@BioDecoded

A daily digest of 3 articles about biomedical research and tech industry, with an emphasis on bringing data science and AI to life science and medicine.

 Mountain View, CA
biodecoded.com/
Joined May 2018
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6.7KMedia
Improving microbial phylogeny with citizen science within a mass-market video game nature.com/articles/s41587-0… #CitizenScience
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Topological benchmarking of algorithms to infer Gene Regulatory Networks from Single-Cell RNA-seq Data academic.oup.com/bioinformat… #Bioinformatics
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Prediction of tumor origin in cancers of unknown primary origin with cytology-based deep learning nature.com/articles/s41591-0… #Bioinformatics
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scGHOST: identifying single-cell 3D genome subcompartments nature.com/articles/s41592-0… #Bioinformatics
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BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies academic.oup.com/nar/article… #Bioinformatics
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PLMSearch: Protein language model powers accurate and fast sequence search for remote homology nature.com/articles/s41467-0… #Bioinformatics
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Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data nature.com/articles/s41587-0… #Bioinformatics
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Comprehensive transcriptome analysis reveals altered mRNA splicing and post-transcriptional changes in the aged mouse brain academic.oup.com/nar/article… #Bioinformatics
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Accurately clustering biological sequences in linear time by relatedness sorting nature.com/articles/s41467-0… #Bioinformatics
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Identification of clinical disease trajectories in neurodegenerative disorders with natural language processing nature.com/articles/s41591-0… #NLP
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AI-guided pipeline for protein–protein interaction drug discovery identifies a SARS-CoV-2 inhibitor embopress.org/doi/full/10.10… #AI
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Leveraging large language models for predictive chemistry nature.com/articles/s42256-0… #LLM
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Unsupervised ensemble-based phenotyping enhances discoverability of genes related to left-ventricular morphology nature.com/articles/s42256-0… #DeepLearning
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A comparison of methods for detecting DNA methylation from long-read sequencing of human genomes genomebiology.biomedcentral.… #Bioinformatics
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AlphaPept: a modern and open framework for MS-based proteomics nature.com/articles/s41467-0… #Bioinformatics
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Spike sorting with Kilosort4 nature.com/articles/s41592-0… #Bioinformatics
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Genomic language model predicts protein co-regulation and function nature.com/articles/s41467-0… #Bioinformatics
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Deciphering cell types by integrating scATAC-seq data with genome sequences nature.com/articles/s43588-0… #Bioinformatics

Deciphering cell types by integrating scATAC-seq data with genome sequences

Nature Computational Science - This study introduces SANGO, a method for accurate single-cell annotation leveraging genomic sequences around accessibility peaks within single-cell ATAC sequencing...

nature.com
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SimuCell3D: three-dimensional simulation of tissue mechanics with cell polarization nature.com/articles/s43588-0… #Bioinformatics
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PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization genomebiology.biomedcentral.… #Bioinformatics
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