BioLizard
@BioLizard_nv
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A bioinformatics and AI company providing innovative solutions for all your scientific data needs.
Joined July 2019
The #interestingread for today highlights a powerful R package for interpreting gene enrichment results using Gene Ontology (GO) with greater clarity. ๐ก ๐๐๐๐ ๐ฉ๐๐ ๐๐ช๐ก๐ก ๐๐ง๐ฉ๐๐๐ก๐:
nature.com
Scientific Reports - Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance
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Todayโs #interestingread takes us into the world of high-resolution spatial transcriptomics with a side-by-side comparison of ๐๐๐จ๐๐ช๐ข-๐๐ฟ vs ๐๐๐ฃ๐๐ช๐ข-5๐ on the same tissue slide. ๐ ๐๐๐๐ ๐ฉ๐๐ ๐๐ช๐ก๐ก ๐๐ง๐ฉ๐๐๐ก๐:
jeccr.biomedcentral.com
Recent advancements in spatial transcriptomics have been largely triggered by two high-resolution technologies: Visium-HD and Xenium in-situ. While sequencing-based Visium HD features a refined bin...
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Todayโs #interestingread dives into how researchers are tackling one of the biggest obstacles in functional genomics: figuring out exactly what disease-associated variants do inside real human cells. ๐ ๐๐๐๐ ๐ฉ๐๐ ๐๐ช๐ก๐ก ๐๐ง๐ฉ๐๐๐ก๐:
nature.com
Nature - A plate-based assay called CRAFTseq has been developed that uses โmulti-omicโ single-cell RNA sequencing and direct genotyping of CRISPR edits to test the functional effects of...
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Today's #interestingread introduces ๐ฅ๐ถ๐ฏ๐ผ๐ก๐ก, a deep convolutional neural network designed to predict translation efficiency of mRNAs across human and mouse. ๐ก ๐๐๐๐ ๐ฉ๐๐ ๐๐ช๐ก๐ก ๐ฅ๐๐ฅ๐๐ง ๐๐๐ง๐:
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The #interestingread for today takes us into the frontier of genome completeness, with researchers uncovereing thousands of complex structural variants and closed long-standing gaps in regions like centromeres and immune genes. ๐ก ๐๐๐๐ ๐ข๐ค๐ง๐:
nature.com
Nature - Using sequencing and haplotype-resolved assembly of 65 diverse human genomes, complex regions including the major histocompatibility complex and centromeres are analysed.
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Our #interestingread of the day showcases the ๐๐ผ๐๐ ๐
๐๐๐บ๐ฎ๐ป ๐ช๐ต๐ผ๐น๐ฒ ๐ง๐ฟ๐ฎ๐ป๐๐ฐ๐ฟ๐ถ๐ฝ๐๐ผ๐บ๐ฒ ๐๐ผ๐น๐ผ๐ป ๐๐ฎ๐๐ฎ๐๐ฒ๐. ๐ก ๐๐๐๐ ๐ข๐ค๐ง๐:
nanostring.com
With CosMxยฎ Spatial Molecular Imager (SMI) we characterized human colon FFPE tissue with the CosMx Human Whole Transcriptome Panel.ย With over 18,000
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Today's #interestingread examines the performance of AI in predicting the effects of gene perturbation using single-cell data. ๐ก ๐๐๐๐ ๐ฉ๐๐ ๐๐ช๐ก๐ก ๐จ๐ฉ๐ช๐๐ฎ:
nature.com
Nature Methods - The analysis presented in this Brief Communication shows that, despite their complexity, current deep learning models do not outperform linear baselines in predicting gene...
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๐ฆ ๐๐ฒ๐ฎ๐ฑ ๐๐ต๐ฒ ๐ช๐ฎ๐ ๐ถ๐ป ๐๐ฎ๐๐ฎ-๐๐ฟ๐ถ๐๐ฒ๐ป ๐๐ถ๐๐ฐ๐ผ๐๐ฒ๐ฟ๐! Weโre on the hunt for a ๐ง๐ฒ๐ฎ๐บ ๐๐ฒ๐ฎ๐ฑ ๐ถ๐ป ๐๐ฎ๐๐ฎ ๐ฆ๐ฐ๐ถ๐ฒ๐ป๐ฐ๐ฒ to help shape the future of innovation at BioLizard. If youโre ready to lead, letโs talk ๐ https://t.co/lChs3t9Ec4
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Today's #interestingread spotlights ๐๐ฒ๐ป๐ฒ๐๐ด๐ฒ๐ป๐, an AI-powered language agent designed for gene-set analysis. ๐ก ๐๐๐๐ ๐ฉ๐๐ ๐๐ช๐ก๐ก ๐จ๐ฉ๐ช๐๐ฎ:
nature.com
Nature Methods - GeneAgent is a language agent using large language models and self-verification to improve gene-set function annotation.
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๐ฆ ๐ช๐ฒโ๐ฟ๐ฒ ๐ต๐ถ๐ฟ๐ถ๐ป๐ด! Weโre looking for a Marketing coordinator to help us amplify our impact at the intersection of science and strategy. Join the best minds in data-driven life sciences! ๐ Apply now! https://t.co/ql3S0igOyA
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In our #interesting read today, researchers, using in situ cryoโelectron tomography across four mammalian cell lines, found hemifusomes at the cell periphery, making up ~10% of vesicular organelles. ๐ฌ๐๐๐๐ ๐ฉ๐๐ ๐๐ช๐ก๐ก ๐๐ง๐ฉ๐๐๐ก๐:
nature.com
Nature Communications - Cryo-ET reveals hemifused vesicles containing a hemifusion diaphragm and an associated proteolipid nanodroplet. These hemifusomes drive intraluminal vesicle biogenesis and...
