Conditional Screening For Ultra-High Dimensional Covariates With Survival Outcomes,
2016
Michigan State University
Conditional Screening For Ultra-High Dimensional Covariates With Survival Outcomes, Hyokyoung Grace Hong, Jian Kang, Yi Li
The University of Michigan Department of Biostatistics Working Paper Series
Identifying important biomarkers that are predictive for cancer patients' prognosis is key in gaining better insights into the biological influences on the disease and has become a critical component of precision medicine. The emergence of large-scale biomedical survival studies, which typically involve excessive number of biomarkers, has brought high demand in designing efficient screening tools for selecting predictive biomarkers. The vast amount of biomarkers defies any existing variable selection methods via regularization. The recently developed variable screening methods, though powerful in many practical setting, fail to incorporate prior information on the importance of each biomarker and are less powerful in …
A Colletotrichum Graminicola Mutant Deficient In The Establishment Of Biotrophy Reveals Early Transcriptional Events In The Maize Anthracnose Disease Interaction,
2016
University of Kentucky
A Colletotrichum Graminicola Mutant Deficient In The Establishment Of Biotrophy Reveals Early Transcriptional Events In The Maize Anthracnose Disease Interaction, Maria F. Torres, Noushin Ghaffari, Ester A. S. Buiate, Neil Moore, Scott Schwartz, Charles D. Johnson, Lisa J. Vaillancourt
Plant Pathology Faculty Publications
Background: Colletotrichum graminicola is a hemibiotrophic fungal pathogen that causes maize anthracnose disease. It progresses through three recognizable phases of pathogenic development in planta: melanized appressoria on the host surface prior to penetration; biotrophy, characterized by intracellular colonization of living host cells; and necrotrophy, characterized by host cell death and symptom development. A “Mixed Effects” Generalized Linear Model (GLM) was developed and applied to an existing Illumina transcriptome dataset, substantially increasing the statistical power of the analysis of C. graminicola gene expression during infection and colonization. Additionally, the in planta transcriptome of the wild-type was compared with that of …
Session D-1: Science And Spaghetti Monsters: Addressing The Ethical Issues And Controversy Related To Genomics And Evolution In The Biology Classroom,
2016
Illinois Mathematics and Science Academy
Session D-1: Science And Spaghetti Monsters: Addressing The Ethical Issues And Controversy Related To Genomics And Evolution In The Biology Classroom, Sarah O'Leary-Driscoll
Professional Learning Day
As science teachers, we may shy away from addressing the controversy surrounding particular topics in our classrooms in order to maintain focus on content. However, the real world context of knowledge is essential, and the performance expectations in the life sciences as outlined in the NGSS state that students should be able to discuss the ethical issues related to genetic modifications and the nature of science. We will discuss ideas for how to address these topics effectively and help our students understand their importance beyond academics in our global community.
