@YizhakLab

Computational Cancer Genomics Lab - Turn Cancer Data into Knowledge

Joined March 2021
  • Tweets43
  • Following156
  • Followers128
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๐Ÿš€ New preprint! scXpand โ€” the first ML framework to detect T-cell clonal expansion from scRNA-seq (no TCR needed). Built on 2.6M T cells, robust across cancers & TME contexts. ๐Ÿ‘ Led by Ofir Shorer & @RonAmit5 ๐Ÿ”— doi.org/10.1101/2025.09.14.6โ€ฆ
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๐Ÿ’ป Code: github.com/yizhak-lab-ccg/scโ€ฆ ๐Ÿ“š Docs: scxpand.readthedocs.io #MachineLearning #scRNAseq #scTCRseq #CancerResearch #Bioinformatics #bioRxiv
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๐Ÿ“ข Excited to share our new paper in @CellGenomics! We analyzed matched #scRNAseq and #scTCRseq from 767K T cells to uncover clonal programs that predict response to immune checkpoint inhibitors. ๐Ÿ‘‰ cell.com/cell-genomics/fulltโ€ฆ #CancerImmunotherapy

Single-cell meta-analysis of T cells reveals clonal dynamics of response to checkpoint immunotherapy

Shorer et al. perform paired scRNA/TCR-seq meta-analysis of 767,606 T cells obtained from patients with cancer treated with checkpoint immunotherapy across multiple cancer types. Their findings...

cell.com
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๐Ÿ“ข Excited to share our new paper in #npjPrecisionOncology: We present a roadmap for using #scRNAseq and #MachineLearning to study and predict response to immune checkpoint inhibitors. ๐Ÿ‘‰ nature.com/articles/s41698-0โ€ฆ #CancerImmunotherapy
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KerenYizhakLab retweeted
Reut Shalgi@reut_shalgi17 Mar 2025
ืžื–ืžื™ื ื™ื ืืชื›ื/ืŸ ืœื™ื•ื ื”ืคืชื•ื— ืœืžืกืœื•ืœ ื”ื—ื“ืฉ ืœืชื•ืืจ ืฉื ื™ ืขื ื”ืชืžื—ื•ืช ื‘ืจืคื•ืื” ื—ื™ืฉื•ื‘ื™ืช ื‘ืคืงื•ืœื˜ื” ืœืจืคื•ืื” ื‘ื˜ื›ื ื™ื•ืŸ! 20.3, ื‘ืฉืขื” 16:00 . ืœืคืจื˜ื™ื ื ื•ืกืคื™ื : compmed.net.technion.ac.il ืœื”ืจืฉืžื” ืœื™ื•ื ื”ืคืชื•ื—: did.li/n8e6q ื ืชืจืื”!
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๐Ÿšจ New preprint alert! We performed scRNA-seq & scTCR meta-analysis on cancer patients treated with ICIs, revealing key T cell signatures linked to therapeutic response, with insights into clonal replacement vs reinvigoration! #scRNAseq #Immunotherapy biorxiv.org/content/10.1101/โ€ฆ

Single-cell meta-analysis of T cells reveals clonal dynamics of response to checkpoint immunotherapy

Despite the crucial role of T cell clones in the anti-tumor activity, their characterization and association with clinical outcome following immune checkpoint inhibitors (ICI) is lacking. Here we...

biorxiv.org
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We are excited to share the agenda for our 1st annual event, 26/9 @ELSCbrain๐Ÿช… w/ spotlights ๐Ÿ”ฆ@YOrenLab, Amos Tanay, @yizhaklab, @atownfool & @SItzkovitz. A field overview by @mor_nitzan & @naomi_habib, and sc-ience sessions led by @bitonm, Oren Ram, @YosefLab & @OCohenlab
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KerenYizhakLab retweeted
Ayelet Erez@AyeletErez10 Jun 2024
Iโ€™m happy to share our new paper showing moonlighting function of ASS1 in the nucleus. Under the tough circumstances we are facing this paper would have never been published without the help of a wonderful editor, great collaborators and resilient students. Thank you all! โ™ฅ๏ธ
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We celebrate the much-deserved selection of @gaddyg to this yearโ€™s class of 2024 AACR Academy Fellows!! Congrats, Gaddy ๐ŸŽ‰! aacr.org/about-the-aacr/newsโ€ฆ @MGHCancerCenter @broadinstitute

