Search Results - "Systems Biology methods"

Conditional universal differential equations capture population dynamics and interindividual variation in c-peptide production

Authors: de Rooij, Max van Riel, Natal A. W. O’Donovan, Shauna D.

Source: npj Systems Biology and Applications. 11

Subject Terms: Machine Learning, Computer, Type 2/metabolism, Neural Networks, SDG 3 - Good Health and Well-being, Systems Biology/methods, Models, Diabetes Mellitus, Humans, Biological, SDG 3 – Goede gezondheid en welzijn, C-Peptide/biosynthesis, Glucose Intolerance/blood

Access URL: https://research.tue.nl/en/publications/26617f97-c1ad-4149-ba1b-eb8bcaa9e2dd
https://doi.org/10.1038/s41540-025-00570-6
https://pure.amsterdamumc.nl/en/publications/d45be129-8c29-40ae-8eda-c54ec209de12
https://doi.org/10.1038/s41540-025-00570-6

GcMAF, Nagalase Suppression & Fibrin Reduction – A Quantum Oncology OS Expansion

Authors: Mohamed, Anwar

Subject Terms: Tumor Microenvironment/genetics, Clinical Integrative Medicine, Tumor Microenvironment/physiology, Sublingual Immunotherapy/trends, GcMAF, Immunotherapy/standards, Exosomes, Medical Oncology, Tumour Microenvironment, Immunotherapy, Adoptive, Clinical Trial Protocols as Topic, Fibrin/standards, Clinical Protocols, Molecular Chaperones/immunology, Fibrin/immunology, Tumor Microenvironment, Immune Evasion/drug effects, Vision, Monocular/immunology, PEMF, Heparin, Low-Molecular-Weight/immunology, Systems Biology, Clinical Protocols/standards, Nagalase, Redox Medicine, Immunotherapy/classification, Exosomes/immunology, Tumor Microenvironment/drug effects, Fibrin/chemistry, EZ Water, Biofield Science, Exposome, Scalar Fields, CD68 Molecule/immunology, Tumour Holography, Oncology, Quantum Oncology, Cardio-Oncology, Structured Water, Systems Biology/standards, Immunotherapy, Fibrin/pharmacokinetics, Exosomes/physiology, Kininogen, Low-Molecular-Weight/immunology, Molecular Immunology, Integrative Oncology/standards, Systems Biology/methods, Psycho-Oncology, Immunotherapy/psychology, TRPV Cation Channels, Fourth Phase Water, Fibrin/metabolism, Fibrin/physiology, Immunotherapy/ethics, ECS Therapeutics, Tumor Microenvironment/immunology, Integrative Oncology, Cancer Stealth, Systems Biology/education, Immune Evasion/immunology, Exosomes/genetics, Exosomes/classification, Bioelectric Medicine, Systems Biology/ethics, Immune Evasion, Fibrin, Immune Evasion/genetics, Sublingual Immunotherapy, Fibrin/classification, Exosomes/chemistry, Pathogen-Associated Molecular Pattern Molecules/immunology, Fibrin/agonists, Fibrin/genetics, ECS, Immune Reprogramming, Immunotherapy, Active, Systems Biology/trends, Immune Evasion/physiology, Sublingual Immunotherapy/economics, TRPV1, Immunotherapy/trends, Clinical Protocols/classification, AI in Healthcare

A Quantum-Integrated Systems Framework for Epilepsy From Mitochondrial Collapse to Biophotonic Modulation and AI-Driven Intervention

Authors: Mohamed, Anwar

Subject Terms: Hz Resonance, Artificial intelligence, Neuroimmune Interface, Systems Biology/methods, Quantum Biology, Bioenergetics, Frequency Therapy, Endocannabinoid System, Artificial Intelligence, Artificial Intelligence/trends, Systems Biology/education, Neurology/classification, Seizure Modulation, Precision Neurology, miRNA, Epilepsy, Systems Biology, Epilepsy/therapy, Systems Biology/classification, ECS, Systems Biology/trends, Programmed Cell Death, Gut-Brain Axis, Neurology, Mitochondrial Dysfunction, Biophotons

Exploring environmental intra‐species diversity through non‐redundant pangenome assemblies

Authors: Puente‐Sánchez, Fernando Hoetzinger, Matthias Buck, Moritz et al.

