Tools

Bioinformatics tools, software, databases and web servers: what they do and how researchers use them.

Bioinformatics | Health | Infectious Diseases | Machine Learning | News | Tools | Trending

Identifying Imported Plasmodium vivax Malaria Using Molecular Barcoding and Web-Based Data Analysis
ByRiya Vishwakarma December 26, 2022December 26, 2022

Researchers from Indonesia and Australia have developed a molecular barcode and a web-based data analysis tool to identify and track imported cases of Plasmodium vivax malaria. Using a unique molecular identifier, the tool can accurately detect the presence of P. vivax in samples and provide important information for the prevention and treatment of the disease….

Read More Identifying Imported Plasmodium vivax Malaria Using Molecular Barcoding and Web-Based Data Analysis
Bioinformatics | Cancer Research | News | Paper Summary | Phylogenetic Analysis | Precision Medicine | Tools | Trending

Scientists Employed Phylogenetic Approach to Understand the Pattern of Mutation Occurance During Cancer Evolution
ByRiya Vishwakarma December 11, 2022December 11, 2022

Phylogenetic approaches can be used to infer the order in which mutations arise during cancer progression by analyzing patterns of mutation occurrence in a population of cells. By identifying clades of related cells, it is possible to trace the evolutionary history of each cell and determine which mutations occurred first. This information can then be…

Read More Scientists Employed Phylogenetic Approach to Understand the Pattern of Mutation Occurance During Cancer Evolution
Bioinformatics | Metagenomics | News | OMICS | Paper Summary | Tools | Transcriptomics

Metagenomics and Metatranscriptomics: New Insights and Pipelines to Better Navigate Data Analysis
ByCatherene Tomy December 10, 2022December 10, 2022

Scientists at the Institute of Parasitology and Biomedicine and the University of Granada, Spain, collaborated to develop two pipelines that could automate and optimize metagenomics and metatranscriptomics data analysis. These pipelines could be adapted for 16S, shotgun, and RNA-Seq data. Its performance was validated through three studies by assessing their taxonomy classification ability. When Anton…

Read More Metagenomics and Metatranscriptomics: New Insights and Pipelines to Better Navigate Data Analysis
Bioinformatics | Infectious Diseases | News | NGS | Paper Summary | Tools | Trending

TransFlow: a Fast and Efficient Snakemake Workflow for Whole Genome Sequencing Based Transmission Analysis of Mycobacterium tuberculosis
ByRiya Vishwakarma December 9, 2022December 10, 2022

TransFlow (Transmission Workflow), a convenient, quick, effective, and thorough WGS-based transmission analysis pipeline, is presented by Chinese researchers. TransFlow integrates a number of cutting-edge technologies to perform transmission analysis on raw sequencing data. This analysis includes quality control, sequence alignment, variant calling, downstream transmission grouping, transmission network reconstruction, and transmission risk factor inference. TransFlow is…

Read More TransFlow: a Fast and Efficient Snakemake Workflow for Whole Genome Sequencing Based Transmission Analysis of Mycobacterium tuberculosis
Bioinformatics | Health | News | Paper Summary | Tools | Trending

UCL Researchers Unraveled the Hidden Patterns Involved in Patients with Multimorbidities
ByShwetha S December 6, 2022December 6, 2022

Researchers at University College London discovered multimorbidity and comorbidity illness trends using a dataset spanning 3.8 million patients in England. Patients and clinicians can use the study findings and interactive online tools to prevent and detect comorbid conditions. In contrast, biomedical researchers and pharmaceutical manufacturers can use them to provide lead compounds targeting common or…

Read More UCL Researchers Unraveled the Hidden Patterns Involved in Patients with Multimorbidities
Bioinformatics | News | NGS | Paper Summary | RNA-Seq | Sequencing | Tools | Trending

RNAlysis: a Gateway into RNA Sequencing Data Analysis for Less Computer-savvy Researchers
ByRiya Vishwakarma November 29, 2022November 29, 2022

Qualitative data analysis, understanding patterns, finding possible targets/candidates, and intuitively displaying the results are among the crucially difficult aspects of next-generation sequencing experiments. These challenges are even more difficult for researchers who are not accustomed to writing computer code because the bulk of the analysis tools accessible demand programming knowledge. A customizable Python-based analysis program…

Read More RNAlysis: a Gateway into RNA Sequencing Data Analysis for Less Computer-savvy Researchers
Big Data | Bioinformatics | News | NGS | Paper Summary | RNA-Seq | Tools | Transcriptomics | Trending

