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Journal articles on the topic 'SEQ-C'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Ferreira, Daneelly H., Maria das Graças X. Carvalho, Maria J. Nardelli, Francisca G. C. Sousa, and Celso J. B. Oliveira. "Occurrence of enterotoxin-encoding genes in Staphylococcus aureus causing mastitis in lactating goats." Pesquisa Veterinária Brasileira 34, no. 7 (2014): 633–36. http://dx.doi.org/10.1590/s0100-736x2014000700004.

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Staphylococcal enterotoxins are the leading cause of human food poisoning worldwide. Staphylococcus spp. are the main mastitis-causing agents in goats and frequently found in high counts in goat milk. This study aimed to investigate the occurrence of enterotoxin-encoding genes in Staphylococcus aureus associated with mastitis in lactating goats in Paraiba State, Brazil. Milk samples (n=2024) were collected from 393 farms. Staphylococcus aureus was isolated in 55 milk samples. Classical (sea, seb, sec, sed, see) and novel (seg, seh, sei) enterotoxin-encoding genes were investigated by means of

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2

Lee, Kyuwon, Areum Han, and Tae Hui Kim. "Effectiveness of Simulation-Based Empathy Enhancement Program for Caregivers (SEE-C) Evaluated by Older Adults Receiving Care." International Journal of Environmental Research and Public Health 18, no. 15 (2021): 7802. http://dx.doi.org/10.3390/ijerph18157802.

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The aim of this study was to examine whether a Simulation-based Empathy Enhancement program for Caregivers of the Elderly (SEE-C) was effective in increasing program satisfaction and positive emotional changes of older adults. A total of 100 older adults living alone were randomly assigned to experimental and control groups. The experimental group was interviewed by caregivers who experienced SEE-C while the control group was interviewed by caregivers who did not experience SEE-C. In both elderly groups, post session satisfaction and affective state were assessed using a Session Evaluation Que

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3

Wang, Hengtao, Meiling Liang, Jiajia Wu, Xia Peng, Kuangzheng Zhu, and Zhuqing Zheng. "Strategies of Integrated Analysis of ATAC-seq and RNA-seq Data." Science of Advanced Materials 16, no. 1 (2024): 130–40. http://dx.doi.org/10.1166/sam.2024.4599.

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The ATAC-seq and RNA-seq have been widely used in the epigenomes analysis of mammals. However, there is a lack of comprehensive integrated analysis of ATAC-seq and RNA-seq data. Here, we explored two effective strategies for analyzing ATAC-seq and RNA-seq data using proliferation and differentiation myoblast cells as model. One strategy is a joint analysis by integrating Hi-C data with ATAC-seq and RNA-seq data. The other strategy is to investigate the association between ATAC-seq and RNA-seq data only based on genome physical distance in the case of no availability of Hi-C data. Hi-C data-bas

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4

PEXARA, A., A. BOURRIEL, and A. GOVARIS. "Staphylococcus aureus and Staphylococcal enterotoxins in foodborne diseases." Journal of the Hellenic Veterinary Medical Society 61, no. 4 (2018): 316. http://dx.doi.org/10.12681/jhvms.14904.

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Staphylococcal food poisoning (SFP) is one of the most significant foodborne diseases. It is a mild intoxication, which is caused by the ingestion of food containing one or more preformed staphylococcal enterotoxins (SEs). The toxic dose of SEs in human is usually ranged from 20 ng to 1 μg. SEs are proteins produced by Staphylococcus spp in various parts of the environment, including foods. Although several staphylococci can produce SEs, the majority of SFP cases is attributed to S. aureus. Traditionally, five antigenic SE types have been recognized: SEA, SEB, SEC, SED and SEE. During the 1990

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5

Casuso, Antonio, Valentina Valenzuela-Muñoz, and Cristian Gallardo-Escárate. "Dual RNA-Seq Analysis Reveals Transcriptome Effects during the Salmon–Louse Interaction in Fish Immunized with Three Lice Vaccines." Vaccines 10, no. 11 (2022): 1875. http://dx.doi.org/10.3390/vaccines10111875.

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Due to the reduced efficacy of delousing drugs used for sea lice control in salmon aquaculture, fish vaccines have emerged as one of the most sustainable strategies in animal health. Herein, the availability of C. rogercresseyi and Salmo salar genomes increases the capability of identifying new candidate antigens for lice vaccines using RNA sequencing and computational tools. This study aimed to evaluate the effects of two recombinant antigens characterized as peritrophin and cathepsin proteins on the transcriptome profiling of Atlantic salmon during a sea lice infestation. Four experimental g

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Bhardwaj, Vivek, Steffen Heyne, Katarzyna Sikora, et al. "snakePipes: facilitating flexible, scalable and integrative epigenomic analysis." Bioinformatics 35, no. 22 (2019): 4757–59. http://dx.doi.org/10.1093/bioinformatics/btz436.

