19 papers · ranked by Valyu relevance
Francisco Javier Lobo-Cabrera
Complexity is often associated with increasing non-coding DNA (ncDNA). For example, the human genome is in its vast majority ncDNA. Here, it is hypothesized that normalized ncDNA (nncDNA) has in fact diminished in evolution. This definition of ncDNA content takes into consideration total proteomic content. It is shown…
Gaoxiang Jia, Xinlei Wang, Qiwei Li, Wei Lü + 3 more
'Ignacio I. Wistuba' 'Yang Xie'] Formalin-fixed paraffin-embedded (FFPE) samples have great potential for biomarker discovery, retrospective studies and diagnosis or prognosis of diseases. Their application, however, is hindered by the unsatisfactory performance of traditional gene expression profiling techniques on…
Xue-Ying Lyu, Yu-Man Tsui, Ivan Ka-Kit Tam, Po-Man Li + 5 more
'Gary Cheuk-Hang Cheung' 'Joyce Man-Fong Lee' 'Irene Oi-Lin Ng' 'Daniel Wai-Hung Ho' 'David A. Geller'] Simple Summary Mitochondria are important organelles in the human body, and they act as a source of chemical energy for different cellular processes. Multiple copies of mitochondria are normally detected in cells…
Dongsuk Kim, Geonhee Lee, Myung-Jae Lee, Shin Uk Kang + 1 more
In this paper, we propose Normalized Convolutional Neural Network(NCNN). NCNN is more fitted to a convolutional operator than other nomralizaiton methods. The normalized process is similar to a normalization methods, but NCNN is more adapative to sliced-inputs and corresponding the convolutional kernel. Therefor NCNN…
Anastassiia Vertii, Jianhong Ou, Jun Yu, Aimin Yan + 4 more
In interphase eukaryotic cells, almost all heterochromatin is located adjacent to the nucleolus or to the nuclear lamina, thus defining Nucleolus-Associated Domains (NADs) and Lamina–Associated Domains (LADs), respectively. Here, we determined the first genome-scale map of murine NADs in mouse embryonic fibroblasts…
Ruchi Joshi, Anushka Roy, Relestina Lopes, Laxmi Kata + 6 more
Cell-free chromatin particles (cfChPs), primarily derived from non-coding DNA (ncDNA) and released from apoptotic cells into the bloodstream, can be horizontally transferred into living cells^1^. However, their potential role in generating ncDNA within recipient cells remains unknown. We previously reported that…
Wenying He, Ying Ju, Xiangxiang Zeng, Xiangrong Liu + 1 more
With the rapid development of high-speed sequencing technologies and the implementation of many whole genome sequencing project, research in the genomics is advancing from genome sequencing to genome synthesis. Synthetic biology technologies such as DNA-based molecular assemblies, genome editing technology, directional…
Mariya Shtumpf, Kristan V. Piroeva, Shivam P. Agrawal, Divya R. Jacob + 1 more
Nucleosome positioning is involved in many gene regulatory processes happening in the cell and it may change as cells differentiate or respond to the changing microenvironment in a healthy or diseased organism. One important implication of nucleosome positioning in clinical epigenetics is its use in the “nucleosomics”…
David Haughton, Félix Balado
Background In recent times, the application of deoxyribonucleic acid (DNA) has diversified with the emergence of fields such as DNA computing and DNA data embedding. DNA data embedding, also known as DNA watermarking or DNA steganography, aims to develop robust algorithms for encoding non-genetic information in DNA.…
Ciaran Evans, Johanna Hardin, Daniel M. Stoebel
Johanna Hardin is Professor of Mathematics at Pomona College. She works on different types of analyses of high-throughput genetic data that don't conform to the usual assumptions needed for statistical analyses. Daniel Stoebel is Associate Professor of Biology at Harvey Mudd College. He works on the molecular biology…
Carlos P. Roca, Susana I.L. Gomes, Mónica J.B. Amorim, Janeck J. Scott‐Fordsmand
'Janeck J. Scott‐Fordsmand'] RNA-Seq and gene expression microarrays provide comprehensive profiles of gene activity, but lack of reproducibility has hindered their application. A key challenge in the data analysis is the normalization of gene expression levels, which is currently performed following the implicit…
Zuzana Vrablicova, Kristina Tomova, Lubomira Tothova, Janka Babickova + 5 more
'Janka Babickova' 'Barbora Gromova' 'Barbora Konecna' 'Robert Liptak' 'Tibor Hlavaty' 'Roman Gardlik'] Background: The role of cell-free DNA (cfDNA) in the pathogenesis of inflammatory bowel disease (IBD) has been recently suggested. The aim of this study was to analyze circulating cfDNA and deoxyribonuclease (DNase)…
Danielle F. Mello, Luiza Perez, Christina M. Bergemann, Katherine S. Morton + 2 more
Mitochondrial bioenergetic processes are fundamental to development, stress responses, and health. Caenorhabditis elegans is widely used to study developmental biology, mitochondrial disease, and mitochondrial toxicity. Oxidative phosphorylation generally increases during development in many species, and genetic and…
Troy Ruths, Luay Nakhleh
Background The amount of transcription factor binding sites (TFBS) in an organism’s genome positively correlates with the complexity of the regulatory network of the organism. However, the manner by which TFBS arise and accumulate in genomes and the effects of regulatory network complexity on the organism’s fitness are…
Zhenyu Zhang, Kyle Hernandez, Jeremiah Savage, Shenglai Li + 6 more
The goal of the National Cancer Institute (NCI) Genomic Data Commons (GDC) is to provide the cancer research community with a data repository of uniformly processed genomic and associated clinical data that enables data sharing and collaborative analysis in the support of precision medicine. The initial GDC dataset…
Shadrack Barnabas, Timo Böhme, Stephen Boyer, Matthias Irmer + 5 more
The extraction of chemical information from documents is a demanding task in cheminformatics due to the variety of text and image-based representations of chemistry. The present work describes the extraction of chemical compounds with unique chemical structures from the open access CORE (COnnecting REpositories) and…
Shadrack Barnabas, Timo Böhme, Stephen Boyer, Matthias Irmer + 4 more
The extraction of chemical information from documents is a demanding task in cheminformatics due to the variety of text and image-based representations of chemistry. The present work describes the extraction of chemical compounds with unique chemical structures from the open access CORE (COnnecting REpositories) and…
Authors not listed
Long-lived and photostable fluorescent probes for real-time monitoring of cell division, particularly for dynamic visualization of mitosis and interphase, are rare. We have developed a water soluble diazaoxatriangulenium cation based fluorescent probe, Nuc-DAOTA+, that meets these criteria. Nuc-DAOTA+ has a long…
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Large-scale de novo nucleic acid synthesis is a powerful tool enabling researchers to better understand and engineer biological systems. Fields ranging from genomics to nucleic acid therapeutics to synthetic biology make use of high-throughput experimental approaches requiring access to large pools or libraries of DNA…