Mark James Adams
@markjamesadams.bsky.social
Minds, moods, and molecules ␥ Psychological and psychiatric complex trait genetics ␥ Researcher in Edinburgh, Scotland
https://differentialist.info/about/
https://differentialist.info/about/
Reposted by Mark James Adams
The end of an era: the Tree of Life Web Project is going dark after 3 decades. Anyone interested in communicating phylogeny online should read David's account of goals, history, and future. @bembidion.bsky.social
subulatepalpomere.com/2025/11/02/t...
subulatepalpomere.com/2025/11/02/t...
The Passing of the Tree of Life Web Project
The Tree of Life Web Project began its journey almost 40 years ago, and was formally announced in early 1996. It has served thousands of pages of information about the evolutionary tree of life and…
subulatepalpomere.com
November 3, 2025 at 3:54 PM
The end of an era: the Tree of Life Web Project is going dark after 3 decades. Anyone interested in communicating phylogeny online should read David's account of goals, history, and future. @bembidion.bsky.social
subulatepalpomere.com/2025/11/02/t...
subulatepalpomere.com/2025/11/02/t...
Reposted by Mark James Adams
We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT
October 15, 2025 at 3:53 PM
We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT
Reposted by Mark James Adams
This is how I integrate Quarto and Zotero with minimal suffering (long rambling post, scroll down to the section on bibliography or search for Zotero): cameronpatrick.com/post/2023/07...
Cameron Patrick - Some Quarto PDF formatting tips, with particular reference to thesis writing
I’ve just spent most of a day faffing around trying to get Quarto to produce a nice PDF file that I like the look of and which meets my university’s formatting requirements for a PhD thesis. Maybe my ...
cameronpatrick.com
October 3, 2025 at 11:39 PM
This is how I integrate Quarto and Zotero with minimal suffering (long rambling post, scroll down to the section on bibliography or search for Zotero): cameronpatrick.com/post/2023/07...
Reposted by Mark James Adams
🚨 Position Alert! 🚨
I am looking for a full-time Research Scientist 1 to join my lab in Albuquerque, NM at the Center on Alcohol, Substance Use, and Addiction (CASAA). We will be studying how stress and trauma influence cannabis and substance use. 🧠🌿 (1/5)
I am looking for a full-time Research Scientist 1 to join my lab in Albuquerque, NM at the Center on Alcohol, Substance Use, and Addiction (CASAA). We will be studying how stress and trauma influence cannabis and substance use. 🧠🌿 (1/5)
October 2, 2025 at 10:33 PM
🚨 Position Alert! 🚨
I am looking for a full-time Research Scientist 1 to join my lab in Albuquerque, NM at the Center on Alcohol, Substance Use, and Addiction (CASAA). We will be studying how stress and trauma influence cannabis and substance use. 🧠🌿 (1/5)
I am looking for a full-time Research Scientist 1 to join my lab in Albuquerque, NM at the Center on Alcohol, Substance Use, and Addiction (CASAA). We will be studying how stress and trauma influence cannabis and substance use. 🧠🌿 (1/5)
Reposted by Mark James Adams
Non-paywalled link to my commentary on @vw1234.bsky.social and colleagues new paper in @nature.com rdcu.be/eI2NG
October 1, 2025 at 6:17 PM
Non-paywalled link to my commentary on @vw1234.bsky.social and colleagues new paper in @nature.com rdcu.be/eI2NG
Reposted by Mark James Adams
University of Colorado Boulder Department of Psychology & Neuroscience is searching for TWO tenure track assistant professors. This is open to all department areas, including Behavioral, Psychiatric, and Statistical Genetics🧬 jobs.colorado.edu/jobs/JobDeta...
Assistant Professor
jobs.colorado.edu
September 29, 2025 at 3:57 PM
University of Colorado Boulder Department of Psychology & Neuroscience is searching for TWO tenure track assistant professors. This is open to all department areas, including Behavioral, Psychiatric, and Statistical Genetics🧬 jobs.colorado.edu/jobs/JobDeta...
'Is artificial intelligence a scientific study?'
