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Bioinformatics
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Article
Open AccessexpHRD: an individualized, transcriptome-based prediction model for homologous recombination deficiency assessment in cancer
Homologous recombination deficiency (HRD) stands as a clinical indicator for discerning responsive outcomes to platinum-based chemotherapy and poly ADP-ribose polymerase (PARP) inhibitors. One of the conventio...
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TGF-β1-Induced LINC01094 promotes epithelial-mesenchymal transition in hepatocellular carcinoma through the miR-122-5p/TGFBR2–SAMD2–SMAD3 Axis
Hepatocellular carcinoma (HCC) is a common malignancy with a poor prognosis. It has been proven that long non-coding RNAs (lncRNAs) play an essential role in regulating HCC progression. However, the involvemen...
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Open AccessTemplate-independent enzymatic synthesis of RNA oligonucleotides
RNA oligonucleotides have emerged as a powerful therapeutic modality to treat disease, yet current manufacturing methods may not be able to deliver on anticipated future demand. Here, we report the development...
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Enzymatic synthesis of RNA oligonucleotides
Research on enzymatic RNA synthesis has long been eclipsed by work on DNA—but a new method provides a leap forward for RNA.
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Open AccessPrecise in vivo RNA base editing with a wobble-enhanced circular CLUSTER guide RNA
Recruiting the endogenous editing enzyme adenosine deaminase acting on RNA (ADAR) with tailored guide RNAs for adenosine-to-inosine (A-to-I) RNA base editing is promising for safely manipulating genetic inform...
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Exosome theranostics: Comparative analysis of P body and exosome proteins and their mutations for clinical applications
Exosomes are lipid-bilayered vesicles, originating from early endosomes that capture cellular proteins and genetic materials to form multi-vesicular bodies. These exosomes are secreted into extracellular fluid...
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Open AccessTranscriptome- and DNA methylation-based cell-type deconvolutions produce similar estimates of differential gene expression and differential methylation
Changing cell-type proportions can confound studies of differential gene expression or DNA methylation (DNAm) from peripheral blood mononuclear cells (PBMCs). We examined how cell-type proportions derived from...
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Open AccessA strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques
The growing abundance of in vitro omics data, coupled with the necessity to reduce animal testing in the safety assessment of chemical compounds and even eliminate it in the evaluation of cosmetics, highlights...
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Open AccessSimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies
SimSpliceEvol is a tool for simulating the evolution of eukaryotic gene sequences that integrates exon-intron structure evolution as well as the evolution of the sets of transcripts produced from genes. It tak...
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CAR-Ts sweep into autoimmunity
Biotechs are equip** CAR-T cells to destroy B cells — not to treat blood cancers, but to take on multiple sclerosis and a raft of autoimmune disorders.
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Open AccessTFscope: systematic analysis of the sequence features involved in the binding preferences of transcription factors
Characterizing the binding preferences of transcription factors (TFs) in different cell types and conditions is key to understand how they orchestrate gene expression. Here, we develop TFscope, a machine learn...
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Open AccesssciMET-cap: high-throughput single-cell methylation analysis with a reduced sequencing burden
DNA methylation is a key component of the mammalian epigenome, playing a regulatory role in development, disease, and other processes. Robust, high-throughput single-cell DNA methylation assays are now possibl...
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Circ-IP6K2 suppresses tumor progression by modulating the miR-1292-5p/CAMK2N1 signal in clear cell renal cell carcinoma
Renal cell carcinoma (RCC) is a malignant tumor originating from the epithelial cells of the renal tubules. The clear cell RCC subtype is closely linked to a poor prognosis due to its rapid progression. Circul...
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Open Accessgcplyr: an R package for microbial growth curve data analysis
Characterization of microbial growth is of both fundamental and applied interest. Modern platforms can automate collection of high-throughput microbial growth curves, necessitating the development of computati...
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Open AccessProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing
Structural variations play an important role in bacterial genomes. They can mediate genome adaptation quickly in response to the external environment and thus can also play a role in antibiotic resistance. The...
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Open AccessAuthor Correction: CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes
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Open AccessDetection of allele-specific expression in spatial transcriptomics with spASE
Spatial transcriptomics technologies permit the study of the spatial distribution of RNA at near-single-cell resolution genome-wide. However, the feasibility of studying spatial allele-specific expression (ASE...
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Purifying selection drove the adaptation of mitochondrial genes along with correlation of gene rearrangements and evolutionary rates in two subfamilies of Whitefly (Insecta: Hemiptera)
Insect mitochondrial genomes (mitogenomes) are usually represented by a conserved gene order. Whiteflies exhibit gene rearrangement in their mitogenomes; however, understanding how nucleotide substitution rate...
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Open AccessMassively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the yeast noncanonical translatome
Recent studies uncovered pervasive transcription and translation of thousands of noncanonical open reading frames (nORFs) outside of annotated genes. The contribution of nORFs to cellular phenotypes is difficu...
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Open AccessPanpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis
Single-cell multiomic analysis of the epigenome, transcriptome, and proteome allows for comprehensive characterization of the molecular circuitry that underpins cell identity and state. However, the holistic i...