Multi-platform Universal Single-cell RNAseq Data Processing Pipeline – UniverSC
ByRiya Vishwakarma November 23, 2022November 23, 2022

Scientists at the Center for Integrative Medical Sciences Yokohama, Japan, designed a platform-independent application to run UniverSC, a wrapper for the 10X Genomics CellRanger program that works with different single-cell technologies, via a graphical user interface, operable on macOS, Windows, and Linux Ubuntu, eliminating data processing for single-cell RNAseq (scRNAseq) analysis for researchers who are naive to…

Read More Multi-platform Universal Single-cell RNAseq Data Processing Pipeline – UniverSC
Bioinformatics | Computational Models | Genomics | Metagenomics | News | NGS | Paper Summary | Sequencing | Tools | Trending

Researchers Develop a Computational Tool ‘CAMMiQ’ for Strain Level Microbial Detection and Quantification Using High Throughput Sequencing Data
ByMahi Sharma November 5, 2022November 5, 2022

A recent study led under the supervision of Cenk Sahinalp et al. and conducted jointly at the National Institute of Health, UCSD, and Indiana University introduced an optimized framework for strain-level microbial identification. The team has provided a comparative approach with reference to other taxonomic classifiers and embedded results with higher sensitivity and specificity. Introduction…

Read More Researchers Develop a Computational Tool ‘CAMMiQ’ for Strain Level Microbial Detection and Quantification Using High Throughput Sequencing Data
Bioinformatics | Deep Learning | Machine Learning | News | Paper Summary | Tools | Trending

Researchers Identified Deep Learning Tools as the Top Performers for Predicting Long Non-coding RNA
BySrishti Sharma October 3, 2022October 3, 2022

New RNA transcripts have been discovered as a result of the growing amount of transcriptomic data. Bioinformatic tool developers have had difficulty separating long non-coding RNA (lncRNA) from protein-coding messenger RNA (mRNA). Currently, tools implementing deep learning architectures have been developed to accomplish this task, but their potential to discover sequence features and their interactions…

Read More Researchers Identified Deep Learning Tools as the Top Performers for Predicting Long Non-coding RNA
AI | Bioinformatics | Cancer Research | Machine Learning | News | Paper Summary | Tools | Trending

New AI Tool ‘SigProfilerExtractor’ Identifies Mutational Signature Linked To Tobacco Smoking and Bladder Cancer
BySrishti Sharma September 30, 2022September 30, 2022

A new powerful machine learning tool, ‘SigProfilerExtractor‘ has identified a link between bladder cancer and tobacco smoking. The study was led by researchers at the University of California San Diego School of Medicine and published in the journal Cell Genomics. The study may help researchers determine what environmental factors could cause cancer in certain patients, such…

Read More New AI Tool ‘SigProfilerExtractor’ Identifies Mutational Signature Linked To Tobacco Smoking and Bladder Cancer
Bioinformatics | Metagenomics | News | Paper Summary | Sequencing | Tools | Trending

iNAP: An Integrated Network Analysis Pipeline for Microbiome Studies in Complex Ecosystems
ByMahi Sharma September 28, 2022September 28, 2022

Microbial network analysis is an acceptable approach to investigating microbiome and metagenomic datasets and finding insights into a complex ecosystem. Ye Deng et al. introduced an integrated pipeline, iNAP, for network construction and visualization to help researchers understand microbial ecology without prior knowledge of bioinformatics or statistical programming skills. Understanding and deducing information from microbial…

Read More iNAP: An Integrated Network Analysis Pipeline for Microbiome Studies in Complex Ecosystems
AI | Bioinformatics | COVID-19 | Drug Discovery | News | Structural Biology | Tools | Trending

Accelerating the Discovery of New Drugs with AI-based Screening Methods
ByDr. Tamanna Anwar September 25, 2022September 29, 2022

The researchers from the University of Central Florida identified promising drug candidates using an AI-based tool, “AttentionSiteDTI,” that uses natural language to model drug-target protein interactions. Drug discovery has become a major bottleneck in modern medicine. Researchers have developed several methods to speed up the process in recent years, such as high-throughput screening (HTS). HTS…

Read More Accelerating the Discovery of New Drugs with AI-based Screening Methods
Bioinformatics | Deep Learning | News | Paper Summary | Structural Biology | Tools | Trending

DeepFold: A Fast and Accurate Method for Ab Initio Protein Structure Prediction using Deep Learning Potentials
BySrishti Sharma September 20, 2022January 26, 2023

Scientists from the University of Michigan developed an open-source program, DeepFold, to quickly construct accurate protein structure models from deep learning-based potentials. In spite of recent progress in protein structure prediction, it is still necessary to improve the accuracy of models for proteins lacking sequence and/or structure homologs. The DeepFold program uses multi-task deep residual…

