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PATH (phylogenetic analysis of trait heritability) is out Nature Genetics! Excited about tackling the fundamentals of somatic evolution: *measuring cell state heritability *a quantitative definition for cell plasticity (1-heritability) *cell-state transition dynamics 👀🧵👇

Published in 2009, bwa-aln is one of the oldest short-read aligners. It remains a popular choice for aligning ancient DNA reads. The following blog post explains the algorithmic reasons. lh3.github.io/2024/09/28/why…

Excited to have our work out now in Orli Bahcall. @BartDeplancke nature.com/articles/s4158… Few important changes compared to the preprint! see 🧵 below

Flexible differential expression analyses have always been neat in CZ #CellxGene. Now they’re next level! Quickly perform DE analysis across our entire data corpus. For ex: leveraging >125 relevant datasets to compare astrocytes with/without Alzheimer’s📷 bit.ly/4eDt9uU

🧵 Bioinformatics faces a critical challenge: despite its importance, software quality often falls short due to the lack of proper development practices. In our latest paper, we advocate for improving software quality in bioinformatics through teamwork. doi.org/10.1093/bioinf…

Free scientific illustrations for biologists! 😍 NIH has released a library of 500+ free scientific illustrations to create figures, presentations, and illustrations! all freely available in the public domain. Retweet and spread the message! bioart.niaid.nih.gov

My guidelines for exploratory data analysis

VeloCycle, developed by the team of Gioele La Manno and The Naef Lab is a manifold-constrained RNA velocity framework for uncovering cell cycle dynamics. nature.com/articles/s4159…

Excited to visit the Human Technopole 🇮🇹today to share our work on computational approaches in functional genomics! Looking forward to discussions with amazing scientists about #singlecell, #CRISPR, and #syntheticbiology. 🧬Special thanks to Nicole Soranzo for the invitation 🙏

Attending #NeurIPS2024 this week and excited to connect with anyone exploring the intersection of #GenerativeAI, #DeepLearning, and #Genomics! I’m presenting our DNA-diffusion work at the LatinX in AI workshop today at 2:30—drop by if you’re around. Looking forward to connecting!

Amazing new assay that allows testing of multiple DNA sequences, similar to MPRA, but in an endogenous setting. Incredible potential! Congrats Judith Kribelbauer , @BartDeplancke and the entire team – grateful and lucky to be an early adopter. Check it out!

Excited to be visiting Duke University to share insights on computational methods for single-cell genomics and CRISPR genome editing! Thank you for hosting me Yi-zhang-compbio! 🙏

We are thrilled to join the FutureHouse community, Sam Rodriques FutureHouse! We are seeking exceptional machine learning experts to help create predictive virtual 3D mammalian embryos and virtual scientists for advancing human health. As part of the FutureHouse community, we

🚨📰TWEETORIAL time📰🚨 Excited to share recent work from our lab on noncoding genomics 🔎🧬: High-resolution CRISPR mutagenesis of the MYC TAD (~3 Mb) in 6 different human cancer cell lines nature.com/articles/s4146…

In @nature we describe the use of scalable #proteinengineering & #machinelearning to predict millions of bespoke CRISPR-Cas9 enzymes, offering safer & more genome editing tools. 🧬🖥️ Rachel Silverstein CGM at MGH @MGH_RI MassGeneral News Harvard Medical School nature.com/articles/s4158…

Great to see it finally out —such a fantastic collaboration with Ben Kleinstiver, Rachel Silverstein and team!