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Lilly Cummins

@lillycummins.bsky.social
1.1K followers 441 following 59 posts

she/her | Postdoc @ University of Oxford | bacterial evolutionary genomics, pangenomes, AMR | I believe in equality

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Reposted by Lilly Cummins
Robin Hayward 🌳 🏳️‍⚧️ @canopyrobin.com · 25/09/2026
We're publishing new guidance to support trans people who do fieldwork (any work outside the office)! Now we need your help to get them seen so please share! inclusivefieldwork.leeds.ac.uk/trans/
a cartoon of three fieldworkers. One has a small trans flag. The logos of the university of leeds, research england, and canopy robin are shown, as well as the URL: InclusiveFieldwork (dot) Leeds (dot) AC (dot) UK (slash) trans
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Hannah Pugh @hannahpugh.bsky.social · 09/09/2026
Does anyone know where one could can obtain a stock of E. coli UTI89 from? It is unavailable at both NCTC and ATCC. 🧫
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Will Matlock @wtmatlock.bsky.social · 09/09/2026
Does an AMR gene on a plasmid diversify differently to an AMR gene on a chromosome? We are looking for a PhD student to work on this question in Bath!
gw4biomed.ac.uk
Turning up the volume: plasmid copy number and gene duplications as drivers of antimicrobial resistance evolution - GW4 BioMed MRC DTP
Project Code IIAR27Ba Matlock Project Type Wet lab Research Theme Infection, Immunity, and Antimicrobial Resistance Project Summary Download Summary Plasmids are important drivers of antimicrobial res...
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Siobhán O'Brien @siderophile.bsky.social · 21/08/2026
And that’s a wrap on #MENI2026! What a great day of microbial evolution research, and a pleasure to host at Trinity with @paulinedscanlan.bsky.social
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Paul Hoskisson 🧫 🦠🐸 @paulhoskisson.bsky.social · 22/06/2026
This is an awesome review from @sheppardlab.bsky.social - Epistasis and co-adaptation in bacterial genome #evolution www.nature.com/articles/s41...
nature.com
Epistasis and co-adaptation in bacterial genome evolution - Nature Reviews Genetics
Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic interactions into population-...
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Laurie Belcher @lauriebelch.bsky.social · 26/05/2026
We’re hiring for OrthoFinder! Great role for someone who enjoys scientific software development: Python, data analysis, workflows, Git, scalability, and making tools nicer to use. Comparative genomics or open-source bioinformatics experience would be a lovely bonus. my.corehr.com/pls/uoxrecru...
my.corehr.com
Job Details
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Fiona J Whelan @whelanfj.bsky.social · 13/05/2026
After a few technical glitches... 📣 Whelan lab is hiring 📣 We are looking for an entry level technician to help us with our culturing and DNA sequencing prep of cystic fibrosis lung microbiome samples. Applications close 28 May 2026 Any queries, please reach out!
jobs.manchester.ac.uk
Research Technician in Microbiology and Molecular Biology:Oxford Road
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Fiona J Whelan @whelanfj.bsky.social · 11/05/2026
📣 Whelan lab is hiring 📣 We are looking for an entry level technician to help us with our culturing and DNA sequencing prep of cystic fibrosis lung microbiome samples. Applications close 20 May 2026. www.jobs.manchester.ac.uk/Job/JobDetai...
jobs.manchester.ac.uk
Research Technician in Microbiology and Molecular Biology:Oxford Road
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Ilyas Alav @ilyasalav.bsky.social · 01/05/2026
I’m looking to hire a talented postdoctoral research assistant to work with me on my Wellcome Trust-funded project at the @dunnschool.bsky.social If you’re interested in bacterial pathogenesis and host-pathogen interactions, please apply below! my.corehr.com/pls/uoxrecru...
my.corehr.com
Job Details
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Laura Hollis @laurahollis.bsky.social · 30/04/2026
Thrilled to have passed my PhD viva yesterday! A wonderful way to end 4 great years in the Geoghegan lab.
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Lilly Cummins @lillycummins.bsky.social · 29/04/2026
🚨 The @microbiologysociety.org summer conference this year is in Birmingham! A great place for ECRs to network, share science and chat about careers Submit your abstract by end of day tomorrow 👇
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Microbiology Society @microbiologysociety.org · 21/04/2026
Registration is open for our Early Career Summer Conference 🤝👩‍🔬 Join us on 6–7 July 2026 at the University of Birmingham for chance to network with peers and experienced colleagues in various fields of Microbiology, secure your place today: microb.io/ECConf26 #ECConf26
Two people discussing scientific posters at the Microbiology Society Early Career Summer Conference 2025.
