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1. Towards a Change in the Diagnostic Algorithm of Autism Spectrum Disorders: Evidence Supporting Whole Exome Sequencing as a First-Tier Test

Author:
Arteche-López, Ana; Gómez Rodríguez, Maria José; Sánchez Calvin, Maria Teresa; Quesada-Espinosa, Juan Francisco; Lezana Rosales, Jose Miguel; Palma Milla, Carmen; Gómez-Manjón, Irene; Hidalgo Mayoral, Irene; Pérez de la Fuente, Rubén; Díaz de Bustamante, Arancha; Darnaude, María Teresa; Gil-Fournier, Belén; Ramiro León, Soraya; Ramos Gómez, Patricia; Sierra Tomillo, Olalla; Juárez Rufián, Alexandra; Arranz Cano, Maria Isabel; Villares Alonso, Rebeca; Morales-Pérez, Pablo; Segura-Tudela, Alejandro; Camacho, Ana; Nuñez, Noemí; Simón, Rogelio; Moreno-García, Marta; Alvarez-Mora, Maria Isabel
Source:
Genes 2021 v.12 no.4
ISSN:
2073-4425
Subject:
microarray technology,   etc   ; algorithms; autism; etiology;     Show all 4 Subjects
Abstract:
... Autism spectrum disorder (ASD) is a prevalent and extremely heterogeneous neurodevelopmental disorder (NDD) with a strong genetic component. In recent years, the clinical relevance of de novo mutations to the aetiology of ASD has been demonstrated. Current guidelines recommend chromosomal microarray (CMA) and a FMR1 testing as first-tier tests, but there is increasing evidence that support the use ...
DOI:
10.3390/genes12040560

2. Circular RNA ciRS-7 affects the propagation of Cryptosporidium parvum in HCT-8 cells by sponging miR-1270 to activate the NF-κB signaling pathway

Author:
Yin, Yan-Ling; Liu, Ting-Li; Yao, Qian; Wang, Yu-Xin; Wu, Xue-Mei; Wang, Xue-Ting; Yang, Xin; Song, Jun-Ke; Zhao, Guang-Hui
Source:
Parasites & vectors 2021 v.14 no.1 pp. 238
ISSN:
1756-3305
Subject:
microarray technology,   etc   ; Cryptosporidium parvum; circular RNA; pathogens;     Show all 4 Subjects
Abstract:
... BACKGROUND: Cryptosporidium is an important zoonotic pathogen responsible for severe enteric diseases in humans and animals. However, the molecular mechanisms underlying host and Cryptosporidium interactions are still not clear. METHODS: To study the roles of circRNAs in host cells during Cryptosporidium infection, the expression profiles of circRNAs in HCT-8 cells infected with C. parvum were inv ...
DOI:
10.1186/s13071-021-04739-w

3. On the optimistic performance evaluation of newly introduced bioinformatic methods

Author:
Buchka, Stefan; Hapfelmeier, Alexander; Gardner, Paul P.; Wilson, Rory; Boulesteix, Anne-Laure
Source:
Genome biology 2021 v.22 no.1 pp. 152
ISSN:
1474-760X
Subject:
microarray technology,   etc   ; bioinformatics; data collection; epigenetics; genome;     Show all 5 Subjects
Abstract:
... Most research articles presenting new data analysis methods claim that “the new method performs better than existing methods,” but the veracity of such statements is questionable. Our manuscript discusses and illustrates consequences of the optimistic bias occurring during the evaluation of novel data analysis methods, that is, all biases resulting from, for example, selection of datasets or compe ...
DOI:
10.1186/s13059-021-02365-4

4. MicroRNA-mRNA expression profiles and functional network after injection of botulinum toxin type A into submandibular glands

Author:
Mao, Qian-Ying; Xie, Shang; Wu, Li-Ling; Xiang, Ruo-Lan; Cai, Zhi-Gang
Source:
Toxicon 2021 v.199 pp. 31-40
ISSN:
0041-0101
Subject:
microarray technology,   etc   ; bioinformatics; botulinum toxin; microRNA; secretion;     Show all 5 Subjects
Abstract:
... Botulinum toxin type A (BTXA) is effective for the treatment of sialorrhea. MicroRNAs (miRNAs) have significant functions in salivary diseases, but the role of miRNAs during BTXA-inhibited salivary secretion is not yet clear. A total of 19 differentially expressed (DE) miRNAs and 1072 DE mRNAs were identified following BTXA injected into submandibular glands of rats (n = 4) through miRNA sequencin ...
DOI:
10.1016/j.toxicon.2021.05.011

