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Full-Text Articles in Life Sciences
Winner's Curse Correction And Variable Thresholding Improve Performance Of Polygenic Risk Modeling Based On Genome-Wide Association Study Summary-Level Data, Jianxin Shi, Ju-Hyun Park, Jubao Duan, Sonja T. Berndt, Winton Moy, Kai Yu, Lei Song, William Wheeler, Xing Hua, Debra Silverman, Montserrat Garcia-Closas, Chao Agnes Hsiung, Jonine D. Figueroa, Victoria K. Cortessis, Nuria Malats, Margaret R. Karagas
Winner's Curse Correction And Variable Thresholding Improve Performance Of Polygenic Risk Modeling Based On Genome-Wide Association Study Summary-Level Data, Jianxin Shi, Ju-Hyun Park, Jubao Duan, Sonja T. Berndt, Winton Moy, Kai Yu, Lei Song, William Wheeler, Xing Hua, Debra Silverman, Montserrat Garcia-Closas, Chao Agnes Hsiung, Jonine D. Figueroa, Victoria K. Cortessis, Nuria Malats, Margaret R. Karagas
Dartmouth Scholarship
Recent heritability analyses have indicated that genome-wide association studies (GWAS) have the potential to improve genetic risk prediction for complex diseases based on polygenic risk score (PRS), a simple modelling technique that can be implemented using summary-level data from the discovery samples. We herein propose modifications to improve the performance of PRS. We introduce threshold-dependent winner’s-curse adjustments for marginal association coefficients that are used to weight the single-nucleotide polymorphisms (SNPs) in PRS. Further, as a way to incorporate external functional/annotation knowledge that could identify subsets of SNPs highly enriched for associations, we propose variable thresholds for SNPs selection. We applied …
Promises And Challenges Of Eco-Physiological Genomics In The Field: Tests Of Drought Responses In Switchgrass. Plant Physiology, John T. Lovell, Eugene V. Shakirov, Scott Schwartz, David B. Lowry, Michael J. Aspinwall, Samuel H. Taylor, Jason Bonnette, Juan Diego Palacio-Mejia, Christine V. Hawkes, Philip A. Fay, Thomas E. Juenger
Promises And Challenges Of Eco-Physiological Genomics In The Field: Tests Of Drought Responses In Switchgrass. Plant Physiology, John T. Lovell, Eugene V. Shakirov, Scott Schwartz, David B. Lowry, Michael J. Aspinwall, Samuel H. Taylor, Jason Bonnette, Juan Diego Palacio-Mejia, Christine V. Hawkes, Philip A. Fay, Thomas E. Juenger
Biological Sciences Faculty Research
Identifying the physiological and genetic basis of stress tolerance in plants has proven to be critical to understanding adaptation in both agricultural and natural systems. However, many discoveries were initially made in the controlled conditions of greenhouses or laboratories, not in the field. To test the comparability of drought responses across field and greenhouse environments, we undertook three independent experiments using the switchgrass reference genotype Alamo AP13. We analyzed physiological and gene expression variation across four locations, two sampling times, and three years. Relatively similar physiological responses and expression coefficients of variation across experiments masked highly dissimilar gene expression responses …
Genome-Wide Annotation, Identification, And Global Transcriptomic Analysis Of Regulatory Or Small Rna Gene Expression In Staphylococcus Aureus, Ronan K. Carroll, Andy Weiss, William H. Broach, Richard E Wiemels, Austin B. Mogen, Kelly C. Rice, Lindsey N. Shaw
Genome-Wide Annotation, Identification, And Global Transcriptomic Analysis Of Regulatory Or Small Rna Gene Expression In Staphylococcus Aureus, Ronan K. Carroll, Andy Weiss, William H. Broach, Richard E Wiemels, Austin B. Mogen, Kelly C. Rice, Lindsey N. Shaw
Molecular Biosciences Faculty Publications
In Staphylococcus aureus, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in S. aureus, we generated updated GenBank files for three commonly used S. aureus strains (MRSA252, NCTC 8325, and USA300), in which we added annotations for >260 previously identified sRNAs. These files, the first to include genome-wide annotation of sRNAs in S. aureus, were …
Can The Insertion Of An E. Coli Shine-Dalgarno Sequence Upstream Of M. Ruber Proa Of The Proba Operon Enhance Its Expression, As Measured By A Complementation Assay Using E. Coli Null Strains?, Matthew D. Murphy, Dr. Lori Scott
Can The Insertion Of An E. Coli Shine-Dalgarno Sequence Upstream Of M. Ruber Proa Of The Proba Operon Enhance Its Expression, As Measured By A Complementation Assay Using E. Coli Null Strains?, Matthew D. Murphy, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
The process by which the thermophilic bacteria Meiothermus ruber (M. ruber) synthesizes the amino acid proline is examined in this paper. In the well-studied E. coli system, proline biosynthesis involves three enzymes ProA, ProB and ProC; proA and proB form the proBA operon and both proA and proB possess an upstream Shine-Delgarno sequence; and ProB is functionally dependent on ProA as components of a ProBA complex. In previous studies in Dr. Scott’s lab, the putative M. ruber proA (locus tag Mrub1079), proB (Mrub1080) and proC (Mrub1345) genes were cloned into the pKt1 expression vector, transformed into the corresponding …
Tick Genome Assembled: New Opportunities For Research On Tick-Host-Pathogen Interactions, Jose De La Fuente, Robert M. Waterhouse, Daniel E. Sonenshine, R. Michael Roe, Jose M. Ribeiro, David B. Sattelle, Catherine A. Hill
Tick Genome Assembled: New Opportunities For Research On Tick-Host-Pathogen Interactions, Jose De La Fuente, Robert M. Waterhouse, Daniel E. Sonenshine, R. Michael Roe, Jose M. Ribeiro, David B. Sattelle, Catherine A. Hill
Biological Sciences Faculty Publications
As tick-borne diseases are on the rise, an international effort resulted in the sequence and assembly of the first genome of a tick vector. This result promotes research on comparative, functional and evolutionary genomics and the study of tick-host-pathogen interactions to improve human, animal and ecosystem health on a global scale.