Read More DeepFold: A Fast and Accurate Method for Ab Initio Protein Structure Prediction using Deep Learning Potentials
AI | Bioinformatics | Cancer Research | Deep Learning | Health | News | Precision Medicine | Tools | Trending

Scientists Develop an Improved Method for Detecting Myeloma Bone Disease using Deep Learning Coupled Photon-counting CT
ByDr. Tamanna Anwar September 13, 2022September 13, 2022

Scientists have developed a new CT technique using artificial intelligence (AI) to spot multiple myeloma-related bone diseases, using lower radiation doses than conventional CT, according to a study published in Radiology, a journal of the Radiological Society of North America. After nearly two decades of development, the technology was used in clinical practice in 2021….

Read More Scientists Develop an Improved Method for Detecting Myeloma Bone Disease using Deep Learning Coupled Photon-counting CT
Bioinformatics | Cancer Research | News | NGS | OMICS | Paper Summary | RNA-Seq | Tools | Trending

Cancer Omics Data Analysis Simplified with a Graphical Interface-driven Bioinformatics Pipeline ‘iCOMIC’
BySrishti Sharma September 10, 2022January 3, 2024

Researchers from the Indian Institute of Technology, Madras, present iCOMIC, a tool for quickly analyzing genomic data. With iCOMIC, users can analyze whole genome and exome sequencing data as well as RNA-Seq data using several pre-configured workflows. Developed as an open-source, standalone tool characterized by a Python-based GUI and automated bioinformatics pipelines for DNA-Seq and…

Read More Cancer Omics Data Analysis Simplified with a Graphical Interface-driven Bioinformatics Pipeline ‘iCOMIC’
Bioinformatics | COVID-19 | Infectious Diseases | News | Tools | Trending

MVsim – A Toolset for Simulating Complex Molecular Interactions Could Improve Cancer and COVID-19 Treatments
ByDr. Tamanna Anwar September 8, 2022September 8, 2022

MVsim is a new application suite that enables the quantification, design, and mechanistic evaluation of multivalent binding interactions. It can be used to simulate both monospecific and multispecific multivalent ligand-receptor interactions accurately, having potential applications for protein engineering, molecular and cellular analysis, as well as drug design. The University of Minnesota Twin Cities biomedical engineers have…

Read More MVsim – A Toolset for Simulating Complex Molecular Interactions Could Improve Cancer and COVID-19 Treatments
Bioinformatics | Genetic Engineering | Metabolomics | News | Paper Summary | Proteomics | Tools | Transcriptomics | Trending

Scientists Introduce an Automated Pipeline ‘Galaxy-SynBioCAD’ for Synthetic Biology Design and Engineering
BySrishti Sharma September 6, 2022October 22, 2026

A toolshed for synthetic biology, metabolic engineering, and industrial biotechnology is available through the Galaxy-SynBioCAD portal. Using the tools and workflows available on the portal, one can create libraries of strains that produce the desired chemical targets, spanning a comprehensive metabolic pathway design and engineering process from selecting strains and targets, designing DNA parts to…

Read More Scientists Introduce an Automated Pipeline ‘Galaxy-SynBioCAD’ for Synthetic Biology Design and Engineering
Bioinformatics | COVID-19 | Covid-19 News | News | Paper Summary | SARS-CoV-2 | Tools | Trending

Epitope-Evaluator: A Shiny/R-based Web Tool for Interactively Analysing Predicted T-cell Epitopes
BySrishti Sharma September 1, 2022September 1, 2022

T-cell epitopes are predicted based on amino acid sequences of proteins from different MHC alleles using multiple immunoinformatic tools. Many of these tools produce hundreds of potential peptide candidates, but they are either non-graphical or unfriendly to non-programmers. Epitope-Evaluator is a web application developed in the Shiny/R framework for analyzing predicted T-cell epitopes interactively. A…

Read More Epitope-Evaluator: A Shiny/R-based Web Tool for Interactively Analysing Predicted T-cell Epitopes
AI | Bioinformatics | Deep Learning | Featured | News | Paper Summary | Structural Biology | Tools | Trending

Meta’s AI Protein Structure Prediction Model ‘ESMFold’ Predicts as Accurately and 6x Faster than AlphaFold2
BySrishti Sharma August 13, 2022October 6, 2022

Researchers at Meta AI developed an artificial intelligence (AI) model that can precisely predict entire atomic protein structures from a single sequence of a protein. The use of language model representations to replace the requirement for explicit homologous sequences distinguishes ESMFold from AlphaFold2. As a result of this simplification, ESMFold is significantly faster than the…

