Evolution Of Alternative Splicing After Gene Duplication, 2017 Zhejiang University
Evolution Of Alternative Splicing After Gene Duplication, Zhixi Su, Jianmin Wang, Xiaoqiu Huang, Xun Gu
Alternative splicing and gene duplication are two major sources of proteomic function diversity. Here, we study the evolutionary trend of alternative splicing after gene duplication by analyzing the alternative splicing differences between duplicate genes. We observed that duplicate genes have fewer alternative splice (AS) forms than single-copy genes, and that a negative correlation exists between the mean number of AS forms and the gene family size. Interestingly, we found that the loss of alternative splicing in duplicate genes may occur shortly after the gene duplication. These results support the subfunctionization model of alternative splicing in the early stage after gene ...
Cap3: A Dna Sequence Assembly Program, 2017 Iowa State University
Cap3: A Dna Sequence Assembly Program, Xiaoqiu Huang, Anup Madan
This article is from Genome Research 9 (1999): 867, doi: 10.1101/gr.9.9.868. Posted with permission.
Penetrance Estimates For Incidental Genomic Findings In Acmg-59, 2017 Yale University
Penetrance Estimates For Incidental Genomic Findings In Acmg-59, James A. Diao
Yale Day of Data
The dropping costs and rising popularity of next-generation sequencing has introduced the possibility of personalizing medical treatments and screening for genetic diseases. Still, the clinical community’s understanding remains incomplete, with limited consensus on the proper interpretation for many genetic variants. Thus, the standard procedure when returning sequencing results has been to report findings only in genes related to the diagnostic indication, and not incidental findings in other genes. To balance the threat of false positives with the medical benefits of true findings, the American College on Medical Genetics and Genomics (ACMG) recommends an exception: that clinical sequencing laboratories seek ...
Detecting Discordance Enrichment Among A Series Of Two-Sample Genome-Wide Expression Data Sets, 2017 George Washington University
Detecting Discordance Enrichment Among A Series Of Two-Sample Genome-Wide Expression Data Sets, Yinglei Lai, Fanni Zhang, Tapan Nayak, Reza Modarres, Norman H. Lee, Timothy A. Mccaffrey
Epidemiology and Biostatistics Faculty Publications
With the current microarray and RNA-seq technologies, two-sample genome-wide expression data have been widely collected in biological and medical studies. The related differential expression analysis and gene set enrichment analysis have been frequently conducted. Integrative analysis can be conducted when multiple data sets are available. In practice, discordant molecular behaviors among a series of data sets can be of biological and clinical interest.
In this study, a statistical method is proposed for detecting discordance gene set enrichment. Our method is based on a two-level multivariate normal mixture model. It is statistically efficient with linearly increased parameter space when ...
Mrub_2642, Mrub_1054, And Mrub_1059 Genes Are Orthologs Of The Escherichia Coli Genes B2942, B0159, And B2687 Genes, Respectively, Which Code For Methionine Adenosyltransferase, Adenosylhomocysteine Nucleosidase, And S-Ribosylhomocysteine Lyase, 2017 Augustana College, Rock Island Illinois
Mrub_2642, Mrub_1054, And Mrub_1059 Genes Are Orthologs Of The Escherichia Coli Genes B2942, B0159, And B2687 Genes, Respectively, Which Code For Methionine Adenosyltransferase, Adenosylhomocysteine Nucleosidase, And S-Ribosylhomocysteine Lyase, Nicholas M. Orslini, Dr. Lori R. Scott
Meiothermus ruber Genome Analysis Project
This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_2642, Mrub_1054, and Mrub_1059.
We predict that Mrub_2642 encodes the enzyme methionine adenosyltransferase (DNA coordinates [2677251…2678426] on the reverse strand), the first step of the methionine degradation pathway (KEGG map number 00270). Methionine adenosyltransferase catalyzes the conversion of the substrates, ATP, L-methionine, and water, to yield the products S-adenosyl-L-methionine (SAM), inorganic phosphate, and diphosphate. Mrub_1054 encodes adenosylhomocysteine nucleosidase (DNA ...
