Stephen Doyle
stephenrdoyle.bsky.social
Stephen Doyle
@stephenrdoyle.bsky.social
Group Leader @ Wellcome Sanger Institute. UKRI Future Leaders Fellow.

Molecular & computational biology of parasitic worms of humans and animals.

https://helminthgenomics.sanger.ac.uk/

🇦🇺Aussie dad of 🧒+👶^2.
Pinned
I am delighted to share that my UKRI Future Leaders Fellowship has been renewed/extended. Some fun science planned, so I am really happy to have the opportunity.

Many thanks to a wonderfully smart and productive team and to the generous support of mentors and collaborators past and present.
New paper, now in Nature Communications!

Thanks to a massive effort by PhD student @marinapapaiakovou.bsky.social, I am excited to share our work "Global diversity of soil-transmitted helminths reveals population-biased genetic variation that impacts diagnostic targets".

doi.org/10.1038/s414...
Global diversity of soil-transmitted helminths reveals population-biased genetic variation that impacts diagnostic targets - Nature Communications
This study analysed genetic data of soil-transmitted helminths from 27 countries, revealing diversity impacting molecular test accuracy and highlighting the need to adapt diagnostics for effective STH...
doi.org
July 14, 2025 at 8:32 AM
I am proud to see our latest work on hybridisation capture in soil-transmitted helminths, led by PhD student @marinapapaiakovou.bsky.social , now published in Molecular Ecology Resources. I am looking forward to scaling this up into larger populations. In the meantime, 🥳

doi.org/10.1111/1755...
Enrichment of Helminth Mitochondrial Genomes From Faecal Samples Using Hybridisation Capture
New approaches are urgently needed to enrich rare or low-abundant DNA in complex samples. Soil-transmitted helminths (STHs) inhabit heterogeneous environments, including the gastrointestinal tract of...
doi.org
July 12, 2025 at 8:55 PM
Job advert - Please share!

Mark Viney (lnkd.in/dwkZf7mG) and I are seeking a motivated postdoctoral fellow to work on drug treatment responses of soil-transmitted helminth and hookworm genomics in Southeast Asia.

Do reach out if you are keen!

www.jobs.ac.uk/job/DMR456/p...
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
April 22, 2025 at 9:57 PM
Reposted by Stephen Doyle
We are advertising for a PhD position to study bacterial metabolites in C. elegans, funded by the MRC Microbes, Microbiomes and Bioinformatics training programme @uniofeastanglia.bsky.social @biouea.bsky.social. Open to UK and international students. www.findaphd.com/phds/project...
Uncovering bacterial metabolites that can attenuate vitamin B12 deficiency (AKAY_U25MMB) at University of East Anglia on FindAPhD.com
PhD Project - Uncovering bacterial metabolites that can attenuate vitamin B12 deficiency (AKAY_U25MMB) at University of East Anglia, listed on FindAPhD.com
www.findaphd.com
March 16, 2025 at 10:57 AM
Very excited to see our latest work, led by @marinapapaiakovou.bsky.social , on @biorxiv-genomic.bsky.social !

Enrichment of helminth mitochondrial genomes from faecal samples using hybridisation capture

doi.org/10.1101/2025...
Enrichment of helminth mitochondrial genomes from faecal samples using hybridisation capture
New approaches are urgently needed to enrich rare or low-abundant DNA in complex samples. Soil-transmitted helminths (STHs) inhabit heterogeneous environments, including the gastrointestinal tract of ...
doi.org
February 28, 2025 at 3:53 PM
Reposted by Stephen Doyle
Enrichment of helminth mitochondrial genomes from faecal samples using hybridisation capture https://www.biorxiv.org/content/10.1101/2025.02.24.639427v1
February 28, 2025 at 2:40 AM
Reposted by Stephen Doyle
globally, there are ~3500 described mosquito species in the Culicidae family and many of these are important vectors of disease but only a small percentage have genomic resources. we are launching a pilot project to generate high quality reference genomes for 100 important mosquito species [1/3]
February 24, 2025 at 10:51 AM
Less than one week to apply - deadline 25th of Feb!