Source: Molecular Ecology Resources. 23:1724-1736

Subject Terms: Evolutionary Biology, Ecology, Bacteria, Microbiota, Bioinformatics and Systems Biology (methods development to be 10203), Metagenome, Metagenomics, 15. Life on land, Phylogeny, Algorithms

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/37382302
https://pub.epsilon.slu.se/32081/

Symbolic Biology and Recursive Informational Metabolism: Modeling Self-Organization, Replication, and Evolution via RHCM Recursive Collapse

Authors: Keel, Christopher orcid:0000-0002-9086-

Subject Terms: Computational Biology, Computational Biology/classification, Computational Biology/standards, Computational Biology/methods, Theoretical Biophysics, Information Theory, Artificial Life, Artificial Life/methods, Systems Biology, Systems Biology/methods, Systems Biology/classification, Systems Biology/statistics & numerical data, Cognitive Science, Cognitive Science/classification, Complexity Theory

Relation: https://zenodo.org/records/15851683; oai:zenodo.org:15851683; https://doi.org/10.5281/zenodo.15851683

Availability: https://doi.org/10.5281/zenodo.15851683
https://zenodo.org/records/15851683

Predicting Wounds Before They Break: A Coherence-Based Model for Lower Limb Preservation

Authors: Mcgeough, Fiona

Subject Terms: Wound Healing, Peripheral Nerves/abnormalities, Systems Biology/methods, Systems Biology, Diabetic Foot/complications, Diabetic Foot/economics, Systems Biology/economics, Limb Salvage, DFU, Diabetic Foot, PAD, Diabetes Complications, PVD, chronic wounds, Venous Ulcer, Peripheral vascular disease, Diabetic Foot/pathology, Diabetic Foot/classification, Systems Biology/education, Limb Salvage/methods, Peripheral Nerves, Diabetic Foot/therapy

Fractal Risk Architecture (FRA): A New Mathematical Framework for Functional HIV Cure and Immune System Control

Authors: AdmailFRA

Subject Terms: Systems Biology/methods, CRISPR-Associated Proteins, HIV reservoirs, biomedicine, microdosing, HIV Infections, Systems Biology/economics, HIV/classification, Global Health, Global Health/education, Phase Transition, Immune System Exhaustion, HIV Testing, Immune System/chemistry, Immune System Phenomena, Global Health/classification, CRISPR-Cas Systems/physiology, functional cure, Immune System/parasitology, HIV Enhancer, HIV monitoring, immune gradients, Systems Biology, Immune System/microbiology, mathematical modeling, HIV, CRISPR-Cas Systems/genetics, Phase Transition/drug effects, Systems Biology/trends, therapy algorithms, Personalized medicine, viral dynamics, HIV/physiology, Immune system, Immune System/pathology, Immune System Diseases, Immune System/virology, ART optimization, CRISPR, latent reservoirs, HIV/genetics, HIV Enteropathy, Phase Transition/radiation effects, Immune System/ultrastructure, Systems Biology/standards, Global Health/economics, CRISPR-Cas Systems, FRAmodel, HIV/immunology

Parasitic plant small RNA analyses unveil parasite-specific signatures of microRNA retention, loss, and gain

Authors: Zahra Zangishei Maria Luz Annacondia Heidrun Gundlach et al.

Source: Plant Physiol
Zangishei, Z, Annacondia, M L, Gundlach, H, Didriksen, A, Bruckmüller, J, Salari, H, Krause, K & Martinez, G 2022, ' Parasitic plant small RNA analyses unveil parasite-specific signatures of microRNA retention, loss, and gain ', Plant Physiology, vol. 190, no. 2, pp. 1242-1259 . https://doi.org/10.1093/plphys/kiac331
Plant Physiol. 190, 1242-1259 (2022)

Subject Terms: 0301 basic medicine, Cuscuta Degradome, Cuscuta Srnas, Rna-directed Dna Methylation, Microrna, Parasitic Plant, Transposable Elements, Evolutionary Biology, 0303 health sciences, Regular Issue Content, Orobanche, Botany, Cuscuta, MicroRNAs, 03 medical and health sciences, RNA, Plant, Bioinformatics and Systems Biology (methods development to be 10203), Animals, Parasites

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/35861439
https://hdl.handle.net/10037/27122
https://pub.epsilon.slu.se/29902/
https://curis.ku.dk/ws/files/320762371/kiac331.pdf
https://push-zb.helmholtz-muenchen.de/frontdoor.php?source_opus=65760

