# Bioinformatics Commons™

## All Articles in Bioinformatics

592 full-text articles. Page 1 of 16.

2014 Georgia State University

#### Statistical Analysis Of Enhanced Ctl Killing Activity Against Irradiated Tumor Cells, Catannian Sanogo

##### Georgia State Undergraduate Research Conference

No abstract provided.

2014 Georgia State University

#### Bioinformatic Analysis Of Plant-Like Vacuole (Plv) Proteins In Toxoplasma Gondii, Javier A. Tovar

##### Georgia State Undergraduate Research Conference

No abstract provided.

Computational Model For Survey And Trend Analysis Of Patients With Endometriosis : A Decision Aid Tool For Ebm, 2014 COBRA

#### Computational Model For Survey And Trend Analysis Of Patients With Endometriosis : A Decision Aid Tool For Ebm, Salvo Reina, Vito Reina, Franco Ameglio, Mauro Costa, Alessandro Fasciani

##### COBRA Preprint Series

Endometriosis is increasingly collecting worldwide attention due to its medical complexity and social impact. The European community has identified this as a “social disease”. A large amount of information comes from scientists, yet several aspects of this pathology and staging criteria need to be clearly defined on a suitable number of individuals. In fact, available studies on endometriosis are not easily comparable due to a lack of standardized criteria to collect patients’ informations and scarce definitions of symptoms. Currently, only retrospective surgical stadiation is used to measure pathology intensity, while the Evidence Based Medicine (EBM) requires shareable methods and correct ...

Time Series Data For 3b Image Processing, 2014 The University of Texas

#### Time Series Data For 3b Image Processing, George Mcnamara

##### George McNamara

Time series data for 3B image processing

Four time series data sets of Stellaris single molecules RNA FISH (fluorescence in situ hybridization). All four datasets are 301 imaqe planes. FISH probes are to TOP1 mRNA (Topoisomerase I)in Saos osterosarcoma cells.

One dataset is 10 millisecond exposures (very dim), acquired in Streaming acquisition mode (no hardware overhead).

The other three datasets are a three consecutive planes of the same XY field of view.

I have included image processing results for:

PiMP - a fast method developed by Sebastian Munck et al 2012, http://www.ncbi.nlm.nih.gov/pubmed/?term=22357945 ...

2014 SelectedWorks

#### Software To Accompany "A Kernel Machine Approach For Differential Expression Analysis Of Mass Spectrometry-Based Metabolomics Data", Debashis Ghosh

##### Debashis Ghosh

No abstract provided.

Computational Molecular Coevolution, 2013 Western University

#### Computational Molecular Coevolution, Russell J. Dickson

##### University of Western Ontario - Electronic Thesis and Dissertation Repository

A major goal in computational biochemistry is to obtain three-dimensional structure information from protein sequence. Coevolution represents a biological mechanism through which structural information can be obtained from a family of protein sequences. Evolutionary relationships within a family of protein sequences are revealed through sequence alignment. Statistical analyses of these sequence alignments reveals positions in the protein family that covary, and thus appear to be dependent on one another throughout the evolution of the protein family. These covarying positions are inferred to be coevolving via one of two biological mechanisms, both of which imply that coevolution is facilitated by inter-residue ...

Characterizing The Human Vaginal Microbiome Using High-Throughput Sequencing, 2013 Western University

#### Characterizing The Human Vaginal Microbiome Using High-Throughput Sequencing, Jean Megan E. Macklaim

##### University of Western Ontario - Electronic Thesis and Dissertation Repository

The human vaginal microbiome undoubtedly has a significant role in reproductive health and for protection from infectious organisms. Recent efforts to characterize the bacterial species of the vagina using molecular techniques have uncovered an unexpected diversity. Using high-throughput sequencing I sought to describe the structure and function of the vaginal microbiome under different physiological states including healthy, bacterial vaginosis (BV), post-menopausal vaginal atrophy, and acute vulvovaginal candidiasis (VVC).

Partial 16S rRNA gene sequencing revealed that healthy, asymptomatic women most often have vaginal biotas dominated by Lactobacillus iners or L. crispatus. In contrast, BV is a heterogeneous, highly diversified condition with ...

2013 Texas Medical Center Library

#### Introducing A Novel Method For Genetic Analysis Of Autism Spectrum Disorder, Sepideh Nouri

##### UT GSBS Dissertations and Theses (Open Access)

Autism is a spectrum of neurological disorders that is characterized by repetitive and stereotyped behaviors, lack of social skills in verbal and non-verbal communications, and intellectual disability. Recent statistics shows that 1 out of every 88 children in the US is affected by autism.

