News
July 2021:
Trupti Gore joins the group to do her LIDo BBSRC Studentship with
second supervisor Dr Michele Mishto at KCL/Crick.
April 2021:
Xianli Li joins the group from the ESIEE in Paris to do an internship
looking at viral mutation patterns over time.
Congratualtions to Martin Rosellen for passing his PhD viva.
March 2021:
MSc Bioinformatics students Joan Amaya Cuesta, Zak Downey, Varada
Krishnadas, Georgina Leslie, Rory McDaid, Rosie Mottram,
Hirushi Rajapakse and Anna Sidera have joined the group to do
their MSc research projects.
November 2020:
Colin Straton (MRes Bioinformatics) has joined the group to do an MRes
project on immune repertoire visual analytics.
October 2020:
Trupti Gore (LIDo DTG PhD student) has joined the group to do a
rotation project applying deep learning and data augmentation
in the field of adaptive immunology.
Justin Barton has joined the group to do a PhD applying deep learning
to challenges in the field of cancer immunology.
September 2020:
Congratulations to Dr Lenka Stejskal for having a paper published in
Journal of Biological Chemistry (Cholesterol sensing by CD81
is important for hepatitis C virus entry), work conducted
during her PhD.
July 2020:
Congratulations to Tapasvi Modi for completing her thesis corrections
and having a paper on the UK anthrax vaccine accepted for
publication.
Congratulations to William Lees on having a poster about antibody
repertoire responses to therapeutic treatment of haemophilia A
at ISTH 2020 on 12th to 14th of the month (with our
collaborators at QMUL).
June 2020:
Ryan Dowsell (Wellcome Trust PhD student) has joined the group to do a
rotation project on methods for predicting the impact of
susbtitutions on antibody-antigen binding.
April 2020:
MSc Bioinformatics students Sucharitha Balu, Kieran Drake, Kyvi
Nguyen, Vuyelwa Nkomo
and Ruchira Sachdeva have joined the group to do their projects on
B-cell germline genes, T-cell receptors, and SARS-CoV-2.
March 2020:
Adrian Shepherd is giving a talk about the group's computational
immunology research at the Royal Veterinary College on the
4th.
February 2020:
Congratulations to Lenka Stejkal and other group members for having a
paper on the hepatitis C virus E2 glycoprotein published
in PLOS
Computational Biology.
January 2020:
Sarah Griffiths joins the group to do an internship aimed at
evaluating
different antibody repertoire annotation tools.
November
2019:
Adrian Shepherd is giving a talk on alloimmunity and our proteome
scanning strategy at
the Immunogenicity
and Tolerance Seminar in Amsterdam on the 15th. Three members of the group are co-authors on a paper
in Frontiers in
Immunology abouta statistical package for analysing and
comparing immune receptor repertoires called sumrep.
October 2019:
Zainab Aziz and Trupti Gore join the group to do internships on MHC
molecule binding signatures and HLA allele prediction from T-cell receptor
sequences respectively.
September 2019:
Congratulations to Dr William Lees for having two papers accepted in
Nucleic Acids Research — one for our
database OGRDB, and
one for VDJbase, which we
host and jointly develop with Gur Yaari's lab.
June 2019:
Adrian Shepherd is giving a talk about antibody repertoire sequencing
at
the Antibody
Engineering & Therapeutics Europe
conference in Amsterdam on the 13th.
April 2019:
MSc Bioinformatics students Esther Adebanjo, Sam Dougan, Diego, Miruna
Serian and Nikita Sharma join the group to do their Masters projects.
March 2019:
Congratulations to William Lees for having
a
paper
on inferred allelic variants of immunoglobulin receptor genes
published in Frontiers in Immunology.
October 2018:
Congratulations to Lenka Stejskal for giving the Best Oral
Presentation at the HCV2018,
the 25th International Symposium on Hepatitis C Virus and Related
Viruses in Dublin!
September 2018:
Several present and former members of the group have had a paper
about missense mutation haemophilia A accepted by
Haematologica, the
journal of the European Hematology Association.
June 2018:
Congratulations to Lenka Stejkal for having an oral presentation on
her research accepted by HCV2018 (the 25th International Symposium
on hepatitis C virus).
March 2018:
Three MSc Bioinformatics students have joined the group to work on
their Masters projects: Trupti Gore (plasmid fertility
inhibition), Georgina Toye (antibody binding motifs) and Ifigenia
Tsitsa (Pepscan epitope mapping data).
Adrian Shepherd is giving a lunchtime seminar on the group's
haemophilia A
research (T-cell tolerance prediction, antibody
repertoire analytics, molecular dynamics) at the School of
Biosciences, University of Kent, Canterbury on the 27th.