Read More Meta’s AI Protein Structure Prediction Model ‘ESMFold’ Predicts as Accurately and 6x Faster than AlphaFold2
Bioinformatics | Data Science | News | Paper Summary | Tools | Trending

Graph Based Visualization and Analysis of High Dimensional Data Using the Platform ‘Graphia’
ByTanveen Kaur August 3, 2022August 3, 2022

Scientists from the University of Edinburgh developed an open-source platform, ‘Graphia’, for the graph-based visualization and analysis of the high dimensional data being produced from research on cells, genes, proteins, and metabolites. A brand-new visual analytics platform called Graphia was developed especially for network-based analysis of enormous and complicated data, such as the vast volumes…

Read More Graph Based Visualization and Analysis of High Dimensional Data Using the Platform ‘Graphia’
AI | Algorithm | Bioinformatics | News | Paper Summary | Tools | Trending

DeepBacs: A Deep Learning Approach to Analyze Bacterial Microscopy Images
BySrishti Sharma August 2, 2022August 2, 2022

Scientists from University College London demonstrate the use of various cutting-edge artificial neural networks to analyze images of bacterial microscopy. The approach will help future researchers to explore the prospective deep learning (DL) applications and employ pre-trained models in their research on a designated platform. Microbiology, the study of microorganisms and their community, is a…

Read More DeepBacs: A Deep Learning Approach to Analyze Bacterial Microscopy Images
AI | Algorithm | Bioinformatics | Database | Drug Discovery | News | Structural Biology | Tools | Trending

Deepmind’s AlphaFold Predicted the Structures of all the Proteins Known to Science, Expanding the AlphaFold DB by Over 200x
ByDr. Tamanna Anwar July 30, 2022October 22, 2026

The AlphaFold Protein Structure Database, created by DeepMind and EMBL’s European Bioinformatics Institute (EMBL-EBI), makes AI-enabled predictions of the 3D structures of nearly all cataloged proteins available to the scientific community for free and without restrictions. It has been a year since AlphaFold was made available for free worldwide distribution and AlphaFold Protein Structure Database…

Read More Deepmind’s AlphaFold Predicted the Structures of all the Proteins Known to Science, Expanding the AlphaFold DB by Over 200x
AI | Bioinformatics | Biomedical Engineering | Health | Infectious Diseases | Machine Learning | News | Tools | Trending

AI-Based Early Warning System for Sepsis Prevents Thousands of Deaths
ByDr. Tamanna Anwar July 22, 2022November 9, 2022

The new AI-based technology developed by the scientists at Johns Hopkins University recognizes patients susceptible to sepsis, which is otherwise notoriously hard to detect and progresses rapidly. Early diagnosis and treatment of sepsis are associated with better patient outcomes. Early warning systems based on machine learning may shorten the diagnosis time, but only a few…

Read More AI-Based Early Warning System for Sepsis Prevents Thousands of Deaths
AI | Algorithm | Bioinformatics | Computational Models | Deep Learning | Drug Discovery | News | Paper Summary | Structural Biology | Tools

A Geometric Deep-Learning Model ‘EquiBind’ the Fastest Computational Molecular Docking Model
ByTanveen Kaur July 17, 2022October 22, 2026

MIT researchers have developed a geometric deep-learning model, EquiBind, which is 1,200 times faster than one of the fastest computational molecular docking models currently in use, QuickVina2-W, for effective binding of drug-like substances to proteins. One of the main challenges in drug discovery is to predict the binding properties of a drug-like chemical to a…

Read More A Geometric Deep-Learning Model ‘EquiBind’ the Fastest Computational Molecular Docking Model
AI | Bioinformatics | Drug Discovery | News | OMICS | Paper Summary | Tools | Trending

PandaOmics: An AI-Enabled Biological Target Discovery Platform Used to Identify Amyotrophic Lateral Sclerosis Therapeutic Targets
ByTanveen Kaur July 12, 2022October 22, 2026

Scientists use PandaOmics, an AI-driven target identification tool, to examine the expression profiles of direct iPSC-derived motor neurons from Answer Amyotrophic Lateral Sclerosis (ALS) and central nervous system samples from public datasets. The discovery of novel therapy regimens is urgently needed for the severe neurological disease amyotrophic lateral sclerosis, which has unclear pathophysiology. Here, the…

Read More PandaOmics: An AI-Enabled Biological Target Discovery Platform Used to Identify Amyotrophic Lateral Sclerosis Therapeutic Targets
AI | Bioinformatics | Corona Virus | COVID-19 | Health | Infectious Diseases | News | Tools | Trending

