Bioinformatics and computational biology news: new methods, tools and findings from recent research, explained clearly.
A platform for separation-free detection of bacteria in arbitrary medium has been developed by the researchers from Korea Advanced Institute of Science and Technology (KAIST), using a synergistic integration of surface-enhanced Raman spectroscopy and deep learning. Bacterial identification can take hours, if not days, to complete, wasting valuable time for diagnosing diseases and choosing treatments….
New software built by Princeton University researchers may determine whether someone is infected with COVID-19 in minutes by combining questions about a person’s health with data from wristwatch sensors. The study led by Niraj Jha, a professor of electrical and computer engineering at Princeton University, resulted in this new diagnostic tool. His group is working…
The team of researchers led by the Technical University of Munich (TUM) was able to destroy the genetic code of SARS-CoV-2 by using particular enzymes, shortly after the virus had invaded the cell. The data might be utilized to design a novel COVID-19 treatment. The building instructions for proteins and other compounds are found in…
Yale scientists report in the journal Nature Biotechnology this week that a novel data analysis technique they created has uncovered the particular immune cell types linked to an elevated risk of mortality from COVID-19. A variety of technologies provide high-throughput biological data by measuring dozens to tens of thousands of features in millions of cells…
According to recent research published in Nature Communications, a new AI algorithm creates novel compounds based on desired properties. Researchers are searching for innovative chemicals in a variety of fields, including health, battery research, and materials science. They can typically forecast the necessary chemical and physical features in great precision during this process, down to…
Researchers looked at data from over 200,000 people and discovered unusual genetic variations linked to diseases including diabetes and heart failure. Last year, the UK Biobank containing a large-scale collection of genetic and health information from half a million UK participants released additional protein sequence data (exome data). After analyzing whole-exome sequencing data from around…
Stanford University researchers established the record in collaboration with NVIDIA, Oxford Nanopore Technologies, Google, Baylor College of Medicine, and the University of California, Santa Cruz. This week, Guinness World Records awarded a Stanford University-led research team the first record for quickest DNA sequencing technology — a benchmark established utilizing a workflow enhanced by AI and…
The researchers from Curtin University, Australia, and the University of Western Australia developed a system to carry out the complete process of directed evolution in silico. Thanks to revolutionary software that mimics evolution, the building blocks of life-saving treatments might be produced in days rather than years. According to the research published this week in…
Scientists from the University of North Carolina School of Medicine, led by Scott Magness, Ph.D., sequenced the genes expressed in single cells from human digestive tracts to discover new cell-type characteristics and learn more about essential cell functions like nutrient absorption and immune defense. You could feel uneasy in your tummy if you get nervous….
The researchers at the Mayo Clinic Cancer Center in Florida, in a recent study published in Nature Communications, validate the use of genetic sequencing to predict whether patients with gastric cancer would benefit from chemotherapy or immunotherapy. Gastric cancer is one of the significant reasons for cancer-related deaths worldwide. Most patients with gastric cancer receive…
A new research reveals how a protein removes harmful chemicals from bacterial cells. The structure of a protein that may pump hazardous chemicals out of bacterial cells has been identified by MIT researchers. Proteins like this one, discovered in E. coli, are thought to aid in developing antibiotic resistance in bacteria. Multidrug resistance (MDR) is…
Scientists from the Duke University with collaborators at the University of Connecticut are aiming to create novel enzyme inhibitors to combat Methicillin-resistant Staphylococcus aureus (MRSA). The researchers revealed how a single small mutation affects therapeutic efficacy in a study published in PLOS Computational Biology. Antimicrobial resistance is an important public health issue worldwide. New resistance…
Scientists from MIT probed into how proteins recognize and bind to one another, informing drug treatments for cancer. A single cell, despite its small size, has billions of molecules that buzz around and bond to one another, performing critical tasks. About 20,000 proteins are encoded in the human genome, the majority of which interact with…
Scientists at The University of Milan-Bicocca, Milan, Italy, have proposed INTEGRATE, a computational pipeline that incorporates metabolomics and transcriptomics data, by applying constraint-based stoichiometric metabolic models as a scaffold. The pipeline might aid in developing personalized treatments for people suffering from complicated disorders. From cancer to neurodegeneration and aging, many physio-pathological states and multifactorial disorders…
Neurons are surprisingly complicated, for something so small, not only because there are billions of them in the brain but also because their function is impacted by a variety of factors such as their structure and genetic composition. A research group led by Daifeng Wang, professor at the University of Wisconsin–Madison, is using machine learning…
The Researchers at The University of Chicago, Chicago, developed 24 binary classifiers of MTB drug resistance condition across eight anti-MTB drugs and three different Machine Learning algorithms: logistic regression, random forest, and 1D CNN with the use of a training dataset of 10,575 MTB isolates obtained from 16 countries, where an extended pan-genome reference was…
Researchers from Göttingen University have found a protein switch that controls enzymes in pathogens. An allosteric lysine–cysteine redox switch with a covalent NOS bridge modulates enzyme activity in response to redox changes. Proteins are the “workhorses” of all living cells and the chemical foundation of life. These little machines are required for performing various activities…
