Dr Emma Hodcroft

@firefoxx66.bsky.social

17587 Followers 185 Following

Die Virenjägerin! 🏹🧬! Using programming & phylogenetics, I study & track viruses. Co-developer of Nextstrain, based at Swiss TPH & Uni Basel. Founder of CoVariants.org, co-founder of @pathoplexus.org I like 🐈 & 🛫 @firefoxx66@mstdn.science

Banner for the 1st Swiss Enterovirus Symposium 2026. Shows a virus to the left and a picture of a monastery in the Alps on the right. Tagline says: "Enterovirus Research and Surveillance: Strengthening Networks in Europe and Beyond". Dates: 5-8 October 2026 Location: Disentis, Switzerland Information: In-person only Website: ses2026.org
Photo of a lone green rolling suitcase sitting completely alone in the middle of a busy airport gate area tarmac surrounded by aircraft stairs and airport vehicles, in the sun.
A phylogenetic tree showing linked sequences from the S and L segment of ANDV virus (Andes Hantavirus)
Banner for the 1st Swiss Enterovirus Symposium 2026. Shows a virus to the left and a picture of a monastery in the Alps on the right. Tagline says: "Enterovirus Research and Surveillance: Strengthening Networks in Europe and Beyond". Dates: 5-8 October 2026 Location: Disentis, Switzerland Information: In-person only Website: ses2026.org
#OnThisDay 1930: the BBC's news announcer said, "there is no news" and piano music was played for the remainder of the 15 minute segment.
Email from amazon announcing they will no longer support Kindle devices from 2012 or earlier - even if they are working fine.
A screenshot of the arguments table for SimPlotCL, just giving a brief view of some of the arguments and what they do, such as --metadata, --colors, --windowsize, --stepsize, etc.
A figure showing a 'Simplot' which plots the similarity of a genome to other genomes across a graph, with similarity on the Y-axis and the genome position on the x-axis. Many coloured lines show the sequences being compared - those closest to the top (similarity of 1) are the closest matches in different parts of the genome.
A "lantern" from Basel Fasnacht (carnival) celebrations, showing an upside down white abstract dove holding a neon green leaf in its beak
A screenshot of a FB memories post from 6 years ago today, 23 Feb 2020. Emma Hodcroft posts: "So yea. This is it. This is the post. SARS-CoV-2 is extremely likely to become (if not already) pandemic. What's most important right now is getting a handle on how quickly it is spreading and where. This means increasing testing and trying to slow the spread to buy time."
Screenshot showing the results screen of Nextclade, with example D68 sequences having been run, showing the sequence name, QC status, clade assignment, and mutations relative to the reference
Screenshot showing the EV-D68 dataset on Nextclade, with some example data loaded, ready to run
A gif of the Nextclade interface, using the new EV-D68 dataset, showing how to upload files, the resulting panel with QC and clade assignment, and the position of the sequences on the reference tree.
A cartoon version of the EVE lab, generated by ChatGPT from a similar photo, showing Nosihle, Emma, Nadia, and Keno
Screenshot of the Collaborations page of the Eve-lab website, showing some of our collaborations: ARTIC2, Center for Pathogen Bioinformatics, ENPEN, ESCAPE, Pathoplexus, & VIM
Image showing information on the BC2 (Basel Computational Biology Conference) from 8-10 Sept 2025. Says: "Tutorial: build a microbial genomic sequence database with Loculus - Register now. 8 Sept 2025 - Biozentrum, Basel. Early bird until 30 June 2025"
An image showing the ARTIC and Pathoplexus logos connected by blue lines, with the text "Hiring: post-doc/software engineer" and "Global open-source pathogen tools" and "Join Swiss TPH, Work on ARTIC2 and Pathoplexus, Basel, Switzerland"
"The main contradiction of liberal democracy is that it has largely been shaped through a history of various friends of illegal civil disobedience against entrenched power structures. Such civil disobedience is (retrospectively) seen as justified, and the people committing it are (retrospectively) seen as heroes... But each successive generation is asked to believe that any further civil disobedience would be unreasonable."
A picture of Emma, the post author, on a train holding a homemade sign stating "the power of the people is stronger than the people in power"
A photo of the poster, Emma Hodcroft, on 5 May 2015. She is wearing a dark blue top and orange-and-blue patterned skirt, and looking nervous but smiling. She holds a very thick copy of her thesis (printed one-sided and double-spaced as regulations required) with many coloured page-marking tabs sticking out of the sides & top. She stands before a wooden desk covered in notes, notebooks, post-its, small knick-nacks and toys (and a computer), in Ashworth Building at University of Edinburgh, where she did her PhD.
A screenshot of the In Vivo website showing 30 selected 'Rising Leaders' for 2020, including Emma Hodcroft.
A screenshot of the shared mutations view on CoVariants, showing columns labelled with the Nextstrain names of variants
