Papers

Published software and methods

  1. scClonetoire - Quantifies intra/inter subset clonality and other repertoire features (2023) (https://github.com/rbr1/scIsoTyper).
  2. scReptransition - Measures clonal overlap within/between samples (2023) (https://github.com/rbr1/scIsoTyper).
  3. SVMcelltransfer - Annotates single cells in a scRNA-seq dataset confidently from a reference dataset containing multi-omics (2023) (https://github.com/rbr1/scIsoTyper).
  4. scIsotyper - Assigns high confidence VDJ chains per droplet (2023) (https://github.com/rbr1/scIsoTyper).
  5. MLtiplet - scRNA-seq doublet/multiplet detection using multi-omic profiling (2020) (https://github.com/rbr1/MLtiplet_2.0).
  6. Ultrasensitive amplicon barcoding for next-generation sequencing facilitating sequence error and amplification-bias correction (2020) (https://github.com/rbr1/sUMI_processing_pipeline).
  7. Immune-Repertoire-Network-Generation: open-source program that performs population analyses on B and T cell repertoires (2013)

(https://github.com/rbr1/Immune_receptor_NETWORK-GENERATION).

Preprints

  • Tissue-resident NK cells support survival in pancreatic cancer through promotion of cDC1-CD8T activity (2023)

(https://www.biorxiv.org/content/10.1101/2023.10.14.562332v1)

Simei Go, Constantinos Demetriou, Sophie Hughes, Simone Lanfredini, Giampiero Valenzano, Helen Ferry, Edward Arbe-Barnes, Shivan Sivakumar, Rachael Bashford-Rogers, Mark R. Middleton, Somnath Mukherjee, Jennifer Morton, Keaton Jones,  Eric O’Neill

  • Single-cell immune multi-omics and repertoire analyses in pancreatic ductal adenocarcinoma reveal differential immunosuppressive mechanisms within different tumour microenvironments (2023)

(https://www.biorxiv.org/content/10.1101/2023.08.31.555730v1)

Shivan Sivakumar, Ashwin Jainarayanan, Edward Arbe-Barnes, Piyush Kumar Sharma, Maire Ni Leathlobhair, Sakina Amin, Lara Heij, Samarth Hegde,  Assaf Magen, Felicia Tucci, Bo Sun, Shihong Wu, Nithishwer Mouroug Anand, Hubert Slawinski, Santiago Revale, Isar Nassiri, Jonathon Webber, Adam Frampton, Georg Wiltberger, Ulf Neumann, Philip Charlton, Laura Spiers, Tim Elliott, Pallavur V. Sivakumar, Alexander V. Ratushny, Mark Middleton, Dimitra Peppa,  Benjamin Fairfax, Miriam Merad, Michael L. Dustin,  Enas Abu-Shah, Rachael Bashford-Rogers

  • Shared Hypermutated Disease Specific B Cell Clones in Crohn's Disease (2022)

(https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4212404)

Prasanti Kotagiri, William M. Rae, Laura Bergamaschi, Diana Pombal, Lukas W. Unger, Nurulamin M. Noor, Sofie H. Tolmeijer, Giulia Manferrari, Rachael J.M. Bashford-Rogers, Anton Stift, James C. Lee, Kenneth G.C. Smith, Eoin F. McKinney, Paul A. Lyons

Publications

 

Tissue-resident B cells orchestrate macrophage polarisation and function (Nature Communications, 2023)

(https://www.nature.com/articles/s41467-023-42625-4?trk=feed_main-feed-card_feed-article-content)

Ondrej Suchanek, John R. Ferdinand, Zewen K. Tuong, Sathi Wijeyesinghe, Anita Chandra, Ann-Katrin Clauder, Larissa N. Almeida, Simon Clare, Katherine Harcourt, Christopher J. Ward, Rachael Bashford-Rogers, Trevor Lawley, Rudolf A. Manz, Klaus Okkenhaug, David Masopust & Menna R. Clatworthy

 

Temporality of body mass index, blood tests, comorbidities and medication use as early markers for pancreatic ductal adenocarcinoma (PDAC): a nested case–control study (Gut, 2023)