In this thesis, I first review previous studies on genetic association analyses of autism spectrum disorder. A large number of these studies fall into two categories: Genome Wide Association Studies (GWAS) and sequencing studies. Although GWAS are able to identify multiple common risk variants associated with different diseases, these common variants explain only a small portion ...

2013 Syracuse University

#### Filter-Based Multiscale Entropy Analysis Of Complex Physiological Time Series, Liang Zhao

##### Dissertations - ALL

The multiscale entropy (MSE) has been widely and successfully used in analyzing the complexity of physiologic time series. In this thesis, we re-interpret the averaging process in MSE as filtering a time series by a filter of a piecewise constant type. From this viewpoint, we introduce the {\it filter-based multiscale entropy} (FME) which filters a time series by filters to generate its multiple frequency components and then compute the {\it blockwise} entropy of the resulting components. By choosing filters adapted to the feature of a given time series, FME is able to better capture its multiscale information and to provide ...

2013 SelectedWorks

#### Ultra-Deep Pyrosequencing Of Partial Surface Protein Genes From Infectious Salmon Anaemia Virus (Isav) Suggest Novel Mechanisms Involved In Transition To Virulence, Torstein Tengs Dr.

##### Dr. Torstein Tengs

Uncultivable HPR0 strains of infectious salmon anaemia viruses (ISAVs) infecting gills are non-virulent putative precursors of virulent ISAVs (vISAVs) causing systemic disease in farmed Atlantic salmon (Salmo salar). The transition to virulence involves two molecular events, a deletion in the highly polymorphic region (HPR) of the hemagglutinin-esterase (HE) gene and a Q266→L266 substitution or insertion next to the putative cleavage site (R267) in the fusion protein (F). We have performed ultra-deep pyrosequencing (UDPS) of these gene regions from healthy fish positive for HPR0 virus carrying full-length HPR sampled in a screening program, and a vISAV strain from an ISA ...

High Variance In Reproductive Success Generates A False Signature Of A Genetic Bottleneck In Populations Of Constant Size: A Simulation Study, 2013 University of Tennessee, Knoxville

#### Background

Demographic bottlenecks can severely reduce the genetic variation of a population or a species. Establishing whether low genetic variation is caused by a bottleneck or a constantly low effective number of individuals is important to understand a species’ ecology and evolution, and it has implications for conservation management. Recent studies have evaluated the power of several statistical methods developed to identify bottlenecks. However, the false positive rate, i.e. the rate with which a bottleneck signal is misidentified in demographically stable populations, has received little attention. We analyse this type of error (type I) in forward computer simulations of ...

The Cytochrome P450 Superfamily Complement (Cypome) In The Annelid Capitella Teleta, 2013 McMaster University

#### The Cytochrome P450 Superfamily Complement (Cypome) In The Annelid Capitella Teleta, Christopher A. Dejong

##### Open Access Dissertations and Theses

CYPs are a large and diverse protein superfamily found in all domains of life and are able to metabolize a wide array of both exogenous and endogenous molecules. The CYPome of the polychaete annelid Capitella teleta has been robustly identified and annotated with the genome assembly available (version 1). Annotation of 84 full length and 12 partial CYP sequences predicted a total of 96 functional CYPs in C. teleta. A further 13 CYP fragments were found but these may be pseudogenes. The C. teleta CYPome contained 24 novel CYP families and seven novel CYP subfamilies within existing families. A phylogenetic ...

Sasd: The Synthetic Alternative Splicing Database For Identifying Novel Isoform From Proteomics, 2013 University of North Texas Health Science Center

#### Background

Alternative splicing is an important and widespread mechanism for generating protein diversity and regulating protein expression. High-throughput identification and analysis of alternative splicing in the protein level has more advantages than in the mRNA level. The combination of alternative splicing database and tandem mass spectrometry provides a powerful technique for identification, analysis and characterization of potential novel alternative splicing protein isoforms from proteomics.

Therefore, based on the peptidomic database of human protein isoforms for proteomics experiments, our objective is to design a new alternative splicing database to 1) provide more coverage of genes, transcripts and alternative splicing, 2) exclusively ...

2013 McMaster University

#### Increased Substitution Rates In Dna Surrounding Low-Complexity Regions, Carolyn Lenz

##### Open Access Dissertations and Theses

Previous studies have found that DNA flanking low-complexity regions (LCRs) have an increased substitution rate. Here, the substitution rate was confirmed to increase in the vicinity of LCRs in several primate species, including humans. This effect was also found within human sequences from the 1000 Genomes Project. A strong correlation was found between average substitution rate per site and distance from the LCR, as well as between the proportion of genes with gaps in the alignment at each site and distance from the LCR. Along with substitution rates, dN/dS ratios were also determined for each site, and the proportion ...

