Yifan Zhao

New online! Advances in single-cell DNA sequencing enable insights into human somatic mosaicism bit.ly/3EGIyxQ

We open our wonderful @HiTSeq session today at #ISMBECCB2023 with our keynote speaker Dr Jan Korbel @JanKorbel5 and his talk about using single-Celll and single-molecule seq to decipher disease and aging. Follow us for more! hitseq.org #scseq #lovebionformatics

The Park lab is looking for a recent college grad to work as scientific programmer/RA, who will help with projects in the lab as well as doing independent research. Last 5 people in this role: 4 went onto PhD programs at Harvard (3) and MIT (1), 1 to Google. Send CV to me.

Motivated by my earlier tweet and the responses, I wrote a blog post to explain my views on the design of command-line interface. lh3.github.io/2022/09/28/add…

Excited to announce that our protein ML platform TorchProtein (torchprotein.ai) are now released as a part of TorchDrug! Tired of processing proteins? Struggle with protein seq & struct representation models? Come and have a try!

Can we identify single nucleotide variants and indels accurately at the single cell level? Joe Luquette developed SCAN2 to examine >50 neurons and finds enrichment of indels at brain-specific enhancers/promoters. Collab with @ChrisAWalsh1 lab. Full text: rdcu.be/cWmNb

Excited to share our paper describing Numbat, a haplotype-aware CNV caller for scRNA-seq, out today on @NatureBiotech! nature.com/articles/s4158… (1/5)

We are excited to share our work applying PTA genomic amplification to human #neurons to study somatic mutations! Out today in @NatureGenet. Beautiful analysis by Joe Luquette @peter_j_park leading this collaboration w/ @zinan_zhou and @ChrisAWalsh1 nature.com/articles/s4158… [1/n]

I'm thrilled to share our MuSiCal (Mutational Signature Calculator) manuscript: biorxiv.org/content/10.110… Mutational signature analysis, pioneered by colleagues at Sanger, has become a key tool for interpreting somatic mutations identified in sequencing data. 3 main concepts (1/8):

Happy worms make great movies😉

Out today is our review "Computational analysis of cancer genome sequencing data" describing the key steps/algorithms especially for whole-genome analysis. The indefatigable Isidro Cortes-Ciriano (@isidrolauscher), a former postdoc now a group leader at EBI, is the lead author.

Interested in single-cell RNA sequencing analysis? We proposed single-cell Embedded Topic Model, which learns a transferrable cell encoder and an interpretable decoder, inferring both gene and topic embeddings. Published at Nature Communications:nature.com/articles/s4146…

Would like to identify transposable element insertions from your whole-genome data? The latest tool from my lab is xTea (x-Transposable element analyzer), developed by the talented Simon Chu. nature.com/articles/s4146…

Another positive publishing experience @MBoCjournal. 🙏 to the reviewers for their constructive feedback.

Preprint time 🥳 Awesome job Réda, @yifnzhao, Vincent & @RamyaSingh! Live imaging C. elegans GSC mitosis in happy cells/worms, automated analysis via centrosome tracking/pairing (it's not just for worms😉) & what we see by looking at lots of cells. doi.org/10.1101/2020.1…