Search Results - "computational biology/methods"

Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics

Authors: Jones, Christopher Hallin, Sara Sveriges lantbruksuniversitet, Originator

Contributors: Jones, Christopher Hallin, Sara Sveriges lantbruksuniversitet, Originator

Source: ISME Communications. 5

Subject Terms: Microbiology, Mikrobiologi, Bioinformatics and Computational Biology (Methods development to be 10203), Bioinformatik och beräkningsbiologi (Metodutveckling under 10203)

Access URL: https://res.slu.se/id/publ/144795
https://pub.epsilon.slu.se/id/eprint/38952/contents

Making Sense of Missense: Benchmarking MutScore for Variant Interpretation in Inherited Cardiac Diseases

Authors: Alessandra Pia Porretta Véronique Fressart Elodie Surget et al.

Source: Mol Diagn Ther
Molecular diagnosis & therapy, vol. 29, no. 4, pp. 539-552

Subject Terms: Original Research Article, Humans, Mutation, Missense, Heart Diseases/genetics, Heart Diseases/diagnosis, Computational Biology/methods, Genetic Predisposition to Disease, Male, Benchmarking, Retrospective Studies, Female, Genetic Testing

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/40397311
http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_989C4B2B208D3
https://serval.unil.ch/resource/serval:BIB_989C4B2B208D.P001/REF.pdf
https://serval.unil.ch/notice/serval:BIB_989C4B2B208D

Benchmarking scRNA-seq copy number variation callers

Authors: Schmid, Katharina T Symeonidi, Aikaterini Hlushchenko, Dmytro et al.

Source: Nature Communications. 16(1)

Subject Terms: Benchmarking, Single-Cell Analysis/methods, Humans, DNA Copy Number Variations/genetics, RNA-Seq/methods, Computational Biology/methods, Neoplasms/genetics, Single-Cell Gene Expression Analysis

Access URL: https://research.rug.nl/en/publications/e0d47017-c370-4bf5-abd0-8854923f8733
https://hdl.handle.net/11370/e0d47017-c370-4bf5-abd0-8854923f8733