Phagephisher: A Pipeline For The Discovery Of Covert Viral Sequences In Complex Genomic Datasets,
2016
Loyola University Chicago
Phagephisher: A Pipeline For The Discovery Of Covert Viral Sequences In Complex Genomic Datasets, Thomas Hatzopoulos, Siobhan C. Watkins, Catherine Putonti
Bioinformatics Faculty Publications
Obtaining meaningful viral information from large sequencing datasets presents unique challenges distinct from prokaryotic and eukaryotic sequencing efforts. The difficulties surrounding this issue can be ascribed in part to the genomic plasticity of viruses themselves as well as the scarcity of existing information in genomic databases. The open-source software PhagePhisher (http://www.putonti-lab.com/phagephisher) has been designed as a simple pipeline to extract relevant information from complex and mixed datasets, and will improve the examination of bacteriophages, viruses, and virally related sequences, in a range of environments. Key aspects of the software include speed and ease of use; PhagePhisher can be used with …
Transcriptional Profile Of Immediate Response To Ionizing Radiation Exposure,
2016
University of Louisville
Transcriptional Profile Of Immediate Response To Ionizing Radiation Exposure, Eric C. Rouchka, Robert M. Flight, Brigitte H. Fasciotto, Rosendo Estrada, John W. Eaton, Phani K. Patibandla, Sabine J. Waigel, Dazhuo Li, John K. Kirtley, Palaniappan Sethu, Robert S. Keynton
Molecular and Cellular Biochemistry Faculty Publications
Astronauts participating in long duration space missions are likely to be exposed to ionizing radiation associated with highly energetic and charged heavy particles. Previously proposed gene biomarkers for radiation exposure include phosphorylated H2A Histone Family, Member X (γH2AX), Tumor Protein 53 (TP53), and Cyclin-Dependent Kinase Inhibitor 1A (CDKN1A). However, transcripts of these genes may not be the most suitable biomarkers for radiation exposure due to a lack of sensitivity or specificity. As part of a larger effort to develop lab-on-a-chip methods for detecting radiation exposure events using blood samples, we designed a dose–course microarray study in order to determine coding …
Bacteriophage Ems9: Preliminary Genomic Description,
2016
Bowling Green State University
Bacteriophage Ems9: Preliminary Genomic Description, Hallie Rae Zimmer
Honors Projects
EMS9 is a bacteriophage that was recently isolated from an Escherichia coli strain present in horse feces. Bacteriophage EMS9 consists of 98,771 base pairs that are organized into 139 predicted open reading frames (ORFs). These predicted genes potentially encode specific bacteriophage proteins. The genomic sequence of bacteriophage EMS9 is arranged intro three groups: early, middle, and late genes. Considerable homology between the ORFs of bacteriophage EMS9 and bacteriophages T5 and H8 exists. All of these bacteriophages are believed to use a rare two-step transfer mechanism to invade host cells. This annotation of the genomic sequence of EMS9 will provide a …
Bioinformatics Comparison Of M. Ruber Mrub_2507 To E. Coli Pdxk/B1636 And M. Ruber Mrub_2888 To E. Coli Pdxh/B1638 To Determine The Orthologous Nature,
2016
Augustana College, Rock Island Illinois
Bioinformatics Comparison Of M. Ruber Mrub_2507 To E. Coli Pdxk/B1636 And M. Ruber Mrub_2888 To E. Coli Pdxh/B1638 To Determine The Orthologous Nature, Adam Bernardi, Dr. Lori 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_2507 and Mrub_2888. We predict that Mrub_2507 encodes the enzyme pyridoxal kinase (DNA coordinates 2555521..2556402), which is in the Vitamin B6 Metabolism pathway (KEGG map number 00750). It catalyzes the conversion of pyridoxine, pyridoxamine, or pyridoxal to pyridoxine 5’-phosphate, pyridoxamine 5’-phosphate, or pyridoxal 5’-phosphate respectively. The E. coli K12 MG1655 ortholog is predicted to be b1636, which has …
Comparing Apples And Oranges?: Next Generation Sequencing And Its Impact On Microbiome Analysis,
