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Keywords: functional analysis
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Journal Article
Current approaches and outstanding challenges of functional annotation of metabolites: a comprehensive review
Quang-Huy Nguyen and others
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae498, https://doi.org/10.1093/bib/bbae498
Published: 13 October 2024
... support metabolite annotation. The column Cluster Analysis indicates whether the methods support cluster analysis of the input samples. The column Differential Analysis indicates the methods support differential analysis and marker detection. The next two columns under Functional Analysis describes...
Journal Article
Taxonomic and functional metagenomic assessment of a Dolichospermum bloom in a large and deep lake south of the Alps
Nico Salmaso and others
FEMS Microbiology Ecology, Volume 100, Issue 10, October 2024, fiae117, https://doi.org/10.1093/femsec/fiae117
Published: 03 September 2024
... to the use of aquatic resources for drinking and bathing purposes (Chorus and Welker 2021 ). European Union 10.13039/501100000780 CN00000033 CUPD43C22001280006 ADA Anabaena/Dolichospermum/Aphanizomenon cyanobacterial blooms Dolichospermum genome mining KEGG functional analysis...
Journal Article
Maternal exposure to Di-n-butyl phthalate (DBP) inhibit orexin receptor 1 (OX1R) expression to prevent Sertoli cells proliferation through the AKT signaling pathway
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Zhiwen Xie and others
Toxicology Research, Volume 13, Issue 5, October 2024, tfae140, https://doi.org/10.1093/toxres/tfae140
Published: 03 September 2024
... analysis was used to demonstrate the apoptotic rates of PSCs after DBP exposure. Results: The Orexin receptor 1 (OX1R) was screened out by qRT-PCR array. Our results showed that DBP could significantly suppress the OX1R expression of Sertoli cells in vivo and in vitro. Functional analysis showed the AKT...
Journal Article
Reevaluating the splice-altering variant in TECTA as a cause of nonsyndromic hearing loss DFNA8/12 by functional analysis of RNA
Yan Yang and others
Human Molecular Genetics, ddae071, https://doi.org/10.1093/hmg/ddae071
Published: 27 April 2024
....com TECTA functional analysis of RNA DFNA8/12 splice-site variant Provincial Health Commission Program of Jiangxi 202211156 Key Research and Development Program of Jiangxi Province 10.13039/501100013064 20202BBG73015 Nature Science Research Project of Jiangxi 20232BAB216025...
Journal Article
CellGO: a novel deep learning-based framework and webserver for cell-type-specific gene function interpretation
Peilong Li and others
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad417, https://doi.org/10.1093/bib/bbad417
Published: 22 November 2023
... genes. Accessible as a Python package, CellGO also provides a user-friendly web interface, making it a versatile and accessible tool for researchers in the field. cell-type-specific pathway analysis gene functional analysis artificial neural network disease risk genes Gene Ontology Shanghai Center...
Journal Article
Robust functional ANOVA with application to additive manufacturing
Fabio Centofanti and others
Journal of the Royal Statistical Society Series C: Applied Statistics, Volume 72, Issue 5, November 2023, Pages 1210–1234, https://doi.org/10.1093/jrsssc/qlad074
Published: 09 August 2023
... University Press, Standard Journals Publication Model ( https://dbpia.nl.go.kr/pages/standard-publication-reuse-rights ) Abstract In this paper, we propose a new robust non-parametric functional analysis of variance method (RoFANOVA) that reduces the weights of outlying curves on the functional analysis...
Journal Article
PCR-based gene targeting in Hanseniaspora uvarum
Jennifer Badura and others
FEMS Yeast Research, Volume 23, 2023, foad034, https://doi.org/10.1093/femsyr/foad034
Published: 27 July 2023
... with primers adding the S1 and S2 primer annealing regions [primer set 5/6 (5′-hygXL/3′-hygXL)] and ligated into pGEM-T Easy. (B and C) This generated functional analysis plasmids pFA-hygXL and pFA-clnXL. Corresponding author. Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von...
Journal Article
Bi-Level Structured Functional Analysis for Genome-Wide Association Studies
Mengyun Wu and others
in
Biometrics
Biometrics, Volume 79, Issue 4, December 2023, Pages 3359–3373, https://doi.org/10.1111/biom.13871
Published: 26 April 2023
... unique structures of SNP data and the relative lack of development in functional genetic analysis, we propose a bi-level structured functional analysis method with applications to grouped SNP measurements, with which we investigate disease-associated genetic variants at the SNP level and SNP group level...
Journal Article
Isolation and characterization of gut bacteria associated with the degradation of host-specific terpenoids in Pagiophloeus tsushimanus (Coleoptera: Curculionidae) larvae
Heng Qiao and others
Journal of Insect Science, Volume 23, Issue 2, March 2023, 14, https://doi.org/10.1093/jisesa/iead019
Published: 19 April 2023
... of China 10.13039/501100001809 32271884 Pagiophloeus tsushimanus intestinal bacteria plant secondary metabolite Cinnamomum camphora functional analysis Abstract Insect intestinal bacteria play an important role in resisting defensive substances of host plants. Pagiophloeus...
Journal Article
The hitchhikers’ guide to RNA sequencing and functional analysis
Jiung-Wen Chen and others
Briefings in Bioinformatics, Volume 24, Issue 1, January 2023, bbac529, https://doi.org/10.1093/bib/bbac529
Published: 08 January 2023
... and interpretation. RNA sequencing differential expression functional analysis machine learning multi-omics National Institutes of Health 10.13039/100000002 1R01HD102690 In this step, one needs to define a statistic to measure gene expression levels. The default choice are counts, which entails the number...
