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
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Hyperbolic matrix factorization improves prediction of drug-target associations
- Scientific Reports
- VOL. 13
on Jan 18, 2023
- Research In Computational Biology
- Low Dimensional Euclidean Space
- Drug-target Interaction Prediction
- Numerical Optimization Techniques
- Euclidean Methods
- DTI
- More +
Connecting genomic islands across prokaryotic and phage genomes via protein families
- Scientific Reports
- VOL. 13
on Jan 7, 2023
- Computational Biology Research
- Prokaryotic Genomes
- GIs
- HGT
- Phage Genomes
- Bacterial Kingdom
- 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
The in silico lab: Improving academic code using lessons from biology
- Cell Systems
- VOL. 14
on Jan 1, 2023
- Computational Biology Research
- Improving Code Quality
- Rigorous Computer Science
- Good Code
- FAIR Practices
- Scientific Research Practices
- More +
"Good code" is often regarded as a nebulous, impractical ideal. Common best practices toward improving code quality can be inaccessible to those without a rigorous computer science or software engineering background, contributing to a gap between adv... Read More
Trade-off between conservation of biological variation and batch effect removal in deep generative modeling for single-cell transcriptomics
- BMC Bioinformatics
- VOL. 23
on Nov 3, 2022
- Researchers In Computational Biology
- Batch Effect Removal
- Batch Effect
- Pareto Front
- Deep Generative Model
- scRNA-seq Data
- More +
BackgroundSingle-cell RNA sequencing (scRNA-seq) technology has contributed significantly to diverse research areas in biology, from cancer to development. Since scRNA-seq data is high-dimensional, a common strategy is to learn low-dimensional latent... Read More
FPocketWeb: protein pocket hunting in a web browser
- Journal of Cheminformatics
- VOL. 14
on Aug 26, 2022
- Computational-biology Research
- Computer-aided Drug Discovery
- Web Browser
- Command-line Interface
- Remote Server
- Version Of App
- More +
Detecting macromolecular (e.g., protein) cavities where small molecules bind is an early step in computer-aided drug discovery. Multiple pocket-detection algorithms have been developed over the past several decades. Among them, fpocket, created by Sc... Read More
FPocketWeb: protein pocket hunting in a web browser.
- Journal of cheminformatics
- VOL. 14
on Aug 26, 2022
- Computational-biology Research
- Computer-aided Drug Discovery
- Web Browser
- Command-line Interface
- User's Computer
- Remote Server
- More +
Detecting macromolecular (e.g., protein) cavities where small molecules bind is an early step in computer-aided drug discovery. Multiple pocket-detection algorithms have been developed over the past several decades. Among them, fpocket, created by Sc... Read More
A survey of researchers’ code sharing and code reuse practices, and assessment of interactive notebook prototypes
- PeerJ
- VOL. 10
on Aug 22, 2022
- Researchers In Computational Biology
- PLOS Computational Biology
- Survey Of Researchers
- Gather Feedback
- Good Documentation
- Models For Funding
- More +
This research aimed to understand the needs and habits of researchers in relation to code sharing and reuse; gather feedback on prototype code notebooks created by NeuroLibre; and help determine strategies that publishers could use to increase code s... Read More
Microbiome, Metabolism, and Immunoregulation of Asthma: An American Thoracic Society and National Institute of Allergy and Infectious Diseases Workshop Report
- American Journal of Respiratory Cell and Molecular Biology
- VOL. 67
on Aug 1, 2022
- American Thoracic Society
- Pediatric Asthma Exacerbations
- Pathways In Asthma
- Heterogeneity In Asthma
- Function In Adipose Tissue
- Asthma Immunology
- More +
This report presents the proceedings from a workshop titled "Microbiome, Metabolism and Immunoregulation of Asthma" that was held virtually May 13 and 14, 2021. The workshop was jointly sponsored by the American Thoracic Society (Assembly on Allergy,... Read More
Michael Waterman's Contributions to Computational Biology and Bioinformatics
- Journal of Computational Biology
- VOL. 29
on Jul 1, 2022
- RECOMB
- Computational Biology
- Computational Bioinformatics
- Alignment-free Sequence Comparison
- Computational Genome Analysis
- Computational Molecular Biology
- More +
On the occasion of Dr. Michael Waterman's 80th birthday, we review his major contributions to the field of computational biology and bioinformatics including the famous Smith-Waterman algorithm for sequence alignment, the probability and statistics t... Read More
IFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets
- Nucleic Acids Research
- VOL. 50
on May 7, 2022
- Research In Computational Biology
- Ligand Data Sets
- Command Line Interface
- Molecular Data
- Largest Scope
- Research In Bioinformatics
- More +
Abstract The rapid accumulation of molecular data motivates development of innovative approaches to computationally characterize sequences, structures and functions of biological and chemical molecules in an efficient, accessible and a... Read More
PyProtModel: An easy to use GUI for comparative protein modeling
- Journal of Molecular Graphics and Modelling
- VOL. 112
