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Ultra-Fast Alterations in mRNA Levels Uncover Multiple Players in Light Stress Acclimation in Plants

Description: This article contains RNA sequencing analysis of Arabidopsis thaliana plants subjected to light stress in order to identify and characterize rapid changes in the steady-state level of different transcripts in response to light stress.
Date: September 26, 2015
Creator: Suzuki, Nobuhiro; Devireddy, Amith R.; Inupakutika, Madhuri A.; Baxter, Aaron; Miller, Gad; Song, Luhua et al.
Item Type: Refine your search to only Article
Partner: UNT College of Arts and Sciences
open access

DiseaseNet: a transfer learning approach to noncommunicable disease classification

Description: This article presents a neural network trained on one class of noncommunicable diseases, cancer, as the basis for a transfer learning approach to non-cancer noncommunicable disease modeling. The authors used a concept based explanation method called Testing with Concept Activation Vectors to investigate the importance of the sample sources and understand how future training datasets for multiple noncommunicable disease models may be improved.
Date: March 11, 2024
Creator: Gore, Steven; Meche, Bailey; Shao, Danyang; Ginnett, Benjamin; Zhou, Kelly & Azad, Rajeev K.
Item Type: Refine your search to only Article
Partner: UNT College of Science
open access

Phylogenetic analysis of eukaryotic NEET proteins uncovers a link between a key gene duplication event and the evolution of vertebrates

Description: This article describes the use of three members of the human NEET protein family (CISD1, mitoNEET; CISD2, NAF-1 or Miner 1; and CISD3, Miner2) as guides to conduct a phylogenetic analysis of eukaryotic NEET proteins and their evolution.
Date: February 16, 2017
Creator: Inupakutika, Madhuri A.; Sengupta, Soham; Nechushtai, Rachel; Jennings, Patricia A.; Onuchic, José N.; Azad, Rajeev K. et al.
Item Type: Refine your search to only Article
Partner: UNT College of Arts and Sciences
open access

Interactions between mitoNEET and NAF-1 in cells

Description: This article uses yeast two-hybrid to demonstrate through vivo bimolecular fluorescence complementation (BiFC), direct coupling analysis (DCA), RNA-sequencing, ROS and iron imaging, and single and double shRNA lines with suppressed mNT, NAF-1 and mNT/NAF-1 expression, that mNT and NAF-1 directly interact in mammalian cells and could function in the same cellular pathway.
Date: April 20, 2017
Creator: Karmi, Ola; Holt, Sarah H.; Song, Luhua; Tamir, Sagi; Luo, Yuting; Bai, Fang et al.
Item Type: Refine your search to only Article
Partner: UNT College of Arts and Sciences
open access

Environmental vibrios represent a source of antagonistic compounds that inhibit pathogenic Vibrio cholerae and Vibrio parahaemolyticus strains

Description: This article predicts that marine-derived bacteria should inhibit Vibrio pathogens and may be a source of unique antibiotic compounds.
Date: May 16, 2017
Creator: Burks, David J.; Norris, Stephen; Kauffman, Kathryn M.; Joy, Abigail; Arevalo, Philip; Azad, Rajeev K. et al.
Item Type: Refine your search to only Article
Partner: UNT College of Science
open access

POSMM: an efficient alignment-free metagenomic profiler that complements alignment-based profiling

Description: Article presents POSMM, Python-Optimized Standard Markov Model classifier, which is a new incarnation of the Markov model approach to metagenomic sequence analysis. The authors claim that by combining POSMM with ultrafast classifiers such as Kraken2, their complementary strengths can be leveraged to produce higher overall accuracy in metagenomic sequence classification than by either as a standalone classifier. POSMM is a user-friendly and highly adaptable tool designed for broad use by the met… more
Date: March 8, 2023
Creator: Burks, David J.; Pusadkar, Vaidehi & Azad, Rajeev K.
Item Type: Refine your search to only Article
Partner: UNT College of Science
open access

Detection and Classification of Cancer and Other Noncommunicable Diseases Using Neural Network Models

Description: Here, we show that training with multiple noncommunicable diseases (NCDs) is both feasible and beneficial to modeling this class of diseases. We first use data from the Cancer Genome Atlas (TCGA) to train a pan cancer model, and then characterize the information the model has learned about the cancers. In doing this we show that the model has learned concepts that are relevant to the task of cancer classification. We also test the model on datasets derived independently of the TCGA cohort and s… more
Date: July 2023
Creator: Gore, Steven Lee
Item Type: Refine your search to only Thesis or Dissertation
Partner: UNT Libraries
open access

