Susan Holmes🎲🖥️🧬
@sherlockpholmes.bsky.social
Statistician,Mother,Prof,Grandmother(she/her)🇫🇷🇵🇹🇺🇸🧪.
🖋️with @wkhuber.bsky.social:Modern Statistics for Modern Biology (https://www.huber.embl.de/msmb/) #stats,#rstats.OSS,arXiv, microbial ecology,cytof,multi-omics,Bioconductor:phyloseq, DADA2
🖋️with @wkhuber.bsky.social:Modern Statistics for Modern Biology (https://www.huber.embl.de/msmb/) #stats,#rstats.OSS,arXiv, microbial ecology,cytof,multi-omics,Bioconductor:phyloseq, DADA2
Pinned
My career path:
-- Develop computational methods so that when distributional assumptions are not met we can evaluate uncertainty.
-- Make fancy multivariate statistics easier to understand.
-- Help biologists use rank based tests correctly.
-- Ask biologists to plot their data.
-- Develop computational methods so that when distributional assumptions are not met we can evaluate uncertainty.
-- Make fancy multivariate statistics easier to understand.
-- Help biologists use rank based tests correctly.
-- Ask biologists to plot their data.
Reposted by Susan Holmes🎲🖥️🧬
Open position at the Swiss Institute of Bioinformatics:
We are looking for a Director of the Center of Pathogen Bioinformatics
apply.refline.ch/499599/0346/...
I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and
We are looking for a Director of the Center of Pathogen Bioinformatics
apply.refline.ch/499599/0346/...
I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and
Director, Center for Pathogen Bioinformatics
The Centre for Pathogen Bioinformatics (CPB) is a unit of SIB which offers expertise and services in pathogen bioinformatics, computational molecular epidemiology and related multi-site project manage...
apply.refline.ch
October 25, 2025 at 1:03 PM
Open position at the Swiss Institute of Bioinformatics:
We are looking for a Director of the Center of Pathogen Bioinformatics
apply.refline.ch/499599/0346/...
I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and
We are looking for a Director of the Center of Pathogen Bioinformatics
apply.refline.ch/499599/0346/...
I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and
Reposted by Susan Holmes🎲🖥️🧬
Hi! Florence Hommais, @nicolasparisot.bsky.social , and I are looking for a postdoctoral candidate to investigate the molecular dialogue between three weevil species and their endosymbiotic bacteria #symbiosis! Please see the #post-doc offer for more information. #SymbioSky #Bioinformatics
November 3, 2025 at 11:50 AM
Hi! Florence Hommais, @nicolasparisot.bsky.social , and I are looking for a postdoctoral candidate to investigate the molecular dialogue between three weevil species and their endosymbiotic bacteria #symbiosis! Please see the #post-doc offer for more information. #SymbioSky #Bioinformatics
Reposted by Susan Holmes🎲🖥️🧬
6 hours 30 mins they could do from this December, with one change in Badajoz or Elvas - but they're likely not going to do though
So 🤷♂️
Whenever I hear about these long term plans for ES-PT rail, I wonder why they're not doing the basics with what they have right now?
#CrossBorderRail
So 🤷♂️
Whenever I hear about these long term plans for ES-PT rail, I wonder why they're not doing the basics with what they have right now?
#CrossBorderRail
🇵🇹🚉🇪🇸 “Five-hour Lisbon-Madrid rail link to go ahead by 2030, say Portuguese and Spanish governments and the European Commission.”
www.euronews.com/travel/2025/...
www.euronews.com/travel/2025/...
Five-hour Lisbon-Madrid rail link to go ahead by 2030, officials say
The agreement between the Portuguese and Spanish governments and the European Commission also foresees, among other goals, a high-speed connection between the two capitals by 2034.
www.euronews.com
October 30, 2025 at 6:02 PM
6 hours 30 mins they could do from this December, with one change in Badajoz or Elvas - but they're likely not going to do though
So 🤷♂️
Whenever I hear about these long term plans for ES-PT rail, I wonder why they're not doing the basics with what they have right now?
#CrossBorderRail
So 🤷♂️
Whenever I hear about these long term plans for ES-PT rail, I wonder why they're not doing the basics with what they have right now?
#CrossBorderRail
Reposted by Susan Holmes🎲🖥️🧬
Spread the word! There is a professor position opening at our University @upcite.bsky.social. There are several possible (great) labs to join, but if you are interested in DNA methylation and epigenetics in mammals, don't hesitate to contact me directly!
