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Viper: Visualization Pipeline For Rna-Seq, A Snakemake Workflow For Efficient And Complete Rna-Seq Analysis, MacIntosh Cornwell, Mahesh Vangala, Len Taing, Zachary Herbert, Johannes Koster, Bo Li, Hanfei Sun, Taiwen Li, Jian Zhang, Xintao Qiu, Matthew Pun, Rinath Jeselsohn, Myles Brown, X Shirley Liu, Henry W. Long 2018 Dana-Farber Cancer Institute

Viper: Visualization Pipeline For Rna-Seq, A Snakemake Workflow For Efficient And Complete Rna-Seq Analysis, Macintosh Cornwell, Mahesh Vangala, Len Taing, Zachary Herbert, Johannes Koster, Bo Li, Hanfei Sun, Taiwen Li, Jian Zhang, Xintao Qiu, Matthew Pun, Rinath Jeselsohn, Myles Brown, X Shirley Liu, Henry W. Long

Open Access Articles

BACKGROUND: RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology has led to the continuous development of new tools for every step of analysis from alignment to downstream pathway analysis. However, effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts.

RESULTS: Using the workflow management system Snakemake we have developed a user friendly, fast, efficient, and comprehensive pipeline for RNA-seq analysis. VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis ...


Rates And Patterns Of Evolution In A Duplicated Genome In The Family Catostomidae, Megann Schmidt 2018 University of Northern Iowa

Rates And Patterns Of Evolution In A Duplicated Genome In The Family Catostomidae, Megann Schmidt

Research in the Capitol

Whole genome duplication (WGD) is a process in which the entire genome of an organism is duplicated, making redundant genes which are subject to unique evolutionary forces. Various modes of selection create different genetic fates such as retention of ancestral function, development of new function, or loss of function. Because of these differing fates, WGD is hypothesized to be a major driving force behind diversification. In this project, DNA sequences from fish species in the family Catostomidae were examined to observe patterns of evolution following a known WGD. Gene trees were generated for 179 loci to determine the amount of ...


Numerous Recursive Sites Contribute To Accuracy Of Splicing Of Long Introns In Flies, Athma A. Pai, Joseph Paggi, Karen Adelman, Christopher B. Burge 2018 University of Massachusetts Medical School

Numerous Recursive Sites Contribute To Accuracy Of Splicing Of Long Introns In Flies, Athma A. Pai, Joseph Paggi, Karen Adelman, Christopher B. Burge

University of Massachusetts Medical School Faculty Publications

Recursive splicing, a process by which a single intron is removed from pre-mRNA transcripts in multiple distinct segments, has been observed in a small subset of Drosophila melanogaster introns. However, detection of recursive splicing requires observation of splicing intermediates which are inherently unstable, making it difficult to study. Here we developed new computational approaches to identify recursively spliced introns and applied them, in combination with existing methods, to nascent RNA sequencing data from Drosophila S2 cells. These approaches identified hundreds of novel sites of recursive splicing, expanding the catalog of recursively spliced fly introns by 4-fold. Recursive sites occur in ...


A Genetic Screen To Identify Fission Yeast Genes With Roles In Protecting Against Perturbation Of The Actin Cytoskeleton, Dorota Michalski 2018 The University of Western Ontario

A Genetic Screen To Identify Fission Yeast Genes With Roles In Protecting Against Perturbation Of The Actin Cytoskeleton, Dorota Michalski

Electronic Thesis and Dissertation Repository

In the fission yeast, Schizosaccharomyces pombe, stress upon the cell division machinery leads to the activation of a cytokinesis checkpoint. This checkpoint results in a delay in cell cycle progression and the prolonged maintenance of a cytokinesis competent cellular state. In this state the cell is able to continuously reform/repair the actomyosin ring until cell division is achieved. To uncover genes that play a role in enforcing this checkpoint, the actin depolymerizing drug Latrunculin A (LatA) was used to perturb the cytokinetic machinery in a set of 3400 viable haploid S. pombe gene deletion mutants. Thirty-eight gene deletion mutants ...