AACR Announces Newly Elected 2024 Class of Fellows of the AACR Academy

AACR Announces Newly Elected 2024 Class of Fellows of the AACR Academy

aacr.org
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KerenYizhakLab retweeted
Tal Shay@tal_shay26 Dec 2023
My second cousin Yagev Buchshtab was kidnapped on October 7 and is being held in Gaza for 81 days now. Please listen to his sister Nufar and share.
SternLab @sternadi.bsky.social@SternLab26 Dec 2023
My brilliant PhD student Nufar, whose brother is a hostage in Gaza for over 80 days. Nothing prepared me to being a mentor under such a scenario. How can we even continue research in the lab?? Please help her, help us, spread this heart-breaking humanitarian call.
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KerenYizhakLab retweeted
OncoHost@OncoHost4 Dec 2023
We are thrilled to announce that OncoHost has been named one of the Top 10 Precision Oncology Solutions Companies of 2023 by @HealthCareTO! ๐Ÿ† Thank you for this honor ๐Ÿ’™ Read more: bit.ly/4a4BjdT #PrecisionOncology #HealthcareInnovation #CancerResearch #Proteomics
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Happy to share this work lead by Daniel Schaffer, using a deep learning model to identify microbial RNAseq reads that are assembled into longer contigs. We find that the presence of several microbial genes strongly predicts outcomes in esophageal cancer nature.com/articles/s43705-0โ€ฆ

Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers...

ISME Communications - Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes

nature.com
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ื ืขื ื“ืŸ, ืžืžืฉืคื—ืชื ืฉืœ ืกื”ืจ ื•ืืจื– ืงืœื“ืจื•ืŸ ืฉืฉื•ื—ืจืจื• ืืš ืื‘ื™ื”ื ืขื•ืคืจ ืขื“ื™ื™ืŸ ื—ื˜ื•ืฃ, ื˜ืœื˜ืœื” ืืชืžื•ืœ ืืช ืื•ืœืคืŸ ื—ื“ืฉื•ืช 12. ื”ื ื” ืฉื•ื‘ ืงื˜ืข ืžื“ื‘ืจื™ื”, ืขื ื›ืชื•ื‘ื™ื•ืช. ืœืฆืคื•ืช, ืœื”ืคื™ืฅ ืœื›ืœ ืขื‘ืจ
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In these darkest days our country have ever known, we somehow manage to do science. Our new paper shows how #metabolism of immune cells predicts patients response to ICI. Ofir finished this paper while in reserve duty helping to bring our people back home cell.com/iscience/fulltext/Sโ€ฆ

Metabolic predictors of response to immune checkpoint blockade therapy

Human metabolism; Immunology; Cancer

cell.com
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ื”ืกืจื˜ ื”ื–ื” ื”ื•ื ื—ื•ื‘ื” ืื–ืจื—ื™ืช - ืื™ืŸ ืคื” ื—ื•ืžืจื™ื ืžื–ืขื–ืขื™ื ื•ืจื’ื™ืฉื™ื - ื›ื ืกื• ืœื”ืงืฉื™ื‘ ืœื›ืจืžื™ืช ืฉืื‘ื™ื” ื ืจืฆื—, ืืžื” ื ื—ื˜ืคื” ื•ืื—ื™ื” ื ืขื“ืจ
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KerenYizhakLab retweeted
Shai Davidai
@ShaiDavidai19 Oct 2023
An Open Letter to Every Parent In America Please help me get this message out to every parent in the United States. Please help me protect your children. I am BEGGING you - "liking" this is not enough. Please retweet right NOW. youtube.com/watch?v=uo7fdxrjโ€ฆ

An Open Letter to Every Parent in America

Please help me share this video as widely as possible.I am beggin...

youtube.com
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Ayelet Erez@AyeletErez21 Sep 2023
Before we have to pay to tweet, I want to post an opening for a PhD position at the Weizmann Institute for a student interested in characterizing the tumor MACROenvironment for therapeutic implications.
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Check out our new #preprint on the metabolism of immune cells in the TME of patients treated with #immunotherapy led by Ofir Shorer. We analyzed scRNA-seq from >1M cells and found a metabolic signature predictive of response across cancer types. biorxiv.org/content/10.1101/โ€ฆ

Metabolic predictors of response to immune checkpoint blockade therapy

Metabolism of immune cells in the tumor microenvironment (TME) plays a critical role in cancer patient response to immune checkpoint inhibitors (ICI). Yet, a metabolic characterization of immune...

biorxiv.org
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We had a great time at the #ILANIT2023 meeting. Very proud of my team with 4 talks, 3 posters, 3 runners and one fun lab outing which as usual, we forgot to take a photo of.
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Noam Kaplan@Noam_Kaplan11 Jan 2023
Our work on genomic compartments is now out in @NAR_Open! I really have to commend both the reviewers and NAR team for very professional and speedy handling of the manuscript ๐Ÿ‘๐Ÿ‘๐Ÿ‘ academic.oup.com/nar/advanceโ€ฆ

Hypothesis-driven probabilistic modelling enables a principled perspective of genomic compartments

Abstract. The Hi-C method has revolutionized the study of genome organization, yet interpretation of Hi-C interaction frequency maps remains a major challe

academic.oup.com
Noam Kaplan@Noam_Kaplan5 Oct 2022
New preprint! biorxiv.org/content/10.1101/โ€ฆ So whatโ€™s the deal with this checkered Hi-C pattern, aka genomic compartments (GC)? Led by the one and only Hagai Kariti @hakariti Tweetorial>>
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