Search results | J. Murrey Atkins Library

Title: A comparison of transgenic and wild type soybean seeds : analysis of transcriptome profiles using RNA-Seq
Author: Loraine, Ann, Lambirth, Kevin C., Whaley, Adam M., Piller, Kenneth J.
Date Created: 2015
Subjects--Topical: Gene expression, Biotechnology
Description: Background: Soybean (Glycine max) has been bred for thousands of years to produce seeds rich in protein for human and animal consumption, making them an appealing bioreactor for producing valuable recombinant proteins at high levels. However, the ...

Title: A novel machine learning framework for comparison of viral COVID-19–related Sina Weibo and Twitter posts : workflow development and content analysis
Author: Chen, Shi, Zhou, Lina, Song, Yunya, Xu, Qian, Wang, Ping, Wang, Kanlun, Ge, Yaorong, Janies, Daniel
Date Created: 2021
Subjects--Topical: COVID-19 (Disease), Twitter (Firm), Social media, Machine learning
Description: Background: Social media plays a critical role in health communications, especially during global health emergencies such as the current COVID-19 pandemic. However, there is a lack of a universal analytical framework to extract, quantify, and comp...

Title: A subterminal growth zone at arm tip likely underlies life-long indeterminate growth in brittle stars
Author: Janies, Daniel, Machado, Denis Jacob, Reid, Robert, Kofsky, Janice
Date Created: 2022
Subjects--Topical: Genomics, Biology
Description: Background Echinoderms are a phylum of marine invertebrates with close phylogenetic relationships to chordates. Many members of the phylum Echinodermata are capable of extensive post-traumatic regeneration and life-long indeterminate growth. Diffe...

Title: A virtual pebble game to ensemble average graph rigidity
Author: Jacobs, Donald J., Gonzalez, Luis C., Wang, Hui, Livesay, Dennis R.
Date Created: 2015
Subjects--Topical: Probabilities, Proteins
Description: Background: The body-bar Pebble Game (PG) algorithm is commonly used to calculate network rigidity properties in proteins and polymeric materials. To account for fluctuating interactions such as hydrogen bonds, an ensemble of constraint topologies...

Title: Active Notch signaling is required for arm regeneration in a brittle star
Author: Janies, Daniel, Machado, Denis Jacob, Reid, Robert
Date Created: 2020
Subjects--Topical: Genomics, Biology
Description: Cell signaling pathways play key roles in coordinating cellular events in development. The Notch signaling pathway is highly conserved across all multicellular animals and is known to coordinate a multitude of diverse cellular events, including pr...

Title: An updated synthesis of and outstanding questions in the olfactory and vomeronasal systems in bats : genetics asks questions only anatomy can answer
Author: Yohe, Laurel R., Krell, Nicholas T.
Date Created: 2023
Subjects--Topical: Bats, Ecology
Description: The extensive diversity observed in bat nasal chemosensory systems has been well-documented at the histological level. Understanding how this diversity evolved and developing hypotheses as to why particular patterns exist require a phylogenetic pe...

Title: Analysis of pollen-specific alternative splicing in Arabidopsis thaliana via semi-quantitative PCR
Author: Loraine, Ann, Estrada, April, Freese, Nowlan H., Blakley, Ivory
Date Created: 2015
Subjects--Topical: Bioinformatics, Pollen, Nucleic acids
Description: Alternative splicing enables a single gene to produce multiple mRNA isoforms by varying splice site selection. In animals, alternative splicing of mRNA isoforms between cell types is widespread and supports cellular differentiation. In plants, at ...

Title: Arabidopsis bioinformatics resources : the current state, challenges, and priorities for the future
Author: Loraine, Ann, Doherty, Colleen, Friesner, Joanna, Gregory, Brian
Date Created: 2019
Subjects--Topical: Bioinformatics, Arabidopsis thaliana
Description: Effective research, education, and outreach efforts by the Arabidopsis thaliana community, as well as other scientific communities that depend on Arabidopsis resources, depend vitally on easily available and publicly-shared resources. These resour...

Title: Calculating ensemble averaged descriptions of protein rigidity without sampling
Author: Jacobs, Donald J., Gonzalez, Luis C., Wang, Hui, Livesay, Dennis R.
Date Created: 2012
Subjects--Topical: Biology, Proteins
Description: Previous works have demonstrated that protein rigidity is related to thermodynamic stability, especially under conditions that favor formation of native structure. Mechanical network rigidity properties of a single conformation are efficiently cal...

Title: Cell-specific cis-natural antisense transcripts (cis-NATs) in the sperm and the pollen vegetative cells of Arabidopsis thaliana
Author: Loraine, Ann, Qin, Peng, McCormick, Sheila
Date Created: 2018
Subjects--Topical: Gene expression, Pollen
Description: Background: cis-NATs (cis-natural antisense transcripts ) are transcribed from opposite strands of adjacent genes and have been shown to regulate gene expression by generating small RNAs from the overlapping region. cis-NATs are important for plan...

