Alignment-Based DNA Language Models: The GPN-MSA Approach Enables Accurate Genome-wide Variant...
In the dynamic landscape of biology, researchers around the world aim to unlock the secrets held in the genetic code. With the introduction of...
New Deep Learning Framework ‘DEMINING’ Distinguishes DNA and RNA Mutations Directly...
Researchers have introduced a groundbreaking computational framework called DEMINING, designed to directly identify expressed DNA and RNA mutations in RNA deep sequencing data. This...
Visualizing Complex Biological Networks with ‘ggkegg’
The Kyoto Encyclopedia of Genes and Genomes (KEGG) database serves as an invaluable resource for systems biology research across diverse fields. It provides comprehensive...
Meet BTR: A Deep Learning Powered Bioinformatics Tool Recommendation System Revolutionizing...
With the rise in popularity of the field of bioinformatics in recent years, researchers have created multiple computational tools that help streamline and optimize...
Meet ggCaller: A Fast and Accurate Solution for Pangenome Annotation and...
Pangenomic annotation is critical for understanding the bacterial genomic variety and depends on recognizing core and accessory genes through gene prediction and clustering. These...
Deep Learning Unveils Antimalarial Drug’s Potential to Combat Osteoporosis
Scientists at Peking University School and Hospital for Stomatology, China, have used deep learning to identify dihydroartemisinin (DHA), an antimalarial drug, as a potential...
Mosaic Variant Calling: Benchmarking Approaches and Unveiling Best Practices
Scientists from Yonsei University College of Medicine, Republic of Korea, have developed a new benchmark for evaluating mosaic variant calling methods, which are used...
Machine Learning Modeling Helps Uncover Links Between Gut Microbiome and Heart...
Heart failure is widely recognized as a leading cause of mortality worldwide. Though there have been great strides made in medical technology over the...
A Comprehensive Look at Lactic Acid Bacteria: Pangenome Analysis Reveals New...
Researchers from the University of California, San Diego, and the Technical University of Denmark have conducted a comprehensive pangenomic analysis of the Lactobacillaceae family, a crucial...
Decoding Cellular Interactions with DeepCCI: A Deep Learning Approach to Analyze...
Cell-cell interactions (CCIs) are pivotal in various biological functions, including cellular differentiation, tissue maintenance, and immune reactions. As single-cell RNA sequencing (scRNA-seq) techniques advance,...
MIT Scientists Discover Thousands of New Programmable DNA-Cutting Enzymes Opening the...
Through the advent of CRISPR-Cas12, scientists have managed to unlock a new world of gene editing and reprogramming, with important applications for diagnostics, therapeutics,...
Fast-tracking CNS Tumor Diagnosis: New AI System ‘Sturgeon’ Accurately Diagnoses Brain...
Tumors that affect the central nervous system are among the most fatal kinds of cancer, especially in pediatric cases. Surgical removal of the tumor...
Pharmacophore-Guided Deep Learning: A New Paradigm for Generating Bioactive Molecules in...
One of the biggest challenges to drug discovery is designing molecules that express desired biological activity, also referred to as bioactivity. This is of...
Meta-analysis of 13000 Salmonella Typhi Genomes Unravels Global Diversity and Drug...
Typhoid, once a disease that ravaged countries, had been considered tamed by the introduction of new antibiotics in the mid-20th century. Awareness of the...
Variational Auto-encoders for Ligand Generation: A New Approach to Drug Discovery
The search for molecules that bind effectively to specific proteins is crucial from a drug discovery point of view. The existing methods for creating...
A New Deep Neural Networks-Based Method Predicts Protein Abundance Based on...
With the potential to have significant impacts on various fields, like therapeutics and agritech, protein engineering has recently been a subject that has incited...
Researchers Develop Neural Network for Genomics that can Explain its Prediction...
A breakthrough by a group of researchers at New York University resulted in the development of an interpretable neural network that can explain the...
New Findings Challenge Traditional Rules of Genetics: UAA and UAG Codons...
Scientists from the Earlham Institute and the University of Oxford have unexpectedly altered our understanding of the rules of genetics while testing a new...
The Rise of mRNA Vaccines: A Game-Changer for Public Health?