Journal Article
Separating the chaff from the wheat: antibody-based removal of DNA-fragmented sperm
L B Belardin and others
Human Reproduction, Volume 38, Issue 2, February 2023, Pages 204–215, https://doi.org/10.1093/humrep/deac260
Published: 20 December 2022
... protein-1 functional analysis sperm sperm sub-populations spermiogram male infertility magnetic cell-sorter magnetic beads References Agarwal A , Farkouh A , Parekh N , Zini A , Arafa M , Kandil H , Tadros N , Busetto GM , Ambar R , Parekattil S et al...
Journal Article
Biological characteristics and whole‐genome analysis of the potential probiotic, Lactobacillus reuteri S5
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Shuiqin Shi and others
Letters in Applied Microbiology, Volume 74, Issue 4, 1 April 2022, Pages 593–603, https://doi.org/10.1111/lam.13644
Published: 01 April 2022
...:https://dbpia.nl.go.kr/journals/pages/open_access/funder_policies/chorus/standard_publication_model ) biological characteristics functional analysis L. reuteri S5 lactic acid bacteria whole genome sequencing Anhui Natural Science Foundation 2108085QC138 Key research and development plan of Anhui Province...
Journal Article
Elucidation of dynamic microRNA regulations in cancer progression using integrative machine learning
Haluk Dogan and others
Briefings in Bioinformatics, Volume 22, Issue 6, November 2021, bbab270, https://doi.org/10.1093/bib/bbab270
Published: 09 August 2021
... competitive binding in human cancers, as well as modulated miRNA regulation. However, this previous model was focused on miRNA regulation at each individual gene, not accounting for gene-gene interactions, and therefore showed limitations in general functional analysis. In this study, we explore integrated...
Journal Article
Overexpression of MdVQ37 reduces drought tolerance by altering leaf anatomy and SA homeostasis in transgenic apple
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Qinglong Dong and others
Tree Physiology, Volume 42, Issue 1, January 2022, Pages 160–174, https://doi.org/10.1093/treephys/tpab098
Published: 29 July 2021
... Duan two authors contributed equally to this work and are considered as co-first authors. 18 4 2021 16 7 2021 20 7 2021 23 10 2021 apple drought stress functional analysis SA signaling pathway VQ protein © The Author(s) 2021. Published by Oxford University Press. All rights...
Journal Article
Whole-exome sequencing reveals potential germline and somatic mutations in 60 malignant ovarian germ cell tumors
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Juan Chen and others
Biology of Reproduction, Volume 105, Issue 1, July 2021, Pages 164–178, https://doi.org/10.1093/biolre/ioab052
Published: 19 March 2021
... sequencing functional analysis Malignant ovarian germ cell tumors (MOGCTs) are aggressive tumors, which primarily affect young females, with a peak incidence below the age of 20 [ 1–4 ]. MOGCTs consist of several histologically different types, including dysgerminoma (DG), immature teratoma (IT), embryonal...
Journal Article
PSIII-16 Genome-wide association mapping and functional analysis of body weight, feed intake and walking ability in turkeys
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Emhimad Abdalla and others
Journal of Animal Science, Volume 98, Issue Supplement_4, November 2020, Pages 234–235, https://doi.org/10.1093/jas/skaa278.429
Published: 30 November 2020
... association mapping and Breeding Protocols in Dairy Cattle. functional analysis of body weight, feed intake and walking ability in turkeys. Colin Lynch1, Gerson Oliveira1, Flavio Emhimad Abdalla1, Bayode Makanjuola1, Schenkel1, Christine F. Baes1, 1University of Benjamin Wood2, Christine F. Baes3, Guelph...
Journal Article
Visualizing the Effects of Predictor Variables in Black Box Supervised Learning Models
Daniel W. Apley and Jingyu Zhu
Journal of the Royal Statistical Society Series B: Statistical Methodology, Volume 82, Issue 4, September 2020, Pages 1059–1086, https://doi.org/10.1111/rssb.12377
Published: 11 June 2020
... with correlated predictors. Moreover, accumulated local effects plots are far less computationally expensive than partial dependence plots. We also provide an R package ALEPlot as supplementary material to implement our proposed method. Functional analysis of variance Marginal plots Partial dependence plots...
Journal Article
Genomics-enabled analysis of specialized metabolism in bioenergy crops: current progress and challenges
Kira Tiedge and others
Synthetic Biology, Volume 5, Issue 1, 2020, ysaa005, https://doi.org/10.1093/synbio/ysaa005
Published: 01 June 2020
... DNA synthesis gene discovery enzyme functional analysis terpenoid metabolism Meeting the needs of a growing world population while addressing urgent sustainability challenges has spurred intensive efforts in renewable energy production including biofuels ( 1 , 2 ). In 2018, global biofuel...
Journal Article
TGPred: a tumor gene prediction webserver for analyzing structural and functional impacts of variants
Jixiang Liu and others
Journal of Molecular Cell Biology, Volume 12, Issue 7, July 2020, Pages 556–558, https://doi.org/10.1093/jmcb/mjaa007
Published: 03 April 2020
..., provided the original work is properly cited. For commercial re-use, please contact [email protected] cancer web service structure prediction variation and functional analysis visualization National Key Research and Development Program of China 10.13039/501100012166 2018YFC0910500...
Journal Article
A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs
Meik Kunz and others
Briefings in Bioinformatics, Volume 21, Issue 4, July 2020, Pages 1391–1396, https://doi.org/10.1093/bib/bbz066
Published: 03 October 2019
... expression analysis sequence-structure analysis integrated functional analysis In recent years, long non-coding RNAs (lncRNAs) have been identified as functional players that regulate important biological processes and signaling pathways associated with pathogenesis and disease progression [ 1–6...
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