ON THE HARDNESS OF THE BORDER LENGTH MINIMIZATION PROBLEM ON A RECTANGULAR ARRAY

2010 ◽  
Vol 21 (06) ◽  
pp. 1089-1100 ◽  
Author(s):  
VAMSI KUNDETI ◽  
SANGUTHEVAR RAJASEKARAN
Keyword(s):  
Gene Expression ◽  
Expression Profiling ◽  
State Of The Art ◽  
Combinatorial Problem ◽  
Np Hard ◽  
Microarray Technology ◽  
Rectangular Grid ◽  
Rectangular Array ◽  
Current State ◽  
Invaluable Tool

DNA microarray technology has proven to be an invaluable tool for molecular biologists. Microarrays are used extensively in SNP detection, genomic hybridization, alternative splicing and gene expression profiling. However the manufacturers of the microarrays are often stuck with the problem of minimizing the effects of unwanted illumination (border length minimization (BLM)) which is a hard combinatorial problem. In this paper we prove that the BLM problem on a rectangular grid is NP-hard – this however does not mean the BLM problem on a square grid is NP-hard. We also give the first integer linear programming (ILP) formulation to solve BLM problem optimally. Experimental results indicate that our ILP method produces superior results (both in runtime and cost) compared to the current state of the art algorithms to solve the BLM problem optimally.

Custom microarray for glycobiologists: considerations for glycosyltransferase gene expression profiling

2002 ◽  
Vol 69 ◽  
pp. 135-142 ◽  
Author(s):  
Elena M. Comelli ◽  
Margarida Amado ◽  
Steven R. Head ◽  
James C. Paulson
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Affymetrix Genechip ◽  
Microarray Technology ◽  
Gene Arrays ◽  
Glycosyltransferase Gene

The development of microarray technology offers the unprecedented possibility of studying the expression of thousands of genes in one experiment. Its exploitation in the glycobiology field will eventually allow the parallel investigation of the expression of many glycosyltransferases, which will ultimately lead to an understanding of the regulation of glycoconjugate synthesis. While numerous gene arrays are available on the market, e.g. the Affymetrix GeneChip® arrays, glycosyltransferases are not adequately represented, which makes comprehensive surveys of their gene expression difficult. This chapter describes the main issues related to the establishment of a custom glycogenes array.

Study of Basic Concepts on the Development of Protein Microarray - Gene Expression Profiling

2016 ◽  
pp. 263-295
Author(s):  
P. Sivashanmugam ◽  
Arun C. ◽  
Selvakumar P.
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Protein Microarray ◽  
Microarray Technology ◽  
Microarray Gene Expression ◽  
High Throughput Technology ◽  
Multiple Cell ◽  
Stressed Cell ◽  
Microarray Gene

The physical and biological activity of any organisms is mainly depended on the genetic information which stored in DNA. A process at which a gene gives rise to a phenotype is called as gene expression. Analysis of gene expression can be used to interpret the changes that occur at biological level of a stressed cell or tissue. Hybridization technology helps to study the gene expression of multiple cell at a same time. Among them microarray technology is a high- throughput technology to study the gene expression at transcription level (DNA) or translation level (Protein). Analysis the protein only can predict the accurate changes that happens in a tissue, when they are infected by a disease causing organisms. Protein microarray mainly used to identify the interactions and activities of proteins with other molecules, and to determine their function for a system at normal state and stressed state. The scope of this chapter is to outline a detail description on the fabrication, types, data analysis, and application of protein microarray technology towards gene expression profiling.

scholarly journals Sonoporation: Underlying Mechanisms and Applications in Cellular Regulation

2021 ◽  
Author(s):  
Yue Li ◽  
Zhiyi Chen ◽  
Shuping Ge
Keyword(s):  
Gene Expression ◽  
Cell Membrane ◽  
State Of The Art ◽  
Cellular Functions ◽  
Cellular Regulation ◽  
Current State ◽  
Cellular Apoptosis ◽  
Ultrasonic Parameters ◽  
Or Gene ◽  
Underlying Mechanisms

Ultrasound combined with microbubble-mediated sonoporation has been applied to enhance drug or gene intracellular delivery. Sonoporation leads to the formation of openings in the cell membrane, triggered by ultrasound-mediated oscillations and destruction of microbubbles. Multiple mechanisms are involved in the occurrence of sonoporation, including ultrasonic parameters, microbubbles size, and the distance of microbubbles to cells. Recent advances are beginning to extend applications through the assistance of contrast agents, which allow ultrasound to connect directly to cellular functions such as gene expression, cellular apoptosis, differentiation, and even epigenetic reprogramming. In this review, we summarize the current state of the art concerning microbubble–cell interactions and sonoporation effects leading to cellular functions.

scholarly journals DNA microarrays, a novel approach in studies of chromatin structure.

