Pollination of Orchid Flowers: Quantitative and Domain-Specific Analysis of Ethylene Biosynthetic and Hormone-Induced Gene Expression

2017 ◽  
Vol 178 (3) ◽  
pp. 188-210 ◽  
Author(s):  
Sharman D. O’Neill ◽  
Anhthu Q. Bui ◽  
Daniel Potter ◽  
Xian Sheng Zhang
Keyword(s):  
Gene Expression ◽  
Domain Specific ◽  
Specific Analysis

Nucleomics of glucose sensing cells: methodology for cell‐type specific analysis of gene expression

2007 ◽  
Vol 21 (5) ◽  
Author(s):  
Ronald M. Lynch ◽  
Roger Barthelson ◽  
Julia Cates ◽  
Heddwen L. Brooks ◽  
David W. Galbraith
Keyword(s):  
Gene Expression ◽  
Glucose Sensing ◽  
Cell Type ◽  
Specific Analysis ◽  
Cell Type Specific

scholarly journals A domain-specific analysis system for examining nuclear reactor simulation data for light-water and sodium-cooled fast reactors

2015 ◽  
Vol 85 ◽  
pp. 856-868 ◽  
Author(s):  
Jay Jay Billings ◽  
Jordan H. Deyton ◽  
S. Forest Hull ◽  
Eric J. Lingerfelt ◽  
Anna Wojtowicz
Keyword(s):  
Nuclear Reactor ◽  
Fast Reactors ◽  
Simulation Data ◽  
Light Water ◽  
Domain Specific ◽  
Specific Analysis ◽  
Analysis System

scholarly journals Pathway-Specific Analysis of Gene Expression Data Identifies the PI3K/Akt Pathway as a Novel Therapeutic Target in Cervical Cancer

2012 ◽  
Vol 18 (5) ◽  
pp. 1464-1471 ◽  
Author(s):  
Julie K. Schwarz ◽  
Jacqueline E. Payton ◽  
Ramachandran Rashmi ◽  
Tao Xiang ◽  
Yunhe Jia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cervical Cancer ◽  
Gene Expression Data ◽  
Therapeutic Target ◽  
Akt Pathway ◽  
Expression Data ◽  
Specific Analysis ◽  
Novel Therapeutic

scholarly journals Interpretable factor models of single-cell RNA-seq via variational autoencoders

2019 ◽  
Author(s):  
Valentine Svensson ◽  
Lior Pachter
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Statistical Inference ◽  
Factor Models ◽  
Rna Seq ◽  
Cell Type ◽  
Massive Datasets ◽  
Domain Specific ◽  
Variational Autoencoder ◽  
Inference Methods

Single cell RNA-seq makes possible the investigation of variability in gene expression among cells, and dependence of variation on cell type. Statistical inference methods for such analyses must be scalable, and ideally interpretable. We present an approach based on a modification of a recently published highly scalable variational autoencoder framework that provides interpretability without sacrificing much accuracy. We demonstrate that our approach enables identification of gene programs in massive datasets. Our strategy, namely the learning of factor models with the auto-encoding variational Bayes framework, is not domain specific and may be of interest for other applications.

The transcription factor Schnurri plays a dual role in mediating Dpp signaling during embryogenesis

Development ◽  
2001 ◽  
Vol 128 (9) ◽  
pp. 1657-1670 ◽  
Author(s):  
J. Torres-Vazquez ◽  
S. Park ◽  
R. Warrior ◽  
K. Arora
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Cell Fate ◽  
Target Genes ◽  
Gene Activation ◽  
Nuclear Accumulation ◽  
Embryonic Patterning ◽  
Specific Analysis ◽  
Positive Input ◽  
Affect Gene Expression

Decapentaplegic (Dpp), a homolog of vertebrate bone morphogenic protein 2/4, is crucial for embryonic patterning and cell fate specification in Drosophila. Dpp signaling triggers nuclear accumulation of the Smads Mad and Medea, which affect gene expression through two distinct mechanisms: direct activation of target genes and relief of repression by the nuclear protein Brinker (Brk). The zinc-finger transcription factor Schnurri (Shn) has been implicated as a co-factor for Mad, based on its DNA-binding ability and evidence of signaling dependent interactions between the two proteins. A key question is whether Shn contributes to both repression of brk as well as to activation of target genes. We find that during embryogenesis, brk expression is derepressed in shn mutants. However, while Mad is essential for Dpp-mediated repression of brk, the requirement for shn is stage specific. Analysis of brk; shn double mutants reveals that upregulation of brk does not account for all aspects of the shn mutant phenotype. Several Dpp target genes are expressed at intermediate levels in double mutant embryos, demonstrating that shn also provides a brk-independent positive input to gene activation. We find that Shn-mediated relief of brk repression establishes broad domains of gene activation, while the brk-independent input from Shn is crucial for defining the precise limits and levels of Dpp target gene expression in the embryo.

A NOVEL APPROACH OF REQUIREMENT GATHERING AND ANALYSIS FOR AGENT ORIENTED SOFTWARE ENGINEERING (AOSE)

2009 ◽  
Vol 19 (01) ◽  
pp. 79-111
Author(s):  
PRABHAT RANJAN ◽  
A. K. MISRA
Keyword(s):  
System Development ◽  
Specific Model ◽  
Agent Based Modeling ◽  
Agent Based ◽  
Domain Specific ◽  
Analysis Methodology ◽  
Analysis Process ◽  
Agent Oriented Software Engineering ◽  
Novel Approach ◽  
Specific Analysis

In this paper, an agent-based open and adaptive system development process has been proposed which continuously change and evolve to meet new requirements. The proposed methodology is based on a model-based technique that provides a specific model for the type of information to be gathered and uses this model to drive the domain specific analysis process. The focus is on a clear separtion between the requirement gathering and analysis phases. The analysis methodology further splits the analysis phase into the user_centric analysis and the system_centric analysis phases. Optimization of the system performance has also been proposed by exploiting the relationships and dependencies among roles and mapping criteria between roles to agents. The Gaia and ROADMAP models have been used as a basis to the proposed agent-based modeling method.

scholarly journals VAR2CSA Domain-Specific Analysis of Naturally Acquired Functional Antibodies toPlasmodium falciparumPlacental Malaria

2016 ◽  
Vol 214 (4) ◽  
pp. 577-586 ◽  
Author(s):  
Justin Yai Alamou Doritchamou ◽  
Raul Herrera ◽  
Joan A. Aebig ◽  
Robert Morrison ◽  
Vu Nguyen ◽  
...  
Keyword(s):  
Domain Specific ◽  
Specific Analysis ◽  
Functional Antibodies
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