Pui San Tan, Cesar Garriga, Ashley Clift, Weiqi Liao, Martina Patone, Carol Coupland, Rachael Bashford-Rogers, Shivan Sivakumar, Julia Hippisley-Cox
 
 
Pseudotime dynamics of T-cells in pancreatic ductal adenocarcinoma inform distinct functional states within the regulatory and cytotoxic T-cells (iScience, 2023)
Ashwin Kumar Jainarayanan; Nithishwer Mouroug-Anand; Edward H. Arbe-Barnes; Adam J. Bush; Rachael Bashford-Rogers; Adam Frampton; Lara Heij; Mark Middleton; Michael L. Dustin; Enas Abu-Shah; Shivan Sivakumar

 

Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19 (Lancet Digital Health, 2022) 

Christos P Kotanidis, Cheng Xie, Donna Alexander, Jonathan C L Rodrigues, Katie Burnham, Alexander Mentzer, Daniel O’Connor, Julian Knight, Muhammad Siddique, Helen Lockstone, Sheena Thomas, Rafail Kotronias, Evangelos K Oikonomou, Ileana Badi, Maria Lyasheva, Cheerag Shirodaria, Sheila F Lumley, Bede Constantinides, Nicholas Sanderson, Gillian Rodger, Kevin K Chau, Archie Lodge, Maria Tsakok, Fergus Gleeson, David Adlam, Praveen Rao, Das Indrajeet, Aparna Deshpande, Amrita Bajaj, Benjamin J Hudson, Vivek Srivastava, Shakil Farid, George Krasopoulos, Rana Sayeed, Ling-Pei Ho, Stefan Neubauer, David E Newby, Keith M Channon, John Deanfield, Charalambos Antoniades, COMBAT Consortium and ORFAN investigators
 

Temporality of body mass index, blood tests, comorbidities and medication use as early markers for pancreatic ductal adenocarcinoma (PDAC): a nested case–control study (Gut, 2022)

Pui San Tan, Ashley Kieran Clift, Weiqi Liao, Martina Patone, Carol Coupland, Rachael Bashford-Rogers, Shivan Sivakumar, David Clifton, Stephen P Pereira, Julia Hippisley-Cox
 
Clonally Expanded B Cells in Multiple Sclerosis Bind EBV EBNA1 and GlialCAM (Nature, 2022)
Tobias V. Lanz, R. Camille Brewer, Peggy P. Ho, Kevin M. Jude, Daniel Fernandez, Ricardo A. Fernandes, Alejandro Gomez, Gabriel Nadj, Ryan D. Schubert, Bianca Teegen, Jeffrey E. Dunn, Christopher B. Lock, Lucas B. Kipp, Victoria C. Cotham, Beatrix M. Ueberheide, Blake T. Aftab, Michael R. Wilson, Rachael J.M. Bashford-Rogers, Michael Platten, Raymond A. Sobel, Christopher K. Garcia, Lawrence Steinman, William H. Robinson
 
B Cell Receptor Repertoire Kinetics after SARS-CoV-2 Infection and Vaccination (Cell Reports, 2022)
Prasanti Kotagiri, Federica Mescia, William Rae, Laura Bergamaschi, Zewen Tuong, Lorinda Turner, Kelvin Hunter, Federico Pehuen Pereyra Gerber, Myra Hosmillo, Christoph Hess, Menna R Clatworthy, Ian Goodfellow, Nicholas J Matheson, Eoin McKinney, Mark R Wills, Ravindra K Gupta, John R Bradley, Rachael JM Bashford-Rogers, Paul A Lyons, Kenneth GC Smith
 
A blood atlas of COVID-19 defines hallmarks of disease severity and specificity (Cell, 2022)
The Covid-19 Multi-omics Blood Atlas (COMBAT) Consortium
 