Profiling Of Pluripotency Factors In Individual Stem Cells And Early Embryos, Sarah J. Hainer, Ana Boskovic, Oliver J. Rando, Thomas G. Fazzio 2018 University of Massachusetts Medical School

Profiling Of Pluripotency Factors In Individual Stem Cells And Early Embryos, Sarah J. Hainer, Ana Boskovic, Oliver J. Rando, Thomas G. Fazzio

University of Massachusetts Medical School Faculty Publications

Major cell fate decisions are governed by sequence-specific transcription factors (TFs) that act in small cell populations within developing embryos. To understand how TFs regulate cell fate it is important to identify their genomic binding sites in these populations. However, current methods cannot profile TFs genome-wide at or near the single cell level. Here we adapt the CUT&RUN method to profile chromatin proteins in low cell numbers, mapping TF-DNA interactions in single cells and individual pre-implantation embryos for the first time. Using this method, we demonstrate that the pluripotency TF NANOG is significantly more dependent on the SWI/SNF ...


Copy Number Variation In The Porcine Genome Detected From Whole-Genome Sequence, Rebecca Anderson 2018 University of Nebraska-Lincoln

Copy Number Variation In The Porcine Genome Detected From Whole-Genome Sequence, Rebecca Anderson

Honors Theses, University of Nebraska-Lincoln

Copy number variations (CNVs) are large insertions, deletions, and duplications in the genome that vary between individuals in a species. These variations are known to impact a broad range of phenotypes from molecular-level traits to higher-order clinical phenotypes. CNVs have been linked to complex traits in humans such as autism, attention deficit hyperactivity disorder, nervous system disorders, and early-onset extreme obesity. In this study, whole-genome sequence was obtained from 72 founders of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC) in Clay Center, Nebraska. This included 24 boars (12 Duroc and 12 Landrace ...


Atacseqqc: A Bioconductor Package For Post-Alignment Quality Assessment Of Atac-Seq Data, Jianhong Ou, Haibo Liu, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson, Lihua Julie Zhu 2018 Duke University

Atacseqqc: A Bioconductor Package For Post-Alignment Quality Assessment Of Atac-Seq Data, Jianhong Ou, Haibo Liu, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson, Lihua Julie Zhu

University of Massachusetts Medical School Faculty Publications

BACKGROUND: ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers. However, to ensure a successful ATAC-seq experiment, step-by-step quality assurance processes, including both wet lab quality control and in silico quality assessment, are essential. While several tools have been developed or adopted for assessing read quality, identifying nucleosome occupancy and accessible regions from ATAC-seq data, none of the ...


Evidence For A Unique Dna-Dependent Rna Polymerase In Cereal Crops, Joshua T. Trujillo, Arun S. Seetharam, Matthew B. Hufford, Mark A. Beilstein, Rebecca A. Mosher 2018 University of Arizona

Evidence For A Unique Dna-Dependent Rna Polymerase In Cereal Crops, Joshua T. Trujillo, Arun S. Seetharam, Matthew B. Hufford, Mark A. Beilstein, Rebecca A. Mosher

Genome Informatics Facility Publications

Gene duplication is an important driver for the evolution of new genes and protein functions. Duplication of DNA-dependent RNA polymerase (Pol) II subunits within plants led to the emergence of RNA Pol IV and V complexes, each of which possess unique functions necessary for RNA-directed DNA Methylation. Comprehensive identification of Pol V subunit orthologs across the monocot radiation revealed a duplication of the largest two subunits within the grasses (Poaceae), including critical cereal crops. These paralogous Pol subunits display sequence conservation within catalytic domains, but their carboxy terminal domains differ in length and character of the Ago-binding platform, suggesting unique ...


