Open Access. Powered by Scholars. Published by Universities.®

Genomics Commons

Open Access. Powered by Scholars. Published by Universities.®

1,043 Full-Text Articles 3,597 Authors 92,108 Downloads 94 Institutions

All Articles in Genomics

Faceted Search

1,043 full-text articles. Page 43 of 44.

Molecular Probes For The Detection Of Cyanophage As-1 And Its Cyanobacterial Hosts., Tin-Chun Chu, Jonathan Jimenez, Lauren Strawn, Michelle Reed, Lauren Pohren, Lee Lee 2010 Seton Hall University

Molecular Probes For The Detection Of Cyanophage As-1 And Its Cyanobacterial Hosts., Tin-Chun Chu, Jonathan Jimenez, Lauren Strawn, Michelle Reed, Lauren Pohren, Lee Lee

Tin-Chun Chu, Ph.D.

No abstract provided.


Following Tetraploidy In Maize, A Short Deletion Mechanism Removed Genes Preferentially From One Of The Two Homeologs, Margaret R. Woodhouse, James C. Schnable, Brent S. Pedersen, Eric Lyons, Damon Lisch, Shabarinath Subramaniam, Michael Freeling 2010 University of California - Berkeley

Following Tetraploidy In Maize, A Short Deletion Mechanism Removed Genes Preferentially From One Of The Two Homeologs, Margaret R. Woodhouse, James C. Schnable, Brent S. Pedersen, Eric Lyons, Damon Lisch, Shabarinath Subramaniam, Michael Freeling

Agronomy & Horticulture -- Faculty Publications

Previous work in Arabidopsis showed that after an ancient tetraploidy event, genes were preferentially removed from one of the two homeologs, a process known as fractionation. The mechanism of fractionation is unknown. We sought to determine whether such preferential, or biased, fractionation exists in maize and, if so, whether a specific mechanism could be implicated in this process. We studied the process of fractionation using two recently sequenced grass species: sorghum and maize. The maize lineage has experienced a tetraploidy since its divergence from sorghum approximately 12 million years ago, and fragments of many knocked-out genes retain enough sequence similarity ...


Genomic Patterns Of Nucleotide Diversity In Divergent Populations Of U.S. Weedy Rice, Michael Reagon, Carrie Thurber, Brian Gross, Kenneth Olsen, Yulin Jia, Ana Caicedo 2010 University of Massachusetts - Amherst

Genomic Patterns Of Nucleotide Diversity In Divergent Populations Of U.S. Weedy Rice, Michael Reagon, Carrie Thurber, Brian Gross, Kenneth Olsen, Yulin Jia, Ana Caicedo

Biology Department Faculty Publication Series

Background: Weedy rice (red rice), a conspecific weed of cultivated rice (Oryza sativa L.), is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP) variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution. Results: We find greater population structure than has been previously reported ...


Genomic Patterns Of Nucleotide Diversity In Divergent Populations Of U.S. Weedy Rice, Michael Reagon, Carrie S. Thurber, Brian L. Gross, Kenneth M. Olsen, Yulin Jia, Ana Lucia Caicedo 2010 University of Massachusetts - Amherst

Genomic Patterns Of Nucleotide Diversity In Divergent Populations Of U.S. Weedy Rice, Michael Reagon, Carrie S. Thurber, Brian L. Gross, Kenneth M. Olsen, Yulin Jia, Ana Lucia Caicedo

Ana Lucia Caicedo

Background: Weedy rice (red rice), a conspecific weed of cultivated rice (Oryza sativa L.), is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP) variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution. Results: We find greater population structure than has been previously reported ...


The Prospects For Sequencing The Western Corn Rootworm Genome, Nicholas J. Miller, S. Richards, Thomas W. Sappington 2010 Iowa State University

The Prospects For Sequencing The Western Corn Rootworm Genome, Nicholas J. Miller, S. Richards, Thomas W. Sappington

Entomology Publications

Historically, obtaining the complete sequence of eukaryotic genomes has been an expensive and complex task. For this reason, efforts to sequence insect genomes have largely been confined to model organisms, species that are important to human health and representative species from a few insect orders. This situation is set to change as a number of ‘next generation’ sequencing technologies are making large-scale DNA sequencing both affordable and accessible. Sequencing the genome of the western corn rootworm, Diabrotica virgifera virgifera, is likely to become a realistic proposition within the next 2 years. In the meantime, there is an active community of ...


