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Gene network inference
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Carbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistance determinants to unrelated bacterial hosts.
22p
viellison
28-03-2024
3
2
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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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The application of cell-specific construction of transcription regulatory networks (TRNs) to identify their master regulators (MRs) in EMP2 induced vascular proliferation disorders has been largely unexplored.
10p
vihagrid
30-01-2023
6
3
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Transcription factor (TF) binding to regulatory DNA sites is a key determinant of cell identity within multi-cellular organisms and has been studied extensively in relation to site affinity and chromatin modifications. There has been a strong focus on the inference of TF-gene regulatory networks and TF-TF physical interaction networks.
23p
vigalileogalilei
27-02-2022
15
1
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Diverse molecular alterations associated with smoking in normal and precursor lung cancer cells have been reported, yet their role in lung cancer etiology remains unclear. A prominent example is hypomethylation of the aryl hydrocarbon-receptor repressor (AHRR) locus, which is observed in blood and squamous epithelial cells of smokers, but not in lung cancer.
18p
vialfrednobel
29-01-2022
5
0
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SCANPY is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and simulation of gene regulatory networks.
5p
vialfrednobel
29-01-2022
6
0
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It has proven exceedingly difficult to ascertain rare copy number alterations (CNAs) that may have strong effects in individual tumors. We show that a regulatory network inferred from gene expression and gene copy number data of 768 human cancer cell lines can be used to quantify the impact of patient-specific CNAs on survival signature genes.
25p
viaristotle
29-01-2022
7
0
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We present a novel approach, the Local Edge Machine, for the inference of regulatory interactions directly from time-series gene expression data. We demonstrate its performance, robustness, and scalability on in silico datasets with varying behaviors, sizes, and degrees of complexity. Moreover, we demonstrate its ability to incorporate biological prior information and make informative predictions on a well-characterized in vivo system using data from budding yeast that have been synchronized in the cell cycle.
13p
viaristotle
29-01-2022
9
0
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Most methods for inferring gene-gene interactions from expression data focus on intracellular interactions. The availability of high-throughput spatial expression data opens the door to methods that can infer such interactions both within and between cells. To achieve this, we developed Graph Convolutional Neural networks for Genes (GCNG).
16p
viarchimedes
26-01-2022
10
0
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Dropouts distort gene expression and misclassify cell types in single-cell transcriptome. Although imputation may improve gene expression and downstream analysis to some degree, it also inevitably introduces false signals. We develop DISC, a novel deep learning network with semi-supervised learning to infer gene structure and expression obscured by dropouts.
28p
viarchimedes
26-01-2022
8
0
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Ablepharus Lichtenstein, 1823, which includes ten species, is distributed in eastern Europe and Asia. Four species are recorded in Turkey: A. kitaibelii, A. chernovi, A. bivittatus, and A. budaki. After molecular and morphological studies in Anatolia, the phylogenetic relationship of the genus is still very complicated. Here, we investigate the taxonomic status of Ablepharus in Anatolia using morphological and molecular methods. The genetic structure of Ablepharus populations in Anatolia was analyzed using both the nuclear (CMOS) and mitochondrial (cyt b and COI) gene regions.
12p
dolomite36
30-12-2021
16
1
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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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MicroRNA regulation is fundamentally responsible for fine-tuning the whole gene network in human and has been implicated in most physiological and pathological conditions. Studying regulatory impact of microRNA on various cellular and disease processes has resulted in numerous computational tools that investigate microRNA-mRNA interactions through the prediction of static binding site highly dependent on sequence pairing.
11p
vitzuyu2711
29-09-2021
14
1
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Cluster analysis of replicated alternative polyadenylation data using canonical correlation analysis
Alternative polyadenylation (APA) has emerged as a pervasive mechanism that contributes to the transcriptome complexity and dynamics of gene regulation. The current tsunami of whole genome poly(A) site data from various conditions generated by 3′ end sequencing provides a valuable data source for the study of APArelated gene expression.
15p
vigiselle2711
30-08-2021
6
1
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Single-cell gene expression measurements offer opportunities in deriving mechanistic understanding of complex diseases, including cancer. However, due to the complex regulatory machinery of the cell, gene regulatory network (GRN) model inference based on such data still manifests significant uncertainty.
11p
visilicon2711
20-08-2021
6
1
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The filamentous fungus Fusarium graminearum causes devastating crop diseases and produces harmful mycotoxins worldwide. Understanding the complex F. graminearum transcriptional regulatory networks (TRNs) is vital for effective disease management
14p
vijeeni2711
24-07-2021
15
0
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Reference genome and transcriptome assemblies of helminths have reached a level of completion whereby secondary analyses that rely on accurate gene estimation or syntenic relationships can be now conducted with a high level of confidence.
22p
vijeeni2711
24-07-2021
18
0
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Genes are regulated by various types of regulators and most of them are still unknown or unobserved. Current gene regulatory networks (GRNs) reverse engineering methods often neglect the unknown regulators and infer regulatory relationships in a local and sub-optimal manner.
14p
vijeeni2711
30-06-2021
14
1
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High-throughput transcriptomic datasets are often examined to discover new actors and regulators of a biological response. To this end, graphical interfaces have been developed and allow a broad range of users to conduct standard analyses from RNA-seq data, even with little programming experience.
15p
vilichoo2711
23-06-2021
10
1
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Psychrotrophic lactic acid bacteria (LAB) species are the dominant species in the microbiota of coldstored modified-atmosphere-packaged food products and are the main cause of food spoilage. Despite the importance of psychrotrophic LAB, their response to cold or heat has not been studied.
16p
vilichoo2711
25-06-2021
21
1
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