Evolution In Light Of Mitonuclear Landscapes An Examination Of Mitochondrial Replacement In Killifish (Fundulus Spp.), 2016 University of Southern Mississippi
Evolution In Light Of Mitonuclear Landscapes An Examination Of Mitochondrial Replacement In Killifish (Fundulus Spp.), Stephen D. Flanagan
The mitochondria are responsible for the bulk of energy production in eukaryotes. They possess their own genome that works in conjunction with the nuclear genome to accomplish the extraordinarily important task of energy conversion. When species hybridize there will be a mismatch in evolutionary histories between these two genomes. The deleterious interactions of these genomes have been studied in great detail (i.e. hybrid breakdown). However, little work has been conducted to understand the population genetic, and morphological consequences of wide-ranging replacement. The Fundulus notatus complex is comprised of 3 species: F. notatus, F. olivaceus, and F. euryzonus. Within the ...
Peering Below The Diffraction Limit: Robust And Specific Sorting Of Viruses With Flow Cytometry, 2016 University of California, San Francisco
Peering Below The Diffraction Limit: Robust And Specific Sorting Of Viruses With Flow Cytometry, Shea T. Lance, David J. Sukovich, Kenneth M. Stedman, Adam R. Abate
Biology Faculty Publications and Presentations
Background: Viruses are incredibly diverse organisms and impact all forms of life on Earth; however, individual virions are challenging to study due to their small size and mass, precluding almost all direct imaging or molecular analysis. Moreover, like microbes, the overwhelming majority of viruses cannot be cultured, impeding isolation, replication, and study of interesting new species. Here, we introduce PCR-activated virus sorting, a method to isolate specific viruses from a heterogeneous population. Specific sorting opens new avenues in the study of uncultivable viruses, including recovering the full genomes of viruses based on genetic fragments in metagenomes, or identifying the hosts ...
Investigating The Functional Role Of Tick Antioxidants In Hematophagy And Vector Competence, 2016 University of Southern Mississippi
Investigating The Functional Role Of Tick Antioxidants In Hematophagy And Vector Competence, Deepak Kumar
Ticks are obligate hematophagous arthropods and harbor several pathogens which transmit various diseases to humans and their domesticated animals. Host blood- digestion in a tick midgut (MG) generates several reactive oxygen species (ROS), which are extremely toxic to essential macromolecules (e.g. DNA, proteins, and lipids) within the cell, resulting in high oxidative stress. Thus, this dissertation focuses on the questions of how tick homeostasis responds to high oxidative stress, and how ticks and their harbored pathogens survive the high surge of oxidative stress during blood digestion. We are specifically interested in the tick-pathogen, Rickettsia parkeri (R. parkeri, Rp), harbored ...
Rna Sequencing Analysis Of The Developing Chicken Retina, 2016 James Madison University
Rna Sequencing Analysis Of The Developing Chicken Retina, Christophe Langouet-Astrie*, Annamarie Meinsen*, Emily R. Grunwald*, Stephen Turner, Raymond A. Enke
Ray Enke Ph.D.
Genomes Of Gardnerella Strains Reveal An Abundance Of Prophages Within The Bladder Microbiome, 2016 Loyola University Chicago
Genomes Of Gardnerella Strains Reveal An Abundance Of Prophages Within The Bladder Microbiome, Kema Malki, Jason W. Shapiro, Travis Kyle Price, Evann Elizabeth Hilt, Krystal Thomas-White, Trina Sircar, Amy B. Rosenfeld, Michael J. Zilliox, Alan J. Wolfe, Catherine Putonti
Bioinformatics Faculty Publications
Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance of many similar bacterial taxa. As the bladder was once thought to be sterile, the complex interactions between microbes within the bladder have yet to be characterized. To initiate this process, we have begun sequencing isolates, including the clinically relevant genus Gardnerella. Herein, we present the genomic sequences of four Gardnerella strains isolated from the bladders of women with symptoms of urgency urinary incontinence; these are the first Gardnerella genomes produced from this niche. Congruent to genomic characterization of Gardnerella isolates from the reproductive tract, isolates from ...
