23 papers · ranked by Valyu relevance
Sang-Jin Park, Eun Hye Jung, Ran-Suk Ryu, Hyun Woong Kang + 5 more
'Jung-Min Ko' 'Hyon J Kim' 'Chong Kun Cheon' 'Sang-Hyun Hwang' 'Ho-Young Kang'] Background Array comparative genomic hybridization (CGH) is currently the most powerful method for detecting chromosomal alterations in pre and postnatal clinical cases. In this study, we developed a BAC based array CGH analysis platform…
Björn Menten, Filip Pattyn, Katleen De Preter, Piet Robbrecht + 11 more
Background The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic…
Raj Chari, William W. Lockwood, Wan L. Lam
Array comparative genomic hybridization (array CGH) is a technique for assaying the copy number status of cancer genomes. The widespread use of this technology has lead to a rapid accumulation of high throughput data, which in turn has prompted the development of computational strategies for the analysis of array CGH…
Raj Chari, William W Lockwood, Bradley P Coe, Anna Chu + 5 more
'Andrew Thomson' 'Jonathan J Davies' 'Calum MacAulay' 'Wan L Lam'] Background The prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the public domain are gene expression…
Wei Chen, Fikret Erdogan, H-Hilger Ropers, Steffen Lenzner + 1 more
'Reinhard Ullmann'] Background Array CGH (Comparative Genomic Hybridisation) is a molecular cytogenetic technique for the genome wide detection of chromosomal imbalances. It is based on the co-hybridisation of differentially labelled test and reference DNA onto arrays of genomic BAC clones, cDNAs or oligonucleotides…
Ganesh Shankar, Michael R. Rossi, Devin E. McQuaid, Jeffrey M. Conroy + 4 more
'Jeffrey M. Conroy' 'Daniel G. Gaile' 'John K. Cowell' 'Norma J. Nowak' 'Ping Liang'] Array-Comparative Genomic Hybridization (aCGH) is a powerful high throughput technology for detecting chromosomal copy number aberrations (CNAs) in cancer, aiming at identifying related critical genes from the affected genomic…
Bin Zhu, Jeremy M. G. Taylor, Peter X.‐K. Song
Array comparative genomic hybridization(CGH) is a high resolution technique to assess DNA copy number variation. Identifying breakpoints where copy number changes will enhance the understanding of the pathogenesis of human diseases, such as cancers. However, the biological variation and experimental errors contained in…
Majid Mohammadi, Hossein Sharifi Noghabi
Mat-aCGH is an application toolbox for analysis and visualization of microarray-comparative genomic hybridization (array-CGH or aCGH) data which is based on Matlab. Full process of aCGH analysis, from denoising of the raw data to the visualization of the desired results, can be obtained via Mat-aCGH straightforwardly.…
Xian Fan, Mohammadamin Edrisi, Nicholas Navin, Luay Nakhleh
Single-cell DNA sequencing technologies are enabling the study of mutations and their evolutionary trajectories in cancer. Somatic copy number aberrations (CNAs) have been implicated in the development and progression of various types of cancer. A wide array of methods for CNA detection has been either developed…
Jing Liu, Francois Bernier, Julie Lauzon, R. Brian Lowry + 1 more
'Judy Chernos'] Microarray-based comparative genomic hybridization (array CGH) is a newly emerged molecular cytogenetic technique for rapid evaluation of the entire genome with sub-megabase resolution. It allows for the comprehensive investigation of thousands and millions of genomic loci at once and therefore enables…
Xiao Fang, Jian Li, David Siegmund
To segment a sequence of independent random variables at an unknown number of change-points, we introduce new procedures that are based on thresholding the likelihood ratio statistic. We also study confidence regions based on the likelihood ratio statistic for the changepoints and joint confidence regions for the…
Sangwon Hyun, Kevin Lin, Max G’Sell, Ryan J. Tibshirani
Changepoint detection methods are used in many areas of science and engineering, e.g., in the analysis of copy number variation data, to detect abnormalities in copy numbers along the genome. Despite the broad array of available tools, methodology for quantifying our uncertainty in the strength (or presence) of given…