The Harmonic Model:First Principles Theory of Everything

Authors: Sowersby, Scott

Subject Terms: Volition, Electric, Electric vehicles, Photons/history, Computational Biology/history, Math, Quarks, Crystal Arthropathies/etiology, Atomic, Microscopy, Atomic Force/trends, Mathematical model, Absorptiometry, Photon, Crystal Arthropathies/blood, Nuclear Reactors, Mathematics/economics, Chromium Isotopes, Phonons/classification, Raphe Nuclei/abnormalities, Silicon/analysis, Electric Organ, Higgs bosons, Electric power generation, Computational Biology/instrumentation, Particle accelerator, Computational Biology/education, Music Therapy/ethics, Volition/physiology, Electric Injuries, Silicon/poisoning, Computational Biology/trends, Phonons/history, Septal Nuclei/cytology, Protons, Cerebellar Nuclei/microbiology, Calcium Isotopes, Music Therapy/classification, Crystal Arthropathies/classification, Microscopy, Atomic Force/classification, Music Therapy/education, Spectrophotometry, Atomic/history, Physics/instrumentation, Computational Chemistry/education, FOS: Electrical engineering, electronic engineering, information engineering, Crystal Arthropathies/mortality, Lactic Acid, Cerebellar Nuclei/physiology, Particle Physics, Computational Biology/classification, Particle separator, Heat (physics), Physics/education, Computational Biology, Music Therapy/instrumentation, Models, Theoretical, Vestibular Nuclei, Acidosis, Lactic/classification, Cerebellar Nuclei/virology, Raphe Nuclei/chemistry, Electric batteries, Ringer's Solution, Computational neuroscience, Music/psychology, Silicon/standards, Isotopes/poisoning, Particle Accelerators, Mathematics/ethics, Health Physics, Photons/adverse effects, Music Therapy/trends, Music Therapy/economics, Protons/history, Electric vehicle, Computational Chemistry/instrumentation, Z bosons, Soliton, Music Therapy/methods, Photons/classification, Crystal Arthropathies/nursing, Spectrophotometry, Atomic/economics, Solar physics, Isotopes/history, Music/history, Mathematical method, Raphe Nuclei/physiopathology, Isotope, Crystal Arthropathies/parasitology, Discrete mathematics, Alpha Particles, Computational Chemistry/history, Quantum field theory, Beyond the Standard Model, Cerebellar Nuclei, Computational Chemistry/ethics, Crystal Arthropathies/enzymology, Computational Biology/ethics, Computational Chemistry/standards, Zinc Isotopes, Theoretical physics, Microscopy, Atomic Force/ethics, Isotopes/agonists, Silicon, Crystal Arthropathies/therapy, Submitochondrial Particles, Atomic Bomb Survivors/history, Surgical Attire, Nuclear, Photons/therapeutic use, Fermions, Music Therapy, Phonons/therapeutic use, Mathematics/trends, Lattice, Electric Conductivity, W bosons, Applied mathematics, Atomic Bomb Survivors, Elementary Particle Interactions, Isotopes/analysis, Transport (physics), Mesoscopic physics, Potassium Isotopes, Electric Fish, Acidosis, Lactic/complications, Electric energy, Music Therapy/history, Crystal Arthropathies, Computational Chemistry/methods, Quantum physics, Crystal Arthropathies/pathology, Microscopy, Atomic Force, Signal Recognition Particle/biosynthesis, Computational topology, Phonons/adverse effects, Crystal Arthropathies/urine, Mathematical Computing, Crystal Arthropathies/microbiology, Microscopy, Atomic Force/standards, Mesons, Spectrophotometry, Atomic/classification, Burns, Electric/complications, Particle Accelerators/history, Physics, Particle physics, Burns, Electric, Crystal Arthropathies/psychology, Computational Chemistry/trends, Particle Accelerators/economics, Mathematics/education, Spectrophotometry, Atomic/veterinary, Mathematical physics, Thalamic Nuclei, Grand Unification Theory, Septal Nuclei/parasitology, Crystal Arthropathies/virology, Spectrophotometry, Atomic/trends, Popular music studies, Saline Solution, Music Therapy/legislation & jurisprudence, Trigeminal Nuclei/abnormalities, Elementary Particles, Particle Accelerators/classification, Crystal Arthropathies/epidemiology, Trigeminal Nuclei/cytology, Electric Countershock, Spectrophotometry, Atomic/standards, Electric Capacitance, Isotopes/pharmacology, Spectrophotometry, Atomic/instrumentation, FOS: Mathematics, Crystal Arthropathies/diagnosis, Electrical engineering, electronic engineering, information engineering, Particle Size, Computational intelligence, Crystal Arthropathies/immunology, Spectrophotometry, Atomic/methods, Computational, Pure mathematics, Phosphorus Isotopes, Mathematical Concepts, Computational Biology/methods, Crystal Arthropathies/surgery, Electric Stimulation, Beta Particles, Laser physics, Electric line, Music Therapy/statistics & numerical data, Signal Recognition Particle, Mathematics, Particle Accelerators/instrumentation, Silicon/toxicity, Isotopes/chemistry, Protons/classification, Computational creativity, Protons/adverse effects, Nuclear physics, Particle, Cerebellar Nuclei/ultrastructure, Computational fluid dynamics, Electric battery, Single particle characterisation, Trigeminal Nuclei, Isotopes/immunology, Isotopes/standards, Computational Chemistry, Isotopes, Iodine Isotopes, Crystal, Electric Impedance, Atomic Bomb Survivors/classification, Theory of Everything, Gallium Isotopes, Septal Nuclei/immunology, Raphe Nuclei/pathology, Computational science, Solid particle, Music Therapy/organization & administration, Iron Isotopes, Electric power, Cobalt Isotopes, Physics/methods, Spectrophotometry, Atomic/ethics, Phonons, Acidosis, Lactic, Computational Biology/organization & administration, Electric Wiring, Cerebellar Nuclei/surgery, Silicon/urine, Mathematical analysis, Gold Isotopes, Crystals, Atomic physics, Plasma physics, Mathematics/standards, Crystal Arthropathies/metabolism, Computational Chemistry/classification, Music Therapy/standards, Mathematics/history, Particle Accelerators/standards, Photons, Computational Biology/economics, Spectrophotometry, Atomic, Volition/classification, Silicon/metabolism, Physics/standards, Leptons, Nuclei, Computational Chemistry/economics, Microscopy, Atomic Force/instrumentation, Mathematical logic, Raphe Nuclei, Septal Nuclei, Mathematics/classification, Music