'Not really…'
— Muriel Spark, Symposium, 1990
'Not really…'
— Muriel Spark, Symposium, 1990
September 19, 2025 at 12:51 PM
'Is artificial intelligence a scientific study?'
'Not really…'
— Muriel Spark, Symposium, 1990
'Not really…'
— Muriel Spark, Symposium, 1990
Reposted by Mark James Adams
Brilliant paper by Visscher et al.
Populations differ in traits/disease burden. Are these differences due to genetics?
Comparing single variants or polygenic scores between populations is biased due to environmental confounders correlated with the variants.
1/3
www.medrxiv.org/content/10.1...
Populations differ in traits/disease burden. Are these differences due to genetics?
Comparing single variants or polygenic scores between populations is biased due to environmental confounders correlated with the variants.
1/3
www.medrxiv.org/content/10.1...
Direct effect of genetic ancestry on complex traits in a Mexican population
Human populations differ in disease prevalences and in average values of phenotypes, but the extent to which differences are caused by genetic or environmental factors is unknown for most complex trai...
www.medrxiv.org
September 11, 2025 at 5:57 AM
Brilliant paper by Visscher et al.
Populations differ in traits/disease burden. Are these differences due to genetics?
Comparing single variants or polygenic scores between populations is biased due to environmental confounders correlated with the variants.
1/3
www.medrxiv.org/content/10.1...
Populations differ in traits/disease burden. Are these differences due to genetics?
Comparing single variants or polygenic scores between populations is biased due to environmental confounders correlated with the variants.
1/3
www.medrxiv.org/content/10.1...
At a symposium celebrating the 20th year of the @genscot.bsky.social cohort. David Porteous giving an overview of the origins of the cohort, answering the question "Why Scotland"
August 26, 2025 at 9:31 AM
At a symposium celebrating the 20th year of the @genscot.bsky.social cohort. David Porteous giving an overview of the origins of the cohort, answering the question "Why Scotland"
We're looking at setting up a trusted research environment (TRE) for our cohort, to enable observability and governance, smooth rollout of updates, limit proliferation of outdated copies.
Need some pointers on how to provision these environments up so that they aren't exasperating to researchers.
Need some pointers on how to provision these environments up so that they aren't exasperating to researchers.
August 26, 2025 at 5:51 AM
We're looking at setting up a trusted research environment (TRE) for our cohort, to enable observability and governance, smooth rollout of updates, limit proliferation of outdated copies.
Need some pointers on how to provision these environments up so that they aren't exasperating to researchers.
Need some pointers on how to provision these environments up so that they aren't exasperating to researchers.
Good evening from Scotland.
Go Home Tae Yer Bed [Fhalbh Dhachaigh Don Leabaidh Agad] — Brògeal feat. Josie Duncan
youtu.be/__ezRGsYsuo
Go Home Tae Yer Bed [Fhalbh Dhachaigh Don Leabaidh Agad] — Brògeal feat. Josie Duncan
youtu.be/__ezRGsYsuo
Go Home Tae Yer Bed - Brògeal [Acoustic Video]
YouTube video by Brògeal
youtu.be
August 25, 2025 at 6:49 PM
Good evening from Scotland.
Go Home Tae Yer Bed [Fhalbh Dhachaigh Don Leabaidh Agad] — Brògeal feat. Josie Duncan
youtu.be/__ezRGsYsuo
Go Home Tae Yer Bed [Fhalbh Dhachaigh Don Leabaidh Agad] — Brògeal feat. Josie Duncan
youtu.be/__ezRGsYsuo
<Me clicking a reCaptcha checkbox>
August 22, 2025 at 6:17 AM
<Me clicking a reCaptcha checkbox>
Reposted by Mark James Adams
Excited to share our new preprint for the tskit_arg_visualizer Python package! ARGs can sometimes feel like a black box, so
@yanwong.bsky.social and I have been developing a method to programmatically drawing these graphs.
🔗 arxiv.org/abs/2508.03958
1/6
@yanwong.bsky.social and I have been developing a method to programmatically drawing these graphs.