2016
Department of Biological Sciences Cork Institute of Technology, Cork, Ireland, APC Microbiome Institute, University College Cork, Cork, Ireland
Comparing Apples And Oranges?: Next Generation Sequencing And Its Impact On Microbiome Analysis, Adam G. Clooney, Fiona Fouhy, Roy D. Sleator, Aisling O'Driscoll, Stanton Catherine, Paul D. Cotter, Marcus J. Claesson
Department of Biological Sciences Publications
Rapid advancements in sequencing technologies along with falling costs present widespread opportunities for microbiome studies across a vast and diverse array of environments. These impressive technological developments have been accompanied by a considerable growth in the number of methodological variables, including sampling, storage, DNA extraction, primer pairs, sequencing technology, chemistry version, read length, insert size, and analysis pipelines, amongst others. This increase in variability threatens to compromise both the reproducibility and the comparability of studies conducted. Here we perform the first reported study comparing both amplicon and shotgun sequencing for the three leading next-generation sequencing technologies. These were applied to …
Meiothermus Ruber Mrub_0976 And Mrub_1641 Share The Same Functions As Escherichia Coli B3940 And B3433 In The Biosynthesis Of Homoserine,
2016
Augustana College, Rock Island Illinois
Meiothermus Ruber Mrub_0976 And Mrub_1641 Share The Same Functions As Escherichia Coli B3940 And B3433 In The Biosynthesis Of Homoserine, Cody Stephans, Dr. Lori 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_0976 and Mrub_1641. We predict that Mrub_0976 encodes the enzyme aspartate kinase (DNA coordinates 964404..965630) which is the 1st step of the homoserine biosynthesispathway (KEGG map number M00018). It catalyzes the conversion L-aspartate to L-asparyl-4-phospate. The E. coli K12 MG1655 ortholog is predicted to be b3940, which has the gene identifier ‘thrA’. We …
Possible Orthologs Of Trpa And Trpb Genes Between E. Coli (B1260 And B1261) And M. Ruber (Mrub_1512 And Mrub_1511),
2016
Augustana College, Rock Island Illinois
Possible Orthologs Of Trpa And Trpb Genes Between E. Coli (B1260 And B1261) And M. Ruber (Mrub_1512 And Mrub_1511), John J. Stenger, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
Mrub_1512 encodes the enzyme tryptophan A (DNA coordinates 1544300..1545091), which is the 6th step of the Tryptophan Biosynthesis pathway (KEGG map number 00400). It catalyzes the conversion of Chorismate to L-Tryptophan. The E. coli K12 MG1655 ortholog is predicted to be b1260, which has the gene identifier trpA. We predict that Mrub_1512 (DNA coordinates 1544300..1545091) is a alpha subunit of the Tryptophan Synthase (KEGG map number 00400). Mrub_1511 encodes the enzyme tryptophan B (DNA coordinates 1543083..1544303), which is the 7th step of the Tryptophan Biosynthesis pathway (KEGG map number 00400). It catalyzes the conversion of Chorismate to L-Tryptophan. The E. …
Mrub_2765 Is The Version Of E. Coli Fabz In Meiothermus Ruber, While Mrub_0266 Is The Version Of E. Coli Fabi In Meiothermus Ruber,
2016
Augustana College, Rock Island Illinois
Mrub_2765 Is The Version Of E. Coli Fabz In Meiothermus Ruber, While Mrub_0266 Is The Version Of E. Coli Fabi In Meiothermus Ruber, Amanda M. Narkis, Dr. Lori 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_2765 and Mrub_0266. We predict that Mrub_2765 encodes the enzyme β-hydroxyacyl-Acyl carrier protein (ACP) dehydratase (DNA coordinates 2805770..2806213 on the reverse strand), which is the 3rd step of the fatty acid elongation pathway (KEGG map number 00780). It catalyzes the conversion of (3R)-3-hydroxyacyl-[ACP] to trans-2-enoyl-[ACP]. The E. coli K12 MG1655 ortholog is predicted to be …
Pyruvate Metabolism In M. Ruber When Compared To E. Coli,
2016
Augustana College, Rock Island Illinois
