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Bioinformatics
Microbial Genetics and Genomics
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Article
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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CRISPR-Cas9-mediated deletion enhancer of MECOM play a tumor suppressor role in ovarian cancer
MDS1 and EVI1 complex locus (MECOM), a transcription factor encoding several variants, has been implicated in progression of ovarian cancer. The function of regulatory regions in regulating MECOM expression in...
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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 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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Open AccessLateral root enriched Massilia associated with plant flowering in maize
Beneficial associations between plants and soil microorganisms are critical for crop fitness and resilience. However, it remains obscure how microorganisms are assembled across different root compartments and ...
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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 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...
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Open AccessThe contribution of silencer variants to human diseases
Although disease-causal genetic variants have been found within silencer sequences, we still lack a comprehensive analysis of the association of silencers with diseases. Here, we profiled GWAS variants in 2.8 ...
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Open AccessTaqTth-hpRNA: a novel compact RNA-targeting tool for specific silencing of pathogenic mRNA
Pathogenic allele silencing is a promising treatment for genetic hereditary diseases. Here, we develop an RNA-cleaving tool, TaqTth-hpRNA, consisting of a small, chimeric TaqTth, and a hairpin RNA guiding prob...
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Open AccessCultivation of novel Atribacterota from oil well provides new insight into their diversity, ecology, and evolution in anoxic, carbon-rich environments
The Atribacterota are widely distributed in the subsurface biosphere. Recently, the first Atribacterota isolate was described and the number of Atribacterota genome sequences retrieved from environmental samples ...
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Open AccessFecal microbiota transplantation alters gut phage communities in a clinical trial for obesity
Fecal microbiota transplantation (FMT) is a therapeutic intervention used to treat diseases associated with the gut microbiome. In the human gut microbiome, phages have been implicated in influencing human hea...
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Open AccessAuthor Correction: The shaky foundations of simulating single-cell RNA sequencing data
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Open AccessMetatranscriptomics-guided genome-scale metabolic reconstruction reveals the carbon flux and trophic interaction in methanogenic communities
Despite rapid advances in genomic-resolved metagenomics and remarkable explosion of metagenome-assembled genomes (MAGs), the function of uncultivated anaerobic lineages and their interactions in carbon mineral...
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Open AccessLongTR: genome-wide profiling of genetic variation at tandem repeats from long reads
Tandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatl...
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Sha** Drosophila eggs: unveiling the roles of Arpc1 and cpb in morphogenesis
The Drosophila egg chamber (EC) starts as a spherical tissue at the beginning. With maturation, the outer follicle cells of EC collectively migrate in a direction perpendicular to the anterior-posterior axis, to ...
