scholarly journals Distance and Similarity Measures in Comparative Genomics

2020 ◽  
Author(s):  
Diego P. Rubert ◽  
Jens Stoye ◽  
Fábio H. V. Martinez
Keyword(s):  
Comparative Genomics ◽  
Molecular Biology ◽  
Similarity Measures ◽  
Central Question ◽  
Similarities And Differences

Research in comparative genomics supports the investigation of important questions in molecular biology, genetics and biomedicine. A central question in this field is the elucidation of similarities and differences between genomes by means of different measures. This summary, submitted to CTD 2020, briefly describes the main contributions, originality and impact possibilities of the thesis entitled "Distance and Similarity Measures in Comparative Genomics", by Diego P. Rubert.

FPGA-Based Accelerators for Bioinformatics Applications

2013 ◽  
pp. 605-635
Author(s):  
Alba Cristina Magalhaes Alves de Melo ◽  
Nahri Moreano
Keyword(s):  
Molecular Biology ◽  
Research Area ◽  
Sequence Profile ◽  
Huge Amount ◽  
Computational Tools ◽  
Computing Power ◽  
Open Questions ◽  
Similarities And Differences

The recent and astonishing advances in Molecular Biology, which led to the sequencing of an unprecedented number of genomes, including the human, would not have been possible without the help of Bioinformatics. Bioinformatics can be defined as a research area where computational tools and algorithms are developed to help biologists in the task of understanding the organisms. Some Bioinformatics applications, such as pairwise and sequence-profile comparison, require a huge amount of computing power and, therefore, are excellent candidates to run in FPGA platforms. This chapter discusses in detail several recent proposals on FPGA-based accelerators for these two Bioinformatics applications, highlighting the similarities and differences among them. At the end of the chapter, research tendencies and open questions are presented.

Conspiracy Thinking, Tolerance, and Democracy

2018 ◽  
pp. 187-198 ◽  
Author(s):  
Steven M. Smallpage
Keyword(s):  
Central Question ◽  
University Professors ◽  
Conspiracy Theories ◽  
The Public ◽  
Thoughtful Reflection ◽  
Conspiracy Beliefs ◽  
Similarities And Differences ◽  
The One ◽  
Independent Thinking ◽  
Conspiracy Thinking

When university professors engage with conspiracy theories, the public is pushed to the limit in terms of what it will or will not tolerate. Professors that publicly hold conspiracy beliefs force the central question of political tolerance: what is the line between the intellectual inquiry that allows for communities to flourish, on the one hand, and the expression of viewpoints that undermine that community’s integrity altogether, on the other? The line is blurry, as careful skepticism underlies both the best academic work and the psychology of conspiracy thinking. Since conspiracy theorists often anger, provoke, and sometimes harass the public, we must decide as a community if we will tolerate professors who hold controversial conspiracy beliefs. Such decisions require thoughtful reflection on the similarities and differences between conspiracy thinking and its relationship to desirable traits of democratic citizens, like tolerance, independent thinking, and academic freedom.

scholarly journals Comparative Genomics of Bacillus species and its Relevance in Industrial Microbiology

2013 ◽  
Vol 6 ◽  
pp. GEI.S12732 ◽  
Author(s):  
Archana Sharma ◽  
T. Satyanarayana
Keyword(s):  
Comparative Genomics ◽  
Molecular Biology ◽  
Genome Sequencing ◽  
High Throughput Sequencing ◽  
Bacterial Species ◽  
Bacillus Species ◽  
Genome Sequences ◽  
Wide Range ◽  
Sequencing Platforms ◽  
Analytical Tools

With the advent of high throughput sequencing platforms and relevant analytical tools, the rate of microbial genome sequencing has accelerated which has in turn led to better understanding of microbial molecular biology and genetics. The complete genome sequences of important industrial organisms provide opportunities for human health, industry, and the environment. Bacillus species are the dominant workhorses in industrial fermentations. Today, genome sequences of several Bacillus species are available, and comparative genomics of this genus helps in understanding their physiology, biochemistry, and genetics. The genomes of these bacterial species are the sources of many industrially important enzymes and antibiotics and, therefore, provide an opportunity to tailor enzymes with desired properties to suit a wide range of applications. A comparative account of strengths and weaknesses of the different sequencing platforms are also highlighted in the review.

scholarly journals Combined comparative genomics and molecular biology approaches provide insights into the terpene synthases inventory in Trichoderma

2020 ◽  
Author(s):  
Isabel Vicente ◽  
Riccardo Baroncelli ◽  
Mar a Eugenia Mor n Diez ◽  
Rodolfo Bernardi ◽  
Grazia Puntoni ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Molecular Biology ◽  
Terpene Synthases

