Marc Suchard
@msuchard.bsky.social
Striving to provide better evidence to improve health globally! Professor, Departments of Biostatistics, Computational Medicine and Human Genetics, UCLA
Open science!
1/ 🚀 Big thanks to our community - since August we’ve added thousands of new sequences, rolled out major new features, and welcomed fresh faces into the #Pathoplexus world. Let’s dive into what’s new.👇🏻
Read the full update: pathoplexus.org/news/2025-11...
Read the full update: pathoplexus.org/news/2025-11...
November 19, 2025 at 4:46 AM
Open science!
Very much enjoyed reading this paper!
academic.oup.com/evlett/advan...
So exciting to see a new method to model the evolution of G (and P) matrices on phylogenies. Another step in the direction of trying to bridge micro and macroevolution
So exciting to see a new method to model the evolution of G (and P) matrices on phylogenies. Another step in the direction of trying to bridge micro and macroevolution
Multivariate trait evolution: models for the evolution of the quantitative genetic G-matrix on phylogenies
Abstract. Genetic covariance matrices (G-matrices) are a key focus for research and predictions from quantitative genetic evolutionary models of multiple t
academic.oup.com
November 7, 2025 at 1:57 PM
Very much enjoyed reading this paper!
Reposted by Marc Suchard
Gill, @lemeylab.bsky.social et al. develop Bayesian infinite mixture models for phylogenetic inference, finding that infinite hidden Markov models best capture complex patterns in large datasets; they implement this framework in BEAST X.
🔗 doi.org/10.1093/molbev/msaf199
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf199
#evobio #molbio
Infinite Mixture Models for Improved Modeling of Across-Site Evolutionary Variation
Abstract. Scientific studies in many areas of biology routinely employ evolutionary analyses based on inference of phylogenetic trees from molecular sequen
doi.org
August 29, 2025 at 9:37 AM
Gill, @lemeylab.bsky.social et al. develop Bayesian infinite mixture models for phylogenetic inference, finding that infinite hidden Markov models best capture complex patterns in large datasets; they implement this framework in BEAST X.
🔗 doi.org/10.1093/molbev/msaf199
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf199
#evobio #molbio
Erick is an incredible mentor, working on the most cutting-edge research at the intersection of biology, probability and computing. If I were an early-career researcher, I would jump at this opportunity -- you should too!
Interested in doing a PhD or postdoc in our group? Here is a letter to you: matsen.group/general/202...
We are ready to recruit a trainee who can help develop the next generation of our transformer-based models of natural selection. See the "joining" tab of our website for details.
We are ready to recruit a trainee who can help develop the next generation of our transformer-based models of natural selection. See the "joining" tab of our website for details.
Dear future trainee:
Let's have fun, work hard, and feel lucky that our job is to expand the boundary of knowledge.
matsen.group
August 21, 2025 at 12:01 PM
Erick is an incredible mentor, working on the most cutting-edge research at the intersection of biology, probability and computing. If I were an early-career researcher, I would jump at this opportunity -- you should too!
Reposted by Marc Suchard
BEAST X v10.5.0 finally released – you can't just do beta releases forever. github.com/beast-dev/be...
Details and instructions for installing on the BEAST website: beast.community
Details and instructions for installing on the BEAST website: beast.community
July 2, 2025 at 8:32 PM
BEAST X v10.5.0 finally released – you can't just do beta releases forever. github.com/beast-dev/be...
Details and instructions for installing on the BEAST website: beast.community
Details and instructions for installing on the BEAST website: beast.community
Am also a proud 6502 assembly programmer!
Yes! I graduated from the class of 6502 :) #retrocomputing
June 25, 2025 at 2:38 PM
Am also a proud 6502 assembly programmer!