Clonal Spread Of Methicillin-Resistant Staphylococcus Pseudintermedius In Europe And North America: An International Multicentre Study, V Perreten, K Kadlec, S Schwarz, U Grönlund Andersson, M Finn, C Greko, A Moodley, Stephen Kania, L Frank, D Demis, A Franco, M Iurescia, A Battisti, B Duim, J Wagenaar, E van Duijkeren, J Weese, J Fitzgerald, A Rossano, L Guardabassi 2010 University of Tennessee - Knoxville

Clonal Spread Of Methicillin-Resistant Staphylococcus Pseudintermedius In Europe And North America: An International Multicentre Study, V Perreten, K Kadlec, S Schwarz, U Grönlund Andersson, M Finn, C Greko, A Moodley, Stephen Kania, L Frank, D Demis, A Franco, M Iurescia, A Battisti, B Duim, J Wagenaar, E Van Duijkeren, J Weese, J Fitzgerald, A Rossano, L Guardabassi

Stephen A Kania

OBJECTIVES: The aim of this study was to determine the phenotypic and genotypic resistance profiles of methicillin-resistant Staphylococcus pseudintermedius (MRSP) and to examine the clonal distribution in Europe and North America. METHODS: A total of 103 MRSP isolates from dogs isolated from several countries in Europe, the USA and Canada were characterized. Isolates were identified by PCR-restriction fragment length polymorphism (RFLP), antimicrobial susceptibility was determined by broth dilution or gradient diffusion, and antimicrobial resistance genes were detected using a microarray. Genetic diversity was assessed by multilocus sequence typing (MLST), PFGE and spa typing. Staphylococcal cassette chromosome mec (SCCmec) elements were ...


Chippeakanno: A Bioconductor Package To Annotate Chip-Seq And Chip-Chip Data, Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Herve Pages, Simon M. Lin, David S. Lapointe, Michael R. Green 2010 University of Massachusetts Medical School

Chippeakanno: A Bioconductor Package To Annotate Chip-Seq And Chip-Chip Data, Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Herve Pages, Simon M. Lin, David S. Lapointe, Michael R. Green

Open Access Articles

BACKGROUND: Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identification of DNA-binding protein target sites. A number of algorithms have been developed in parallel that allow identification of binding sites from ChIP-seq or ChIP-chip datasets and subsequent visualization in the University of California Santa Cruz (UCSC) Genome Browser as custom annotation tracks. However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome.

RESULTS: We have developed ...


A Brain-Specific Cytochrome P450 Responsible For The Majority Of Deltamethrin Resistance In The Qtc279 Strain Of Tribolium Castaneum, Fang Zhu, R. Parthasarathy, Hua Bai, Katharina Woithe, Martin Kaussmann, Ralf Nauen, Douglas A. Harrison, Subba R. Palli 2010 University of Kentucky

A Brain-Specific Cytochrome P450 Responsible For The Majority Of Deltamethrin Resistance In The Qtc279 Strain Of Tribolium Castaneum, Fang Zhu, R. Parthasarathy, Hua Bai, Katharina Woithe, Martin Kaussmann, Ralf Nauen, Douglas A. Harrison, Subba R. Palli

Entomology Faculty Publications

Cytochrome P450-mediated detoxification is one of the most important mechanisms involved in insecticide resistance. However, the molecular basis of this mechanism and the physiological functions of P450s associated with insecticide resistance remain largely unknown. Here, we exploited the functional genomics and reverse genetic approaches to identify and characterize a P450 gene responsible for the majority of deltamethrin resistance observed in the QTC279 strain of Tribolium castaneum. We used recently completed whole-genome sequence of T. castaneum to prepare custom microarrays and identified a P450 gene, CYP6BQ9, which showed more than a 200-fold higher expression in the deltamethrin-resistant QTC279 strain when compared ...