Scientists from the York University, Toronto, Canada, investigated a novel deep learning-based methodology to predict breast cancer response to neo-adjuvant chemotherapy (NAC) using the quantitative ultrasound (QUS) multiparametric imaging at pre-treatment. Breast cancer is the most general type of cancer in women and the leading cause of cancer-related death. Locally advanced breast cancer (LABC) is…
The researchers from Syntelly — a startup that originated at Skoltech — Lomonosov Moscow State University, and Sirius University present a Transformer-based artificial neural network that can turn images of organic structures into molecular templates. The model is capable of automatically detecting chemical formulae on research paper scans. The findings were published in Chemistry-Methods, that…
The researchers from MIT Cambridge, USA, and collaborators at the University of Pittsburgh School of Medicine, present DYNAMO – an analytical framework that infers absolute RNA velocity, reconstruct continuous vector fields that predict cell fates, uses differential geometry to obtain underlying regulations, and anticipates optimal reprogramming routes and perturbation results. The capability of a single…
Researchers from the Rockefeller University, United States revealed that FMRP, a protein that has been linked to fragile X syndrome, intellectual impairment, and some types of autism, has been found to play a critical role in various brain activities, assisting in the regulation of synaptic connections between neurons. When we memorize a password or learn…
Researchers at Yale University, in collaboration with Karolinska Institutet in Stockholm, Sweden, have created a technology that allows them to look at epigenetic mechanisms driving tissue formation concurrently at a spatial and genome-wide level, a breakthrough with several scientific and medical applications. While existing technology allows scientists to study epigenetic information in the bulk of…
The researchers at Michigan State University in the United States used extensive structural datasets along with a refined and annotated collection of antiviral phytochemicals to determine which naturally derived medicines have the best chance of provoking strong binding interactions with SARS-CoV-2 proteins and thus preventing or disrupting the viral infection process. Millions of people have…
Deep Docking (DD) is artificial intelligence (AI) driven method that provides very economical yet highly reliable access to ultra-large docking. It was developed by Scientists at the University of British Columbia, Vancouver, to address the global lack of computational docking power and to enable structure-based screening of chemical libraries having billions of molecules without using…
A new study reveals the lifespans and locations of the cells that produce HIV and delay the virus’s elimination. Scientists may be able to discover new strategies to lower the number of cells in the future, with the ultimate objective of curing HIV infection, if they can better understand the dynamics of the cells. “When…
Synthetic DNA is becoming a popular alternative to electronic-based technology in areas including data storage, product tagging, and signal processing, etc. To date, DNA has shown to be the ideal material for use in information technology. Watson–Crick base pairing is a fundamental feature of nucleic acids that provides the foundation for various DNA handling methods,…
According to the latest research published this week in the journal Science Advances, many modern marine invertebrates, such as sponges and jellyfish, contain chromosomes with the same old structure acquired from their primordial ancestors more than 600 million years ago. The surprising discovery serves as a reminder that evolution is conservative, keeping things that operate…
Researchers at the University of Copenhagen, Denmark, introduce the Clinical Knowledge Graph (CKG), an open-source platform with about 20 million nodes and 220 million relationships representing relevant experimental data, public databases, and literature. Evidence-based precision medicine has grown to include a more thorough examination of disease characteristics. This necessitates the seamless integration of a wide…
Researchers from MIT have developed a machine-learning model that can predict how two proteins bind, not in hours or minutes but just in a few seconds. Scientists may be able to use this machine-learning model to speed up the development of new drugs. Antibodies, which are small proteins generated by the immune system, can bind…
Researchers from the Helmholtz Centre Munich, Germany, provide CellRank, a method for single-cell fate mapping in a variety of circumstances where the direction is unclear, such as regeneration, reprogramming, and disease. During numerous biological processes, cells go through state transitions in a highly asynchronous manner. Single-cell RNA sequencing (scRNA-seq) successfully captures the heterogeneity that comes…
Researchers of Central South University, Changsha proposed an end-to-end bio-inspired model based on the convolutional neural network (CNN) and attention mechanism, named HyperAttentionDTI, for predicting drug-target interactions. In today’s world of biomedicine, drug discovery and repurposing are highly valued. Drug–target interactions (DTIs) are an essential part of drug discovery and repurposing. However, finding DTIs in…
GPU-accelerated software developed by the researchers at the University of Illinois at Urbana-Champaign simulates a 2-billion-atom cell that metabolizes and grows like a biological cell. Researchers present a whole-cell fully dynamical kinetic model that replicates the physical and chemical characteristics at a particle scale of a minimal living cell-JCVI-syn3A. The study of the simplest living…
A team of scientists led by a former University of British Columbia (UBC) postdoctoral researcher in medical genetics discovered over ten times the number of RNA viruses previously thought to exist, including many novel coronavirus species. By re-analyzing all publicly accessible RNA sequencing data, the researchers were able to make the finding. They established a…