Reposted by Marc Suchard
The OHDSI Collaborator Showcase is a chance to share your research with a global community passionate about real-world data, open science, and collaboration. Submit your abstract for a poster, demo or talk by July 1! 🌍📊 #OHDSI2025 #JoinTheJourney
🔗 https://ohdsi.org/2025-collaborator-showcase
🔗 https://ohdsi.org/2025-collaborator-showcase
June 17, 2025 at 7:03 PM
The OHDSI Collaborator Showcase is a chance to share your research with a global community passionate about real-world data, open science, and collaboration. Submit your abstract for a poster, demo or talk by July 1! 🌍📊 #OHDSI2025 #JoinTheJourney
🔗 https://ohdsi.org/2025-collaborator-showcase
🔗 https://ohdsi.org/2025-collaborator-showcase
Reposted by Marc Suchard
Excited to share my new preprint developed with @matsen.bsky.social, in collaboration with Marius Brusselmans, Luiz Carvalho, @msuchard.bsky.social, and @guybaele.bsky.social, on the biological causes and impacts of tree space ruggedness in phylodynamic inference. 1/
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
June 17, 2025 at 1:25 AM
Excited to share my new preprint developed with @matsen.bsky.social, in collaboration with Marius Brusselmans, Luiz Carvalho, @msuchard.bsky.social, and @guybaele.bsky.social, on the biological causes and impacts of tree space ruggedness in phylodynamic inference. 1/
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Marc Suchard
🚨 Calling all ATLAS users! As we continue to build an ATLAS roadmap, we ask for you to fill out Survey #2, which focuses on data sources & vocabularies. These features were discussed at our last community call (https://youtu.be/Mfi5N6NHdRA).
Survey #2: https://forms.cloud.microsoft/r/NWjAG1gS33
Survey #2: https://forms.cloud.microsoft/r/NWjAG1gS33
June 11, 2025 at 3:58 PM
🚨 Calling all ATLAS users! As we continue to build an ATLAS roadmap, we ask for you to fill out Survey #2, which focuses on data sources & vocabularies. These features were discussed at our last community call (https://youtu.be/Mfi5N6NHdRA).
Survey #2: https://forms.cloud.microsoft/r/NWjAG1gS33
Survey #2: https://forms.cloud.microsoft/r/NWjAG1gS33
Reposted by Marc Suchard
Using administrative claims and EHR databases rates of benign tumors and thyroid #cancer were not different in 460,032 users of GLP-1RAs vs. Users of other glucose lowering agents #diabetes @hmkyale.bsky.social diabetesjournals.org/care/article...
June 4, 2025 at 11:11 PM
Using administrative claims and EHR databases rates of benign tumors and thyroid #cancer were not different in 460,032 users of GLP-1RAs vs. Users of other glucose lowering agents #diabetes @hmkyale.bsky.social diabetesjournals.org/care/article...
Reposted by Marc Suchard
OHDSI is on Bluesky! What is OHDSI? Glad you asked.
OHDSI (Observational Health Data Sciences and Informatics) is a global community using open-source tools & real-world data to generate reliable, reproducible evidence that improves health outcomes. Get to know us and #JoinTheJourney!
ohdsi.org
OHDSI (Observational Health Data Sciences and Informatics) is a global community using open-source tools & real-world data to generate reliable, reproducible evidence that improves health outcomes. Get to know us and #JoinTheJourney!
ohdsi.org
June 5, 2025 at 6:23 PM
OHDSI is on Bluesky! What is OHDSI? Glad you asked.
OHDSI (Observational Health Data Sciences and Informatics) is a global community using open-source tools & real-world data to generate reliable, reproducible evidence that improves health outcomes. Get to know us and #JoinTheJourney!
ohdsi.org
OHDSI (Observational Health Data Sciences and Informatics) is a global community using open-source tools & real-world data to generate reliable, reproducible evidence that improves health outcomes. Get to know us and #JoinTheJourney!
ohdsi.org
Reposted by Marc Suchard
Our consortium's paper on Mpox in West Africa is finally out today: "Genomics reveals zoonotic and sustained human Mpox spread in West Africa" rdcu.be/emGKq. Extremely fortunately to get to work with such an exceptional team of African public health scientists, and our partners!
