Tools

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

AI | Bioinformatics | Computational Models | Data Science | Deep Learning | Drug Discovery | Featured | News | Paper Summary | Structural Biology | Tools | Trending
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
Bioinformatics | Cancer Research | Computational Models | Drug Discovery | News | Paper Summary | Precision Medicine | Tools | Trending
Scientists Discover the Landscape of Receptor-Mediated Precision Cancer Combination Therapy through a Single-Cell Perspective
ByTanveen Kaur April 1, 2022October 22, 2026
Scientists from the National Cancer Institute, Bethesda, and the University of Maryland have developed a computational tool to determine gene-target combinations for personalized cancer therapies. The tool has the potential to aid in the creation of novel combinatorial treatments for cancer patients. For mining a vast cohort of single-cell transcriptomics information, the scientists utilize combinatorial…
Read More Scientists Discover the Landscape of Receptor-Mediated Precision Cancer Combination Therapy through a Single-Cell Perspective
Bioinformatics | Cancer Research | Cell | Drug Discovery | Featured | News | OMICS | Precision Medicine | RNA-Seq | Tools | Trending
A New Tool ‘FORALL’ for Profiling Multi-Omics and Drug Response in Childhood Acute Lymphoblastic Leukemia
ByDr. Tamanna Anwar March 31, 2022October 22, 2026
In a report published in Nature Communications, researchers from the Department of Oncology-Pathology at Karolinska Institutet, Sweden established a cell line resource dataset and analysis tool ‘Functional Omics Resource of ALL (FORALL)’ that could be used to uncover the features that make specific leukemias vulnerable to new forms of targeted medicines. The researchers used proteomics,…
Read More A New Tool ‘FORALL’ for Profiling Multi-Omics and Drug Response in Childhood Acute Lymphoblastic Leukemia
Bioinformatics | Cancer Research | News | RNA-Seq | Sequencing | Tools | Trending
Scientists Developed a Computational Tool ‘CellTrek’ for Spatial Mapping of Single-Cell Data Within Tissues
ByDr. Tamanna Anwar March 28, 2022June 18, 2022
‘CellTrek’ can accurately map single cells in diverse tissue types to resolve their spatial organization. The tool identifies the location of particular cell types to drive biological insights. Scientists at The University of Texas MD Anderson Cancer Center have created a new computational methodology that successfully combines data from simultaneous gene-expression profiling approaches to build…
Read More Scientists Developed a Computational Tool ‘CellTrek’ for Spatial Mapping of Single-Cell Data Within Tissues
AI | Bioinformatics | Data Science | Deep Learning | Genomics | Machine Learning | Neural Network | News | NGS | Tools | Trending
Scientists from the University of California Developed a Highly Accurate Algorithm ‘La Jolla Assembler (LJA)’ to Scale-up Complete Genome Assembly
ByDr. Tamanna Anwar March 12, 2022June 18, 2022
A team of international researchers led by the University of California San Diego’s Department of Computer Science and Engineering has demonstrated that the La Jolla Assembler (LJA), a new genome assembly algorithm, vastly improves large genome reconstruction, the process of arranging DNA snippets into complete genomes, which is a crucial part of genomic sequencing. Furthermore,…
Read More Scientists from the University of California Developed a Highly Accurate Algorithm ‘La Jolla Assembler (LJA)’ to Scale-up Complete Genome Assembly
Bioinformatics | Drug Discovery | Featured | Genomics | News | NGS | OMICS | Precision Medicine | Tools | Trending
Scientists at Garvan Institute Developed a Single Test for Over 50 Genetic Diseases, Cutting Diagnosis Time from Decades to Days
ByDr. Tamanna Anwar March 11, 2022October 22, 2026
Garvan Institute researchers have demonstrated how new genomic sequencing technologies might help individuals with uncommon neurological and neuromuscular conditions avoid a “diagnostic odyssey.” – A single DNA test capable of screening a patient’s genome for over 50 genetic neurological and neuromuscular diseases (e.g., Huntington’s disease, muscular dystrophies, and fragile X syndrome) has been developed. -…
