Drug repositioning aims to discover novel clinical benefits of existing drugs, is an effective way to develop drugs for complex diseases such as cancer and may facilitate the process of traditional drug development. Meanwhile, network-based computati... Read More
Computational Biology Research Articles
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Guiding Drug Repositioning for Cancers Based on Drug Similarity Networks
- International Journal of Molecular Sciences
- VOL. 24
on Jan 23, 2023
- Prognosis Of NSCLC
- Drug Similarity Network
- NSCLC
- Cancer-related Pathways
- Network-based Computational Approaches
- Drug Repurposing
- More +
Geometric analysis enables biological insight from complex non-identifiable models using simple surrogates
- PLOS Computational Biology
- VOL. 19
on Jan 20, 2023
- Computational Biology
- Non-identifiable Parameters
- Map In Parameter Space
- Identifiable Parameter Combinations
- Gompertz Growth Models
- Surrogate Model
- More +
An enduring challenge in computational biology is to balance data quality and quantity with model complexity. Tools such as identifiability analysis and information criterion have been developed to harmonise this juxtaposition, yet cannot always reso... Read More
PGAGP: Predicting pathogenic genes based on adaptive network embedding algorithm
- Frontiers in Genetics
- VOL. 13
on Jan 20, 2023
- Gaussian Random Projection
- Field Of Computational Biology
- Heterogeneous Network
- Features Of Nodes
- Meaningful Task
- Low-dimensional Features
- More +
The study of disease-gene associations is an important topic in the field of computational biology. The accumulation of massive amounts of biomedical data provides new possibilities for exploring potential relations between diseases and genes through... Read More
Female Dynamics in Authorship of Scientific Publications in the Public Library of Science: A 10-year Bibliometric Analysis of Biomedical Research
- European Journal of Investigation in Health, Psychology and Education
- VOL. 13
on Jan 20, 2023
- PLoS Computational Biology
- Proportion Of Female First Authors
- PLoS Journals
- Authorship Of Scientific Publications
- Gender Of Authors
- PLoS Pathogens
- More +
Women are generally underrepresented in science, technology, engineering, and mathematics (STEM). As scientific production reflects scholarly impact and participation in the scientific process, the number of journal publications forms a pertinent mea... Read More
Hyperbolic matrix factorization improves prediction of drug-target associations
- Scientific Reports
- VOL. 13
on Jan 18, 2023
- Low Dimensional Euclidean Space
- Drug-target Interaction Prediction
- Numerical Optimization Techniques
- Euclidean Methods
- DTI
- Geometry Of Space
- More +
Past research in computational systems biology has focused more on the development and applications of advanced statistical and numerical optimization techniques and much less on understanding the geometry of the biological space. By representing bio... Read More
Learning the structure of the mTOR protein signaling pathway from protein phosphorylation data
- Journal of Applied Statistics
- VOL. ahead-of-print
on Jan 18, 2023
- Computational Biology
- Protein Phosphorylation Data
- Network Reconstruction Methods
- Data Imputation Methods
- Computational Systems Biology
- Protein Signaling Pathway
- More +
Statistical learning of the structures of cellular networks, such as protein signaling pathways, is a topical research field in computational systems biology. To get the most information out of experimental data, it is often required to develop a tai... Read More
Advancing our knowledge of antigen processing with computational modelling, structural biology, and immunology
- Biochemical Society Transactions
on Jan 16, 2023
- Antigen Processing
- Antigen Processing Pathway
- MHC-I Pathway
- Intracellular Peptides
- Cell Vaccines
- Machine Learning Techniques
- More +
Antigen processing is an immunological mechanism by which intracellular peptides are transported to the cell surface while bound to Major Histocompatibility Complex molecules, where they can be surveyed by circulating CD8+ or CD4+ T-cells, potentiall... Read More
GPCR Allostery: a View from Computational Biology
- Current Medicinal Chemistry
- VOL. 30
on Jan 13, 2023
- Computational Biology
- GPCR
- Conformational Dynamics
- Protein-coupled Receptor
- Current Limitations
- Pathological Processes
- More +
Abstract: G protein-coupled receptors (GPCRs) represent a large superfamily of cell-surface proteins that mediate cell signaling and regulate virtually various aspects of physiological and pathological processes, therefore serving as a rich source o... Read More
Discovering untapped microbial communities through metagenomics for microplastic remediation: recent advances, challenges, and way forward
- Environmental Science and Pollution Research
on Jan 13, 2023
- Computational Biology
- MP
- Role Of MGs
- MGs
- MP Accumulation
- Prediction Of Genes
- More +
Microplastics (MPs) are ubiquitous pollutants persisting almost everywhere in the environment. With the increase in anthropogenic activities, MP accumulation is increasing enormously in aquatic, marine, and terrestrial ecosystems. Owing to the slow d... Read More
Sherlock: an open-source data platform to store, analyze and integrate Big Data for computational biologists
- F1000Research
- VOL. 10
on Jan 12, 2023
- JSON
- Specific File Formats
- Big Data
- Era Of Big Data
- Big Data Technologies
- Expression Databases
- More +
