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TcellInflamedDetector: an R package to distinguish T cell inflamed tumor types from non–T cell inflamed tumor types

Yang SD, Park HS

A major issue in the use of immune checkpoint inhibitors is their lack of efficacy in many patients. Previous studies have reported that the T cell inflamed signature can help...
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Transcriptome Analysis Identifies Altered Biological Processes and Novel Markers in Human Immunodeficiency Virus-1 Long-Term Non-Progressors

Lee D, Yoon CH, Choi SY, Kim JE, Cho YK, Choi BS, Park J

Background: The latent reservoir of Human Immunodificiency Virus-1 (HIV-1) has been a major barrier to the complete eradication of HIV-1 and the development of HIV therapy. Longterm non-progressors (LTNPs) are...
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Age-Dependent Sensitivity to the Neurotoxic Environmental Metabolite, 1,2-Diacetylbenzene

Hoang NMH, Kim S, Nguyen HD, Kim M, Kim J, Kim BC, Park D, Lee S, Yu BP, Chung HY, Kim MS

1,2-Diacetylbenzene (DAB) is a metabolite of 1,2-diethylbenzene, which is commonly used in the manufacture of plastics and gasoline. We examined the neurotoxic effects of DAB in young and old rats,...
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Identification of a Novel CSNK2A1-PDGFRB Fusion Gene in a Patient with Myeloid Neoplasm with Eosinophilia

Xu X, Lu Q, Wang Z, Cai P, Zeng Z, Zhang L, Wang M, Ma L, Ruan C, Chen S

Platelet-derived growth factor receptor beta (PDGFRB) rearrangements play an important role in the pathogenesis of eosinophilia-associated myeloid/lymphoid neoplasms. Up to now, more than 70 PDGFRB fusions have been identified. Here,...
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Analysis of H3K4me3-ChIP-Seq and RNA-Seq data to understand the putative role of miRNAs and their target genes in breast cancer cell lines

Kotipalli A, Banerjee R, Kasibhatla SM, Joshi R

Breast cancer is one of the leading causes of cancer in women all over the world and accounts for ~25% of newly observed cancers in women. Epigenetic modifications influence differential...
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A protein interactions map of multiple organ systems associated with COVID-19 disease

Bharne D

Coronavirus disease 2019 (COVID-19) is an on-going pandemic disease infecting millions of people across the globe. Recent reports of reduction in antibody levels and the re-emergence of the disease in...
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Valproic Acid Enhance Reprogramming of Bactrian Camel Cells through Promoting the Expression of Endogenous Gene c-Myc and the Process of Angiogenesis

Li Z, Ge W, Li Y, Zhang Y, Zhao X, Hu J

Background and Objectives: Induced pluripotent stem cells (iPSCs) are usually generated by reprogramming differentiated cells through the introduction of specific transcription factors, but this is a difficult and inefficient process. Valproic...
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Reprogramming of Cancer Cells into Induced Pluripotent Stem Cells Questioned

Bang JS, Choi NY, Lee M, Ko K, Park YS, Ko K

BACKGROUND AND OBJECTIVES: Several recent studies have claimed that cancer cells can be reprogrammed into induced pluripotent stem cells (iPSCs). However, in most cases, cancer cells seem to be resistant...
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In silico approach to calculate the transcript capacity

Lee YS, Won KH, Oh JD, Shin D

We sought the novel concept, transcript capacity (TC) and analyzed TC. Our approach to estimate TC was through an in silico method. TC refers to the capacity that a transcript...
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FusionScan: accurate prediction of fusion genes from RNA-Seq data

Kim P, Jang YE, Lee S

Identification of fusion gene is of prominent importance in cancer research field because of their potential as carcinogenic drivers. RNA sequencing (RNA-Seq) data have been the most useful source for...
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Differential Gene Expression Common to Acquired and Intrinsic Resistance to BRAF Inhibitor Revealed by RNA-Seq Analysis

