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1 month ago | 
biorxiv.org | Katherine S. Pollard |Nilah M. Ioannidis |Ryan L. Keivanfar |Forest Yang
AbstractDeep learning models in genomics that predict molecular phenotypes from DNA sequence traditionally focus on one-hot encoded representations. Here, we develop a novel model that extends this approach by incorporating DNA structural attributes indicative of local shape alongside canonical sequence inputs. This augmentation provides an additional axis for model interpretability and aids in identifying regulatory patterns not apparent from sequence alone.
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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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Sep 30, 2024 | 00324-x&sz=64)
cell.com | Lee Reicher |Katherine S. Pollard
Keywordsmicrobiotamicrobiomeprokaryotesbacteriaantibioticsantibiotic resistancegeneticsgenomicsstrainsgutGet full text accessLog in, subscribe or purchase for full access. References1. Lynch, S.V. ∙ Pedersen, O. The human intestinal microbiome in health and diseaseN. Engl. J. Med. 2016; 375:2369-23792. Van Rossum, T. ∙ Ferretti, P. ∙ Maistrenko, O.M. ... Diversity within species: interpreting strains in microbiomesNat. Rev. Microbiol. 2020; 18:491-5063. McInerney, J.O. ∙ McNally, A.
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Jul 28, 2024 | 
nature.com | Shuzhen Kuang |Katherine S. Pollard
AbstractRecent studies have highlighted the impact of both transcription and transcripts on 3D genome organization, particularly its dynamics. Here, we propose a deep learning framework, called AkitaR, that leverages both genome sequences and genome-wide RNA-DNA interactions to investigate the roles of chromatin-associated RNAs (caRNAs) on genome folding in HFFc6 cells.
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Jul 28, 2024 | 
flipboard.com | Shuzhen Kuang |Katherine S. Pollard
The Brain2 hours agoNeurologist diagnosed with dementia in his 60s reveals his 'first clue' - and it was 'smelly'gbnews.com - Adam Chapman • 2hA neurologist diagnosed with dementia in his 60s has revealed his first symptom.
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Jun 30, 2024 | 
biorxiv.org | Miriam Goldman |Chunyu Zhao |Katherine S. Pollard
AbstractMicrobiome association studies typically link host disease or other traits to summary statistics measured in metagenomics data, such as diversity or taxonomic composition. But identifying disease-associated species based on their relative abundance does not provide insight into why these microbes act as disease markers, and it overlooks cases where disease risk is related to specific strains with unique biological functions.
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May 17, 2024 | 
biorxiv.org | Zhirui Hu |Pawel F. Przytycki |Katherine S. Pollard
AbstractCellWalker2 is a graph diffusion-based method for single-cell genomics data integration. It extends the CellWalker model by incorporating hierarchical relationships between cell types, providing estimates of statistical significance, and adding data structures for analyzing multi-omics data so that gene expression and open chromatin can be jointly modeled.
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Nov 22, 2023 | 
biorxiv.org | Laura M Gunsalus |Michael Keiser |Katherine S. Pollard
AbstractThe investigation of chromatin organization in single cells holds great promise for identifying causal relationships between genome structure and function. However, analysis of single-molecule data is hampered by extreme yet inherent heterogeneity, making it challenging to determine the contributions of individual chromatin fibers to bulk trends.
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Nov 17, 2023 | 
biorxiv.org | Pawel F. Przytycki |Katherine S. Pollard |Chan Zuckerberg Biohub
AbstractWhile context-type-specific regulation of genes is largely determined by cis-regulatory regions, attempts to identify cell-type specific eQTLs are complicated by the nested nature of cell types. We present a network-based model for hierarchical annotation of bulk-derived eQTLs to levels of a cell type tree using single cell chromatin accessibility data and no clustering of cells into discrete cell types.