2004 ◽  
Vol 51 (1) ◽  
pp. 1-8
Author(s):  
Piotr Widłak
Keyword(s):  
Gene Expression ◽  
Dna Microarray ◽  
Chromatin Structure ◽  
Expression Profiling ◽  
Genetic Information ◽  
Dna Microarrays ◽  
Microarray Technology ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale

The DNA microarray technology delivers an experimental tool that allows surveying expression of genetic information on a genome-wide scale at the level of single genes--for the new field termed functional genomics. Gene expression profiling--the primary application of DNA microarrays technology--generates monumental amounts of information concerning the functioning of genes, cells and organisms. However, the expression of genetic information is regulated by a number of factors that cannot be directly targeted by standard gene expression profiling. The genetic material of eukaryotic cells is packed into chromatin which provides the compaction and organization of DNA for replication, repair and recombination processes, and is the major epigenetic factor determining the expression of genetic information. Genomic DNA can be methylated and this modification modulates interactions with proteins which change the functional status of genes. Both chromatin structure and transcriptional activity are affected by the processes of replication, recombination and repair. Modified DNA microarray technology could be applied to genome-wide study of epigenetic factors and processes that modulate the expression of genetic information. Attempts to use DNA microarrays in studies of chromatin packing state, chromatin/DNA-binding protein distribution and DNA methylation pattern on a genome-wide scale are briefly reviewed in this paper.

Embryonic gene expression profiling using microarray analysis

2009 ◽  
Vol 21 (1) ◽  
pp. 22 ◽  
Author(s):  
Sadie L. Marjani ◽  
Daniel Le Bourhis ◽  
Xavier Vignon ◽  
Yvan Heyman ◽  
Robin E. Everts ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiling ◽  
Nuclear Transfer ◽  
Lower Cost ◽  
Preimplantation Embryos ◽  
Microarray Technology ◽  
In Vitro Production ◽  
Vitro Production ◽  
Level Of Analysis

Microarray technology enables the interrogation of thousands of genes at one time and therefore a systems level of analysis. Recent advances in the amplification of RNA, genome sequencing and annotation, and the lower cost of developing microarrays or purchasing them commercially, have facilitated the analysis of single preimplantation embryos. The present review discusses the components of embryonic expression profiling and examines current research that has used microarrays to study the effects of in vitro production and nuclear transfer.

Mining Largest Maximal Quasi-Cliques

2021 ◽  
Vol 15 (5) ◽  
pp. 1-21
Author(s):  
Seyed-Vahid Sanei-Mehri ◽  
Apurba Das ◽  
Hooman Hashemi ◽  
Srikanta Tirthapura
Keyword(s):  
Social Network ◽  
Social Network Analysis ◽  
Network Analysis ◽  
Heuristic Algorithm ◽  
State Of The Art ◽  
Experimental Results ◽  
Np Hard ◽  
Challenging Problem ◽  
Current State ◽  
Clique Enumeration

Quasi-cliques are dense incomplete subgraphs of a graph that generalize the notion of cliques. Enumerating quasi-cliques from a graph is a robust way to detect densely connected structures with applications in bioinformatics and social network analysis. However, enumerating quasi-cliques in a graph is a challenging problem, even harder than the problem of enumerating cliques. We consider the enumeration of top- k degree-based quasi-cliques and make the following contributions: (1) we show that even the problem of detecting whether a given quasi-clique is maximal (i.e., not contained within another quasi-clique) is NP-hard. (2) We present a novel heuristic algorithm K ernel QC to enumerate the k largest quasi-cliques in a graph. Our method is based on identifying kernels of extremely dense subgraphs within a graph, followed by growing subgraphs around these kernels, to arrive at quasi-cliques with the required densities. (3) Experimental results show that our algorithm accurately enumerates quasi-cliques from a graph, is much faster than current state-of-the-art methods for quasi-clique enumeration (often more than three orders of magnitude faster), and can scale to larger graphs than current methods.

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