Immunodominant NP105-113-B*0702 cytotoxic T cell response controls viral replication and is associated with less severe COVID-19 disease (Nature Immunology, 2021)
Tao Dong, Graham Ogg, Yan-Chun Peng, Suet Felce, Danning Dong, Frank Penkava, Alexander Mentzer, Xuan Lao, Guihai Liu, Zixi Yin, Ji-Li Chen, YongXu Lu, Dannielle Wellington, Peter Wing, Delaney Dominey-Foy, Julian Knight, Chen Jin, Wenbo Wang, Megat Abd Hamid, Ricardo Fernandes, Beibei Wang, Anastasia Fries, Xiaodong Zhuang, Neil Ashley, Timothy Rostron, Craig Waugh, Paul Sopp, Philip Hublitz, Ryan Beveridge, Tiong Kit Tan, Christina Dold, Andrew Kwok, Charlotte Rich-Griffin, Wanwisa Dejnirattisai, Isar Nassiri, Robert Watson, Orion Tong, Chelsea Taylor, Piyush Kumar Sharma, Fabiola Curion, Santiago Revale, Lucy Garner, Kathrin Jansen, Ricardo Ferreira, Moustafa Attar, Jeremy Fry, Rebecca Russell, Hans Stauss, William James, Alain Townsend, Ling-Pei Ho, Juthathip Mongkolsapaya, Paul Klenerman, Gavin Screaton, Calliope Dendrou, Stephen Sansom, Rachael Bashford-Rogers, Benny Chain, Geoffrey Smith, Jane McKeating, Benjamin Fairfax, Paul Bowness, Andrew McMichael
 
Research Recommendations Following the Discovery of Pain Sensitising IgG Autoantibodies in Fibromyalgia Syndrome (Pain Medicine, 2021)
Andreas Goebel, David Andersson, Chris Barker, Neil Basu, Craig Bullock, Stuart Bevan, Rachael J.M. Bashford-Rogers, Ernest Choy, David Clauw, Debra Dulake, Richard Dulake, Herta Flor, Marcia Glanvill, Zsuzsanna Helyes, Sarosh Irani, Eva Kosek Jennifer Laird, Gary MacFarlane, Hayley McCullough, Andrew Marshall, Robert Moots, Serge Perrot, Nick Shenker, Emanuele Sher, Claudia Sommer, Camilla I Svensson, Amanda Williams, Geoff Wood, and Emma R. Dorris
 
Analysis of T cell receptor clonotypes in tumor microenvironment identifies shared cancer‑type‑specific signatures (Cancer Immunology, Immunotherapy, 2021)
Yvonne H. F. Teng,Hong Sheng Quah, Lisda Suteja, João M. L. Dias, Annalisa Mupo, Rachael J. M. Bashford‑Rogers, George S. Vassiliou, Melvin L. K. Chua, Daniel S. W. Tan, Darren W. T. Lim, N. Gopalakrishna Iyer
 
Using de novo assembly to identify structural variation of complex immune system gene regions (PLOS Computational Biology, 2021)
Jia-Yuan Zhang, Hannah Roberts, David S. C. Flores,  Antony J. Cutler, Andrew C. Brown,  Justin P. Whalley, Olga Mielczarek, David Buck, Helen Lockstone, Barbara Xella, Karen Oliver,  Craig Corton,  Emma Betteridge, Rachael Bashford-Rogers, Julian C. Knight, John A. Todd,  Gavin Band
 
Double-Jeopardy: scRNA-seq Doublet/Multiplet Detection Using Multi-Omic Profiling (Cell Reports Methods, 2021)
Bo Sun, Emmanuel Bugarin-Estrada, Lauren E. Overend, Felicia A. Tucci, Rachael J. M. Bashford-Rogers 
 
Activated regulatory T-cells, dysfunctional and senescent T-cells hinder the immunity in pancreatic cancer (Cancers, 2021)
Shivan Sivakumar,  Enas Abu-Shah,  David Ahern,  Edward H Arbe-Barnes,  Nagina Mangal,  Srikanth Reddy, Aniko Rendek, Alistair Easton, Elke Kurz, Michael Silva,  Lara R
Heij, Zahir Soonawalla,  Rachael Bashford-Rogers,  Mark R Middleton,  Michael Dustin
 
