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Blokirali ste korisnika/cu @spence_jeffrey_
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jeffrey spence proslijedio/la je Tweet
I'm looking for a computational postdoc for analyzing palaeogenomic data, co-advised with
@ras_nielsen, to start around September 2020. Deadline for applying is March 15th. Link here: https://candidate.hr-manager.net/ApplicationInit.aspx/?cid=1307&departmentId=19217&ProjectId=151105&MediaId=5&SkipAdvertisement=false …Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
It's great to see careful consideration of the invariances present in popgen data and rigorous comparison of different architectures. It looks like ABC with summary statistics is still competitive, though, and that there's room for improvement by combining DL and ABC approaches.
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Nice work by
@florajay_ 's group using deep learning in population genetics:https://www.biorxiv.org/content/10.1101/2020.01.20.910539v1 …Prikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
jeffrey spence proslijedio/la je Tweet
Our preprint on ancestral haplotype reconstruction is out (and associated code "thread" https://github.com/mathiesonlab/thread …). Feedback welcome!https://twitter.com/biorxivpreprint/status/1217986491567263744 …
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jeffrey spence proslijedio/la je Tweet
Ever wonder if other people dream of flying? Help us find out
#whywedream using our questionnaire https://stanforduniversity.qualtrics.com/jfe/form/SV_8wufxlPcx77CzDT …Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
jeffrey spence proslijedio/la je Tweet
Thanks to the heroic efforts of
@roshan_m_rao we have re-released our TAPE code as a pytorch repository! Take it for a spin https://github.com/songlab-cal/tape … At NeurIPS? Come chat with us about proteins on Thursday at our poster! https://neurips.cc/Conferences/2019/Schedule?showEvent=15841 …Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
Interesting math fact: take a PSD matrix and take the absolute value of every entry. In dimensions 2 and 3 the result is guaranteed to still be PSD, but for any dimension greater than 4 there exist matrices where the resulting matrix is no longer PSD
https://math.stackexchange.com/questions/1355088/is-the-absolute-value-of-a-p-d-s-matrix-p-d-s …Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
jeffrey spence proslijedio/la je Tweet
iSMC is finally here! The much improved version our paper with
@natashapuzovic and@jydutheil is out in@PLOSGenetics. We develop a new model of the recombination landscape and show that it can infer recombination maps with a single pair of genomes:https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008449 …Prikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
jeffrey spence proslijedio/la je Tweet
Felix Wu's work comparing sex-specific germline mutation rates in baboons to humans:https://www.biorxiv.org/content/10.1101/844910v1 …
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jeffrey spence proslijedio/la je Tweet
We all know the written history of Roman civ. With an awesome resource of DNA from 10k+ years and cutting-edge popgen analysis,
@antmarge,@ziyue_gao,@mootspoints, et al. articulate a new, genetics-based perspective of Roman history/pop migration patternshttps://science.sciencemag.org/content/366/6466/708 …Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
jeffrey spence proslijedio/la je Tweet
Can we learn the language of proteins? Check out our
@berkeley_ai blog post where we discuss Sesame Street, protein plagiarism, and manage to fit in some machine learning along the way.https://bair.berkeley.edu/blog/2019/11/04/proteins/ …Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
jeffrey spence proslijedio/la je Tweet
Our work using geostatistical modeling with ancient DNA to reconstruct ancient migrations in Europe: https://www.biorxiv.org/content/10.1101/826149v1 …pic.twitter.com/rXv6GPRisJ
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What's the etymology of the "Tower Property" of conditional expectation in probability? Is "Tower" a person or does it refer to the building?
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I should also say that it's fast, can handle unphased data, and has some utilities to compute the expected value and percentiles of the distribution of r^2 for SNPs at different genetic distances for a given demographic history.
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Fine-scale recombination rates are complex traits, likely influenced by many cis and trans factors.
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In particular, chromatin states characterized by H3K27me3 have particularly elevated recombination rates, and the mechanism for that is not clear. In any case, it's clear there is much more to the story than just PRDM9 binding.
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The last thing we looked at was whether there are other determinants of recombination rate beyond PRDM9, and we found that chromatin structure appears to modulate recombination rates by about an order of magnitude, but the effect doesn't line up with "open" vs. "closed" chromatin
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We found some evidence of this, but the effect was much weaker than we had originally expected. Some of this might be because we used binding motifs instead of known PRDM9 binding sites, but there are also a lot of hotspots and not very many recombinations per generation.
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There's also an interesting story that the double strand breaks involved in recombination events are repaired via homology directed repair, which should cause mutations that disrupt a PRDM9 binding site to increase in frequency.
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PRDM9 is a protein that positions recombination hotspots, and the C allele of PRDM9 is present at appreciable frequencies only in African populations. Correspondingly we find increased recombination rates at PRDM9-C binding sites only in those populations.
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