February 2018:
The group has a "spotlight" paper published in Journal of
Virology with our
collaborators at NYU School of Medicine and Iowa State
— see the abstract
here.
October 2017:
Pejvak Moghimi (BBSRC CASE studentship) has joined the group
to do a PhD on antibody repertoire analytics (in
collaboration with UCB).
June 2017:
Adrian Shepherd is giveng a talk — Antibody repertoire
analytics: deep sequencing meets “the evolution
within us” — at
a BIDA workshop
on
the 20th.
May 2017:
William Lees be presenting a poster about our antibody
repertoire sequencing work at
the SysIms: Systems
Biology of Adaptive Immunity conference in Ascona,
Switzerland, 14-17 May.
February 2017: Martin Rosellen has joined
the group to do a LIDo PhD rotation project modelling Factor
VIII interactions using Molecular Dynamics.
January 2017: The group has its first
publication
in Frontiers
in Immunology.
December 2016: Congratulations to William
Lees and Jan Czarnecki for having chapters
on antibody
repertoires analysis with NGS
and metabolic
pathway mining published in Bioinformatics Volume II:
Structure, Function, and Applications.
Guy Williamson (MRes Bioinformatics with Systems Biology) has
joined the research group to do a research project on
antibody-antigen complexes.
October 2016: There is
a BBSRC-funded PhD position
available in the group — a
collaboration with biopharma company UCB. It's a project
on antibody repertoires focusing on the visualisation and
analysis of NGS (Rep-seq) data. The application deadline
is 20th Jan. More information is
available here.
Lenka Stejskal (Wellcome Trust PhD Programme) has
joined the group to do a PhD on B-cell responses to
hepatitis C virus (in collaboration with Joe Grove at
UCL).
September 2016:
William Lees has added more tools for antibody clonal
analysis (including ClusterStats
and Spectratype) to
the TRIgS
GitHub site.
July 2016:
William Lees has added clustering and germline analysis
tools to
our Phylogenetic
Analysis Tools.
Congratulations to Kevin Pentiah for successfully completing his
PhD.
Congratulations to Anna Hernandez for having
a paper
accepted by Molecular & Cellular Proteomics.
June 2016: Elise Parey (Masters in Bioinformatics and Modelling, Pierre and Marie Curie
University, Paris) has joined the group to do a summer internship on antibody VH genes.
March 2016: Four MSc Bioinformatics students have joined the group to do their Masters projects:
Daniel Bugembe-Lule (HIV), Sandy MacPherson (chronic hepatitis B infections), Sam McGreig (fungal growth and
climate change) and Mark Warren (T-cell epitope immunodominance).
February 2016:
Congratulations to Michael Denyer for having a paper accepted
by PLOS ONE.
November 2015:
Adrian Shepherd was a plenary speaker and chaired the computational
biology session at VAAVV 2015, the Vaccines Against
Antigenically Variable Viruses Symposium, Ames, Iowa, US on
the 6th. William Lees presented an abstract and poster at the
same conference. Charles Bird, Frough Froghi and Jacob Househam (MRes Bioinformatics
with Systems Biology) have joined the group to do
computational immunology research projects.
October 2015: William Lees has added new functionality to our Phylogenetic Analysis
Tools: a tool for analysing IgBLAST reports; a tool for
extracting sequences and sequence fragments from IMGT and
IgBLAST reports; and expanded and improved documentation, now
available via GitHub. Arundhati Maitra and Lenka Stejskal have joined the group to do
Wellcome Trust PhD rotation projects.
September 2015:
William Lees has added the generation of WebLogo
sequence logos to the output from
our Phylogenetic
Analysis Tools.
July 2015:
Congratulations to William Lees for having a paper accepted by Journal
of Immunology Research.
April 2015:
Adrian Shepherd will be giving a talk at PHE (Public Health
England) Porton on the 23rd.
March 2015:
Adrian Shepherd gave a talk at the Pirbright Institute on
the 5th. Paul Buckley and Adam Shepherd (MSc Bioinformatics with Systems
Biology) have joined the group to do research projects on
T-cell responses to influenza A and antibody germline
polymorphisms.
February 2015:
Sukhuma Starkings (MSc Microbiology) has joined the
group to do a project on viral surface glycoproteins.
January 2015:
Tapasvi Modi has joined the group to do a PhD on anthrax
vaccines in collaboration with Public Health England.
Siobhan Titre-Johnson (MSc Health and Disease) has joined the
group to do a project on influenza B virus.
November 2014:
Anna Laddach and Zheli Tan (MRes Bioinformatics with Systems
Biology) have joined the group to do research projects on NGS
antibody repertoire sequencing.
October 2014:
Roxana Mironska has joined the group to do a Wellcome Trust PhD
rotation project.