In the era of Big Data, data collection underpins biological research more than ever before. In many cases, this can be as time-consuming as the analysis itself. It requires downloading multiple public databases with various data structures, and in g... Read More
ISCB Student Council Symposium 2021, a virtual global venue: challenges and lessons learned
- F1000Research
- VOL. 12
on Jan 12, 2023
- Computational Biologists
- ISCB Student Council
- SCS
- Student Council
- COVID-19
- Pandemic Situation
- More +
Since 2004, the ISCB Student Council has been organizing different symposia worldwide, gathering together the community of young computational biologists. Due to the coronavirus disease 2019 (COVID-19) pandemic situation, the world scientific communi... Read More
Understanding respiratory microbiome–immune system interactions in health and disease
- Science Translational Medicine
- VOL. 15
on Jan 11, 2023
- Computational Biology
- Immune System In Early Life
- System In Early Life
- Early Life Colonization
- Maturing Immune System
- Respiratory Microbiome
- More +
Interactions between the developing microbiome and maturing immune system in early life are critical for establishment of a homeostasis beneficial to both host and commensals. The lung harbors a diverse community of microbes associated with health an... Read More
Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes
- Annual Review of Biophysics
- VOL. 52
on Jan 10, 2023
- Protein Structure Prediction Field
- Experimental Structural Biology
- Structure Prediction Field
- Modeling Of Complexes
- Blind Experiments
- Deep Learning Methods
- More +
Advances in a scientific discipline are often measured by small, incremental steps. In this review, we report on two intertwined disciplines in the protein structure prediction field, modeling of single chains and modeling of complexes, that have ov... Read More
Deciphering the interaction mechanism of natural actives against larval proteins of Aedes aegypti to identify potential larvicides: a computational biology analysis
- Journal of Biomolecular Structure and Dynamics
- VOL. ahead-of-print
on Jan 10, 2023
- Larval Proteins
- Toxicity Estimation Software Tool
- Potential Larvicides
- Molecular Mechanisms Of Interactions
- Natural Larvicides
- Computational Insights
- More +
Aedes aegypti is the target for repellents to curb incidences of vector-borne diseases. Stopping breeding of this mosquito species at its larval stages helps in controlling spread of insect-borne diseases. Therefore, the present study focused on de... Read More
Connecting genomic islands across prokaryotic and phage genomes via protein families
- Scientific Reports
- VOL. 13
on Jan 7, 2023
- Prokaryotic Genomes
- GIs
- HGT
- Phage Genomes
- Bacterial Kingdom
- Biological Connections
- More +
Prokaryotic genomes evolve via horizontal gene transfer (HGT), mutations, and rearrangements. A noteworthy part of the HGT process is facilitated by genomic islands (GIs). While previous computational biology research has focused on developing tools ... Read More
After a Century of Research into Environmental Mutagens and Carcinogens, Where Do We Stand?
- International Journal of Environmental Research and Public Health
- VOL. 20
on Jan 6, 2023
- Computational Biology
- High-throughput Toxicology
- Impact Risk Assessment
- Mutagenic Pollutants
- Percentage Of Neoplasms
- Environmental Mutagens
- More +
Cancer is one of the longest-known human diseases, yet only in recent times have we begun to perceive that the percentage of neoplasms caused by environmental factors, lifestyle and chemicals, is likely underestimated. The first medical reports assoc... Read More
Challenges in predicting stabilizing variations: An exploration
- Frontiers in Molecular Biosciences
- VOL. 9
on Jan 5, 2023
- Computational Biology
- Abundant Class
- Experimental Biology
- Wild-type Form
- Input Features
- Protein Stability
- More +
An open challenge of computational and experimental biology is understanding the impact of non-synonymous DNA variations on protein function and, subsequently, human health. The effects of these variants on protein stability can be measured as the di... Read More
Ten simple rules for defining a computational biology project
- PLOS Computational Biology
- VOL. 19
on Jan 5, 2023
- Computational Biology
- Computational Project
- Simple Rules
Single-cell computational machine learning approaches to immune-mediated inflammatory disease: New tools uncover novel fibroblast and macrophage interactions driving pathogenesis
- Frontiers in Immunology
- VOL. 13
on Jan 4, 2023
- Computational Techniques
- Computational Biology Techniques
- Cell Types In Tissues
- Cross-tissue Analysis
- Immune-mediated Inflammatory Disease
- Trajectory Inference
- More +
Recent advances in single-cell sequencing technologies call for greater computational scalability and sensitivity to analytically decompose diseased tissues and expose meaningful biological relevance in individual cells with high resolution. And whil... Read More
Metabolic reprogramming and its clinical implication for liver cancer.
- Hepatology (Baltimore, Md.)
on Jan 3, 2023
- NAFLD
- Metabolic Reprogramming
- Alterations In HCC
- Generation Of Lactate
- Liver Cancer
- HCC
- More +
Cancer cells often encounter hypoxic and hypo-nutrient conditions, which force them to make adaptive changes to meet their high demands for energy and various biomaterials for biomass synthesis. As a result, enhanced catabolism (breakdown of macromol... Read More