ProEnd: a comprehensive database for identifying HbYX motif-containing proteins across the tree of life

Authors: Gutierrez Diaz, Aimer

Subject Terms: Bioinformatics and Systems Biology (methods development to be 10203)

File Description: application/pdf

Access URL: https://pub.epsilon.slu.se/35601/

The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered

Authors: Lindahl, Björn

Subject Terms: Microbiology (Microbiology in the medical area to be 30109), Bioinformatics and Systems Biology (methods development to be 10203), Biological Systematics

File Description: application/pdf

Access URL: https://pub.epsilon.slu.se/33071/

Maboss for HPC environments: implementations of the continuous time Boolean model simulator for large CPU clusters and GPU accelerators.

Authors: Šmelko, Adam KRATOCHVIL, Miroslav Barillot, Emmanuel et al.

Contributors: Šmelko, Adam KRATOCHVIL, Miroslav Barillot, Emmanuel et al.

Source: BMC Bioinformatics, 25 (1), 199 (2024-05-24)

Subject Terms: Boolean models, Computational biology, High performance computing, Systems Biology/methods, Computational Biology/methods, Algorithms, Computer Graphics, Software, Computer Simulation, Boolean modeling, Computational modelling, Continous time, Experimental techniques, GPU accelerators, Large models, Performance computing, Systems biology, Structural Biology, Biochemistry, Molecular Biology, Computer Science Applications, Applied Mathematics, Life sciences, Biotechnology, Engineering, computing & technology, Computer science, Sciences du vivant, Biotechnologie, Ingénierie

Relation: info:eu-repo/grantAgreement/EC/H2020/951773; https://link.springer.com/content/pdf/10.1186/s12859-024-05815-5.pdf; urn:issn:1471-2105; https://orbilu.uni.lu/handle/10993/64540; info:hdl:10993/64540; info:pmid:38789933; wos:001232515000002

Availability: https://orbilu.uni.lu/handle/10993/64540
https://orbilu.uni.lu/bitstream/10993/64540/1/s12859-024-05815-5.pdf
https://doi.org/10.1186/s12859-024-05815-5

The Quintuple Whammy Effect

Authors: Mohamed, Anwar

Subject Terms: DNA Mismatch Repair/immunology, DNA Repair, DNA Repair Enzymes/standards, Systems Biology/methods, DNA Mismatch Repair/physiology, Quantum Biology, DNA Mismatch Repair, Licensing Ready Framework, NRF2, Neuroimmune Plasticity, Therapeutic Platform, DNA Repair/genetics, Onclogic, DNA Repair/physiology, CRISPR-Cas Systems/immunology, Precision Oncology, Warburg Effect, Oncologic, Quintuple Whammy, Systems Biology/education, DNA Repair/immunology, Bioelectric Medicine, Systems Biology/ethics, miRNA, CRISPR-Associated Proteins/immunology, Gene Editing, Gene Editing/methods, Quantum Biocomputing, Gene Editing/standards, Systems Biology, Systems Biology/classification, Gene Editing/trends, Bioactive Modulation, Systems Biology/trends, Gene Editing / CRISPR, Epigenetic Reprogramming, Biomedicine, DNA Repair Enzymes, CRISPR, Translational Medicine

Strategies for sample labelling and library preparation in DNA metabarcoding studies

Authors: Alex J. Dumbrell Christian Carøe Mathew Seymour et al.

Contributors: Alex J. Dumbrell Christian Carøe Mathew Seymour et al.

Source: Mol Ecol Resour
Bohmann, K, Elbrecht, V, Carøe, C, Bista, I, Leese, F, Bunce, M, Yu, D W, Seymour, M, Dumbrell, A J & Creer, S 2022, ' Strategies for sample labelling and library preparation in DNA metabarcoding studies ', Molecular Ecology Resources, vol. 22, no. 4, pp. 1231-1246 . https://doi.org/10.1111/1755-0998.13512
Molecular Ecology Resources, 22 (4)
Molecular Ecology Resources

Subject Terms: 0301 basic medicine, amplicon sequencing, biodiversity assessment, eDNA, environmental DNA, high-throughput sequencing, Illumina sequencing, library preparation, 0303 health sciences, Invited Technical Review, Ecology, Biodiversity, Polymerase Chain Reaction, 03 medical and health sciences, Bioinformatics and Systems Biology (methods development to be 10203), DNA Barcoding, Taxonomic, Biologie, DNA Primers, Gene Library