A New Tumor Suppressor Gene Candidate Regulated By The Non-Coding Rna Pca3 In Human Prostate Cancer, Alessandro K. Lee 2010 University of Texas Graduate School of Biomedical Sciences at Houston

A New Tumor Suppressor Gene Candidate Regulated By The Non-Coding Rna Pca3 In Human Prostate Cancer, Alessandro K. Lee

UT GSBS Dissertations and Theses (Open Access)

Prostate cancer is the second leading cause of cancer-related death and the most common non-skin cancer in men in the USA. Considerable advancements in the practice of medicine have allowed a significant improvement in the diagnosis and treatment of this disease and, in recent years, both incidence and mortality rates have been slightly declining. However, it is still estimated that 1 man in 6 will be diagnosed with prostate cancer during his lifetime, and 1 man in 35 will die of the disease.

In order to identify novel strategies and effective therapeutic approaches in the fight against prostate cancer, it ...


A Systems Genetics Approach To The Characterization Of Differential Low Dose Radiation Responses In Bxd Recombinant Inbred Mice, Rachel Marie Lynch 2010 University of Tennessee, Knoxville

A Systems Genetics Approach To The Characterization Of Differential Low Dose Radiation Responses In Bxd Recombinant Inbred Mice, Rachel Marie Lynch

Doctoral Dissertations

High doses of radiation (HDR) are clearly detrimental to human health, but relatively little is known about the health consequences following exposure to low doses of radiation (LDR, <10cGy). Understanding the risks associated with LDR is of great importance to the general public due to the recent dramatic increase in diagnostic radiological imaging. While HDR clearly suppress immune function, there is evidence that LDR can be immunostimulatory. Within the organism, defining the consequences of LDR is further complicated by the impact of genetic background, particularly in systems such as the immune system for which both radiosensitivity and genetic effects are profound.

We addressed the issue of genetic susceptibility to LDR using the immune system as a target system and treated the LDR response as a complex trait analyzed using a systems genetics framework. Using the BXD recombinant inbred strain mouse panel as a genetic reference population allowed us to address the radiation response within the context of natural genetic variation. Our overarching hypothesis is that, within a population, the immunological effects of LDR ...


Metagenomes From High-Temperature Chemotrophic Systems Reveal Geochemical Controls On Microbial Community Structure And Function, William P. Inskeep, Douglas B. Rusch, Zackary J. Jay, Markus J. Herrgard, Mark A. Kozubal, Toby H. Richardson, Richard E. Macur, Natsuko Hamamura, Ryan deM. Jennings, Bruce W. Fouke, Anna-Louise Reysenbach, Frank Roberto, Mark Young, Ariel Schwartz, Eric S. Boyd, Jonathan H. Badger, Eric J. Mathur, Alice C. Ortmann, Mary Bateson, Gill Geesey 2010 Montana State University - Bozeman

Metagenomes From High-Temperature Chemotrophic Systems Reveal Geochemical Controls On Microbial Community Structure And Function, William P. Inskeep, Douglas B. Rusch, Zackary J. Jay, Markus J. Herrgard, Mark A. Kozubal, Toby H. Richardson, Richard E. Macur, Natsuko Hamamura, Ryan Dem. Jennings, Bruce W. Fouke, Anna-Louise Reysenbach, Frank Roberto, Mark Young, Ariel Schwartz, Eric S. Boyd, Jonathan H. Badger, Eric J. Mathur, Alice C. Ortmann, Mary Bateson, Gill Geesey

Biology Faculty Publications and Presentations

The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14-15,000 Sanger reads per site) was obtained for five hightemperature (>65°C) chemotrophic microbial communities sampled ...


Identification Of Functional Modules That Correlate With Phenotypic Difference: The Influence Of Network Topology, Jui-Hung Hung, Troy W. Whitfield, Tun-Hsiang Yang, Zhenjun Hu, Zhiping Weng, Charles Delisi 2010 Boston University

Identification Of Functional Modules That Correlate With Phenotypic Difference: The Influence Of Network Topology, Jui-Hung Hung, Troy W. Whitfield, Tun-Hsiang Yang, Zhenjun Hu, Zhiping Weng, Charles Delisi

Open Access Articles

One of the important challenges to post-genomic biology is relating observed phenotypic alterations to the underlying collective alterations in genes. Current inferential methods, however, invariably omit large bodies of information on the relationships between genes. We present a method that takes account of such information - expressed in terms of the topology of a correlation network - and we apply the method in the context of current procedures for gene set enrichment analysis.


