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1. A regression framework for assessing covariate effects on the reproducibility of high‐throughput experiments

Author:
Li, Qunhua; Zhang, Feipeng
Source:
Biometrics 2018 v.74 no.3 pp. 803-813
ISSN:
0006-341X
Subject:
microarray technology,   etc   ; biometry; models;     Show all 3 Subjects
Abstract:
... The outcome of high‐throughput biological experiments is affected by many operational factors in the experimental and data‐analytical procedures. Understanding how these factors affect the reproducibility of the outcome is critical for establishing workflows that produce replicable discoveries. In this article, we propose a regression framework, based on a novel cumulative link model, to assess th ...
DOI:
10.1111/biom.12832

2. Bio-orthogonal fluorinated resist for biomolecules patterning applications

Author:
Machairioti, Fotini; Petrou, Panagiota; Oh, Hyun-Taek; Lee, Jin-Kyun; Kakabakos, Sotirios; Argitis, Panagiotis; Chatzichristidi, Margarita
Source:
Colloids and surfaces 2019 v.178 pp. 208-213
ISSN:
0927-7765
Subject:
microarray technology,   etc   ; adsorption; biochemical compounds; chemical bonding; fluorocarbon polymers; solvents;     Show all 6 Subjects
Abstract:
... The patterning of organic materials on solid substrate surfaces has been demonstrated by several methods, such as photolithography, soft lithography, imprint lithography and ink-jet printing. Fluorinated polymers and solvents provide attractive material systems to develop new patterning approaches, as they are chemically orthogonal to non-fluorinated organic molecules, allowing their efficient inc ...
DOI:
10.1016/j.colsurfb.2019.03.006

3. Microfluidic device embedding electrodes for dielectrophoretic manipulation of cells‐A review

Author:
Yao, Jiafeng; Zhu, Guiping; Zhao, Tong; Takei, Masahiro
Source:
Electrophoresis 2019 v.40 no.8 pp. 1166-1177
ISSN:
0173-0835
Subject:
microarray technology,   etc   ; dielectrophoresis; electric field; electrodes; electrophoresis; medicine; microfluidic technology;     Show all 7 Subjects
Abstract:
... Microfluidic device embedding electrodes realizes cell manipulation with the help of dielectrophoresis. Cell manipulation is an important technology for cell sorting and cell population purification. Till now, the theory of dielectrophoresis has been greatly developed. Microfluidic devices with various arrangements of electrodes have been reported from the beginning of the single non‐uniform elect ...
DOI:
10.1002/elps.201800440

4. Cytogenetic microarray in structurally normal and abnormal foetuses: a five years experience elucidating increasing acceptance and clinical utility

Author:
Lallar, Meenakshi; Srivastava, Priyanka; Rai, Archana; Saxena, Deepti; Mandal, Kausik; Phadke, Shubha R.
Source:
Journal of genetics 2019 v.98 no.1 pp. 6
ISSN:
0022-1333
Subject:
microarray technology,   etc   ; aneuploidy; fetus; fluorescence; karyotyping; polymerase chain reaction; risk;     Show all 7 Subjects
Abstract:
... The aim of the present study was to evaluate the diagnostic yield of prenatal cytogenetic microarray (CMA) in structurally normal and abnormal foetuses and record the acceptance rate of CMA for prenatal diagnosis over a course of five years. In 128 structurally normal and abnormal foetuses, CMA was performed along with foetal karyotype, after exclusion of aneuploidy by quantitative fluorescence po ...
DOI:
10.1007/s12041-018-1050-5

5. Micropatterning of porous silicon Bragg reflectors with poly(ethylene glycol) to fabricate cell microarrays: Towards single cell sensing

Author:
Piya, Ranjana; Zhu, Ying; Soeriyadi, Alexander H.; Silva, Saimon M.; Reece, Peter J.; Gooding, J. Justin
Source:
Biosensors & bioelectronics 2019 v.127 pp. 229-235
ISSN:
0956-5663
Subject:
microarray technology,   etc   ; biosensors; hydrogels; macrophages; polyethylene glycol; silicon;     Show all 6 Subjects
Abstract:
... The work presented here describes the development of an optical label-free biosensor based on a porous silicon (PSi) Bragg reflector to study heterogeneity in single cells. Photolithographic patterning of a poly(ethylene glycol) (PEG) hydrogel with a photoinitiator was employed on RGD peptide-modified PSi to create micropatterns with cell adhesive and cell repellent areas. Macrophage J774 cel ...
DOI:
10.1016/j.bios.2018.12.001