Ahn JH, Hwang SH, Cho HS, Lee M

Melanoma cells have been shown to respond to BRAF inhibitors; however, intrinsic and acquired resistance limits their clinical application. In this study, we performed RNA-Seq analysis with BRAF inhibitor-sensitive (A375P)...
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RNA-sequencing Profiles of Cell Cycle–Related Genes Upregulated during the G2-Phase in Giardia lamblia

Kim J, Shin MY, Park SJ

To identify the component(s) involved in cell cycle control in the protozoan Giardia lamblia, cells arrested at the G1/S- or G2-phase by treatment with nocodazole and aphidicolin were prepared from...
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Identification of ERBB Pathway-Activated Cells in Triple-Negative Breast Cancer

Cho SY

Intratumor heterogeneity within a single tumor mass is one of the hallmarks of malignancy and has been reported in various tumor types. The molecular characterization of intratumor heterogeneity in breast...
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NFATC3–PLA2G15 Fusion Transcript Identified by RNA Sequencing Promotes Tumor Invasion and Proliferation in Colorectal Cancer Cell Lines

Jang JE, Kim HP, Han SW, Jang H, Lee SH, Song SH, Bang D, Kim TY

PURPOSE: This study was designed to identify novel fusion transcripts (FTs) and their functional significance in colorectal cancer (CRC) lines. MATERIALS AND METHODS: We performed paired-end RNA sequencing of 28 CRC...
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COEX-Seq: Convert a Variety of Measurements of Gene Expression in RNA-Seq

Kim SC, Yu D, Cho SB

Next generation sequencing (NGS), a high-throughput DNA sequencing technology, is widely used for molecular biological studies. In NGS, RNA-sequencing (RNA-Seq), which is a short-read massively parallel sequencing, is a major...
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RNA-Seq De Novo Assembly and Differential Transcriptome Analysis of Korean Medicinal Herb Cirsium japonicum var. spinossimum

Roy NS, Kim JA, Choi AY, Ban YW, Park NI, Park KC, Yang HS, Choi IY, Kim S

Cirsium japonicum belongs to the Asteraceae or Compositae family and is a medicinal plant in Asia that has a variety of effects, including tumour inhibition, improved immunity with flavones, and...
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RNA-Seq for Gene Expression Profiling of Human Necrotizing Enterocolitis: a Pilot Study

Jung K, Koh I, Kim JH, Cheong HS, Park T, Nam SH, Jung SM, Sio CA, Kim SY, Jung E, Lee B, Kim HR, Shin E, Jung SE, Choi CW, Kim BI, Jung E, Shin HD

Necrotizing enterocolitis (NEC) characterized by inflammatory intestinal necrosis is a major cause of mortality and morbidity in newborns. Deep RNA sequencing (RNA-Seq) has recently emerged as a powerful technology enabling...
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Investigation of Splicing Quantitative Trait Loci in Arabidopsis thaliana

Yoo W, Kyung S, Han S, Kim S

The alteration of alternative splicing patterns has an effect on the quantification of functional proteins, leading to phenotype variation. The splicing quantitative trait locus (sQTL) is one of the main...
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A known expressed sequence tag, BM742401, is a potent lincRNA inhibiting cancer metastasis

Park SM, Park SJ, Kim HJ, Kwon OH, Kang TW, Sohn HA, Kim SK, Moo Noh S, Song KS, Jang SJ, Sung Kim Y, Kim SY

  • KMID: 2154250
  • Exp Mol Med.
  • 2013 Jul;45(7):e31.
Long intergenic non-coding RNAs (lincRNAs) have historically been ignored in cancer biology. However, thousands of lincRNAs have been identified in mammals using recently developed genomic tools, including microarray and high-throughput...
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Bioinformatics Approaches for the Identification and Annotation of RNA Editing Sites

Lee SY, Kim JH

Post-transcriptional nucleotide sequence modification of transcripts by RNA editing is an important molecular mechanism in the regulation of protein function and is associated with a variety of human disease phenotypes....
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