www.bioinf.org.uk

Previous group members

Post docs and contractors
  • 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)
  • Matt Couch rewrote the abYsis interface. (2013-2014)
  • Annabel Cook did various analysis on the abYsis project. (2013-2015)
  • Avneet Saini was a visiting post doc performing computational analyses of tubulin binding peptides (2014-2015)
  • The Research Software Development Team at UCL are acting in lieu of a post doc on development of abYsis (2014-2015)
  • Nouf Alnumair continued work on a phenotype predictor for functional evaluation of beta-myosin heavy chain missense variants and distinguishing between HCM and DCM associated mutations. She was also extending work of an undergraduate project student to look at the use of protein models rather than structures in the analysis of the effects of mutations. (2014-2015)
  • Ian Carruthers worked on abYsis and abYmod. (2015-2016)
  • Rob Miller worked on abYsis. (2016)
  • Mark Dibley worked on processing antibody sequences from nextgen sequencing using Mixcr (2016-2017)
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)
  • Tom Peskett was a Wellcome Trust rotation student working on protein modelling (2013)
  • Grace Jeremy was a Wellcome Trust rotation student working on regulation of moonlighting proteins (2015).
  • Alina Chrzastek was a Wellcome Trust rotation student working on analysis of the disulphide bridge between light and heavy chains of antibodies (2019).
  • James Sweet-Jones LIDo rotation PhD student working on an antibody triage pipeline (2020-2021)
  • Chris Dulson Wellcome Trust rotation PhD student working on greating a summary of TCR crystal structures (2021)
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)
  • 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.
  • Abhinandan Raghavan analysis of antibody sequence and structure. (2004-2008) He then took up a Presidential Fellowship at Novartis.
  • Lisa McMillan worked on prediction of the effects of mutations at a local structual level and extrapolating to predict whether a mutation will be disease-causing. (2005-2009)
  • Irena Sani was working on interactions of RNA (2008-2010)
  • Anja Baresic was 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)
  • Nouf Alnumair worked on building a prediction server (SAAPpred) based on our SAAPdap analysis of the structural effects of mutations. She also extended that to predict detailed phenotype information. (2010-2014)
  • Francesco Carbone was a UCL IMPACT studend sponsored by the Foundation for Innovative New Diagnostics working on mutations in G6PD. (2012-2016)
  • Tom Northey was a BBSRC CASE student sponsored by UCB, working on antibody stability and prediction of B-cell epitopes - particularly those that may occur on antibodies. (2012-2016)
  • Narayan Jayaram was a UCL IMPACT student working on looking at the effects of mutations at the DNA level (i.e. effects on splice sites and transcription factor binding sites) and integrating this into SAAPdb. (2011-2016)
  • Kirsty Wood was a visiting PhD student looking at amyloidogenic antibody sequences. (2016-2017)
  • Saba Ferdous was a UCL-ORS student working on the nature of antibody-antigen interactions with a view to developing peptide vaccines. (2013-2016)
  • Sam Ireland was a Wellcome Trust student working on the characterization and prediction of zinc binding sites. (2017-2021)
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 looked at clustering of mutations in protein structures (2011-2012)
  • Tarit Puvanuttrai worked on GroEL-dependent proteins (2011-2012)
  • Catherine Orr did a literature project on the TGN1412 drug trial (2011-2012)
  • Jennifer Dhingra did a literature project 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)
  • Charles Dunn worked on analysis of HumsaVar data using our SAAPdap and SAAPpred pipeline (2013/14)
  • James Coughtrey worked on analysis of potential glycosylation sites in antibodies (2013/14)
  • Zachary Wilson was a Pomona student who looked at the performance of our SAAPdap/SAAPpred method on modelled structures rather than crystal structures of proteins (2014).
  • Daniel James was comparing the performance of Shirai's H3 rules for CDR-H3 conformation prediction with a simple sequence-identity approach. (2014)
  • Jonathan Ekwonna was doing a literature survey on methods for antigenicity prediction. (2014)
  • Abbie Rogan did a literature project on antibody modelling methods. (2015)
  • Ernie Zheng re-evaluated our 'contact definition' of antibody loops. (2015)
  • Qian Ding did a literature project on antibody humanization. (2015)
  • Tanner Byer was a Pomona student working on automating our structural classification of antibody CDRs. (2015)
  • David Choi was a Pomona student working on analyzing the clusters in our structural classification of antibody CDRs. (2015)
  • Charles Stewart was an MSci student analyzing the presence of non-standard cysteines and disulphide bonds in antibody variable regions.
