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Design of 2D Genome Visualization Tool for DNA Sequence Analysis
2017
International Journal of Computer Applications
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transform for visualizing DNA sequence. [2] The choice of the graphical representation technique for a DNA sequence affects how well its biological properties can be reflected in the graphical domain ...
for visualization and analysis of the characteristics of special regions of interest within the DNA sequence. ...
The original plot of a DNA sequence as a random walk on a TwoD grid using the four cardinal directions to represent the four bases was done by Gatesand then rediscovered independently by Nandy and Leong ...
doi:10.5120/ijca2017913525
fatcat:jqvjzdcxfnclnhtzgxdgxjy72m
RNA-Seq profiling of single bovine oocyte transcript abundance and its modulation by cytoplasmic polyadenylation
2015
Molecular Reproduction and Development
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Results Single oocyte transcriptome sequencing Single-oocyte, whole-cell lysates from GV (n=3) and MII (n=3) samples were used as template for cDNA synthesis, with an anchored oligo(dT) primer, and for ...
amplification using a whole-transcript PCR amplification approach. ...
award number R01HD070044 to PJR. ...
doi:10.1002/mrd.22445
pmid:25560149
pmcid:PMC4651626
fatcat:ybxbwl43ljerxhdvskcseurhmm
On the Origin of Macromolecular Sequences
1961
Biophysical Journal
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unrestricted primeval sequences capable of self-replication, since the biological process of replication is itself dependent on the pre-existence of such order, and since the number of sequences that ...
The origin of the degree and type of order found in biological macromolecules is not adequately explained solely as an accumulation of genetic restrictions acquired through natural selection from otherwise ...
biological macromolecules, except in so far as such order pre-exists in genetic sequences. ...
doi:10.1016/s0006-3495(61)86917-8
pmid:14484391
pmcid:PMC1366362
fatcat:aztafopd2ben5e76chrk3q53ye
Delivery of Macromolecules into Cytosol Using Liposomes Containing Hemolysin fromListeria monocytogenes
1996
Journal of Biological Chemistry
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1 The abbreviations used are: ...
Alfred Goldberg for the generous gift of MG132 (courtesy of ProScript Inc.) and Dr. C. Harding for the OVA-specific CD8 ϩ T cell line. ...
Howard Goldfine, Andreas Gallusser, and Tomas Kirchhausen and Eun Ji Shin for help in purification of LLO. We also thank Dr. ...
doi:10.1074/jbc.271.13.7249
fatcat:tufihitas5eanliqb3ictnw4vm
Bioinorganic motifs: towards functional classification of metalloproteins
2000
Bioinformatics
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The habitat of bioinorganic motifs (BIMs) is at the interface of biological inorganic chemistry and bioinformatics. ...
A number of specialized databases dealing with BIMs and attempts to classify them are reviewed. ...
/
3D and quaternary structures of biological
macromolecules
PDB
http://www.rcsb.org/pdb/
http://pdb-browsers.ebi.ac.uk/
3D structures of biological macromolecules
Berman et al., 2000
PDBsum ...
doi:10.1093/bioinformatics/16.10.851
pmid:11120676
fatcat:khqiuredorduzinwaafidf2wlm
Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology
2015
Journal of Molecular Graphics and Modelling
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for a variety of simulation studies. ...
A model for the cytoplasm of Mycoplasma genitalium is presented that integrates data from a variety of sources into a physically and biochemically consistent model. ...
Computer resources were used at RIKEN-RICC (RIKEN Integrated Cluster of Clusters). ...
doi:10.1016/j.jmgm.2015.02.004
pmid:25765281
pmcid:PMC4388805
fatcat:2vzgxnpu7ncsbfqeqnguubbusq
The generation of phosphoserine stretches in phosphoproteins: mechanism and significance
2015
Molecular Biosystems
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generate a kind of "phosphoclusterome". ...
A STRING analysis of proteins containing clusters of 3 or more adjacent phosphoserine residues reveals that the great majority of these proteins are interconnected by physical and/or functional links to ...
Indeed a large number of phosphoproteins (26%) include more than 12 phosphoresidues in their sequence. ...
doi:10.1039/c5mb00337g
pmid:26211804
fatcat:tnc3mvf3bva3dkim2jwfwentuy
Updates in Rhea—a manually curated resource of biochemical reactions
2014
Nucleic Acids Research
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Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities of Biological Interest) ...
These include significant growth in the number of Rhea reactions and the inclusion of reactions involving complex macromolecules such as proteins, nucleic acids and other polymers that lie outside the ...