Draft Genome Sequence For A Urinary Isolate Of Nosocomiicoccus Ampullae, 2016 Loyola University Chicago
Draft Genome Sequence For A Urinary Isolate Of Nosocomiicoccus Ampullae, Evann Elizabeth Hilt, Travis Kyle Price, Katherine Diebel, Catherine Putonti, Alan J. Wolfe
Bioinformatics Faculty Publications
A draft genome sequence for a urinary isolate of Nosocomiicoccus ampullae (UMB0853) was investigated. The size of the genome was 1,578,043 bp, with an observed G+C content of 36.1%. Annotation revealed 10 rRNA sequences, 40 tRNA genes, and 1,532 protein-coding sequences. Genome coverage was 727× and consisted of 32 contigs, with an N50 of 109,831 bp.
Sequence Annotation & Designing Gene-Specific Qpcr Primers (Computational), 2016 email@example.com
Sequence Annotation & Designing Gene-Specific Qpcr Primers (Computational), Raymond A. Enke
Ray Enke Ph.D.
- Obtaining and annotating genomic DNA and mRNA sequence information
- Designing primers for quantitative PCR (qPCR) analysis of a cDNA library
Qpcr Primer Standard Curve Assay (Wet Lab) + Kegg Pathway Analysis (Computational), 2016 firstname.lastname@example.org
Qpcr Primer Standard Curve Assay (Wet Lab) + Kegg Pathway Analysis (Computational), Raymond A. Enke
Ray Enke Ph.D.
- analyzing qPCR standard curve data to determine primer efficiency
- analyzing differential gene expression experimental qPCR data
- applying KEGG pathway analysis of selected candidates genes
A Gene-Centered C. Elegans Protein-Dna Interaction Network Provides A Framework For Functional Predictions, 2016 University of Massachusetts Medical School
A Gene-Centered C. Elegans Protein-Dna Interaction Network Provides A Framework For Functional Predictions, Juan Fuxman Bass, Carles Pons, Lucie Kozlowski, John S. Reece-Hoyes, Shaleen Shrestha, Amy D. Holdorf, Akihiro Mori, Chad L. Myers, Albertha J. M. Walhout
Open Access Articles
Transcription factors (TFs) play a central role in controlling spatiotemporal gene expression and the response to environmental cues. A comprehensive understanding of gene regulation requires integrating physical protein-DNA interactions (PDIs) with TF regulatory activity, expression patterns, and phenotypic data. Although great progress has been made in mapping PDIs using chromatin immunoprecipitation, these studies have only characterized ~10% of TFs in any metazoan species. The nematode C. elegans has been widely used to study gene regulation due to its compact genome with short regulatory sequences. Here, we delineated the largest gene-centered metazoan PDI network to date by examining interactions between 90 ...
Mammalian Keratin Associated Proteins (Krtaps) Subgenomes: Disentangling Hair Diversity And Adaptation To Terrestrial And Aquatic Environments, Imran Khan, Emanuel Maldonado, Vitor Vasconcelos, Stephen J. O'Brien, Warren E. Johnson, Agostinho Antunes
Background: Adaptation of mammals to terrestrial life was facilitated by the unique vertebrate trait of body hair, which occurs in a range of morphological patterns. Keratin associated proteins (KRTAPs), the major structural hair shaft proteins, are largely responsible for hair variation.
Results: We exhaustively characterized the KRTAP gene family in 22 mammalian genomes, confirming the existence of 30 KRTAP subfamilies evolving at different rates with varying degrees of diversification and homogenization. Within the two major classes of KRTAPs, the high cysteine (HS) subfamily experienced strong concerted evolution, high rates of gene conversion/recombination and high GC content. In contrast, high ...
General Equations For Natural Selection Under Complete Dominance, 2016 New York University
General Equations For Natural Selection Under Complete Dominance, Kasthuri Kannan, Adriana Heguy
Annual Symposium on Biomathematics and Ecology: Education and Research
No abstract provided.