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Abstract Summary Due to the rapidly increasing scale and diversity of epigenomic data, modular and scalable analysis workflows are of wide interest. Here we present snakePipes, a workflow package for processing and downstream analysis of data from common epigenomic assays: ChIP-seq, RNA-seq, Bisulfite-seq, ATAC-seq, Hi-C and single-cell RNA-seq. snakePipes enables users to assemble variants of each workflow and to easily install and upgrade the underlying tools, via its simple command-line wrappers and yaml files. Availability and implementation snakePipes can be installed via conda: `conda in

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7

Leung, Ka-Man, Pak-Kwong Chung, Tin-Lok Yuen, Jing Dong Liu, and Donggen Wang. "Psychometric Properties of the Modified Social Environment Questionnaire in Chinese Older Adults." Journal of Aging and Physical Activity 26, no. 4 (2018): 530–36. http://dx.doi.org/10.1123/japa.2017-0044.

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This study evaluated the psychometric properties of a Chinese version of the 24-item Social Environment Questionnaire (SEQ-C). Confirmatory factor analysis was used to examine the factor validity and measurement invariance (Purpose 1) of the SEQ-C in 453 older adults in Hong Kong. Convergent validity (Purpose 2) and test–retest reliability (Purpose 3) were also measured. The results of the confirmatory factor analysis and measurement invariance supported the four-factor structure (representing companionship, encouragement, neighborhood social cohesion, and role models) of the SEQ-C, in a 15-it

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8

Semaan, Karl, Marc Eid, Damien Vasseur, et al. "Abstract 5926: Determining classical-basal transcriptional subtypes of pancreatic ductal adenocarcinoma using circulating tumor DNA epigenomic profiling." Cancer Research 85, no. 8_Supplement_1 (2025): 5926. https://doi.org/10.1158/1538-7445.am2025-5926.

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Abstract Introduction: Classical (C) and basal (B) transcriptional subtypes are key prognostic biomarkers of pancreatic ductal adenocarcinoma (PDAC). The B subtype is associated with higher rates of metastases, chemoresistance and poor outcomes. Early data suggest that the B subtype may predict response to KRAS inhibition. Current subtyping methods rely on tissue biopsies, which may not capture subtype heterogeneity, and are difficult to implement clinically. Here, we report a novel non-invasive approach for PDAC subtyping based on profiling circulating tumor chromatin. Methods: RNA-seq, chrom

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Mladineo, Ivona, Jerko Hrabar, Željka Trumbić, et al. "Community Parameters and Genome-Wide RAD-Seq Loci of Ceratothoa oestroides Imply Its Transfer between Farmed European Sea Bass and Wild Farm-Aggregating Fish." Pathogens 10, no. 2 (2021): 100. http://dx.doi.org/10.3390/pathogens10020100.

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Wild fish assemblages that aggregate within commercial marine aquaculture sites for feeding and shelter have been considered as a primary source of pathogenic parasites vectored to farmed fish maintained in net pens at an elevated density. In order to evaluate whether Ceratothoa oestroides (Isopoda, Cymothoidae), a generalist and pestilent isopod that is frequently found in Adriatic and Greek stocks of farmed European sea bass (Dicentrarchus labrax), transfers between wild and farmed fish, a RAD-Seq (restriction-site-associated DNA sequencing)-mediated genetic screening approach was employed.

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10

Uyar, B., J. S. C. Chu, I. A. Vergara, et al. "RNA-seq analysis of the C. briggsae transcriptome." Genome Research 22, no. 8 (2012): 1567–80. http://dx.doi.org/10.1101/gr.134601.111.

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11

Yuan, Fang, Ying Bi, Paulina Siejka-Zielinska, Ying-Lin Zhou, Xin-Xiang Zhang, and Chun-Xiao Song. "Bisulfite-free and base-resolution analysis of 5-methylcytidine and 5-hydroxymethylcytidine in RNA with peroxotungstate." Chemical Communications 55, no. 16 (2019): 2328–31. http://dx.doi.org/10.1039/c9cc00274j.

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WO-Seq: a bisulfite-free and base-resolution sequencing method based on peroxotungstate oxidation is presented for the identification of hm<sup>5</sup>C sites in the transcriptome. Combining the peroxotungstate oxidation with TET enzyme oxidation, m<sup>5</sup>C can also be detected in a procedure termed TET-Assisted WO-Seq (TAWO-Seq).

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Abdesselam, Djihane, Mallory Frederick, and Saima N. Hassan. "Abstract 5722: Gene expression analysis of different PARPi combination approaches with carboplatin at primary tumor and metastatic site in xenograft model of triple-negative breast cancer." Cancer Research 85, no. 8_Supplement_1 (2025): 5722. https://doi.org/10.1158/1538-7445.am2025-5722.

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Introduction: Patients with triple-negative breast cancer (TNBC) do not overexpress hormone receptors or HER2, leaving limited therapeutic options. Despite the improvement in outcomes for patients with early TNBC, patients only benefit from one targeted therapeutic agent: PARP inhibitors (PARPi). By targeting PARP-1/2, PARPi function via catalytic inhibition, thereby inducing synthetic lethality in BRCA1/2-mutant contexts, or via PARP-DNA trapping. Two potent PARPi have demonstrated efficacy in the clinic amongst BRCA1/2-mutant patients, with talazoparib and olaparib improving progression-free

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Dohn, Ryan, Bingqing Xie, Rebecca Back, et al. "mDrop-Seq: Massively Parallel Single-Cell RNA-Seq of Saccharomyces cerevisiae and Candida albicans." Vaccines 10, no. 1 (2021): 30. http://dx.doi.org/10.3390/vaccines10010030.