Pyruvate Metabolism In M. Ruber When Compared To E. Coli, Amanda M. Johnson, Dr. Lori 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_0476, Mrub_1516, Mrub_1517, Mrub_0477, and Mrub_2322. We predict that Mrub_0476, Mrub_1516, and Mrub_1517 (DNA coordinates 461643..464366, 1548957..1549955, 1549952..1550986, respectively) are a paralogous a subunit of the pyruvate dehydrogenase complex E1(KEGG map number 00620). We predict that Mrub_0477 and Mrub_2322 (DNA coordinates 464402..465697 and 2371690..2373090, respectively) are a paralogous subunit of the pyruvate dehydrogenase complex …
A Bioinformatics Study On Whether Or Not Mrub_2763 Gene In M. Ruber Is Similar To The Lpxb Gene In E. Coli And If Mrub_2768 Is Similar To The Lpxd Gene In E. Coli.,
2016
Augustana College, Rock Island Illinois
A Bioinformatics Study On Whether Or Not Mrub_2763 Gene In M. Ruber Is Similar To The Lpxb Gene In E. Coli And If Mrub_2768 Is Similar To The Lpxd Gene In E. Coli., Frank J. Habura, Dr. Lori 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 gene Mrub_2768 and Mrub_2763. We predict that Mrub_2768 (DNA coordinates 2808186..2809178 on the reverse strand) encodes the enzyme UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase (LpxD), which is the third step of the Lipopolysaccharide biosynthesis pathway (KEGG map number 00540). It catalyzes the conversion of UDP-3-O-(3-hydroxymyristoyl)-α-D-glucosamine + a(3R)-3-hydroxymyristoyl-[acp] → a holo-[acyl-carrier protein] + UDP-2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-α-D-glucosamine. The E. coli K12 MG1655 ortholog is predicted to be b0179, which …
Comparing Meiothermus Ruber And Myxococcus Xanthus In The Purine Metabolism Pathway,
2016
Augustana College - Rock Island
Comparing Meiothermus Ruber And Myxococcus Xanthus In The Purine Metabolism Pathway, Linnea J. Ritchie, Dr. Lori 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. I investigated the biological functions of Mrub_1053 Mrub_2281 and Mrub_2299. I predicted that Mrub_1053 and Mrub_2281 (DNA coordinates 1053364..1054359 on the forward strand and 2333172..2334113 on the forward strand respectively) encodes the enzyme phosphoribose-1-pyrophosphate synthetase (PRS) which is the first step of the purine synthesis pathway (KEGG). I also predicted that Mrub_2299 (DNA coordinates: 2352378..2353775 on the forward strand) encodes for Phosphoribosyl pyrophosphate (PRPP) amidotransferase, which is …
Valine Biosynthesis: Mrub_2994 Is Orthologous To E. Coli B3770 And Mrub_1844 Is Orthologous To E. Coli B3771,
2016
Augustana College, Rock Island Illinois
Valine Biosynthesis: Mrub_2994 Is Orthologous To E. Coli B3770 And Mrub_1844 Is Orthologous To E. Coli B3771, Bennett A. Hartmann, Dr. Lori 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_2994 and Mrub_1844. We predict that Mrub_1884 encodes the enzyme dihydroxy-acid dehydratase (DNA coordinates 1901362..1903026 on the forward strand), which is the third step of the valine biosynthesis pathway (KEGG map number 00290). It catalyzes the conversion of 2,3-dihydroxy-3methylbutanoate to 3-methyl-2-oxobutanoate. The E. coli K12 MG1655 ortholog is predicted to be b3771, which has the gene identifier ilvD. …
Bioinformatic Comparison Of Genes In The Leucine Biosynthesis Pathway Of Escherichia Coli To Meiothermus Ruber,
2016
Augustana College, Rock Island Illinois
Bioinformatic Comparison Of Genes In The Leucine Biosynthesis Pathway Of Escherichia Coli To Meiothermus Ruber, Isaac D. Schmied, Benjamin T. Ryan, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
We predict that Mrub_1905 and Mrub_1906 encode the enzyme 2-isopropylmalate synthase (Mrub_1906 DNA coordinates complement(1965044..1966603) Mrub_1905 DNA coordinates complement(1963455..1965041)), which is the first step of the leucine biosynthesis pathway (KEGG map number 00290). It catalyzes the conversion of (2S)-2-isopropylmalate to 2-isopropylmaleate. The E. coli K12 MG1655 ortholog is predicted to be b0074, which has the gene identifier leuA. We predict that Mrub_1846 encodes the enzyme 3-isopropylmalate dehydrogenase (DNA coordinates complement(1903909..1904961)), which is the third step of the leucine biosynthesis pathway (KEGG map number 00290). It catalyzes the conversion of (2R,3S)-3-isopropylmalate to (2S)-2-isopropyl-3-oxosuccinate. The E. coli K12 MG1655 ortholog is predicted …
