing void-causing mutations (2007).

Nouf Alnumair was an M.Sc. student from Birkbeck working looking at mutation data in SAAPdb where there are multiple structures available (2009).

Liaqat Latif was an M.Sc. student from Birkbeck who is updating and automating our analysis of antibody canonical classes (2007-8).

Katerina Blaveri was an M.Sc. student from Birkbeck who is updating our analysis of humanization patents and implementing a server. (2008-9).

Peter Halls was a Birkbeck MSc student evaluating the performance of out mutmodel program for sidechain replacement. (2010)

Minu Bhatt was a Birkbeck MSc student looking at analysis and prediction of ubiquitination sites. (2010)

Palab Bhowmick was a Birkbeck MSc student looking at preferred pairing of mouse antibody germline sequences using Abysis. (2010)

Adam Denyer was a Birkbeck MSc student looking at predicting ubiquitination sites from sequence. (2011)

Kajendiran Mahendiran was a Birkbeck MSc student looking at predicting ubiquitination sites from structure. (2011)

Narayan Jayaram was a part-time Birkbeck MSc student looking at preferred pairing of human antibody germline sequences using Abysis. (2009-2011)

Nick Tu was working on analysis of luciferase structure with a view to modifying its specificity (2011-12)

Anna Pham was working on conformational changes in antibodies on forming a complex with an antigen (2012)

Visitors

Veronica Lam and Colin Kwok were visitors from Hong Kong University working on the database of G6PD mutations. (Summer 2000)

Filippo Ledda was a visiting Ph.D. student from the group of Giuliano Armano at the University of Cagliari. He is working on the prediction of misalignments and improvement of alignment for protein modelling. (May 2010)

Pawan Shree Poudel was a summer intern building a new web server to run our analysis tools on the effects of mutations, providing both a visual web site and RESTful web services. (Summer 2011)

Interns

Carles Monterrubio was a summer intern assessing the performance of a new antibody numbering program.

Other

James Allen worked on a temporary student basis for 10 weeks to help with the SAAP database (2005)

Oliver Huish worked on a temporary student basis for 2 months developing our G-score for antibody humanness and analyzing Macaque antibody sequences (2009)