After a period of downtime and maintenance, I am excited to announce that locuscompare.com is back with a more enriched feature set. The new locuscompare suite includes: 1) The locuscomparer R package 2) The locuscomparepy Python module 3) The locuscompare website (locuscompare.com)

If you are interested in single-cell splicing QTL analysis, it will worth trying ISSAC. My talk at the Biology of Genomes 2026: youtu.be/ObWtjpYBie4 ISSAC Preprint: www.medrxiv.org/content/10.6...

Single-cell splicing analysis with ISSAC links cell type-specific and cell state-dependent sQTLs to neurological disorders

Single-cell RNA sequencing enables comprehensive profiling of gene expression and splicing at cellular resolution, revealing cell type-specific and cell state-dependent regulation (variation within ce...

medrxiv.org

Sharing our exciting single-cell splicing method ISSAC. Key features include: 1) ISSAC is 1.4 to 2.5-fold power increase over LeafCutter on single-cell sQTL discovery, and scalable to millions of cells 2) ISSAC is able to map cell-state-dependent sQTLs and intron-retention sQTLs.

Excited to share our new paper on Cell Genomics: We mapped how genetics shape the muscle transcriptome in response to exercise and diet intervention. 📄 www.cell.com/cell-genomic...

Collaborative work led by Zhihao and me finally online at Nature Communications! nature.com/articles/s41... Huge congratulations to Zhihao and his outstanding leadership. Also, to first author Foozhan Tahmasebinia, and key contributions from Yinglu Tang and Rushi Tang!

The 40S ribosomal subunit recycling complex modulates mitochondrial dynamics and endoplasmic reticulum - mitochondria tethering at mitochondrial fission/fusion hotspots - Nature Communications

Coordinating protein translation with energy supply is a significant challenge faced by cells. Here, the authors found that the protein quality control network may provide a link between the two.

nature.com

Exciting new benchmark for DNA language models!

Arpita Singhal@arpita-s.bsky.social · 2y ago

Excited to announce DART-Eval, our latest work on benchmarking DNALMs! Catch us at #NeurIPS!

This study is truly amazing.

Danny IncaRNAto@incarnatolab.bsky.social · 2y ago

This is huge. Mis-splicing of a 24nt-long micro-exon in the CPEB4 #RNA binding protein leads to formation of irreversible aggregates, which normally would dissolve after depolarization, and consequent deregulation of genes associated with autism spectrum disorders www.nature.com/articles/s41...

The next Human Cell Atlas will be held in Singapore in June 2025. The early-bird registration is already open: 2025events.humancellatlas.org/2025GM I highly encourage single-cell folks to register. Many exciting talks ahead!

2025 Human Cell Atlas General Meeting

The 2025 HCA General Meeting will convene our community to share updates on assembling HCA Atlases of specific tissues, and to plan for the release of the first draft Human Cell Atlas. We will discuss...

2025events.humancellatlas.org

Our paper on single-cell splicing QTL is now published as a cover article in Nature Genetics. www.nature.com/articles/s41... Congratulations to co-first authors Chi Tian, Yihan Tong, and Yuntian Zhang! Huge thanks to AIDA leaders Shyam Prabhakar, @jayshin.bsky.social, Woong-Yang, and Kian Hong!

Single-cell RNA sequencing of peripheral blood links cell-type-specific regulation of splicing to autoimmune and inflammatory diseases - Nature Genetics

This analysis of single-cell RNA sequencing data from peripheral blood mononuclear cells for 474 individuals of diverse Asian ancestries in the Asian Immune Diversity Atlas links cell-type-specific sp...

nature.com

Very exciting work for biology and drug discovery!

Anne Carpenter@drannecarpenter.bsky.social · 2y ago

Now on biorxiv! The JUMP-Cell Painting Consortium’s paper: “Morphological map of under- and over-expression of genes in human cells” This is the genetic perturbation portion of the JUMP’s dataset; our chemical perturbation paper will come in a few months www.biorxiv.org/content/10.1...

QC is arguably the most important step in any single cell analysis. Low quality data can lead to incorrect conclusions.

Tomàs Montserrat Ayuso@tmontsay.bsky.social · 2y ago

scRNA-seq has revolutionized biology, but it’s not without challenges. We uncovered significant quality issues in widely used reference cell atlases like the Human Cell Atlas and Tabula Sapiens. Up to 85% of cells in some datasets are low-quality or misidentified! 2/8

HCA Asia 2024 off to a great start!

En route to HCA Hong Kong. Excited to reconnect with old friends and making new ones!

Comprehensive knockdown of 305 splicing-related proteins and their effect on splicing. Such a tour de force!!

Here is a starter pack for functional genomics on bluesky. Not sure if there is one already but do let me know if so. Let me know if you want to be added to the list. go.bsky.app/SvBtD4d

The SG Academies South-East Asia Fellowship Programme (2024 Round) application is now open and will close on 31 Jan 2025. snas.org.sg/saseaf.

Is there a starter pack for functional genomics? Should I start one?

Has anyone used Video Byte or Graphical Abstract service by Springer Nature? Is it worth it?