Genomics reveals zoonotic and sustained human Mpox spread in West Africa
Nature - Genomics reveals zoonotic and sustained human Mpox spread in West Africa
rdcu.be
May 19, 2025 at 4:58 PM
Our consortium's paper on Mpox in West Africa is finally out today: "Genomics reveals zoonotic and sustained human Mpox spread in West Africa" rdcu.be/emGKq. Extremely fortunately to get to work with such an exceptional team of African public health scientists, and our partners!
A truly amazing scientist, colleague and friend!
Mike is both a brilliant, principled scientist & also one of the most generous, kind people I’ve worked with. His leadership & groundbreaking research has profoundly transformed how we understand pandemics.
Congratulations, Mike, this is so richly deserved! 🍾🎉🇨🇦❤️
www.statnews.com/status-list/...
Congratulations, Mike, this is so richly deserved! 🍾🎉🇨🇦❤️
www.statnews.com/status-list/...
STATUS List | Michael Worobey
Michael Worobey's University of Arizona team monitors genetic sequencing data made available by the USDA to track the trajectory of disease outbreaks.
www.statnews.com
April 11, 2025 at 5:37 PM
A truly amazing scientist, colleague and friend!
Reposted by Marc Suchard
🚀 𝐏𝐡𝐃 𝐎𝐩𝐩𝐨𝐫𝐭𝐮𝐧𝐢𝐭𝐲 𝐚𝐭 𝐈𝐦𝐩𝐞𝐫𝐢𝐚𝐥
Looking for my first PhD student
🔬 Project: 𝐈𝐦𝐩𝐚𝐜𝐭 𝐨𝐟 𝐞𝐧𝐯𝐢𝐫𝐨𝐧𝐦𝐞𝐧𝐭𝐚𝐥, 𝐯𝐢𝐫𝐚𝐥, 𝐛𝐞𝐡𝐚𝐯𝐢𝐨𝐮𝐫𝐚𝐥 & 𝐩𝐬𝐲𝐜𝐡𝐨-𝐬𝐨𝐜𝐢𝐚𝐥 𝐞𝐱𝐩𝐨𝐬𝐮𝐫𝐞𝐬 𝐨𝐧 𝐡𝐞𝐚𝐥𝐭𝐡
Joint with LSHTM & UKHSA
See links below.
📅 𝐃𝐞𝐚𝐝𝐥𝐢𝐧𝐞: 7 March 2024
📩 Questions? DM me!
#PhD #HealthEquity #ImperialCollege
Looking for my first PhD student
🔬 Project: 𝐈𝐦𝐩𝐚𝐜𝐭 𝐨𝐟 𝐞𝐧𝐯𝐢𝐫𝐨𝐧𝐦𝐞𝐧𝐭𝐚𝐥, 𝐯𝐢𝐫𝐚𝐥, 𝐛𝐞𝐡𝐚𝐯𝐢𝐨𝐮𝐫𝐚𝐥 & 𝐩𝐬𝐲𝐜𝐡𝐨-𝐬𝐨𝐜𝐢𝐚𝐥 𝐞𝐱𝐩𝐨𝐬𝐮𝐫𝐞𝐬 𝐨𝐧 𝐡𝐞𝐚𝐥𝐭𝐡
Joint with LSHTM & UKHSA
See links below.
📅 𝐃𝐞𝐚𝐝𝐥𝐢𝐧𝐞: 7 March 2024
📩 Questions? DM me!
#PhD #HealthEquity #ImperialCollege
January 30, 2025 at 12:01 PM
🚀 𝐏𝐡𝐃 𝐎𝐩𝐩𝐨𝐫𝐭𝐮𝐧𝐢𝐭𝐲 𝐚𝐭 𝐈𝐦𝐩𝐞𝐫𝐢𝐚𝐥
Looking for my first PhD student
🔬 Project: 𝐈𝐦𝐩𝐚𝐜𝐭 𝐨𝐟 𝐞𝐧𝐯𝐢𝐫𝐨𝐧𝐦𝐞𝐧𝐭𝐚𝐥, 𝐯𝐢𝐫𝐚𝐥, 𝐛𝐞𝐡𝐚𝐯𝐢𝐨𝐮𝐫𝐚𝐥 & 𝐩𝐬𝐲𝐜𝐡𝐨-𝐬𝐨𝐜𝐢𝐚𝐥 𝐞𝐱𝐩𝐨𝐬𝐮𝐫𝐞𝐬 𝐨𝐧 𝐡𝐞𝐚𝐥𝐭𝐡
Joint with LSHTM & UKHSA
See links below.
