fan of functional genomics Postdoc at UCSF
Joined October 2018
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Starting to think Guardiola struck a deal with the Premier League: he loses ~10 games, the League drops the FFP charges. The bald wizard plays his 'win if I want, lose if I want' game and plays his role of being heartbroken after every loss beautifully. What a fantastic actor!
Thrilled to share that our paper "Systematic identification of post-transcriptional regulatory modules" has been featured on the Editors' Highlights webpage by @NatureComms! A big thank you to the editors for selecting our work. Check it out here: nature.com/ncomms/editorshig…
Matvei Khoroshkin retweeted
The final version of is now published: nature.com/articles/s41467-0…
Congratulations @khorms57 and our team across 3 groups, ours, @FKHM, and @halfacrocodile!
Thanks to @vishvak2000 we are also releasing an RNA binding protein (RBP) browser for dynamic visualization of RBP-RBP interactions in our preprint (1/7) goodarzilab.shinyapps.io/RBP…
Matvei Khoroshkin retweeted
Excited to share our latest preprint on two innovative click-chemistry-aided methods: Click-Fluoro-Quant and Click-Code-Seq, enabling precise sequencing of DNA oxidation and nucleobase loss at single-nucleotide resolution in the human genome. 1/4
biorxiv.org/content/10.1101/…
Excited to see our work on human RNA switches published in Nature Methods today! nature.com/articles/s41592-0…
RNA folding affects gene expression, but this link is not well explored in Eukaryotes. We researched RNA structural switches and discovered hundreds of them in the human transcriptome. We even visualized some of their 3D folds with CryoEM. Thread below: biorxiv.org/content/10.1101/…
In the blog post below, I discuss the implications of this work for the field of RNA biology communities.springernature.c…
Matvei Khoroshkin retweeted
We’re thrilled to welcome Hani Goodarzi @genophoria, Associate Professor of Biochemistry & Biophysics @UCSF, as our newest Core Investigator
His groundbreaking research uses machine learning models and experimental frameworks to dig into cancer progression and metastasis.
Check out our new preprint led by Artemii! We focus on inherent biases present in biological annotations and ways to adjust for them when doing pathway enrichment analysis
A long time ago, @ElementoLab and I came up with our solution to the gene-set enrichment analysis. We used mutual information to measure the association between gene-set membership and input. After a decade, a talented undergrad spearheaded an update: biorxiv.org/content/10.1101/…
Go Albertas!
Links between translation and alternative polyadenylation in metastasis? The story is out today! A great collab between @genophoria, @AndreiGoga_SF and @FKHM labs! Shout out to co-authors @Gentremet, @JulianeScience, @lisacfishsci among others! nature.com/articles/s41556-0…
Matvei Khoroshkin retweeted
We're excited to introduce our latest database - NucleosomeDB! With its help, you can easily browse through all known nucleosome structures, compare their shape and DNA geometry parameters, and find structures of chromatin protein complexes. We hope you enjoy using it!
NucleosomeDB - a database of 3D nucleosome structures and their complexes with comparative analysis toolkit biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
Matvei Khoroshkin retweeted
Super excited to share the results of our highly collaborative project co-led by @MNaghipourfar, Ali Saberi, @DelaramPB, Amirhossein Zarezadeh and supervised by my incredible mentor @genophoria.
Matvei Khoroshkin retweeted
Happy to share one more story (journal pre-proof) I led working at @Caltech with William Goddard and Stephen Liggett with great support from Brian Guthrie and @Cargill!
Predicted structure and cell signaling of TAS2R14 reveal receptor hype... sciencedirect.com/science/ar…
RNA folding affects gene expression, but this link is not well explored in Eukaryotes. We researched RNA structural switches and discovered hundreds of them in the human transcriptome. We even visualized some of their 3D folds with CryoEM. Thread below: biorxiv.org/content/10.1101/…
We believe this to be a sole example among hundreds if not thousands of such RNA structural elements across the human transcriptome. And we are confident that such elements will emerge as hitherto ignored regulators of gene expression in health and disease. #RNAfolding
A huge thank you to @genophoria, @a_navickas, @dabiophysicist, Mark Ansel, @yifan_ucsf, @LukeGilbertSF, who generously supported my plan to work on what seemed to be a quite risky idea. I had a ton of fun working on this problem! #geneexpression