To facilitate the clinical implementation of genomic medicine by next-generation sequencing, it will be critically important to obtain accurate and consistent variant calls on personal genomes. Multiple software tools for calling are available, but is unclear how comparable these or what their relative merits in real-world scenarios might be.We sequenced 15 exomes from four families using commercial kits (Illumina HiSeq 2000 platform Agilent SureSelect version 2 capture kit), with...

Abstract Introgression is an important biological process affecting at least 10% of the extant species in animal kingdom. significantly impacts inference phylogenetic relationships where a strictly binary tree model cannot adequately explain reticulate net-like relationships. Here, we use phylogenomic approaches to understand patterns introgression along evolutionary history unique, nonmodel insect system: dragonflies and damselflies (Odonata). We demonstrate that pervasive force across...

Gene duplication plays a central role in adaptation to novel environments by providing new genetic material for functional divergence and evolution of biological complexity. Several evolutionary models have been proposed gene explain how copies are preserved natural selection, but these rarely tested using empirical data. Opsin proteins, when combined with chromophore, form photopigment that is responsible the absorption light, first step phototransduction cascade. Adaptive duplications...

Pyrenophora semeniperda (anamorph Drechslera campulata) is a necrotrophic fungal seed pathogen that has wide host range within the Poaceae. One of its hosts cheatgrass (Bromus tectorum), species exotic to United States invaded natural ecosystems Intermountain West. As cheatgrass, P. potential as biocontrol agent due effectiveness at killing seeds bank; however, few genetic resources exist for fungus. Here, genome isolate assembled from sequence reads 454 pyrosequencing presented. The total...

Genome assemblers to date have predominantly targeted haploid reference reconstruction from homozygous data. When applied diploid genome assembly, these perform poorly, owing the violation of assumptions during both contigging and scaffolding phases. Effective tools overcome problems are in growing demand. Increasing parameter stringency is an effective solution obtaining haplotype-specific contigs; however, algorithms for such contigs lacking.We present a stand-alone algorithm,...

Error correction is an important step in increasing the quality of next-generation sequencing data for downstream analysis and use. Polymorphic datasets are a challenge many bioinformatic software packages that designed or assume homozygosity input dataset. This assumption ignores true genomic composition organisms diploid polyploid. In this survey, two different error packages, Quake ECHO, examined to see how they perform on sequence from heterozygous genomes. ECHO well were able correct...

Genome-wide association studies (GWAS) have effectively identified genetic factors for many diseases. Many diseases, including Alzheimer's disease (AD), epistatic causes, requiring more sophisticated analyses to identify groups of variants which together affect phenotype. Based on the GWAS statistical model, we developed a multi-SNP analysis pairs whose common occurrence signaled Despite not having sufficient data demonstrate significance, our preliminary experimentation high correlation...

The contig orientation problem, which we formally define as the MAX-DIR has at times been addressed cursorily and using various heuristics. In setting forth a linear-time reduction from MAX-CUT problem to prove latter is NP-complete. We compare relative performance of novel greedy approach with several other heuristic solutions.Our results suggest that our algorithm not only works well but also outperforms algorithms due nature scaffold graphs. Our demonstrate method for identifying inverted...

Conway's law, the idea that a software system reflects structure of organization built it, is one most well-known "laws" in engineering. However, seemingly straightforward phenomenon described by Conway appears to be subject nuances personal and organizational dynamics as well contextual factors, which are neither well-understood nor well-studied. As pilot study intended foster discussion within RESER community, we performed small somewhat informal qualitative designed elucidate some these...

A challenge in the domain of creative story generation is generating stories that reflect a consistent theme or genre. We present GREEN, computational (CC) system designed to generate short whose genre customized user's tastes literature. Given book title, GREEN uses association rule mining identify appropriate recommendations from which train long short-term memory model (LSTM) then produce new story. The forms its intention based on input, thereby aiming artifacts will be value and...

SUMMARY Introgression is arguably one of the most important biological processes in evolution groups related species, affecting at least 10% extant species animal kingdom. reduces genetic divergence between and some cases can be highly beneficial, facilitating rapid adaptation to ever-changing environmental pressures. also significantly impacts inference phylogenetic relationships where a strictly binary tree model cannot adequately explain reticulate net-like relationships. Here we use...

We present kleuren, a novel assembly-free method to reconstruct phylogenetic trees using the Colored de Bruijn Graph. kleuren works by constructing Graph and then traversing it, finding bubble structures in graph that provide signal. The bubbles are aligned concatenated form supermatrix, from which tree is inferred. introduce algorithms uses accomplish this task, show its performance on reconstructing of 12 Drosophila species. reconstructed established accurately, viable tool for...

Although music is full of repetitive motifs and themes, artificially intelligent temporal sequence models have yet to demonstrate the ability model or generate musical compositions that satisfy steerable, long-range constraints needed evoke such repetitions. Markovian approaches inherently assume a strictly limited range memory while neural approaches—despite recent advances in evoking dependencies—remain largely unsteerable. More been published attempt by imposing unary at intervals...

In recent years, the viability of hash cracking has been questioned as industry encryption standards, salting, and timeouts have risen in popularity. John Ripper emerged one most sophisticated open-source tool on market. The is used by cybercriminals well security specialists. Research Questions formulated to answer questions related Ripper. To these questions, three experiments are defined performed with varying results. We find that while struggles a brute force attacker without complex...

We address the problem of building and evaluating a computational system whose primary objective is creativity. illustrate seven characteristics for creativity in context that autonomously composes Western lyrical music. conduct an external evaluation which respondents rated with regard to each characteristic as well overall Average scores exceeded ratings any single characteristic, suggesting may be emergent property unique research opportunities exist CC systems design attempts comprehend all known

This research employs an exhaustive search of different attribute selection algorithms in order to provide a more structured approach learning design for prediction Alzheimer's clinical dementia rating (CDR).

In the context of genome assembly, contig orientation problem is described as removing sufficient edges from scaffold graph so that remaining subgraph assigns a consistent to all sequence nodes in graph. This can also be phrased weighted MAX-CUT problem. The performance heuristics this application untested. We present greedy heuristic solution and compare its semi-definite programming on several graphs. note used identify inverted repeats haplotypes, these represent sequences whose appears...

Comparing genomes to identify polymorphisms is a difficult task, especially beyond single nucleotide poly-morphisms. Polymorphism detection important in disease association studies as well phylogenetic tree reconstruc-tion. We present method for identifying by using modified version de Bruijn graphs, data structures widely used genome assembly from Next-Generation Sequencing. Using our method, we are able that exist within see graph form the particular types of (translocations, etc.).