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Quantitative GWAS & QTL studies

February 25, 2023

Primer
Published: 25 January 2023

Molecular quantitative trait loci

François Aguet, Kaur Alasoo, Yang I. Li, Alexis Battle, Hae Kyung Im, Stephen B. Montgomery & Tuuli Lappalainen

Nature Reviews Methods Primers volume 3, Article number: 4 (2023)

Related to the discussion about quantitative GWAS and QTL, this primer review (and in particular box 1) is helpful in clarifying the (non) difference between the two types of studies:

https://www.nature.com/articles/s43586-022-00188-6

The statistics behind quantitative GWAS and QTL studies is the same, the only main difference might be the multiple testing correction procedure.
In general, it’s more a nomenclature distinction, as the term “QTL” is often used specifically for molecular traits.

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Lynn Williams obituary

January 25, 2023

https://www.nytimes.com/1983/01/01/obituaries/albert-l-williams-dies-at-71-ibm-president-in-the-1960-s.html

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Audm – Listen to feature stories from The Atlantic, WIRED, and more.

January 3, 2023

https://www.audm.com/

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Chat GPT

December 18, 2022

https://chat.openai.com/

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Deep learning guided optimization of human antibody against SARS-CoV-2 variants with broad neutralization

October 13, 2022

https://www.pnas.org/doi/10.1073/pnas.2122954119

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www.brimr.org/NIH_Awards/NIH_Awards.htm

October 5, 2022

http://www.brimr.org/NIH_Awards/NIH_Awards.htm

Nice listing of NIH money by field & PI

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Lab leaders wrestle with paucity of postdocs

September 4, 2022

https://www.nature.com/articles/d41586-022-02781-x

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SLC6A4 Gene – GeneCards | SC6A4 Protein | SC6A4 Antibody

August 1, 2022

https://www.genecards.org/cgi-bin/carddisp.pl?gene=SLC6A4

QT:{{”
This gene encodes an integral membrane protein that transports the neurotransmitter serotonin from synaptic spaces into presynaptic neurons. The encoded protein terminates the action of serotonin and recycles it in a sodium-dependent manner. This protein is a target of psychomotor stimulants, such as amphetamines and cocaine, and is a member of the sodium:neurotransmitter symporter family. A repeat length polymorphism in the promoter of this gene has been shown to affect the rate of serotonin uptake. There have been conflicting results in the literature about the possible effect, if any, that this polymorphism may play in behavior and depression. [provided by RefSeq, May 2019]
“}}
famous serotonin re-update transporter

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Eisenhower’s Urgent/Important Principle/Matrix

July 11, 2022

https://todoist.com/productivity-methods/eisenhower-matrix

https://www.mindtools.com/pages/article/newHTE_91.htm#:~:text=Eisenhower%2C%20who%20was%20quoting%20Dr,organized%20his%20workload%20and%20priorities.

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Mutation bias reflects natural selection in Arabidopsis thaliana | Nature

April 14, 2022

https://www.nature.com/articles/s41586-021-04269-6

https://twitter.com/MarkGerstein/status/1510065060806283269

Interesting paper, relating de novo mutation rate to epigenetic features. Wonder exactly how this connects to the fact that the background mutation rate in cancer genomes depends strongly on epigenetics.

Important genomic regions mutate less often than do other regions https://www.nature.com/articles/d41586-022-00017-6

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