The Future of Blood Testing Is the Immunome ( Frontiers in Immunology, 2021)
Ramy A. Arnaout, Eline T. Luning Prak, Nicholas Schwab, Florian Rubelt and the Adaptive Immune Receptor Repertoire Community
 
Deep sequencing of B cell receptor repertoires from COVID-19 patients reveals strong convergent immune signatures (Frontiers in Immunology, 2020)
Jacob D. Galson, Sebastian Schaetzle, Rachael J. M. Bashford-Rogers, Matthew I. J. Raybould, Aleksandr Kovaltsuk, Gavin J. Kilpatrick, Ralph Minter, Donna K. Finch, Jorge Dias, Louisa James, Gavin Thomas, Wing-Yiu Jason Lee, Jason Betley, Olivia Cavlan, Alex Leech,  Charlotte M. Deane, Joan Seoane, Carlos Caldas, Dan Pennington, Paul Pfeffer, Jane Osbourn
 
Gut-educated IgA plasma cells form an immunological defense at meningeal venous sinuses (Nature, 2020)
Zachary Fitzpatrick, Gordon Frazer, Ashley Ferro, Simon Clare, Nicolas Bouladoux, John Ferdinand, Zewen Kelvin Tuong, Maria Luciana Negro-Demontel, Ondrej Suchanek, Tamara Tajsic, Katherine Harcourt, Kirsten Scott, Rachael Bashford-Rogers, Adel Helmy, Daniel S. Reich, Yasmine Belkaid, Trevor Lawley, Dorian B. McGavern and Menna R. Clatworthy
 
Dynamic regulation of HIF-1 activity is essential for normal B cell development (Nature Immunology, 2020)
Natalie Burrows, Rachael J.M. Bashford-Rogers, Vijesh J. Bhute, Ana Peñalver, John R. Ferdinand, Benjamin J. Stewart, Joscelin E.G. Smith, Mukta Deobagkar-Lele, Girolamo Giudice, Thomas M Connor, Akimichi Inaba, Laura Bergamaschi, Sam Smith, Maxine G.B. Tran, Evangelia Petsalaki, Paul A. Lyons, Marion Espeli, Brian J.P. Huntly, Kenneth G.C. Smith, Richard J. Cornall, Menna R. Clatworthy, Patrick H. Maxwell
 
The B cell immunobiology that underlies CNS autoantibody-mediated diseases (Nature Reviews Neurology, 2020)
Bo Sun, Melanie Ramberger, Kevin C. O’Connor, Rachael J. M. Bashford-Rogers & Sarosh R. Irani
 
Ultrasensitive amplicon barcoding for next-generation sequencing facilitating sequence error and amplification-bias correction (Scientific Reports, 2020)
Ibrahim Ahmed, Felicia A. Tucci, Aure Aflalo, Kenneth G. C. Smith, Rachael Bashford-Rogers
 
Shared D-J rearrangements reveal cell of origin of TCF3-ZNF384 and PTPN11 mutations in monozygotic twins with concordant BCP-ALL (Blood, 2020)
Clara Bueno, Paola Ballerini, Ignacio Varela, Pablo Menendez, Rachael Bashford-Rogers
 
Distinctive binding properties of patient-derived LGI1-autoantibodies determine pathogenicity (Brain, 2020)
Melanie Ramberger,* Antonio Berretta,* Jeanne MM Tan,* Bo Sun, Sophia Michael, Tianrong Yeo, Jakob Theorell, Rachael Bashford-Rogers, Sofija Paneva, Victoria O’Dowd, Neesha Dedi, Sarfaraj Topia, Robert Griffin, Jorge Ramirez-Franco PhD, Oussama El Far, Stéphanie Baulac, Maria I Leite, Arjune Sen, Alexander Jeans, David McMillan,5 Diane Marshall, Daniel Anthony, Daniel Lightwood, Patrick Waters, Sarosh R Irani.
 
