Search Results - "network inference algorithms"

Benchmarking of biological regulatory network inference algorithms of microbiome- metabolome interaction

Authors: Müller, Mattea Zacharias, Helena Altenbuchinger, Michael

Evaluation of network inference algorithms for derivation of metabolic relationships from lipidomic and metabolomic datasets

Authors: Finn Archinuk Haley Greenyer Ulrike Stege et al.

Cross-validation for training and testing co-occurrence network inference algorithms

Authors: Daniel Agyapong Jeffrey Ryan Propster Jane Marks et al.

Source: BMC Bioinformatics
BMC Bioinformatics, Vol 26, Iss 1, Pp 1-24 (2025)

Subject Terms: FOS: Computer and information sciences, Computer Science - Machine Learning, Bacteria, QH301-705.5, Research, Microbiota, Computer applications to medicine. Medical informatics, R858-859.7, Network Validation, Computational Biology, LASSO, Microbiome Analysis, Quantitative Biology - Quantitative Methods, Machine Learning (cs.LG), FOS: Biological sciences, Machine learning, Cross-Validation, Biology (General), Co-occurrence network inference, Algorithms, Quantitative Methods (q-bio.QM)

Access URL: https://pubmed.ncbi.nlm.nih.gov/40045231
http://arxiv.org/abs/2309.15225
https://doaj.org/article/d8504249d11249a3990e5350d7b920b0

Are the tools fit for purpose? Network inference algorithms evaluated on a simulated lipidomics network.

Authors: Archinuk F Greenyer H Stege U et al.

Source: Bioinformatics advances [Bioinform Adv] 2025 Nov 09; Vol. 5 (1), pp. vbaf286. Date of Electronic Publication: 2025 Nov 09 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9918282081306676 Publication Model: eCollection Cited Medium: Internet ISSN: 2635-0041 (Electronic) Linking ISSN: 26350041 NLM ISO Abbreviation: Bioinform Adv Subsets: PubMed not MEDLINE

Enhancing Collaborative Filtering- Based Recommender System Through Information Theory-Based Network Inference Algorithms

Authors: Mustafa Özgür Cingiz

Revealing ecological networks using Bayesian network inference algorithms

Authors: Milns, Isobel Beale, Colin M. Smith, V. Anne

Source: Ecology, 2010 Jul 01. 91(7), 1892-1899.

Access URL: https://www.jstor.org/stable/25680438

Cross-Validation for Training and Testing Co-occurrence Network Inference Algorithms

Authors: Agyapong, Daniel Propster, Jeffrey Ryan Marks, Jane et al.

Index Terms: Computer Science - Machine Learning, Quantitative Biology - Quantitative Methods, text

URL: http://arxiv.org/abs/2309.15225

Assessing Gene Regulatory Network Inference Algorithms Using Word Embeddings: A Novel Approach for NLP and Systems Biology Integration

Authors: Peignier, Sergio Zapata, Patricia

Contributors: Peignier, Sergio Zapata, Patricia

Subject Terms: Gene Regualtory Network inference, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-TT] Computer Science [cs]/Document and Text Processing, Poilitical Discourse analysis

File Description: application/pdf

Access URL: https://hal.science/hal-04783589v1

Additional file 1 of Cross-validation for training and testing co-occurrence network inference algorithms

Authors: Agyapong, Daniel Propster, Jeffrey Ryan Marks, Jane et al.

Investigation of association estimators in network inference algorithms on breast cancer proteomic data

Authors: Cihat Erdogan Zeyneb Kurt Banu Diri

Source: 2017 25th Signal Processing and Communications Applications Conference (SIU). :1-4

Subject Terms: 0301 basic medicine, 0303 health sciences, 03 medical and health sciences, 13. Climate action, 10. No inequality, 3. Good health

Evaluating the Reproducibility of Single-Cell Gene Regulatory Network Inference Algorithms

Authors: Yoonjee Kang Denis Thieffry Laura Cantini

Source: Frontiers in Genetics, Vol 12 (2021)

Subject Terms: biological networks, scRNA-seq, single-cell, transcriptome, network inference, network theory, Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fgene.2021.617282/full; https://doaj.org/toc/1664-8021

Access URL: https://doaj.org/article/126b9198d38241a5b2ae694c15aa69ed

Evaluating the reproducibility of single-cell gene regulatory network inference algorithms

Authors: Yoonjee Kang Denis Thieffry Laura Cantini

Source: Front Genet
Frontiers in Genetics, Vol 12 (2021)

Subject Terms: network theory, 0301 basic medicine, biological networks, 03 medical and health sciences, network inference, scRNA-seq, 0206 medical engineering, Genetics, 02 engineering and technology, single-cell, QH426-470, transcriptome

Access URL: https://www.frontiersin.org/articles/10.3389/fgene.2021.617282/pdf
https://pubmed.ncbi.nlm.nih.gov/33828580
https://doaj.org/article/126b9198d38241a5b2ae694c15aa69ed
https://europepmc.org/article/MED/33828580
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8019823
https://hal.archives-ouvertes.fr/hal-03358193
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8019823
https://www.frontiersin.org/articles/10.3389/fgene.2021.617282/full
https://pubmed.ncbi.nlm.nih.gov/33828580/
https://www.biorxiv.org/content/biorxiv/early/2020/11/10/2020.11.10.375923.full.pdf
https://biorxiv.org/content/10.1101/2020.11.10.375923v1.full.pdf
https://www.biorxiv.org/content/10.1101/2020.11.10.375923v1

Improving network inference algorithms using resampling methods

Authors: Sean M Colby Ryan S McClure Christopher C Overall et al.

