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Dr Wendi Bacon

Profile summary

Professional biography

2023 - Present: Senior Lecturer in Health Science, The Open University

2021 - 2023: Lecturer in Health Science, The Open University

2019 - 2021: Single-cell Analysis Training Officer, European Bioinformatics Institute (EMBL-EBI)

2016 - 2019: Postdoctoral Researcher, Centre for Trophoblast Research, University of Cambridge, UK

2012 - 2016: PhD in Haematology, Cambridge Institute for Medical Research, University of Cambridge, UK

2008 - 2012: BSc in Biochemistry & Spanish, Hobart & William Smith Colleges, New York, USA

Wendi’s academic experience and research interests lie in crossing scientific disciplines. As a PhD student, she applied developmental biology techniques in a cancer context, creating mouse and cell models for infant leukemia. As a postdoc, she continued her passion for method development in applying single cell transcriptomics in a reproductive biology context, examining the developmental defects occurring in cases of birth complications such as preeclampsia or fetal growth restriction. At the EBI, Wendi bridged the gap between wet-lab researchers and computer scientists to train biologists and develop bioinformatics resources as part of the Human Cell Atlas. Ultimately, Wendi enjoys learning and applying knowledge in new ways - scientists no longer need to be single entities in dusty labs, but can share expertise and knowledge to collaborate beyond what anyone could do alone.

Research interests

Bioinformatics Education

Bioinformatics is one of the biggest skill gaps in modern biology and biomedical science. The Galaxy Project is an open science consortium to create a means for scientists to analyse their big data (Omics data in particular, such as DNA or RNA sequencing) without access to expensive computational infrastructure or programming skills. By providing more flexibility and connection to users, Wendi aims to improve bioinformatics learning, assess student experiences, and evaluate impact of bioinformatics skills on career trajectories. In line with both The Open University and The Galaxy Project's ethos towards democratising science, she has led projects on tutorial translations to increase the participation of Latin America within the Galaxy community (you can check out the project video for a Spanish bioinformatics workshop here) and advocates for improvements in platform accessibility.

Single-cell Biology

Wendi’s particular bioinformatic skillset is in single-cell analysis. We now have the technology to isolate all of the RNA (or DNA, or chromatin structure...or - increasingly - protein!) from a single cell, across thousands (or even millions!) of cells in a tissue or body. With such quantities of data comes challenging data analysis. The analytical field is moving quickly to answer key questions, for instance, “How many cell types are there in a human lung?” or “Which cell is affected by this oncogene?”, or “How does this drug affect the RNA and DNA structure in particular cell types?”. Leveraging the workflow features within the Galaxy interface, Wendi collaborates with multiple members of the LHCS community as well as academics at the University of Cambridge, the Babraham Institute, and beyond, to provide bioinformatics analysis. She is particularly interested in repurposing publicly available data to answer novel questions.

Widening participation for women in sport

Outside of science, Wendi is a martial arts instructor, dedicated to widening participation for underprivileged groups. This hobby grew into a research consortium focusing on physical, social, and infrastructural barriers to women's healthy high impact sport participation. Having experienced an ACL tear and subsequent rehabilitation herself, Wendi is particularly interested in preventing similar injuries for others, improving injury recording, and developing better tools for recreational coaches to safely train their participants.

​Group Members

  • Marisa Loach - PhD Student, Single cell transcriptomics in health & disease
  • Brenda McCartney - PhD Student, Building confidence in bioinformatics learning
  • Kayleigh Smith - PhD Student, Identification of B-cell Dysfunction in Therapy and Disease
  • Jurgi Giraud - PhD Student in Linguistic Sciences, The Art of Translation: Developing Multilingual Digital Resources using Artifical Intelligence to Support Translation in Bioinformatics
  • Julia Jakiela - EPSRC Intern & EOSC-Life Training intern, Single cell trajectory analysis in Galaxy
  • Morgan Howells - EPSRC Intern, Automated cell annotation for single cell analysis in Galaxy

Former Members

  • Camila Goclowski - Intern, Batch correction & Seurat analysis in Galaxy
  • Stefy Dreptate - Intern, Spanscriptomics Workshop: Análisis de células únicas usando Galaxy | Single cell analysis using Galaxy

Teaching interests

Within the health, biology, & biomedical modules, Wendi emphasises quantitative analysis and bioinformatics in order to upskill students for the careers of tomorrow. Additionally, she remains active with the Galaxy Training Network, providing resources and tutorials for scientists across the globe.

