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BioLizard

@BioLizard_nv

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A bioinformatics and AI company providing innovative solutions for all your scientific data needs.

Joined July 2019
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@BioLizard_nv
BioLizard
7 days
The #interestingread for today highlights a powerful R package for interpreting gene enrichment results using Gene Ontology (GO) with greater clarity. ๐Ÿ’ก ๐™๐™š๐™–๐™™ ๐™ฉ๐™๐™š ๐™›๐™ช๐™ก๐™ก ๐™–๐™ง๐™ฉ๐™ž๐™˜๐™ก๐™š:
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nature.com
Scientific Reports - Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance
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@BioLizard_nv
BioLizard
14 days
Todayโ€™s #interestingread takes us into the world of high-resolution spatial transcriptomics with a side-by-side comparison of ๐™‘๐™ž๐™จ๐™ž๐™ช๐™ข-๐™ƒ๐˜ฟ vs ๐™“๐™š๐™ฃ๐™ž๐™ช๐™ข-5๐™† on the same tissue slide. ๐Ÿ“– ๐™๐™š๐™–๐™™ ๐™ฉ๐™๐™š ๐™›๐™ช๐™ก๐™ก ๐™–๐™ง๐™ฉ๐™ž๐™˜๐™ก๐™š:
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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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@BioLizard_nv
BioLizard
21 days
Todayโ€™s #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. ๐Ÿ“– ๐™๐™š๐™–๐™™ ๐™ฉ๐™๐™š ๐™›๐™ช๐™ก๐™ก ๐™–๐™ง๐™ฉ๐™ž๐™˜๐™ก๐™š:
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nature.com
Nature - A plate-based assay called CRAFTseq has been developed that uses โ€˜multi-omicโ€™ single-cell RNA sequencing and direct genotyping of CRISPR edits to test the functional effects of...
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@BioLizard_nv
BioLizard
1 month
Today's #interestingread introduces ๐—ฅ๐—ถ๐—ฏ๐—ผ๐—ก๐—ก, a deep convolutional neural network designed to predict translation efficiency of mRNAs across human and mouse. ๐Ÿ’ก ๐™๐™š๐™–๐™™ ๐™ฉ๐™๐™š ๐™›๐™ช๐™ก๐™ก ๐™ฅ๐™–๐™ฅ๐™š๐™ง ๐™๐™š๐™ง๐™š:
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@BioLizard_nv
BioLizard
2 months
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. ๐Ÿ’ก ๐™๐™š๐™–๐™™ ๐™ข๐™ค๐™ง๐™š:
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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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@BioLizard_nv
BioLizard
2 months
Our #interestingread of the day showcases the ๐—–๐—ผ๐˜€๐— ๐˜… ๐—›๐˜‚๐—บ๐—ฎ๐—ป ๐—ช๐—ต๐—ผ๐—น๐—ฒ ๐—ง๐—ฟ๐—ฎ๐—ป๐˜€๐—ฐ๐—ฟ๐—ถ๐—ฝ๐˜๐—ผ๐—บ๐—ฒ ๐—–๐—ผ๐—น๐—ผ๐—ป ๐——๐—ฎ๐˜๐—ฎ๐˜€๐—ฒ๐˜. ๐Ÿ’ก ๐™๐™š๐™–๐™™ ๐™ข๐™ค๐™ง๐™š:
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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@BioLizard_nv
BioLizard
2 months