The Pandemic Readiness Platform ‘IDentif.AI-x’ for Rapid Prioritization of Effective COVID-19 Combination Therapy Regimens
ByTanveen Kaur July 6, 2022November 9, 2022

Scientists from the National University of Singapore and DSO National Laboratories, Singapore develop IDentif.AI-x, a pandemic readiness platform powered by artificial intelligence for the rapid prioritization of COVID-19 optimized combination therapy regimens. By combining a prospective, experimental validation of multi-drug efficacy on a SARS-CoV-2 live virus and Vero E6 assay with a quadratic optimization workflow,…

Read More The Pandemic Readiness Platform ‘IDentif.AI-x’ for Rapid Prioritization of Effective COVID-19 Combination Therapy Regimens
AI | Algorithm | Bioinformatics | Cancer Research | Deep Learning | Health | Neural Network | News | Tools | Trending

TranSalNet – AI System that Simulates Human Vision Holds Potential Application in Cancer Detection
ByDr. Tamanna Anwar July 5, 2022December 28, 2022

Scientists at Cardiff University have developed a state-of-the-art artificial intelligence (AI) system, ‘TranSalNet,’ which precisely anticipates the regions of an image where a person is most likely to gaze. The researchers claim that the unique method more accurately simulates human vision than any previous system based on human brain mechanics and its ability to discriminate…

Read More TranSalNet – AI System that Simulates Human Vision Holds Potential Application in Cancer Detection
Bioinformatics | Infectious Diseases | News | NGS | Sequencing | Tools | Trending

Computer Scientists from Rice University Develop a Software ‘Emu’ for Accurate Microbial Community Profiling
ByDr. Tamanna Anwar July 1, 2022July 1, 2022

Emu, an approach that uses an expectation-maximization algorithm to generate taxonomic abundance profiles from full-length 16S rRNA reads profiles microbial populations using common genes. According to results generated from simulated datasets and mock communities, Emu is capable of accurate microbial community profiling while obtaining fewer false positives and false negatives than alternative approaches, When determining…

Read More Computer Scientists from Rice University Develop a Software ‘Emu’ for Accurate Microbial Community Profiling
Algorithm | Bioinformatics | Computational Models | Machine Learning | News | Tools | Trending

Scientists Develop a Novel GPU-based Machine Learning Model to Discover Human Brain Connectivity
ByDr. Tamanna Anwar June 30, 2022July 1, 2022

Indian Institute of Science (IISc) researchers have created a novel GPU-based machine learning model to better understand and predict human brain connections across various brain regions. The researchers present “Regularized, Accelerated, Linear Fascicle Evaluation (ReAl-LiFE)”, a GPU-based execution of a state-of-the-art streamline pruning algorithm (LiFE), which achieves >100× speedups over previous CPU-based implementations. The ReAl-LiFE…

Read More Scientists Develop a Novel GPU-based Machine Learning Model to Discover Human Brain Connectivity
AI | Bioinformatics | Cancer Research | Cell | News | Tools | Trending

PICASSO Technique Helps Scientists Visualize Biological Molecules into Technicolor
ByDr. Tamanna Anwar June 27, 2022December 28, 2022

Scientists from the Korea Advanced Institute of Science and Technology propose the PICASSO technique, which enables more than 15-color imaging of spatially overlapping proteins in a single imaging round without using any reference emission spectra. For a wide spectrum of researchers, the PICASSO technique offers a multiplexed imaging tool with great accessibility and accuracy. According…

Read More PICASSO Technique Helps Scientists Visualize Biological Molecules into Technicolor
Bioinformatics | Genomics | News | Paper Summary | Tools | Trending

Scientists Develop a New Computational Tool ‘Grit’ to Identify Upstream Transcription Factor Binding Sites More Accurately
ByTanveen Kaur June 16, 2022June 16, 2022

Scientists from Yangtze University, Jingzhou, China developed a computational tool, “Grit,” to identify the upstream transcription factor binding sites in orthologous genes by the utilization of mixed Student’s t-test statistics. The transcription factor (TF) regulates the transcription of DNA to messenger RNA or mRNA by binding to upstream sequence motifs. Distinguishing the locations of known…

Read More Scientists Develop a New Computational Tool ‘Grit’ to Identify Upstream Transcription Factor Binding Sites More Accurately
Bioinformatics | Data Science | Featured | Genomics | News | NGS | Sequencing | Tools | Trending

Scientists Use CRISPR Technology and Perturb-seq to Map Every Human Gene to its Function
ByDr. Tamanna Anwar June 11, 2022June 18, 2022

