Identification and Cross-Platform Validation of Sparse Molecular Classifiers for Antibody-Mediated and T-Cell–Mediated Rejection After Kidney Transplantation by Jasper Callemeyn, Josué Manik Nava-Sedeño, Dany Anglicheau, Jack Beadle, Jan Hinrich Bräsen, Marian C. Clahsen-van Groningen, Iacopo Cristoferi, Henriette de Loor, Andreas Deutsch, Marie Essig, Wilfried Gwinner, Philip F. Halloran, Dennis A. Hesselink, Priyanka Koshy, Dirk Kuypers, Evelyne Lerut, Pierre Marquet, Robert C. Minnee, Candice Roufosse, Ben Sprangers, Amaryllis H. Van Craenenbroeck, Haralampos Hatzikirou, Maarten Naesens

“…Methods: In a discovery cohort of 224 kidney transplant biopsies, lasso regression was applied on microarray gene expression data to derive a molecular classifier for ABMR and TCMR, respectively. …”
Get full text

Rapid changes in transcription profiles of the Plasmodium yoelii yir multigene family in clonal populations: lack of epigenetic memory? by Deirdre Cunningham, Jannik Fonager, William Jarra, Celine Carret, Peter Preiser, Jean Langhorne

“…Using microarray and quantitative RT-PCR, we show that despite this very restricted transcription in a single cell, many yir genes are transcribed throughout the intra-erythrocytic asexual cycle. …”
Get full text

Analysis of Gene Expression in Human Dermal Fibroblasts Treated with Senescence-Modulating COX Inhibitors by Jeong A. Han, Jong-Il Kim

“…In contrast, celecoxib, another COX-2–selective inhibitor, and aspirin, a non-selective COX inhibitor, accelerated the senescence and aging. …”
Get full text

The Differential Gene Expression Pattern of Mycobacterium tuberculosis in Response to Capreomycin and PA-824 versus First-Line TB Drugs Reveals Stress- and PE/PPE-Related Drug Targ... by Li M. Fu, Shu C. Tai

“…Six among the 42 genes identified in this study are on the list of the top 100 persistence targets selected by the TB Structural Genomics Consortium. …”
Get full text

Reprogramming‐derived gene cocktail increases cardiomyocyte proliferation for heart regeneration by Yuan‐Yuan Cheng, Yu‐Ting Yan, David J Lundy, Annie HA Lo, Yu‐Ping Wang, Shu‐Chian Ruan, Po‐Ju Lin, Patrick CH Hsieh

“…Several candidate genes were selected and tested for their ability to induce CM proliferation. …”
Get full text

Comparing gene-gene co-expression network approaches for the analysis of cell differentiation and specification on scRNAseq data by Alisa Pavel, Manja Gersholm Grønberg, Line H. Clemmensen

“…Gene-gene co-expression network analysis has been widely applied to bulk RNA sequencing and microarray data to investigate different phenotypes and compound exposures. …”
Get full text

Infection of Human Coronary Artery Endothelial Cells by Group B Streptococcus Contributes to Dysregulation of Apoptosis, Hemostasis, and Innate Immune Responses by Claudia Beyrich, Jürgen Löffler, Anna Kobsar, Christian P. Speer, Susanne Kneitz, Martin Eigenthaler

Get full text

Tissue-restricted expression of Nrf2 and its target genes in zebrafish with gene-specific variations in the induction profiles. by Hitomi Nakajima, Yaeko Nakajima-Takagi, Tadayuki Tsujita, Shin-Ichi Akiyama, Takeshi Wakasa, Katsuki Mukaigasa, Hiroshi Kaneko, Yutaka Tamaru, Masayuki Yamamoto, Makoto Kobayashi

“…Seven zebrafish genes (gstp1, mgst3b, prdx1, frrs1c, fthl, gclc and hmox1a) suitable for WISH analysis were selected from candidates for Nrf2 targets identified by microarray analysis. …”
Get full text

Inferring pathway activity toward precise disease classification. by Eunjung Lee, Han-Yu Chuang, Jong-Won Kim, Trey Ideker, Doheon Lee

“…The advent of microarray technology has made it possible to classify disease states based on gene expression profiles of patients. …”
Get full text

Prevalence and characteristics of Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) isolated from chicken meat in the province of Quebec, Canada. by Jocelyn Bernier-Lachance, Julie Arsenault, Valentine Usongo, Éric Parent, Josée Labrie, Mario Jacques, François Malouin, Marie Archambault