6. Preparation of giant lipid vesicles with controllable sizes by a modified hydrophilic polydimethylsiloxane microarray chip

Author:
Fan, Ting; Wang, Qiong; Hu, Ning; Liao, Yanjian; Chen, Xi; Wang, Zhenyu; Yang, Zhong; Yang, Jun; Qian, Shizhi
Source:
Journal of colloid and interface science 2019 v.536 pp. 53-61
ISSN:
0021-9797
Subject:
microarray technology,   etc   ; glass; hydrophilicity; lipids; polydimethylsiloxane; statistical analysis;     Show all 6 Subjects
Abstract:
... This paper presents an accessible method to prepare giant lipid vesicles (GLVs) with controllable sizes based on the quick formation of patterned lipid films. Lipid solutions naturally penetrate into arrayed micro-apertures on a modified hydrophilic Polydimethylsiloxane (PDMS) chip, and excess lipid films on the surface are removed by a glass slide. Three main factors, the depth and diameter of th ...
DOI:
10.1016/j.jcis.2018.10.034

7. Ultrasensitive Single-Molecule Enzyme Detection and Analysis Using a Polymer Microarray

Author:
Duan, Barrett K.; Cavanagh, Peter E.; Li, Xiang; Walt, David R.
Source:
Analytical chemistry 2018 v.90 no.5 pp. 3091-3098
ISSN:
1520-6882
Subject:
microarray technology,   etc   ; enzymes; oils; olefin; polymers;     Show all 5 Subjects
Abstract:
... This report describes a novel method for isolating and detecting individual enzyme molecules using polymer arrays of picoliter microwells. A fluidic flow-cell device containing an array of microwells is fabricated in cyclic olefin polymer (COP). The use of COP microwell arrays simplifies experiments by eliminating extensive device preparation and surface functionalization that are common in other ...
DOI:
10.1021/acs.analchem.7b03980

8. Spatial Control of Crystallographic Direction in 2D Microarrays of Anisotropic Nanoblocks on Trenched Substrates

Author:
Matsumoto, Riho; Nakagawa, Yoshitaka; Kato, Kazumi; Oaki, Yuya; Imai, Hiroaki
Source:
Langmuir 2017 v.33 no.48 pp. 13805-13810
ISSN:
1520-5827
Subject:
microarray technology,   etc   ; evaporation rate; silicon;     Show all 3 Subjects
Abstract:
... Elaborate two-dimensional (2D) microarrays of tetragonal Mn₃O₄ nanocuboids 10–20 nm in size were constructed with parallel trenches 500 nm wide and 500 nm deep on a silicon substrate. By adjusting the conditions, including the dispersion medium, particle concentration, and evaporation rate, the a-face and c-face 2D arrays were selectively deposited on the upper and lower stages of the trenches, re ...
DOI:
10.1021/acs.langmuir.7b03264

9. Convex biclustering

Author:
Chi, Eric C.; Allen, Genevera I.; Baraniuk, Richard G.
Source:
Biometrics 2017 v.73 no.1 pp. 10-19
ISSN:
0006-341X
Subject:
microarray technology,   etc   ; algorithms; biometry; genes;     Show all 4 Subjects
Abstract:
... In the biclustering problem, we seek to simultaneously group observations and features. While biclustering has applications in a wide array of domains, ranging from text mining to collaborative filtering, the problem of identifying structure in high‐dimensional genomic data motivates this work. In this context, biclustering enables us to identify subsets of genes that are co‐expressed only within ...
DOI:
10.1111/biom.12540

10. RnBeads 2.0: comprehensive analysis of DNA methylation data

Author:
Müller, Fabian; Scherer, Michael; Assenov, Yassen; Lutsik, Pavlo; Walter, Jörn; Lengauer, Thomas; Bock, Christoph
Source:
Genome biology 2019 v.20 no.1 pp. 55
ISSN:
1474-760X
Subject:
microarray technology,   etc   ; DNA methylation; bisulfites; cell differentiation; computer software; epigenetics; neoplasms; sequence analysis; user interface;     Show all 9 Subjects
Abstract:
... DNA methylation is a widely investigated epigenetic mark with important roles in development and disease. High-throughput assays enable genome-scale DNA methylation analysis in large numbers of samples. Here, we describe a new version of our RnBeads software - an R/Bioconductor package that implements start-to-finish analysis workflows for Infinium microarrays and various types of bisulfite sequen ...
DOI:
10.1186/s13059-019-1664-9