Pathway Realizability in Chemical Networks

Authors: Jakob L. Andersen Sissel Banke Rolf Fagerberg et al.

Source: Journal of Computational Biology. 32:164-187

Subject Terms: 104027 Computational chemistry, FOS: Computer and information sciences, Discrete Mathematics (cs.DM), 104022 Theoretical chemistry, Molecular Networks (q-bio.MN), pentose phosphate pathway, cheminformatics, Computational Biology, Petri net, Computational Biology/methods, Biological, Models, Biological, 104027 Computational Chemistry, Pentose Phosphate Pathway, 104022 Theoretische Chemie, Models, FOS: Biological sciences, chemical reaction network, directed multi-hypergraph, Quantitative Biology - Molecular Networks, Metabolic Networks and Pathways, Algorithms, Computer Science - Discrete Mathematics

Access URL: https://pubmed.ncbi.nlm.nih.gov/39899362
http://arxiv.org/abs/2309.10629
https://ucrisportal.univie.ac.at/de/publications/20918760-cfa2-43c2-9bed-889d642fb20c
https://doi.org/10.1089/cmb.2024.0521
https://portal.findresearcher.sdu.dk/da/publications/417ecefc-7648-4472-9903-254204ab8031
https://doi.org/10.1089/cmb.2024.0521

Stacked Graph Attention Network With Temporal Modeling for lncRNA-miRNA Association Network

Authors: Rizvi, Ahsan Zaigam Sveriges lantbruksuniversitet, Originator

Contributors: Rizvi, Ahsan Zaigam Sveriges lantbruksuniversitet, Originator

Source: IEEE transactions on computational biology and bioinformatics. 22:2216-2229

Subject Terms: Bioinformatics and Computational Biology (Methods development to be 10203), Bioinformatik och beräkningsbiologi (Metodutveckling under 10203)

Access URL: https://res.slu.se/id/publ/144449

Identification of malignant cells in single-cell transcriptomics data

Authors: Andreatta, Massimo Garnica Caparros, Josep Carmona, Santiago

Source: Communications Biology. 8

Subject Terms: Gene Expression Profiling / methods, Gene Expression Regulation, Neoplastic, Biomarkers, Tumor / genetics, Computational Biology / methods, Neoplasms / pathology, DNA Copy Number Variations, Single-Cell Analysis / methods, Humans, 616.07, Neoplasms / genetics, Transcriptome

File Description: application/pdf

Access URL: https://archive-ouverte.unige.ch/unige:187363
https://doi.org/10.1038/s42003-025-08695-4

Seasonal variability of the rumen microbiome in indigenous African cattle: a bioinformatics approach : from pasture to pathways

Authors: Van Damme, Renaud Sveriges lantbruksuniversitet, Originator

Contributors: Van Damme, Renaud Sveriges lantbruksuniversitet, Originator

Source: Acta Universitatis Agriculturae Sueciae.

Subject Terms: Microbiology, Mikrobiologi, Bioinformatics (Computational Biology), Bioinformatik (beräkningsbiologi), Bioinformatics and Computational Biology (Methods development to be 10203), Bioinformatik och beräkningsbiologi (Metodutveckling under 10203)

Access URL: https://res.slu.se/id/publ/142461
https://pub.epsilon.slu.se/id/eprint/38162/contents

Ouroboros: cross-linking protein expression perturbations and cancer histology imaging with generative-predictive modeling: cross-linking protein expression perturbations and cancer histology imaging with generative-predictive modeling

Authors: Srijay Deshpande Sokratia Georgaka Michael Haley et al.