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Advances in high-throughput single-cell RNA sequencing (scRNA-seq) have been limited by technical challenges such as tough cell walls and low RNA quantity that prevent transcriptomic profiling of microbial species at throughput. We present microbial Drop-seq or mDrop-seq, a high-throughput scRNA-seq technique that is demonstrated on two yeast species, Saccharomyces cerevisiae, a popular model organism, and Candida albicans, a common opportunistic pathogen. We benchmarked mDrop-seq for sensitivity and specificity and used it to profile 35,109 S. cerevisiae cells to detect variation in mRNA leve

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Rosen, Jonathan D., Yuchen Yang, Armen Abnousi, et al. "HPRep: Quantifying Reproducibility in HiChIP and PLAC-Seq Datasets." Current Issues in Molecular Biology 43, no. 2 (2021): 1156–70. http://dx.doi.org/10.3390/cimb43020082.

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HiChIP and PLAC-Seq are emerging technologies for studying genome-wide long-range chromatin interactions mediated by the protein of interest, enabling more sensitive and cost-efficient interrogation of protein-centric chromatin conformation. However, due to the unbalanced read distribution introduced by protein immunoprecipitation, existing reproducibility measures developed for Hi-C data are not appropriate for the analysis of HiChIP and PLAC-Seq data. Here, we present HPRep, a stratified and weighted correlation metric derived from normalized contact counts, to quantify reproducibility in Hi

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15

Qian, Jianpu, Wenli Liu, Yanna Shi, et al. "C-CorA: A Cluster-Based Method for Correlation Analysis of RNA-Seq Data." Horticulturae 8, no. 2 (2022): 124. http://dx.doi.org/10.3390/horticulturae8020124.

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Correlation analysis is a routine method of biological data analysis. In the process of RNA-Seq analysis, differentially expressed genes could be identified by calculating the correlation coefficients in the comparison of gene expression vs. phenotype or gene expression vs. gene expression. However, due to the complicated genetic backgrounds of perennial fruit, the correlation coefficients between phenotypes and genes are usually not high in fruit quality studies. In this study, a cluster-based correlation analysis method (C-CorA) is presented for fruit RNA-Seq analysis. C-CorA is composed of

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16

Affandi, Ghozali Rusyid, Widyastuti Widyastuti, and Mohammad Faizal Amir. "Adaptation and Validation of the Self-Efficacy Questionnaire for Children (SEQ-C) for Indonesian Orphanage Students." Jurnal Kependidikan: Jurnal Hasil Penelitian dan Kajian Kepustakaan di Bidang Pendidikan, Pengajaran dan Pembelajaran 8, no. 3 (2022): 521. http://dx.doi.org/10.33394/jk.v8i3.5809.

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This study aims to adapt the Self-Efficay Questionnaire for Children (SEQ-C) into Indonesian and analyze the quality of its psychometric properties. The adaptation model refers to the concept developed by Beaton with 5 (five) stages, including initial translation, synthesis of the translations, back translation, expert committee, and pre-final version testing. This research method used descriptive quantitative by adapting measuring instruments. This research was conducted offline and online on students who live in the Aisyiyah Orphanage in East Java and students who are cared for by their pare

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17

Zhong, Hui, Ran Zhang, Guihuan Li, et al. "c-JUN is a barrier in hESC to cardiomyocyte transition." Life Science Alliance 6, no. 11 (2023): e202302121. http://dx.doi.org/10.26508/lsa.202302121.

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Loss of c-JUN leads to early mouse embryonic death, possibly because of a failure to develop a normal cardiac system. How c-JUN regulates human cardiomyocyte cell fate remains unknown. Here, we used the in vitro differentiation of human pluripotent stem cells into cardiomyocytes to study the role of c-JUN. Surprisingly, the knockout of c-JUN improved cardiomyocyte generation, as determined by the number of TNNT2+ cells. ATAC-seq data showed that the c-JUN defect led to increased chromatin accessibility on critical regulatory elements related to cardiomyocyte development. ChIP-seq data showed t

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18

Chan, Kok-Gan, Kumutha Priya, Chien-Yi Chang, Ahmad Yamin Abdul Rahman, Kok Keng Tee, and Wai-Fong Yin. "Transcriptome analysis ofPseudomonas aeruginosaPAO1 grown at both body and elevated temperatures." PeerJ 4 (July 19, 2016): e2223. http://dx.doi.org/10.7717/peerj.2223.

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Functional genomics research can give us valuable insights into bacterial gene function. RNA Sequencing (RNA-seq) can generate information on transcript abundance in bacteria following abiotic stress treatments. In this study, we used the RNA-seq technique to study the transcriptomes of the opportunistic nosocomial pathogenPseudomonas aeruginosaPAO1 following heat shock. Samples were grown at both the human body temperature (37 °C) and an arbitrarily-selected temperature of 46 °C. In this work using RNA-seq, we identified 133 genes that are differentially expressed at 46 °C compared to the hum

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Liu, Tong, and Zheng Wang. "DeepChIA-PET: Accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks." PLOS Computational Biology 19, no. 7 (2023): e1011307. http://dx.doi.org/10.1371/journal.pcbi.1011307.

