AnimalTFDB 4.0: a comprehensive animal transcription factor database updated with variation and expression annotations

Nucleic Acids Research, Journal Year: 2022, Volume and Issue: 51(D1), P. D39 - D45

Published: Oct. 5, 2022

Abstract Transcription factors (TFs) are proteins that interact with specific DNA sequences to regulate gene expression and play crucial roles in all kinds of biological processes. To keep up new data provide a more comprehensive resource for TF research, we updated the Animal Factor Database (AnimalTFDB) version 4.0 (http://bioinfo.life.hust.edu.cn/AnimalTFDB4/) up-to-date functions. We refined family rules prediction pipeline predict TFs genome-wide protein from Ensembl. As result, predicted 274 633 genes 150 726 transcription cofactor AnimalTFDB 183 animal genomes, which 86 species than 3.0. Besides double volume, also added following annotations functions database: (i) variations (including mutations) on various human cancers other diseases; (ii) post-translational modification sites phosphorylation, acetylation, methylation ubiquitination sites) 8 species; (iii) regulation autophagy; (iv) annotation 38 (v) exact batch search allow users flexibly. is useful studying regulation, contains classification cofactors.

Language: Английский

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Universal Cell Embeddings: A Foundation Model for Cell Biology

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 29, 2023

Developing a universal representation of cells which encompasses the tremendous molecular diversity cell types within human body and more generally, across species, would be transformative for biology. Recent work using single-cell transcriptomic approaches to create definitions in form atlases has provided necessary data such an endeavor. Here, we present Universal Cell Embedding (UCE) foundation model. UCE was trained on corpus atlas from other species completely self-supervised way without any annotations. offers unified biological latent space that can represent cell, regardless tissue or species. This embedding captures important variation despite presence experimental noise diverse datasets. An aspect UCE's universality is new organism mapped this with no additional labeling, model training fine-tuning. We applied Integrated Mega-scale Atlas, 36 million cells, than 1,000 uniquely named types, hundreds experiments, dozens tissues eight uncovered insights about organization space, leveraged it infer function newly discovered types. exhibits emergent behavior, uncovering biology never explicitly for, as identifying developmental lineages novel not included set. Overall, by enabling every state type, provides valuable tool analysis, annotation hypothesis generation scale single datasets continues grow.

Language: Английский

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Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

Nature Methods, Journal Year: 2024, Volume and Issue: 21(8), P. 1492 - 1500

Published: Feb. 16, 2024

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes conservation and diversification cell types. However, interspecies genomic differences limit the joint analysis cross-species homologous genes. Here we present SATURN, a deep learning method for universal embeddings that encodes genes' biological properties using protein language models. By coupling models with RNA expression, SATURN integrates profiled different species regardless their similarity. can detect functionally related genes coexpressed across species, redefining differential expression analysis. Applying three whole-organism atlases frog zebrafish embryogenesis datasets, show effectively transfer annotations even when they are evolutionarily remote. We also demonstrate be used find potentially divergent gene functions between glaucoma-associated in humans four other species.

Language: Английский

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One-step green synthesis of collagen nanoparticles using Ulva fasciata, network pharmacology and functional enrichment analysis in hepatocellular carcinoma treatment

International Journal of Biological Macromolecules, Journal Year: 2025, Volume and Issue: unknown, P. 139244 - 139244

Published: Jan. 1, 2025

Language: Английский

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DNA‐Coated Upconversion Nanoparticles for Sensitive Nucleic Acid FRET Biosensing

Advanced Functional Materials, Journal Year: 2022, Volume and Issue: 32(37)

Published: May 1, 2022

Abstract Despite the significant advancements of developing upconversion nanoparticles (UCNPs) for high performance biosensing and bioimaging, development DNA‐functionalized UCNPs with thin coatings, efficient surface passivation, fully functional DNAs hybridization sensing in biological media remains extremely challenging. Here, a straightforward concept labeling DNA to polysulfonate polymer layer on is presented. Both preserve their full functionality as demonstrated by Förster resonance energy transfer (FRET) assays Cy3‐conjugated complementary DNA. The important bioanalytical benefits UCNP‐DNA nanohybrids are implementation into rapid wash‐free microRNA FRET assays. Using simple fiber‐coupled USB‐spectrometer 980 nm diode laser excitation 96‐well microplate, ratiometric from UCNP‐to‐Cy3 can quantify miR20a 0.01–10 × 10 −9 m concentration range detection limit 30 −12 (4.5 fmol miR20a), which more than 20‐fold lower compared quantum dot‐based thin‐coating DNA‐UCNP have strong potential translating advanced DNA‐based biosensing, high‐throughput point‐of‐care clinical diagnostics.

