scholarly journals A priori Considerations When Conducting High‐Throughput Amplicon‐Based Sequence Analysis

ael ◽  
2016 ◽  
Vol 1 (1) ◽  
pp. 150010 ◽  
Author(s):  
Aditi Sengupta ◽  
Warren A. Dick
Keyword(s):  
Sequence Analysis ◽  
High Throughput ◽  
A Priori

scholarly journals Identification of Driver and Passenger Mutations of FLT3 by High-Throughput DNA Sequence Analysis and Functional Assessment of Candidate Alleles

Cancer Cell ◽  
2007 ◽  
Vol 12 (6) ◽  
pp. 501-513 ◽  
Author(s):  
Stefan Fröhling ◽  
Claudia Scholl ◽  
Ross L. Levine ◽  
Marc Loriaux ◽  
Titus J. Boggon ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Dna Sequence ◽  
High Throughput ◽  
Functional Assessment ◽  
Dna Sequence Analysis ◽  
Passenger Mutations

Applications of Supercomputers in Sequence Analysis and Genome Annotation

2015 ◽  
pp. 149-175
Author(s):  
Gerard G. Dumancas
Keyword(s):  
Sequence Analysis ◽  
High Throughput ◽  
Genome Annotation ◽  
Critical Role ◽  
Time Saving ◽  
Genetic Causes ◽  
Modern Era

In the modern era of science, bioinformatics play a critical role in unraveling the potential genetic causes of various diseases. Two of the most important areas of bioinformatics today, sequence analysis and genome annotation, are essential for the success of identifying the genes responsible for different diseases. These two emerging areas utilize highly intensive mathematical calculations in order to carry out the processes. Supercomputers facilitate such calculations in an efficient and time-saving manner generating high-throughput images. Thus, this chapter thoroughly discusses the applications of supercomputers in the areas of sequence analysis and genome annotation. This chapter also showcases sophisticated software and algorithms utilized by the two mentioned areas of bioinformatics.

scholarly journals High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: Alternative expression modes and gene function correlates

2010 ◽  
Vol 20 (5) ◽  
pp. 636-645 ◽  
Author(s):  
J. Matsumoto ◽  
K. Dewar ◽  
J. Wasserscheid ◽  
G. B. Wiley ◽  
S. L. Macmil ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
High Throughput ◽  
Gene Function ◽  
Ciona Intestinalis ◽  
Alternative Expression

scholarly journals Improved resolution of bacteria by high throughput sequence analysis of the rRNA internal transcribed spacer

2014 ◽  
Vol 105 ◽  
pp. 82-87 ◽  
Author(s):  
Paul M. Ruegger ◽  
Robin T. Clark ◽  
John R. Weger ◽  
Jonathan Braun ◽  
James Borneman
Keyword(s):  
Sequence Analysis ◽  
High Throughput ◽  
Internal Transcribed Spacer

Bacterial Diversity of Grapevine Rhizosphere Soil Revealed by High-Throughput Sequence Analysis from Different Vineyards in China

2018 ◽  
Vol 12 (2) ◽  
pp. 194-202 ◽  
Author(s):  
Ping Zhao ◽  
Wenxu Xia ◽  
Jiabin Wang ◽  
Xinguo Zhang ◽  
Yan Zhuang ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Bacterial Diversity ◽  
High Throughput ◽  
Rhizosphere Soil

scholarly journals Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 230 ◽  
Author(s):  
Nicolas C Nalpas ◽  
Stephen DE Park ◽  
David A Magee ◽  
Maria Taraktsoglou ◽  
John A Browne ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Mycobacterium Bovis ◽  
High Throughput ◽  
Macrophage Response ◽  
Rna Sequence ◽  
Bovine Macrophage ◽  
Whole Transcriptome

scholarly journals High-throughput DNA sequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria

Gut Microbes ◽  
2013 ◽  
Vol 4 (2) ◽  
pp. 125-135 ◽  
Author(s):  
Matthew J. Hamilton ◽  
Alexa R. Weingarden ◽  
Tatsuya Unno ◽  
Alexander Khoruts ◽  
Michael J. Sadowsky
Keyword(s):  
Sequence Analysis ◽  
Gut Microbiota ◽  
Dna Sequence ◽  
High Throughput ◽  
Dna Sequence Analysis ◽  
Fecal Bacteria

scholarly journals A High-Throughput Analysis Method to Detect Regions of Interest and Quantify Zebrafish Embryo Images

2010 ◽  
Vol 15 (9) ◽  
pp. 1152-1159 ◽  
Author(s):  
Xiaoyan Xu ◽  
Xiaoyin Xu ◽  
Xin Huang ◽  
Weiming Xia ◽  
Shunren Xia
Keyword(s):  
High Throughput ◽  
Neural Development ◽  
Zebrafish Embryo ◽  
A Priori ◽  
Region Of Interest ◽  
Real Data ◽  
Zebrafish Embryos ◽  
High Throughput Analysis ◽  
Single Experiment ◽  
Priori Information

Zebrafish is widely used to understand neural development and model various neurodegenerative diseases. Zebrafish embryos are optically transparent, have a short development period, and can be kept alive in microplates for days, making them amenable to high-throughput microscopic imaging. As a result of high-throughput experiments, a large number of images can be generated in a single experiment, posing a challenge to researchers to analyze them efficiently and quantitatively. In this work, we develop an image processing focused on detecting and quantifying pigments in zebrafish embryos. The algorithm automatically detects a region of interest (ROI) enclosing an area around the pigments and then segment the pigments for quantification. In this process, the algorithm identifies the head and torso at first, and then finds the boundaries corresponding to the back and abdomen by taking advantage of a priori information about the anatomy of zebrafish embryos. The method is robust in terms that it can detect and quantify pigments even when the embryos have different orientations and curvatures. We used real data to demonstrate the performance of the method to extract phenotypic information from zebrafish embryo images and compared its results with manual analysis for verification.

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