Methods of Molecular Biology
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#1Marie Zufferey (Swiss Institute of Bioinformatics)H-Index: 2
#2Daniele Tavernari (Swiss Institute of Bioinformatics)H-Index: 6
Last. Giovanni Ciriello (Swiss Institute of Bioinformatics)H-Index: 42
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Chromatin folding in the 3D space of the nucleus can be explored through high-throughput chromosome conformation capture (Hi-C) approaches. These experiments quantify the number of interactions between any pair of genomic loci in the genome and, thus, allow building genome-scale maps of intra- and inter-chromosomal contacts (contact maps). Statistical and algorithmic analyses of Hi-C data consist in extracting information from these contact maps. One of the most striking patterns observed in int...
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#2Jens AllmerH-Index: 16
Last. Malik YousefH-Index: 18
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Gene regulation is of utmost importance to cell homeostasis; thus, any dysregulation in it often leads to disease. MicroRNAs (miRNAs) are involved in posttranscriptional gene regulation and consequently, their dysregulation has been associated with many diseases.MiRBase version 21 contains microRNAs from about 200 species organized into about 70 clades. It has been shown that not all miRNAs collected in the database are likely to be real and, therefore, novel routes to delineate between correct ...
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#1Harsh Dweep (Wistar Institute)H-Index: 14
#2Louise C. Showe (Wistar Institute)H-Index: 57
Last. Andrew V. Kossenkov (Wistar Institute)H-Index: 47
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MicroRNAs (miRNAs) are endogenous small noncoding RNAs that are involved in most biological signaling pathways, including the cell cycle, apoptosis, proliferation, immune response, metabolism as well as in biological processes including organ development and in human diseases like cancers. During the past two decades, high-throughput transcriptomic profiling using next generation sequencing and microarrays have been extensively utilized to identify differentially expressed miRNAs across differen...
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Processing, storing, and visualizing high-resolution Hi-C data required development of efficient data formats. A sparse matrix format saving only nonzero values has become the norm. A "zoomable" matrix style also became popular, storing multiple resolutions in a single file for interactive visualization. This chapter discusses the latest matrix file formats such as .hic and .mcool, and other intermediate formats including SAM/BAM and random-accessible contact lists.
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#1Bünyamin Akgül (İzmir Institute of Technology)H-Index: 5
#2Peter F. Stadler (Leipzig University)H-Index: 113
Last. Yusuf Tutar (UHSA: University of Health Sciences Antigua)H-Index: 16
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Mature microRNAs (miRNAs) are short RNA sequences about 18-24 nucleotide long, which provide the recognition key within RISC for the posttranscriptional regulation of target RNAs. Considering the canonical pathway, mature miRNAs are produced via a multistep process. Their transcription (pri-miRNAs) and first processing step via the microprocessor complex (pre-miRNAs) occur in the nucleus. Then they are exported into the cytosol, processed again by Dicer (dsRNA) and finally a single strand (matur...
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#1Martial Marbouty (Pasteur Institute)H-Index: 17
#2Romain Koszul (Pasteur Institute)H-Index: 31
Microbial communities are key components of all ecosystems, but characterization of their complete genomic structure remains challenging. Typical analysis tends to elude the complexity of the mixes in terms of species, strains, as well as extrachromosomal DNA molecules. Recently, approaches have been developed that bins DNA contigs into individual genomes and episomes according to their 3D contact frequencies. Those contacts are quantified by chromosome conformation capture experiments (3C, Hi-C...
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#1Hanane Hadj-Moussa (Carleton University)H-Index: 8
#2Liam J. Hawkins (Carleton University)H-Index: 4
Last. Kenneth B. Storey (Carleton University)H-Index: 90
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The critical role microRNAs play in modulating global functions is emerging, both in the maintenance of homeostatic mechanisms and in the adaptation to diverse environmental stresses. When stressed, cells must divert metabolic requirements toward immediate survival and eventual recovery and the unique features of miRNAs, such as their relatively ATP-inexpensive biogenesis costs, and the quick and reversible nature of their action, renders them excellent "master controllers" for rapid responses. ...
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#1Cristian A. Velandia-Huerto (Leipzig University)H-Index: 2
#2Ali M. Yazbeck (Leipzig University)H-Index: 2
Last. Peter F. Stadler (Leipzig University)H-Index: 113
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MicroRNAs are important regulators in many eukaryotic lineages. Typical miRNAs have a length of about 22nt and are processed from precursors that form a characteristic hairpin structure. Once they appear in a genome, miRNAs are among the best-conserved elements in both animal and plant genomes. Functionally, they play an important role in particular in development. In contrast to protein-coding genes, miRNAs frequently emerge de novo. The genomes of animals and plants harbor hundreds of mutually...
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#1Bala Gur Dedeoglu (Ankara University)H-Index: 6
#2Senem Noyan (Ankara University)H-Index: 3
microRNAs (miRNAs) have recently been recognized as a new dimension of posttranscriptional regulation. It is well defined that most human protein-coding genes are regulated by one or more miRNAs. Therefore, it is crucial to identify genes targeted by the miRNAs to better understand their functions. Although bioinformatics tools have the ability to identify target candidates it is still essential to identify physiological targets by experimental approaches. Currently, the majority of miRNA-target...
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#1Erez Uzuner (İzmir Institute of Technology)
#2Gizem Tuğçe Ulu (İzmir Institute of Technology)
Last. Yusuf Baran (İzmir Institute of Technology)H-Index: 27
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Cancer is also determined by the alterations of oncogenes and tumor suppressor genes. These gene expressions can be regulated by microRNAs (miRNA). At this point, researchers focus on addressing two main questions: "How are oncogenes and/or tumor suppressor genes regulated by miRNAs?" and "Which other mechanisms in cancer cells are regulated by miRNAs?" In this work we focus on gathering the publications answering these questions. The expression of miRNAs is affected by amplification, deletion o...
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