Scientists from Whitehead Institute and collaborators used Perturb-seq, a single-cell sequencing technology, to link every expressed gene in the human genome to its function in the cell, offering a free resource for other researchers that can be accessed via the internet. The Human Genome Project was a huge undertaking that aimed to sequence every single…

Read More Scientists Use CRISPR Technology and Perturb-seq to Map Every Human Gene to its Function
Bioinformatics | Chronic Diseases | Computer Vision | Health | Machine Learning | News | Precision Medicine | Tools | Trending

Scientists Develop a New Computer Vision Model with Improved Proficiency to Differentiate Rheumatoid Arthritis from Osteoarthritis in Damaged Joint Tissue
ByDr. Tamanna Anwar June 9, 2022June 18, 2022

Hospital for Special Surgery (HSS) researchers in New York City have developed a computer vision tool that effectively identifies rheumatoid arthritis (RA) from osteoarthritis (OA) in joint tissue collected from patients who had total knee replacements (TKR). The findings show that the new computer vision model with improved proficiency to differentiate rheumatoid arthritis from osteoarthritis…

Read More Scientists Develop a New Computer Vision Model with Improved Proficiency to Differentiate Rheumatoid Arthritis from Osteoarthritis in Damaged Joint Tissue
Bioinformatics | News | Paper Summary | Structural Biology | Tools | Trending

ColabFold: A Freely Accessible Protein Folding Tool for Accelerated Prediction of Protein Structures and Complexes
ByTanveen Kaur June 8, 2022February 5, 2024

Scientists have developed ColabFold, an open-source software to accelerate the prediction of protein structures as well as complexes by integrating fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold offers a sped-up prediction of protein structures and complexes by consolidating the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. The 40−60-overlap quicker search…

Read More ColabFold: A Freely Accessible Protein Folding Tool for Accelerated Prediction of Protein Structures and Complexes
AI | Bioinformatics | Cancer Research | Infectious Diseases | News | Tools

An Automated AI-Based Software ‘TrackMate v7’ for Tracking Things in Bioimages
ByDr. Tamanna Anwar June 4, 2022June 18, 2022

Scientists from Akademi University, Turku, Finland, and Pasteur Institute, Paris, France have developed a new software TrackMate v7 that may allow tracking things in photos. The technology, which is based on artificial intelligence, will serve as a catalyst for future discoveries in the biological sciences. Object tracking, or following objects across time, is a critical…

Read More An Automated AI-Based Software ‘TrackMate v7’ for Tracking Things in Bioimages
AMR Alert | Antibiotic Resistance | News | Paper Summary | Tools

Scientists Develop a Mathematical Model to Predict the Efficiency of Phage Therapy Against Pathogenic Bacteria
ByTanveen Kaur May 25, 2022November 9, 2022

Scientists from Inserm, Université Sorbonne Paris Nord, and Université Paris-Cité at the IAME Laboratory, with their collaborators at Institut Pasteur and the Paris Public Hospitals Group (AP-HP), develop an in silico model in combination with in vivo phage therapy data to highlight vital parameters for increasing the efficiency of pneumonia treatment. The clinical (re)development of…

Read More Scientists Develop a Mathematical Model to Predict the Efficiency of Phage Therapy Against Pathogenic Bacteria
AI | Algorithm | Bioinformatics | Deep Learning | Health | Machine Learning | News | Paper Summary | Tools

Scientists Develop a Machine Learning Algorithm that uses Electronic Health Records to Predict Mental Health Crisis
ByTanveen Kaur May 23, 2022December 28, 2022

Scientists from Koa Health and Birmingham and Solihull Mental Health NHS Foundation Trust developed a machine learning model that uses electronic health records to detect the risk of a mental health crisis in patients over 28 days. The machine-learning algorithm continuously monitors patients for the possibility of a mental health crisis using anonymized electronic health…

Read More Scientists Develop a Machine Learning Algorithm that uses Electronic Health Records to Predict Mental Health Crisis
Algorithm | Bioinformatics | Genomics | Machine Learning | News | NGS | Sequencing | Tools | Trending

‘BWA-MEME’ – Machine Learning-Based Short Read Alignment Algorithm to Speed up DNA Sequencing
ByDr. Tamanna Anwar May 21, 2022June 18, 2022

The algorithm is the first full-fledged machine learning-based short read alignment algorithm to speed up DNA sequencing, that efficiently uses learned indices to solve the exact match search issue for efficient seeding. The human genome is made up of a whole set of DNA that is around 6.4 billion letters long. Reading the entire genome…

