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Efficient Alignment Algorithms For Dna Sequencing Data, Nilesh Vinod Khiste 2018 The University of Western Ontario

Efficient Alignment Algorithms For Dna Sequencing Data, Nilesh Vinod Khiste

Electronic Thesis and Dissertation Repository

The DNA Next Generation Sequencing (NGS) technologies produce data at a low cost, enabling their application to many ambitious fields such as cancer research, disease control, personalized medicine etc. However, even after a decade of research, the modern aligners and assemblers are far from providing efficient and error free genome alignments and assemblies respectively. This is due to the inherent nature of the genome alignment and assembly problem, which involves many complexities. Many algorithms to address this problem have been proposed over the years, but there still is a huge scope for improvement in this research space.

Many new genome ...


The Genome Of The Hi5 Germ Cell Line From Trichoplusia Ni, An Agricultural Pest And Novel Model For Small Rna Biology, Yu Fu, Yujing Yang, Han Zhang, Gwen Farley, Junling Wang, Kaycee A. Quarles, Zhiping Weng, Phillip D. Zamore 2018 Boston University

The Genome Of The Hi5 Germ Cell Line From Trichoplusia Ni, An Agricultural Pest And Novel Model For Small Rna Biology, Yu Fu, Yujing Yang, Han Zhang, Gwen Farley, Junling Wang, Kaycee A. Quarles, Zhiping Weng, Phillip D. Zamore

Open Access Articles

We report a draft assembly of the genome of Hi5 cells from the lepidopteran insect pest, Trichoplusia ni, assigning 90.6% of bases to one of 28 chromosomes and predicting 14,037 protein-coding genes. Chemoreception and detoxification gene families reveal T. ni-specific gene expansions that may explain its widespread distribution and rapid adaptation to insecticides. Transcriptome and small RNA data from thorax, ovary, testis, and the germline-derived Hi5 cell line show distinct expression profiles for 295 microRNA- and > 393 piRNA-producing loci, as well as 39 genes encoding small RNA pathway proteins. Nearly all of the W chromosome is devoted to ...


Taming The Beast—A Community Teaching Material Resource For Beast 2, Joelle Barido-Sottani, Veronika Boskova, Louis du Plessis, Denise Kuhnert, Carsten Magnus, Venelin Mitov, Nicola F. Muller, Julia Pecerska, David A. Rasmussen, Chi Zhang, Alexei J. Drummond, Tracy A. Heath, Oliver G. Pybus, Timothy G. Vaughan, Tanja Stadler 2018 ETH Zurich

Taming The Beast—A Community Teaching Material Resource For Beast 2, Joelle Barido-Sottani, Veronika Boskova, Louis Du Plessis, Denise Kuhnert, Carsten Magnus, Venelin Mitov, Nicola F. Muller, Julia Pecerska, David A. Rasmussen, Chi Zhang, Alexei J. Drummond, Tracy A. Heath, Oliver G. Pybus, Timothy G. Vaughan, Tanja Stadler

Ecology, Evolution and Organismal Biology Publications

Phylogenetics and phylodynamics are central topics in modern evolutionary biology. Phylogenetic methods reconstruct the evolutionary relationships among organisms, whereas phylodynamic approaches reveal the underlying diversification processes that lead to the observed relationships. These two fields have many practical applications in disciplines as diverse as epidemiology, developmental biology, palaeontology, ecology, and linguistics. The combination of increasingly large genetic data sets and increases in computing power is facilitating the development of more sophisticated phylogenetic and phylodynamic methods. Big data sets allow us to answer complex questions. However, since the required analyses are highly specific to the particular data set and question, a ...


Mrub_1325, Mrub_1326, Mrub_1327, And Mrub_1328 Are Orthologs Of B_3454, B_3455, B_3457, B_3458, Respectively Found In Escherichia Coli Coding For A Branched Chain Amino Acid Atp Binding Cassette (Abc) Transporter System, Bennett Tomlin, Adam Buric, Dr. Lori Scott 2018 Augustana College, Rock Island Illinois

Mrub_1325, Mrub_1326, Mrub_1327, And Mrub_1328 Are Orthologs Of B_3454, B_3455, B_3457, B_3458, Respectively Found In Escherichia Coli Coding For A Branched Chain Amino Acid Atp Binding Cassette (Abc) Transporter System, Bennett Tomlin, Adam Buric, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_1325, Mrub_1326, Mrub_1327, and Mrub_1328 (KEGG map number 02010). We predict these genes encode components of a Branched Chain Amino Acid ATP Binding Cassette (ABC) transporter: 1) Mrub_1325 (DNA coordinates 1357399-1358130 on the reverse strand) encodes the ATP binding domain; 2) Mrub_1326 (DNA coordinates 1358127-1359899 on the reverse strand) encodes the ATP-binding domain and permease domain; 3) Mrub_1327 (DNA coordinates 1359899-1360930 on the reverse strand) encodes a permease domain; and 4)Mrub_1328 (DNA coordinates 1711022-1712185 on the reverse strand) encodes the substrate binding domain. This system is not predicted ...