5. Recent progress and advanced technology in carbohydrate-based drug development

Author:
Pan, Lin; Cai, Chao; Liu, Chanjuan; Liu, Di; Li, Guoyun; Linhardt, Robert J; Yu, Guangli
Source:
Current opinion in biotechnology 2021 v.69 pp. 191-198
ISSN:
0958-1669
Subject:
microarray technology,   etc   ; biotechnology; carbohydrates; drug development; microbiome;     Show all 5 Subjects
Abstract:
... Carbohydrates, one of the most abundant and widespread biomolecules in nature, play indispensable roles in diverse biological functions, and represent a treasure trove of untapped potential for pharmaceutical applications. Here, we provide a brief overview of carbohydrate-based drug development (CBDD) over the past two decades. More importantly, advanced techniques and methodologies related to CBD ...
DOI:
10.1016/j.copbio.2020.12.023

6. High-Throughput Methods in the Discovery and Study of Biomaterials and Materiobiology

Author:
Yang, Liangliang; Pijuan-Galito, Sara; Rho, Hoon Suk; Vasilevich, Aliaksei S.; Eren, Aysegul Dede; Ge, Lu; Habibović, Pamela; Alexander, Morgan R.; de Boer, Jan; Carlier, Aurélie; van Rijn, Patrick; Zhou, Qihui
Source:
Chemical reviews 2021 v.121 no.8 pp. 4561-4677
ISSN:
1520-6890
Subject:
microarray technology,   etc   ; biocompatible materials; homeostasis; medicine; transcriptomics;     Show all 5 Subjects
Abstract:
... The complex interaction of cells with biomaterials (i.e., materiobiology) plays an increasingly pivotal role in the development of novel implants, biomedical devices, and tissue engineering scaffolds to treat diseases, aid in the restoration of bodily functions, construct healthy tissues, or regenerate diseased ones. However, the conventional approaches are incapable of screening the huge amount o ...
DOI:
10.1021/acs.chemrev.0c00752

7. PD_BiBIM: Biclustering-based biomarker identification in ESCC microarray data

Author:
Patowary, Pallabi; Bhattacharyya, Dhruba K.
Source:
Journal of biosciences 2021 v.46 no.3 pp. 56
ISSN:
0250-5991
Subject:
microarray technology,   etc   ; biomarkers; data collection; squamous cell carcinoma; topology;     Show all 5 Subjects
Abstract:
... To promote diligent analysis of the progression of a disease, it is important to identify interesting biomarkers for the disease. Biclustering has already been established as an effective technique to help identify such biomarkers of high biological significance. Although in the recent past, a good number of biclustering techniques have been introduced, most of them fail to perform consistently ac ...
DOI:
10.1007/s12038-021-00171-5

8. Ensemble sparse estimation of covariance structure for exploring genetic disease data

Author:
Kang, Xiaoning; Wang, Mingqiu
Source:
Computational statistics & data analysis 2021 v.159 pp. 107220
ISSN:
0167-9473
Subject:
microarray technology,   etc   ; data analysis; genetic disorders; models; variance covariance matrix;     Show all 5 Subjects
Abstract:
... High-dimensional data often occur nowadays in various areas, such as genetic and microarray data. The covariance matrix is of fundamental importance in analyzing the relationship between multivariate variables. A powerful tool for estimating a covariance matrix is the modified Cholesky decomposition, which allows for unconstrained estimation and guarantees the positive definiteness of the estimate ...
DOI:
10.1016/j.csda.2021.107220

9. Trace the profile and function of circular RNAs in Sertoli cell only syndrome

Author:
Zhu, Fang; Luo, Yang; Bo, Hao; Gong, Guanghui; Tang, Ruiling; Fan, Jingyu; Zhang, Huan; Liu, Gang; Zhu, Wenbing; Tan, Yueqiu; He, Zuping; Fan, Liqing
Source:
Genomics 2021 v.113 no.4 pp. 1845-1854
ISSN:
0888-7543
Subject:
microarray technology,   etc   ; Sertoli cells; cell communication; cell cycle; genomics;     Show all 5 Subjects
Abstract:
... Studies increasingly show the involvement of circular RNAs (circRNAs) in several diseases. This study aims to explore the circRNA expression pattern in the testicular tissues of patients with Sertoli only cell syndrome (SCOS) and their potential functions. High throughput circRNA microarray analysis indicated that 399 circRNAs were upregulated and 1195 were down-regulated (fold change >2, P < 0.05 ...
DOI:
10.1016/j.ygeno.2021.04.022