🔗 arxiv.org/abs/2508.03958
1/6
tskit_arg_visualizer: interactive plotting of ancestral recombination graphs
Summary: Ancestral recombination graphs (ARGs) are a complete representation of the genetic relationships between recombining lineages and are of central importance in population genetics. Recent brea...
arxiv.org
August 19, 2025 at 2:12 PM
Excited to share our new preprint for the tskit_arg_visualizer Python package! ARGs can sometimes feel like a black box, so
@yanwong.bsky.social and I have been developing a method to programmatically drawing these graphs.
🔗 arxiv.org/abs/2508.03958
1/6
@yanwong.bsky.social and I have been developing a method to programmatically drawing these graphs.
🔗 arxiv.org/abs/2508.03958
1/6
Reposted by Mark James Adams
Our study in @JAMAPsych ja.ma/4lVx1eu Using 🧬 we found that disruptions in #energy pathways link to specific #MDD symptoms (⬆️ appetite & sleep). This suggests a #depression profile linked to #metabolic risk, opening doors to targeted treatments. #metabolicpsychiatry
Energy Homeostasis in Depression Pathophysiology and Heterogeneity
This study examines whether the genetic liability of metabolic, interoceptive, and motivational pathways involved in energy homeostasis regulation is associated with specific symptoms of major depress...
ja.ma
August 10, 2025 at 2:19 PM
Our study in @JAMAPsych ja.ma/4lVx1eu Using 🧬 we found that disruptions in #energy pathways link to specific #MDD symptoms (⬆️ appetite & sleep). This suggests a #depression profile linked to #metabolic risk, opening doors to targeted treatments. #metabolicpsychiatry
In Lilongwe for the kick-off meeting of the Genetics of Anxiety in Malawi project. Toward African-led, context-specific genomic research, supported by @wellcometrust.bsky.social
Meeting at the Kwaza Arts centre.
Meeting at the Kwaza Arts centre.
August 4, 2025 at 9:17 AM
In Lilongwe for the kick-off meeting of the Genetics of Anxiety in Malawi project. Toward African-led, context-specific genomic research, supported by @wellcometrust.bsky.social
Meeting at the Kwaza Arts centre.
Meeting at the Kwaza Arts centre.
Reposted by Mark James Adams
"Behavior drives morphological change during human evolution"
Our new article is out in @science.org today
www.science.org/doi/10.1126/...
Our new article is out in @science.org today
www.science.org/doi/10.1126/...
July 31, 2025 at 10:02 PM
"Behavior drives morphological change during human evolution"
Our new article is out in @science.org today
www.science.org/doi/10.1126/...
Our new article is out in @science.org today
www.science.org/doi/10.1126/...
Reposted by Mark James Adams
Thanks! This is amazing! So the term 'Manhattan Plot' is not originally a GWAS term at all.
Screenshotting the image here from a 1994 book on nuclear physics, for others who may be interested:
Screenshotting the image here from a 1994 book on nuclear physics, for others who may be interested:
July 29, 2025 at 6:18 PM
Thanks! This is amazing! So the term 'Manhattan Plot' is not originally a GWAS term at all.
Screenshotting the image here from a 1994 book on nuclear physics, for others who may be interested:
Screenshotting the image here from a 1994 book on nuclear physics, for others who may be interested:
The University of Edinburgh has published its Race Review.
The report goes way deeper than just ties to slavery: "…the UoE formed a central point in a network of knowledge about 'civilization' and 'race' from the period of the Enlightenment onward."
www.ed.ac.uk/about/race-r...
The report goes way deeper than just ties to slavery: "…the UoE formed a central point in a network of knowledge about 'civilization' and 'race' from the period of the Enlightenment onward."
www.ed.ac.uk/about/race-r...
Review of Race and History | The University of Edinburgh
The academically-led review explores historic racial and colonial injustices, including enslavement, linked to the University as well as reassessing current policies and procedures.
www.ed.ac.uk
July 27, 2025 at 6:15 AM
The University of Edinburgh has published its Race Review.
The report goes way deeper than just ties to slavery: "…the UoE formed a central point in a network of knowledge about 'civilization' and 'race' from the period of the Enlightenment onward."
www.ed.ac.uk/about/race-r...
The report goes way deeper than just ties to slavery: "…the UoE formed a central point in a network of knowledge about 'civilization' and 'race' from the period of the Enlightenment onward."
www.ed.ac.uk/about/race-r...