Identification and characterization of a core set of ROS wave‐associated transcripts involved in the systemic acquired acclimation response of Arabidopsis to excess light

Description: Article reveal that the systemic transcriptomic response of plants to excess light stress is extensive in the context of systemic acquired acclimation and involves an early (2 min) and transient stage of transcript expression that includes thousands of genes.
Date: December 6, 2018
Creator: Zandalinas, Sara I.; Sengupta, Soham; Burks, David; Azad, Rajeev K. & Mittler, Ron
Item Type: Refine your search to only Article
Partner: UNT College of Science
open access

Glucose or Altered Ceramide Biosynthesis Mediate Oxygen Deprivation Sensitivity Through Novel Pathways Revealed by Transcriptome Analysis in Caenorhabditis elegans

Description: This article discusses how RNA-sequencing analysis was performed to assess how a glucose-supplemented diet and/or a hyl-2 mutation altered the transcriptome.
Date: August 5, 2016
Creator: Ladage, Mary L.; King, Skylar D.; Burks, David J.; Quan, Daniel L.; Garcia, Anastacia M.; Azad, Rajeev K. et al.
Item Type: Refine your search to only Article
Partner: UNT College of Arts and Sciences
open access

Identification of Novel Genomic Islands in Liverpool Epidemic Strain of Pseudomonas aeruginosa Using Segmentation and Clustering

Description: This article utilizes a recursive segmentation and cluster procedure presented as a genome-mining tool, GEMINI, to decipher genomic islands and understand their contributions to the evolution of virulence and antibiotic resistance in Pseudomonas aeruginosa.
Date: August 3, 2016
Creator: Jani, Mehul; Mathee, Kalal & Azad, Rajeev K.
Item Type: Refine your search to only Article
Partner: UNT College of Arts and Sciences
open access

Local and Systemic Metabolic Responses during Light-Induced Rapid Systemic Signaling

Description: This article reports that local application of light stress to one rosette leaf of bolting Arabidopsis (Arabidopsis thaliana) plants resulted in a metabolic response that encompassed local, systemic and transport tissues, demonstrating a high degree of physical and metabolic continuity between different tissues throughout the plant.
Date: December 2018
Creator: Choudhury, Feroza K.; Devireddy, Amith R.; Azad, Rajeev K.; Shulaev, Vladimir & Mittler, Ron
Item Type: Refine your search to only Article
Partner: UNT College of Science
open access

Analysis of transcribed sequences from young and mature zebrafish thrombocytes

Description: Article studying thrombocyte function and development in adult zebrafish. The authors performed single-cell RNA sequencing of the young and mature zebrafish thrombocytes and compared the two datasets for young and mature thrombocyte transcripts.
Date: March 23, 2022
Creator: Fallatah, Weam; De, Ronika; Burks, David J.; Azad, Rajeev K. & Jagadeeswaran, Pudur
Item Type: Refine your search to only Article
Partner: UNT College of Science
open access

The Arabidopsis gene co-expression network

Description: Article presents an Arabidopsis gene co-expression network constructed using RNA-Seq datasets, which will serve as a useful resource for the Arabidopsis research community to gain insights into Arabidopsis gene interactions and functions.
Date: April 26, 2022
Creator: Burks, David J.; Sengupta, Soham; De, Ronika; Mittler, Ron & Azad, Rajeev K.
Item Type: Refine your search to only Article
Partner: UNT College of Science
open access

The impact of multifactorial stress combination on plant growth and survival

Description: Article studying seedlings of wild-type and different mutants of Arabidopsis thaliana plants subjected to a multifactorial stress combination of six different stresses, each applied at a low level, and their survival, physiological and molecular responses. Findings reveal that further polluting our environment could result in higher complexities of multifactorial stress combinations that in turn could drive a critical decline in plant growth and survival.
Date: January 26, 2021
Creator: Zandalinas, Sandra I.; Sengupta, Soham; Fritschi, Felix B.; Azad, Rajeev K.; Nechushtai, Rachel & Mittler, Ron
Item Type: Refine your search to only Article
Partner: UNT College of Science
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