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A novel totivirus alters gene expression and vacuolar morphology in Malassezia cells and induces a TLR3-mediated inflammatory immune response

Our analysis also revealed that a viral nucleic acid from MrV40 induces a TLR3-mediated inflammatory immune response in bone marrow-derived dendritic cells (BMDCs) and this result suggests that a viral element contributes to the pathogenesis of Malassezia. Expand abstract.
39 days ago
8/10 relevant
bioRxiv

Machine learning applied to atopic dermatitis transcriptome reveals distinct therapy-dependent modification of the keratinocyte immunophenotype

Using co-expression clustering and machine learning tools, we resolved the gene expression of bulk skin (n=7 datasets, n=406 samples), firstly, into unsupervised keratinocyte immune response phenotypes and, secondly, into 19 cutaneous cell signatures of purified populations from publicly available datasets. Expand abstract.
40 days ago
4/10 relevant
medRxiv

Precision Sub-phenotyping of Histologically Stable Kidney Transplants by a Composite Molecular and Cellular Instability Score

By applying a machine learning model, a substantive number of hSTA samples were found to be molecularly similar to AR (mAR); these have been reclassified in this study as clinical and histological stable samples with transcriptional signatures overlapping with AR (hSTA/mAR), with the predominant expression of a subset of 6 genes... Expand abstract.
40 days ago
4/10 relevant
bioRxiv

Two tandem mechanisms control bimodal expression of the flagellar genes in Salmonella enterica

In this work, a second mechanism was found to govern bimodal expression of class 3 genes. Expand abstract.
40 days ago
8/10 relevant
bioRxiv

Finding a suitable library size to call variants in RNA-seq

To extend this result to another cancer type, an exploration of the characteristics of its mutations and gene expression patterns is suggested Expand abstract.
40 days ago
7/10 relevant
bioRxiv

Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation

In eutherian mammals, X chromosome inactivation (XCI) in females proceeds via the lncRNA Xist, which coats one of the two X chromosomes and recruits repressive proteins to epigenetically silence gene expression in cis. Expand abstract.
40 days ago
5/10 relevant
bioRxiv

Accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis

Based on an analysis of Genotype-Tissue Expression (GTEx) data we demonstrate the existence of sets of genes that show predominant DGE or DAST across a comparison of 20 tissue types, and show that these sets have pervasive differences with respect to gene structure, function, membership in protein complexes,... Expand abstract.
40 days ago
7/10 relevant
bioRxiv

Transcriptome profiling of Variovorax paradoxus EPS under different growth conditions reveals regulatory and structural novelty in biofilm formation

A small set of genes (103/6020) were differentially expressed in opposing fashions in biofilm and stationary phase, indicating potentially substantial shifts in phenotype. Expand abstract.
41 days ago
7/10 relevant
bioRxiv

Gene expression data support the hypothesis that Isoetes rootlets are true roots and not modified leaves

RSL genes which positively regulate cell differentiation in roots were either exclusively or preferentially expressed in the I. echinospora rootlets, S. moellendorffii roots and A. thaliana roots compared to the leaves of each respective species. Expand abstract.
41 days ago
10/10 relevant
bioRxiv

Hierarchical Markov Random Field model captures spatial dependency in gene expression, demonstrating regulation via the 3D genome

Some functional groups of genes show strong spatial dependency in gene expression as well, providing new insights into the regulation mechanisms of these molecular functions. Expand abstract.
41 days ago
10/10 relevant
bioRxiv