📅 𝐃𝐞𝐚𝐝𝐥𝐢𝐧𝐞: 7 March 2024
📩 Questions? DM me!
#PhD #HealthEquity #ImperialCollege
Looking for my first PhD student
🔬 Project: 𝐈𝐦𝐩𝐚𝐜𝐭 𝐨𝐟 𝐞𝐧𝐯𝐢𝐫𝐨𝐧𝐦𝐞𝐧𝐭𝐚𝐥, 𝐯𝐢𝐫𝐚𝐥, 𝐛𝐞𝐡𝐚𝐯𝐢𝐨𝐮𝐫𝐚𝐥 & 𝐩𝐬𝐲𝐜𝐡𝐨-𝐬𝐨𝐜𝐢𝐚𝐥 𝐞𝐱𝐩𝐨𝐬𝐮𝐫𝐞𝐬 𝐨𝐧 𝐡𝐞𝐚𝐥𝐭𝐡
Joint with LSHTM & UKHSA
See links below.
📅 𝐃𝐞𝐚𝐝𝐥𝐢𝐧𝐞: 7 March 2024
📩 Questions? DM me!
#PhD #HealthEquity #ImperialCollege
Reposted by Marc Suchard
There is a new alternative to the MCC summary tree in BEAST X - the 'highest independent posterior sub-tree reconstruction' or HIPSTR tree. First implemented over 5 years ago (something distracted us from writing it up) we now have a preprint describing it: www.biorxiv.org/content/10.1...
HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X
In Bayesian phylogenetic and phylodynamic studies it is common to summarise the posterior distribution of trees with a time-calibrated consensus phylogeny. While the maximum clade credibility (MCC) tr...
eur02.safelinks.protection.outlook.com
December 11, 2024 at 1:05 PM
There is a new alternative to the MCC summary tree in BEAST X - the 'highest independent posterior sub-tree reconstruction' or HIPSTR tree. First implemented over 5 years ago (something distracted us from writing it up) we now have a preprint describing it: www.biorxiv.org/content/10.1...
Reposted by Marc Suchard
Clinicians, your voice matters! 🩺 @JACCJournals & @US_FDA are teaming up to tackle urgent evidence gaps in cardiovascular care. Share the key questions you face in practice about FDA-regulated products and help shape the future of research. www.jacc.org/doi/10.1016/...
Giving Cardiovascular Clinicians a Voice in Evidence Generation: A Collaboration Between FDA and JACC
www.jacc.org
December 11, 2024 at 11:13 PM
Clinicians, your voice matters! 🩺 @JACCJournals & @US_FDA are teaming up to tackle urgent evidence gaps in cardiovascular care. Share the key questions you face in practice about FDA-regulated products and help shape the future of research. www.jacc.org/doi/10.1016/...
Reposted by Marc Suchard
Preliminary report on genomic epidemiology of the 2024 H5N1 influenza A virus outbreak in U.S. cattle.
Thanks to everyone who contributed to this and, of course, first and foremost the data producers and those involved in the response.
virological.org/t/preliminar...
Thanks to everyone who contributed to this and, of course, first and foremost the data producers and those involved in the response.
virological.org/t/preliminar...
Preliminary report on genomic epidemiology of the 2024 H5N1 influenza A virus outbreak in U.S. cattle (Part 1 of 2)
Due to length constraints on virological.org posts, we are splitting this report into two parts that should be read as a single report. This is Part 1, containing Background, Data, Methods, and Findi...
virological.org
May 3, 2024 at 6:51 PM
Preliminary report on genomic epidemiology of the 2024 H5N1 influenza A virus outbreak in U.S. cattle.