  • Zi Chen Liu was a Pomona student working on evaluating the performance of our antibody modelling code and integrating VH/VL packing angle prediction. (2016)
  • Anran Tang was a Pomona student working on the problem of rapid assignment of germline information to antibody sequences from nextgen sequencing. (2016)
  • Adam Mohd Nadir was a literature project BSc student investigating antibody humanization. (2016-2017)
  • Lydia Dinsmore was a literature project student looking at the nomenclature of antibody-based drugs and their second indications. (2017-2018)
  • Mariana Costa was a literature project student looking at antibody-based cancer therapies. (2017-2018)
  • Josh Bhathal was a literature project student looking at the state of the art in protein structure prediction. (2017-2018)
  • Natalya Chapman was a literature project student looking at the involvement of IgE in allergy and asthma. (2018-2019)
  • Ho Hin (Nicholas) Wong was a literature project student looking at CAR-T cell therapy. (2018-2019)
  • Mahnoor Mahmood was a literature project student looking at antibody therapeutics for rheumatoid arthritis. (2018-2019)
  • Siyuan Ji was a literature project student looking at transcriptomics and RNA sequencing in cancer biomarker discovery. (2018-2019)
  • Ho Ting Chan was a literature project student looking at antibody Fc fragments and glyco-engineering. (2018-2019)
  • Elizabeth Stephens Undergraduate literature project student looking at GPCR-targeted antibodies. (2019-2020)
  • Fabian Spoendlin Undergraduate literature project student looking at multi-specific antibody formats in cancer therapy. (2019-2020)
  • Francesca Jacklin Undergraduate literature project student looking at molecular mechanisms of ebola pathogenesis and potential antibody therapeutics. (2019-2020)
  • Janvi Patel literature project student looking at bispecific antibodies. (2020-2021)
  • Ivan Filippov literature project student looking at evolution of moonlighting proteins (2020-2021)
  • Reuben Martin literature project student looking at antibody drug conjugates (2020-2021)
  • Ruiqi Hu literature project student looking at antibody Fc engineering (2021-2022)
  • Mehzabeen Hairsoo literature project student looking at vaccines against Covid-19 and the role of bioinformatics (2021-2022)
  • Hugo Shaw literature project student looking at antibody-based treatments for cancer (2021-2022)
MSci project students
  • Echo Ziyi Chi was an MSci student working on immunogenicity and analysis of unusual features in antibodies. (2016-2017)
  • Charlie Barker was an MSci student optimizing our antibody modelling software, abYmod.
  • Ho Hin (Nicholas) Wong MSci student working on prediction of sudden cardiac events resulting from mutations in cardiac beta-myosin. (2019-2020)
  • Lilian Denzler MSci student continuing work on prediction of CDR-H3 modelling quality in antibodies (2020-2021)
  • Khushboo Matwani MSci student co-supervised with Prof. Snezana Djordjevic working on evolution of neuropilin (2020-2021)
  • Barbara Mickucka A 4th year MSci student working on prediction of the effects of mutations (2021-2022)
  • Oliver Hood A 4th year MSci student evaluating different docking methods when applied to antibody/antigen complexes (2021-2022)
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 was an M.Res. student from Birkbeck who was 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 was updating and automating our analysis of antibody canonical classes (2007-8).
  • Katerina Blaveri was an M.Sc. student from Birkbeck who was 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)
  • Mehboob Patel (Mehbs) was working on automated classification of antigens (2014)
  • Jeff Hurst was working on automated classification of antigens (2014)
  • Irene Del Hierro was a Birkbeck Masters student working on incorporating VH/VL packing prediction into antibody modelling (2016).
  • Shanghao Rong was a Birkbeck Masters student working on analysis of rabbit gene conversion (2016).
  • Ben Blundell was a Birkbeck MRes student looking at using neural networks for prediction of CDR-H3 conformation (2018).
  • Joe Lawson was a Birkbeck MSc student looking at the occurrence of cis-prolines and developing a cis-proline predictor. (2018)
  • Oliver Roberts was a part-time Birkbeck MSc student looking at the effects of prolines in breaking alpha-helices. (2018-19)
  • Yobi Livingstone was a Birkbeck MSc student looking at VH/VL packing in antibodies. (2019)
  • Sam Addis was a Birkbeck MSc student looking at VH/VL packing in antibodies. (2019)
  • Maham Ahmad was a Birkbeck MSc student working on description of the structure of antibody-based drugs, particularly complex bi- and multi-specifics. (2020)
  • Matthew Brown was a UCL MRes student working on prediction of quality of CDR-H3 modelling (2019-2020)
  • Lanre Sosan Part-time Birkbeck MSc student working on an online database of antibody-based drugs using MongoDB. (2020-2021)
  • Marianthi (Mara) Tatari Part-time Birkbeck MSc student working on prediction of cis-prolines. (2020-2021)
  • Ayub Hareed Birkbeck MSc student working on prediction of cis-prolines. (2021)
  • Kenen D'Souza was a Birkbeck MSc student continuing work on prediction of glycosylation sites (2021)
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 worked on the prediction of misalignments and improvement of alignment for protein modelling. (May 2010)
  • Emanuele Tamponi was a visiting Ph.D. student from the group of Giuliano Armano at the University of Cagliari. He worked on a novel machine learning approach for dealing with small unbalanced datasets including our mutation phenotype data. (February-May 2014)
  • Rubakan Thuraban was a visiting student funded by Erasmus working on prediction of the effects of mutations in MYH7 (Summer 2019)
Interns
  • 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)
  • Carles Monterrubio was a summer intern assessing the performance of a new antibody numbering program.
  • Giovanni Ordonez Work Experience student from Depauw University working on using NoSQL databases for antibody sequence storage. (2019)
  • Zi (Rita) Zhu Work Experience student developing code to generate AbML from INN antibody annotations. (2022)
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)