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Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) can capture genome-wide chromatin interactions mediated by a specific DNA-associated protein. The ChIA-PET experiments have been applied to explore the key roles of different protein factors in chromatin folding and transcription regulation. However, compared with widely available Hi-C and ChIP-seq data, there are not many ChIA-PET datasets available in the literature. A computational method for accurately predicting ChIA-PET interactions from Hi-C and ChIP-seq data is needed that can save the efforts of performing wet-lab

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Savary, Romain, Daniel J. Barshis, Christian R. Voolstra, et al. "Fast and pervasive transcriptomic resilience and acclimation of extremely heat-tolerant coral holobionts from the northern Red Sea." Proceedings of the National Academy of Sciences 118, no. 19 (2021): e2023298118. http://dx.doi.org/10.1073/pnas.2023298118.

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Corals from the northern Red Sea and Gulf of Aqaba exhibit extreme thermal tolerance. To examine the underlying gene expression dynamics, we exposed Stylophora pistillata from the Gulf of Aqaba to short-term (hours) and long-term (weeks) heat stress with peak seawater temperatures ranging from their maximum monthly mean of 27 °C (baseline) to 29.5 °C, 32 °C, and 34.5 °C. Corals were sampled at the end of the heat stress as well as after a recovery period at baseline temperature. Changes in coral host and symbiotic algal gene expression were determined via RNA-sequencing (RNA-Seq). Shifts in co

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Fukuda, Akari, Tatsuro Hirose, Yoichi Hashida, Naohiro Aoki, and Atsushi J. Nagano. "Selection of transcripts related to low-temperature tolerance using RNA sequencing from F2 plants between japonica and indica rice (Oryza sativa L.) cultivars." Functional Plant Biology 48, no. 10 (2021): 984. http://dx.doi.org/10.1071/fp21088.

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At low temperatures (18°C), seedlings of an indica rice (Oryza sativa L.) cultivar Kasalath showed symptoms of chlorosis, although the leaves of a japonica cultivar Arroz da Terra remained green. In this study, transcripts related to the chlorophyll content of rice seedlings grown at 18°C were investigated using RNA-sequencing (RNA-Seq) data for F2 crosses between cultivars Arroz da Terra and Kasalath, as well as their parental cultivars. Differential expression analysis revealed that gene ontology terms related to ‘photosynthesis’ were significantly enriched in lowly expressed genes at 18°C t

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OH, SU KYUNG, NARI LEE, YOUNG SUN CHO, DONG-BIN SHIN, SOON YOUNG CHOI, and MINSEON KOO. "Occurrence of Toxigenic Staphylococcus aureus in Ready-to-Eat Food in Korea." Journal of Food Protection 70, no. 5 (2007): 1153–58. http://dx.doi.org/10.4315/0362-028x-70.5.1153.

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Toxigenic Staphylococcus aureus contamination in ready-to-eat (RTE) food is a leading cause of foodborne illness in Korea. To monitor food contamination by S. aureus, a total of 3,332 RTE food samples were selected from nationwide wholesale marts between 2003 and 2004 and examined. A total of 285 (8.6%) of the overall samples were contaminated by S. aureus. According to the analysis, 31.6% of the tested cream-cakes, 19.8% of the raw fish, and 19.3% of the rice cakes with filling were contaminated with S. aureus. Forty-seven percent of the strains isolated from the contaminated food were entero

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23

Kim, Youngmi, Kyeongmo Kim, and Shinhye Lee. "Testing the Self-Efficacy Questionnaire With Korean Children in Institutionalized Care." Research on Social Work Practice 27, no. 6 (2015): 734–42. http://dx.doi.org/10.1177/1049731515606219.

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Purpose: We tested the reliability and validity of the Self-Efficacy Questionnaire for Children (SEQ-C) in a sample of children living in orphanages in South Korea. Methods: Our study sample consisted of 334 children aged 13–18 obtained using a convenience sampling method. We conducted a confirmatory factor analysis to identify the factor structure of the 24 self-efficacy items and used a Pearson correlation to explore the scale’s validity. Results: The findings show the SEQ-C is a reliable scale with a three-factor model measuring social, academic, and emotional self-efficacy. Construct valid

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Purwanasari, HN, N. Fitria, D. Kusuma, F. Aziz, R. Widayanti, and S. I. O. Salasia. "Multiplex PCR detection of the classical enterotoxin genes of Staphylococcus aureus in humans and animal isolates." IOP Conference Series: Earth and Environmental Science 1174, no. 1 (2023): 012010. http://dx.doi.org/10.1088/1755-1315/1174/1/012010.

