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Infer gene function
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Ebook "Prokaryotic systems biology (Advances in experimental medicine and biology, Volume 883)" focuses on innovative experimental and computational approaches for charting interaction networks in bacterial species.
326p
duongthandue0501
28-02-2024
3
1
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DNA methylation is a key epigenetic modification in human development and disease, yet there is limited understanding of its highly coordinated regulation. Here, we identify 818 genes that affect DNA methylation patterns in blood using large-scale population genomics data.
24p
viarchimedes
26-01-2022
7
1
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Chromatin interactions are important for gene regulation and cellular specialization. Emerging evidence suggests many-body spatial interactions play important roles in condensing super-enhancer regions into a cohesive transcriptional apparatus. Chromosome conformation studies using Hi-C are limited to pairwise, population-averaged interactions; therefore unsuitable for direct assessment of many-body interactions.
17p
viarchimedes
26-01-2022
13
0
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Phylogenetic trees are useful tools to infer evolutionary relationships between genetic entities. Phylogenetics enables not only evolution-based gene clustering but also the assignment of gene duplication and deletion events to the nodes when coupled with statistical approaches such as bootstrapping. However, extensive gene duplication and deletion events bring along a challenge in interpreting phylogenetic trees and require manual inference.
7p
langthannam
29-12-2021
14
0
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A large number of disease resistance genes or QTLs in crop plants are identified through conventional genetics and genomic tools, but their functional or molecular characterization remains costly, labor-intensive and inaccurate largely due to the lack of deep sequencing of large and complex genomes of many important crops such as allohexaploid wheat (Triticum aestivum L.). On the other hand, gene annotation and relevant genomic resources for disease resistance and other defense-related traits are more abundant in model plant Arabidopsis (Arabidopsis thaliana).
13p
vilarryellison
29-10-2021
12
0
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Inference of protein’s membership in metabolic pathways has become an important task in functional annotation of protein. The membership information can provide valuable context to the basic functional annotation and also aid reconstruction of incomplete pathways. Previous works have shown success of inference by using various similarity measures of gene ontology.
10p
vitzuyu2711
29-09-2021
19
1
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In forest trees, genetic markers have been used to understand the genetic architecture of natural populations, identify quantitative trait loci, infer gene function, and enhance tree breeding.
17p
vijeeni2711
24-07-2021
3
0
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Genetic mutation, selective pressure for translational efficiency and accuracy, level of gene expression, and protein function through natural selection are all believed to lead to codon usage bias (CUB). Therefore, informative measurement of CUB is of fundamental importance to making inferences regarding gene function and genome evolution.
10p
viwyoming2711
16-12-2020
9
1
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The concept of orthology is key to decoding evolutionary relationships among genes across different species using comparative genomics. QuartetS is a recently reported algorithm for large-scale orthology detection.
9p
viwyoming2711
16-12-2020
5
0
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Knockdown or overexpression of genes is widely used to identify genes that play important roles in many aspects of cellular functions and phenotypes. Because next-generation sequencing generates high-throughput data that allow us to detect genes, it is important to identify genes that drive functional and phenotypic changes of cells.
14p
vikentucky2711
26-11-2020
5
0
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Biomedical ontologies are increasingly instrumental in the advancement of biological research primarily through their use to efficiently consolidate large amounts of data into structured, accessible sets. However, ontology development and usage can be hampered by the segregation of knowledge by domain that occurs due to independent development and use of the ontologies.
15p
vikentucky2711
26-11-2020
9
1
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The nonrandom radial organization of eukaryotic chromosome territories (CTs) inside the nucleus plays an important role in nuclear functional compartmentalization. Increasingly, chromosome conformation capture (Hi-C) based approaches are being used to characterize the genome structure of many cell types and conditions.
28p
vikentucky2711
24-11-2020
12
1
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Deep mutational scanning is a technique to estimate the impacts of mutations on a gene by using deep sequencing to count mutations in a library of variants before and after imposing a functional selection. The impacts of mutations must be inferred from changes in their counts after selection.
13p
vikentucky2711
24-11-2020
10
1
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Predicting protein subcellular localization is indispensable for inferring protein functions. Recent studies have been focusing on predicting not only single-location proteins, but also multi-location proteins. Almost all of the high performing predictors proposed recently use gene ontology (GO) terms to construct feature vectors for classification.
17p
vioklahoma2711
19-11-2020
6
1
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Inference of active regulatory cascades under specific molecular and environmental perturbations is a recurring task in transcriptional data analysis. Commercial tools based on large, manually curated networks of causal relationships offering such functionality have been used in thousands of articles in the biomedical literature.
15p
vioklahoma2711
19-11-2020
12
1
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MiRNAs play a critical role in the response of plants to abiotic and biotic stress. However, the functions of most plant miRNAs remain unknown. Inferring these functions from miRNA functional similarity would thus be useful. This study proposes a new method, called PPImiRFS, for inferring miRNA functional similarity.
11p
vioklahoma2711
19-11-2020
6
1
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Loss-of-function phenotypes are widely used to infer gene function using the principle that similar phenotypes are indicative of similar functions. However, converting phenotypic to functional annotations requires careful interpretation of phenotypic descriptions and assessment of phenotypic similarity.
12p
vioklahoma2711
19-11-2020
10
1
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Gene Ontology (GO) is a community effort to represent functional features of gene products. GO annotations (GOA) provide functional associations between GO terms and gene products. Due to resources limitation, only a small portion of annotations are manually checked by curators, and the others are electronically inferred.
13p
viflorida2711
30-10-2020
9
2
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An improved approach to infer protein-protein interaction based on a hierarchical vector space model
Comparing and classifying functions of gene products are important in today’s biomedical research. The semantic similarity derived from the Gene Ontology (GO) annotation has been regarded as one of the most widely used indicators for protein interaction.
14p
viconnecticut2711
28-10-2020
15
1
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Identification of homologous genes is fundamental to comparative genomics, functional genomics and phylogenomics. Extensive public homology databases are of great value for investigating homology but need to be continually updated to incorporate new sequences.
11p
viconnecticut2711
28-10-2020
11
1
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