Tag

Bioinformatics

All articles tagged with #bioinformatics

science28 days ago•13 min saved

AlphaFold Opens a Free Global Library of Protein Shapes

AI-powered AlphaFold2 transformed protein folding by predicting 3D structures from sequence in minutes, leading to a public database with roughly 214 million predicted protein structures available for free. Most entries are highly accurate or confidently useful, but about a fifth have low confidence and users should filter by pLDDT. The data is CC-BY-4.0 licensed and widely used, enabling rapid research while raising questions about openness for future commercial tools and the handling of multiple conformations and disordered regions. Ongoing updates include isoforms and alignments; methods like AF-Cluster have had mixed results in extracting alternative conformations.

via Space Daily|

#alphafold #bioinformatics #deepmind

biotechnology2 months ago•6 min saved

Open-source AI atlas maps 1.1B protein structures, widening the protein universe

An open-access atlas called the ESM Atlas, generated with the ESMFold2 AI model, predicts about 1.1 billion protein structures and 6.8 billion sequences, outperforming AlphaFold in scale and openness and enabling new biology discoveries through a freely available resource.

via Nature|

#ai-in-biology #alphafold #bioinformatics

technology5 months ago•6 min saved

AlphaFold’s database adds protein pairs to map how molecules work together

AlphaFold’s database now includes 1.7 million predicted homodimer protein complexes, expanding its 200 million monomer structures to show how two copies of the same protein interact. The complex predictions were produced by a international consortium and are freely accessible via EMBL-EBI, broadening the resource’s biological and medical relevance across 20 studied species.

via Nature|

#alphafold #bioinformatics #homodimer

science5 months ago•76 min saved

Evo 2: An Open-Source AI for Genome-Scale Prediction and Design Across Life

Evo 2 is a large, open biological foundation model trained on 9 trillion base pairs across all life, with a 1‑million‑token context, available in 7B and 40B sizes. It predicts mutational effects on DNA, RNA and proteins without task-specific fine-tuning, can generate genome-scale sequences and chromatin-accessibility designs, and supports exon–intron annotation and variant-effect prediction across diverse species. The model and data (OpenGenome2) are fully open-source, with training/inference code and tools (Evo Designer, Evo Mech Interp), plus safety safeguards such as virus-data exclusions to mitigate misuse.

via Nature|

#artificial-intelligence #bioinformatics #genome-design

health8 months ago•3 min saved

New Tool Unveils Hidden Communication Networks in Cancer

Researchers at the University of Navarra have developed RNACOREX, an open-source software that maps gene regulation networks in cancer, helping to understand tumor behavior and predict patient survival with clear, interpretable results, advancing personalized cancer treatment.

via ScienceDaily|

#bioinformatics #cancer #cancer-research

science9 months ago•74 min saved

Chat-Based Exploration of Single-Cell Data Through Multimodal Learning

The article introduces CellWhisperer, a multimodal AI framework that enables chat-based exploration and analysis of single-cell RNA-seq data using natural language, integrating transcriptome profiles with biological text understanding to facilitate intuitive data interrogation and hypothesis generation.

via Nature|

#bioinformatics #cell-data-exploration #multimodal-learning

science10 months ago•97 min saved

Advanced DNA Search Engine Enhances Genetic Data Analysis

The article discusses MetaGraph, a scalable framework for indexing petabase-scale biological sequence repositories, enabling efficient and accurate full-text search across vast datasets like the SRA and ENA, with potential to revolutionize genomic research and data accessibility.

via Nature|

#bioinformatics #dna-sequencing #metagraph

technology10 months ago•8 min saved

Trimodal Protein Model Enhances Search Capabilities

A new trimodal protein language model enhances the accuracy and efficiency of protein searches, leveraging advanced deep learning techniques to improve understanding of protein structures and functions.

via Nature|

#bioinformatics #deep-learning #protein-language-model

technology11 months ago•42 min saved

LexicMap Enables Rapid Alignment of Prokaryotic Genomes

LexicMap is a high-performance tool designed for efficient sequence alignment against millions of prokaryotic genomes, using a novel seeding approach with variable-length prefix and suffix matching, enabling rapid and scalable analysis suitable for large genomic databases.

via Nature|

#bioinformatics #lexicmap #prokaryotic-genomes

science1 year ago•3 min saved

Marine Researcher Discovers New Lifeform in Black Goo Inside Ship

Marine researchers discovered a new species of archaea in a mysterious black goo found inside a ship's rudder, revealing an unexpected habitat for extremophiles and potential applications in biofuel production, highlighting the importance of exploratory science.

via Yahoo|

#archaea #bioinformatics #marine-biology

finance1 year ago•0 min saved

Dimension Secures $500M for Biotech and AI Convergence Fund

Dimension, a venture capital firm, has successfully raised a $500 million second fund to invest in the intersection of biotechnology and machine learning, an area they describe as 'still contrary.' The firm, led by managing partners in New York and the Bay Area, aims to capitalize on the growing synergy between biological sciences and AI technologies.

via Endpoints News|

#bioinformatics #dimension #finance

science-and-technology1 year ago•3 min saved

Evo: The AI Revolutionizing Genetic Prediction and Design

Scientists have developed Evo, a machine learning model that predicts the effects of genetic mutations and generates new DNA sequences with high accuracy. Unlike traditional large language models, Evo is trained on microbial genomes, using base pairs as "words" to analyze genetic patterns. While Evo shows promise in understanding DNA and RNA functions, it currently lacks the ability to predict human genetic mutations. The researchers emphasize the importance of ethical guidelines to prevent misuse as the technology advances.

via Livescience.com|

#ai #bioinformatics #dna

science2 years ago•5 min saved

"New Atlas Reveals Gene Functions in Early Embryo Development"

Researchers at UC San Diego have developed a "genetic atlas" using the model organism C. elegans to profile the function of nearly 500 genes during embryonic development. By blocking each gene one at a time and using time-lapse 4D imaging and computer vision, they tracked how these genes influence tissue formation and cell identity. This study, published in Cell, provides new insights into gene functions and their roles in development, with implications for understanding human developmental disorders. The data is now available through an online resource called PhenoBank.

via Phys.org|

#bioinformatics #c-elegans #embryonic-development

science-and-technology2 years ago•3 min saved

"Next-Generation CRISPR: Advancements in Precision Gene Editing"

The recent development of CRISPR-COPIES by the Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) represents a significant advancement in genetic engineering, streamlining the identification of optimal genetic integration sites and accelerating the pace of scientific discovery and innovation. This high-tech upgrade to the CRISPR/Cas system offers a powerful and accessible tool for precision genome editing, with applications spanning agriculture, biofuel production, and gene therapy, promising to drive forward the boundaries of what’s possible in genetic engineering.

via Earth.com|

#bioinformatics #crispr #crispr-copies

science-and-technology2 years ago•3 min saved

"Revolutionizing R&D: AI Unlocks Unknown Protein Functions"

Researchers at KAUST have developed an innovative AI tool, DeepGO-SE, that excels in predicting the functions of unknown proteins, outperforming existing methods and ranking in the top 20 of over 1,600 algorithms in an international competition. Leveraging large language models and logical entailment, this tool can deduce molecular functions even for proteins without existing database matches, offering a groundbreaking approach to understanding cellular mechanisms. The team aims to apply this tool to explore proteins in extreme environments, opening new doors for biotechnological advancements.

via Neuroscience News|

#ai #bioinformatics #drug-discovery