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Abstract Staphylococcus aureus is a prevalent bacterial causative agent of bovine mastitis and human food illness by secreting enterotoxins. This study aims to identify the seven classic Staphylococcus aureus enterotoxin genes (SEA to SEH) isolated from humans and animals. A total of 173 human isolates and 14 mastitis (goat and cow) isolates were amplified with a 23S rRNA genes. The presence of classical enterotoxins genes (sea-seh) was amplified using multiplex polymerase chain reaction (m-PCR). Amplification of the SEs genes singly and in combination was observed from both isolates. Of 173 h

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Park, Sangmi, Tae Hui Kim, Tae Rim Um, et al. "THE EFFECTS OF SIMULATION-BASED EMPATHY ENHANCEMENT PROGRAM FOR CARER OF THE ELDERLY ON COUNSELLING." Innovation in Aging 3, Supplement_1 (2019): S920—S921. http://dx.doi.org/10.1093/geroni/igz038.3354.

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Abstract Empathy of the caregiver can influence both the caregiver’s performance and the receiver’s enhanced life. The aim of this study is to examine whether Simulation-based Empathy Enhancement program for the Carer of the Elderly (SEE-C) is effective in increasing care receivers’ session satisfaction and positive emotional change. We developed SEE-C by modifying the Dementia Live(TM) program and adding with a brief mindfulness. The effect on counselling was assessed using the Session Evaluation Questionnaire (SEQ), which is self-report tool asking the client about their experience with the

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Qian, Yuqing, Quan Zou, Mengyuan Zhao, Yi Liu, Fei Guo, and Yijie Ding. "scRNMF: An imputation method for single-cell RNA-seq data by robust and non-negative matrix factorization." PLOS Computational Biology 20, no. 8 (2024): e1012339. http://dx.doi.org/10.1371/journal.pcbi.1012339.

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Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool in genomics research, enabling the analysis of gene expression at the individual cell level. However, scRNA-seq data often suffer from a high rate of dropouts, where certain genes fail to be detected in specific cells due to technical limitations. This missing data can introduce biases and hinder downstream analysis. To overcome this challenge, the development of effective imputation methods has become crucial in the field of scRNA-seq data analysis. Here, we propose an imputation method based on robust and non-negative matr

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Wiejak, Jolanta, Boy van Basten, Graham Hamilton та Stephen J. Yarwood. "Genome-Wide Mapping Defines a Role for C/EBPβ and c-Jun in Non-Canonical Cyclic AMP Signalling". Cells 8, № 10 (2019): 1253. http://dx.doi.org/10.3390/cells8101253.

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The novel exchange protein activated by cyclic AMP (EPAC1) activator, I942, induces expression of the suppressor of cytokine signalling 3 (SOCS3) gene, thereby inhibiting interleukin 6 (IL6) inflammatory processes in human umbilical vein endothelial cells (HUVECs). Here we use RNA-SEQ and ChIP-SEQ to determine global gene responses to I942, in comparison with cyclic AMP production promoted by forskolin and rolipram (F/R). We found that I942 promoted significant changes in the RNA expression of 1413 genes, largely associated with microtubule stability and cell cycle progression, whereas F/R reg

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Golov, Arkadiy K., Sergey V. Ulianov, Artem V. Luzhin, et al. "C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries." Methods 170 (January 2020): 48–60. http://dx.doi.org/10.1016/j.ymeth.2019.06.022.

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Zhou, Yuenan, Pei Yang, Shuang Xie, et al. "Comparative Transcriptome Analysis Reveals Sex-Based Differences during the Development of the Adult Parasitic Wasp Cotesia vestalis (Hymenoptera: Braconidae)." Genes 12, no. 6 (2021): 896. http://dx.doi.org/10.3390/genes12060896.

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The endoparasitic wasp Cotesia vestalis is an important biological agent for controlling the population of Plutella xylostella, a major pest of cruciferous crops worldwide. Though the genome of C. vestalis has recently been reported, molecular mechanisms associated with sexual development have not been comprehensively studied. Here, we combined PacBio Iso-Seq and Illumina RNA-Seq to perform genome-wide profiling of pharate adult and adult development of male and female C. vestalis. Taking advantage of Iso-Seq full-length reads, we identified 14,466 novel transcripts as well as 8770 lncRNAs, wi

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Ruchika, Chisato Okudaira, Matomo Sakari, and Toshifumi Tsukahara. "Genome-Wide Identification of U-To-C RNA Editing Events for Nuclear Genes in Arabidopsis thaliana." Cells 10, no. 3 (2021): 635. http://dx.doi.org/10.3390/cells10030635.

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Cytosine-to-Uridine (C-to-U) RNA editing involves the deamination phenomenon, which is observed in animal nucleus and plant organelles; however, it has been considered the U-to-C is confined to the organelles of limited non-angiosperm plant species. Although previous RNA-seq-based analysis implied U-to-C RNA editing events in plant nuclear genes, it has not been broadly accepted due to inadequate confirmatory analyses. Here we examined the U-to-C RNA editing in Arabidopsis tissues at different developmental stages of growth. In this study, the high-throughput RNA sequencing (RNA-seq) of 12-day

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Mallik, Saurav, and Zhongming Zhao. "Multi-Objective Optimized Fuzzy Clustering for Detecting Cell Clusters from Single-Cell Expression Profiles." Genes 10, no. 8 (2019): 611. http://dx.doi.org/10.3390/genes10080611.