Source: Bioinformatics
Deshpande, S, Georgaka, S, Haley, M, Sellers, R, Minshull, J, Nallala, J, Fergie, M, Stone, N, Rajpoot, N, Baker, S M, Iqbal, M, Couper, K, Roncaroli, F & Minhas, F 2024, 'Ouroboros : cross-linking protein expression perturbations and cancer histology imaging with generative-predictive modeling', Bioinformatics (Oxford, England), vol. 40, no. Supplement_2, pp. ii174-ii181. https://doi.org/10.1093/bioinformatics/btae399

Subject Terms: Image Processing, Computer-Assisted/methods, Brain Neoplasms, Image Processing, Computer-Assisted/methods, Image Processing, Computer-Assisted, Digital Health, Humans, Computational Biology, Glioblastoma/metabolism, Computational Biology/methods, Glioblastoma, Brain Neoplasms/metabolism

Access URL: https://pubmed.ncbi.nlm.nih.gov/39230703
https://research.manchester.ac.uk/en/publications/d62fb1d8-c128-4302-8650-a7e47eb66d08
https://doi.org/10.1093/bioinformatics/btae399
https://research.manchester.ac.uk/en/publications/d62fb1d8-c128-4302-8650-a7e47eb66d08
http://www.scopus.com/inward/record.url?scp=85203168010&partnerID=8YFLogxK
https://doi.org/10.1093/bioinformatics/btae399

RNA dynamics from experimental and computational approaches

Authors: Bussi, Giovanni Bonomi, Massimiliano Gkeka, Paraskevi et al.

Contributors: Bussi, Giovanni Bonomi, Massimiliano Gkeka, Paraskevi et al.

Source: Structure

Subject Terms: 0301 basic medicine, 0303 health sciences, FOS: Physical sciences, Biomolecules (q-bio.BM), Molecular Dynamics Simulation, Computational Biology/methods, RNA/metabolism, 3. Good health, [SDV] Life Sciences [q-bio], 03 medical and health sciences, Quantitative Biology - Biomolecules, Biological Physics (physics.bio-ph), FOS: Biological sciences, Nucleic Acid Conformation, Humans, Physics - Biological Physics

File Description: application/pdf

Access URL: http://arxiv.org/abs/2404.02789
https://cnrs.hal.science/hal-04781704v1
https://doi.org/10.1016/j.str.2024.07.019
https://cnrs.hal.science/hal-04781704v1/document

Innovative construction of the first reliable catalogue of bovine circular RNAs

Authors: Robic, Annie Hadlich, Frieder Costa Monteiro Moreira, Gabriel et al.

Contributors: Robic, Annie Hadlich, Frieder Costa Monteiro Moreira, Gabriel et al.

Source: RNA Biol
RNA Biology, Vol 21, Iss 1, Pp 716-738 (2024)

Subject Terms: lariat-derived circRNA, [SDV]Life Sciences [q-bio], circular transcriptome, Genetics & genetic processes, bovine circRNAs, Sequence Analysis, RNA/methods, QH426-470, intron circle, Génétique & processus génétiques, Genetics, Animals, Molecular Biology, artificial annotation, Sequence Analysis, RNA, Gene Expression Profiling, Computational Biology, Cell Biology, RNA, Circular, Exons, Computational Biology/methods, Life sciences, artificial circRNA, Introns, 3. Good health, [SDV] Life Sciences [q-bio], RNA, Circular/genetics, Exonic circRNA, backsplicing, Sciences du vivant, Cattle, Gene Expression Profiling/methods, Transcriptome, Research Paper

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/38989833
https://doaj.org/article/eb86ff58292c434c83d3a7ca3858587e

Annotation matters: the effect of structural gene annotation on orthology inference

Authors: Silvia Prieto-Baños Yannis Nevers Adrian Altenhoff et al.