If you are from Latin America, work on helminths, and are interested in genetics/bioinformatics, this could be a great opportunity for you 👇
Are you based in South America and work on helminths?

Join me & a great group of instructors on the Helminth Bioinformatics course in Montevideo during 18–24 May!

We'll cover expenses, you just need to come, interact, and learn.

Please share & apply!

t.co/Dlj4DyG1ul
https://coursesandconferences.wellcomeconnectingscience.org/event/helminth-bioinformatics-latin-america-the-caribbean-20250518/
t.co
February 19, 2025 at 10:45 AM
Reposted by Stephen Doyle
I am hiring! 2 year Post-Doc microbiologist to identify gut bacteria inhibiting fungal pathogens. Join new, expanding gut microbiome research group at @apcmicrobiomeirel.bsky.social and @uccmicrobiology.bsky.social in Cork. Further details and apply here:
ore.ucc.ie
Job ID: 084031
University College Cork Vacancies
ore.ucc.ie
February 15, 2025 at 4:51 PM
Reposted by Stephen Doyle
We're looking for a post-doc to work on anthelminthic resistance in a new pan-European project. It will involve generating and analysing targeted and whole-genome data from well-phenotyped livestock GIN populations.

Please get in touch if you have any questions.

www.jobs.gla.ac.uk/job/research...
Research Assistant/Research Associate (anthelmintic resistance management)
Job Purpose We have an exciting opportunity for a Research Assistant/Associate to contribute/make a leading contribution to the project ‘Anthelmogram: the next generation decision making tool for a...
www.jobs.gla.ac.uk
February 15, 2025 at 1:04 PM
Are you based in South America and work on helminths?

Join me & a great group of instructors on the Helminth Bioinformatics course in Montevideo during 18–24 May!

We'll cover expenses, you just need to come, interact, and learn.

Please share & apply!

t.co/Dlj4DyG1ul
https://coursesandconferences.wellcomeconnectingscience.org/event/helminth-bioinformatics-latin-america-the-caribbean-20250518/
t.co
February 13, 2025 at 6:44 PM
Reposted by Stephen Doyle
📣📣Genomic data sharing: you don’t know what you’ve got (till it’s gone) www.nature.com/articles/s41...

A comment @natrevgenet.bsky.social from @katholt.bsky.social and me
February 13, 2025 at 9:10 AM
Any suggestions for tracking worms like C.elegans and other things from live imaging fluorescence data? Would like an open source tool.
February 11, 2025 at 10:45 PM
Reposted by Stephen Doyle
Hookworm genes encoding intestinal excreted-secreted proteins are transcriptionally upregulated in response to the host's immune system https://www.biorxiv.org/content/10.1101/2025.02.01.636063v1
February 4, 2025 at 2:34 AM
Reposted by Stephen Doyle
Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq https://www.biorxiv.org/content/10.1101/2025.02.02.636107v1
February 4, 2025 at 2:33 AM
Really fun to write this paper on spatial transcriptomics with Sarah. It’s an exciting technique that has a lot of potential in Parasitology for new insights.
In our Jan issue: Entering the #spatial age of parasite #genomics, authored by Sarah Buddenborg & @stephenrdoyle.bsky.social highlighting Simone Haeberlein & colleagues’ @naturecomms.bsky.social article. #Transcriptomics #Fasciola #hepatica @sangerinstitute.bsky.social

www.cell.com/trends/paras...
January 28, 2025 at 8:58 AM
This is too much fun to be called work. #scalingup @sangerinstitute.bsky.social #ukriflf
January 27, 2025 at 9:51 PM
Today was a great reminder that I work with some really amazing people. Shout out to Joana and Javi for kicking big goals today 🤩 @sangerinstitute.bsky.social
January 22, 2025 at 8:36 PM
Reposted by Stephen Doyle
We share a lot of our ideas, code, datasets (that we spend years sanitizing) early. Often way before we release preprints. We do this so that others can use, build on, improve & even "beat" our approaches. But I want to say a few things about some simple expectations 1/
January 17, 2025 at 5:16 PM
Reposted by Stephen Doyle
If you are a budding parasitologist and you would like to spend a great summer full of science, networking, and fun with your peers, there is still time to apply for Biology of Parasitism course at @mblscience.bsky.social! Deadline 29th of January.

