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Articles by Ence Yang
Transposable elements drive species-specific and tissue-specific transcriptomes in human development - Genome Biology
We collected 9,175 short-read RNA-seq samples from several public databases, including the GTEx (by dbGaP, study accession: phs000424.v8.p2), ENCODE, and HPA project [30, 31, 62]. Long-read RNA-seq datasets were download from the GTEx, ENCODE, and the Gene Expression Omnibus database (GSE192955) [30, 31, 33]. CAGE datasets were download from the Fantom5 project (https://fantom.gsc.riken.jp/5/datafiles/latest/) [32].
Molecular landscape, subtypes, and therapeutic vulnerabilities of central nervous system solitary fibrous tumors - Nature Communications
Abstract Solitary fibrous tumors (SFTs) of the central nervous system (CNS) are rare, aggressive mesenchymal neoplasms with high recurrence and metastasis rates. Here, we perform a comprehensive multi-omics analysis of 189 cases of CNS SFTs integrating 94 whole genome sequencing, 88 transcriptomics, 7 single-nucleus RNA sequencing and 3 spatial transcriptome sequencing.
Common signatures of neutrophils in diverse disease conditions - Cell Discovery
Dear Editor, Neutrophils are traditionally recognized for their pro-inflammatory roles. However, accumulating evidence has begun to highlight the plasticity of transcriptional states of neutrophils during pathological insults. Whether such unconventional neutrophils share commonality across diverse disease conditions is incompletely understood.
Competitive antagonism of KAT7 crotonylation against acetylation affects procentriole formation and colorectal tumorigenesis - Nature Communications
Abstract Accurate procentriole formation is critical for centriole duplication. However, the holistic transcriptional regulatory mechanisms underlying this process remain elusive. Here, we show that KAT7 crotonylation, facilitated by the crotonyltransferase hMOF, competes against its acetylation regulated by the deacetylase HDAC2 at the K432 residue upon DNA damage stimulation.
Disease-specific suppressive granulocytes participate in glioma progression
Research topic(s) CP: Cancer Introduction The tumor immune microenvironment plays a determinant role in cancer progression and metastasis.
Lower ratio of IMPDH1 to IMPDH2 sensitizes gliomas to chemotherapy - Cancer Gene Therapy
Abstract Gliomas are the most common primary tumors of the central nervous system, with approximately half of patients presenting with the most aggressive form of glioblastoma. Although several molecular markers for glioma have been identified, they are not sufficient to predict the prognosis due to the extensive genetic heterogeneity within glioma. Our study reveals that the ratio of IMPDH1 to IMPDH2 expression levels serves as a molecular indicator for glioma treatment prognosis.
Regulatory basis for reproductive flexibility in a meningitis-causing fungal pathogen - Nature Communications
Media and growth conditions Yeast cells were grown routinely at 30 °C on YPD (1% yeast extract, 2% Bacto peptone, 2% dextrose, and 2% Bacto agar) medium. Sexual differentiation and bisexual cell–cell fusion assays were conducted on V8 agar (0.5 g/liter KH2PO4, 4% Bacto agar and 5% V8 juice, pH = 7.0) at 25 °C in the dark for the designated time period.
The landscape of hervRNAs transcribed from human endogenous retroviruses across human body sites - Genome Biology
Public dataset description In total, we collected 9466 samples across 42 body sites from 686 individuals in the GTEx Project [52], including RNA-seq data (FASTQ files), imputation genotyping data (VCF file), and whole-genome sequencing (WGS) data (FASTQ files). The details regarding the samples and sequencing methods are available by dbGaP (study accession: phs000424.v8.p2).
MTM: a multi-task learning framework to predict individualized tissue gene expression profiles
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Predicting individualized tissue gene expression profiles with multi-task learning
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Proceedings of the National Academy of Sciences of the United States of America
Carnivorism is one of the basic life strategies of fungi. Carnivorous fungi possess the ability to trap and digest their preys by sophisticated trapping devices. However, the origin and development of fungal carnivorism remains a gap in evolution biology.
Aberrant Gene Expression in Humans
Copyright: © 2015 Zeng et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Data Availability:All relevant data are within the paper and its Supporting Information files.
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