Leafhopper Comparative Genomics - Identifying Similarities and Differences across Leafhopper Vectors ofXylella fastidiosa

2011 ◽  
Vol 36 (3) ◽  
pp. 305-321
Author(s):  
E. W. Welch ◽  
W. B. Hunter ◽  
K. S. Shelby ◽  
R. F. Mizell ◽  
C. Tipping ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Similarities And Differences

scholarly journals A Content-Based Retrieval Framework for Whole Metagenome Sequencing Samples

2018 ◽  
Vol 15 (4) ◽  
Author(s):  
Duygu Dede Şener ◽  
Daniele Santoni ◽  
Giovanni Felici ◽  
Hasan Oğul
Keyword(s):  
Latent Semantic Analysis ◽  
System Performance ◽  
Semantic Analysis ◽  
Similarity Measures ◽  
Ground Truth ◽  
Selection Methods ◽  
Content Based Retrieval ◽  
Source Codes ◽  
Similarities And Differences ◽  
Metagenome Sequencing

AbstractFinding similarities and differences between metagenomic samples within large repositories has been rather a significant issue for researchers. Over the recent years, content-based retrieval has been suggested by various studies from different perspectives. In this study, a content-based retrieval framework for identifying relevant metagenomic samples is developed. The framework consists of feature extraction, selection methods and similarity measures for whole metagenome sequencing samples. Performance of the developed framework was evaluated on given samples. A ground truth was used to evaluate the system performance such that if the system retrieves patients with the same disease, -called positive samples-, they are labeled as relevant samples otherwise irrelevant. The experimental results show that relevant experiments can be detected by using different fingerprinting approaches. We observed that Latent Semantic Analysis (LSA) Method is a promising fingerprinting approach for representing metagenomic samples and finding relevance among them. Source codes and executable files are available atwww.baskent.edu.tr/∼hogul/WMS_retrieval.rar.

Beyond Jewish Christianity: Ancient Social Taxonomies and the Christianity-Judaism Divide

2020 ◽  
pp. 144-184
Author(s):  
Matt Jackson-Mccabe
Keyword(s):  
Social Interaction ◽  
Late Antiquity ◽  
Social Experience ◽  
Social Consequences ◽  
Central Question ◽  
The Social ◽  
Jewish Christianity ◽  
Per Se ◽  
Similarities And Differences ◽  
Primary Division

This concluding chapter demonstrates how one can get around the problems created by Jewish Christianity by approaching the question of the origins of Christianity and the Christianity–Judaism division as a study in the production and dissemination of ancient social taxonomies. The central question from this perspective is neither the similarities and differences in culture nor even the social interaction among ancient Christians and Jews, but how early Jesus groups imagined themselves and their characteristic cultures in relation to Judeans and theirs. At what point did some Jesus groups begin to assert that Judeans and their distinguishing culture were, per se, “other” and to reify that difference by postulating a distinction between Christianism and Judaism? Whatever its various social consequences, how widespread was this taxonomy before its imperial adoption in the centuries after Constantine? Through an examination of a few exemplary cases, a significant distinction can be observed well into late antiquity between Jesus groups who made sense of their social experience with reference to such a notion of Christianism and those who did not; between those who came to differentiate a new “us” from the Judeans and the Nations alike, and those for whom Judeans and the Nations remained the primary division.

scholarly journals Odor Discrimination by Similarity Measures of Abstract Odor Factor Maps from Electronic Noses

Sensors ◽  
2018 ◽  
Vol 18 (8) ◽  
pp. 2658
Author(s):  
Weiqing Guo ◽  
Haohui Kong ◽  
Junzhang Wu ◽  
Feng Gan
Keyword(s):  
Similarity Measure ◽  
Electronic Nose ◽  
Similarity Measures ◽  
Discrimination Performance ◽  
Odor Discrimination ◽  
New Method ◽  
Data Array ◽  
Electronic Noses ◽  
Similarities And Differences ◽  
Factor Maps

The aim of this study is to improve the discrimination performance of electronic noses by introducing a new method for measuring the similarity of the signals obtained from the electronic nose. We constructed abstract odor factor maps (AOFMs) as the characteristic maps of odor samples by decomposition of three-way signal data array of an electronic nose. A similarity measure for two-way data was introduced to evaluate the similarities and differences of AOFMs from different samples. The method was assessed by three types of pipe and powder tobacco samples. Comparisons were made with other techniques based on PCA, SIMCA, PARAFAC and PARAFAC2. The results showed that our method had significant advantages in discriminating odor samples with similar flavors or with high VOCs release.

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