B cell receptor repertoire analysis in six immune-mediated diseases (Nature, 2019)
RJM Bashford-Rogers, L Bergamaschi, EF McKinney, DC Pombal, F Mescia, JC Lee, DC Thomas, SM Flint, P Kellam, DRW Jayne, PA Lyons, KGC Smith
 
Natural history and cell-of-origin of TCF3-ZNF384 & PTPN11 mutations in twins with concordant B-ALL (Blood, 2019)
Clara Bueno*, J Ramón Tejedor*, Rachael Bashford-Rogers*,Laura González-Silva*, Rafael Valdés-Mas, Antonio Agraz-Doblás, Rafael Díaz de la Guardia, Chrystele Bilhou-Nabera, Nassera Abermil, Hélène Guermouche, Mario F Fraga, Agustín F Fernández, Paola Ballerini, Ignacio Varela, Pablo Menendez.
 
The integrated genomic and immune landscapes of lethal metastatic breast cancer. (Cell Reports, 2019) 
Leticia De Mattos-Arruda, Stephen-John Sammut, Edith M. Ross, Rachael Bashford-Rogers,Erez Greenstein, Havell Markus,  Sandro Morganella, Yvonne Teng, Yosef Maruvka, Bernard Pereira, Oscar Rueda, Suet-Feung Chin, Tania Contente-Cuomo, Regina Mayor, Alexandra Arias, Raza Ali, Wei Cope, Daniel Tiezzi, Dan Reshef,  Elena Martinez, Vicente Peg, Santiago Ramon y Cajal, Javier Cortes, George Vassiliou, Gad Getz, Serena Nik-Zainal, Muhammed Murtaza, Nir Friedman, Florian Markowetz, Joan Seoane and Carlos Caldas 
 
Genetic modification of primary human B cells generates translationally-relevant models of high-grade lymphoma (Nature Communications, 2019 and bioRxiv, 2019) 
Rebecca Caeser, Miriam Di Re, Joanna A Krupka, Jie Gao, Maribel Lara-Chica, João M.L Dias, Susanna L Cooke, Rachel Fenner, Zelvera Usheva, Hendrik Runge, Philip A Beer, Hesham Eldaly, Hyo-Kyung Pak, Chan-Sik Park, George Vassiliou, Brian J.P Huntly, Annalisa Mupo, Rachael JM Bashford-Rogers, Daniel J Hodson
 
FcgRIIb differentially regulates pre-immune and germinal center B cell tolerance in mouse and human. (Nature Communications, 2019) 
Marion Espeli, Rachael Bashford-Rogers, John Sowerby, Nagham Alouche, Limy Wong, Alice Denton, Michelle Linterman, and Ken Smith
 
Unravelling The Cellular Origin And Clinical Prognostic Markers Of Infant B-Cell Acute Lymphoblastic Leukemia Using Genome-Wide Analysis (Heamatologica, 2019)
Antonio Agraz-Doblas, Clara Bueno, Rachael Bashford-Rogers, Anindita Roy, Pauline Schneider, Michela Bardini, Paola Ballerini, Gianni Cazzaniga, Thaidy Moreno, Carlos Revilla, Marta Gut, Maria G Valsecchi, Irene Roberts, Rob Pieters, Paola De Lorenzo, Ignacio Varela, Pablo Menendez, Ronald W Stam
 
Combined influence of B-cell receptor rearrangement and somatic hypermutation on B-cell class-switch fate in health and in chronic lymphocytic leukaemia (Frontiers Immunology, 2018)
Velislava N Petrova, Luke Muir, Paul F McKay, George S Vassiliou, Kenneth GC Smith, Paul A Lyons, Colin A Russell, Carl A Anderson, Paul Kellam, Rachael JM Bashford-Rogers
 
Antibody repertoire analysis in polygenic autoimmune diseases (Immunology, 2018)
Rachael J.M. Bashford-Rogers, Kenneth G.C. Smith and David C. Thomas
 