Reconstructability Analysis As A Tool For Identifying Gene-Gene Interactions In Studies Of Human Diseases, Stephen Shervais, Patricia L. Kramer, Shawn K. Westaway, Nancy J. Cox, Martin Zwick 2010 Eastern Washington University

Reconstructability Analysis As A Tool For Identifying Gene-Gene Interactions In Studies Of Human Diseases, Stephen Shervais, Patricia L. Kramer, Shawn K. Westaway, Nancy J. Cox, Martin Zwick

Systems Science Faculty Publications and Presentations

There are a number of common human diseases for which the genetic component may include an epistatic interaction of multiple genes. Detecting these interactions with standard statistical tools is difficult because there may be an interaction effect, but minimal or no main effect. Reconstructability analysis (RA) uses Shannon’s information theory to detect relationships between variables in categorical datasets. We applied RA to simulated data for five different models of gene-gene interaction, and find that even with heritability levels as low as 0.008, and with the inclusion of 50 non-associated genes in the dataset, we can identify the interacting ...


Aata Is A Novel Autotransporter And Virulence Factor Of Avian Pathogenic Escherichia Coli, Ganwu Li, Yaping Feng, Subhashinie Kariyawasam, Kelly A. Tivendale, Yvonne Wannemuehler, Fanghong Zhou, Catherine M. Logue, Cathy L. Miller, Lisa K. Nolan 2010 Iowa State University

Aata Is A Novel Autotransporter And Virulence Factor Of Avian Pathogenic Escherichia Coli, Ganwu Li, Yaping Feng, Subhashinie Kariyawasam, Kelly A. Tivendale, Yvonne Wannemuehler, Fanghong Zhou, Catherine M. Logue, Cathy L. Miller, Lisa K. Nolan

Veterinary Microbiology and Preventive Medicine Publications

Autotransporters (AT) are widespread in Gram-negative bacteria, and many of them are involved in virulence. An open reading frame (APECO1_O1CoBM96) encoding a novel AT was located in the pathogenicity island of avian pathogenicEscherichia coli (APEC) O1's virulence plasmid, pAPEC-O1-ColBM. This 3.5-kb APEC autotransporter gene (aatA) is predicted to encode a 123.7-kDa protein with a 25-amino-acid signal peptide, an 857-amino-acid passenger domain, and a 284-amino-acid β domain. The three-dimensional structure of AatA was also predicted by the threading method using the I-TASSER online server and then was refined using four-body contact potentials. Molecular analysis of AatA revealed ...


Sequence Analysis And Characterization Of A Transferable Hybrid Plasmid Encoding Multidrug Resistance And Enabling Zoonotic Potential For Extraintestinal Escherichia Coli, Timothy J. Johnson, Dianna Jordan, Subhashinie Kariyawasam, Adam L. Stell, Nathan P. Bell, Yvonne Wannemuehler, Claudia Fernández Alarcón, Ganwu Li, Kelly A. Tivendale, Catherine M. Logue, Lisa K. Nolan 2010 Iowa State University

Sequence Analysis And Characterization Of A Transferable Hybrid Plasmid Encoding Multidrug Resistance And Enabling Zoonotic Potential For Extraintestinal Escherichia Coli, Timothy J. Johnson, Dianna Jordan, Subhashinie Kariyawasam, Adam L. Stell, Nathan P. Bell, Yvonne Wannemuehler, Claudia Fernández Alarcón, Ganwu Li, Kelly A. Tivendale, Catherine M. Logue, Lisa K. Nolan

Veterinary Microbiology and Preventive Medicine Publications

ColV plasmids of extraintestinal pathogenic Escherichia coli (ExPEC) encode a variety of fitness and virulence factors and have long been associated with septicemia and avian colibacillosis. These plasmids are found significantly more often in ExPEC, including ExPEC associated with human neonatal meningitis and avian colibacillosis, than in commensal E. coli. Here we describe pAPEC-O103-ColBM, a hybrid RepFIIA/FIB plasmid harboring components of the ColV pathogenicity island and a multidrug resistance (MDR)-encoding island. This plasmid is mobilizable and confers the ability to cause septicemia in chickens, the ability to cause bacteremia resulting in meningitis in the rat model of human ...