#JobOffer
💼 Un poste susceptible d’être vacant de Professeur en stabilité des génomes devrait s’ouvrir pour la rentrée 2026 au sein de l’Institut Jacques Monod
➡️ Informations concernant ce poste et la procédure de candidature 🔗 www.ijm.fr/poste-de-pro...
💼 Un poste susceptible d’être vacant de Professeur en stabilité des génomes devrait s’ouvrir pour la rentrée 2026 au sein de l’Institut Jacques Monod
➡️ Informations concernant ce poste et la procédure de candidature 🔗 www.ijm.fr/poste-de-pro...
October 28, 2025 at 1:51 PM
Spread the word! There is a professor position opening at our University @upcite.bsky.social. There are several possible (great) labs to join, but if you are interested in DNA methylation and epigenetics in mammals, don't hesitate to contact me directly!
Reposted by Susan Holmes🎲🖥️🧬
My fantastic department at CU Boulder is hiring a tenure-track Assistant Professor! This is a broad search spanning nearly all areas of biology. Applications are due Nov 13, 2025. Feel free to reach out to me with questions, and please share widely.
jobs.colorado.edu/jobs/JobDeta...
jobs.colorado.edu/jobs/JobDeta...
October 17, 2025 at 4:00 PM
My fantastic department at CU Boulder is hiring a tenure-track Assistant Professor! This is a broad search spanning nearly all areas of biology. Applications are due Nov 13, 2025. Feel free to reach out to me with questions, and please share widely.
jobs.colorado.edu/jobs/JobDeta...
jobs.colorado.edu/jobs/JobDeta...
Reposted by Susan Holmes🎲🖥️🧬
A reminder that the PhD program for EMBL is open for winter recruitment round. If you want to understand life at a molecular level and have a quantitative science (you don't have to have done biology - we love our mathematicians/physcists/chemists!) apply www.embl.org/about/info/e...
Application – EMBL International PhD Programme
www.embl.org
October 9, 2025 at 4:51 AM
A reminder that the PhD program for EMBL is open for winter recruitment round. If you want to understand life at a molecular level and have a quantitative science (you don't have to have done biology - we love our mathematicians/physcists/chemists!) apply www.embl.org/about/info/e...
Reposted by Susan Holmes🎲🖥️🧬
The Data Science team at EMBL is hiring for two open positions! First, for a Scientific Community Manager, focusing on community aspects and training on data science. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Scientific Community Manager
EMBL is Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation with more than 110 independent research groups and teams performing scientific research in disci...
embl.wd103.myworkdayjobs.com
October 8, 2025 at 7:08 AM
The Data Science team at EMBL is hiring for two open positions! First, for a Scientific Community Manager, focusing on community aspects and training on data science. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Reposted by Susan Holmes🎲🖥️🧬
I'm looking for a doctoral student with Bayesian background to work on Bayesian workflow and cross-validation (see my publication list users.aalto.fi/~ave/publica... for my recent work) at Aalto University.
Apply through the ELLIS PhD program (dl October 31) ellis.eu/news/ellis-p...
Apply through the ELLIS PhD program (dl October 31) ellis.eu/news/ellis-p...
ELLIS PhD Program: Call for Applications 2025
The ELLIS mission is to create a diverse European network that promotes research excellence and advances breakthroughs in AI, as well as a pan-European PhD program to educate the next generation of AI...
ellis.eu
October 6, 2025 at 9:28 AM
I'm looking for a doctoral student with Bayesian background to work on Bayesian workflow and cross-validation (see my publication list users.aalto.fi/~ave/publica... for my recent work) at Aalto University.
Apply through the ELLIS PhD program (dl October 31) ellis.eu/news/ellis-p...
Apply through the ELLIS PhD program (dl October 31) ellis.eu/news/ellis-p...
Reposted by Susan Holmes🎲🖥️🧬
We are thrilled to announce that our NEW Large Language Model will be released on 11.18.25.
October 1, 2025 at 2:38 PM
We are thrilled to announce that our NEW Large Language Model will be released on 11.18.25.
Reposted by Susan Holmes🎲🖥️🧬
A 2-y postdoc position in my former group at University of Copenhagen is available in microbial ecology and bioinformatics.
See more: employment.ku.dk/faculty/?sho...
Feel free to contact me if you have questions about the environment.
Please share the ad.
See more: employment.ku.dk/faculty/?sho...
Feel free to contact me if you have questions about the environment.
Please share the ad.