Read More ‘BWA-MEME’ – Machine Learning-Based Short Read Alignment Algorithm to Speed up DNA Sequencing
AI | Bioinformatics | Cancer Research | Deep Learning | Machine Learning | News | Paper Summary | Tools | Trending

‘CancerVar’ – A New Machine Learning Empowered Tool to Interpret Somatic Variants in Cancer
ByTanveen Kaur May 18, 2022November 9, 2022

CancerVar leverages machine learning frameworks to evaluate the potential relevance of somatic cancer mutations in terms of cancer diagnosis, prognosis, and targetability, in addition to simply discovering them. Researchers at Children’s Hospital of Philadelphia (CHOP) developed CancerVar, a novel machine learning empowered tool to interpret somatic variants in cancer. CancerVar can be accessed either as…

Read More ‘CancerVar’ – A New Machine Learning Empowered Tool to Interpret Somatic Variants in Cancer
Bioinformatics | Deep Learning | Neural Network | News | Paper Summary | Tools | Trending

‘DeepRank’ – A Deep Learning Framework for Data Mining Protein-Protein Interfaces Using 3D Convolutional Neural Networks
ByTanveen Kaur May 16, 2022November 9, 2022

Scientists formulate a deep learning framework, DeepRank, for the data mining of 3D protein-protein interfaces. They demonstrated the efficiency and readiness of DeepRank on two unique difficulties in structural biology. 3D structures of protein complexes give essential data to decipher biological processes at the molecular scale. The huge measure of experimentally and computationally resolved protein-protein…

Read More ‘DeepRank’ – A Deep Learning Framework for Data Mining Protein-Protein Interfaces Using 3D Convolutional Neural Networks
Biomedical Engineering | News | Tools | Trending

Scientists Engineered a New Tool to Precisely Switch Gene Expression ‘On’ and ‘Off’
ByDr. Tamanna Anwar May 5, 2022February 3, 2024

Scientists have developed a new approach for harnessing electrical signals to turn genes on and off. A team led by Imperial College London experts has created a new way for precisely altering gene expression by adding and withdrawing electrons. Experts from Imperial College’s Departments of Chemistry, Life Sciences, and Bioengineering, the Imperial College Translation &…

Read More Scientists Engineered a New Tool to Precisely Switch Gene Expression ‘On’ and ‘Off’
AI | Bioinformatics | Cancer Research | Computational Models | Health | News | Precision Medicine | Tools | Trending

Artificial Intelligence Enables Physicians to Better Evaluate the Effectiveness of Bladder Cancer Treatment
ByDr. Tamanna Anwar April 26, 2022June 18, 2022

Consultation with a machine learning tool helped providers determine more accurately whether patients had a complete response to chemotherapy. Scientists from the University of Michigan investigated the impact of a computerized artificial intelligence (AI)-based decision support system (CDSS-T) on physicians’ diagnostic accuracy in measuring bladder cancer treatment response. The CDSS-T has the potential to increase…

Read More Artificial Intelligence Enables Physicians to Better Evaluate the Effectiveness of Bladder Cancer Treatment
Bioinformatics | News | Paper Summary | Systems Biology | Tools | Trending

‘BioCRNpyler’ – A Python Package to Build, Manage and Explore Intricate Biochemical Models
ByTanveen Kaur April 25, 2022April 25, 2022

Scientists from the California Institute of Technology, United States, have developed a python package, ‘BioCRNpyler’, to build, manage, and explore intricate biochemical models. BioCRNpyler can be used to speed up the computer-assisted design of biochemical circuits and the creation of model-driven hypotheses in biology. Biochemical interactions in systems and synthetic biology are frequently modeled with…

Read More ‘BioCRNpyler’ – A Python Package to Build, Manage and Explore Intricate Biochemical Models
Bioinformatics | Deep Learning | News | Paper Summary | Tools | Trending

Scientists Develop a Deep Learning Model ‘CAESAR’ to Connect High-Resolution 3-Dimensional Chromatin Organization With Epigenomics
ByDr. Tamanna Anwar April 22, 2022June 18, 2022

Researchers from the University of Michigan, USA, developed a deep learning model, CAESAR (Chromosomal structure And EpigenomicS AnalyzeR), to predict nucleosome-resolution 3D chromatin contact maps from existing epigenomic features and lower-resolution Hi-C contact maps. The imputed high-resolution contact maps could help in target finding, hypotheses generation, and other downstream analyses. The resolution of chromatin conformation…