tinyurl.com/applyBoP
Biology of Parasitism: Modern Approaches | Marine Biological Laboratory
A unique course for advanced graduate students, postdocs, and independent investigators, who are seeking in-depth training in modern approaches to the study of protozoan parasites and parasitic worms.
www.mbl.edu
January 9, 2025 at 4:11 PM
Reposted by Stephen Doyle
Two postdoctoral positions at the Wellcome Sanger Institute focus on symbiosis genomics, analyzing eukaryotic and prokaryotic cobionts. Closing date: Jan 26, … https://sanger.wd103.myworkdayjobs.com/en-US/WellcomeSangerInstitute/details/Postdoctoral-Fellow--Microbiomes-of-Tree-of-Life-_JR102528 #job
Postdoctoral Fellow (Microbiomes of Tree of Life)
Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenges. We have an exciting opportunity for a Postdoctoral Fellow to work with Tree of Life and Parasites and Microbes teams to identify cobionts in genome sequence datasets as they are generated and thus build a catalogue of host-microbe associations. This PDF contract will be 3 years fixed term at the Sanger Institute Life on planet Earth is a complex web of interactions between organisms, some mutualistic, some harmful, some neutral. While sequencing diverse eukaryotic species, the Tree of Life programme at the Sanger Institute is also able to assemble the genomes of many (often unexpected) bacterial, archaeal and eukaryotic microbial organisms. We already have assemblies for over 6,000 bacterial, archaeal and eukaryotic microbes. These “cobionts” represent a subsampling of the organisms associated with the target species, and may be pathogens, parasites, components of the microbiome or chance encounters. To understand these cobionts more fully, we are seeking a Postdoctoral Fellow to work in a collaboration between the Tree of Life (ToL) and the Parasites and Microbes (PaM) programmes to collate, annotate and explore the biology of the bacterial and archaeal cobionts we discover. About the Role: You will work with ToL and PaM teams to identify cobionts in genome sequence datasets as they are generated and thus build a catalogue of host-microbe associations. You will explore the evolutionary and systems biology of host-microbiome interactions, including identification of phylogenetic associations between hosts and microbes, exploration of virulence and other phenotypes in pathogens, exploration of phage metagenomes, definition and functional analysis of horizontal DNA transfers into host genomes, and other topics. Where required, additional data will be commissioned to better evidence particular aspects of host and microbe. About Us: The post is shared between the Blaxter group (which has a focus on large scale analysis of genome evolution across diversity) and groups within PaM who have interests in (respectively) the genomic epidemiology of human pathogens and human microbiomes in health and disease. You will be embedded in a supportive and dynamic environment to produce significant work of wide impact. About You: You should have a PhD in Biomedical science, statistical genetics, microbial genomics, computational biology or similar related discipline or equivalent working experience in bioinformatics. You will have the ability to analyse and interpret data with strong quantitative/computational skills. You will have relevant programming skills in modern languages including Python and R and experience with software development and good practice in coding. Applicants should have excellent communication and organisational skills, and have the ability to work collaboratively with a range of stakeholders. When you join us as a Postdoctoral Fellow, you will benefit from a unique and well-resourced learning environment that will equip you for your future career. We are proud to produce and analyse genetic and cellular data on a scale unmatched by other institutes in Europe to advance biological and medical science. Essential Scientific and Technical Skills: PhD in relevant subject area, or on track to be awarded your PhD within 6 months of starting the role Proven ability to deliver research projects A track record of demonstrating research excellence and expertise in your area of research Knowledge, skills and experience as appropriate to the research area including: Ability to analyse and interpret data with strong quantitative/computational skills Programming in relevant, modern languages, including Python and R; experience with software development and good practice