External collaborations

Sarah Morgan, Cath Brooksbank, Irene Papatheodorou and Pablo Moreno (EMBL-EBI, UK)

Andrew Stubbs & Helena Rasche (Erasmus-MC, Netherlands)

Saskia Hiltemann, Mehmet Tekman & Beatriz Serrano-Solano (University of Freiberg)

Rowan Wilson (Physio-Fit, Cambridge, UK)

EMBL-EBI Single Cell Scientific Organiser

ELIXIR-UK Steering Group

ELIXIR-UK Galaxy Working Group

ELIXIR-UK Single Cell Omics Working Group

ELIXIR-UK DaSH Fellowship Mentor

Galaxy Single Cell Community of Practice Chair

Galaxy Single Cell Editorial Board

Galaxy Executive Board


The Influence of Gender Dynamics on Women’s Experiences in Martial Arts: A Scoping Review (2023-08-01)
Lindsay, Rosie; Horne, Jo; Shaw, Jill; Kentzer, Nichola and Bacon, Wendi
International Journal of the Sociology of Leisure

Applications of single-cell RNA sequencing in drug discovery and development (2023-06)
Van de Sande, Bram; Lee, Joon Sang; Mutasa-Gottgens, Euphemia; Naughton, Bart; Bacon, Wendi; Manning, Jonathan; Wang, Yong; Pollard, Jack; Mendez, Melissa; Hill, Jon; Kumar, Namit; Cao, Xiaohong; Chen, Xiao; Khaladkar, Mugdha; Wen, Ji; Leach, Andrew and Ferran, Edgardo
Nature Reviews Drug Discovery, 22 (pp. 496-520)

Galaxy Training: A powerful framework for teaching! (2023)
Hiltemann, Saskia; Rasche, Helena; Gladman, Simon; Hotz, Hans-Rudolf; Larivière, Delphine; Blankenberg, Daniel; Jagtap, Pratik D.; Wollmann, Thomas; Bretaudeau, Anthony; Goué, Nadia; Griffin, Timothy J.; Royaux, Coline; Le Bras, Yvan; Mehta, Subina; Syme, Anna; Coppens, Frederik; Droesbeke, Bert; Soranzo, Nicola; Bacon, Wendi; Psomopoulos, Fotis; Gallardo-Alba, Cristóbal; Davis, John; Föll, Melanie Christine; Fahrner, Matthias; Doyle, Maria A.; Serrano-Solano, Beatriz; Fouilloux, Anne Claire; van Heusden, Peter; Maier, Wolfgang; Clements, Davx; Heyl, Florian; Grüning, Björn and Batut, Bérénice
PLOS Computational Biology, 19, Article e1010752(1)

Training Infrastructure as a Service (2023)
Rasche, Helena; Hyde, Cameron; Davis, John; Gladman, Simon; Coraor, Nate; Bretaudeau, Anthony; Cuccuru, Gianmauro; Bacon, Wendi; Serrano-Solano, Beatriz; Hillman-Jackson, Jennifer; Hiltemann, Saskia; Zhou, Miaomiao; Grüning, Björn and Stubbs, Andrew
GigaScience, 12, Article giad048

Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses (2022-07-28)
Bacon, Wendi; Holinski, Alexandra; Pujol, Marina; Wilmott, Meredith and Morgan, Sarah L
PLOS Computational Biology, 18, Article e1010220(7)

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update (2022-07-05)
Bacon, Wendi and The Galaxy Community,
Nucleic Acids Research, 50(W1) (W345-W351)

Deciphering Tumour Microenvironment of Liver Cancer through Deconvolution of Bulk RNA-Seq Data with Single-Cell Atlas (2022)
Zhang, Shaoshi; Bacon, Wendi; Peppelenbosch, Maikel P.; van Kemenade, Folkert and Stubbs, Andrew Peter
Cancers, 15, Article 153(1)