Postdoc in Microbial bioinformatics
employment.ku.dk
October 2, 2025 at 5:51 AM
A 2-y postdoc position in my former group at University of Copenhagen is available in microbial ecology and bioinformatics.
See more: employment.ku.dk/faculty/?sho...
Feel free to contact me if you have questions about the environment.
Please share the ad.
See more: employment.ku.dk/faculty/?sho...
Feel free to contact me if you have questions about the environment.
Please share the ad.
Reposted by Susan Holmes🎲🖥️🧬
Professor (full) or Associate Professor (tenure track) in Microbial Genetics of Health (U. Turku Finland). Competitive starting package included! Please share.
duunitori.fi/tyopaikat/ty...
duunitori.fi/tyopaikat/ty...
Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto - Työpaikat - Duunitori
Avoin työpaikka: Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto, Turku. Duunitorilla lisäksi yli 30 000 muuta avointa työpaikkaa. Lue lisää nyt!
duunitori.fi
September 30, 2025 at 8:37 AM
Professor (full) or Associate Professor (tenure track) in Microbial Genetics of Health (U. Turku Finland). Competitive starting package included! Please share.
duunitori.fi/tyopaikat/ty...
duunitori.fi/tyopaikat/ty...
Reposted by Susan Holmes🎲🖥️🧬
#Exposition #Peluchologie 🧸 | L’exposition invite petits et grands à plonger dans l’univers des ours en peluche à travers un regard à la fois scientifique et historique
📆 du 22/09 au 13/11
📌 Médiathèque Émile Zola, Montpellier
🔗 infos : www.umontpellier.fr/agenda/expos...
📆 du 22/09 au 13/11
📌 Médiathèque Émile Zola, Montpellier
🔗 infos : www.umontpellier.fr/agenda/expos...
October 1, 2025 at 9:05 AM
#Exposition #Peluchologie 🧸 | L’exposition invite petits et grands à plonger dans l’univers des ours en peluche à travers un regard à la fois scientifique et historique
📆 du 22/09 au 13/11
📌 Médiathèque Émile Zola, Montpellier
🔗 infos : www.umontpellier.fr/agenda/expos...
📆 du 22/09 au 13/11
📌 Médiathèque Émile Zola, Montpellier
🔗 infos : www.umontpellier.fr/agenda/expos...
Reposted by Susan Holmes🎲🖥️🧬
Reposted by Susan Holmes🎲🖥️🧬
I feel like I should be able to crochet elliptic curves 🧶 Has anyone done this yet?
September 18, 2025 at 5:18 AM
I feel like I should be able to crochet elliptic curves 🧶 Has anyone done this yet?
Reposted by Susan Holmes🎲🖥️🧬
As someone who came to R from computer science a lot of this post resonates
Also, I had not previously connected the inconsistencies of the base R API to the same philosophy that makes CRAN work
Also, I had not previously connected the inconsistencies of the base R API to the same philosophy that makes CRAN work
Really insightful post from Julie Tibshirani (spotted in LinkedIn, can't find on Bsky) reflecting on #rstats 's unique governance structure and what can be learned for other languages
jtibs.substack.com/p/if-all-the...
jtibs.substack.com/p/if-all-the...
If all the world were a monorepo
The R ecosystem and the case for extreme empathy in software maintenance
jtibs.substack.com
September 15, 2025 at 1:45 PM
As someone who came to R from computer science a lot of this post resonates
Also, I had not previously connected the inconsistencies of the base R API to the same philosophy that makes CRAN work
Also, I had not previously connected the inconsistencies of the base R API to the same philosophy that makes CRAN work
Reposted by Susan Holmes🎲🖥️🧬
This xkcd is utterly brilliant and should be shared more:
Vaccine research: xkcd.com/2515/
Rollover text: Honestly feel a little sheepish about the amount of time and effort I spent confirming "yes, the vaccine helps protect people from getting sick and dying" but I guess everyone needs a hobby.
Vaccine research: xkcd.com/2515/
Rollover text: Honestly feel a little sheepish about the amount of time and effort I spent confirming "yes, the vaccine helps protect people from getting sick and dying" but I guess everyone needs a hobby.
![[White Hat is talking to Cueball.]
White Hat: I've been hearing about vaccines.
White Hat: But I decided to do my own research.
[In a frame-less panel White Hat continues to talk to Cueball.]
White Hat: So I spent months on the Internet reading hundreds of studies.
[Close up of White Hat as he speaks to Cueball, who replies from off-panel.]