Rapid Screening For Crispr-Directed Editing Of The Drosophila Genome Using White Coconversion, 2016 University of Massachusetts Medical School
Rapid Screening For Crispr-Directed Editing Of The Drosophila Genome Using White Coconversion, Daniel Tianfang Ge, Cindy Tipping, Michael H. Brodsky, Phillip D. Zamore
Open Access Articles
Adoption of a streamlined version of the bacterial clustered regular interspersed short palindromic repeat (CRISPR)/Cas9 defense system has accelerated targeted genome engineering. The Streptococcus pyogenes Cas9 protein, directed by a simplified, CRISPR-like single-guide RNA, catalyzes a double-stranded DNA break at a specific genomic site; subsequent repair by end joining can introduce mutagenic insertions or deletions, while repair by homologous recombination using an exogenous DNA template can incorporate new sequences at the target locus. However, the efficiency of Cas9-directed mutagenesis is low in Drosophila melanogaster Here, we describe a strategy that reduces the time and effort required to identify flies ...
Genome Sequences And Annotation Of Two Urinary Isolates Of E. Coli, 2016 Loyola University Chicago
Genome Sequences And Annotation Of Two Urinary Isolates Of E. Coli, Travis Kyle Price, Arya Mehtash, Laurynas Kalesinskas, Kema Malki, Evann Elizabeth Hilt, Catherine Putonti, Alan J. Wolfe
Bioinformatics Faculty Publications
The genus Escherichia includes pathogens and commensals. Bladder infections (cystitis) result most often from colonization of the bladder by uropathogenic E. coli strains. In contrast, a poorly defined condition called asymptomatic bacteriuria results from colonization of the bladder with E. coli strains without symptoms. As part of an on-going attempt to identify and characterize the newly discovered female urinary microbiota, we report the genome sequences and annotation of two urinary isolates of E. coli: one (E78) was isolated from a female patient who self-reported cystitis; the other (E75) was isolated from a female patient who reported that she did not ...
A Widely Employed Germ Cell Marker Is An Ancient Disordered Protein With Reproductive Functions In Diverse Eukaryotes, Michelle A. Carmell, Gregoriy A. Dokshin, Helen Skaletsky, Yueh-Chiang Hu, Josien C. Van Wolfswinkel, Kyomi J. Igarashi, Daniel W. Bellott, Michael Nefedov, Peter W. Reddien, George C. Enders, Vladimir N. Uversky, Craig C. Mello, David C. Page
Open Access Articles
The advent of sexual reproduction and the evolution of a dedicated germline in multicellular organisms are critical landmarks in eukaryotic evolution. We report an ancient family of GCNA (germ cell nuclear antigen) proteins that arose in the earliest eukaryotes, and feature a rapidly evolving intrinsically disordered region (IDR). Phylogenetic analysis reveals that GCNA proteins emerged before the major eukaryotic lineages diverged; GCNA predates the origin of a dedicated germline by a billion years. Gcna gene expression is enriched in reproductive cells across eukarya - either just prior to or during meiosis in single-celled eukaryotes, and in stem cells and germ cells ...
Dnapi: A De Novo Adapter Prediction Algorithm For Small Rna Sequencing Data, 2016 University of Massachusetts Medical School Worcester
Dnapi: A De Novo Adapter Prediction Algorithm For Small Rna Sequencing Data, Junko Tsuji, Zhiping Weng
Program in Bioinformatics and Integrative Biology Publications and Presentations
With the rapid accumulation of publicly available small RNA sequencing datasets, third-party meta-analysis across many datasets is becoming increasingly powerful. Although removing the 3 adapter is an essential step for small RNA sequencing analysis, the adapter sequence information is not always available in the metadata. The information can be also erroneous even when it is available. In this study, we developed DNApi, a lightweight Python software package that predicts the 3 adapter sequence de novo and provides the user with cleansed small RNA sequences ready for down stream analysis. Tested on 539 publicly available small RNA libraries accompanied with 3 ...