Title: Changes in Lysozyme flexibility upon mutation are frequent, large and long-ranged
Author: Jacobs, Donald J., Verma, Deeptak, Livesay, Dennis R.
Date Created: 2012
Subjects--Topical: Bioinformatics, Statistics
Description: We investigate changes in human c-type lysozyme flexibility upon mutation via a Distance Constraint Model, which gives a statistical mechanical treatment of network rigidity. Specifically, two dynamical metrics are tracked. Changes in flexibility ...

Title: Changing of the genomic pattern of Salmonella enteritidis strains isolated in Brazil over a 48 year-period revealed by whole genome SNP analyses
Author: Janies, Daniel
Date Created: 2018
Subjects--Topical: Genomics, Salmonella
Description: Salmonella Enteritidis became the main serovar isolated from gastroenteritis cases in Brazil after the 90's. In this study we used whole genome sequence analysis to determine the phylogenetic relationships among a collection of strains isolated in...

Title: Characterization of the cytokinin-responsive transcriptome in rice
Author: Loraine, Ann, Raines, Tracy, Blakley, Ivory, Kieber, Joseph J.
Date Created: 2016
Subjects--Topical: Gene expression, Cytokinins
Description: Background: Cytokinin activates transcriptional cascades important for development and the responses to biotic and abiotic stresses. Most of what is known regarding cytokinin-regulated gene expression comes from studies of the dicotyledonous plant...

Title: Commonality of functional annotation : a method for prioritization of candidate genes from genome-wide linkage studies
Author: Loraine, Ann, Shriner, Daniel, Baye, Tesfaye M., Padilla, Miguel A.
Date Created: 2008
Subjects--Topical: Gene expression, Alzheimer's disease
Description: Linkage studies of complex traits frequently yield multiple linkage regions covering hundreds of genes. Testing each candidate gene from every region is prohibitively expensive and computational methods that simplify this process would benefit gen...

Title: Comparative phylogenetic studies on Schistosoma japonicum and its snail intermediate host Oncomelania hupensis : origins, dispersal and coevolution
Author: Attwood, Stephen W., Ibaraki, Motomu, Saitoh, Yasuhide, Janies, Daniel
Subjects--Topical: Parasites, Coevolution, Public health
Description: Schistosoma japonicum causes major public health problems in China and the Philippines; this parasite, which is transmitted by freshwater snails of the species Oncomelania hupen- sis, causes the disease intestinal schistosomiasis in humans and cat...

Title: ComparePD : improving protein–DNA complex model comparison with hydrogen bond energy-based metrics
Author: Guo, Jun-tao, Malik, Fareeha Kanwal
Date Created: 2023
Subjects--Topical: DNA, Nucleic acids
Description: Computational modeling of protein–DNA complex structures has important implications in biomedical applications such as structure-based, computer aided drug design. A key step in developing methods for accurate modeling of protein–DNA complexes is ...

Title: Conformational entropy of an ideal cross-linking polymer chain
Author: Jacobs, Donald J., Vorov, Oleg, Livesay, Dennis R.
Date Created: 2008
Subjects--Topical: Proteins, Entropy
Description: We present a novel analytical method to calculate conformational entropy of ideal cross-linking polymers from the configuration integral by employing a Mayer series expansion. Mayer-functions describing chemical bonds within the chain and for cros...

Title: Consistency analysis of redundant probe sets on Affymetrix three-prime expression arrays and applications to differential mRNA processing
Author: Loraine, Ann, Cui, Xiangqin
Date Created: 2009
Subjects--Topical: Gene expression, Nucleic acids
Description: Affymetrix three-prime expression microarrays contain thousands of redundant probe sets that interrogate different regions of the same gene. Differential expression analysis methods rarely consider probe redundancy, which can lead to inaccurate in...

Title: Content and sentiment surveillance (CSI) : A critical component for modeling modern epidemics
Author: Janies, Daniel, Chen, Shi, Zhang, Dongsong
Date Created: 2023
Subjects--Topical: Communicable diseases, Biology
Description: Comprehensive surveillance systems are the key to provide accurate data for effective modeling. Traditional symptom-based case surveillance has been joined with recent genomic, serologic, and environment surveillance to provide more integrated dis...

Title: Detection of high prevalence of Plasmodium falciparum histidine-rich protein 2/3 gene deletions in Assosa zone, Ethiopia : implication for malaria diagnosis
Author: Janies, Daniel, Blackburn, Kayla, Lopez, Karen, Lo, Eugenia
Date Created: 2021
Subjects--Topical: Communicable diseases, Malaria
Description: Background Rapid diagnostic tests (RDTs) targeting histidine rich protein 2(HRP2) are widely used for diagnosis of Plasmodium falciparum infections. Besides PfHRP2, the PfHRP3 antigen contributes to the detection of P. falciparum infections in PfH...