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Rapid advance in single-cell RNA sequencing (scRNA-seq) allows measurement of the expression of genes at single-cell resolution in complex disease or tissue. While many methods have been developed to detect cell clusters from the scRNA-seq data, this task currently remains a main challenge. We proposed a multi-objective optimization-based fuzzy clustering approach for detecting cell clusters from scRNA-seq data. First, we conducted initial filtering and SCnorm normalization. We considered various case studies by selecting different cluster numbers ( c l = 2 to a user-defined number), and appli

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Min, Alan, Timothy Durham, Louis Gevirtzman, and William Stafford Noble. "Matrix prior for data transfer between single cell data types in latent Dirichlet allocation." PLOS Computational Biology 19, no. 5 (2023): e1011049. http://dx.doi.org/10.1371/journal.pcbi.1011049.

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Single cell ATAC-seq (scATAC-seq) enables the mapping of regulatory elements in fine-grained cell types. Despite this advance, analysis of the resulting data is challenging, and large scale scATAC-seq data are difficult to obtain and expensive to generate. This motivates a method to leverage information from previously generated large scale scATAC-seq or scRNA-seq data to guide our analysis of new scATAC-seq datasets. We analyze scATAC-seq data using latent Dirichlet allocation (LDA), a Bayesian algorithm that was developed to model text corpora, summarizing documents as mixtures of topics def

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Li, Jianping, Priscillia Lhoumaud, Alberto Riva, et al. "Dysregulation of Epigenetic Landscape Uncovered the Mechanisms Underlying the Relapse of Pediatric Acute Lymphoblastic Leukemia with NSD2 Mutation." Blood 138, Supplement 1 (2021): 3297. http://dx.doi.org/10.1182/blood-2021-149985.

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Abstract Background: Relapse from acute lymphoblastic leukemia (ALL) is one of the most common causes of pediatric cancer-related death. Early relapse of ALL is associated with recurrent mutations of histone methyltransferase NSD2 (nuclear receptor binding SET domain protein 2), which is specific for H3K36me2, suggesting a link to therapy resistance or other mechanisms underlying relapse such as central neural system (CNS) infiltration. NSD2 p.E1099K affects gene expression through disturbing the balance of H3K36me2/H3K27me3. Using CRISPR/Cas9-edited isogenic ALL cell lines and PDX cells, we f

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Carducci, Federica, Maria Assunta Biscotti, Alessandro Mosca, et al. "The Mantle Transcriptome of Chamelea gallina (Mollusca: Bivalvia) and Shell Biomineralization." Animals 12, no. 9 (2022): 1196. http://dx.doi.org/10.3390/ani12091196.

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The striped venus Chamelea gallina is a bivalve mollusc that represents one of the most important fishery resources of the Adriatic Sea. In this work, we investigated for the first time the ability of this species to modulate the expression of genes encoding proteins involved in biomineralization process in response to biotic and abiotic factors. We provided the first comprehensive transcriptome from the mantle tissue of clams collected in two sampling sites located along the Italian Adriatic coast and characterized by different environmental features. Moreover, the assessment of environmental

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ADESIYUN, ABIODUN A., IFEDAPO RAJI, and VIVIAN YOBE. "Enterotoxigenicity of Staphylococcus aureus from Anterior Nares of Dining Hall Workers." Journal of Food Protection 49, no. 12 (1986): 955–57. http://dx.doi.org/10.4315/0362-028x-49.12.955.

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The frequency of isolation of enterotoxigenic Staphylococcus aureus in dining hall workers of a Nigerian University was determined. Of a total of 186 workers sampled, 47 (25.3%) were carriers of enterotoxigenic S. aureus in their anterior nares, including 19 (22.4%) of 85 cooks and 11 (23.9%) of 46 stewards. Fifty-five (26.6%) of 207 strains of S. aureus tested produced staphylococcal enterotoxins A (SEA), B (SEB), C (SEC), D (SED) or E (SEE). SEA predominated, with 18 (8.7%) strains elaborating it and representing 32.7% of all enterotoxigenic strains. SEC and SED were produced by 14 (6.8%) an

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Ooi, Wen Fong, Amrita M. Nargund, Kevin Junliang Lim, et al. "Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma." Gut 69, no. 6 (2019): 1039–52. http://dx.doi.org/10.1136/gutjnl-2018-317612.

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ObjectiveGenomic structural variations (SVs) causing rewiring of cis-regulatory elements remain largely unexplored in gastric cancer (GC). To identify SVs affecting enhancer elements in GC (enhancer-based SVs), we integrated epigenomic enhancer profiles revealed by paired-end H3K27ac ChIP-sequencing from primary GCs with tumour whole-genome sequencing (WGS) data (PeNChIP-seq/WGS).DesignWe applied PeNChIP-seq to 11 primary GCs and matched normal tissues combined with WGS profiles of >200 GCs. Epigenome profiles were analysed alongside matched RNA-seq data to identify tumour-associated enhanc

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Zhou, Huimin, Minghua Chen, Cong Zhao, Rongguang Shao, Yanni Xu, and Wuli Zhao. "The Natural Product Secoemestrin C Inhibits Colorectal Cancer Stem Cells via p38–S100A8 Feed-Forward Regulatory Loop." Cells 13, no. 7 (2024): 620. http://dx.doi.org/10.3390/cells13070620.