White Hat: And wow, I gotta say,
White Hat: these vaccines are pretty good.
Cueball (off-panel): Oh, really.
[Zoomed back out, to White Hat and Cueball talking.]
White Hat: Yeah, seems like it'd be great if lots of people got them.
White Hat: Is anyone working on that?
Cueball: There's been some effort.
White Hat: Okay, cool.
Brilliant ALT text from: https://www.explainxkcd.com/wiki/index.php/2515:_Vaccine_Research](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:dcug5hr3622ym4zaueassqao/bafkreifpyph3vquc5ivszpehxpjhn6hvtqdwzhzvonbpzbrx3kb4bk3dka@jpeg)
September 14, 2025 at 6:05 PM
This xkcd is utterly brilliant and should be shared more:
Vaccine research: xkcd.com/2515/
Rollover text: Honestly feel a little sheepish about the amount of time and effort I spent confirming "yes, the vaccine helps protect people from getting sick and dying" but I guess everyone needs a hobby.
Vaccine research: xkcd.com/2515/
Rollover text: Honestly feel a little sheepish about the amount of time and effort I spent confirming "yes, the vaccine helps protect people from getting sick and dying" but I guess everyone needs a hobby.
Reposted by Susan Holmes🎲🖥️🧬
I keep stumbling when, in biological data analysis, someone uses the word "noise" as if it represented an objectively existing, tangible thing.
It is not. Noise is just another word for ignorance. Complicated but in principle deterministic stuff that ...
(1/2)
It is not. Noise is just another word for ignorance. Complicated but in principle deterministic stuff that ...
(1/2)
September 14, 2025 at 10:11 AM
I keep stumbling when, in biological data analysis, someone uses the word "noise" as if it represented an objectively existing, tangible thing.
It is not. Noise is just another word for ignorance. Complicated but in principle deterministic stuff that ...
(1/2)
It is not. Noise is just another word for ignorance. Complicated but in principle deterministic stuff that ...
(1/2)
New paper with Sourav Chatterjee and Persi Diaconis: Estimating the size of a set with cascading exclusion, see arxiv.org/abs/2508.05901 and a whole github repo of examples in R spholmes.github.io/SetSize/, thank you #rstats and #quarto.
Estimating the size of a set using cascading exclusion
Let $S$ be a finite set, and $X_1,\ldots,X_n$ an i.i.d. uniform sample from $S$. To estimate the size $|S|$, without further structure, one can wait for repeats and use the birthday problem. This requ...
arxiv.org
September 11, 2025 at 1:56 PM
New paper with Sourav Chatterjee and Persi Diaconis: Estimating the size of a set with cascading exclusion, see arxiv.org/abs/2508.05901 and a whole github repo of examples in R spholmes.github.io/SetSize/, thank you #rstats and #quarto.
Reposted by Susan Holmes🎲🖥️🧬
I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN.
It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package.
Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats
It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package.
Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats
ggplot2 4.0.0
A new major version of ggplot2 has been released on CRAN. Find out what is new here.
www.tidyverse.org
September 11, 2025 at 11:20 AM
Reposted by Susan Holmes🎲🖥️🧬
#Formation | Présentation des 148 projets lauréats des appels à projets "Formation" de l'Université de Montpellier #PedagoNUM
#COMP en 2024 et 2025 en faveur de la réussite étudiante, du numérique, de la formation à l'IA ou à la transition écologique, des équipements pédagogiques innovants...
#COMP en 2024 et 2025 en faveur de la réussite étudiante, du numérique, de la formation à l'IA ou à la transition écologique, des équipements pédagogiques innovants...
September 10, 2025 at 8:01 AM
#Formation | Présentation des 148 projets lauréats des appels à projets "Formation" de l'Université de Montpellier #PedagoNUM
#COMP en 2024 et 2025 en faveur de la réussite étudiante, du numérique, de la formation à l'IA ou à la transition écologique, des équipements pédagogiques innovants...
#COMP en 2024 et 2025 en faveur de la réussite étudiante, du numérique, de la formation à l'IA ou à la transition écologique, des équipements pédagogiques innovants...
Reposted by Susan Holmes🎲🖥️🧬
Join EMBL as a research group leader in AI in biology. EMBL AI is our new initiative aiming to exploit the full potential of ML/AI-based approaches to advance our understanding of the most complex system in the known universe - life on Earth.
