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Dr Wendi Bacon

Profile summary

Professional biography

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

STEM Education for Bioinformatics

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 heavy and expensive computational infrastructure or programming skills. By providing more flexibility and connection to users, Wendi aims to assess improvements in learning experiences and research utility for would-be-bioinformaticians, as well as widening participation, for instance in Latin America with a suite of translated tutorials. You can check out the project video for a Spanish bioinformatics workshop here.

Single-cell Biology

Wendi’s particular bioinformatic skillset is in single-cell analysis. We now have the technology to isolate all of the RNA 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 try and best answer many 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 of a cell?”. Wendi is collaborating with multiple members of the LHCS community to provide bioinformatics analysis for wet-lab work, as well as repurposing publicly available data to answer novel questions.

Widening participation for women in sport

Outside of science, Wendi is a martial arts instructor, aiming at widening participation for underprivileged groups. With an emphasis on tradition and qualification outside of the modern coaching professional development, martial arts can both offer excellent mental and physical health benefits, as well as provide unsafe environments or outdated practices in training. As part of a wider multidisciplinary collaboration, Wendi is aiming to study the effect of this phenomenon of tradition versus innovation, and the impact on diversity and participation of women in combat sport.

​Group Members

  • Graeme Tyson - PhD Student, Galaxy tools for Immunologists: User design meets T-cell biologists
  • 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

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 sciences modules, Wendi will be providing quantitative analysis and bioinformatics elements 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 & Saskia Hiltemann (Erasmus-MC, Netherlands)

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

Rowan Wilson (Physio-Fit, Cambridge, UK)


Applications of single-cell RNA sequencing in drug discovery and development (2023-04-28)
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 ((Early access))

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)

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)