The emergence of mRNA vaccine technology represents a monumental leap forward in disease prevention. A review article published in Nature Reviews Drug Discovery by...
A New Active Learning Model Makes Cellular Reprogramming and Genetic Intervention...
Millennia of evolution has allowed life to flourish in a million different ways, each suited to the niches it fills. The advent of CRISPR...
Massive Structural Clustering of the AlphaFold Database using Foldseek Cluster Reveals New...
Hundreds of millions of protein structures can be clustered using the new AI algorithm "Foldseek Cluster," which was developed by a team of researchers...
The Rise of Scientific Language Models: Revolutionizing Molecular Discovery
In a groundbreaking collaboration spanning IBM Research in Switzerland and the USA, scientists have illuminated the pivotal role of language models (LMs) in molecular...
Advancing Continuous Blood Pressure Monitoring: Accurate Measurements with Multichannel Sensing Signals...
Hypertension has long been known to be a causative factor for a multitude of medical ailments. Hypertension has further been noticed to have significantly...
GeneCompass: A New Foundation Model that Unlocks the Secrets of Gene...
A team of researchers from the University of Chinese Academy of Sciences, China, and collaborators developed GeneCompass, one of the first foundation models of...
IM3PACT: A New Computational Model to Improve the Design of Glucose-Responsive...
IM3PACT is a unique approach to improve MK-2640, glucose-responsive insulin (GRI). However, it did not function as well on humans as it did on...
The 2023 Nobel Prize in Physiology or Medicine: Pioneers Katalin Karikó...
The 2023 Nobel Prize in Physiology or Medicine has been jointly awarded to Katalin Karikó and Drew Weissman for their outstanding discoveries concerning nucleoside...
BigRNA: A Foundation Model for RNA Biology that Revolutionizes Personalized RNA...
A team of researchers at Deep Genomics Inc. developed BigRNA, a foundation model for understanding the biological functions and mechanisms of RNA molecules. Two...
Integrative Multi-Omics Analysis Reveals Molecular Responses to PARP Inhibition: A Focus...
Understanding diverse molecular mechanisms is necessary for the research of complex diseases. Using COSMOS, the integration of Thermal Proteome Profiling (TPP) with phosphoproteomics and...
Machine Learning Model ‘HASTEN’ Enables Giga-Scale Virtual Screening of Enumerated Chemical...
A team of researchers utilized HASTEN, a machine-learning (ML) model, to perform virtual screening on ultra-large chemical compound libraries. Several challenges are faced when...
Protein Engineering Tournament: A Competition Aiming to Revolutionize Computational Protein Design
Protein engineering is an emerging field in biological research – the improvement of existing proteins or the creation of new ones in order to...
Using EzMechanism to Unravel the Mysteries of Enzyme Catalysis
Enzyme mechanisms, intricate sequences of events within an enzyme's active site facilitating chemical reactions, are key to understanding enzyme function and evolution. Experimental approaches...
MitoSpace: A Novel Mitochondrial Phenotypic Atlas for Drug Discovery and Diagnostics
A collaborative effort between the Departments of Pharmacology, Chemistry, and Biochemistry at the University of California, San Diego, led to the development of MitoSpace,...
Streamlining Differential Expression Analysis on Bulk RNA-seq Data with PyDESeq2
Exploring bulk RNA-seq data has become a cornerstone for uncovering crucial insights into gene expression patterns and their relationship to phenotypes in biomedical research....
Achieving RNA’s AlphaFold Moment: How Close Are We?
AlphaFold's breakthrough in solving the protein structure prediction problem has ignited enthusiasm to apply similar methods to predict the 3D structures of RNAs. However,...
Accurate Annotation of Eukaryotic Genomes Made Easy: The BRAKER3 Advantage
Researchers from the University of Greifswald, Germany, introduced a new version of the BRAKER software BRAKER3, notably improving the annotation of eukaryotic genomes. Its...
DrugChat: A ChatGPT-like System for Drug Compound Discovery
A team of researchers at the University of California, San Diego, came together to develop a chatbot specifically catered to drug discovery called DrugChat....
Google’s DeepMind Unveils AlphaMissense: A Breakthrough AI Tool for Decoding Genetic...
Google's DeepMind scientists have made a monumental stride with the inception of AlphaMissense, an AI tool that can pinpoint genes responsible for diseases. This...