John Wiedenhoeft, Eric Brugel, Alexander Schliep
By combining Haar wavelets with Bayesian Hidden Markov Models, we improve detection of genomic copy number variants (CNV) in array CGH experiments compared to the state-of-the-art, including standard Gibbs sampling. At the same time, we achieve drastically reduced running times, as the method concentrates computational…
Gemma M Jenkins, Michael E Goddard, Michael A Black, Rudiger Brauning + 5 more
Background. Copy number variants (CNVs) are a type of polymorphism found to underlie phenotypic variation, both in humans and livestock. Most surveys of CNV in livestock have been conducted in the cattle genome, and often utilise only a single approach for the detection of copy number differences. Here we performed a…
Benjamin L. Rambo-Martin, Jennifer G. Mulle, David J. Cutler, Lora J.H. Bean + 8 more
One in five people with Down syndrome (DS) are born with an atrioventricular septal defect (AVSD), an incidence 2,000 times higher than in the euploid population. The genetic loci that contribute to this risk are poorly understood. In this study, we tested two hypotheses: 1) individuals with DS carrying chromosome 21…
Koki Murano, Tomoyoshi Shimobaba, Atsushi Sugiyama, Naoki Takada + 3 more
'Takashi Kakue' 'Minoru Oikawa' 'Tomoyoshi Ito'] We report fast computation of computer-generated holograms (CGHs) using Xeon Phi coprocessors, which have massively x86-based processors on one chip, recently released by Intel. CGHs can generate arbitrary light wavefronts, and therefore, are promising technology for…
Munkyu Kang, Murray, Elizabeth, Leyla Kabuli + 2 more
Computer generated holography requires high-speed spatial light modulators (SLMs) for dynamically patterning light in 3D. Pistonmotion micromirror-based SLMs support high-speed (≥ 10 kHz) phase modulation; however, fabricating micromirror arrays with sufficient fill factor necessary for high diffraction efficiency is…
Nathan Tessema Ersaro, Cem Yalcin, Liz Murray, Leyla Kabuli + 2 more
'Laura Waller' 'Rikky Muller'] Abstract: Recently developed iterative and deep learning-based approaches to computergenerated holography (CGH) have been shown to achieve high-quality photorealistic 3D images with spatial light modulators. However, such approaches remain overly cumbersome for patterning sparse…
Chin Hong Ooi, Nam-Trung Nguyen, Gregor Kijanka
Protein arrays are systematically arranged, large collections of annotated proteins on planar surfaces commonly used for the characterisation of protein binding events against a wide range of possible probes. These may include analyses of protein-protein, peptide-protein, enzyme-substrate or antibody-antigen…
Paul Morris, Cory Simon
In many gas sensing tasks, we simply wish to become aware of gas compositions that deviate from normal, "business-as-usual" conditions. We provide a methodology, illustrated by example, to computationally predict the performance of a gas sensor array design for detecting anomalous gas compositions. Specifically, we…
Margaux L.A. Hujoel, Maxwell A. Sherman, Alison R. Barton, Ronen E. Mukamel + 2 more
The human genome contains hundreds of thousands of regions exhibiting copy number variation (CNV). However, the phenotypic effects of most such polymorphisms are unknown because only larger CNVs (spanning tens of kilobases) have been ascertainable from the SNP-array data generated by large biobanks. We developed a new…
Authors not listed
Large-scale graphene films enable the integration of graphene field-effect transistor (GFET) arrays onto chips. However, the transfer characteristics display variability across the array. This significant statistical variation in graphene quality, combined with the lack of standardized protocols, poses a major…
Jürgen Behr, Timm Michel, Maya Giridhar, Santra Santhosh + 11 more
Large- to ultra-large-scale synthesis of nucleic acids is becoming an increasingly important tool for understanding and manipulating biological systems, as well as for developing new technologies based on engineered biological materials, including DNA-based nanofabrication, aptamers and writing digital data at the…