A Systematic Approach To Rna-Associated Motif Discovery, Tian Gao, Jiang Shu, Juan Cui 2018 University of Nebraska-Lincoln

A Systematic Approach To Rna-Associated Motif Discovery, Tian Gao, Jiang Shu, Juan Cui

CSE Journal Articles

Background: Sequencing-based large screening of RNA-protein and RNA-RNA interactions has enabled the mechanistic study of post-transcriptional RNA processing and sorting, including exosome-mediated RNA secretion. The downstream analysis of RNA binding sites has encouraged the investigation of novel sequence motifs, which resulted in exceptional new challenges for identifying motifs from very short sequences (e.g., small non-coding RNAs or truncated messenger RNAs), where conventional methods tend to be ineffective. To address these challenges, we propose a novel motif-finding method and validate it on a wide range of RNA applications.

Results: We first perform motif analysis on microRNAs and longer RNA fragments ...


Transcripity Split: Course-Based Rna-Seq Analysis Using The Ultrafast Kallisto-Sleuth Pipeline, Raymond A. Enke 2017 enkera@jmu.edu

Transcripity Split: Course-Based Rna-Seq Analysis Using The Ultrafast Kallisto-Sleuth Pipeline, Raymond A. Enke

Ray Enke Ph.D.

No abstract provided.


Integrative Microrna And Mrna Deep-Sequencing Expression Profiling In Endemic Burkitt Lymphoma, Cliff I. Oduor, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John Michael Ong'echa, Ann M. Moormann, Jeffrey A. Bailey 2017 Maseno University

Integrative Microrna And Mrna Deep-Sequencing Expression Profiling In Endemic Burkitt Lymphoma, Cliff I. Oduor, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John Michael Ong'echa, Ann M. Moormann, Jeffrey A. Bailey

Ann M. Moormann

BACKGROUND: Burkitt lymphoma (BL) is characterized by overexpression of the c-myc oncogene, which in the vast majority of cases is a consequence of an IGH/MYC translocation. While myc is the seminal event, BL is a complex amalgam of genetic and epigenetic changes causing dysregulation of both coding and non-coding transcripts. Emerging evidence suggest that abnormal modulation of mRNA transcription via miRNAs might be a significant factor in lymphomagenesis. However, the alterations in these miRNAs and their correlations to their putative mRNA targets have not been extensively studied relative to normal germinal center (GC) B cells.

METHODS: Using more sensitive ...


Identifying Genetic Factors Influencing Sperm Mobility Phenotype In Chicken Using Genome Wide Association Studies, Primordial Germ Cell Transplantation, And Rnaseq., Sohita Ojha 2017 University of Arkansas, Fayetteville

Identifying Genetic Factors Influencing Sperm Mobility Phenotype In Chicken Using Genome Wide Association Studies, Primordial Germ Cell Transplantation, And Rnaseq., Sohita Ojha

Theses and Dissertations

Sperm mobility is a major determinant of male fertility in chicken. In spite of low heritability of reproductive traits, sperm mobility has high heritability index which suggests presence of quantitative trait loci (QTLs) governing the trait. Our research focused on three objectives: i) to identify the QTLs affecting low mobility phenotype in chicken, ii) to understand the impact of Sertoli-cells and germ cells interactions in influencing the mobility phenotype and iii) to identify the genes and gene networks differentially expressed in male and female PGCs. To detect the QTLs, genome wide association studies (GWAS) was conducted which revealed the presence ...


Integrative Cancer Immunogenomic Analysis Of Serial Melanoma Biopsies Reveals Correlates Of Response And Resistance To Sequential Ctla-4 And Pd-1 Blockade Treatment, Whijae Roh 2017 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

Integrative Cancer Immunogenomic Analysis Of Serial Melanoma Biopsies Reveals Correlates Of Response And Resistance To Sequential Ctla-4 And Pd-1 Blockade Treatment, Whijae Roh

UT GSBS Dissertations and Theses (Open Access)

Melanoma is the most malignant form of skin cancer. The five-year survival rate for metastatic melanoma is 19.9%. Although targeted therapy of BRAF and MEK inhibitors were developed for melanoma, resistance to therapy is inevitable. Immune checkpoint blockade, which reverses the suppression of the immune system, on the other hand, has shown a durable response in 20-30% of patients with metastatic melanoma. However, more predictive and robust biomarkers of response to this therapy are still needed, and resistance mechanisms remain incompletely understood. To address this, we examined a cohort of metastatic melanoma patients treated with sequential checkpoint blockade against ...