Reposted by Mark James Adams
In #GENETICS, Williams et al. present a novel statistics—haplotype score—for summarizing identity-by-descent (IBD) sharing that can distinguish half-sibling pairs from avuncular or grandparent-grandchildren pairs and assign individuals to ancestor vs descendant generation.
buff.ly/SaZP3CA
buff.ly/SaZP3CA
July 25, 2025 at 6:03 PM
In #GENETICS, Williams et al. present a novel statistics—haplotype score—for summarizing identity-by-descent (IBD) sharing that can distinguish half-sibling pairs from avuncular or grandparent-grandchildren pairs and assign individuals to ancestor vs descendant generation.
buff.ly/SaZP3CA
buff.ly/SaZP3CA
My university has new guidance about generative AI. Requirements and restrictions are set on a course-by-course basis, but AI outputs must not be presented as a student's own work and the exact use must be acknowledged.
information-services.ed.ac.uk/computing/co...
information-services.ed.ac.uk/computing/co...
Using generative AI in your studies: guidelines for students | Computing | Information Services
• The University trusts you to act with integrity in your use of generative AI for your studies. • It does not ban the use of generative AI, though its use is restricted for assessment. • Some of your...
information-services.ed.ac.uk
July 25, 2025 at 8:20 AM
My university has new guidance about generative AI. Requirements and restrictions are set on a course-by-course basis, but AI outputs must not be presented as a student's own work and the exact use must be acknowledged.
information-services.ed.ac.uk/computing/co...
information-services.ed.ac.uk/computing/co...
If you are new to GWAS, the lectures by Matti Pirinen are a good place to start. Conceptual foundations rather than how to use software.
www.mv.helsinki.fi/home/mjxpiri...
www.mv.helsinki.fi/home/mjxpiri...
July 25, 2025 at 8:08 AM
If you are new to GWAS, the lectures by Matti Pirinen are a good place to start. Conceptual foundations rather than how to use software.
www.mv.helsinki.fi/home/mjxpiri...
www.mv.helsinki.fi/home/mjxpiri...
Reposted by Mark James Adams
Very happy to share our new paper now on @medrxivpreprint: “Genetic risk effects on psychiatric disorders act in sets”, a great effort led my PhD student @jolienrietkerk.bsky.social, and performed together with collaborators Andy Dahl, Jonathan Flint, Andrew Schork etc. Thread 1/n
July 24, 2025 at 5:24 AM
Very happy to share our new paper now on @medrxivpreprint: “Genetic risk effects on psychiatric disorders act in sets”, a great effort led my PhD student @jolienrietkerk.bsky.social, and performed together with collaborators Andy Dahl, Jonathan Flint, Andrew Schork etc. Thread 1/n
Reposted by Mark James Adams
🧬 New @emblebi.bsky.social service beta launched:
Perturbation Catalogue
🔎 Browse genetic perturbation datasets
🧠 Train models
🧬 Interpret variant function
🧭 Explore gene dependencies
Search, test APIs, suggest datasets, send feedback!
🔗 www.ebi.ac.uk/perturbation...
Funded by @opentargets.org
Perturbation Catalogue
🔎 Browse genetic perturbation datasets
🧠 Train models
🧬 Interpret variant function
🧭 Explore gene dependencies
Search, test APIs, suggest datasets, send feedback!
🔗 www.ebi.ac.uk/perturbation...
Funded by @opentargets.org
July 23, 2025 at 10:06 AM
🧬 New @emblebi.bsky.social service beta launched:
Perturbation Catalogue
🔎 Browse genetic perturbation datasets
🧠 Train models
🧬 Interpret variant function
🧭 Explore gene dependencies
Search, test APIs, suggest datasets, send feedback!
🔗 www.ebi.ac.uk/perturbation...
Funded by @opentargets.org
Perturbation Catalogue
🔎 Browse genetic perturbation datasets
🧠 Train models
🧬 Interpret variant function
🧭 Explore gene dependencies
Search, test APIs, suggest datasets, send feedback!
🔗 www.ebi.ac.uk/perturbation...
Funded by @opentargets.org