Early loss of Crebbp confers malignant stem cell properties on lymphoid progenitors (Nature Cell Biology, 2017)
Sarah Horton, George Giotopoulos, Haiyang Yun, Shabana Vohra, Olivia Sheppard, Rachael Bashford-Rogers, Mamunur Rashid, Alex Clipson, Wai-In Chan, Daniel Sasca, Loukia Yiangou, Hikari Osaki, Faisal Basheer, Paolo Gallipoli, Natalie Burrows, Aysegul Erdem, Anastasiya Sybirna, Sarah Förster, Wanfeng Zhao, Tonci Sustic, Anna Petrukina Harrison, Elisa Laurenti, Jessica Okosun, Daniel Hodson, Penny Wright, Kenneth Smith, Patrick Maxwell, Jude Fitzgibbon, Ming-Qing Du, David Adams, and Brian Huntly
 
Novel pre/pro-B cells generates macrophage populations during homeostasis and inflammation (PNAS, 2017)
Tatsiana Audzevich, Rachel Bashford-Rogers, Neil A. Mabbott, Dan Frampton, Tom C Freeman, Alexandre Potocnik, Paul Kellam, Derek W Gilroy
 
Dynamic variation of CD5 surface expression levels within individual chronic lymphocytic leukaemia clones (Experimental Hematology, 2017)
Rachael J. M. Bashford-Rogers, Anne L. Palser, Clare Hodkinson, Joanna Baxter, George A. Follows, George S. Vassiliou, and Paul Kellam.
 
RNA-seq de novo assembly of clonal immunoglobulin rearrangements identifies interesting biology and uncovers prognostic features in multiple myeloma. (Blood, 2016, 128(22); 195)
Mosen-Ansorena D, Bashford-Rogers R, Bolli N, Minvielle S, Magrangeas F, Anderson KC, AveTLoiseau H, Parmigiani G, Munshi NC.
 
Eye on the B ALL: B cell receptor repertoires reveal persistence of numerous B lymphoblastic leukemia subclones from diagnosis to relapse. (Leukemia, 2016)
Rachael Bashford-Rogers*, Katerina A. Nicolaou*, Jack Bartram, Nicholas J. Goulden, Loizos Loizou, Laura Koumas, Jianxiang Chi, Mike Hubank, Paul Kellam, Paul A. Costeas and George S. Vassiliou.
 
Epstein-Barr virus nuclear protein EBNA3C directly induces expression of AID and somatic mutations in EBV-infected B cells (The Journal of Experimental Medicine, 2016)
Jens S Kalchschmidt, Rachael Bashford-Rogers, Adam CT Gillman, Kostas Paschos, Paul Kellam and Martin J Allday.
 
Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals (Philosophical Transactions B, 2015)
Kenneth B Hoehn, Astrid Gall, Rachael Bashford-Rogers, SJ Fidler, S Kaye, JN Weber, MO McClure, SPARTAC Trial Investigators, Paul Kellam, Oliver G Pybus.
 
Molecular evolution of broadly neutralizing llama antibodies to the CD4 binding site of HIV-1. (Plos Pathogens 2014)
McCoy, L. E., Rutten, L., Frampton, D., Anderson, I., Granger, L., Bashford-Rogers, R , Webb, B., Dekkers, G., Seaman, M., Koh, W., Wagner, R., Verrips, T., Kellam, P., Fassati, A., and Weiss, R. A.
 
Capturing needles in haystacks: comparison of B cell receptor sequencing methods. (BMC Immunology 2014).
Bashford-Rogers, R., Palser, A, Idris, S, Carter, L, Epstein, M, Callard, R, Douek, D., Vassiliou, G., Follows, G., Hubank, M. and Kellam, P.
 
Network properties derived from deep sequencing of the human B cell receptor repertoires delineates B cell populations. (Genome Research 2013).
Bashford-Rogers, RJM. Palser AL, Huntly BJ, Rance R, Vassiliou GS, Follows GA, Kellam P.
 
Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study. (LANCET, 2013).
Cotten M, Watson SJ, Kellam P, Al-Rabeeah AA, Makhdoom HQ, Assiri A, Al-Tawfiq JA, Alhakeem RF, Madani H, Alrabiah FA, Hajjar, S. A., Al-Nassir, W. N., Albarrak, A., Flemban, H., Balkhy, H. H., Alsubaie, S., Palser, A. L., Gall, A., Bashford-Rogers, R., Rambaut, A., Zumla, A. I. & Memish, Z. (2013).