A screenshot of the per-country view on CoVariants, with the mouse-hover legend appearing, showing variant names labelled with Nextstrain names
A gif showing a new toggle at the top of CoVariants, showing the left-hand menu switching between Nextstrain and Pango lineages
A photo from the 1990s showing 2 girls, aged roughly 5 and 3, making sandcastles on a UK beach on an overcast summer day. Both are bundled up against the cold - wearing long trousers, shoes, and thick parka-style jackets with faux-fur trimming. The post author (Emma) is the girl on the left, barely visible peeking out cheekily from her huge furry hood.
Photo of the World Reference Centre for Emerging Viruses and Arboviruses University of Texas Medical Branch and some description of their work.
Myself and my mother at the protest today with signs "no scientific future = no scientific funding" and "defiance for science"
A screenshot of an email from a travel-alert-security program sending alerts about upcoming protests "denouncing national government policies", with a neat list of places, dates, and times.
Photo credit: https://www.flickr.com/photos/au_ears/25373576072/
Photo from etsy user StickemUK whose shop unfortunately seems to be closed, or I would link it. Photo is of many overlapping stickers with slogans like 'empowered women empower women' 'black lives matter' 'strength in unity' 'equal' 'we need more empathy' in many colours and beautiful designs.
Image with text that reads: It's happening now: - All US health meetings around the world remain cancelled indefinitely. This includes critical ones on ‘bird flu,’ flu vaccines, and seasonal flu - and things like the recent Ebola case in Uganda, and other global health crises. Disease respects no borders. To combat disease we must benefit from and contribute to international information and dialogue. (Source: Reuters)
Image with text that reads: It's happening now: The NIH (National Institute of Health) has issued guidance to terminate all contracts or grants that include 'gender ideology'. This includes using the word 'gender' according to the memo issued. That means potentially all studies that say 'gender: M/F' instead of 'sex: M/F' on a survey or intake form could be cancelled. It could also impact studies specifically designed to better understand treatments and drugs on diverse populations - including women (traditionally excluded from medical trials!), people of different sexuality, different races, different gender presentations, and people with disabilities. Potentially years of research and studies lost. (Source: Science.org)
Image with text that reads: It's happening now: - The NSF (National Science Foundation) has frozen payments on all grants. PhD student and Post-doc salary requests were denied this Tuesday. No news on when they will get paid. This applies to ALL NSF grants (which are hugely prestigious) - work on evolution, geology (earthquakes), cancer, novel chemicals, and more. If funds stay frozen, animals will have to be euthanized, and billions of dollars of experiments will be lost. This impacts all kinds of work, in the name of stopping programs that may list DEI principles. (Source: NPR)
Image with text that reads: It's happening now: All of the American Public Health Labs (APHL) Global Health team has been furloughed. This is everyone outside of the US, including deployed staff and locally employed staff. These are people working on infectious diseases (and more) all over the world. Designing tests. Improving diagnostics. Improving lab procedures. This is a huge team, doing critical work.
Image with text that reads: It's happening now: Critical disease-related publications like MMWR (Morbidity and Mortality Weekly Report) are frozen, with no release this week. This report is a lifeblood of health events in the USA. it has been published weekly without pause since 1960. It is essential for keeping all US (and global) researchers updated on outbreaks and investigations. This week alone there were reportedly to be 3 publications on the bird flu. The publication is also a likely venue for further information about the ongoing Tuberculosis outbreak in Kansas. (Source: Reuters)
Image with text that reads: It's happening now: I know it's totally overwhelming but here are just a handful of things happening in US Science & public health RIGHT NOW. I need you to know, so you can realise how you are being defrauded from a healthy, disease free future, with thriving science. I need you to know, so you can tell others.
Emma sits in front of a real, fully decorated Christmas tree, smiling. She wears a red top and black jumper with a sparkly snowflake pin and golden necklace. Her earrings say "Ho Ho" in shiny red and on her head are a pair of toy, fluffy reindeer ears and antlers, with small sprigs of holly.
Screenshot of the Nature 10 for 2024 article, showing the 'ones to watch 2025' list at the bottom of the page, which lists Mark Thomson (incoming director of CERN), Emma Hodcroft (for Pathoplexus), and Donald Trump (incoming present of US).