Thanks to everyone who contributed to this and, of course, first and foremost the data producers and those involved in the response.
virological.org/t/preliminar...
Thanks to everyone who contributed to this and, of course, first and foremost the data producers and those involved in the response.
virological.org/t/preliminar...
Reposted by Marc Suchard
My colleagues and I have just posted a
"Note about availability of #H5N1 2.3.4.4b consensus sequences from cattle and other species" on virological.org.
Consensus genomes and metadata.
virological.org/t/note-about...
"Note about availability of #H5N1 2.3.4.4b consensus sequences from cattle and other species" on virological.org.
Consensus genomes and metadata.
virological.org/t/note-about...
Note about availability of H5N1 2.3.4.4b consensus sequences from cattle and other species:
On Sunday, April 21st, 2024, “in the interest of public transparency and ensuring the scientific community has access to this information as quickly as possible to encourage disease research and devel...
virological.org
April 28, 2024 at 3:30 PM
My colleagues and I have just posted a
"Note about availability of #H5N1 2.3.4.4b consensus sequences from cattle and other species" on virological.org.
Consensus genomes and metadata.
virological.org/t/note-about...
"Note about availability of #H5N1 2.3.4.4b consensus sequences from cattle and other species" on virological.org.
Consensus genomes and metadata.
virological.org/t/note-about...
Reposted by Marc Suchard
I want to re-emphasize how critically important it will be to not repeat our mistake from the COVID-19 pandemic of letting an opaque organization with highly questionable governance be the main source for critical, publicly funded, genomic data for H5N1.
www.science.org/content/arti...
www.science.org/content/arti...
April 28, 2024 at 6:29 PM
I want to re-emphasize how critically important it will be to not repeat our mistake from the COVID-19 pandemic of letting an opaque organization with highly questionable governance be the main source for critical, publicly funded, genomic data for H5N1.
www.science.org/content/arti...
www.science.org/content/arti...
Reposted by Marc Suchard
I love that the Department of Biostatistics at UCLA still has manual pencil sharpeners on the walls.... #statistics
February 3, 2024 at 6:50 PM
I love that the Department of Biostatistics at UCLA still has manual pencil sharpeners on the walls.... #statistics
Reposted by Marc Suchard
New paper from "SEARCH" just landed!
By sequencing 80k+ SARS2 genomes from San Diego & Baja, we looked at connectedness between waves since the start of the pandemic.
Clear heterogeneity over time and very limited effect of the US-Mexico border 'closure'.
t.co/AdtUN7VuKK
By sequencing 80k+ SARS2 genomes from San Diego & Baja, we looked at connectedness between waves since the start of the pandemic.
Clear heterogeneity over time and very limited effect of the US-Mexico border 'closure'.
t.co/AdtUN7VuKK
December 14, 2023 at 5:20 PM
New paper from "SEARCH" just landed!
By sequencing 80k+ SARS2 genomes from San Diego & Baja, we looked at connectedness between waves since the start of the pandemic.
Clear heterogeneity over time and very limited effect of the US-Mexico border 'closure'.
t.co/AdtUN7VuKK
By sequencing 80k+ SARS2 genomes from San Diego & Baja, we looked at connectedness between waves since the start of the pandemic.
Clear heterogeneity over time and very limited effect of the US-Mexico border 'closure'.
t.co/AdtUN7VuKK
Do you want to deliver reliable evidence from observational healthcare data or develop tomorrow's hottest phylodynamics model? Find computational statistics and data science fascinating? Let me hire you as a Postdoctoral Fellow. Please email me directly ASAP! (flexible start)
September 5, 2023 at 12:53 AM
Do you want to deliver reliable evidence from observational healthcare data or develop tomorrow's hottest phylodynamics model? Find computational statistics and data science fascinating? Let me hire you as a Postdoctoral Fellow. Please email me directly ASAP! (flexible start)