RNA features
-
We developed subclone multiplicity allocation and somatic heterogeneity (SMASH), a new statistical method for intra-tumor heterogeneity (ITH) inference. SMASH is tailored to the purpose of large-scale association studies with one tumor sample per patient. In a pan-cancer study of 14 cancer types, we studied the associations between survival time and ITH quantified by SMASH, together with other features of somatic mutations.
15p vibransone 28-03-2024 7 2 Download
-
A challenge in the post-GWAS era is to assign function to disease-associated variants. However, available resources do not include all tissues or environmental exposures that are relevant to all diseases. For example, exaggerated bronchoconstriction of airway smooth muscle cells (ASMCs) defines airway hyperresponsiveness (AHR), a cardinal feature of asthma.
14p vibransone 28-03-2024 9 2 Download
-
Many immunotherapies rely on the presence of neoepitopes derived from somatic mutations that lead to altered peptide sequences. Several studies have now analyzed the neoepitope landscape of different cancer subtypes, predominantly for adult samples, which tend to feature significantly higher mutational burden.
4p vioraclene 31-03-2024 2 2 Download
-
IL-4-driven alternative macrophage activation and proliferation are characteristic features of both antihelminthic immune responses and wound healing in contrast to classical macrophage activation, which primarily occurs during inflammatory responses.
22p vioraclene 31-03-2024 4 2 Download
-
Recent studies have suggested that individual variants do not sufficiently explain the variable expressivity of phenotypes observed in complex disorders. For example, the 16p12.1 deletion is associated with developmental delay and neuropsychiatric features in affected individuals, but is inherited in > 90% of cases from a mildly-affected parent.
21p vibransone 28-03-2024 8 2 Download
-
Malignant pleural mesothelioma (MPM) has a poor overall survival with few treatment options. Whole genome sequencing (WGS) combined with the immune features of MPM ofers the prospect of identifying changes that could inform future clinical trials.
18p viellison 28-03-2024 2 2 Download
-
The RNA profiles of tumor-educated platelets (TEPs) possess pathological features that could be used for early cancer detection. However, the utility of TEP RNA profiling in detecting early colorectal cancer (CRC) versus noncancerous colorectal diseases has not yet been investigated.
11p viellison 28-03-2024 7 2 Download
-
Mixed phenotype acute leukemia (MPAL), a rare subgroup of leukemia characterized by blast cells with myeloid and lymphoid lineage features, is difficult to diagnose and treat. A better characterization of MPAL is essential to understand the subtype heterogeneity and how it compares with acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL).
25p vicwell 29-02-2024 3 2 Download
-
Pituitary neuroendocrine tumors (PitNETs) are one of the most common types of intracranial tumors. Currently, the cellular characteristics of normal pituitary and various other types of PitNETs are still not completely understood.
17p vicwell 29-02-2024 3 2 Download
-
Ebook "Argonaute proteins: Methods and protocols" aids researchers in examining these versatile proteins in a wide variety of cell types; features practical, step-by-step protocols which open the door to future progress in the field of molecular therapeutics; contains expert tips and vital implementation advice to ensure success;...
262p lucchinguyen 28-12-2023 6 2 Download
-
Emerging proof shows that abnormal lipometabolism affects invasion, metastasis, stemness and tumor microenvironment in carcinoma cells. However, molecular markers related to lipometabolism have not been further established in breast cancer. In addition, numerous studies have been conducted to screen for prognostic features of breast cancer only with RNA sequencing profiles.
13p vialfrednobel 23-12-2023 5 3 Download
-
Researches have manifested that the disorder of iron metabolism is participated in Gastric cancer (GC), but whether iron metabolism-relevant genes (IMRGs) is related to the survival outcome of GC remain unknown.
16p vialfrednobel 23-12-2023 9 2 Download
-
In this paper, we proposed a new method to predict lncRNA-disease associations using multiple features and deep learning. Our method uses a weighted
10p visystrom 22-11-2023 6 5 Download
-
As an essential regulator of type I interferon (IFN) response, TMEM173 participates in immune regulation and cell death induction. In recent studies, activation of TMEM173 has been regarded as a promising strategy for cancer immunotherapy. However, transcriptomic features of TMEM173 in B-cell acute lymphoblastic leukemia (B-ALL) remain elusive.
14p vischultz 20-10-2023 5 1 Download
-
Organogenesis is crucial for proper organ formation during mammalian embryonic development. However, the similarities and shared features between different organs and the cellular heterogeneity during this process at single-cell resolution remain elusive.
20p vimichaelfaraday 25-03-2022 16 1 Download
-
We perform a large-scale RNA sequencing study to experimentally identify genes that are downregulated by 25 miRNAs. This RNA-seq dataset is combined with public miRNA target binding data to systematically identify miRNA targeting features that are characteristic of both miRNA binding and target downregulation.
10p vigalileogalilei 27-02-2022 10 1 Download
-
Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes
General translational cis-elements are present in the mRNAs of all genes and affect the recruitment, assembly, and progress of preinitiation complexes and the ribosome under many physiological states. These elements include mRNA folding, upstream open reading frames, specific nucleotides flanking the initiating AUG codon, protein coding sequence length, and codon usage.
24p vielonmusk 30-01-2022 16 2 Download
-
Single nucleotide variants (SNVs) in intronic regions have yet to be systematically investigated for their diseasecausing potential. Using known pathogenic and neutral intronic SNVs (iSNVs) as training data, we develop the RegSNPs-intron algorithm based on a random forest classifier that integrates RNA splicing, protein structure, and evolutionary conservation features.
16p vielonmusk 30-01-2022 20 0 Download
-
Adenosine-to-inosine (A-to-I) editing of dsRNA by ADAR proteins is a pervasive epitranscriptome feature. Tens of thousands of A-to-I editing events are defined in the mouse, yet the functional impact of most is unknown. Editing causing protein recoding is the essential function of ADAR2, but an essential role for recoding by ADAR1 has not been demonstrated.
18p vialfrednobel 29-01-2022 8 0 Download
-
Single-cell transcriptomics reveals gene expression heterogeneity but suffers from stochastic dropout and characteristic bimodal expression distributions in which expression is either strongly non-zero or non-detectable. We propose a two-part, generalized linear model for such bimodal data that parameterizes both of these features.
13p viaristotle 29-01-2022 13 0 Download