Predicting Human Splicing Branchpoints By Combining Sequence-Derived Features And Multi-Label Learning Methods, Wen Zhang, Xiaopeng Zhu, Yu Fu, Junko Tsuji, Zhiping Weng 2017 Wuhan University

Predicting Human Splicing Branchpoints By Combining Sequence-Derived Features And Multi-Label Learning Methods, Wen Zhang, Xiaopeng Zhu, Yu Fu, Junko Tsuji, Zhiping Weng

Program in Bioinformatics and Integrative Biology Publications and Presentations

BACKGROUND: Alternative splicing is the critical process in a single gene coding, which removes introns and joins exons, and splicing branchpoints are indicators for the alternative splicing. Wet experiments have identified a great number of human splicing branchpoints, but many branchpoints are still unknown. In order to guide wet experiments, we develop computational methods to predict human splicing branchpoints.

RESULTS: Considering the fact that an intron may have multiple branchpoints, we transform the branchpoint prediction as the multi-label learning problem, and attempt to predict branchpoint sites from intron sequences. First, we investigate a variety of intron sequence-derived features, such as ...


Linking Taxonomic Diversity And Trophic Function: A Graph-Based Theoretical Approach, Marcella M. Jurotich, Kaitlyn Dougherty, Barbara Hayford, Sally Clark 2017 Wayne State College

Linking Taxonomic Diversity And Trophic Function: A Graph-Based Theoretical Approach, Marcella M. Jurotich, Kaitlyn Dougherty, Barbara Hayford, Sally Clark

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

The purpose of this study is to develop a novel, visual method in analyzing complex functional trait data in freshwater ecology. We focus on macroinvertebrates in stream ecosystems under a gradient of habitat degradation and employ a combination of taxonomic and functional trait diversity analyses. Then we use graph theory to link changes in functional trait diversity to taxonomic richness and habitat degradation. We test the hypotheses that: 1) taxonomic diversity and trophic functional trait diversity both decrease with increased habitat degradation; 2) loss of taxa leads to a decrease in trophic function as visualized using a bipartite graph; and ...


The Hoxd Cluster Is A Dynamic And Resilient Tad Boundary Controlling The Segregation Of Antagonistic Regulatory Landscapes, Eddie Rodriguez-Carballo, Lucille Lopez-Delisle, Ye Zhan, Pierre J. Fabre, Leonardo Beccari, Imane El-Idrissi, Thi Hanh Nguyen Huynh, Hakan Ozadam, Job Dekker, Denis Duboule 2017 University of Geneva

The Hoxd Cluster Is A Dynamic And Resilient Tad Boundary Controlling The Segregation Of Antagonistic Regulatory Landscapes, Eddie Rodriguez-Carballo, Lucille Lopez-Delisle, Ye Zhan, Pierre J. Fabre, Leonardo Beccari, Imane El-Idrissi, Thi Hanh Nguyen Huynh, Hakan Ozadam, Job Dekker, Denis Duboule

Program in Systems Biology Publications and Presentations

The mammalian HoxD cluster lies between two topologically associating domains (TADs) matching distinct enhancer-rich regulatory landscapes. During limb development, the telomeric TAD controls the early transcription of Hoxd genes in forearm cells, whereas the centromeric TAD subsequently regulates more posterior Hoxd genes in digit cells. Therefore, the TAD boundary prevents the terminal Hoxd13 gene from responding to forearm enhancers, thereby allowing proper limb patterning. To assess the nature and function of this CTCF-rich DNA region in embryos, we compared chromatin interaction profiles between proximal and distal limb bud cells isolated from mutant stocks where various parts of this boundary region ...


Integrative Microrna And Mrna Deep-Sequencing Expression Profiling In Endemic Burkitt Lymphoma, Cliff I. Oduor, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John Michael Ong'echa, Ann M. Moormann, Jeffrey A. Bailey 2017 Maseno University

Integrative Microrna And Mrna Deep-Sequencing Expression Profiling In Endemic Burkitt Lymphoma, Cliff I. Oduor, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John Michael Ong'echa, Ann M. Moormann, Jeffrey A. Bailey

UMass Center for Clinical and Translational Science Supported Publications

BACKGROUND: Burkitt lymphoma (BL) is characterized by overexpression of the c-myc oncogene, which in the vast majority of cases is a consequence of an IGH/MYC translocation. While myc is the seminal event, BL is a complex amalgam of genetic and epigenetic changes causing dysregulation of both coding and non-coding transcripts. Emerging evidence suggest that abnormal modulation of mRNA transcription via miRNAs might be a significant factor in lymphomagenesis. However, the alterations in these miRNAs and their correlations to their putative mRNA targets have not been extensively studied relative to normal germinal center (GC) B cells.