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Siobhán O'Brien @siderophile.bsky.social · 20/04/2026
Just over two weeks left to register for MENI 2026! A !!free!! microbial evolution meeting in Ireland with some fantastic keynote speakers @jpjhall.bsky.social @rachelmwheatley.bsky.social @drrebeccajhall.bsky.social @tweethinking.bsky.social #Evolution #microbes www.eventbrite.com/e/3rd-microb...
eventbrite.com
3rd Microbial Evolution Network Ireland meeting
2026 Microbial Evolution Network Ireland meeting, at Trinity College Dublin
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MEEhubs @meehubs.bsky.social · 17/04/2026
2 days left ‼️ Don't forget to submit your abstract to MEEHubs2026: Aug 3-5, 2026 meehubs.org
meehubs.org
Home
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Fiona J Whelan @whelanfj.bsky.social · 15/04/2026
The Whelan lab is well represented at #microbio26 today! @fgyapong.bsky.social culturing the 🐟 microbiome (10:45 Microbiome f.& B182) @melissalawson.bsky.social a 🪰 model pathogen-microbe int. (14:30 Infection f.) @michelle-micro.bsky.social on microbe-microbe int. (15:00 Und. Microbe Function f)
First slide of Francis Gyapong's (3rd year PhD student) talk on culturing the stickleback microbiome.First slide of Mel Lawson's (PDRA) talk on using a Drosophila model of pathogen-microbe interactions.First slide of Michelle Hardman's (PDRA) talk on microbe-microbe interactions.
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Lilly Cummins @lillycummins.bsky.social · 15/04/2026
Really looking forward to today’s pangenomics session at #MicroBio26 ! I’ll be speaking at 10:45 to discuss how a successful pathogen can alter the evolution of an entire species pangenome 🦠
A screenshot from the conference app sharing the title, abstract and location for my talk at 10:45-11:00 in Hall 2A
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Rachel M. Wheatley @rachelmwheatley.bsky.social · 30/03/2026
🔊 Looking for a Research Assistant in Bacterial Evolution to join my lab 🦠 🥼Main duties: Research (AMR + microbiome) + lab assistance. ⏲️ Post duration: 30 months 🗓️ Closing date for applications: 20th April 2026 💰 Salary: ~£35k Details and how to apply: tinyurl.com/2a3v66y7 Please share!
lnkd.in
LinkedIn
This link will take you to a page that’s not on LinkedIn
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Alan McNally @alanmcn1.bsky.social · 19/03/2026
Am stoked and thrilled that our latest paper is now out. A longitudinal study of invasive E. coli from children in the Netherlands over 50 years www.sciencedirect.com/science/arti...
sciencedirect.com
Lineage dynamics of invasive Escherichia coli isolates in the Netherlands from 1975 to 2021: a retrospective longitudinal genomic analysis
Escherichia coli is a common cause of invasive infections such as bloodstream and cerebrospinal fluid infections in neonates. Strains positive for the…
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Fiona J Whelan @whelanfj.bsky.social · 13/03/2026
📣 The Whelan lab is hiring a bioinformatics postdoc 📣 Together with @fabricejpierre.bsky.social, we are offering a 1-year bioinformatic PDRA position in comparative genomics of Pseudomonas aeruginosa. To find out more please visit whelanlab.co.uk/contact/. Applications close 3 April 2026!
jobs.manchester.ac.uk
Research Associate in Microbial Genomics:Manchester
This postdoctoral research position is part of a Cystic Fibrosis Canada Early Career Investigator Award funded for 3-years led by Dr. Fabrice Jean-Pierre and Dr. Fiona Whelan. The aim of this project is to identify the genetic changes that arise in the Pseudomonas aeruginosa genome following perturbations – such as antibiotic treatment – in an in vitro system. The PDRA will use a large dataset of P. aeruginosa genomes and experimental metadata to predict key mutationsto the organism.
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Nature Reviews Genetics @natrevgenet.nature.com · 09/03/2026
ICYMI: New online! Epistasis and co-adaptation in bacterial genome evolution
dlvr.it
Epistasis and co-adaptation in bacterial genome evolution
Nature Reviews Genetics, Published online: 02 March 2026; doi:10.1038/s41576-026-00941-7Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic interactions into population-scale analyses can improve genotype–phenotype mapping and provide a deeper understanding of the complex traits that shape the microbial world.
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Nature Reviews Genetics @natrevgenet.nature.com · 02/03/2026
New online! Epistasis and co-adaptation in bacterial genome evolution
dlvr.it
Epistasis and co-adaptation in bacterial genome evolution
Nature Reviews Genetics, Published online: 02 March 2026; doi:10.1038/s41576-026-00941-7Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic interactions into population-scale analyses can improve genotype–phenotype mapping and provide a deeper understanding of the complex traits that shape the microbial world.