11. Lasso ANOVA decompositions for matrix and tensor data

Author:
Griffin, Maryclare; Hoff, Peter D.
Source:
Computational statistics & data analysis 2019 v.137 pp. 181-194
ISSN:
0167-9473
Subject:
microarray technology,   etc   ; analysis of variance; data collection; magnetic resonance imaging; plant diseases and disorders; wheat;     Show all 6 Subjects
Abstract:
... Consider the problem of estimating the entries of an unknown mean matrix or tensor given a single noisy realization. In the matrix case, this problem can be addressed by decomposing the mean matrix into a component that is additive in the rows and columns, i.e. the additive ANOVA decomposition of the mean matrix, plus a matrix of elementwise effects, and assuming that the elementwise effects may b ...
DOI:
10.1016/j.csda.2019.02.005

12. Omics approaches to understand sourdough fermentation processes

Author:
Weckx, Stefan; Van Kerrebroeck, Simon; De Vuyst, Luc
Source:
International journal of food microbiology 2019 v.302 pp. 90-102
ISSN:
0168-1605
Subject:
microarray technology,   etc   ; DNA; automation; databases; fermentation; genes; lactic acid bacteria; metabolites; metagenomics; sourdough; terminology; transcriptomics; yeasts;     Show all 13 Subjects
Abstract:
... The application of omics methodologies helps to further unravel sourdough fermentation processes. Of all methodologies applied, metagenetics is the most used one to analyse sourdoughs, allowing to elucidate their microbial structure, albeit that it is based on the sequencing of a very small part of whole-community DNA. Although shotgun metagenomics, metatranscriptomics, metaproteomics, and meta-me ...
DOI:
10.1016/j.ijfoodmicro.2018.05.029

13. A graph Laplacian prior for Bayesian variable selection and grouping

Author:
Chakraborty, Sounak; Lozano, Aurelie C.
Source:
Computational statistics & data analysis 2019 v.136 pp. 72-91
ISSN:
0167-9473
Subject:
microarray technology,   etc   ; Arabidopsis thaliana; Bayesian theory; algorithms; regression analysis; social identification; statistical models;     Show all 7 Subjects
Abstract:
... Variable selection, or subset selection, plays a fundamental role in modern statistical modeling. In many applications, interactions exist between the selected variables. Statistical modeling of such dependence structure is of great importance. In this paper, the focus is on cases in which some correlated predictors have similar effects on the response, and will be grouped into predictive clusters ...
DOI:
10.1016/j.csda.2019.01.003

14. Unique arrangement of bone matrix orthogonal to osteoblast alignment controlled by Tspan11-mediated focal adhesion assembly

Author:
Nakanishi, Yohei; Matsugaki, Aira; Kawahara, Kosuke; Ninomiya, Takafumi; Sawada, Hiroshi; Nakano, Takayoshi
Source:
Biomaterials 2019 v.209 pp. 103-110
ISSN:
0142-9612
Subject:
microarray technology,   etc   ; apatite; collagen; extracellular matrix; focal adhesions; gene expression regulation; integrins; isotropy; osteoblasts;     Show all 9 Subjects
Abstract:
... During tissue construction, cells coordinate extracellular matrix (ECM) assembly depending on the cellular arrangement. The traditional understanding of the relationship between the ECM and cells is limited to the orientation-matched interaction between them. Indeed, it is commonly accepted that the bone matrix (collagen/apatite) is formed along osteoblast orientation. Nonetheless, our recent find ...
DOI:
10.1016/j.biomaterials.2019.04.016

15. Copy number variants detection by microarray and multiplex ligation-dependent probe amplification in congenital heart diseases

Author:
Nagy, Orsolya; Szakszon, Katalin; Biró, Brigitta Orsolya; Mogyorósy, Gábor; Nagy, Dóra; Nagy, Bálint; Balogh, István; Ujfalusi, Anikó
Source:
Journal of biotechnology 2019 v.299 pp. 86-95
ISSN:
0168-1656
Subject:
microarray technology,   etc   ; congenital abnormalities; environmental factors; etiology; genes; genomics; heart diseases; humans; pathogenesis; patients; phenotype;     Show all 11 Subjects
Abstract:
... Congenital heart diseases (CHDs) are the most common birth defects among life births, which could be presented as isolated or syndromic with other congenital malformations. The etiology of CHD largely unknown, genetic and environmental factors contribute to the disease. Recurrent copy number variants (CNVs) have been reported in the pathogenesis of CHD. The aim of this study was to evaluate the cl ...
DOI:
10.1016/j.jbiotec.2019.04.025