2013 California Polytechnic State University

#### Identifying Chromosome Rearrangements In The Allopolyploid Brassica Napus Using Pyrosequencing, Alexandra R. Barbella

##### Master's Theses and Project Reports

Allopolyploids form through the hybridization of two or more diploid genomes. A challenge to reproduction in allopolyploids is that pairing can occur between homologous chromosomes or homeologous chromosomes (i.e.different subgenomes.). Crossover between homeologous chromosomes can result in chromosome rearrangements that lower fertility and overall fitness. Rearrangements can alter the dosage of either entire chromosomes or just parts of chromosomes. Understanding the frequency and extent of rearrangements will help to explain the evolution and genome stabilization of agriculturally important allopolyploid species. Pyrosequencing is a useful tool in the study dosage changes in allopolyploids because it allows quantification of the ...

2013 University of Nebraska - Lincoln

#### The Origin And Molecular Evolution Of Two Multigene Families: G-Protein Coupled Receptors And Glycoside Hydrolase Families, Seong-Il Eyun

##### Dissertations and Theses in Biological Sciences

Multigene family is a group of genes that arose from a common ancestor by gene duplication. Gene duplications are a major driving force of new function acquisition. Multigene family thus has a fundamental role in adaptation. To elucidate their molecular evolutionary mechanisms, I chose two multigene families: chemosensory receptors and glycoside hydrolases. I have identified complete repertoires of trace amine-associated receptors (TAARs), a member of chemosensory receptors, from 38 metazoan genomes. An ancestral-type TAAR emerged before the divergence between gnathostomes (jawed vertebrates) and sea lamprey (jawless fish). Primary amine detecting TAARs (TAAR1-4) are found to be older and have evolved ...

2013 Rochester Institute of Technology

#### Quantifying Mutational Impacts On Intrinsic Dna Flexibility In Prokaryotic Genomes, Mohammed Alawad

##### Theses

The existence of synonymous codon biases across all taxonomic groups is a long standing problem in biology. While codon bias seems to be adequately explained by the maintenance of translation efficiency and accuracy in some organisms, there is still no adequate explanation of why codon biases universally track the intergenic gc content, as these regions of the genome would not be under selection pressures affecting translation. One part of the story may come from the triplet nature of codon in which each third position defines the minor groove width and thus affects the basic structure of the DNA by altering ...

Detecting Modules In Multiplex Networks – An Application For Integrating Expression Profiles Across Multiple Species, 2013 Yale University

#### Detecting Modules In Multiplex Networks – An Application For Integrating Expression Profiles Across Multiple Species, Koon-Kiu Yan, Daifeng Wang, Joel Rozowsky, Henry Zheng, Baikang Pei, Mark Gerstein

##### Yale Day of Data

Multiplex network, a set of networks linked through interconnected layers, is a useful mathematical framework for data integration. Here, we present a general method to detect modules in multiplex networks and apply it in a specific biological context: to simultaneously cluster the genome-wide expression profiles of C. elegans and D. melanogaster generated by the ENOCDE and modENCODE consortia. The method revealed modules that are fundamentally cross-species and can either be conserved or species-specific. In general, the method could be applied in various contexts like the integration of different social networks.

2013 Western University

#### Modeling Leafhopper Populations And Their Role In Transmitting Plant Diseases., Ji Ruan

##### University of Western Ontario - Electronic Thesis and Dissertation Repository

This M.Sc. thesis focuses on the interactions between crops and leafhoppers.

Firstly, a general delay differential equations system is proposed, based on the infection age structure, to investigate disease dynamics when disease latencies are considered. To further the understanding on the subject, a specific model is then introduced. The basic reproduction numbers $\cR_0$ and $\cR_1$ are identified and their threshold properties are discussed. When $\cR_0 < 1$, the insect-free equilibrium is globally asymptotically stable. When $\cR_0 > 1$ and $\cR_1 < 1$, the disease-free equilibrium exists and is locally asymptotically stable. When $\cR_1>1$, the disease will persist.

Secondly, we derive another general delay differential equations system to examine how different life stages of leafhoppers affect crops. The basic reproduction numbers $\cR_0$ is determined ...

2013 University of Wisconsin Milwaukee

#### Alcohol Biomarkers As Predictive Factors Of Rearrest In High Risk Repeat Offense Drunk Drivers, Brian Charles Kay

##### Theses and Dissertations

Alcohol biomarkers, or naturally occurring molecules which occur in response to one's alcohol consumption, are proving to be a value tool in objectively monitoring one's alcohol consumption. Coupling this assessment tool, with advances in computing power, new and powerful predictions are becoming evermore possible. In this retrospective study, data was first collected that consisted of a sample of 249 drivers convicted of driving under the influence charge and who monitored over the course of a year by biomarker blood tests. This data was then analyzed using machine learning methods. TwoStep cluster analysis showed distinct drinking groups within the ...