Riboflavin Metabolism: A Study To See If Mrub_1256 Is Orthologous To E. Coli B0415, And If Mrub_1254 Is Orthologous To E. Coli B1662,
2016
Augustana College, Rock Island Illinois
Riboflavin Metabolism: A Study To See If Mrub_1256 Is Orthologous To E. Coli B0415, And If Mrub_1254 Is Orthologous To E. Coli B1662, Anish Sora Reddy, Dr. Lori 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_1256 and Mrub_1254. We predict that Mrub_1256 encodes the enzyme 6,7-dimethyl-8-ribityllumazine synthase (Dna Coordinates 1282509..1282982 forward strand), which is part of the Riboflavin Metabolism pathway (KEGG map number 00740). It catalyzes the conversion of 3,4-Dihydroxy-2-butanone-4-phosphate or 5-amino-6-ribityl-aminouracil to Quinone. The E. coli K12 MG1655 ortholog is predicted to be E. coli b0415, which has the gene identifier …
The Meiothermus Ruber Mrub_2572 Gene Is An Ortholog Of The Escherichia Coli Pyre B3642 Gene And The Meiothermus Ruber Mrub_2071 Gene Is An Ortholog Of The Escherichia Coli Pyrf B1281 Gene,
2016
Augustana College, Rock Island Illinois
The Meiothermus Ruber Mrub_2572 Gene Is An Ortholog Of The Escherichia Coli Pyre B3642 Gene And The Meiothermus Ruber Mrub_2071 Gene Is An Ortholog Of The Escherichia Coli Pyrf B1281 Gene, Cale J. Mccormick, Dr. Lori 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_2572 and Mrub_2071. We predict that Mrub_2572 encodes the enzyme orotate phosphoribosyltransferase (DNA coordinates 2617545..2618096 on the forward strand), which is the 5th step of the UMP biosynthesis pathway (KEGG map number 00240). It catalyzes the conversion of orotate + PRPP to orotidine 5’-phosphate. The E. coli K12 MG1655 ortholog is predicted to be b3642, which has the gene …
Bioinformatics Indicates That Meiothermus Ruber Genes Mrub_1710 And Mrub_1712 Are Homologs Of The Escherichia Coli Genes B2903 (P-Protein; Glycine Dehydrogenase) And B2905 (T-Protein; Aminomethyltransferase), Respectively,
2016
Augustana College, Rock Island Illinois
Bioinformatics Indicates That Meiothermus Ruber Genes Mrub_1710 And Mrub_1712 Are Homologs Of The Escherichia Coli Genes B2903 (P-Protein; Glycine Dehydrogenase) And B2905 (T-Protein; Aminomethyltransferase), Respectively, Malory J. Groen, Dr. Lori 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_1710 and Mrub_1712. We predict that Mrub_1710 encodes the enzyme glycine dehydrogenase (DNA coordinates 3046168.. 3049041 on the reverse strand), which is the first step of the glycine degradation pathway (KEGG map number 00260). It catalyzes the conversion of glycine to S-Amino-methyldihydro-lipoylprotein. The E. coli K12 MG1655 ortholog is predicted to be b2903, which has the gene identifier gcvP. …
Mrub_0258 Gene Is An Ortholog Of The B4226 Gene (Ppa) Found In Escherichia Coli; Mrub_1198 Gene Is An Ortholog Of The B2501 Gene (Ppk) Found In Escherichia Coli;,
2016
Augustana College, Rock Island Illinois
Mrub_0258 Gene Is An Ortholog Of The B4226 Gene (Ppa) Found In Escherichia Coli; Mrub_1198 Gene Is An Ortholog Of The B2501 Gene (Ppk) Found In Escherichia Coli;, Brandon M. Wills, Dr. Lori 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_0258 and Mrub_1198. We predict that Mrub_0258 encodes the enzyme inorganic pyrophosphatase (226403..226942), which is indirectly involved with the oxidative phosphorylation pathway (KEGG map number 00190). It catalyzes the conversion of the diphosphate ions made by Mrub_1198 into two orthophosphate ions, which can then be used by ATP synthase to produce energy. The E. coli K12 MG1655 ortholog is predicted …