10. Image-Based Live Cell Sorting

Author:
LaBelle, Cody A.; Massaro, Angelo; Cortés-Llanos, Belén; Sims, Christopher E.; Allbritton, Nancy L.
Source:
Trends in biotechnology 2021 v.39 no.6 pp. 613-623
ISSN:
0167-7799
Subject:
microarray technology,   etc   ; biomedical research; biotechnology; cell structures; drug development; medicine;     Show all 6 Subjects
Abstract:
... Technologies capable of cell separation based on cell images provide powerful tools enabling cell selection criteria that rely on spatially or temporally varying properties. Image-based cell sorting (IBCS) systems utilize microfluidic or microarray platforms, each having unique characteristics and applications. The advent of IBCS marks a new paradigm in which cell phenotype and behavior can be exp ...
DOI:
10.1016/j.tibtech.2020.10.006

11. Microarray Technology May Reveal the Contribution of Allergen Exposure and Rhinovirus Infections as Possible Triggers for Acute Wheezing Attacks in Preschool Children

Author:
Niespodziana, Katarzyna; Stenberg-Hammar, Katarina; Papadopoulos, Nikolaos G.; Focke-Tejkl, Margarete; Errhalt, Peter; Konradsen, Jon R.; Söderhäll, Cilla; van Hage, Marianne; Hedlin, Gunilla; Valenta, Rudolf
Source:
Viruses 2021 v.13 no.5
ISSN:
1999-4915
Subject:
microarray technology,   etc   ; Enterovirus; allergens; biomarkers; childhood; peptides; therapeutics;     Show all 7 Subjects
Abstract:
... Allergen exposure and rhinovirus (RV) infections are common triggers of acute wheezing exacerbations in early childhood. The identification of such trigger factors is difficult but may have therapeutic implications. Increases of IgE and IgG in sera, were shown against allergens and the N-terminal portion of the VP1 proteins of RV species, respectively, several weeks after allergen exposure or RV i ...
DOI:
10.3390/v13050915

12. Activin A activation drives renal fibrosis through the STAT3 signaling pathway

Author:
Yuan, Cheng; Ni, Lihua; Wu, Xiaoyan
Source:
The international journal of biochemistry & cell biology 2021 v.134 pp. 105950
ISSN:
1357-2725
Subject:
microarray technology,   etc   ; bioinformatics; collagen; fibronectins; fibrosis; protein-protein interactions;     Show all 6 Subjects
Abstract:
... The present study investigated whether TGF-β1 promotes fibrotic changes in HK-2 cells through the Activin A and STAT3 signaling pathways in vitro. Bioinformatics analysis of microarray profiles (GSE20247 and GSE23338) and a protein-protein interaction (PPI) analysis were performed to select hub genes. For the in vitro study, HK-2 cells were exposed to TGF-β1. The expression of Activin A and STAT3 ...
DOI:
10.1016/j.biocel.2021.105950

13. K-Module Algorithm: An Additional Step to Improve the Clustering Results of WGCNA Co-Expression Networks

Author:
Hou, Jie; Ye, Xiufen; Li, Chuanlong; Wang, Yixing
Source:
Genes 2021 v.12 no.1
ISSN:
2073-4425
Subject:
microarray technology,   etc   ; algorithms; data collection; genes; sequence analysis; trees;     Show all 6 Subjects
Abstract:
... Among biological networks, co-expression networks have been widely studied. One of the most commonly used pipelines for the construction of co-expression networks is weighted gene co-expression network analysis (WGCNA), which can identify highly co-expressed clusters of genes (modules). WGCNA identifies gene modules using hierarchical clustering. The major drawback of hierarchical clustering is th ...
DOI:
10.3390/genes12010087

14. CRISPR-based enrichment strategies for targeted sequencing

Author:
Schultzhaus, Zachary; Wang, Zheng; Stenger, David
Source:
Biotechnology advances 2021 v.46 pp. 107672
ISSN:
0734-9750
Subject:
microarray technology,   etc   ; ; DNA; RNA; biotechnology; diagnostic techniques; oligonucleotides; sequence analysis;     Show all 8 Subjects
Abstract:
... The ability to easily produce or procure sequencing data has expanded to be within the reach of most clinics and research laboratories, but the complexity of sequence analysis remains a hurdle for many scientists, and a decline in sequencing cost means that the generation of gratuitous information in a given experiment is a challenge that is more and more often being encountered. To address this i ...
DOI:
10.1016/j.biotechadv.2020.107672