Identifying Protein Complexes From Interaction Networks Based On Clique Percolation And Distance Restriction, Jianxin Wang, Binbin Liu, Min Li, Yi Pan 2010 Georgia State University

Identifying Protein Complexes From Interaction Networks Based On Clique Percolation And Distance Restriction, Jianxin Wang, Binbin Liu, Min Li, Yi Pan

Computer Science Faculty Publications

Background: Identification of protein complexes in large interaction networks is crucial to understand principles of cellular organization and predict protein functions, which is one of the most important issues in the post-genomic era. Each protein might be subordinate multiple protein complexes in the real protein-protein interaction networks.Identifying overlapping protein complexes from protein-protein interaction networks is a considerable research topic.

Result: As an effective algorithm in identifying overlapping module structures, clique percolation method (CPM) has a wide range of application in social networks and biological networks. However, the recognition accuracy of algorithm CPM is lowly. Furthermore, algorithm CPM is unfit ...


Wavelet-Based Functional Linear Mixed Models: An Application To Measurement Error–Corrected Distributed Lag Models, Elizabeth J. Malloy, Jeffrey S. Morris, Sara D. Adar, Helen Suh, Diane R. Gold, Brent A. Coull 2010 American University

Wavelet-Based Functional Linear Mixed Models: An Application To Measurement Error–Corrected Distributed Lag Models, Elizabeth J. Malloy, Jeffrey S. Morris, Sara D. Adar, Helen Suh, Diane R. Gold, Brent A. Coull

Jeffrey S. Morris

Frequently, exposure data are measured over time on a grid of discrete values that collectively define a functional observation. In many applications, researchers are interested in using these measurements as covariates to predict a scalar response in a regression setting, with interest focusing on the most biologically relevant time window of exposure. One example is in panel studies of the health effects of particulate matter (PM), where particle levels are measured over time. In such studies, there are many more values of the functional data than observations in the data set so that regularization of the corresponding functional regression coefficient ...


Members’ Discoveries: Fatal Flaws In Cancer Research, Jeffrey S. Morris 2010 The University of Texas M.D. Anderson Cancer Center

Members’ Discoveries: Fatal Flaws In Cancer Research, Jeffrey S. Morris

Jeffrey S. Morris

A recent article published in The Annals of Applied Statistics (AOAS) by two MD Anderson researchers—Keith Baggerly and Kevin Coombes—dissects results from a highly-influential series of medical papers involving genomics-driven personalized cancer therapy, and outlines a series of simple yet fatal flaws that raises serious questions about the veracity of the original results. Having immediate and strong impact, this paper, along with related work, is providing the impetus for new standards of reproducibility in scientific research.


Statistical Contributions To Proteomic Research, Jeffrey S. Morris, Keith A. Baggerly, Howard B. Gutstein, Kevin R. Coombes 2010 The University of Texas M.D. Anderson Cancer Center

Statistical Contributions To Proteomic Research, Jeffrey S. Morris, Keith A. Baggerly, Howard B. Gutstein, Kevin R. Coombes

Jeffrey S. Morris

Proteomic profiling has the potential to impact the diagnosis, prognosis, and treatment of various diseases. A number of different proteomic technologies are available that allow us to look at many proteins at once, and all of them yield complex data that raise significant quantitative challenges. Inadequate attention to these quantitative issues can prevent these studies from achieving their desired goals, and can even lead to invalid results. In this chapter, we describe various ways the involvement of statisticians or other quantitative scientists in the study team can contribute to the success of proteomic research, and we outline some of the ...


Informatics And Statistics For Analyzing 2-D Gel Electrophoresis Images, Andrew W. Dowsey, Jeffrey S. Morris, Howard G. Gutstein, Guang Z. Yang 2010 Imperial College London

Informatics And Statistics For Analyzing 2-D Gel Electrophoresis Images, Andrew W. Dowsey, Jeffrey S. Morris, Howard G. Gutstein, Guang Z. Yang

Jeffrey S. Morris

Whilst recent progress in ‘shotgun’ peptide separation by integrated liquid chromatography and mass spectrometry (LC/MS) has enabled its use as a sensitive analytical technique, proteome coverage and reproducibility is still limited and obtaining enough replicate runs for biomarker discovery is a challenge. For these reasons, recent research demonstrates the continuing need for protein separation by two-dimensional gel electrophoresis (2-DE). However, with traditional 2-DE informatics, the digitized images are reduced to symbolic data though spot detection and quantification before proteins are compared for differential expression by spot matching. Recently, a more robust and automated paradigm has emerged where gels are ...


Digital Commons powered by bepress