“…A total of 309 chicken drumsticks and thighs were randomly selected in 2013 from 43 retail stores in the Monteregie. …”
Get full text

urg1: a uracil-regulatable promoter system for fission yeast with short induction and repression times. by Stephen Watt, Juan Mata, Luis López-Maury, Samuel Marguerat, Gavin Burns, Jürg Bähler

“…The kanMX6 and natMX6 markers allow selection under urg1 induced and repressed conditions, respectively. …”
Get full text

Quantification of the heterogeneity of prognostic cellular biomarkers in ewing sarcoma using automated image and random survival forest analysis. by Claudia Bühnemann, Simon Li, Haiyue Yu, Harriet Branford White, Karl L Schäfer, Antonio Llombart-Bosch, Isidro Machado, Piero Picci, Pancras C W Hogendoorn, Nicholas A Athanasou, J Alison Noble, A Bassim Hassan

“…Using material from cohorts of genetically diagnosed Ewing sarcoma with EWSR1 chromosomal translocations, confocal images of tissue microarrays were segmented with level sets and watershed algorithms. …”
Get full text

MicroRNA biomarkers of type 2 diabetes: A protocol for corroborating evidence by computational genomics and meta-analyses. by Hongmei Zhu, Siu-Wai Leung

“…Biologically relevant microRNAs will then be selected through genomic database corroboration. Their association with T2D is further measured by area under the curve (AUC) of receive operating characteristic (ROC). …”
Get full text

Integrated Bioinformatics Analysis of Hub Genes and Pathways in Anaplastic Thyroid Carcinomas by Xueren Gao, Jianguo Wang, Shulong Zhang

“…The aim of the present study was to identify hub genes and pathways in ATC by microarray expression profiling. Two independent datasets (GSE27155 and GSE53072) were downloaded from GEO database. …”
Get full text

A Synopsis of Serum Biomarkers in Cutaneous Melanoma Patients by Pierre Vereecken, Frank Cornelis, Nicolas Van Baren, Valérie Vandersleyen, Jean-François Baurain

“…However, the poor sensitivity and specificity of those markers and many other molecules are serious limitations for their routine use in both early (AJCC stage I and II) and advanced stages of melanoma (AJCC stage III and IV). Microarray technology and proteomic research will surely provide new candidates in the near future allowing more accurate definition of the individual prognosis and prediction of the therapeutic outcome and select patients for early adjuvant strategies.…”
Get full text

Maternal bisphenol a exposure impacts the fetal heart transcriptome. by Kalyan C Chapalamadugu, Catherine A Vandevoort, Matthew L Settles, Barrie D Robison, Gordon K Murdoch

“…At the end of treatment, fetal heart tissues were collected and chamber specific transcriptome expression was assessed using genome-wide microarray. Quantitative real-time PCR was conducted on select genes and ventricular tissue glycogen content was quantified. …”
Get full text

Identification and validation of TSPAN13 as a novel temozolomide resistance-related gene prognostic biomarker in glioblastoma. by Haofei Wang, Zhen Liu, Zesheng Peng, Peng Lv, Peng Fu, Xiaobing Jiang

“…Using LASSO Cox analysis, we selected 12 TMZR-RDEGs to construct a risk score model, which was evaluated for performance through survival analysis, time-dependent ROC, and stratified analyses. …”
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

“…In this study, we used a network mining algorithm to identify tightly connected gene co-expression networks that are frequently present in microarray datasets from 33 types of cancer which were derived from 16 organs/tissues. …”
Get full text

Have maternal or paternal ages any impact on the prenatal incidence of genomic copy number variants associated with fetal structural anomalies? by Marta Larroya, Marta Tortajada, Eduard Mensión, Montse Pauta, Laia Rodriguez-Revenga, Antoni Borrell

“…We conducted a non-paired case-control study (1:2 ratio) among pregnancies undergoing chromosomal microarray analysis (CMA) because of fetal ultrasound anomalies, from December 2012 to May 2020. …”
Get full text

Identification of the Exercise and Time Effects on Human Skeletal Muscle through Bioinformatics Methods by Mufang Feng, Jie Ji, Xiaoliu Li, Xinming Ye

“…To determine the effects of exercise and time on human skeletal muscle, we downloaded the microarray expression profile of GSE1832 and analyzed it to select differentially expressed genes (DEGs). …”
Get full text