Sol Shenker

[Sol Shenker @solshenker]

@JohnDoench Thank you, will to!

[Sol Shenker @solshenker]

@JohnDoench I've got a quick question about CFD scores, if I could steal a second of your time

[Sol Shenker @solshenker]

@JohnDoench If you have some examples of bulged alignments and their CFD scores I could make sure the implementation I'm using is correct. It looks like the sites in supplementary table 20 don't include bulges.

[Sol Shenker @solshenker]

@JohnDoench is there a reference implementation of the CFD score that includes bulges? The code with the supplementary materials for the 2016 paper only uses mismatches. It's also a little unclear how positions should be numbered in case of an RNA deletion.

[Sol Shenker @solshenker]

@iskander I'd like one please

[Sol Shenker @solshenker]

@eColi_virus I just happened across this, and it caught my eye because I've got a good solution to do this. Is this still something that you still need a solution for?

[Sol Shenker @solshenker]

@sroyyors and outputs the closest aligned position (rang) in the other genome. It can get a little hairy since one part of the genome can align to many places in the other genome.

[Sol Shenker @solshenker]

@sroyyors The liftover file is a piecewise description of the pairwise alignment of two genomes. If you have the reference sequence of each genome you can convert it to a fasta-format pairwise alignment. Liftover takes a coordinate (or range) in one genome, looks at the alignment...

[Sol Shenker @solshenker]

Beautiful work by my brilliant wife @t_ouspenskaia @broadinstitute, now on to bigger and brighter things at #FL69 @FlagshipPioneer

[Nature Biotechnology @NatureBiotech]

Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer https://t.co/yiecuBOzRC

[B. Arman Aksoy @armish]

At @moma_tx, we are looking for scientifically unapologetic computational biologists who can help us decipher molecular machines in unprecedented ways: https://t.co/BlFNV2GlxG

My DMs are open in case you have questions about this role. Please help us spread the news by RTing🙏

[Sol Shenker @solshenker]

Excited for the public debut of our USP1 program, come listen if you can tomorrow morning (EST)

[KSQ Therapeutics Inc @KSQ_TX]

We are ready for #ENASymp! Don’t miss the presentation of new data from our lead targeted oncology program, a USP1 inhibitor.

https://t.co/L2ncm9ikek

[KSQ Therapeutics Inc @KSQ_TX]

Our USP1 inhibitor program was selected for a plenary at the 32nd Annual #ENASymp, @EORTC, taking place Oct. 24-25, 2020. We look forward to presenting on the promise of this approach and details on clinical candidate KSQ-4279. We’ll see you virtually! https://t.co/SS70wzXWFQ

[Tamara Ouspenskaia @t_ouspenskaia]

Very excited to share our work on unannotated proteins and their contribution to the MHC I immunopeptidome. Could not have been possible without my awesome co-authors and collaborators from @broadinstitute @DanaFarber @Harvard
https://t.co/kShe2tqsPq

[bioRxiv @biorxivpreprint]

Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer https://t.co/KSIoeTeti1 #bioRxiv

[Sol Shenker @solshenker]

@David_McGaughey @gatk_dev

[KSQ Therapeutics Inc @KSQ_TX]

KSQ secures $80M financing and advances broad pipeline of cancer therapies, including its first drug program: an Adoptive T Cell Therapy for PD-1 resistant solid tumors. https://t.co/IystqzuuYc

[KSQ Therapeutics Inc @KSQ_TX]

Proud to unveil KSQ’s pipeline today with 12 new cancer drug discovery programs generated in 12 months, including adoptive T cell therapies, immuno-oncology monotherapies and targeted therapies. https://t.co/ajZqZWURpp

[Olivier Elemento @ElementoLab]

Sol Shenker @cbm_student in Eric Lai's group being grilled on his thesis work by thesis examination committee !

[Fabrice Leclerc @rnomics]

#bioRxiv : A comprehensive analysis of 3' end sequencing data sets reveals novel… https://t.co/7kUcI4UlBs #condmatstrel #biorXiv

[Sol Shenker @solshenker]

@yokofakun @aaronquinlan @neilfws the perl api http://t.co/d6gXs9adSt has some domain info