September 2014:
Adrian Shepherd gave a talk at the Respiratory Viruses 2014
symposium in Oxford on the 8th.
Sebastiaan Klein has joined the group on an internship from the
University of Applied Sciences Leiden. Aaron Yi Long Lam (BSc
Biochemistry, UCL) has joined the group to do his third year
research project on heterologous immunity.
August 2014:
Congratulations to Kevin Pentiah for having a paper
accepted by Glycobiology.
July 2014:
Congratulations to Stuart Skelton for having a paper
accepted by the British Journal of
Haematology.
June 2014: Adrian Shepherd gave a talk at the Institute of Hepatology on the 4th of
the month.
March 2014: Ginny Devonshire and Paddy
MacMahon (MSc Bioinformatics with Systems Biology) join the
group to do their research projects. Our recent paper on
broad-spectrum antibodies against influenza A (Lees, Moss
& Shepherd, 2014) is featured on the Society for General
Microbiology blog, Microbe
Post, here.
February 2014:
Adrian Shepherd has joined the Programme Committee for SMBM
2014 (the 6th International Symposium on Semantic Mining in
Biomedicine)
January 2014: Rute Magalhaes and Paula
Luz Horne (MSc Microbiology students) join the group to do
their research projects. Claire Winship has joined the
group to do a postgraduate internship on influenza
pseudoviruses.
November 2013:
Adrian Shepherd gave a talk on
computational virology at the
Center for Advanced Host Defense, Immunobiotics, and
Translational Comparative Medicine (CAHDIT), Iowa State
University on the 14th of the month. Michael Denyer (MRes
Bioinformatics with Systems Biology) joins the group to work
on T cell responses to influenza A.
October 2013:
Congratulations to William Lees for having a paper
accepted by Journal of General Virology.
September 2013: Congratulations to William Lees for
passing his PhD viva and giving a talk at the Influenza2013 conference
in Oxford. The following students have joined the group: Mary Bispham,
Naz Uzun and Charlie Watson to start their part-time PhDs on
herpesviruses, HBV and influenza A respectively; Jake Saklatvala (BSc
Biochemistry, UCL) to do his final year research project; and Sander
van Boom as an intern, part of his bioinformatics degree at the
University of Leiden, Netherlands.
August 2013: Adrian Shepherd has joined the Programm
Committee for LBM 2013 (the 5th International Symposium on Languages
in Biology and Medicine)
June 2013: Mike Doyle (BSc Chemical and Molecular
Biology) joins the group to work on his research and literature
projects.
May 2013: Richard Lee (MSc Bioinformatics with Systems Biology)
joins the
group to work on the immunogenicity of therapeutic proteins.
January 2013:
Lisa Byer, Anthony Folami and Duldip Sidhu (MSc Health and
Disease students) join the
group to work on their research projects.
December 2012:
Dr James Smith joins the
group to work on SysMIC.
November 2012:
Claire Haskins (MRes Bioinformatics with Systems
Biology) joins the group to work on the evolution of immune regulation. Adrian Shepherd gave a talk
on the stratification of haemophilia A patients at the
Centre for Systems and Synthetic Biology, Brunel
University on the 7th.
September 2012:
William Otterburn (BSc Biochemistry student at UCL)
joins the
group to do his third year research project on
functional
epitopes.
August 2012:
Cangratulation to Simon Corrigan for having his
poster accepted for ECCB'12.
July 2012:
Congratulations to Jan for having a paper
based on his 1st-yr PhD
rotation project accepted by BMC
Bioinformatics.
June 2012:
Oliver King (BSc Biochemistry student at UCL)
joins the group to do an internship in protein
modelling.
April 2012: Sumona Mitra (MSc
Bioinformatics graduate from King's College London)
joins the group to do an internship in
immunoinformatics. Congratulations to Ganesh for
having
a paper
based on his 1st-yr PhD rotation project accepted
by Molecular Immunology.
March 2012: Alison Kakoschke, Nazmiye
Uzun and Shavin Fonseka (MSc Bioinformatics with
Systems Biology) join the group to do their research
projects. Adrian Shepherd has joined the Programme
Committee of the 5th International Symposium on
Semantic Mining in Biomedicine (SMBM 2012, Zurich, 3/4
September).
February 2012:
Christian Search and Patience Tetteh (MSc Health and
Disease
students) join the group to do their
research projects.
January 2012:
The SysMIC (Systems Training in Maths, Informatics and
Computational Biology) project has started. More
information
here.
November 2011:
Johnathan Watkins joins the group to work on a joint
project
with Dr Anita Grigoriadis at
the Breakthrough Breast Cancer Research Unit, King's
College
London.
July 2011:
Congratulations to group member Jan Czarnecki for
winning
first prize for his presentation
at the ISMB 2011 Graduate Symposium!