METHODS: Using more sensitive ...


A Systems Level Approach To Temporal Expression Dynamics In Drosophila Reveals Clusters Of Long Term Memory Genes, Julianna Bozler, Balint Z. Kacsoh, Hao Chen, William E. Theurkauf, Zhiping Weng, Giovanni Bosco 2017 Geisel School of Medicine at Dartmouth

A Systems Level Approach To Temporal Expression Dynamics In Drosophila Reveals Clusters Of Long Term Memory Genes, Julianna Bozler, Balint Z. Kacsoh, Hao Chen, William E. Theurkauf, Zhiping Weng, Giovanni Bosco

Program in Bioinformatics and Integrative Biology Publications and Presentations

The ability to integrate experiential information and recall it in the form of memory is observed in a wide range of taxa, and is a hallmark of highly derived nervous systems. Storage of past experiences is critical for adaptive behaviors that anticipate both adverse and positive environmental factors. The process of memory formation and consolidation involve many synchronized biological events including gene transcription, protein modification, and intracellular trafficking: However, many of these molecular mechanisms remain illusive. With Drosophila as a model system we use a nonassociative memory paradigm and a systems level approach to uncover novel transcriptional patterns. RNA sequencing ...


A Polyglot Approach To Bioinformatics Data Integration: A Phylogenetic Analysis Of Hiv-1, Steven Reisman, Thomas Hatzopoulos, Konstantin Laufer, George K. Thiruvathukal, Catherine Putonti 2017 Loyola University Chicago

A Polyglot Approach To Bioinformatics Data Integration: A Phylogenetic Analysis Of Hiv-1, Steven Reisman, Thomas Hatzopoulos, Konstantin Laufer, George K. Thiruvathukal, Catherine Putonti

Konstantin Läufer

As sequencing technologies continue to drop in price and increase in throughput, new challenges emerge for the management and accessibility of genomic sequence data. We have developed a pipeline for facilitating the storage, retrieval, and subsequent analysis of molecular data, integrating both sequence and metadata. Taking a polyglot approach involving multiple languages, libraries, and persistence mechanisms, sequence data can be aggregated from publicly available and local repositories. Data are exposed in the form of a RESTful web service, formatted for easy querying, and retrieved for downstream analyses. As a proof of concept, we have developed a resource for annotated HIV-1 ...


A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer 2017 Loyola University Chicago

A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer

Konstantin Läufer

RNA-interference has potential therapeutic use against HIV-1 by targeting highly-functional mRNA sequences that contribute to the virulence of the virus. Empirical work has shown that within cell lines, all of the HIV-1 genes are affected by RNAi-induced gene silencing. While promising, inherent in this treatment is the fact that RNAi sequences must be highly specific. HIV, however, mutates rapidly, leading to the evolution of viral escape mutants. In fact, such strains are under strong selection to include mutations within the targeted region, evading the RNAi therapy and thus increasing the virus’ fitness in the host. Taking a phylogenetic approach, we ...


Cytonuclear Evolution Of Rubisco In Four Allopolyploid Lineages, Lei Gong, Mischa Olson, Jonathan F. Wendel 2017 Iowa State University

Cytonuclear Evolution Of Rubisco In Four Allopolyploid Lineages, Lei Gong, Mischa Olson, Jonathan F. Wendel

Jonathan F. Wendel

Allopolyploidization in plants entails the merger of two divergent nuclear genomes, typically with only one set (usually maternal) of parental plastidial and mitochondrial genomes and with an altered cytonuclear stoichiometry. Thus, we might expect cytonuclear coevolution to be an important dimension of allopolyploid evolution. Here, we investigate cytonuclear coordination for the key chloroplast protein rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), which is composed of nuclear-encoded, small subunits (SSUs) and plastid-encoded, large subunits. By studying gene composition and diversity as well as gene expression in four model allopolyploid lineages, Arabidopsis, Arachis, Brassica, and Nicotiana, we demonstrate that paralogous nuclear-encoded rbcS genes ...


Chromosome Conformation In Context, James Taylor 2017 Illinois State University

Chromosome Conformation In Context, James Taylor

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Cage: A Tool For Identifying Genes With Correlated Spatiotemporal Expression, Basheer Becerra 2017 Illinois State University

Cage: A Tool For Identifying Genes With Correlated Spatiotemporal Expression, Basheer Becerra

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Study Of Antidepressant Molecular Structure Leading To Safer Dosing, Meera Garg 2017 Illinois State University

Study Of Antidepressant Molecular Structure Leading To Safer Dosing, Meera Garg

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


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