Alireza Karbalayghareh
@karbalayghareh
Senior Research Scientist at CZ Biohub New York @czbiohub, AI/ML Platform. Building causal AI models of immune cells.
Hi all, I am currently on the academic job market. I am a postdoctoral researcher in Dr. Christina Leslie's lab at the Computational and Systems Biology Program at Memorial Sloan Kettering Cancer Center. My research focuses on deciphering causal and dynamic gene regulation…
Our paper is now in @NatureBiotech! Topological velocity inference from spatial transcriptomic data. TopoVelo infers the direction of differentiation/migration; quantifies spatial cell influence; and identifies morphology changes during differentiation. 🧵rdcu.be/ewqMB
Great workshop and fantastic talks!
Exciting lineup of presenters at today's #CZBiohubNY Mini Workshop hosted by @YaleMed, @TsangLab and @YaleCSEI. Thrilled to welcome @czbiohub and @czi investigators and team members to Yale for this day of science and interaction.
Great opportunity!
@sara_mostafavi (@genentech ) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/
Looks like a great venue!
I’m excited to co-host the new #AIxBio conference alongside @Avsecz, @ferruz_noelia, @pdhsu, @BenLehner, @ml19, @deboramarks, @p_tingying, @CarolineUhlerat at @wellcomegenome/ @sangerinstitute! We’ll focus on modellingz and designing DNA, RNA, proteins, and cells, as well as…
[SAVE THE DATE] MLCB 2025 is happening Sep 10-11 at the NY Genome Center—NYC! Attend the premier conference at the intersection of ML & Bio, share your research and make lasting connections! Submission deadline: Jun 1 Details: mlcb.github.io Spread the word—please RT!
We are hiring 🎺🎺🎺! As part of our immuno-oncology transformation @MSKCancerCenter we are building the Computational Immuno-Oncology Shared Resource. CIOSR is a key pillar supporting expanded immune monitoring & broad IO efforts. We have two open positions: bioinformatics…
Introducing scE2G: a new model to link enhancers to target genes using single-cell data. Excited that scE2G will enable building enhancer maps in hundreds of cell types in the human body! Wonderful collaboration with @robin_andersson @613weilin @mayayayas and others 👇
Excited to share our latest preprint on scE2G – a new model to link enhancers to target genes using single-cell data – with state-of-the-art performance across multiple perturbation benchmarks. biorxiv.org/cgi/content/sh… Read more below! 1/12
Happy to share HiC2Self, a self-supervised tool for denoising bulk and single-cell Hi-C contact maps! biorxiv.org/content/10.110…
My goal is to understand the regulatory role of every nucleotide in the genome, and how this changes across every cell in the human body. If you are interested in doing a Ph.D. with me @UMassGCB, see the links below. Deadline is Dec 1st.
Delighted to have worked on this perspective on the cis-regulatory code with @JuliaZeitlinger, @JasonErnstLab, @ferhatay, @AMathelier, @AleMedinaRivera, @mahonylab, @sinhasaur arxiv.org/abs/2411.04363. We provide an overview of current progress and some challenges to think about.
ChromaFold is out! Very effective and robust model to predict 3D contact maps from scATAC-seq.
Out in @NatureComms ! ChromaFold predicts 3D contact maps using single-cell ATAC-seq alone. nature.com/articles/s4146…
BREAKING NEWS The Royal Swedish Academy of Sciences has decided to award the 2024 #NobelPrize in Physics to John J. Hopfield and Geoffrey E. Hinton “for foundational discoveries and inventions that enable machine learning with artificial neural networks.”
Enjoyed the talks and meeting the old and new friends at #SCG2024. Huge thanks for the organizers!
Great lab to join! Darko's lab has a lot of cool single cell multiome data to understand the role of chromatin remodelers in boold cancers! Great potential for high-impact research plus he is very insightful and kind mentor!
Thrilled to share we are @theNCI R00-funded. 🥳 Looking for computational biologists or bioinformaticians. 👩💻👨💻 We have many exciting projects on the role of chromatin remodelers in blood cancers. 🩸🦀 Please share/DM/email if relevant. Our latest story: cell.com/cancer-cell/ab…
I met so many people (students, researchers, and even investors) say they are so interested in understanding intelligence. Yet, they never bother to prepare themselves with the basic mathematical background. They wouldn't be able to understand anything even if a perfect theory is…
Excited to share the white paper for the IGVF Consortium, supported by @genome_gov Deciphering the impact of genomic variation on function rdcu.be/dSZdm
Understanding the function of an entire genome is no easy task! Most genes likely have more than one function. To understand the functional effects of genomic variation, NHGRI launched a consortium called Impact of Genomic Variation on Function (IGVF). genome.gov/news/IGVF
Heading to #ISMB2024 in Montreal. Looking forward to meet everyone who are around!
Happy to share the final version of our #GAGEseq published today @NatureGenet! The single-cell co-assay for #scHiC and #scRNA reveals 3D genome & gene expression interplay in mouse cortex (also integration w/ #MERFISH) and during human hematopoiesis. 1/3 nature.com/articles/s4158…