User-friendly, scalable tools and workflows for single-cell RNA-seq analysis (2021)
Moreno, Pablo; Huang, Ni; Manning, Jonathan R.; Mohammed, Suhaib; Solovyev, Andrey; Polanski, Krzysztof; Bacon, Wendi; Chazarra, Ruben; Talavera-López, Carlos; Doyle, Maria A.; Marnier, Guilhem; Grüning, Björn; Rasche, Helena; George, Nancy; Fexova, Silvie Korena; Alibi, Mohamed; Miao, Zhichao; Perez-Riverol, Yasset; Haeussler, Maximilian; Brazma, Alvis; Teichmann, Sarah; Meyer, Kerstin B. and Papatheodorou, Irene
Nature Methods, 18(4) (pp. 327-328)

Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice (2018-11)
Bacon, Wendi A.; Hamilton, Russell S.; Yu, Ziyi; Kieckbusch, Jens; Hawkes, Delia; Krzak, Ada M.; Abell, Chris; Colucci, Francesco and Charnock-Jones, D. Stephen
Frontiers in Immunology, 9, Article 2523

High-dose BCNU/Melphalan conditioning regimen before autologous stem cell transplantation in newly diagnosed multiple myeloma (2018-01)
Sivaraj, D.; Bacon, Wendi; Long, G. D.; Rizzieri, D. A.; Horwitz, M. E.; Sullivan, K. M.; Kang, Y.; Li, Z.; Chao, N. J. and Gasparetto, C.
Bone Marrow Transplantation, 53(1) (pp. 34-38)

Efficacy and safety of high-dose chemotherapy with autologous stem cell transplantation in senior versus younger adults with newly diagnosed multiple myeloma (2017-12)
Huang, Li-Wen; Bacon, Wendi; Cirrincione, Constance; Peterson, Bercedis; Long, Gwynn; Rizzieri, David; Sullivan, Keith M.; Corbet, Kelly; Horwitz, Mitchell; Chao, Nelson; Gasparetto, Cristina and Tuchman, Sascha A.
Hematological Oncology, 35(4) (pp. 752-759)

Mll-AF4 Confers Enhanced Self-Renewal and Lymphoid Potential during a Restricted Window in Development (2016-07-26)
Barrett, Neil A.; Malouf, Camille; Kapeni, Chrysa; Bacon, Wendi A.; Giotopoulos, George; Jacobsen, Sten Eirik W.; Huntly, Brian J. and Ottersbach, Katrin
Cell Reports, 16(4) (pp. 1039-1054)

Analysis of Jak2 signaling reveals resistance of mouse embryonic hematopoietic stem cells to myeloproliferative disease mutation (2016-05-12)
Mascarenhas, Maria I.; Bacon, Wendi A.; Kapeni, Chrysa; Fitch, Simon R.; Kimber, Gillian; Cheng, S. W. Priscilla; Li, Juan; Green, Anthony R. and Ottersbach, Katrin
Blood, 127(19) (pp. 2298-2309)

Cyclophosphamide-based hematopoietic stem cell mobilization before autologous stem cell transplantation in newly diagnosed multiple myeloma (2015-06)
Tuchman, Sascha A; Bacon, Wendi A; Huang, Li-Wen; Long, Gwynn; Rizzieri, David; Horwitz, Mitchell; Chute, John P.; Sullivan, Keith; Morris Engemann, Ashle; Yopp, Amanda; Li, Zhiguo; Corbet, Kelly; Chao, Nelson and Gasparetto, Cristina
Journal of Clinical Apheresis, 30(3) (pp. 176-182)

Measurement of Heterogeneous Reaction Rates: Three Strategies for Controlling Mass Transport and Their Application to Indium-Mediated Allylations (2011)
Olson, Isabel A.; Bacon, Wendi A.; Baez Sosa, Yessica Y.; Delaney, Katherine M.; Forte, Salvador A.; Guglielmo, Michael A.; Hill, Alexa N.; Kiesow, Katrina H.; Langenbacher, Rachel E.; Xun, Yuhan; Young, Ryan O. and Bowyer, Walter J.
The Journal of Physical Chemistry A, 115(40) (pp. 11001-11007)