Philipp Rentzsch
@AervaI
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Research Scientist with @tuuliel_lab @scilifelab
Joined August 2015
Many thanks to all collaborators and especially my coauthors Aaron, @Pejminister and our great PI @tuuliel! Tuuli recently got funded as a Wallenberg Scholar, so it is safe to say that we are looking for more colleagues in our Swedish-American lab. 4/4
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Ranking genes by "recalibrated" fold changes enriches results for biological processes related to metabolic and regulatory activity, while simultaneously serving as correction against highly variable genes.
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Here, we introduce a new concept of how to view fold changes that are the result of an RNA-Seq differential expression study. Building upon prior work from the lab lead by @Pejminister, we use the genetic population variance in expression (V^G) to adjust expression fold changes.
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Very happy to share our latest work from my postdoc with @tuuliel_lab on recalibrating gene expression changes relative to natural dosage variance:
biorxiv.org
Differential expression (DE) analysis is a widely used method for identifying genes that are functionally relevant for an observed phenotype or biological response. However, typical DE analysis...
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The Morris Lab at the @DonnellyCentre for Cellular and Biomolecular Research and the University of Toronto is officially open for business, and the lab website is live! Check it out for info on our research and how you can join:
morris-lab.org
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Folks at #BoG23 and others - I'm recruiting postdocs to my Stockholm and New York teams. Reach out if interested - experimental or computational opportunities in gene expression dosage (talk #39), GWAS+CRISPR+molQTLs, developmental GTEx, etc. https://t.co/IGJtJWrLB8
science.org
High-throughput single-cell CRISPR screens help in the understanding of noncoding human genetic variants for blood cell traits.
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Philipp Rentzsch #GRD23: Many diseases are caused by changes in gene dosage. Genes have varying levels of gene expression in the population. V^G is a metric of dosage variation (introduced here: https://t.co/SFbZgQOIQF) Now found that haploinsufficient genes have smaller V^G.
pubmed.ncbi.nlm.nih.gov
Transcriptome data can facilitate the interpretation of the effects of rare genetic variants. Here, we introduce ANEVA (analysis of expression variation) to quantify genetic variation in gene dosage...
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https://t.co/5kz6erU8s0 is recruiting 2 PostDocs ( https://t.co/3KpZlUJaJT.
https://t.co/FavbcrgfBL). Apply by Oct 10, 22. We are part of #IGVF, analyze reg. variant effects (MPRAs/CRISPR screens) and develop new comp. models & tools w/ @JShendure, @NadavAhituv, @malte_spielmann.
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Science media: still tweeting about a terribly designed, underpowered study a week later because it has cool photos and gets clicks. Also science media: what drives scientists to publish studies that don’t replicate???
Your doppelgänger is out there, and you may share a lot more than a face with them.
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A framework to score the effects of structural variants in health and disease | Genome Research https://t.co/ano1MIX6iC
#Bioinformatics
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We're looking for a postdoc in Stockholm! Co-mentored position at the intersection of biology/genomics and ML. Fantastic environment at @KTHuniversity & @scilifelab's Data Driven Life Science community, with strong international networks. Please RT! https://t.co/uJSHJ3q9dG
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Now official: the offered positions are part of @genome_gov 's #IGVF consortium in close collaboration with @JShendure and @NadavAhituv. Great science to come, apply now!
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My PI is looking for a new PostDoc ( https://t.co/EOUmhc4C7P) and a PhD student ( https://t.co/ksgHGoBb5i) in Bioinformatics/Computational Biology on the topic of non-coding variant effects. Deadline Sep 15. I can fully recommend the lab, feel free to contact me if interested
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CADD-SV - a framework to score the effects of structural variants in health and disease https://t.co/sEFOPIK6Cz
#bioRxiv
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New tracks are available for human assemblies, hg19 and hg38. The new tracks show Combined Annotation Dependent Depletion (CADD) scores for each base in the genome and correspond to the v1.6 developmental release. Read more about the release at: https://t.co/pgttUAzTSO
#CADD
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Hello #ESHG2020, visit me at my poster P17.121.B https://t.co/8DVaUjBXLh to talk about the newest CADD version CADD-Splice. I am opening a zoom video chat, come and join me!
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#ESHG2020 talks need to be played at x1.1 speed (some even x1.5) so that speakers do not go over time. Sessions going over time occupy rooms that can not be used by the next session. #virtualconferenceproblems
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