in coding Excellent communication and organisation skills Ability to work collaboratively and inclusively with a range of stakeholders Essential Competencies and Behavioural Skills: Proven ability to develop and maintain effective working relationships with wide range of persons of differing level, abilities and knowledge Foster an inclusive culture where all can thrive and diversity is celebrated Team player with the ability to work with others in a collegiate and collaborative environment Ability to effectively communicate ideas and results and present orally to groups Commitment to personal development and updating of knowledge and skills Ability to prioritise, multi-task and work independently Detail-orientated, with strong organisational and problem-solving skills Other information Please apply with your CV and a Cover Letter outlining how you would meet the criteria set out above. Salary: PDF £38,000 - £49,156 Role profile Closing Date: 26th January 2025 Recruitment Process: Zoom interviews w/c 3rd Feb, Face to face Interviews w/c 10th Feb Contract Type: 3 years fixed term contract Hybrid Working at Wellcome Sanger: We recognise that there are many benefits to Hybrid Working; including an improved work-life balance, with more focused time, as well as the ability to organise working time so that collaborative opportunities and team discussions are facilitated on campus. The hybrid working arrangement will vary for different roles and teams. The nature of your role and the type of work you do will determine if a hybrid working arrangement is possible. Equality, Diversity and Inclusion: We aim to attract, recruit, retain and develop talent from the widest possible talent pool, thereby gaining insight and access to different markets to generate a greater impact on the world. We have a supportive culture with the following staff networks, LGBTQ+, Parents and Carers, Disability and Race Equity to bring people together to share experiences, offer specific support and development opportunities and raise awareness. The networks are also a place for allies to provide support to others. We want our people to be whoever they want to be because we believe people who bring their best selves to work, do their best work. That’s why we’re committed to creating a truly inclusive culture at Sanger Institute. We will consider all individuals without discrimination and are committed to creating an inclusive environment for all employees, where everyone can thrive. Our Benefits: We are proud to deliver an awarding campus-wide employee wellbeing strategy and programme. The importance of good health and adopting a healthier lifestyle and the commitment to reduce work-related stress is strongly acknowledged and recognised at Sanger Institute. Sanger Institute became a signatory of the International Technician Commitment initiative In March 2018. The Technician Commitment aims to empower and ensure visibility, recognition, career development and sustainability for technicians working in higher education and research, across all disciplines. Life at the Sanger Institute is unique. We are tackling some of the most difficult challenges in genomic research. Our people are shaping the future by delivering life-changing science with the reach, scale, and creativity to solve some of humanity’s greatest challenges. We aim to attract, recruit, retain and develop talent from the widest possible talent pool, thereby gaining insight and access to different markets to generate a greater impact on the world.
sanger.wd103.myworkdayjobs.com
January 7, 2025 at 7:13 AM
Reposted by Stephen Doyle
This seems a useful list, and there are others in the thread of replies. Much as we probably shouldn't care about journal 'prestige', its clear not all academics are over it yet.
Have had some good chats recently about pivoting to non-profit and society journals. A point to share/underline is that such options exist across the "prestige" spectrum. Some examples in the image. All heavily subjective of course; would love to hear thoughts from others!
January 6, 2025 at 8:44 AM
Reposted by Stephen Doyle
Life Sciences summer internship opportunity for talented UK or Ireland undergraduates from underrepresented ethnicities & disadvantaged backgrounds. Join us in Cambridge. Apply by 16 January. www.exppg.lifesci.cam.ac.uk
Experience Postgrad Life Sciences | Enhancing diversity among life scientists of the future
www.exppg.lifesci.cam.ac.uk
January 5, 2025 at 12:34 PM