ACKNOWLEDGEMENTS The authors are grateful for the continuing contributions from many members of the scientific community to the continuing success of Rhea. ...
doi:10.1093/nar/gku961
pmid:25332395
pmcid:PMC4384025
fatcat:rg4drak3onguteit2c7wovb7wy
Protein Crystal Growth
[chapter]
2012
Modern Aspects of Bulk Crystal and Thin Film Preparation
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Table 1 1 Biological parameters Purity of macromolecules Rarity of biological macromolecules Bacterial contaminants Biological sources of organisms and cells Macromolecular contaminants Sequence ...
Whatever the crystallization method used, it requires high concentration of biological macromolecules as compared to normal biochemistry conditions. ...
This book allows a reader to gain insight into selected aspects of the field, including growth of bulk inorganic crystals, preparation of thin films, low-dimensional structures, crystallization of proteins ...
doi:10.5772/29424
fatcat:rhtpafciojfktj6rc2d3dn2kgu
A CRISPR-Cas-Inspired Mechanism for Detecting Hardware Trojans in FPGA Devices
[article]
2020
arXiv
pre-print
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The fundamental concepts of the Type 1-E CRISPR-Cas mechanism are discussed and simulated to predict the flow of genetic information through this biological system. ...
Many parallels can be drawn between hardware and natural systems, and one example creates an analogy between hardware attacks and biological attacks. ...
ACKNOWLEDGMENT The authors thank the University of Cincinnati and the Air Force Research Laboratory for providing the support and resources necessary for success. ...
arXiv:2005.07332v1
fatcat:iusvndz7fjc2lbwfdrrf7hnusq
Intelligent design and biological complexity
2006
Gene
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The complexity of biological systems can increase spontaneously. ...
The general and permanent spectacle of nature's spontaneous tinkering with ... informational macromolecules ... suggests an absence from evolution of design and intelligence. ...
organization of chromosomal behavior; and at higher levels of biological integration, the number of cell types represented by the number of semi-autonomous gene interaction programs that get instated ...
doi:10.1016/j.gene.2006.03.025
pmid:17011142
fatcat:mkbvxk34srfvnotlyxl25kvqpu
Profiling of alternative polyadenylation sites in luminal B breast cancer using the SAPAS method
2014
International Journal of Molecular Medicine
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Among the genes involved in the events, a significantly greater number of genes was found with shortened 3'UTRs in the samples, which were samples of primary cancer with relatively low proliferation. ...
Therefore, in the present study, we profiled APA sites in the luminal B subtype of BC by sequencing APA sites (SAPAS) method, in order to assess the relation of these APA site-switching events to the recognized ...
Thus, the expression level of a gene could be represented by the read number mapped to the corresponding region on the genome. ...
doi:10.3892/ijmm.2014.1973
pmid:25333330
pmcid:PMC4249744
fatcat:l2ghxiz7z5ehxahxlr63ul5zci
Sequence-Controlled Polymers
2013
Science
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In principle, polymers with regulated sequences of monomers can be prepared using either chemical or biological methods. ...
Fig. 2 . 2 Representative chemical approaches to sequence control. ...
doi:10.1126/science.1238149
pmid:23929982
fatcat:4nibvwkfsnabfkixn2iadgkzma
The structure and function of 'active zone material' at synapses
2015
Philosophical Transactions of the Royal Society of London. Biological Sciences
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Sequence of connections formed between undocked synaptic vesicles and active zone material macromolecules during docking In order to observe the relationships between the different classes of AZM macromolecules ...
For example, the structural organization of the AZM may influence the number of synaptic vesicles that can dock at an active zone, the rate and efficiency of docking and priming, and the Ca 2þ -triggering ...
doi:10.1098/rstb.2014.0189
pmid:26009768
pmcid:PMC4455758
fatcat:nxev2ij6zfcc5kqk5pziyqkwnu
Transcriptome sequencing and analysis of the zoonotic parasite Spirometra erinacei spargana (plerocercoids)
2014
Parasites & Vectors
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Total RNA was isolated from spargana and then ESTs were generated, assembled and sequenced. Many biological aspects of spargana were investigated using multi-step bioinformatics tools. ...
Although spargana, which are the plerocercoids of Spirometra erinacei, are of biological and clinical importance, expressed sequence tags (ESTs) from this parasite have not been explored. ...
The top 10 highly represented EC numbers are shown in Table 5 . ...
doi:10.1186/1756-3305-7-368
pmid:25128015
pmcid:PMC4262225
fatcat:prr5utjg5nbgjo6gv5r2yibjwi
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