A low-cost metagenome sequencing technology has been developed by scientists from the Chinese Academy of Sciences’ Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT). It allows high-resolution disclosure of a microbiome’s whole ‘landscape’ of species, even from low-biomass, damaged, or polluted samples. The ‘microbiome‘ is referred to a community of microorganisms (bacteria, fungi, protists, and…
Researchers from Harvard’s Wyss Institute, Harvard Medical School, and the ETH Zurich have predicted and validated genetic safe harbors for therapeutic genes, making gene and cell treatments safer, more efficient, more predictable. According to the researchers, “genomic safe harbors (GSHs)” could enhance the efficacy, persistence, and predictability of future gene and cell therapies that are…
Scientists from the Broad Institute of MIT and Harvard discovered an approach to studying the functional implications of the millions of mutations linked to cancer by pooling Perturb-seq and measuring the impact of TP53 and KRAS variants on RNA profiles in single cancer cells. Precision medicine entails predicting how specific genetic variants affect a patient’s…
To better comprehend the function of cells, scientists examine how different components of a cell – from single molecules to several organelles – work in synchronization. They studied individual molecules using classic structural biology tools, honing individual atoms. However, this method yields only static photographs of molecules in most circumstances. Instead, the scientists used cryo-electron…
New biological components developed by scientists at the University of Bristol can alter the flow of cellular activities along DNA. The scientists provide new insights into how information is encoded in DNA and new tools for developing sustainable biotechnologies, in the research published in the journal Nature Communications. Transcriptional terminators tell RNA polymerases (RNAPs) when…
Cornell researchers have invented new nanophotonic tweezers that can fit on a smaller than one-inch square chip, making it easier and more efficient to control single molecules using light to study biological systems. In a paper published in Nature Communications, Michelle Wang, the James Gilbert White Distinguished Professor in Physical Sciences in the College of…
A group of scientists from the Department of Energy’s Oak Ridge National Laboratory (ORNL) and the Georgia Institute of Technology applied supercomputing and new deep learning technologies (Google’s DeepMind) to anticipate the structures and functions of an organism’s whole proteome. The deep learning-based algorithms developed by the team predict protein structure and function from DNA…
Scientists from the University of California, Berkeley have developed a machine learning-based model that predicts protein fitness from the sequence. Protein fitness is a broad term that includes a wide range of protein properties, such as stability, enzyme activity, and ligand binding. Models of protein fitness based on machine learning typically learn from either unlabeled,…
Scientists from the University of Oklahoma and University of California at Berkeley have developed a framework iDIRECT (Inference of Direct and Indirect Relationships with Effective Copula-based Transitivity) for disentangling direct and indirect relationships in association networks. Despite the importance of networks in understanding the behavior and features of complex systems, recreating networks from large-scale experimental…
Pathogens employ virulence factors called effectors, which are critical for their survival. Homology modeling is one of the most extensively used approaches; however, it necessitates the usage of templates of solved effector structures, and solving all of them is far too difficult. There are just too many effector proteins encoded in pathogen genomes for each…
A worldwide endeavor to map the genomes of all life on Earth (plants, animals, fungi, and other microbes) is entering a new phase as it proceeds from pilot studies to full-scale production sequencing. The Earth BioGenome Project (EBP) has entered a new phase, as evidenced by a group of articles published this week in Proceedings…
A new DNA-based fluorescent nanoantenna is created by getting inspired by the ‘Lego-like’ properties of DNA. The building blocks of the new nanoantenna are typically 20,000 times smaller than human hair. A new DNA-based fluorescent nanoantenna will monitor the structural change of proteins over time. Results may go a long way to helping scientists better…
The PET/CT artificial intelligence model performed better than clinical data in predicting heart attack risk in individuals with established coronary artery disease. Predicting a heart attack in standard clinical practice is difficult. Cardiovascular risk factors and scores are commonly used to predict the chance of a heart attack, especially in individuals with suspected coronary artery…
Scientists from EMBL-EBI, NIH, NHGRI, and collaborators have discovered new micro-organisms (bacterial, fungal species, and viruses) in the human skin microbiome. The human skin microbiome is essential for skin health and illness, and studying its makeup might help us better understand skin-related diseases. Researchers employed metagenomics to create new human skin microbiome reference genomes. Data…
Targeting nucleic acid macromolecules, particularly RNA, for structure-based drug design (SBDD) is gaining research attention as it resulted in several FDA-approved compounds targeting RNA molecules. Scientists from Skoltech’s iMolecule group have created an artificial intelligence-driven approach, “BiteNetN,” to identify sites on the structures of DNA or RNA molecules where drug compounds may bind. The drug-binding…
ChromoMap is a fast and easy-to-use tool for visualizing genomic elements and related data (such as multi-omics data) in relation to their chromosome-by-chromosome occurrence for any genome assembly. ChromoMap provides customizable displays that allow for the comparison of data individually connected with each strand of a specific chromosome, as well as homologous chromosomes of any…
Scientists from Ben-Gurion University, Israel, have developed a method for computer-aided diagnostics of bronchial asthma based on machine learning. The model is trained using the audio file data, including respiratory sound records from healthy and asthmatic patients. The AI-based method developed for bronchial asthma diagnostics predicts with a high accuracy rate: “sensitivity of 89.3%, specificity…
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