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Lilly Cummins @lillycummins.bsky.social · 02/03/2026
I’ve spent a lot of time over the past two years thinking about genome evolution and how recent research revealing complex gene-gene interactions has complicated traditional ‘gene-centric’ genomic approaches to evolution. So here is a review that consolidates these thoughts! rdcu.be/e6pHY
rdcu.be
Epistasis and co-adaptation in bacterial genome evolution
Nature Reviews Genetics - Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic...
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Alex Figueiredo @alexfig.eurosky.social · 18/02/2026
Are you, or do you know, a masters/undergrad looking to take part in a cool research project in bird behaviour, in a lovely field site? Look no further! 👇 (pls share!)
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Siobhán O'Brien @siderophile.bsky.social · 18/02/2026
MENI is back! Join us in Dublin this August 2026 for our 3rd Meeting for Microbial Evolution in Ireland. We are delighted to have @rachelmwheatley.bsky.social @drrebeccajhall.bsky.social @jpjhall.bsky.social and @tweethinking.bsky.social join us as keynote speakers this year. miniurl.com/MENI
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Kasia M Parfitt @kasiamparfitt.bsky.social · 11/02/2026
I am delighted to share our pre-print on a LIN code system for C. jejuni and C. coli 🎊
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Lilly Cummins @lillycummins.bsky.social · 11/02/2026
A great initiative supporting women in microbiology! #microsky
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Rachel M. Wheatley @rachelmwheatley.bsky.social · 05/01/2026
🔊 Job Opportunity: Postdoctoral Research Fellow in Bacterial Evolution. Looking to recruit a postdoc to join a UKRI FLF-funded project on antibiotic resistance evolution in the microbiome 🦠 3 years funding, deadline 26th Jan, please share! hrwebapp.qub.ac.uk/tlive_webrec...
hrwebapp.qub.ac.uk
Job profile
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Microbiology Society @microbiologysociety.org · 02/01/2026
Microbial pangenomics is reshaping our understanding of microbial diversity. Reaching new frontiers of an open and evolving discipline, hear the latest insights at Annual Conference 2026. Registration is open: microb.io/AC26Register #Microbio26
microb.io
Annual Conference 2026
Industry opportunities
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Alan McNally @alanmcn1.bsky.social · 16/12/2025
The first preprint from @izziepotterill.bsky.social PhD. A clone within ST131 clade C with a totally unique capsule region.
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Ineos Oxford Institute for antimicrobial research @ineosoxford.bsky.social · 03/12/2025
We're pleased to announce the annual IOI Early Career Researcher Conference will be held on 20 March 2026 at Saïd Business School, Oxford. A conference for early career researchers, designed by early career researchers. Register for your free place now: www.ineosoxford.ox.ac.uk/event/ioi-ea...
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Contamination Club @contamclub.bsky.social · 28/11/2025
The ContamCalendar 2026 will likely be the final calendar we make, so we wanted it to be a great one. The new design folds out to be A3, perfect for displaying the beautiful microbes inside 😍 Also full of microbe-related days throughout the year 📆🦠🧫🍄
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Contamination Club @contamclub.bsky.social · 24/11/2025
💥CONTAM CALENDAR GIVEAWAY💥 Here's your chance to win a ContamCalendar 2026! 🗓️🍄🦠 Just follow @contamclub.bsky.social and repost this post to enter the competition Winner will be randomly selected from Bluesky or Twitter on Wednesday @ 6pm UTC
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Contamination Club @contamclub.bsky.social · 21/11/2025
‼️🚨🗓️ CONTAMCALENDAR 2026 🗓️🚨‼️ Excited to say the ContamCalendar is back for its fifth edition! We’ve created a fresh new design, folding out for an A3 monthly spread. It’s our best yet, we hope you’ll love it 🗓️🦠🧫🍄 Get yours here ➡️ www.contam.club ⬅️
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Contamination Club @contamclub.bsky.social · 21/11/2025
Look out for an exciting announcement later…. 👀 #ContamCalendar
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Alan McNally @alanmcn1.bsky.social · 20/11/2025
Our latest is out tonight in @microbiologysociety.org MGen. Using long read seq to ID and then control hospital transmission of a CRKp we believe shows genomic and clinical signs of hypervirulence www.microbiologyresearch.org/content/jour...
microbiologyresearch.org
Identification and response to a putatively hypervirulent, carbapenem-resistant Klebsiella pneumoniae ST395 hospital outbreak in the UK
Here, we describe a putatively hypervirulent, carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) outbreak. Nanopore sequencing guided the infection prevention and control (IPC) responses during the ...
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Alan McNally @alanmcn1.bsky.social · 12/11/2025
Brilliant day having a project meeting with @sheppardlab.bsky.social and @lillycummins.bsky.social today on our BBSRC project. I still love my research even if I get less time on it now.