on May 1, 2022
- Researchers In Computational Biology
- Knowledge In Bioinformatics
- 3D Structure
- User Expertise
- Extensive Knowledge
- MODELLER Software
- More +
A deep insight into the 3D structures of the proteins is essential to understand their functions and will be helpful in drug design and making decisions for the treatment of diseases. The 3D structure for less than one-thousandth of the protein seque... Read More
Data-Driven and Knowledge-Based Algorithms for Gene Network Reconstruction on High-Dimensional Data
- IEEE/ACM Transactions on Computational Biology and Bioinformatics
- VOL. 19
on May 1, 2022
- Gaussian Graphical Model Selection
- Gene Network Reconstruction
- Empirical Bayesian Approach
- Statistical Estimation Theory
- Gaussian Graphical Model
- Estimated Covariance Matrix
- More +
Previous efforts in gene network reconstruction have mainly focused on data-driven modeling, with little attention paid to knowledge-based approaches. Leveraging prior knowledge, however, is a promising paradigm that has been gaining momentum in netw... Read More
Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines
- Entropy
- VOL. 24
on Apr 29, 2022
- CG Model
- Static Crystal Structures
- ACLY
- Energy Profiles
- RBD
- Domain Of Spike Protein
- More +
Protein machines are clusters of protein assemblies that function in order to control the transfer of matter and energy in cells. For a specific protein machine, its working mechanisms are not only determined by the static crystal structures, but als... Read More
Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines.
- Entropy (Basel, Switzerland)
- VOL. 24
on Apr 29, 2022
- CG Model
- ACLY
- CG
- Static Crystal Structures
- Energy Profiles
- RBD
- More +
Protein machines are clusters of protein assemblies that function in order to control the transfer of matter and energy in cells. For a specific protein machine, its working mechanisms are not only determined by the static crystal structures, but als... Read More
Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field
- Journal of Chemical Theory and Computation
- VOL. 18
on Apr 1, 2022
- Experimental Hydration Free Energies
- Training Set Molecules
- CGenFF
- Hydration Free Energies
- Set Of LJ Parameters
- FF
- More +
The outcomes of computational chemistry and biology research, including drug design, are significantly influenced by the underlying force field (FF) used in molecular simulations. While improved FF accuracy may be achieved via inclusion of explicit t... Read More
Report of the ML4Microbiome workshop 2021 - Statistical and Machine Learning Techniques for Microbiome Data Analysis
- EMBnet.journal
- VOL. 27
on Mar 21, 2022
- Computational Biology Research
- Microbiome Data Analysis
- Statistical Learning Techniques
- COST Action
- Machine Learning Techniques
- Level Of Satisfaction
- More +
The bacteria living in and on us, over 100 trillion, are essential for human development, immunity and nutrition and ultimately for human health. Researchers awareness of the importance of the microbiome for human wellbeing brought in the latest deca... Read More
Classification of bursting patterns: A tale of two ducks
- PLOS Computational Biology
- VOL. 18
on Feb 24, 2022
- Research In Computational Biology
- Subthreshold Oscillations
- Larger Parameter Region
- Previous Classification Systems
- Folded-node Singularity
- Fast Subsystem
- More +
Bursting is one of the fundamental rhythms that excitable cells can generate either in response to incoming stimuli or intrinsically. It has been a topic of intense research in computational biology for several decades. The classification of bursting... Read More
Lessons from a ten-year-long journey: building a student-driven computational biology society across Turkey
- F1000Research
- VOL. 11
on Jan 26, 2022
- Researchers In Computational Biology
- ISCB
- Society In Turkey
- Computational Biology
- SC
- Bioinformatics Fields
- More +
The Regional Student Group Turkey (RSG-Turkey) is officially associated with the International Society for Computational Biology (ISCB) Student Council (SC). At the RSG-Turkey, we aim to contribute to the early-career researchers in computational bio... Read More
Pr[m]: An Algorithm for Protein Motif Discovery
- IEEE/ACM Transactions on Computational Biology and Bioinformatics
- VOL. 19
on Jan 1, 2022
- Researchers In Computational Biology
- Set Of Protein Sequences
- Wildcard Characters
- Motif Patterns
- Motif Discovery
- Protein Motif
- More +
Motifs are the evolutionarily conserved patterns which are reported to serve the crucial structural and functional role. Identification of motif patterns in a set of protein sequences has been a prime concern for researchers in computational biology.... Read More
Lessons from a ten-year-long journey: building a student-driven computational biology society across Turkey.
- F1000Research
- VOL. 11
on Jan 1, 2022
- Researchers In Computational Biology
- ISCB
- Society In Turkey
- Computational Biology
- Long-standing Community
- SC
- More +
The Regional Student Group Turkey (RSG-Turkey) is officially associated with the International Society for Computational Biology (ISCB) Student Council (SC). At the RSG-Turkey, we aim to contribute to the early-career researchers in computational bio... Read More