Today's #interestingread examines the performance of AI in predicting the effects of gene perturbation using single-cell data. ๐Ÿ’ก ๐™๐™š๐™–๐™™ ๐™ฉ๐™๐™š ๐™›๐™ช๐™ก๐™ก ๐™จ๐™ฉ๐™ช๐™™๐™ฎ:
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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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@BioLizard_nv
BioLizard
2 months
๐ŸฆŽ ๐—Ÿ๐—ฒ๐—ฎ๐—ฑ ๐˜๐—ต๐—ฒ ๐—ช๐—ฎ๐˜† ๐—ถ๐—ป ๐——๐—ฎ๐˜๐—ฎ-๐——๐—ฟ๐—ถ๐˜ƒ๐—ฒ๐—ป ๐——๐—ถ๐˜€๐—ฐ๐—ผ๐˜ƒ๐—ฒ๐—ฟ๐˜†! Weโ€™re on the hunt for a ๐—ง๐—ฒ๐—ฎ๐—บ ๐—Ÿ๐—ฒ๐—ฎ๐—ฑ ๐—ถ๐—ป ๐——๐—ฎ๐˜๐—ฎ ๐—ฆ๐—ฐ๐—ถ๐—ฒ๐—ป๐—ฐ๐—ฒ to help shape the future of innovation at BioLizard. If youโ€™re ready to lead, letโ€™s talk ๐Ÿ‘‰ https://t.co/lChs3t9Ec4
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@BioLizard_nv
BioLizard
3 months
Today's #interestingread spotlights ๐—š๐—ฒ๐—ป๐—ฒ๐—”๐—ด๐—ฒ๐—ป๐˜, an AI-powered language agent designed for gene-set analysis. ๐Ÿ’ก ๐™๐™š๐™–๐™™ ๐™ฉ๐™๐™š ๐™›๐™ช๐™ก๐™ก ๐™จ๐™ฉ๐™ช๐™™๐™ฎ:
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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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@BioLizard_nv
BioLizard
3 months
๐ŸฆŽ ๐—ช๐—ฒโ€™๐—ฟ๐—ฒ ๐—ต๐—ถ๐—ฟ๐—ถ๐—ป๐—ด! Weโ€™re 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! ๐Ÿš€ Apply now! https://t.co/ql3S0igOyA
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@BioLizard_nv
BioLizard
3 months
In our #interesting read today, researchers, using in situ cryoโ€‘electron tomography across four mammalian cell lines, found hemifusomes at the cell periphery, making up ~10% of vesicular organelles. ๐Ÿ”ฌ๐™๐™š๐™–๐™™ ๐™ฉ๐™๐™š ๐™›๐™ช๐™ก๐™ก ๐™–๐™ง๐™ฉ๐™ž๐™˜๐™ก๐™š:
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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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@BioLizard_nv
BioLizard
3 months
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. ๐Ÿ’ก ๐™๐™š๐™–๐™™ ๐™ฉ๐™๐™š ๐™›๐™ช๐™ก๐™ก ๐™–๐™ง๐™ฉ๐™ž๐™˜๐™ก๐™š ๐™๐™š๐™ง๐™š:
nature.com
Nature Methods - This Registered Report presents a comprehensive benchmarking analysis of single-cell multi-modal data-integration methods.
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@BioLizard_nv
BioLizard
3 months
Today's #interestingread takes a look at ๐—˜๐˜ƒ๐—ถ๐—ฑ๐—ฒ๐—ป๐—ฐ๐—ฒ ๐—”๐—ด๐—ด๐—ฟ๐—ฒ๐—ด๐—ฎ๐˜๐—ผ๐—ฟ, a generative AI tool for ๐—ฟ๐—ฎ๐—ฟ๐—ฒ ๐—ฑ๐—ถ๐˜€๐—ฒ๐—ฎ๐˜€๐—ฒ ๐—ฑ๐—ถ๐—ฎ๐—ด๐—ป๐—ผ๐˜€๐—ถ๐˜€. ๐Ÿ’ก ๐™๐™š๐™–๐™™ ๐™ฉ๐™๐™š ๐™›๐™ช๐™ก๐™ก ๐™ฅ๐™ง๐™š๐™ฅ๐™ง๐™ž๐™ฃ๐™ฉ ๐™๐™š๐™ง๐™š: https://t.co/YJQr1Up4WX
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@BioLizard_nv
BioLizard
3 months
Our #interestingread for today is all about advancing biological language modeling! ๐™๐™š๐™–๐™™ ๐™ฉ๐™๐™š ๐™›๐™ช๐™ก๐™ก ๐™–๐™ง๐™ฉ๐™ž๐™˜๐™ก๐™š ๐™ฉ๐™ค ๐™š๐™ญ๐™ฅ๐™ก๐™ค๐™ง๐™š ๐™ฉ๐™๐™š ๐™›๐™ช๐™ฉ๐™ช๐™ง๐™š ๐™ค๐™› ๐™—๐™ž๐™ค๐™ก๐™ค๐™œ๐™ž๐™˜๐™–๐™ก ๐™ก๐™–๐™ฃ๐™œ๐™ช๐™–๐™œ๐™š ๐™ข๐™ค๐™™๐™š๐™ก๐™ž๐™ฃ๐™œ:
