Experimental co-expression data and protein-protein interaction networks are frequently used to analyze the interactions among genes or proteins. Recent studies have investigated methods integrate these two sources of information. We propose a new method obtained through DNA microarray analysis (MA) (PPI) network data, apply it Arabidopsis thaliana. The proposed identifies small subsets highly interacting Based on basis co-localization mRNA developmental expression, we show that groups...

This paper introduces a new approach to applying hyper-heuristic algorithms solve combinatorial problems with less effort, taking into account the modelling and algorithm construction process. We propose unified encoding of solution set low level heuristics which are domain-independent change itself. enables us address NP-hard generate good approximate solutions in reasonable time without large amount additional work required tailor search methodologies for problem hand. In particular, we...

Small non-coding RNAs (sncRNAs) are indispensable for proper germ cell development, emphasizing the need greater elucidation of mechanisms germline development and regulation this process by sncRNAs. We used deep sequencing to characterize three families small (piRNAs, miRNAs, tRFs) present in Sus scrofa gonads focused on RNA fraction both male female gonads. Although similar numbers reads were obtained from types gonads, number unique sequences ovaries was several times lower. Of detected...

An innovative approach to DNA sequencing by hybridization utilizes isothermic oligonucleotide libraries. In this paper, we demonstrate the utility of a genetic algorithm for combinatorial portion new incorporating characteristics in addition Specialized crossover and mutation operators were developed purpose. After initial experiments parameter adjustment, performance was evaluated with respect previous methods literature. The results indicate that proposed is superior approaches. operator...

Resistance to anti-cancer drugs is the main challenge in oncology. In pre-clinical studies, established cancer cell lines are primary tools deciphering molecular mechanisms of this phenomenon. study, we proposed a new, transcriptome-focused approach, utilizing model isogenic with gradually changing resistance. We analyzed trends gene expression aim find out scaffold resistance development process. The ovarian line A2780 was treated stepwise increased concentrations paclitaxel (PTX) generate...

Nicotiana benthamiana has been widely used in laboratories around the world for studying plant-pathogen interactions and posttranscriptional gene expression silencing. Yet exploration of its transcriptome lagged behind due to lack both adequate sequence information genome-wide analysis tools, such as DNA microarrays. Despite increasing use high-throughput sequencing technologies, microarrays still remain a popular tool, because they are cheaper less demanding regarding bioinformatics skills...

Abstract Motivation There are very few methods for de novo genome assembly based on the overlap graph approach. It is considered as giving more exact results than so-called Bruijn approach but in much greater time and of higher memory usage. not uncommon that involving model able to successfully compute datasets, mainly due limitation a computer. This was reason developing last decades Bruijn-based methods, fast fairly accurate. However, latter can fail longer or repetitive genomes, they...

Mammalian Pumilio (PUM) proteins are sequence-specific, RNA-binding (RBPs) with wide-ranging roles. They involved in germ cell development, which has functional implications development and fertility. Although human PUM1 PUM2 closely related to each other recognize the same RNA binding motif, there is some evidence for diversity. To address that problem, first we used RIP-Seq RNA-Seq approaches, identified mRNA pools regulated by TCam-2 line, a male model. Second, applying global mass...

Abstract The problem of DNA sequence assembly is well known for its high complexity. Experimental errors di erent kinds present in data and huge sizes the instances make this very hard to solve. In order deal with such data, advanced efficient heuristics must be constructed. Here, we propose a new approach problem, modeled as searching paths an acyclic digraph. Since graph representing instance not general, it heuristically transformed into form. This reduces time computations significantly...

Although currently available strategies for the preparation of exome-enriched libraries are well established, a final validation in terms exome enrichment efficiency prior to sequencing step is considerable importance. Here, we present strategy evaluation enrichment, i.e., Multipoint Test Targeted-enrichment Efficiency (MTTE), PCR-based approach utilizing multiplex ligation-dependent probe amplification with capillary electrophoresis separation. We used MTTE analysis subsequent steps...

In the light of increasing occurrence antifungal resistance, there is an urgent need to search for new therapeutic strategies overcome this phenomenon. One applied approaches synthesis small-molecule compounds showing properties. Here we present a continuation research on recently discovered anti-Candida albicans agent 4-AN. Using next generation sequencing and transcriptional analysis, revealed that treatment C. with 4-AN can change expression profile large number genes. The highest...

Next generation sequencers produce billions of short DNA sequences in a massively parallel manner, which causes great computational challenge accurately reconstructing genome sequence de novo using these sequences. Here, we propose the GRASShopPER assembler, follows an approach overlap-layout-consensus. It uses efficient GPU implementation for alignment during graph construction stage and greedy hyper-heuristic algorithm at fork detection stage. A two-part method allows us to identify...

DNA assembly problem is well known for its high complexity both on biological and computational levels. Traditional laboratory approach to the problem, which involves sequencing by hybridization or gel electrophoresis, entails a lot of errors coming from experimental algorithmic stages. sequences constituting traditional input have lengths about few hundreds nucleotides they cover each other rather sparsely. A new biochemical gives highly reliable output relatively low cost in short time. It...

ABSTRACT Mammalian Pumilio (PUM) proteins are sequence-specific, RNA-binding with wide-ranging roles, including germ cell development that has functional implications in fertility. Although human PUM1 and PUM2 closely related to each other recognize the same RNA binding motif, there is some evidence for diversity, particularly their roles Here, by sequencing (RNA-Seq) approaches, we identified separate mRNA pools regulated male cells. Using global mass spectrometry-based profiling, distinct...

DNA sequencing is a process of recognizing sequences genomes.The consists in reading short sequences, that are subsequences genome, and merging them into longer preferably the whole genome.In first phase even billions read at once.To simplify speed up second phase, we develop pipeline preprocessing initial set removing low quality reads duplicated reads.We also propose method for preliminary joining overlapping which resulted decreasing cardinality sets to 13.9% 27.8%.We examine possible...

Progress in bioengineering brought a new approach to DNA sequencing, which aim is give highly reliable output of low cost and short time. It 454 based on the pyrosequencing protocol, owned by Life Sciences Corporation. Because sequences reliability this method much better than others for assembly purposes. However, produced are shorter there many more them, indicate that problem harder. Presented algorithm was created process data from sequencing method. Usefulness has been proven tests raw...

Literature reports link psoriasis with insulin resistance characteristic for type 2 diabetes. However, this condition may also affect the clinical course of 1 diabetes (T1D).To investigate whether children mellitus (T1D) and have a different diabetes.We evaluated patients diagnosed T1D in years 2002-2011 presence matched them 1:10 T1D-only by sex duration using propensity score. We collected T1D-onset parameters metabolic control surrogates from six months after diagnosis.We identified 14...