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Cancer stem cells (CSCs) are closely associated with tumor initiation, metastasis, chemoresistance, and recurrence, which represent some of the primary obstacles to cancer treatment. Targeting CSCs has become an important therapeutic approach to cancer care. Secoemestrin C (Sec C) is a natural compound with strong anti-tumor activity and low toxicity. Here, we report that Sec C effectively inhibited colorectal CSCs and non-CSCs concurrently, mainly by inhibiting proliferation, self-renewal, metastasis, and drug resistance. Mechanistically, RNA-seq analysis showed that the pro-inflammation path

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Su, Chen, Rong Yu, Xiaoquan Hong, et al. "CXCR4 Expressed by Tumor-Infiltrating B Cells in Gastric Cancer Related to Survival in the Tumor Microenvironment: An Analysis Combining Single-Cell RNA Sequencing with Bulk RNA Sequencing." International Journal of Molecular Sciences 24, no. 16 (2023): 12890. http://dx.doi.org/10.3390/ijms241612890.

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According to the World Health Organization (WHO), gastric cancer (GC) is the fourth leading cause of tumor-related mortality globally and one of the most prevalent malignant tumors. To better understand the role of tumor-infiltrating B cells (TIBs) in GC, this work used single-cell RNA sequencing (scRNA-Seq) and bulk RNA sequencing (bulk RNA-Seq) data to identify candidate hub genes. Both scRNA-Seq and bulk RNA-Seq data for stomach adenocarcinoma (STAD) were obtained from the GEO and TCGA databases, respectively. Using scRNA-seq data, the FindNeighbors and FindClusters tools were used to group

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Rathe, Susan K., Christopher B. Stoltenberg, and David A. Largaespada. "RNA-Sequencing of the Transcriptome of Ara-C Resistant Murine AML Cell Lines Identifies Potential Drug Targets." Blood 118, no. 21 (2011): 2489. http://dx.doi.org/10.1182/blood.v118.21.2489.2489.

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Abstract Abstract 2489 One frequently reported change to acute myeloid leukemia (AML) cells, as they become resistant to arabinoside cytarabine (Ara-C), is the downregulation of deoxycytidine kinase (Dck) (Veuger et al, Blood, 2000, Shi et al, Pharmacogenetics, 2004, Cai et al, Cancer Res, 2008, Song et al, Int J Oncol, 2009, Rathe et al, Leukemia, 2010). Dck is the rate limiting enzyme in the phosphorylation and activation of Ara-C. Transcriptome deep sequencing (RNA-seq) was performed on the transcriptome of two Ara-C resistant murine leukemia cell lines (B117H and B140H), as well their Ara-

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Wang, Juan, Tina Yi-Ting Huang, Ye Hou, et al. "Epigenomic landscape and 3D genome structure in pediatric high-grade glioma." Science Advances 7, no. 23 (2021): eabg4126. http://dx.doi.org/10.1126/sciadv.abg4126.

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Pediatric high-grade gliomas (pHGGs), including glioblastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG), are morbid brain tumors. Even with treatment survival is poor, making pHGG the number one cause of cancer death in children. Up to 80% of DIPGs harbor a somatic missense mutation in genes encoding histone H3. To investigate whether H3K27M is associated with distinct chromatin structure that alters transcription regulation, we generated the first high-resolution Hi-C maps of pHGG cell lines and tumor tissue. By integrating transcriptome (RNA-seq), enhancer landscape (ChIP-s

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Tourasse, Nicolas J., Jonathan R. M. Millet, and Denis Dupuy. "Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans." Genome Research 27, no. 12 (2017): 2120–28. http://dx.doi.org/10.1101/gr.224626.117.

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Chen, Jiao, Dongxiao Zhu, and Yanni Sun. "Cap-seq reveals complicated miRNA transcriptional mechanisms in C. elegans and mouse." Quantitative Biology 5, no. 4 (2017): 352–67. http://dx.doi.org/10.1007/s40484-017-0123-4.

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Kim, Yewon, Anvith Kakkera, Asher Bryant, et al. "Abstract 995: Leveraging RNA and long-read DNA to improve genetic etiology identification in individuals with elevated cancer risk: A pilot study in individuals with Li-Fraumeni-like phenotype." Cancer Research 85, no. 8_Supplement_1 (2025): 995. https://doi.org/10.1158/1538-7445.am2025-995.

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Abstract Individuals with clinical Li-Fraumeni Syndrome (LFS) are at hereditary risk of developing multiple cancers in their lifetime. Among those meeting classic LFS criteria, about 10% do not have a germline mutation identified in TP53. Long-read DNA sequencing identifies complex and structural variants missed on short-read sequencing. Clinical germline testing labs also recently began using short-read RNA-seq to characterize alternative splicing events. This project aims to explore underlying genetic etiology of those with LFS and no identifiable germline TP53 variant using long-read DNA-se

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White, Shannon M., Michael P. Snyder, and Chunling Yi. "Master lineage transcription factors anchor trans mega transcriptional complexes at highly accessible enhancer sites to promote long-range chromatin clustering and transcription of distal target genes." Nucleic Acids Research 49, no. 21 (2021): 12196–210. http://dx.doi.org/10.1093/nar/gkab1105.