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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@BioLizard_nv
BioLizard
4 months
๐ŸŒŸ 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. ๐™๐™š๐™–๐™™ ๐™ฉ๐™๐™š ๐™›๐™ช๐™ก๐™ก ๐™–๐™ง๐™ฉ๐™ž๐™˜๐™ก๐™š:
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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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@BioLizard_nv
BioLizard
4 months
Curious how AI is unlocking the secrets of our genome? ๐Ÿงฌ Todayโ€™s #interestingread looks at ๐—”๐—น๐—ฝ๐—ต๐—ฎ๐—š๐—ฒ๐—ป๐—ผ๐—บ๐—ฒ. ๐™๐™š๐™–๐™™ ๐™ฉ๐™๐™š ๐™›๐™ช๐™ก๐™ก ๐™–๐™ง๐™ฉ๐™ž๐™˜๐™ก๐™š:
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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@BioLizard_nv
BioLizard
5 months
Today's #interestingread introduces ๐˜€๐—ฐ๐—ฃ๐—ฅ๐—œ๐—ก๐—ง, a model that leverages transformer-based architecture to infer gene regulatory networks from single-cell data. ๐Ÿ”— ๐™๐™š๐™–๐™™ ๐™ฉ๐™๐™š ๐™›๐™ช๐™ก๐™ก ๐™–๐™ง๐™ฉ๐™ž๐™˜๐™ก๐™š:
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nature.com
Nature Communications - Authors present a state-of-the-art cell foundation model trained on 50โ€‰million cells. They show that the model generates a meaningful gene network and has zero-shot...
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@BioLizard_nv
BioLizard
5 months
Mondays are for #interestingreads! ๐—–๐—ผ๐—ฑ๐—ผ๐—ป๐—ง๐—ฟ๐—ฎ๐—ป๐˜€๐—ณ๐—ผ๐—ฟ๐—บ๐—ฒ๐—ฟ, a context-aware neural network, addresses the complexities of codon usage bias and provides a versatile tool for synthetic biology. ๐Ÿ”— ๐™๐™š๐™–๐™™ ๐™ฉ๐™๐™š ๐™›๐™ช๐™ก๐™ก ๐™จ๐™ฉ๐™ช๐™™๐™ฎ:
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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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@BioLizard_nv
BioLizard
5 months
Todayโ€™s #interestingread dives into how ๐—ฒ๐—ป๐˜€๐—ฒ๐—บ๐—ฏ๐—น๐—ฒ ๐—บ๐—ฎ๐—ฐ๐—ต๐—ถ๐—ป๐—ฒ ๐—น๐—ฒ๐—ฎ๐—ฟ๐—ป๐—ถ๐—ป๐—ด ๐—บ๐—ผ๐—ฑ๐—ฒ๐—น๐˜€ can supercharge the analysis of complex biological systems by integrating multi-omics data. ๐ŸŒฑ๐Ÿงฌ ๐Ÿ’ก ๐™๐™š๐™–๐™™ ๐™ฉ๐™๐™š ๐™›๐™ช๐™ก๐™ก ๐™–๐™ง๐™ฉ๐™ž๐™˜๐™ก๐™š: https://t.co/VSCcAe83Ha
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@BioLizard_nv
BioLizard
5 months
Time for another #interestingread! This study introduces the ๐— ๐—œ๐—–๐—ฟ๐—ข๐—ก๐—ฆ functional connectomics dataset that intricately maps the functional and structural connectivity of the mouse visual cortex. ๐Ÿ’ก ๐™๐™š๐™–๐™™ ๐™ฉ๐™๐™š ๐™›๐™ช๐™ก๐™ก ๐™–๐™ง๐™ฉ๐™ž๐™˜๐™ก๐™š:
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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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