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This #interestingread presents a benchmark for 40 single-cell multi-modal integration algorithms involving modalities of DNA, RNA, protein and spatial omics for paired, unpaired and mosaic datasets. ๐ก ๐๐๐๐ ๐ฉ๐๐ ๐๐ช๐ก๐ก ๐๐ง๐ฉ๐๐๐ก๐ ๐๐๐ง๐:
nature.com
Nature Methods - This Registered Report presents a comprehensive benchmarking analysis of single-cell multi-modal data-integration methods.
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Today's #interestingread takes a look at ๐๐๐ถ๐ฑ๐ฒ๐ป๐ฐ๐ฒ ๐๐ด๐ด๐ฟ๐ฒ๐ด๐ฎ๐๐ผ๐ฟ, a generative AI tool for ๐ฟ๐ฎ๐ฟ๐ฒ ๐ฑ๐ถ๐๐ฒ๐ฎ๐๐ฒ ๐ฑ๐ถ๐ฎ๐ด๐ป๐ผ๐๐ถ๐. ๐ก ๐๐๐๐ ๐ฉ๐๐ ๐๐ช๐ก๐ก ๐ฅ๐ง๐๐ฅ๐ง๐๐ฃ๐ฉ ๐๐๐ง๐: https://t.co/YJQr1Up4WX
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Our #interestingread for today is all about advancing biological language modeling! ๐๐๐๐ ๐ฉ๐๐ ๐๐ช๐ก๐ก ๐๐ง๐ฉ๐๐๐ก๐ ๐ฉ๐ค ๐๐ญ๐ฅ๐ก๐ค๐ง๐ ๐ฉ๐๐ ๐๐ช๐ฉ๐ช๐ง๐ ๐ค๐ ๐๐๐ค๐ก๐ค๐๐๐๐๐ก ๐ก๐๐ฃ๐๐ช๐๐๐ ๐ข๐ค๐๐๐ก๐๐ฃ๐:
nature.com
Nature Machine Intelligence - He and colleagues develop LucaOne, a biological foundation model pre-trained on nucleic acid and protein sequences from 169,861 species. It shows an emerging...
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๐ Today's #interestingread dives into the world of single-cell RNA sequencing! This study evaluates the practical aspects and performance of various commercial single-cell RNA sequencing technologies. ๐๐๐๐ ๐ฉ๐๐ ๐๐ช๐ก๐ก ๐๐ง๐ฉ๐๐๐ก๐:
biorxiv.org
The rapid development of updated and new commercially available single-cell transcriptomics platforms provides users with a range of experimental options. Cost, sensitivity, throughput, flexibility,...
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Curious how AI is unlocking the secrets of our genome? ๐งฌ Todayโs #interestingread looks at ๐๐น๐ฝ๐ต๐ฎ๐๐ฒ๐ป๐ผ๐บ๐ฒ. ๐๐๐๐ ๐ฉ๐๐ ๐๐ช๐ก๐ก ๐๐ง๐ฉ๐๐๐ก๐:
deepmind.google
Introducing a new, unifying DNA sequence model that advances regulatory variant-effect prediction and promises to shed new light on genome function โ now available via API.
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Today's #interestingread introduces ๐๐ฐ๐ฃ๐ฅ๐๐ก๐ง, a model that leverages transformer-based architecture to infer gene regulatory networks from single-cell data. ๐ ๐๐๐๐ ๐ฉ๐๐ ๐๐ช๐ก๐ก ๐๐ง๐ฉ๐๐๐ก๐:
nature.com
Nature Communications - Authors present a state-of-the-art cell foundation model trained on 50โmillion cells. They show that the model generates a meaningful gene network and has zero-shot...
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Mondays are for #interestingreads! ๐๐ผ๐ฑ๐ผ๐ป๐ง๐ฟ๐ฎ๐ป๐๐ณ๐ผ๐ฟ๐บ๐ฒ๐ฟ, a context-aware neural network, addresses the complexities of codon usage bias and provides a versatile tool for synthetic biology. ๐ ๐๐๐๐ ๐ฉ๐๐ ๐๐ช๐ก๐ก ๐จ๐ฉ๐ช๐๐ฎ:
nature.com
Nature Communications - Authors report a codon language representation and a model, CodonTransformer, open access and with a user-friendly interface. CodonTransformer generates species-specific DNA...
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Todayโs #interestingread dives into how ๐ฒ๐ป๐๐ฒ๐บ๐ฏ๐น๐ฒ ๐บ๐ฎ๐ฐ๐ต๐ถ๐ป๐ฒ ๐น๐ฒ๐ฎ๐ฟ๐ป๐ถ๐ป๐ด ๐บ๐ผ๐ฑ๐ฒ๐น๐ can supercharge the analysis of complex biological systems by integrating multi-omics data. ๐ฑ๐งฌ ๐ก ๐๐๐๐ ๐ฉ๐๐ ๐๐ช๐ก๐ก ๐๐ง๐ฉ๐๐๐ก๐: https://t.co/VSCcAe83Ha
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Time for another #interestingread! This study introduces the ๐ ๐๐๐ฟ๐ข๐ก๐ฆ functional connectomics dataset that intricately maps the functional and structural connectivity of the mouse visual cortex. ๐ก ๐๐๐๐ ๐ฉ๐๐ ๐๐ช๐ก๐ก ๐๐ง๐ฉ๐๐๐ก๐:
nature.com
Nature - Dense calcium imaging combined with co-registered high-resolution electron microscopy reconstruction of the brain of the same mouse provide a functional connectomics map of tens of...
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