HisCoM-PAGE: software for hierarchical structural component models for pathway analysis of gene expression data by Lydia Mok, Taesung Park

“…It can be applied to various types of gene expression data, such as microarray data or RNA sequencing data. We expect that the HisCoM-PAGE software will make our method more easily accessible to researchers who want to perform pathway analysis for survival times.…”
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Molecular Detection and Characterization of Goat Isolate of Taenia hydatigena in Turkey by Armagan Erdem Utuk, Fatma Cigdem Piskin

“…According to rrnS-PCR results, parasites were identified as Taenia spp., and partial sequence of mt-CO1 gene was corresponding to T. hydatigena. …”
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Outbreak of white piedra in a flock of Extremeña blue hens by García Alfredo, Barraso Carmen

“…The diagnosis of Trichosporon jirovecii was made by morphological identification, and it was confirmed by sequencing amplification product of the PCR using universal primers of the internal transcribed spacer region.…”
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Chemotaxis Away from 4-Chloro-2-nitrophenol, 4-Nitrophenol, and 2,6-Dichloro-4-nitrophenol by Bacillus subtilis PA-2 by Pankaj Kumar Arora, Mi-Jeong Jeong, Hanhong Bae

“…This strain was identified as Bacillus subtilis on the basis of the 16S rRNA gene sequencing. The drop plate assay and the chemical-in-plug method were used to demonstrate negative chemotactic behavior of strain PA-2. …”
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Charcot-Marie-Tooth disease: A case report initially manifested by bilateral vocal cord paralysis by Seyed Hossein Mirlohi, Sanaz Tajfirooz, Mitra Rouhi

“…Diagnosis was confirmed through whole genome sequencing, revealing mutations in genes associated with the disorder.…”
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Molecular Basis of Triple Negative Breast Cancer and Implications for Therapy by Parvin F. Peddi, Matthew J. Ellis, Cynthia Ma

“…Recent genomewide gene expression and DNA sequencing studies indicate that this cancer type is composed of a molecularly heterogeneous group of diseases that carry multiple somatic mutations and genomic structural changes. …”
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One Fungus = One Name: DNA and fungal nomenclature twenty years after PCR by J.W. Taylor

“…A nomenclatorial crisis also looms due to environmental sequencing, which suggests that most fungi will have to be named without a physical specimen. …”
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Description of Two New ABCB11 Mutations Responsible for Type 2 Benign Recurrent Intrahepatic Cholestasis in a French-Canadian Family by Yannick Beauséjour, Fernando Alvarez, Martin Beaulieu, Marc Bilodeau

“…The present report describes two individuals from the same family whose symptoms were typical of the clinical characteristics of type 2 benign recurrent intrahepatic cholestasis. Sequencing of the ABCB11 gene revealed two previously unreported mutations that predict the absence of expression of the protein. …”
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Identification of ERBB Pathway-Activated Cells in Triple-Negative Breast Cancer by Soo Young Cho

“…Using single-cell RNA sequencing (RNA-seq) data from a public resource, an ERBB pathway activated triple-negative cell population was identified. …”
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Molecular Identification of Enterocytozoon bieneusi Isolates from Nigerian Children by Adekunle Bamidele Ayinmode, Oladele Teslim Ojuromi, Lihua Xiao

“…Using nested polymerase chain reaction, 9.3% of the children were identified as positive for Enterocytozoon bieneusi. DNA sequencing of the PCR products showed the presence of three known genotypes (two isolates of genotype D and one of genotype K) and one new genotype. …”
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Severe Congenital Toxoplasmosis: A Case Report and Strain Characterization by Bahador Sarkari, Samaneh Abdolahi Khabisi

“…Amniotic fluid was taken and evaluated by polymerase chain reaction (PCR) assay with a direct amplification of the Toxoplasma URPT gene which was found to be positive. Sequencing and analysis of PCR product revealed that the isolate has the most similarity with type I of Toxoplasma gondii. …”
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The Transcribed-Ultraconserved Regions: A Novel Class of Long Noncoding RNAs Involved in Cancer Susceptibility by Paola Scaruffi

“…A large proportion of the transcriptional output is represented by protein noncoding RNAs (ncRNAs) that arise from the “dark matter” of the genome. Focus on such sequences has revealed numerous RNA subtypes with several functions in RNA processing and gene expression regulation, and deep sequencing studies imply that many remain to be discovered. …”
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ANO7 expression in the prostate modulates mitochondrial function and lipid metabolism by Christoffer Löf, Nasrin Sultana, Neha Goel, Samuel Heron, Gudrun Wahlström, Andrew House, Minna Holopainen, Reijo Käkelä, Johanna Schleutker

