Genome-wide association studies with prolapsed gland of the third eyelid in dogs by Yu Zeng, Yu Zeng, Yu Zeng, Cundong Feng, Zheli Jiang, Zheli Jiang, Zheli Jiang, Weian Du, Shan He, Shan He, Shan He, Xingnuan Li, Xingnuan Li, Xingnuan Li, Yi Fan, Yi Fan, Yi Fan, Xiao Ouyang, Xiao Ouyang, Xiao Ouyang, Bixin Huang, Bixin Huang, Bixin Huang, Yan Su, Yan Su, Yan Su, Siyu Wang, Siyu Wang, Siyu Wang, Rongxing Wei, Zonghao Dai, Peng Jin, Jianyun Liu, Jianyun Liu, Jianyun Liu, Qianyong Yang, Qianyong Yang, Qianyong Yang

“…In this study, 170K SNP microarray data were collected from 653 brachycephalic dogs and 788 brachycephalic and mesocephalic dogs. …”
Get full text

Sex and outcomes of patients with microsatellite instability-high and BRAF V600E mutated metastatic colorectal cancer receiving immune checkpoint inhibitors by Michael Hoffmeister, Hermann Brenner, Chiara Cremolini, Sara Lonardi, Filippo Pietrantonio, Julien Taieb, David Tougeron, Robyn L Ward, Marco Vitellaro, Thierry André, Pierre Laurent-Puig, Jitendra Jonnagaddala, Francesca Bergamo, Raghav Sundar, Claire Gallois, Michael J Overman, Jakob Nikolas Kather, Lisa Salvatore, Romain Cohen, Rossana Intini, Priya Jayachandran, Miriam Koopman, Javier Ros, Marwan Fakih, Vincenzo Nasca, Giacomo Mazzoli, Jeanine M L Roodhart, Filippo Ghelardi, Elena Elez, Durgesh Wankhede, Marta Ligero, Joseph Zhao, Koen Zwart, Jeroen Derksen, Nicholas Hawkins, Javier Carmona

“…Finally, we explored two public microarray and RNA-seq datasets from patients with non-metastatic or metastatic MSI-H CRC to gain translational insights on the association between sex, BRAF status and immune contextures/ICI efficacy.Results Although no differences were observed between females and males either overall or in the BRAF wild-type cohort, male sex was associated with inferior progression-free survival (PFS) and overall survival (OS) in the BRAF mutated cohort (in multivariable models, HR for PFS: 1.79, 95% CI: 1.13 to 2.83, p=0.014, and for OS: 2.33, 95% CI: 1.36 to 3.98, p=0.002). …”
Get full text

VEIKIANTIS GENOMAS - VISUMINIS POŽYMIS: DABARTIES ŽVILGSNIS Į GENETIKĄ by Jonas Rubikas

“…Keywords: genome, genomics, DNA microarrays, proteome. …”
Get full text

Clinical Value and Potential Mechanism of miRNA-33a-5p in Lung Squamous Cell Carcinoma by Xiang-Ming Wang, Shang-Wei Chen, Gang Chen, Hua-Fu Zhou, Ting-Qing Gan, Jing-Jing Zeng, Zu-Yun Li

“…Relationship between miRNA-33a-5p expression and clinicopathological traits was investigated from materials derived from miRNA sequencing and miRNA microarrays. A pool standard mean difference (SMD) and summary receiver operating characteristic curves (SROC) were calculated to evaluate the integrated expression value of miRNA-33a-5p in LUSC. …”
Get full text

Gene Array Studies in Renal Neoplasia by John P.T. Higgins

“…For these reasons, renal cell carcinoma is ideally suited to the genome scale investigation made possible by DNA microarrays. A number of DNA array studies of renal cell carcinoma have been published. …”
Get full text

A Review of Three Different Studies on Hidden Markov Models for Epigenetic Problems: A Computational Perspective by Kyung-Eun Lee, Hyun-Seok Park

“…Recent technical advances, such as chromatin immunoprecipitation combined with DNA microarrays (ChIp-chip) and chromatin immunoprecipitation-sequencing (ChIP-seq), have generated large quantities of high-throughput data. …”
Get full text

From Genetics to Genomics of Epilepsy by Silvio Garofalo, Marisa Cornacchione, Alfonso Di Costanzo

“…The introduction of DNA microarrays and DNA sequencing technologies in medical genetics and diagnostics has been a challenge that has significantly transformed medical practice and patient management. …”
Get full text

Perspectives of Integrative Cancer Genomics in Next Generation Sequencing Era by So Mee Kwon, Hyunwoo Cho, Ji Hye Choi, Byul A Jee, Yuna Jo, Hyun Goo Woo

“…The explosive development of genomics technologies including microarrays and next generation sequencing (NGS) has provided comprehensive maps of cancer genomes, including the expression of mRNAs and microRNAs, DNA copy numbers, sequence variations, and epigenetic changes. …”
Get full text

A Novel Method for Functional Annotation Prediction Based on Combination of Classification Methods by Jaehee Jung, Heung Ki Lee, Gangman Yi

“…NGS is a popular research method since high-throughput technologies such as DNA sequencing and microarrays have created large sets of genes. These huge sequences have greatly increased the need for analysis. …”
Get full text

Gene Expression during Survival of Escherichia coli O157:H7 in Soil and Water by Ashley D. Duffitt, Robert T. Reber, Andrew Whipple, Christian Chauret

“…The in vitro survival of Escherichia coli O157:H7 at 15∘C under two experimental conditions (sterile soil and sterile natural water) was examined. DNA microarrays of the entire set of E. coli O157:H7 genes were used to measure the genomic expression patterns after 14 days. …”
Get full text