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
(1/3)
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
(1/3)
September 9, 2025 at 10:07 AM
Join EMBL as a research group leader in AI in biology. EMBL AI is our new initiative aiming to exploit the full potential of ML/AI-based approaches to advance our understanding of the most complex system in the known universe - life on Earth.
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
(1/3)
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
(1/3)
Reposted by Susan Holmes🎲🖥️🧬
Please do not forget that some scientists were cozying up to Epstein long long long after his horrific behavior was known. Five of them are featured in the Birthday Book.
Gerry Edelman.
Murray Gellman.
Steve Kosslyn.
Martin Nowak.
Lee Smolin.
See docs: oversight.house.gov/release/over...
Gerry Edelman.
Murray Gellman.
Steve Kosslyn.
Martin Nowak.
Lee Smolin.
See docs: oversight.house.gov/release/over...
September 9, 2025 at 2:09 AM
Please do not forget that some scientists were cozying up to Epstein long long long after his horrific behavior was known. Five of them are featured in the Birthday Book.
Gerry Edelman.
Murray Gellman.
Steve Kosslyn.
Martin Nowak.
Lee Smolin.
See docs: oversight.house.gov/release/over...
Gerry Edelman.
Murray Gellman.
Steve Kosslyn.
Martin Nowak.
Lee Smolin.
See docs: oversight.house.gov/release/over...
Reposted by Susan Holmes🎲🖥️🧬
Still possible to apply to this #post-doc position at CESAB #Montpellier.
Application closing date: September 15th 2025 (12:00 PM CET)
How taking intraspecific diversity and evolutionary processes into account in translocation-based programs.
Please share widely #PopGen #NbS #Biodiversity
Application closing date: September 15th 2025 (12:00 PM CET)
How taking intraspecific diversity and evolutionary processes into account in translocation-based programs.
Please share widely #PopGen #NbS #Biodiversity
3-year #postdoc position at Centre de synthèse et d'analyse de la biodiversité (CESAB) in Montpellier to work on how taking intraspecific diversity and evolutionary processes into account in translocation-based programs. Please share widely #PopGen #NbS
[📢 Postdoc offer in Montpellier] Work on intraspecific diversity & translocation in Nature-based Solutions 🌿
Join the EVOLUTION Knowledge-Hub at the #FRB-CESAB
🔗 More informations: bit.ly/43uRz6Z
@cnrs.fr @inrae-france.bsky.social @umontpellier.bsky.social
Join the EVOLUTION Knowledge-Hub at the #FRB-CESAB
🔗 More informations: bit.ly/43uRz6Z
@cnrs.fr @inrae-france.bsky.social @umontpellier.bsky.social
September 2, 2025 at 2:28 PM
Still possible to apply to this #post-doc position at CESAB #Montpellier.
Application closing date: September 15th 2025 (12:00 PM CET)
How taking intraspecific diversity and evolutionary processes into account in translocation-based programs.
Please share widely #PopGen #NbS #Biodiversity
Application closing date: September 15th 2025 (12:00 PM CET)
How taking intraspecific diversity and evolutionary processes into account in translocation-based programs.
Please share widely #PopGen #NbS #Biodiversity
Reposted by Susan Holmes🎲🖥️🧬
We are recruiting two biomedical data scientists as part of a new Centre of Research Excellence (MRC CoRE) in Exposome Immunology hosted jointly by @fbmh-uom.bsky.social and @ox.ac.uk.
www.jobs.manchester.ac.uk/Job/JobDetai...
www.jobs.manchester.ac.uk/Job/JobDetai...
www.jobs.manchester.ac.uk/Job/JobDetai...
www.jobs.manchester.ac.uk/Job/JobDetai...
Senior Biomedical Data Scientist:Oxford Road
As an equal opportunities employer we welcome applicants from all sections of the community regardless of age, sex, gender (or gender identity), ethnicity, disability, sexual orientation and transgender status. All appointments are made on merit.
www.jobs.manchester.ac.uk
September 4, 2025 at 4:31 PM
We are recruiting two biomedical data scientists as part of a new Centre of Research Excellence (MRC CoRE) in Exposome Immunology hosted jointly by @fbmh-uom.bsky.social and @ox.ac.uk.
www.jobs.manchester.ac.uk/Job/JobDetai...
www.jobs.manchester.ac.uk/Job/JobDetai...
www.jobs.manchester.ac.uk/Job/JobDetai...
www.jobs.manchester.ac.uk/Job/JobDetai...
Reposted by Susan Holmes🎲🖥️🧬
August 27, 2025 at 7:44 AM