Identification Of Novel Genetic Variations For Amyotrophic Lateral Sclerosis (Als), Guang Xu 2018 University of Massachusetts Medical School

Identification Of Novel Genetic Variations For Amyotrophic Lateral Sclerosis (Als), Guang Xu

GSBS Dissertations and Theses

A list of genes have been identified to carry mutations causing familial ALS such as SOD1, TARDBP, C9orf72. But for sporadic ALS, which is 90% of all ALS cases, the underlying genetic variants are still largely unknown. There are multiple genome-wide association study (GWAS) for sporadic ALS, but usually a large number nominated SNP can hardly be replicated in larger cohort analysis. Also majority of GWAS SNP lie within noncoding region of genome, imposing a huge challenge to study their biological role in ALS pathology. With the rapid development of next-generation sequencing technology, we are able to sequence exome and ...


Novel Candidate Genes Important For Asthma And Hypertension Comorbidity Revealed From Associative Gene Networks, Olga V. Saik, Pavel S. Demenkov, Timofey V. Ivanisenko, Elena Yu. Bragina, Maxim B. Freidin, Irina A. Goncharova, Victor E. Dosenko, Olga I. Zolotareva, Ralf Hofestaedt, Inna N. Lavrik, Evgeny I. Rogaev, Vladimir A. Ivanisenko 2018 Institute of Cytology and Genetics

Novel Candidate Genes Important For Asthma And Hypertension Comorbidity Revealed From Associative Gene Networks, Olga V. Saik, Pavel S. Demenkov, Timofey V. Ivanisenko, Elena Yu. Bragina, Maxim B. Freidin, Irina A. Goncharova, Victor E. Dosenko, Olga I. Zolotareva, Ralf Hofestaedt, Inna N. Lavrik, Evgeny I. Rogaev, Vladimir A. Ivanisenko

Open Access Articles

BACKGROUND: Hypertension and bronchial asthma are a major issue for people's health. As of 2014, approximately one billion adults, or ~ 22% of the world population, have had hypertension. As of 2011, 235-330 million people globally have been affected by asthma and approximately 250,000-345,000 people have died each year from the disease. The development of the effective treatment therapies against these diseases is complicated by their comorbidity features. This is often a major problem in diagnosis and their treatment. Hence, in this study the bioinformatical methodology for the analysis of the comorbidity of these two diseases have been ...


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 ...


Impact Of Concurrent Genomic Alterations Detected By Comprehensive Genomic Sequencing On Clinical Outcomes In East-Asian Patients With Egfr-Mutated Lung Adenocarcinoma, Seijiro Sato, Stephen Lyle, Toshifumi Wakai, Masanori Tsuchida 2018 Niigata University

Impact Of Concurrent Genomic Alterations Detected By Comprehensive Genomic Sequencing On Clinical Outcomes In East-Asian Patients With Egfr-Mutated Lung Adenocarcinoma, Seijiro Sato, Stephen Lyle, Toshifumi Wakai, Masanori Tsuchida

Open Access Articles

Next-generation sequencing (NGS) has enabled comprehensive detection of genomic alterations in lung cancer. Ethnic differences may play a critical role in the efficacy of targeted therapies. The aim of this study was to identify and compare genomic alterations of lung adenocarcinoma between Japanese patients and the Cancer Genome Atlas (TCGA), which majority of patients are from the US. We also aimed to examine prognostic impact of additional genomic alterations in patients harboring EGFR mutations. Genomic alterations were determined in Japanese patients with lung adenocarcinoma (N = 100) using NGS-based sequencing of 415 known cancer genes, and correlated with clinical outcome. EGFR ...


Orbit: A New Paradigm For Genetic Engineering Of Mycobacterial Chromosomes, Kenan C. Murphy, Samantha J. Nelson, Subhalaxmi Nambi, Kadamba Papavinasasundaram, Christina E. Baer, Christopher M. Sassetti 2018 University of Massachusetts Medical School

Orbit: A New Paradigm For Genetic Engineering Of Mycobacterial Chromosomes, Kenan C. Murphy, Samantha J. Nelson, Subhalaxmi Nambi, Kadamba Papavinasasundaram, Christina E. Baer, Christopher M. Sassetti

