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Transcriptomic complexity
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A comprehensive understanding of the pre-existing genetic variation in genes associated with antibiotic resistance in the Mycobacterium tuberculosis complex (MTBC) is needed to accurately interpret wholegenome sequencing data for genotypic drug susceptibility testing (DST).
8p
vibransone
28-03-2024
3
2
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Tumor cell-intrinsic mechanisms and complex interactions with the tumor microenvironment contribute to therapeutic failure via tumor evolution. It may be possible to overcome treatment resistance by developing a personalized approach against relapsing cancers based on a comprehensive analysis of cell typespecific transcriptomic changes over the clinical course of the disease using single-cell RNA sequencing (scRNA-seq).
21p
vibransone
28-03-2024
3
2
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Systemic sclerosis (SSc) is a genetically complex autoimmune disease mediated by the interplay between genetic and epigenetic factors in a multitude of immune cells, with CD4+ T lymphocytes as one of the principle drivers of pathogenesis.
17p
vibransone
28-03-2024
3
2
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Comprehensive molecular profiling has revealed somatic variations in cancer at genomic, epigenomic, transcriptomic, and proteomic levels. The accumulating data has shown clearly that molecular phenotypes of cancer are complex and influenced by a multitude of factors.
13p
vibransone
28-03-2024
6
1
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The genetic origins of chemotherapy resistance are well established; however, the role of epigenetics in drug resistance is less well understood. To investigate mechanisms of drug resistance, we performed systematic genetic, epigenetic, and transcriptomic analyses of an alkylating agent-sensitive murine lymphoma cell line and a series of resistant lines derived by drug dose escalation.
11p
vioraclene
31-03-2024
2
1
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The genetic regulation of metabolic phenotypes (i.e., metabotypes) in type 2 diabetes mellitus occurs through complex organ-specific cellular mechanisms and networks contributing to impaired insulin secretion and insulin resistance. Genome-wide gene expression profiling systems can dissect the genetic contributions to metabolome and transcriptome regulations.
15p
vioraclene
31-03-2024
4
2
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Molecular measurements of the genome, the transcriptome, and the epigenome, often termed multi-omics data, provide an in-depth view on biological systems and their integration is crucial for gaining insights in complex regulatory processes.
21p
viellison
28-03-2024
8
2
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Spatial multi-omic studies have emerged as a promising approach to comprehensively analyze cells in tissues, enabling the joint analysis of multiple data modalities like transcriptome, epigenome, proteome, and metabolome in parallel or even the same tissue section. This review focuses on the recent advancements in spatial multi-omics technologies, including novel data modalities and computational approaches.
17p
vicwell
29-02-2024
5
2
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Spatial resolved transcriptomics (SRT) encompasses a rapidly developing set of technologies that enable the measurement of gene expression in tissue while retaining spatial localization information. SRT technologies and the enabled SRT studies have provided unprecedent insights into the structural and functional underpinnings of complex tissues.
22p
vicwell
29-02-2024
4
1
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Single-cell RNA-seq has emerged as an innovative technology used to study complex tissues and characterize cell types, states, and lineages at a single-cell level. Classification of bulk tumors by their individual cel‑ lular constituents has also created new opportunities to generate single-cell atlases for many organs, cancers, and developmental models.
16p
visharma
20-10-2023
4
2
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Diospyros oleifera, one of the most economically important Diospyros species, is an ideal model for study‑ ing the fruit development of persimmon. While, the lack of whole-transcriptome has hindered the complex transcrip‑ tional regulation mechanisms of sugar and tannin during fruit development.
5p
vinarcissa
21-03-2023
5
1
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Transgenic poplar (Populus × euramericana ‘Guariento’) plants harboring five exogenous, stress-related genes exhibit increased tolerance to multiple stresses including drought, salt, waterlogging, and insect feeding, but the complex mechanisms underlying stress tolerance in these plants have not been elucidated.
17p
vinarcissa
21-03-2023
2
1
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Horse testis development and spermatogenesis are complex physiological processes. To study these processes, three immature and three mature testes were collected from the Mongolian horse, and six libraries were established using high-throughput RNA sequencing technology (RNA-Seq) to screen for genes related to testis development and spermatogenesis.
10p
vihagrid
30-01-2023
8
3
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Most congenital heart defects (CHDs) result from complex interactions among genetic susceptibilities, epigenetic modifications, and maternal environmental exposures. Characterizing the complex relationship between genetic, epigenetic, and transcriptomic variation will enhance our understanding of pathogenesis in this important type of congenital disorder.
12p
vihagrid
30-01-2023
7
3
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We develop CellSIUS (Cell Subtype Identification from Upregulated gene Sets) to fill a methodology gap for rare cell population identification for scRNA-seq data. CellSIUS outperforms existing algorithms for specificity and selectivity for rare cell types and their transcriptomic signature identification in synthetic and complex biological data.
21p
vigalileogalilei
27-02-2022
12
1
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Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotations to determine cell identities, which are time-consuming and irreproducible
19p
vielonmusk
30-01-2022
14
0
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Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition.
18p
vialfrednobel
29-01-2022
9
0
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All mRNAs are bound in vivo by proteins to form mRNA–protein complexes (mRNPs), but changes in the composition of mRNPs during posttranscriptional regulation remain largely unexplored. Here, we have analyzed, on a transcriptome-wide scale, how microRNA-mediated repression modulates the associations of the core mRNP components eIF4E, eIF4G, and PABP and of the decay factor DDX6 in human cells.
18p
vialfrednobel
29-01-2022
12
0
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While intron retention (IR) is now widely accepted as an important mechanism of mammalian gene expression control, it remains the least studied form of alternative splicing. To delineate conserved features of IR, we performed an exhaustive phylogenetic analysis in a highly purified and functionally defined cell type comprising neutrophilic granulocytes from five vertebrate species spanning 430 million years of evolution.
15p
vialfrednobel
29-01-2022
2
0
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The interaction between a pathogen and a host is a highly dynamic process in which both agents activate complex programs. Here, we introduce a single-cell RNA-sequencing method, scDual-Seq, that simultaneously captures both host and pathogen transcriptomes.
8p
vialfrednobel
29-01-2022
9
0
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