Source: Bioinformatics
Bioinformatics, vol. 41, no. 7
Bioinformatics, 41 (7)

Subject Terms: Original Paper, Molecular Sequence Annotation/methods, Genomics/methods, Databases, Genetic, Genome, Computational Biology/methods

File Description: application/pdf; application/application/pdf

Access URL: http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_1F0C64C7E8640
https://serval.unil.ch/resource/serval:BIB_1F0C64C7E864.P001/REF.pdf
https://serval.unil.ch/notice/serval:BIB_1F0C64C7E864
http://hdl.handle.net/20.500.11850/746800

Federated SPARQL query performance evaluation for exploring disease model mouse: combining gene expression, orthology, and disease knowledge graphs

Authors: Tatsuya Kushida Tarcisio Mendes de Farias Ana C. Sima et al.

Source: BMC Med Inform Decis Mak
BMC Medical Informatics and Decision Making, Vol 25, Iss S1, Pp 1-1 (2025)
BMC medical informatics and decision making, vol. 25, no. Suppl 1, pp. 189

Subject Terms: Knowledge graph, Model organism, Ontology, Research, Animals, Mice, Databases, Genetic, Disease Models, Animal, Humans, Computational Biology/methods, Gene Expression, Database integration, Gene expression, Gene-disease association, Orthology, RDF, SPARQL, Computer applications to medicine. Medical informatics, R858-859.7, Computational Biology

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/40380154
https://doaj.org/article/cfee2c8ffa1e4b5db6df712db840b986
http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_1466DAB257644
https://serval.unil.ch/resource/serval:BIB_1466DAB25764.P001/REF.pdf
https://serval.unil.ch/notice/serval:BIB_1466DAB25764

An algorithmic perspective on deciphering cell–cell interactions with spatial omics data

Authors: van Santvoort, Mike Eduati, Federica

Source: Brief Bioinform

Subject Terms: spatial data, spatial omics, Humans, Cluster Analysis, cell–cell interaction modeling, statistical correlation, Cell Communication, Review, Computational Biology/methods, optimization, supervised learning, Algorithms

Ranking Protein–Protein Models with Large Language Models and Graph Neural Networks

Authors: Xu, Xiaotong Bonvin, Alexandre M J J

Source: Methods in Molecular Biology ISBN: 9781071646229

Subject Terms: Protein Interaction Mapping/methods, FOS: Computer and information sciences, Neural Networks, Protein Conformation, Computer Science - Artificial Intelligence, Molecular, Biomolecules (q-bio.BM), Computational Biology/methods, 3. Good health, Computer, Deep Learning, Large Language Models, Artificial Intelligence (cs.AI), SDG 3 - Good Health and Well-being, Quantitative Biology - Biomolecules, Models, FOS: Biological sciences, Humans, Graph Neural Networks, Protein Interaction Maps, Algorithms, Software, Proteins/chemistry

Access URL: http://arxiv.org/abs/2407.16375

Critical assessment of missense variant effect predictors on disease-relevant variant data

Authors: Ruchir Rastogi Ryan Chung Sindy Li et al.

Contributors: Ruchir Rastogi Ryan Chung Sindy Li et al.

Source: Hum Genet

Subject Terms: Gene Frequency, Mutation, Missense/genetics, Databases, Genetic, Mutation, Missense, Humans, Computational Biology, Genetic Predisposition to Disease, disease-relevant variant data, missense variant effect predictors, CAGI, Computational Biology/methods, ddc, Original Investigation, 3. Good health

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/40113603
https://pubmed.ncbi.nlm.nih.gov/38895200
https://biblio.vub.ac.be/vubir/critical-assessment-of-missense-variant-effect-predictors-on-diseaserelevant-variant-data(633006a4-aa1b-48c9-b84f-8c9838272f93).html
https://hdl.handle.net/11585/1016063
https://doi.org/10.1007/s00439-025-02732-2
https://mediatum.ub.tum.de/1792170

Graph machine learning for integrated multi-omics analysis

Authors: Nektarios A. Valous Ferdinand Popp Inka Zörnig et al.