Read More Scientists at Garvan Institute Developed a Single Test for Over 50 Genetic Diseases, Cutting Diagnosis Time from Decades to Days
Bioinformatics | Computational Models | Corona Virus | COVID-19 | Covid-19 News | Data Science | Machine Learning | Tools | Trending
Scientists from Yale University Developed a New Data Analysis Tool ‘Multiscale PHATE’ that Reveals Significant Covid-19 Clues
ByDr. Tamanna Anwar March 2, 2022June 18, 2022
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…
Read More Scientists from Yale University Developed a New Data Analysis Tool ‘Multiscale PHATE’ that Reveals Significant Covid-19 Clues
Bioinformatics | Cancer Research | Drug Discovery | News | Tools
Simulating Directed Evolution With A New Computational Tool
ByDr. Tamanna Anwar February 26, 2022October 22, 2026
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…
Read More Simulating Directed Evolution With A New Computational Tool
Bioinformatics | Deep Learning | Machine Learning | News | Paper Summary | RNA-Seq | Tools | Trending
Predicting Cell Fates and Genetic Perturbations with a New Computational Tool – ‘Dynamo’
BySwati Yadav February 14, 2022November 8, 2022
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…
Read More Predicting Cell Fates and Genetic Perturbations with a New Computational Tool – ‘Dynamo’
AI | Bioinformatics | Drug Discovery | News | Paper Summary | Structural Biology | Tools | Trending
Virtual Screening of Ultra-Large Chemical Libraries Accelerated up to 100-Fold with Artificial Intelligence Enabled ‘Deep Docking’
BySwati Yadav February 9, 2022October 22, 2026
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…
Read More Virtual Screening of Ultra-Large Chemical Libraries Accelerated up to 100-Fold with Artificial Intelligence Enabled ‘Deep Docking’
AI | Bioinformatics | Corona Virus | Machine Learning | News | Tools | Trending
Artificial Intelligence Model Predicts in Seconds How Two Proteins Will Bind in Real-Time
ByDr. Tamanna Anwar February 2, 2022June 18, 2022
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…
Read More Artificial Intelligence Model Predicts in Seconds How Two Proteins Will Bind in Real-Time
Bioinformatics | News | Paper Summary | RNA-Seq | Tools | Trending
CellRank: A Tool for Directed Single-Cell Fate Mapping
BySwati Yadav February 2, 2022November 8, 2022
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…
Read More CellRank: A Tool for Directed Single-Cell Fate Mapping
Bioinformatics | Deep Learning | Drug Discovery | News | Paper Summary | Tools | Trending
HyperAttentionDTI: Combining Sequence-Based Deep Learning with an Attention Mechanism for Drug-Protein Interaction Prediction
BySwati Yadav February 1, 2022October 22, 2026
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…
Read More HyperAttentionDTI: Combining Sequence-Based Deep Learning with an Attention Mechanism for Drug-Protein Interaction Prediction
Bioinformatics | Cancer Research | Data Science | News | Paper Summary | RNA-Seq | Sequencing | Tools | Trending
Expanding the View of how Mutations Impact Cells with a High-throughput Approach ‘Perturb-seq’
BySwati Yadav January 26, 2022September 8, 2022
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…
Read More Expanding the View of how Mutations Impact Cells with a High-throughput Approach ‘Perturb-seq’
Bioinformatics | Machine Learning | News | Structural Biology | Tools | Trending
Genome-Scale Protein Structure and Function Prediction with High-Performance Computing Toolkit
ByDr. Tamanna Anwar January 23, 2022November 4, 2022
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…
Read More Genome-Scale Protein Structure and Function Prediction with High-Performance Computing Toolkit
Bioinformatics | Genomics | News | OMICS | Tools
Multi-omics Data Visualization and Chromosomes Annotation with an R Package “ChromoMap”
ByDr. Tamanna Anwar January 14, 2022June 18, 2022
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…
Read More Multi-omics Data Visualization and Chromosomes Annotation with an R Package “ChromoMap”

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Simulating Directed Evolution With A New Computational Tool

Multi-omics Data Visualization and Chromosomes Annotation with an R Package “ChromoMap”

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