University of Massachusetts Medical School Faculty Publications

Current methods for genome engineering in mycobacteria rely on relatively inefficient recombination systems that require the laborious construction of a long double-stranded DNA substrate for each desired modification. We combined two efficient recombination systems to produce a versatile method for high-throughput chromosomal engineering that obviates the need for the preparation of double-stranded DNA recombination substrates. A synthetic targeting oligonucleotide is incorporated into the chromosome via homologous recombination mediated by the phage Che9c RecT annelase. This oligo contains a site-specific recombination site for the directional Bxb1 integrase (Int), which allows the simultaneous integration of a payload plasmid that contains a cognate ...


Determining Bioindicators For Coastal Tidal Marsh Health Using The Food Web Of Larvae Of The Greenhead Horse Fly (Tabanus Nigrovittatus), Devika Rajeev Bhalerao 2018 Louisiana State University and Agricultural and Mechanical College

Determining Bioindicators For Coastal Tidal Marsh Health Using The Food Web Of Larvae Of The Greenhead Horse Fly (Tabanus Nigrovittatus), Devika Rajeev Bhalerao

LSU Master's Theses

The greenhead horse fly Tabanus nigrovittatus Macquart is native to coastal marshlands from Texas to Nova Scotia. The larvae are apex invertebrate predators and their development is dependent on the food web in the soil. Surveillance of T. nigrovittatus after the 2010 Deepwater Horizon oil spill in the Gulf of Mexico showed population crashes of adults in the coastal marshes of East Louisiana near places where oil made landfall, but not in West Louisiana where the oil did not reach. Sediment collection in 2011 from West and East Louisiana revealed larval population crashes in the Eastern coastal region. We hypothesized ...


Insights Into Teleost Sex Determination From The Seriola Dorsalis Genome Assembly, Catherine M. Purcell, Arun S. Seetharam, Owyn Snodgrass, Sofia Ortega-García, John R. Hyde, Andrew J. Severin 2018 National Marine Fisheries Service

Insights Into Teleost Sex Determination From The Seriola Dorsalis Genome Assembly, Catherine M. Purcell, Arun S. Seetharam, Owyn Snodgrass, Sofia Ortega-García, John R. Hyde, Andrew J. Severin

Office of Biotechnology Publications

Background: The assembly and annotation of a genome is a valuable resource for a species, with applications ranging from conservation genomics to gene discovery. Genomic resource development is especially important for species in culture, such as the California Yellowtail (Seriola dorsalis), the likely candidate for the establishment of commercial offshore aquaculture production in southern California. Genomic resource development for this species will improve the understanding of sex and other phenotypic traits, and allow for rapid increases in genetic improvement for and economic gain in culture production.

Results: We describe the assembly and annotation of the S. dorsalis genome, and present ...


Early Epstein-Barr Virus Genomic Diversity And Convergence Toward The B95.8 Genome In Primary Infection, Eric R. Weiss, Susanna L. Lamers, Jennifer L. Henderson, Alexandre Melnikov, Mohan Somasundaran, Manuel Garber, Liisa K. Selin, Chad Nusbaum, Katherine Luzuriaga 2018 University of Massachusetts Medical School

Early Epstein-Barr Virus Genomic Diversity And Convergence Toward The B95.8 Genome In Primary Infection, Eric R. Weiss, Susanna L. Lamers, Jennifer L. Henderson, Alexandre Melnikov, Mohan Somasundaran, Manuel Garber, Liisa K. Selin, Chad Nusbaum, Katherine Luzuriaga

Garber Lab Publications

Over 90% of the world's population is persistently infected with Epstein-Barr virus. While EBV does not cause disease in most individuals, it is the common cause of acute infectious mononucleosis (AIM) and has been associated with several cancers and autoimmune diseases, highlighting a need for a preventive vaccine. At present, very few primary, circulating EBV genomes have been sequenced directly from infected individuals. While low levels of diversity and low viral evolution rates have been predicted for double-stranded DNA (dsDNA) viruses, recent studies have demonstrated appreciable diversity in common dsDNA pathogens (e.g., cytomegalovirus). Here, we report 40 full-length ...


