Some extremely interesting results were shown today by Joel Hirschhorn on behalf of GIANT consortium (here I use the word GIANT as both noun and an adjective ;)) x.com/doctorveera/st…

This is a crazy good must read article .. go.nature.com/3vXivK1

🧠UNC Faculty Recruitment🧬: we are looking for a clinician or physician scientist to be a bridge between Genetics and Psychiatry. We have a fantastic environment of both basic neuro/genetics & clinical expertise. Please RT and distribute widely. unc.peopleadmin.com/postings/217557

Here we compared 18 functional weighting methods for identifying novel genetic associations and found enhanced discovery for #GWAS ... but such methods are "unlikely to circumvent the need for larger sample sizes in truly underpowered GWAS." Bryan Quach @bcquach.bsky.social et al. RTI International

Please...stop!

Got an RNA-seq dataset with 50, 100, 200+ samples? Plug it into a differential expression tool and hope for the best? No! You need to consider QC, EDA, and modeling technical variation, or else risk generating spurious results. A thread on papers, methods, and best practices:

The first Corces Lab paper is out today! We've released a step-by-step guide to bulk ATAC-seq Nature Protocols. This was definitely a labor of love by stellar postdoc Fiorella Grandi. nature.com/articles/s4159…

Our paper describing NEAT-seq, a method to simultaneously measure transcription factor protein abundance, ATAC-seq, and RNA-seq in single cells, is now out at Nature Methods! Congrats to Amy and Ben! nature.com/articles/s4159…

Mathematical expressions can now be displayed in Markdown on GitHub using the $$ and $ delimiters - all with the help of the wonderful MathJax project. github.blog/2022-05-19-mat…

Very grateful to have the opportunity to work with Tian Zhang dissecting how genetic variation affects protein phosphorylation. Our great team included Steve Munger, @MTFerris, Gygi Lab, and Gary Churchill The Jackson Laboratory. I'll share a few insights from the manuscript.

Thursday, June 9 at 4pm EST: Jeremy M. Simon, PhD (UNC Chapel Hill) leads a #DataScience Zoominar on "Identification of Novel Oncogenic and Neurodevelopmental Programs Using Bulk and Single-Cell Approaches." RSVP: bit.ly/DSJune9

Excited to announce the release of our new manuscript (mdpi.com/2073-4425/13/6…) on the role of mRNA splicing in opioid use disorder. Great to work with Spencer Huggett Karla Kaun and John McGeary to publish this in Genes MDPI

Is it possible to compare genetic effects across ancestries without biased by environmental and cultural differences? Yes, if the genomic segments representing different ancestries come from the same individuals, i.e., admixed individuals. Brilliant idea! medrxiv.org/content/10.110…

The MPRA review paper I shared last week was a teaser for this one. We have performed MPRA on ~5,000 schizophrenia finemapped variants and detected ~400 variants with allelic regulatory activity (MPRA-positive variants). medrxiv.org/cgi/content/sh…

Always great to run into friends and former colleagues at #ASHG22. This year had the added perk of my son getting a first course in genetics by Jack Kosmicki and 23andMe

Stefano Mangiola Stefano Mangiola & I are planning a tutorial on "Tidy Genomic Analysis" Dec 12, 4:30 PM EST Dec 13, 8:30 AM AEDT 60 min + 30 min Q/A - Tidy single-cell and bulk transcriptomics - Tidy enrichment with plyranges and nullranges Sign up: unc.zoom.us/meeting/regist…

Quantitative assessment of association between noncoding variants and transcription factor binding dlvr.it/SdFXjV

Prof. Giovanni Parmigiani, Prof. Sur & co-authors researched how to improve cross-study replicability of predictions by providing a theoretical rationale for when to select multi-study ensembling over merging. Read more in their ArXiv paper: arxiv.org/abs/2207.04588

Posting my talk for tomorrow's #ISMBECCB2023 Keynote lectures.gersteinlab.org/summary/Gradua… A Gradual Evolution of Bioinformatics Research: 1994-2052

Here's a new preprint from our group. "Identifying compounds to treat opiate use disorder by leveraging multi-omic data integration and multiple drug repurposing databases." medrxiv.org/content/10.110… Caryn Willis Bryan Quach @bcquach.bsky.social RTI International