Read More Scientists Develop a Deep Learning Model ‘CAESAR’ to Connect High-Resolution 3-Dimensional Chromatin Organization With Epigenomics
Algorithm | Bioinformatics | Cell | Computational Models | Deep Learning | Machine Learning | News | OMICS | Paper Summary | Tools

DGCyTOF: Deep Learning with Graphic Cluster Visualisation Model for Predicting Cell Types from Single-Cell Mass Cytometry Data
ByTanveen Kaur April 16, 2022November 9, 2022

Researchers from The Ohio State University utilized deep-learning classification and hierarchical stable-clustering approaches to predict cell types from single-cell mass cytometry data. The DGCyTOF approach could facilitate the analysis of single-cell RNASeq data and other omics data. Single-cell mass cytometry, also called cytometry by time of flight (CyTOF), is a powerful high-throughput technology that permits…

Read More DGCyTOF: Deep Learning with Graphic Cluster Visualisation Model for Predicting Cell Types from Single-Cell Mass Cytometry Data
AMR Alert | Antibiotic Resistance | Bioinformatics | Computational Models | Machine Learning | News | Paper Summary | Precision Medicine | Tools | Trending

Machine Learning-Driven Antibiotic Selection Model that Predicts Personalized Antibiograms
ByTanveen Kaur April 13, 2022November 9, 2022

The World Health Organization (WHO) appraises that 700,000 individuals now die yearly because of antibiotic resistance and anticipates that this number will surpass 10 million every year by 2051. Stanford University scientists developed machine learning models that predict antibiotic susceptibility patterns (personalized antibiograms) using electronic health record data. Personalized empiric antibiotic subscription with personalized antibiograms…

Read More Machine Learning-Driven Antibiotic Selection Model that Predicts Personalized Antibiograms
AI | Bioinformatics | Biomedical Engineering | Cancer Research | Deep Learning | News | Tools | Trending

The Reproducibility Crisis – Robot Scientist ‘Eve’ Finds a Lack of Reproducibility in the Breast Cancer Literature
ByDr. Tamanna Anwar April 12, 2022June 18, 2022

Scientists from the University of Cambridge have used a medley of automated text analysis and the ‘robot scientist – Eve’ to semi-automate the procedure of reproducing research results. The lack of reproducibility is one of the biggest crises facing modern science. Scientific findings should be not only ‘replicable’ (i.e., reproducible in the same lab under…

Read More The Reproducibility Crisis – Robot Scientist ‘Eve’ Finds a Lack of Reproducibility in the Breast Cancer Literature
Bioinformatics | Cancer Research | Featured | News | Tools | Trending

Glyco-Decipher – A New Glycoproteomics Analysis Tool for Sensitive Deciphering of Protein Glycosylation
ByDr. Tamanna Anwar April 11, 2022January 30, 2024

A team of scientists led by Prof. YE Mingliang from the Dalian Institute of Chemical Physics (DICP) of the Chinese Academy of Sciences (CAS) has recently created Glyco-Decipher, a new glycoproteomics software tool for the sensitive interpretation of N-glycopeptide mass spectra with high confidence. Glyco-Decipher is a promising method for enhancing glycoproteomics analysis in biological…

Read More Glyco-Decipher – A New Glycoproteomics Analysis Tool for Sensitive Deciphering of Protein Glycosylation
Antibiotic Resistance | Biotech | Genetic Engineering | News | Tools | Trending

Scientists Developed a New Improved Prime Editor in Plants to Produce Resistant and Improved Crops
ByDr. Tamanna Anwar April 4, 2022June 18, 2022

Scientists from GAO Caixia’s team at the Chinese Academy of Sciences’ Institute of Genetics and Developmental Biology (IGDB) with collaborators have introduced Engineered Plant Prime Editor, a more efficient and enhanced plant prime editing system (ePPE). The new editing approach is projected to broaden the scope of prime editing’s application in agricultural breeding, crop improvement,…

Read More Scientists Developed a New Improved Prime Editor in Plants to Produce Resistant and Improved Crops
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A Deep Learning Model ‘AF2complex’ for Predicting Protein Complex Structures and Protein-Protein Interactions
ByDr. Tamanna Anwar April 2, 2022October 22, 2026

Scientists from the Center for the Study of Systems Biology, Atlanta, in collaboration with the Georgia Institute of Technology, Atlanta, and Oak Ridge National Laboratory, Oak Ridge, USA, have introduced a new method, ‘AF2complex’, in which AlphaFold2 (AF2) can be used to predict protein complex structure and protein-protein interactions. It is expected to provide significant…

Read More A Deep Learning Model ‘AF2complex’ for Predicting Protein Complex Structures and Protein-Protein Interactions

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