File Description: application/pdf; text/xml; application/application/pdf

Access URL: https://research.bangor.ac.uk/portal/files/40606046/Molecular_Ecology_Resources_2021_Bohmann_Strategies_for_sample_labelling_and_library_preparation_in_DNA_metabarcoding.pdf
https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/1755-0998.13512
https://pubmed.ncbi.nlm.nih.gov/34551203
https://www.authorea.com/users/410142/articles/522556-strategies-for-sample-labelling-and-library-preparation-in-dna-metabarcoding-studies
https://research-portal.uea.ac.uk/en/publications/strategies-for-sample-labelling-and-library-preparation-in-dna-me
https://pubmed.ncbi.nlm.nih.gov/34551203/
https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13512
https://europepmc.org/article/PPR/PPR343944
https://www.repository.cam.ac.uk/handle/1810/329339
https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13512
https://ueaeprints.uea.ac.uk/id/eprint/81706/
https://curis.ku.dk/ws/files/310831511/Molecular_Ecology_Resources_2021_Bohmann_Strategies_for_sample_labelling_and_library_preparation_in_DNA_metabarcoding.pdf
https://www.repository.cam.ac.uk/handle/1810/329339
https://doi.org/10.1111/1755-0998.13512
https://doi.org/10.17863/cam.76787
http://hdl.handle.net/20.500.11850/511954

Determination of conifer age biomarker DAL1 interactome using Y2H-seq

Authors: Qianya Zhu Xi Chen Harry X. Wu et al.

Source: For Res (Fayettev)
Forestry Research, Vol 1, Iss 1, Pp 1-12 (2021)

Subject Terms: 0301 basic medicine, Interactome, proteins-interaction, Medical Biotechnology, Evolutionary biology, Plant Science, dal1, Cytokinin Signaling, Gene, Article, Molecular Mechanisms of Plant Development and Regulation, Agricultural and Biological Sciences, Computational biology, 03 medical and health sciences, Biochemistry, Genetics and Molecular Biology, Genetics, Molecular Biology, Biology, y2h-seq, 0303 health sciences, Molecular Mechanisms of Flavonoid Biosynthesis in Plants, Biosynthesis and Engineering of Terpenoids, conifer, Life Sciences, Forestry, SD1-669.5, 15. Life on land, ageing, FOS: Biological sciences, Bioinformatics and Systems Biology (methods development to be 10203), Transcription factor, Developmental Biology

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/39524519
https://doaj.org/article/128e7df4eb11400cbb3f4c0c9b9d859c
http://www.maxapress.com/article/doi/10.48130/FR-2021-0012
https://pub.epsilon.slu.se/28849/

Similarity in milk microbiota in replicates

Authors: Josef Dahlberg Erik Pelve Johan Dicksved

Source: Microbiologyopen
MicrobiologyOpen, Vol 12, Iss 5, Pp n/a-n/a (2023)

Subject Terms: milk, Bacteria, Microbiota, Reproducibility of Results, High-Throughput Nucleotide Sequencing, DNA, Microbiology, QR1-502, mock community, Microbiology (Microbiology in the medical area to be 30109), Milk, RNA, Ribosomal, 16S, Bioinformatics and Systems Biology (methods development to be 10203), microbiota, Commentary, Animals, repeatability, reproducibility

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/37877657
https://doaj.org/article/162f11dd5d5e49a6b80e71800491d99e
https://pub.epsilon.slu.se/32029/
https://publications.scilifelab.se/publication/8c04317c16bd45aa87bc68c221982ad6

Mountain- and brown hare genetic polymorphisms to survey local adaptations and conservation status of the heath hare (Lepus timidus sylvaticus, Nilsson 1831)

Authors: Craig T. Michell Jaakko L. O. Pohjoismäki Göran Spong et al.

Contributors: Craig T. Michell Jaakko L. O. Pohjoismäki Göran Spong et al.

Source: Sci Data
Scientific Data, Vol 9, Iss 1, Pp 1-8 (2022)

Subject Terms: Sweden, 0301 basic medicine, Data Descriptor, Genome, Polymorphism, Genetic, Science, 0206 medical engineering, Sequence Analysis, DNA, 02 engineering and technology, 15. Life on land, Hares, 03 medical and health sciences, Animal and Dairy Science, Bioinformatics and Systems Biology (methods development to be 10203), Animals

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/36329035
https://doaj.org/article/26dd5e68dced4648896db718154fa1d0
https://pub.epsilon.slu.se/29848/
https://erepo.uef.fi/handle/123456789/28962
https://publications.scilifelab.se/publication/5eab650a5a5a402b8a354be7de674cb0

Prognostic model development for classification of colorectal adenocarcinoma by using machine learning model based on feature selection technique boruta

Authors: Maurya, Neha Shree Kushwah, Shikha Kushwaha, Sandeep et al.