Comparative Transcriptional Profiling of Two Contrasting Barley Genotypes under Salinity Stress during the Seedling Stage by Runhong Gao, Ke Duan, Guimei Guo, Zhizhao Du, Zhiwei Chen, Liang Li, Ting He, Ruiju Lu, Jianhua Huang

“…We compared changes in transcriptome between Hua 11 (a salt-tolerant genotype) and Hua 30 (a salt sensitive genotype) in response to salt stress at the seedling stage using barley cDNA microarrays. In total, 557 and 247 salt-responsive genes were expressed exclusively in the shoot and root tissue of the salt-tolerant genotype, respectively. …”
Get full text

Effects of Pooling Samples on the Performance of Classification Algorithms: A Comparative Study by Kanthida Kusonmano, Michael Netzer, Christian Baumgartner, Matthias Dehmer, Klaus R. Liedl, Armin Graber

“…In this paper, we perform a comparative study to model and quantify the effects of virtual pooling on the performance of the widely applied classifiers, support vector machines (SVMs), random forest (RF), k-nearest neighbors (k-NN), penalized logistic regression (PLR), and prediction analysis for microarrays (PAMs). We evaluate a variety of experimental designs using mock omics datasets with varying levels of pool sizes and considering effects from feature selection. …”
Get full text

MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model by Yunhee Jeong, Clarissa Gerhäuser, Guido Sauter, Thorsten Schlomm, Karl Rohr, Pavlo Lutsik

“…Read-level methylomes enable more in-depth analyses, due to their broad genomic coverage and preservation of rare cell-type signals, compared to summarized data such as 450K/EPIC microarrays. Here, we propose MethylBERT, a Transformer-based model for read-level methylation pattern classification. …”
Get full text

Increased aPKC Expression Correlates with Prostatic Adenocarcinoma Gleason Score and Tumor Stage in the Japanese Population by Anthony S. Perry, Bungo Furusato, Raymond B. Nagle, Sourav Ghosh

“…The aim of this study was to validate association of aPKC expression with prostatic adenocarcinoma stages in a Japanese cohort. Methods. Tissue microarrays consisting of 142 malignant prostate cancer cases and 21 benign prostate tissues were subject to immunohistological staining for aPKC. aPKC staining intensity was scored by three independent pathologists and categorized as absent (0), dim (1+), intermediate (2+), and bright (3+). aPKC staining intensities were correlated with Gleason score and tumor stage. …”
Get full text

Differential Gene Expression Profile of Human Neutrophils Cultured with Plasmodium falciparum-Parasitized Erythrocytes by Mohamad Alaa Terkawi, Ryo Takano, Kentaro Kato

“…Therefore, we examined the transcriptional gene profile of human PMNs in response to Plasmodium falciparum-parasitized erythrocytes (iRBCs) by using oligonucleotide microarrays. Results revealed that PMNs induced a broad and vigorous set of changes in gene expression in response to malarial parasites, represented by 118 upregulated and 216 downregulated genes. …”
Get full text

Cyclooxygenase 2 (COX2) and Peroxisome Proliferator-Activated Receptor Gamma (PPARG) Are Stage-Dependent Prognostic Markers of Malignant Melanoma by Stefanie Meyer, Thomas Vogt, Michael Landthaler, Anna Berand, Albrecht Reichle, Frauke Bataille, Andreas H. Marx, Anne Menz, Arndt Hartmann, Leoni A. Kunz-Schughart, Peter J. Wild

“…Using tissue microarrays (TMAs) we studied COX2/PPARG immunoreactivity in a broad spectrum of tumors focussing on clinicopathological correlations and the outcome of patients with malignant melanoma (MM). …”
Get full text

Identification of TTLL8, POTEE, and PKMYT1 as immunogenic cancer-associated antigens and potential immunotherapy targets in ovarian cancer by Esen Yonca Bassoy, Remya Raja, Thomas E. Rubino, Fabian Coscia, Krista Goergen, Paul Magtibay, Kristina Butler, Alessandra Schmitt, Ann L. Oberg, Marion Curtis

“…From this dataset, we identified TTLL8, POTEE, and PKMYT1 peptides as candidate tumor antigens with low expression in normal tissues and upregulated expression in OC. Using tissue microarrays, we assessed the protein expression of TTLL8 and POTEE and their association with patient outcomes in a large cohort of OC patients. …”
Get full text

Application of reproductive technologies to the improvement of dairy cattle genomic selection by N. S. Yudin, K. I. Lukyanov, M. I. Voevoda, N. A. Kolchanov

“…The main trends in the development of genomic selection include improvement of the accuracy of breeding value estimations by combination of reference populations; use genotyping of cows in breeding programs; imputation of genotypes for absent SNPs with low marker density microarrays, and prediction of animal genotypes from the genotypes of relatives. …”
Get full text

Blood Transcriptional Signatures for Disease Progression in a Rat Model of Osteoarthritis by Michał Korostyński, Natalia Małek, Marcin Piechota, Katarzyna Starowicz

“…We used whole-genome microarrays to reveal OA-related transcriptional alterations of 72 transcripts. …”
Get full text

GADD45β Determines Chemoresistance and Invasive Growth of Side Population Cells of Human Embryonic Carcinoma by Toshihiko Inowa, Keiichi Hishikawa, Yumi Matsuzaki, Takayuki Isagawa, Takumi Takeuchi, Hiroyuki Aburatani, Tadaichi Kitamura, Toshiro Fujita

“…To further characterize the NEC8 SP cells, we used DNA microarrays. Among 38,500 genes, we identified 12 genes that were over-expressed in SP cells and 1 gene that was over-expressed in non-SP cells. …”
Get full text