Meiothermus Ruber Mrub_0320 Gene Is An Ortholog Of The B3452 Gene, Mrub_0321 Gene Is An Ortholog Of The B3451 Gene, Mrub_0322 Gene Is An Ortholog Of The B3453 Gene, Mrub_2366 Gene Is An Ortholog Of The B3450 Gene Found In Escherichia Coli, Which Encode For Components Of An Abc Transporter Involved In Sn-Glycerol - 3-Phosphate, Jenna Hall, Dr. Lori Scott 2018 Augustana College, Rock Island Illinois

Meiothermus Ruber Mrub_0320 Gene Is An Ortholog Of The B3452 Gene, Mrub_0321 Gene Is An Ortholog Of The B3451 Gene, Mrub_0322 Gene Is An Ortholog Of The B3453 Gene, Mrub_2366 Gene Is An Ortholog Of The B3450 Gene Found In Escherichia Coli, Which Encode For Components Of An Abc Transporter Involved In Sn-Glycerol - 3-Phosphate, Jenna Hall, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes mrub_0320, mrub_0321, mrub_0322, and mrub_2366 (KEGG map number 02010). We predict these genes encode components of a sn-glycerol-3-phosphate (ABC) transporter: 1) mrub_0320 (DNA coordinates 288469..289401) encodes the permease component (aka transmembrane domain), predicted to be an ortholog; 2) mrub_0321 (DNA coordinates 289394..290218) encodes another permease domain, and also contains a transcriptional regular; ATP-binding domain (aka nucleotide binding domain); 3) mrub_0322 (DNA coordinates 290234..291541) encodes the solute binding protein; and 4) mrub_2366 (DNA coordinates 2418207..2419352 on the reverse strand) encodes for an ATP-binding domain for multiple ...


Draft Genome Sequence Of Streptomyces Sp. Strain Jv178, A Producer Of Clifednamide-Type Polycyclic Tetramate Macrolactams, Yunci Qi, John M. D’Alessandro, Joshua A.V Blodgett 2018 Washington University in St. Louis

Draft Genome Sequence Of Streptomyces Sp. Strain Jv178, A Producer Of Clifednamide-Type Polycyclic Tetramate Macrolactams, Yunci Qi, John M. D’Alessandro, Joshua A.V Blodgett

Biology Faculty Publications & Presentations

Here, we report the draft genome sequence of Streptomyces sp. JV178, a strain originating from Connecticut (USA) garden soil. This strain produces the polycyclic tetramate macrolactam compounds clifednamides A and B. The draft genome contains 10.65 Mb, 9,045 predicted protein coding sequences, and several natural product biosynthetic loci.


Mrub_0680, Mrub_0836, And Mrub_0837 Found To Be Orthologous To E. Coli Ccma, Ccmb, And Ccmc, Respectively, Coding For Abc-Transport Proteins Involved In Cytochrome-C Biogenesis, Sarah N. Church, Dr. Lori Scott 2018 Augustana College, Rock Island Illinois

Mrub_0680, Mrub_0836, And Mrub_0837 Found To Be Orthologous To E. Coli Ccma, Ccmb, And Ccmc, Respectively, Coding For Abc-Transport Proteins Involved In Cytochrome-C Biogenesis, Sarah N. Church, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_0680, Mrub_0836 and Mrub_0837(KEGG map number 02010). We predict these genes encode components of a Heme ATP Binding Cassette (ABC) transporter: 1) Mrub_0836 (DNA coordinates 823734..824399on the reverse strand) encodes the permease component (aka transmembrane domain), predicted to be an ortho; and 2) Mrub_0680(DNA coordinates 659484..660071 on the reverse strand) encodes the ATP-binding domain (aka nucleotide binding domain); and 3) Mrub_0837(DNA coordinates 824570..825262on the reverse strand) encodes the solute binding protein. This gene system encodes a transmembrane exporter and helper proteins ...


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