15. Multiplex serological assay for establishing serological profiles of polymorphic, closely related peptide antigens

Author:
Bolton, Jessica; Chaudhury, Sidhartha; MacGill, Randall S.; Early, Angela M.; King, C. Richter; Locke, Emily; Neafsey, Daniel E.; Bergmann-Leitner, Elke S.
Source:
MethodsX 2021 v.8 pp. 101345
ISSN:
2215-0161
Subject:
microarray technology,   etc   ; ; antibodies; biomarkers; electrochemiluminescence; epitopes; landscapes; pathogens; synthetic peptides;     Show all 9 Subjects
Abstract:
... Profiling of serological responses to establish the landscape of antibody specificities in individuals exposed to pathogens or vaccines is crucial for (a) revealing humoral immune correlates of protection; (b) uncovering markers of pathogen exposure; and (c) identifying antigens and epitopes associated with disease vs. protection. Establishing the antigenic profile of serological responses require ...
DOI:
10.1016/j.mex.2021.101345

16. Adaptive Sparse Estimation With Side Information

Author:
Banerjee, Trambak; Mukherjee, Gourab; Sun, Wenguang
Source:
Journal of the American Statistical Association 2020 v.115 no.532 pp. 2053-2067
ISSN:
1537-274X
Subject:
microarray technology,   etc   ; risk; shrinkage; virology;     Show all 4 Subjects
Abstract:
... The article considers the problem of estimating a high-dimensional sparse parameter in the presence of side information that encodes the sparsity structure. We develop a general framework that involves first using an auxiliary sequence to capture the side information, and then incorporating the auxiliary sequence in inference to reduce the estimation risk. The proposed method, which carries out ad ...
DOI:
10.1080/01621459.2019.1679639

17. Computational Methods for the Analysis of Genomic Data and Biological Processes

Author:
Gómez-Vela, Francisco; Divina, Federico; García-Torres, Miguel
Source:
Genes 2020 v.11 no.10
ISSN:
2073-4425
Subject:
microarray technology,   etc   ; computational methodology; genomics;     Show all 3 Subjects
Abstract:
... Today, new technologies, such as microarrays or high-performance sequencing, are producing more and more genomic data [...] ...
DOI:
10.3390/genes11101230

18. circ_KIAA1429 accelerates hepatocellular carcinoma advancement through the mechanism of m6A-YTHDF3-Zeb1

Author:
Wang, Maoyu; Yang, Yongliang; Yang, Jing; Yang, Juanjuan; Han, Shumei
Source:
Life sciences 2020 v.257 pp. 118082
ISSN:
0024-3205
Subject:
microarray technology,   etc   ; hepatoma; metastasis; therapeutics;     Show all 4 Subjects
Abstract:
... Hepatocellular carcinoma (HCC), one of the most common cancer, causes the fourth cancer-related deaths around the world. N6-methyladenosine (m⁶A) has been reported to mediate circRNA translation in cancer biology. However, the mechanisms by which m⁶A and circRNA in post-transcriptional in HCC progression remain poorly understood. This study aimed to explore the mechanisms by which m⁶A and circRNA ...
DOI:
10.1016/j.lfs.2020.118082

19. Differences in berry skin and pulp cell wall polysaccharides from ripe and overripe Shiraz grapes evaluated using glycan profiling reveals extensin-rich flesh

Author:
Gao, Yu; Fangel, Jonatan U.; Willats, William G.T.; Vivier, Melané A.; Moore, John P.
Source:
Food chemistry 2021 v.363 pp. 130180
ISSN:
0308-8146
Subject:
microarray technology,   etc   ; cell walls; cultivars; epitopes; extensin; food chemistry; grapes; pectins; pulp; shrinkage; winemaking; xyloglucans;     Show all 12 Subjects
Abstract:
... Shiraz is a widely planted cultivar in many of the world’s top wine regions where it is used for the production of top-quality single varietal or blended red wines. Cell wall changes during grape ripening and over-ripening have been investigated, particularly in the context of understanding berry deconstruction thereby facilitating the release of favorable compounds during winemaking. However, no ...
DOI:
10.1016/j.foodchem.2021.130180

20. Prenatal diagnosis of the Dandy–Walker malformation associated with partial trisomy 12p and distal 15q deletion

Author:
Sun, Yanmei; Zhang, Ning; Tian, Haishen; Zhang, Pingping; Li, Yali
Source:
Journal of genetics 2021 v.100 no.2 pp. 40
ISSN:
0022-1333
Subject:
microarray technology,   etc   ; abnormal development; cerebellum; fetus; karyotyping; neurodevelopment; pathogenesis; single nucleotide polymorphism; trisomics; ultrasonics;     Show all 10 Subjects
Abstract:
... Dandy–Walker malformation (DWM) is characterized by complete or partial agenesis of the cerebellar vermis, cyatic dilatation of the forth ventricle, and enlarged posterior fossa. However, the mechanism is still not completely understood up to now. In this study, we reported a rare case that a foetus with DWM showed partial trisomy 12p and distal 15q deletion. Karyotype analysis and chromosomal mic ...
DOI:
10.1007/s12041-021-01290-6