Source: Sci Rep
Scientific Reports, Vol 13, Iss 1, Pp 1-14 (2023)

Subject Terms: Science, Adenocarcinoma, Prognosis, Survival Analysis, Article, 3. Good health, Gene Expression Regulation, Neoplastic, Bioinformatics and Systems Biology (methods development to be 10203), Medicine, Humans, Colorectal Neoplasms, Medical Genetics

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/37076536
https://doaj.org/article/cee5fbb875a6468088c43199e41ed6ea
https://pub.epsilon.slu.se/31783/

Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing

Authors: Riho Gross Kristina Noreikiene Martin Flajšhans et al.

Source: G3 (Bethesda)
G3: Genes, Genomes, Genetics, Vol 10, Iss 11, Pp 3897-3906 (2020)

Subject Terms: 0301 basic medicine, silurus glanis, 0206 medical engineering, Fresh Water, Biological Systematics, 02 engineering and technology, de novo assembly, QH426-470, wels catfish, 03 medical and health sciences, Genetics (medical genetics to be 30107 and agricultural genetics to be 40402), Genetics, Animals, 14. Life underwater, Catfishes, Ecosystem, whole genome sequencing, teleost, Genome, 10x genomics chromium linked-reads, ta1184, 6. Clean water, Genome Report, Europe, Bioinformatics and Systems Biology (methods development to be 10203), ta1181, Female

File Description: application/pdf

Access URL: https://academic.oup.com/g3journal/article-pdf/10/11/3897/37192205/g3journal3897.pdf
https://pubmed.ncbi.nlm.nih.gov/32917720
https://doaj.org/article/234713698b304c94ac653adb48d7b800
https://www.scilit.net/article/08447a479de074b438aa597d11a57ec9
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7642921
https://academic.oup.com/g3journal/article/10/11/3897/6048642
https://europepmc.org/article/MED/32917720
https://pub.epsilon.slu.se/19129/
https://pubmed.ncbi.nlm.nih.gov/32917720/
https://pub.epsilon.slu.se/19129/
https://publications.scilifelab.se/publication/e572bce7ac984e7ea1ff903fed9a1293

The strength and form of natural selection on transcript abundance in the wild

Authors: Ilkka Nousiainen Siim Kahar Anti Vasemägi et al.

Source: Mol Ecol

Subject Terms: 0301 basic medicine, Evolutionary Biology, 0303 health sciences, Trout, From the Cover, Fish Diseases, 03 medical and health sciences, Genetics (medical genetics to be 30107 and agricultural genetics to be 40402), Bioinformatics and Systems Biology (methods development to be 10203), ta1181, Animals, Kidney Diseases, Myxozoa, Selection, Genetic

File Description: application/pdf

Access URL: https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/mec.15743
https://pubmed.ncbi.nlm.nih.gov/33219570
http://juuli.fi/Record/0371830320
https://doi.org/10.1111/mec.15743
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8246785
https://europepmc.org/article/PPR/PPR114412
https://onlinelibrary.wiley.com/doi/10.1111/mec.15743
https://pub.epsilon.slu.se/24766/
https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.15743
https://pubmed.ncbi.nlm.nih.gov/33219570/
https://biorxiv.org/content/biorxiv/early/2020/02/25/2020.02.24.948828.full-text.pdf
https://www.biorxiv.org/content/10.1101/2020.02.24.948828v1.article-metrics
https://www.biorxiv.org/content/10.1101/2020.02.24.948828v1
https://pub.epsilon.slu.se/24766/

Seasonal variability of the rumen microbiome in indigenous African cattle: a bioinformatics approach

Authors: Van Damme, Renaud

Subject Terms: 10203 Bioinformatics (Computational Biology) (applications to be 10610), Microbiology (Microbiology in the medical area to be 30109), Bioinformatics and Systems Biology (methods development to be 10203)

File Description: application/pdf

Access URL: https://pub.epsilon.slu.se/38162/