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Abstract The term ‘super enhancers’ (SE) has been widely used to describe stretches of closely localized enhancers that are occupied collectively by large numbers of transcription factors (TFs) and co-factors, and control the transcription of highly-expressed genes. Through integrated analysis of &gt;600 DNase-seq, ChIP-seq, GRO-seq, STARR-seq, RNA-seq, Hi-C and ChIA-PET data in five human cancer cell lines, we identified a new class of autonomous SEs (aSEs) that are excluded from classic SE calls by the widely used Rank Ordering of Super-Enhancers (ROSE) method. TF footprint analysis reve

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Koyama, Kenta, Gosuke Hayashi, Hiroki Ueda, et al. "Base-resolution analysis of 5-hydroxymethylcytidine by selective oxidation and reverse transcription arrest." Organic & Biomolecular Chemistry 19, no. 29 (2021): 6478–86. http://dx.doi.org/10.1039/d1ob00995h.

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Bishop, Emma. "Probing Dermal Immunity to Mycobacteria through a Controlled Human Infection Model." ImmunoHorizons, September 9, 2024. https://doi.org/10.5281/zenodo.13737809.

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File descriptions: "2022_human_BCG_challenge_metadata.xlsx" -- Subject metadata "BCG_Skin_Biopsy_CD45_Subsets.csv" -- CyTOF cell subset proportions, see Fig. 4A    "deg_heatmap_values.csv" -- Bulk RNA-seq DEGs, see Fig. 3A    "filtered_feature_bc_matrix_day3.h5" -- scRNA-seq Cell Ranger output file for Day 3 samples, see Fig. 5    "Kublin_Human_BCG_Challenge_B_2023_10_04.csv" -- Flow cytometry ICS count table, see Fig. 2B-C    "sample_filtered_feature_bc_matrix_day15.h5" -- scRNA-seq Cell Ranger output file for Day 15 samples, see Fig

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Ghaddar, Abbas, Erick Armingol, Chau Huynh, et al. "Whole-body gene expression atlas of an adult metazoan." April 30, 2025. https://doi.org/10.5281/zenodo.15306483.

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Animals are integrated organ systems composed of interacting cells whose structure and function are in turn defined by their active genes. Understanding what distinguishes physiological and disease states therefore requires systemic knowledge of the gene activities that define the distinct cells that make up an animal. Towards this goal, this study reports the first single-cell resolution transcriptional atlas of a fertile multicellular organism: <em>Caenorhabditis elegans</em>. The scRNA-Seq compendium of wild-type young adult <em>C. elegans</em> comprises 159 distinct cell types with 18,033

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Yang, Weilong, Caibiao Wei, Junxian Chen, et al. "Clonorchis sinensis infection remodels chromatin accessibility in hepatocellular carcinoma." Parasites & Vectors 18, no. 1 (2025). https://doi.org/10.1186/s13071-025-06909-6.

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Abstract Background Hepatocellular carcinoma (HCC) is a major global health concern, accounting for a significant proportion of liver cancer cases and related deaths. Clonorchis sinensis (C. sinensis) infection, a recognized carcinogen, has been implicated in the progression of liver diseases, including HCC. However, the precise epigenetic mechanisms underlying C. sinensis-associated HCC remain to be elucidated. Methods To investigate the role of chromatin accessibility in C. sinensis-related HCC progression, we performed an assay for transposase-accessible chromatin with high-throughput seque

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Pham, Tran Thu Ha, Duc Minh Tran, Tiep Khac Nguyen, and Thanh Huong Phung. "A simple sequencing protocol for genotyping the <i>HLA-C</i>locus by the Sanger method." Tạp chí Nghiên cứu Dược và Thông tin Thuốc 16 (April 24, 2024). http://dx.doi.org/10.59882/1859-364x/165.

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The HLA-C gene, which belongs to the HLA superfamily (Human Leukocyte Antigen), codes for the Major Histocompatibility Complex (MHC), which plays crucial roles in the human immune system. This study aimed to develop a simple sequencing protocol by the Sanger method using fewer primers and reactions for genotyping the HLA-C gene than published protocols. The simple protocol with three primers includes one PCR reaction and two sequencing reactions. The primer set comprising SEQ ID1 and SEQ ID2 was used for the PCR reaction to specifically amplify the exon 2 – exon 3 region of the HLA-C locus, wh

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Hart, Sarah, Veronica Kelsey, and Peter Rowley. "Root cycles in Coxeter groups." Journal of Group Theory, February 2, 2024. http://dx.doi.org/10.1515/jgth-2023-0027.

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Abstract For an element 𝑤 of a Coxeter group 𝑊, there are two important attributes, namely its length, and its expression as a product of disjoint cycles in its action on Φ, the root system of 𝑊. This paper investigates the interaction between these two features of 𝑤, introducing the notion of the crossing number of 𝑤, κ ⁢ ( w ) \kappa(w) . Writing w = c 1 ⁢ ⋯ ⁢ c r w=c_{1}\cdots c_{r} as a product of disjoint cycles, we associate to each cycle c i c_{i} a “crossing number” κ ⁢ ( c i ) \kappa(c_{i}) , which is the number of positive roots 𝛼 in c i c_{i} for which w ⋅ α w\cdot\alpha is negative

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