Tips and tricks for building a good paper: what editors want ( 1/5)

Impressive result from the recent eQTL study of snRNA-seq in brain in Fujita et al [pubmed.ncbi.nlm.nih.gov/38514782/]. Bulk RNA-seq study 2x larger identifies 4x fewer disease colocalizing genes.

New paper from the lab that will soon start the submission process. In this paper we use our previously developped statistical test for changes in covariance (biorxiv.org/content/10.110…) to investigate the impact of environmental factors on communities of the human gut microbiome.

'Egyptian Genome Project aims to sequence genomic variants of 100,000 apparently healthy Egyptian adults, with around 8,000 individuals suspected to have a genetic disease, as well as 200 ancient Egyptian mummies.' 🔥
Elmonem et al. Nat Gen
nature.com/articles/s4158…

this paper on collective intelligence by Michael Levin is one of the most mind-blowing things I've read in a while

it's full of examples of the under-appreciated intelligence of biological systems, with some deep perspective shifts on our understanding of ourselves

thread:

🎉📣 Latest preprint from the lab: Genome-wide analyses of variance in blood cell phenotypes provide new insights into complex trait biology and prediction medrxiv.org/content/10.110…

Led by the exceptional Ruidong Xiang (now head of comp bio at AgriBio Agriculture Victoria)!

Published today, our reasons for optimism that success rates in drug discovery can be improved by picking the right targets using human genetics: nature.com/articles/s4158…

I break the key findings down panel by panel in this thread: x.com/cureffi/status…

Many thanks to all my co-authors Deniz Fettahoglu Léo and hu.asch

New short paper from Joel Hellewell and Sam Horsfield and on making pangenome (specifically frequency estimates) from metagenome data:
biorxiv.org/cgi/content/sh…

For over 4 million insurees, 'free' polygenic risk scores for 8 conditions (including heart disease, multiple cancers, type 2 diabetes, atrial fibrillation) that were deemed to be actionable by 71% people in a pilot study
statnews.com/2024/04/09/mas…

How can cell atlases of human tissues support drug target discovery? In a joint effort between Teichlab @Sanofi and Ensocell we tested whether info on cell type specific expression from scRNA-seq is associated w targets of clinically successful drugs medrxiv.org/content/10.110…

Large-scale whole-exome sequencing of neuropsychiatric diseases and traits in 350,770 adults
nature.com/articles/s4156…

The choice of whether to use Seurat or Scanpy for single-cell RNA-seq analysis typically comes down to a preference of R vs. Python. But do they produce the same results? In biorxiv.org/content/10.110… w/ Joseph Rich et al. we take a close look. The results are 👀 1/🧵

An Update on Human CRISPR | Science | AAAS science.org/content/blog-p…

Lots of discussion of Aw et al. [biorxiv.org/content/10.110…] in our journal club this week. Potentially important implications for polygenic score (PGS) analysis and disease architecture. Curious what other people think. Some thoughts below:

DBC annual retreat: great four days of presentations and discussion with (almost) all teams from the department!

New paper on GxDrug and TxEWAS (where T=gene expression from GTEx, E=Drug) identifying genes that modify drug responses in UKBiobank (statin, metformin, warfarin, methotrexate), by Michal Sadowski Noah Zaitlen Andy Dahl Sriram Sankararaman Ayroles Lab et al

Nature

Memories are made by breaking DNA — and fixing it nature.com/articles/d4158…

Analysis of a random selection of papers shared on social media showed no causative link between posting and citations go.nature.com/3TDj4VJ

Today, I’m proud to say, our new paper on assortative mating was published in Nature Communications. (Link: doi.org/10.1038/s41467…). Here are our key findings 🧵: