Discovering structural cis‐regulatory elements by modeling the behaviors of mRNAs by Barrett C Foat, Gary D Stormo

“…We applied our structural cis‐regulatory element detector (StructRED) to microarray and mRNA sequence data from Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. …”
Get full text

Translational profiling reveals novel gene expression changes in the direct and indirect pathways in a mouse model of levodopa induced dyskinesia by Sabika Jafri, Mahdi Ghani, Natalie Stickle, Carl Virtanen, Lili-Naz Hazrati, Naomi P. Visanji, Naomi P. Visanji, Naomi P. Visanji

“…Extracted ribosomal RNA was amplified, purified, and gene expression was quantified using microarray.ResultsOne hundred ninety-five significantly varying transcripts were identified among the four treatment groups. …”
Get full text

Synchrotron Radiation-Induced X-Ray Emission to Identify Metal Ions in Preparations of Purified Protein by Thomas Pfister, Huan Feng, Eckard Wimmer, Keith W. Jones

“…Thus, SRIXE may have wide use as a particularly effective method for rapidly determining trace metals in microarray samples.…”
Get full text

Development of HuMiChip for functional profiling of human microbiomes. by Qichao Tu, Zhili He, Yan Li, Yanfei Chen, Ye Deng, Lu Lin, Christopher L Hemme, Tong Yuan, Joy D Van Nostrand, Liyou Wu, Xuedong Zhou, Wenyuan Shi, Lanjuan Li, Jian Xu, Jizhong Zhou

“…Here we have developed a functional gene-based microarray for profiling human microbiomes (HuMiChip) with 36,802 probes targeting 50,007 protein coding sequences for 139 key functional gene families. …”
Get full text

Comparison of eleven methods for genomic DNA extraction suitable for large-scale whole-genome genotyping and long-term DNA banking using blood samples. by Androniki Psifidi, Chrysostomos I Dovas, Georgios Bramis, Thomai Lazou, Claire L Russel, Georgios Arsenos, Georgios Banos

“…Over the recent years, next generation sequencing and microarray technologies have revolutionized scientific research with their applications to high-throughput analysis of biological systems. …”
Get full text

An animal model with a cardiomyocyte-specific deletion of estrogen receptor alpha: functional, metabolic, and differential network analysis. by Sriram Devanathan, Timothy Whitehead, George G Schweitzer, Nicole Fettig, Attila Kovacs, Kenneth S Korach, Brian N Finck, Kooresh I Shoghi

“…Estrogen exerts diverse biological effects in multiple tissues in both animals and humans. …”
Get full text

Psicoterapia e neuroscienze: il modello strategico ad orientamento neuroscientifico e il metodo mente - corpo by 1 Mauro Cozzolino, 2 Giovanna Celia

“…In this paper we illustrate an innovative and effective model called Neuroscientific Strategic Psychotherapy. …”
Get full text

Dietary inulin supplementation modifies significantly the liver transcriptomic profile of broiler chickens. by Natalia Sevane, Federica Bialade, Susana Velasco, Almudena Rebolé, Maria Luisa Rodríguez, Luís T Ortiz, Javier Cañón, Susana Dunner

“…As far as we are aware, this is the first report of a microarray based gene expression study on the effect of dietary inulin supplementation, supporting further research on the use of this prebiotic on chicken diets as a useful alternative to antibiotics for improving performance and general immunity in poultry farming, along with a healthier meat lipid profile.…”
Get full text

Atm inhibition decreases lens opacity in a rat model of galactose-induced cataract. by Masaya Nagaya, Fumito Kanada, Masaru Takashima, Yoshihiro Takamura, Masaru Inatani, Masaya Oki

“…The regulatory mechanisms of cataract formation and progression remain unclear, and no effective drug treatments are clinically available. …”
Get full text

Concave Magnetic-Responsive Hydrogel Discs for Enhanced Bioassays by Amin Ghaffarzadeh Bakhshayesh, Huiyan Li

“…In response to this challenge, we presented a rapid and cost-effective technique for fabricating concave magnetic-responsive hydrogel discs (CMDs) by straightforward pipetting directly onto microscope glass slides. …”
Get full text

Thrombospondin-1 in a Murine Model of Colorectal Carcinogenesis. by Zenaida P Lopez-Dee, Sridar V Chittur, Hiral Patel, Aleona Chinikaylo, Brittany Lippert, Bhumi Patel, Jack Lawler, Linda S Gutierrez

“…The intestinal transcriptome was also analyzed using a gene microarray approach. When the area containing tumors was compared with the entire colonic area of each mouse, the tumor burden was decreased in AOM/DSS-treated TSP-1-/- versus wild type (WT) mice. …”
Get full text

Identification and functional analysis of light-responsive unique genes and gene family members in rice. by Ki-Hong Jung, Jinwon Lee, Chris Dardick, Young-Su Seo, Peijian Cao, Patrick Canlas, Jirapa Phetsom, Xia Xu, Shu Ouyang, Kyungsook An, Yun-Ja Cho, Geun-Cheol Lee, Yoosook Lee, Gynheung An, Pamela C Ronald

“…Using a rice NSF45K oligo-microarray to compare 2-week-old light- and dark-grown rice leaf tissue, we identified 365 genes that showed significant 8-fold or greater induction in the light relative to dark conditions. …”
Get full text

Hepatic Gene Expression Profiles Are Altered by Dietary Unsalted Korean Fermented Soybean (Chongkukjang) Consumption in Mice with Diet-Induced Obesity by JuRyoun Soh, Dae Young Kwon, Youn-Soo Cha

“…We found that Chongkukjang, traditional unsalted fermented soybean, has an antiobesity effect in mice with diet-induced obesity and examined the changes in hepatic transcriptional profiles using cDNA microarray. …”
Get full text

AssayBLAST: A Bioinformatic Tool for <i>In Silico</i> Analysis of Molecular Multiparameter Assays by Maximilian Collatz, Sascha D. Braun, Martin Reinicke, Elke Müller, Stefan Monecke, Ralf Ehricht

“…This high accuracy demonstrates the method’s effectiveness in reliably using BLAST hits and mismatch counts to predict microarray results. …”
Get full text

A systems biology approach to prediction of oncogenes and molecular perturbation targets in B‐cell lymphomas by Kartik M Mani, Celine Lefebvre, Kai Wang, Wei Keat Lim, Katia Basso, Riccardo Dalla‐Favera, Andrea Califano

“…Such a strategy provides important insights into tumorigenesis, effectively extending and complementing existing methods. …”
Get full text

Weighted frequent gene co-expression network mining to identify genes involved in genome stability. by Jie Zhang, Kewei Lu, Yang Xiang, Muhtadi Islam, Shweta Kotian, Zeina Kais, Cindy Lee, Mansi Arora, Hui-Wen Liu, Jeffrey D Parvin, Kun Huang

“…Gene co-expression network analysis is an effective method for predicting gene functions and disease biomarkers. …”
Get full text

Integrative analysis of co-expression networks and codon usage bias in maize under biotic stress. by Zahra Zinati, Leyla Nazari

“…Understanding the complex networks underlying the biotic stress response in maize is crucial for developing effective approaches to improve tolerance. We identified 1449 differentially expressed genes (DEGs) by meta-analysis of the public microarray gene expression profile. …”
Get full text

c-Triadem: A constrained, explainable deep learning model to identify novel biomarkers in Alzheimer's disease. by Sherlyn Jemimah, Ferial Abuhantash, Aamna AlShehhi

“…We trained the model with blood genotyping data, microarray, and clinical features from the Alzheimer's Neuroimaging Disease Initiative (ADNI). …”
Get full text

Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis. by Venkata Suresh Bonthala, Katie Mayes, Joanna Moreton, Martin Blythe, Victoria Wright, Sean Tobias May, Festo Massawe, Sean Mayes, Jamie Twycross

“…Therefore, in this study we developed a computational pipeline to identify and analyze the genes and gene modules associated with low temperature stress responses in bambara groundnut using the cross-species microarray technique (as bambara groundnut has no microarray chip) coupled with network-based analysis. …”
Get full text

Cell cycle- and cancer-associated gene networks activated by Dsg2: evidence of cystatin A deregulation and a potential role in cell-cell adhesion. by Abhilasha Gupta, Daniela Nitoiu, Donna Brennan-Crispi, Sankar Addya, Natalia A Riobo, David P Kelsell, Mỹ G Mahoney

“…CSTA is deregulated in several skin cancers, including squamous cell carcinomas (SCC) and loss of function mutations lead to recessive skin fragility disorders. The microarray results were confirmed by qPCR, immunoblotting, and immunohistochemistry. …”
Get full text