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Design of 2D Genome Visualization Tool for DNA Sequence Analysis

Ankita Tripathi, Santosh Mishra
2017 International Journal of Computer Applications  
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

Juan M Reyes, James L. Chitwood, Pablo J. Ross
2015 Molecular Reproduction and Development  
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

Howard H. Pattee
1961 Biophysical Journal  
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

Kyung-Dall Lee, Yu-Kyoung Oh, Daniel A. Portnoy, Joel A. Swanson
1996 Journal of Biological Chemistry  
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

K. Degtyarenko
2000 Bioinformatics  
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 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

Michael Feig, Ryuhei Harada, Takaharu Mori, Isseki Yu, Koichi Takahashi, Yuji Sugita
2015 Journal of Molecular Graphics and Modelling  
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

Luca Cesaro, Lorenzo A. Pinna
2015 Molecular Biosystems  
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

Anne Morgat, Kristian B. Axelsen, Thierry Lombardot, Rafael Alcántara, Lucila Aimo, Mohamed Zerara, Anne Niknejad, Eugeni Belda, Nevila Hyka-Nouspikel, Elisabeth Coudert, Nicole Redaschi, Lydie Bougueleret (+3 others)
2014 Nucleic Acids Research  
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]

Igor Nederlof, Eric van, Flip Hoedemaeker, Jan Pieter, Dilyana Georgiev
2012 Modern Aspects of Bulk Crystal and Thin Film Preparation  
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]

Dillon Staub
2020 arXiv   pre-print
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

Emile Zuckerkandl
2006 Gene  
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  
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

J.-F. Lutz, M. Ouchi, D. R. Liu, M. Sawamoto
2013 Science  
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

Joseph A. Szule, Jae Hoon Jung, Uel J. McMahan
2015 Philosophical Transactions of the Royal Society of London. Biological Sciences  
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)

Dae-Won Kim, Won Yoo, Myoung-Ro Lee, Hye-Won Yang, Yu-Jung Kim, Shin-Hyeong Cho, Won-Ja Lee, Jung-Won Ju
2014 Parasites & Vectors  
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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