Language: Английский

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Bioprinted 3D outer retina barrier uncovers RPE-dependent choroidal phenotype in advanced macular degeneration

Nature Methods, Journal Year: 2022, Volume and Issue: 20(1), P. 149 - 161

Published: Dec. 22, 2022

Language: Английский

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The precision medicine process for treating rare disease using the artificial intelligence tool mediKanren

Frontiers in Artificial Intelligence, Journal Year: 2022, Volume and Issue: 5

Published: Sept. 30, 2022

There are over 6,000 different rare diseases estimated to impact 300 million people worldwide. As genetic testing becomes more common practice in the clinical setting, number of disease diagnoses will continue increase, resulting need for novel treatment options. Identifying treatments these disorders is challenging due a limited understanding mechanisms, small cohort sizes, interindividual symptom variability, and little commercial incentive develop new treatments. A promising avenue drug repurposing, where FDA-approved drugs repositioned as However, linking mechanisms action can be extraordinarily difficult requires depth knowledge across multiple fields, which complicated by rapid pace biomedical discovery. To address challenges, The Hugh Kaul Precision Medicine Institute developed an artificial intelligence tool, mediKanren, that leverages mechanistic insight identify therapeutic Using graphs, mediKanren enables efficient way link all relevant literature databases. This tool has allowed scalable process been used help 500 families. Here, we provide description our process, advantages its on patients.

Language: Английский

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TWAS Atlas: a curated knowledgebase of transcriptome-wide association studies

Nucleic Acids Research, Journal Year: 2022, Volume and Issue: 51(D1), P. D1179 - D1187

Published: Sept. 14, 2022

Abstract Transcriptome-wide association studies (TWASs), as a practical and prevalent approach for detecting the associations between genetically regulated genes traits, are now leading to better understanding of complex mechanisms genetic variants in regulating various diseases traits. Despite ever-increasing TWAS outputs, there is still lack databases curating massive public information knowledge. To fill this gap, here we present Atlas (https://ngdc.cncb.ac.cn/twas/), an integrated knowledgebase findings manually curated from extensive literature. In current implementation, collects 401,266 high-quality human gene–trait 200 publications, covering 22,247 257 traits across 135 tissue types. particular, interactive knowledge graph collected constructed together with single nucleotide polymorphism (SNP)–gene build up comprehensive regulatory networks at multi-omics levels. addition, Atlas, user-friendly web interface, efficiently enables users browse, search download all information, relevant research metadata annotation interest. Taken together, great value promoting utility availability results explaining basis well providing new insights health disease research.

Language: Английский

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Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(28)

Published: July 3, 2023

Plasma cell-free DNA (cfDNA) is a noninvasive biomarker for cell death of all organs. Deciphering the tissue origin cfDNA can reveal abnormal because diseases, which has great clinical potential in disease detection and monitoring. Despite promise, sensitive accurate quantification tissue-derived remains challenging to existing methods due limited characterization methylation reliance on unsupervised methods. To fully exploit cfDNA, here we present one largest comprehensive high-resolution atlas based 521 noncancer samples spanning 29 major types human tissues. We systematically identified fragment-level tissue-specific patterns extensively validated them orthogonal datasets. Based rich atlas, develop first supervised deconvolution approach, deep-learning-powered model, cfSort , cfDNA. On benchmarking data, showed superior sensitivity accuracy compared further demonstrated utilities with two applications: aiding diagnosis monitoring treatment side effects. The fraction estimated from reflected outcomes patients. In summary, enhanced performance thus facilitating cfDNA-based longitudinal

Language: Английский

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Unveiling promising breast cancer biomarkers: an integrative approach combining bioinformatics analysis and experimental verification

BMC Cancer, Journal Year: 2024, Volume and Issue: 24(1)

Published: Jan. 31, 2024

Breast cancer remains a significant health challenge worldwide, necessitating the identification of reliable biomarkers for early detection, accurate prognosis, and targeted therapy.

Language: Английский

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