Source: BMC Bioinformatics, Vol 19, Iss 1, Pp 1-9 (2018)

Subject Terms: Gene regulatory network inference, Random subspace method, Resampling, Bootstrapping, Aggregation, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-018-2402-0; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/d146200cab9d448bbfe882e1a2a52cfd

Empirically determining the sample size for large-scale gene network inference algorithms

Authors: Gökmen Altay

Source: IET Systems Biology. 6:35-43

Subject Terms: 0301 basic medicine, 03 medical and health sciences, Models, Statistical, Time Factors, Sample Size, Systems Biology, 0206 medical engineering, Escherichia coli, Gene Regulatory Networks, 02 engineering and technology, Algorithms, Genome, Bacterial

Access URL: https://pubmed.ncbi.nlm.nih.gov/22519356
http://yadda.icm.edu.pl/yadda/element/bwmeta1.element.ieee-000006186896
https://digital-library.theiet.org/content/journals/10.1049/iet-syb.2010.0091
https://ieeexplore.ieee.org/document/6186896/
https://www.infona.pl/resource/bwmeta1.element.ieee-art-000006186896
http://europepmc.org/abstract/MED/22519356
http://ieeexplore.ieee.org/document/6186896/citations

Global assessment of network inference algorithms based on available literature of gene/protein interactions

Authors: Gökmen Altay David E. Neal Nejla Altay

Source: TURKISH JOURNAL OF BIOLOGY. 37:547-555

Subject Terms: 0301 basic medicine, 0303 health sciences, 03 medical and health sciences

Access URL: https://journals.tubitak.gov.tr/biology/abstract.htm?id=14048
https://journals.tubitak.gov.tr/biology/issues/biy-13-37-5/biy-37-5-6-1210-8.pdf

Assessing Gene Regulatory Network Inference Algorithms Using Word Embeddings: A Novel Approach for NLP and Systems Biology Integration

Authors: Sergio Peignier orcid:0000-0002-9004- Patricia Zapata

Subject Terms: Gene Regualtory Network inference, Poilitical Discourse analysis

Relation: https://zenodo.org/communities/dhbenelux2023/; https://zenodo.org/records/7997511; oai:zenodo.org:7997511; https://doi.org/10.5281/zenodo.7997511

Availability: https://doi.org/10.5281/zenodo.7997511
https://zenodo.org/records/7997511

Cross-validation for training and testing co-occurrence network inference algorithms: Cross-validation for training and testing co-occurrence network...: D. Agyapong et al.

Authors: Agyapong, Daniel Propster, Jeffrey Ryan Marks, Jane et al.

Source: BMC Bioinformatics; 3/6/2025, Vol. 26 Issue 1, p1-24, 24p

Subject Terms: GENE regulatory networks, BIODEGRADATION, MICROBIAL ecology, LIFE sciences, HUMAN ecology

A comprehensive comparison of association estimators for gene network inference algorithms

Authors: Aydın, Nizamettin Kurt, Zeyneb Altay, Gokmen

Source: Bioinformatics. 30:2142-2149

Subject Terms: 0301 basic medicine, 03 medical and health sciences, Time Factors, 13. Climate action, 0206 medical engineering, Computational Biology, Gene Regulatory Networks, Saccharomyces cerevisiae, 02 engineering and technology, Algorithms

Access URL: https://academic.oup.com/bioinformatics/article-pdf/30/15/2142/17143846/btu182.pdf
https://pubmed.ncbi.nlm.nih.gov/24728859
https://www.ncbi.nlm.nih.gov/pubmed/24728859?format=text
http://bioinformatics.oxfordjournals.org/content/30/15/2142.full.pdf
https://academic.oup.com/bioinformatics/article/30/15/2142/2390678
https://researchportal.northumbria.ac.uk/en/publications/a-comprehensive-comparison-of-association-estimators-for-gene-net
https://dblp.uni-trier.de/db/journals/bioinformatics/bioinformatics30.html#KurtAA14
https://avesis.yildiz.edu.tr/publication/details/70b2537b-dd7d-4c02-bdeb-6c2f0115d73b/oai

Revealing differences in gene network inference algorithms on the network level by ensemble methods

Authors: Altay, Gokmen Emmert-Streib, Frank

Source: Bioinformatics. 26:1738-1744

Subject Terms: 0301 basic medicine, B-Lymphocytes, 0206 medical engineering, Genes, myc, name=Biochemistry, name=Molecular Biology, Genomics, 02 engineering and technology, name=Computer Science Applications, name=Computational Theory and Mathematics, 03 medical and health sciences, name=Computational Mathematics, Gene Regulatory Networks, Algorithms, name=Statistics and Probability

Access URL: https://academic.oup.com/bioinformatics/article-pdf/26/14/1738/16893384/btq259.pdf
https://pubmed.ncbi.nlm.nih.gov/20501553

An Analysis of the Association Estimators in Biological Network Inference Algorithms on Glioblastoma Multiforme Proteomic Data

Authors: KURT, Zeyneb Erdoğan, Cihat DİRİ, Banu

Access URL: https://avesis.yildiz.edu.tr/publication/details/1587bb1d-5c43-495f-9d2d-28f856ca3e7f/oai