Source: Br J Cancer

Subject Terms: Machine Learning, Proteomics, 0301 basic medicine, 0303 health sciences, 03 medical and health sciences, Neoplasms, Perspective, Humans, Computational Biology, Genomics, Neural Networks, Computer, Multiomics, Proteomics/methods [MeSH], Multiomics [MeSH], 639/705/1042, Humans [MeSH], perspective, Machine Learning [MeSH], Genomics/methods [MeSH], Neoplasms/genetics [MeSH], Neural Networks, Computer [MeSH], 631/114/2401, Computational Biology/methods [MeSH]

Access URL: https://pubmed.ncbi.nlm.nih.gov/38729996
https://repository.publisso.de/resource/frl:6501144

Variant effect predictors: a systematic review and practical guide

Authors: Cristian Riccio Max L. Jansen Linlin Guo et al.

Source: Hum Genet
Humangenetik, 143(5):625-634

Subject Terms: 0301 basic medicine, 0303 health sciences, 03 medical and health sciences, Phenotype, Databases, Genetic, Humans, Computational Biology, Genetic Variation, Review, Genome-Wide Association Study/methods [MeSH], Humans [MeSH], Software [MeSH], Databases, Genetic [MeSH], Phenotype [MeSH], Genetic Variation [MeSH], Computational Biology/methods [MeSH], Software, Genome-Wide Association Study

Access URL: https://pubmed.ncbi.nlm.nih.gov/38573379
https://repository.publisso.de/resource/frl:6499675

Experimental capture of miRNA targetomes: disease-specific 3′UTR library-based miRNA targetomics for Parkinson’s disease

Authors: Martin Hart Fabian Kern Claudia Fecher-Trost et al.

Source: Exp Mol Med
Experimental and Molecular Medicine, Vol 56, Iss 4, Pp 935-945 (2024)

Subject Terms: ddc:610, Parkinson's disease, 13/89, 631/337/384/331, Parkinson Disease/metabolism [MeSH], Humans [MeSH], 13/106, 692/699/375/1718, Parkinson Disease/genetics [MeSH], Article, Gene Regulatory Networks [MeSH], 82/1, 82/29, Gene Library [MeSH], 631/80/86, Gene Expression Regulation [MeSH], MicroRNAs/genetics [MeSH], 3' Untranslated Regions [MeSH], article, Computational Biology/methods [MeSH], Computational Biology, Parkinson Disease, QD415-436, Biochemistry, MicroRNAs, Gene Expression Regulation, miRNAs, Medicine, Humans, Gene Regulatory Networks, 3' Untranslated Regions, Gene Library, Cell signalling

Access URL: https://pubmed.ncbi.nlm.nih.gov/38556547
https://doaj.org/article/3efe0c622e26455595bea061ca0cb9f0
https://repository.publisso.de/resource/frl:6503022

Quantum Neuro Cells – Neuro-Quantum Integration Dataset & Framework

Authors: Mohamed, Anwar

Subject Terms: Artificial intelligence, Regenerative Medicine/ethics, Psychopharmacology, Psychopharmacology/standards, Quantum physics, Quantum Biology, Artificial Intelligence/standards, Systems Biology/economics, Regenerative Medicine, Psychopharmacology/education, Psychopharmacology/classification, Cognitive Neuroscience/education, Quantum Physics, Neurosciences/classification, Artificial Intelligence/ethics, Systems Biology, Psychopharmacology/trends, Cognitive Neuroscience/ethics, Computational Biology/trends, Computational Biology/ethics, Regenerative Medicine/economics, Computational Biology/standards, Quantum Dots/virology, Neurosciences/standards, Regenerative Medicine/methods, Cognitive Neuroscience, Neurotechnology, FOS: Physical sciences, Molecular neuroscience, Artificial Intelligence, Artificial Intelligence/trends, Bioelectric Medicine, Systems Biology/ethics, Psychopharmacology/ethics, Computational Biology/classification, FOS: Clinical medicine, Neurosciences, Systems Biology/classification, Computational Biology, Regenerative Medicine/classification, Cognitive neuroscience, Systems Biology/trends, Computational Biology/methods, Neurosciences/methods, Immune System/virology, Regenerative Medicine/education, Computational neuroscience, Regenerative Medicine/trends, Neurosciences/trends, Neuroscience, Psychopharmacology/methods