Machine Learning and Phylogenetic Analysis Join Forces to Predict Antibiotic Resistance...
Tuberculosis has been known to be a significant threat for many years now. Despite the development of a number of preventative strategies and medications,...
Meet DRfold: A Novel Method to Predict RNA Tertiary Structures with...
RNAs are essential components of physiological activities, however, accurately modeling their structures has long posed a challenge due to their complex structures. The National...
Meet AutoBA: A New Tool Making Bioinformatics Analysis Easy
Recent advancements in technology have now made it feasible for scientific researchers to be able to collect large amounts of biological data using a...
CodonBERT: A New Large Language Model Could Help Design Optimized mRNA...
A team of researchers at Digital R&D, Sanofi, USA, developed CodonBERT, a transformer-based large language model that is used for performing tasks related to...
Large Language Models Meet Single Cell Transcriptomics: Unlocking Biological Insights with...
Large language models, such as GPT (Generative Pre-trained Transformer), have showcased remarkable proficiency in various natural language processing tasks. Their ability to understand and...
Machine Learning Predicts Mood in Chronic Stroke Patients and Identifies the...
Stanford's scientists used Machine Learning to elucidate the relationship between stroke and depression by identifying a biomarker in stroke survivors. The findings may provide...
Virtual Drug Screening with Less Data: Boosting Predictions with Transfer Learning...
A team of researchers at the Eric and Wendy Schmidt Centre at the Broad Institute of MIT and Harvard developed a model that uses...
3Dmapper: A New Tool for Mapping Genetic Variants to Protein Structures...
Centuries after the first proteins were identified and characterized, their complexity proves a challenge for scientists all over the world. Their creation, evolution, and...
PeptideBERT: A Transformer-based Language Model for Predicting Peptide Properties using Amino...
Scientists at Carnegie Mellon University, USA, introduced PeptideBERT, a language model that is capable of predicting the properties of proteins and peptides solely based...
Deep Learning Powers New Methods for Protein Remote Homology Detection and...
Comprehending sequence–structure–function relationships is challenging for proteins with low similarity to existing proteins. New and improved alignment approaches are required for such proteins to...
Meet BARNACLE: A New Tool to Predict RNA Contacts using Data...
In the pursuit of understanding how RNA structure and function are related, predicting RNA structures becomes a tool alongside experimental approaches. However, the limited...
Meet HighFold: An AlphaFold-based Algorithm to Predict Cyclic Peptide Monomers and...
Cyclic peptides represent an emerging class of drugs that combine the advantageous attributes of small molecules with those of antibodies or protein-based therapeutics. Scientists...
Meet XVir: A Promising Transformer-based Approach to Spot Viral Reads in...
A team of researchers at The University of Texas at Austin developed a novel algorithm, XVir, that combines deep learning methods and transformers to...
Must Read
Solving a Long-Standing Genomics Bottleneck: KAIST Proposes AI-Powered Strategy for Gene Function Prediction
KAIST and UCSD researchers proposed AI-driven strategies for microbial gene function discovery, addressing the long-standing bottleneck where many microbial genes remain uncharacterized despite advances...
AI-Powered Metagenomics: How MetagenBERT Predicts Disease From Raw DNA Sequences
Researchers from Sorbonne University and Dauphine University, France, introduced MetagenBERT, a Transformer-based framework for disease prediction directly from raw metagenomic DNA without relying on...
ToposBio Unveils Topos-1: An All-Atom Foundation Model for Intrinsically Disordered Proteins
Intrinsically disordered proteins (IDPs) are proteins that are central to neurodegenerative diseases and aggressive cancers like prostate cancer, have been considered ‘undruggable’ as structures...
CleaveNet Enables Scalable and Targeted Protease Substrate Design for Diagnostics and Therapeutics
Scientists from MIT and Microsoft Research present CleaveNet, an AI-based pipeline that merges predictive and generative modeling for end-to-end peptide (short protein) design. By...
Advancing Peptide Therapeutics with PeptiVerse’s Unified Prediction Framework
Researchers at the University of Pennsylvania developed PeptiVerse, a single platform that predicts drug-related properties of therapeutic peptides using either amino acid sequences or...