“…Methods We performed RNA-sequencing (RNA-seq) on RWPE1 cells engineered to express ANO7 protein, alongside the analysis of a single-cell RNA-sequencing (scRNA-seq) dataset and RNA-seq from prostate tissues. …”
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Qinggan Yipi capsule ameliorates hepatic fibrosis in rats by down-regulating the TGF-β1/Smad2/3 signaling pathway and improving gut microbiota imbalance by Wenjing Xue, Haiqing Liu, Ziheng Su, Siqi Wang, Junping Cheng, Yunzhi Pan, Lurong Zhang

“…The composition of the gut microbiota was analyzed using 16S rRNA gene sequencing.ResultsHistopathological analysis, serum biochemical tests, and ELISA measurements showed that QgYp effectively decreased the levels of ALT, AST, HA, LN, PCIII, and IV-C while improving collagen deposition and hepatocyte necrosis. …”
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Intercellular TIMP-1-CD63 signaling directs the evolution of immune escape and metastasis in KRAS-mutated pancreatic cancer cells by Chu-An Wang, Ya-Chin Hou, Yi-Kai Hong, Yu-Jing Tai, Chieh Shen, Pei-Chi Hou, Jhao-Lin Fu, Cheng-Lin Wu, Siao Muk Cheng, Daw-Yang Hwang, Yung-Yeh Su, Yan-Shen Shan, Shaw-Jenq Tsai

“…Methods Single-cell RNA sequencing and analysis of primary PDAC tumors were conducted. …”
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Population Structure Based on Microsatellite Length Polymorphism, Antifungal Susceptibility Profile, and Enzymatic Activity of <i>Candida auris</i> Clinical Isolates in Russia by Ellina Oganesyan, Victoria Klimenteva, Irina Vybornova, Valentina Venchakova, Ekaterina Parshikova, Sergey Kovyrshin, Olga Orlova, Alexander Kruglov, Svetlana Gordeeva, Natalya Vasilyeva, Anastasiya Taraskina

“…Species identification was confirmed by ITS sequencing, and genotyping was performed using 12 short tandem repeat (STR) markers. …”
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Hsa-miR-532-3p protects human decidual mesenchymal stem cells from oxidative stress in recurrent spontaneous abortion via targeting KEAP1 by Hong Zhou, Jiaxin Zhou, ShanShan Liu, Jing Niu, Jinghua Pan, Ruiman Li

“…Furthermore, differentially expressed miRNAs in hDMSCs were analyzed through miRNA sequencing. We evaluated the interaction between hsa-miR-532-3p and KEAP1 using a luciferase reporter assay. …”
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Immune infiltration landscape and potential drug-targeted implications for hepatocellular carcinoma with ‘progression/hyper-progression’ recurrence by Jing-Xuan Xu, Yue-Xiang Su, Yuan-Yuan Chen, Yi-Yue Huang, Zu-Shun Chen, Yu-Chong Peng, Lu-Nan Qi

“…Virtual docking was used to identify potential therapeutic targets, and the results were verified using single-nuclei RNA sequencing and histological analysis.Results ITM was closely related to type III–IV recurrence and exhibited immunotherapy potential. …”
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A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators by Yuji Ke, Vincent Pujol, Jasper Staut, Lotte Pollaris, Ruth Seurinck, Thomas Eekhout, Carolin Grones, Maite Saura-Sanchez, Michiel Van Bel, Marnik Vuylsteke, Andrea Ariani, Christophe Liseron-Monfils, Klaas Vandepoele, Yvan Saeys, Bert De Rybel

“…Summary: Despite the broad use of single-cell/nucleus RNA sequencing in plant research, accurate cluster annotation in less-studied plant species remains a major challenge due to the lack of validated marker genes. …”
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Optimized Method to Generate Well-Characterized Macrophages from Induced Pluripotent Stem Cells by Qimin Hai, Peter Bazeley, Juying Han, Gregory Brubaker, Jennifer Powers, Claudia M. Diaz-Montero, Jonathan D. Smith

“…The first three principal components of the RNA sequencing data showed clear clustering by differentiation stage. …”
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