16. Automated DNA hybridization transfer with movable super-paramagnetic microbeads in a microflow reactor

Author:
Penchovsky, Robert
Source:
Biosensors & bioelectronics 2019 v.135 pp. 30-35
ISSN:
0956-5663
Subject:
microarray technology,   etc   ; DNA; automation; biosensors; biotechnology; denaturation; drugs; microbeads; nucleic acid hybridization; pH; screening;     Show all 11 Subjects
Abstract:
... An automated DNA hybridization transfer in a microflow reactor is demonstrated by moving paramagnetic beads between two spatially separate solutions with different pH values. The microbeads-based microfluidic platform is fully automated and programmable. It employs a robust chemical procedure for specific DNA hybridization transfer in microfluidic devices under isothermal conditions based on rever ...
DOI:
10.1016/j.bios.2019.04.014

17. miR-3622a promotes proliferation and invasion of bladder cancer cells by downregulating LASS2

Author:
Fu, Shi; Luan, Ting; Jiang, Changyi; Huang, Yinglong; Li, Ning; Wang, Haifeng; Wang, Jiansong
Source:
Gene 2019 v.701 pp. 23-31
ISSN:
0378-1119
Subject:
microarray technology,   etc   ; bioinformatics; bladder; gene expression; microRNA; neoplasm cells; patients; tumor suppressor genes; urinary bladder neoplasms;     Show all 9 Subjects
Abstract:
... As a tumor metastasis suppressor gene, LASS2 has been found to be negatively associated with the stage of bladder cancer and overall survival of patients. However, the mechanisms regulating LASS2 in bladder cancer remain poorly understood. Here, we aim to identify a miRNA that targets LASS2 from bladder cancer-associated miRNAs and to reveal its potential functions in bladder cancer cells. Through ...
DOI:
10.1016/j.gene.2019.02.083

18. A Reappraisal of Circulating Fetal Cell Noninvasive Prenatal Testing

Author:
Rezaei, Meysam; Winter, Marnie; Zander-Fox, Deirdre; Whitehead, Clare; Liebelt, Jan; Warkiani, Majid Ebrahimi; Hardy, Tristan; Thierry, Benjamin
Source:
Trends in biotechnology 2019 v.37 no.6 pp. 632-644
ISSN:
0167-7799
Subject:
microarray technology,   etc   ; DNA; blood; chlorofluorocarbons; cost effectiveness; diagnostic sensitivity; high-throughput nucleotide sequencing; screening;     Show all 8 Subjects
Abstract:
... New tools for higher-resolution fetal genome analysis including microarray and next-generation sequencing have revolutionized prenatal screening. This article provides commentary on this rapidly advancing field and a future perspective emphasizing circulating fetal cell (CFC) utility. Despite the tremendous technological challenges associated with their reliable and cost-effective isolation from m ...
DOI:
10.1016/j.tibtech.2018.11.001

19. The effect of interaction between EtOH dosage and exposure time on gene expression in DPSC

Author:
Li, Jianqiang; Wang, Zhirui; Qiu, Weiliang; Yang, Ji-Jiang; Wang, Qing; Chen, Shi; Pan, Hui
Source:
Genomics 2019 v.111 no.3 pp. 500-507
ISSN:
0888-7543
Subject:
microarray technology,   etc   ; alcohol drinking; data collection; ethanol; exposure duration; gene expression; genes; human health; synergism;     Show all 9 Subjects
Abstract:
... Alcohol (EtOH) dosage and exposure time can affect gene expression. However, whether there exists synergistic effect is unknown. Here, we analyzed the hDPSC gene microarray dataset GSE57255 downloaded from Gene Expression Omnibus and found that the interaction between EtOH dosage and exposure time on gene expression are statistically significant for two probes: 201917_s_at near gene SLC25A36 and 2 ...
DOI:
10.1016/j.ygeno.2018.03.009

20. Microarray analysis of gene expression of Atlantic cod from different Baltic Sea regions: Adaptation to salinity

Author:
Malachowicz, Magdalena; Wenne, Roman
Source:
Marine genomics 2019
ISSN:
1874-7787
Subject:
microarray technology,   etc   ; Gadus morhua; cell cycle; genes; immune system; lipid metabolism; oligonucleotides; salinity; Baltic Sea;     Show all 9 Subjects
Abstract:
... The Atlantic cod (Gadus morhua L.) is one of the most important species in the Baltic Sea with high ecological and economical value. To explore the differences in adaptation to salinity between Baltic cod from different regions, western (Kiel Bight) and eastern (Gdańsk Bay) samples were analyzed through oligonucleotide microarray. The results showed that a total of 1043 genes were differently expr ...
DOI:
10.1016/j.margen.2019.04.006