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2 months ago | 
nature.com | Michael Snyder |Hayan Lee |Annika K Weimer |Aaron M Horning |Edward D. Esplin |Kristina Ayers Paul | +4 more
Correction to: Nature Cancer https://doi.org/10.1038/s43018-024-00823-z, published online 30 October 2024. In the version of the article initially published, a technique described as “intact Micro-C” should have been called “MNase-digested Intact Hi-C” and has now been corrected throughout the article.
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Jan 16, 2025 | 01008-6?rss=yes&sz=64)
cell.com | Anshul Kundaje |Katherine S. Pollard |Jian Ma |Xing Chang |Mengjie Chen |Remo Rohs
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Jan 16, 2025 | 01008-6&sz=64)
cell.com | Anshul Kundaje |Katherine S. Pollard |Jian Ma |Xing Chang |Mengjie Chen |Remo Rohs
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Oct 30, 2024 | 
nature.com | Hayan Lee |Annika K Weimer |Aaron M Horning |Edward D. Esplin |Kristina Ayers Paul |Thomas V. Karathanos | +3 more
AbstractAlthough three-dimensional (3D) genome architecture is crucial for gene regulation, its role in disease remains elusive. We traced the evolution and malignant transformation of colorectal cancer (CRC) by generating high-resolution chromatin conformation maps of 33 colon samples spanning different stages of early neoplastic growth in persons with familial adenomatous polyposis (FAP).
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Oct 30, 2024 | 
nature.com | Edward D. Esplin |Casey Hanson |Aaron M Horning |Hayan Lee |Aziz K. Khan |Annika K Weimer | +5 more
AbstractFamilial adenomatous polyposis (FAP) is a genetic disease causing hundreds of premalignant polyps in affected persons and is an ideal model to study transitions of early precancer states to colorectal cancer (CRC). We performed deep multiomic profiling of 93 samples, including normal mucosa, benign polyps and dysplastic polyps, from six persons with FAP.
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Oct 29, 2024 | 00604-x?rss=yes&sz=64)
cell.com | Roni Levin-Konigsberg |Koushambi Mitra |Kaitlyn Spees |Akshat Kumar Nigam |katherine liu |Camille Januel | +6 more
Keywordslysosome metabolismSLC12A9ammoniumion transportlysosome volume regulationchlorideGet full text accessLog in, subscribe or purchase for full access. References1. Walker, V. Chapter Three - . Ammonia Metabolism and Hyperammonemic DisordersElsevier,Makowski, S. in: Advances in Clinical Chemistry. 67. 2014; 73-1502. Spinelli, J.B. ∙ Yoon, H. ∙ Ringel, A.E. ... Metabolic recycling of ammonia via glutamate dehydrogenase supports breast cancer biomassScience. 2017; 358:941-9463. Takiguchi, M. ∙ Mori, M.
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Oct 29, 2024 | 
biorxiv.org | Chiho Im |Ryan Zhao |Scott D. Boyd |Anshul Kundaje
AbstractUnderstanding T-Cell receptor (TCR) and epitope interactions is critical for advancing ourknowledge of the human immune system. Traditional approaches that use sequence similarity or structure data often struggle to scale and generalize across diverse TCR/epitope interactions. To address these limitations, we introduce ImmuneCLIP, a contrastive fine-tuning method that leverages pre-trained protein language models to align TCR and epitope embeddings in a shared latent space.
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Jun 6, 2024 | 
biorxiv.org | Georgi K. Marinov |Vivekanandan Ramalingam |William J. Greenleaf |Anshul Kundaje
AbstractIn most eukaryotes, mitochondrial organelles contain their own genome, usually circular, which is the remnant of the genome of the ancestral bacterial endosymbiont that gave rise to modern mitochondria. Mitochondrial genomes are dramatically reduced in their gene content due to the process of endosymbiotic gene transfer to the nucleus; as a result most mitochondrial proteins are encoded in the nucleus and imported into mitochondria.
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Apr 14, 2024 | 
biorxiv.org | Alan Min |Jacob Schreiber |Anshul Kundaje |William Noble
AbstractOver the past 15 years, a variety of next-generation sequencing assays have been developed for measuring the 3D conformation of DNA in the nucleus. Each of these assays gives, for a particular cell or tissue type, a distinct picture of 3D chromatin architecture.
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Mar 19, 2024 | 
nature.com | David Yao |Josh Tycko |Lexi R. Bounds |Benjamin Doughty |Alexander White |Xingjie Ren | +16 more
AbstractThe ENCODE Consortium’s efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to investigate cis-regulatory mechanisms. The ENCODE4 Functional Characterization Centers conducted 108 screens in human cell lines, comprising >540,000 perturbations across 24.85 megabases of the genome.