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Kasia M Parfitt @kasiamparfitt.bsky.social · 10/11/2025
Just submitted my abstracts. Make sure to pop yours in 📝
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Fiona J Whelan @whelanfj.bsky.social · 27/10/2025
So much of this article is full of hope then, "About 43% of respondents had experienced some form of discrimination or harassment.. in around four out of ten bullying cases, a student reported bullying by their supervisor." We need safeguards in place to stop this from happening.
nature.com
What makes PhD students happy? Good supervision
Supervisors who invest in positive mentoring relationships with their PhD candidates also reap the benefits for their own research.
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Microbiology Society @microbiologysociety.org · 23/10/2025
External Event Grant awards of up to £750 are available for eligible members as a contribution towards the costs of registration, travel, and accommodation to attend an event beginning in the period 01 Jan – 30 April 2026. Apply now before the deadline 01 Nov at 23:59 GMT: microb.io/ExternalEven...
microb.io
External Event Grant
Login to apply
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Microbiology Society @microbiologysociety.org · 19/10/2025
Join us online for the Education and Outreach Network Winter Conference on 7 November 2025. Attendance is free, and registration remains open until 4 November 2025 at 23:59 GMT. Register now: Link in bio
Illustration promoting the Education and Outreach Network Winter Conference, featuring scientific icons. The event will take place online on 7 November 2025 and is free to attend.
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Microbiology Society @microbiologysociety.org · 15/10/2025
To celebrate Black in Micro Week, the @blackinmicro.bsky.social have published a new commentary, Reclaiming Microbiology: Scientists as Community Members & Advocacy Leaders. Read the article: doi.org/10.1099/mgen... #MGen #BiM2025
microb.io
Reclaiming microbiology: scientists as community members and advocacy leaders
Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the…
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Eva Heinz @evaheinz7.bsky.social · 15/10/2025
To celebrate and support the great @blackinmicro.bsky.social initiative and what joining could mean for you, please take a look through the commentary in Microbial Genomics @microbiologysociety.org hot off the press today! #MicroSky #MicrobiomeSky 💻🧬🧪🦠 www.microbiologyresearch.org/content/jour...
microbiologyresearch.org
Reclaiming microbiology: scientists as community members and advocacy leaders
Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefi...
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Fiona J Whelan @whelanfj.bsky.social · 10/10/2025
📣 Reminder of the below fully-funded PhD studentships in exposome immunology! Projects interfacing with other areas (e.g. the human microbiome) are also on offer. Please reach out if you have any questions. Applications due 2 Dec 2025 📣
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Erik Bakkeren @erikbakkeren.bsky.social · 07/10/2025
Note it in your calendars! Aug 3-5, 2026. Excited to bring back MEEHubs to a hub near you (Switzerland, USA, Canada, Mexico, UK, Ukraine, or virtual only)‼️
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Alan McNally @alanmcn1.bsky.social · 07/10/2025
After being with the journal since its very inception, the time has come for me to step back from Microbial Genomics. This is a wonderful opportunity to have a leadership role in one of the leading journals for microbial genomics research microbiologysociety.org/news/society...
microbiologysociety.org
<i>Microbial Genomics </i> Deputy Editor-in-Chief: Call for Expressions of interest
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Lilly Cummins @lillycummins.bsky.social · 07/10/2025
Great science-filled afternoon at @microbiologysociety.org HQ watching finalists present at the Early Career Microbiologist of the Year Finals! All the speakers gave fantastic talks on a wide variety of subjects 🦠🧫🔬
Photograph taken from within a seated audience showing a screen with ‘EARLY CAREER MICROBIOLOGIST OF THE YEAR TALK FINAL’
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Microbiology Society @microbiologysociety.org · 30/09/2025
Applications for Outreach and Engagement grant are closing tomorrow at 23.59 BST. Members can apply for up to £1000 to support relevant science outreach or public engagement initiatives. Check your eligibility and apply now: microb.io/OutreachandE....
microb.io
Outreach and Engagement Grant
Eligible members can apply for up to £1000 to support relevant science outreach or public engagement initiatives that engage new audiences in the art and science in any aspect of microbiology.…
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CampyUK2025 @campyuk2025.bsky.social · 25/09/2025
Our fantastic @sheppardlab.bsky.social DPhil student Madison Goforth gives us a global overview of Campylobacter source attribution and the spread of AMR 🌎💊🌎 #CampyUK2025 @microbiologysociety.org @ineosoxford.bsky.social @biology.ox.ac.uk
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CampyUK2025 @campyuk2025.bsky.social · 24/09/2025
Are antibiotics a dead parrot? 🦜Prof Aidan Taylor kicks off the ‘From farm to fork’ session discussing Campylobacter AMR and vaccine development 🧫💉 #CampyUK2025 @microbiologysociety.org @ineosoxford.bsky.social @biology.ox.ac.uk
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