Carnitine-acylcarnitine translocase deficiency caused by gene heterozygous variants in twins: a case report.

The current case report describes the clinical, biochemical and genetic characteristics of carnitine-acylcarnitine translocase deficiency (CACTD) in infant male and female twins that presented with symptoms shortly after elective caesarean delivery. The clinical manifestations were neonatal hypoglycaemia, arrhythmia and sudden death. The age of onset was 1.

MinimapR: A parallel alignment tool for the analysis of large-scale third-generation sequencing data.

The development of third-generation sequencing technology has brought significant changes and influences on genomics. Compared to the second-generation sequencing methods, the third-generation technologies produce around 100 times longer reads to reveal new genomic variations that complete long-term gaps in the human reference genome. However, these reads' excessive length and high error rate severely increase the amount of data and alignment cost.

A Review of Parallel Implementations for the Smith-Waterman Algorithm.

The rapid advances in sequencing technology have led to an explosion of sequence data. Sequence alignment is the central and fundamental problem in many sequence analysis procedure, while local alignment is often the kernel of these algorithms. Usually, Smith-Waterman algorithm is used to find the best subsequence match between given sequences.

VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments.

Background: VISPR is an interactive visualization and analysis framework for CRISPR screening experiments. However, it only supports the output of MAGeCK, and requires installation and manual configuration. Furthermore, VISPR is designed to run on a single computer, and data sharing between collaborators is challenging.

CRISP-view: a database of functional genetic screens spanning multiple phenotypes.

High-throughput genetic screening based on CRISPR/Cas9 or RNA-interference (RNAi) enables the exploration of genes associated with the phenotype of interest on a large scale. The rapid accumulation of public available genetic screening data provides a wealth of knowledge about genotype-to-phenotype relationships and a valuable resource for the systematic analysis of gene functions. Here we present CRISP-view, a comprehensive database of CRISPR/Cas9 and RNAi screening datasets that span multiple phenotypes, including in vitro and in vivo cell proliferation and viability, response to cancer immunotherapy, virus response, protein expression, etc.

OffScan: a universal and fast CRISPR off-target sites detection tool.

Background: The Type II clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) is a powerful genome editing technology, which is more and more popular in gene function analysis. In CRISPR/Cas, RNA guides Cas nuclease to the target site to perform DNA modification.

Results: The performance of CRISPR/Cas depends on well-designed single guide RNA (sgRNA).

Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute.

Genome-wide screening using CRISPR coupled with nuclease Cas9 (CRISPR-Cas9) is a powerful technology for the systematic evaluation of gene function. Statistically principled analysis is needed for the accurate identification of gene hits and associated pathways. Here, we describe how to perform computational analysis of CRISPR screens using the MAGeCKFlute pipeline.

Efficient computation of motif discovery on Intel Many Integrated Core (MIC) Architecture.

Background: Novel sequence motifs detection is becoming increasingly essential in computational biology. However, the high computational cost greatly constrains the efficiency of most motif discovery algorithms.

Results: In this paper, we accelerate MEME algorithm targeted on Intel Many Integrated Core (MIC) Architecture and present a parallel implementation of MEME called MIC-MEME base on hybrid CPU/MIC computing framework.

Review of CRISPR/Cas9 sgRNA Design Tools.

The adaptive immunity system in bacteria and archaea, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-associate (CRISPR/Cas), has been adapted as a powerful gene editing tool and got a broad application in genome research field due to its ease of use and cost-effectiveness. The performance of CRISPR/Cas relies on well-designed single-guide RNA (sgRNA), so a lot of bioinformatic tools have been developed to assist the design of highly active and specific sgRNA. These tools vary in design specifications, parameters, genomes and so on.

A CPU/MIC Collaborated Parallel Framework for GROMACS on Tianhe-2 Supercomputer.

Molecular Dynamics (MD) is the simulation of the dynamic behavior of atoms and molecules. As the most popular software for molecular dynamics, GROMACS cannot work on large-scale data because of limit computing resources. In this paper, we propose a CPU and Intel® Xeon Phi Many Integrated Core (MIC) collaborated parallel framework to accelerate GROMACS using the offload mode on a MIC coprocessor, with which the performance of GROMACS is improved significantly, especially with the utility of Tianhe-2 supercomputer.

Protective Effects of Scutellarin on Human Cardiac Microvascular Endothelial Cells against Hypoxia-Reoxygenation Injury and Its Possible Target-Related Proteins.

Scutellarin (SCU) is one of the main components of traditional Chinese medicine plant Erigeron breviscapus (Vant.) Hand.-Mazz.

A Hybrid Parallel Strategy Based on String Graph Theory to Improve De Novo DNA Assembly on the TianHe-2 Supercomputer.

' The de novo assembly of DNA sequences is increasingly important for biological researches in the genomic era. After more than one decade since the Human Genome Project, some challenges still exist and new solutions are being explored to improve de novo assembly of genomes. String graph assembler (SGA), based on the string graph theory, is a new method/tool developed to address the challenges.

B-MIC: An Ultrafast Three-Level Parallel Sequence Aligner Using MIC.

Sequence alignment is the central process for sequence analysis, where mapping raw sequencing data to reference genome. The large amount of data generated by NGS is far beyond the process capabilities of existing alignment tools. Consequently, sequence alignment becomes the bottleneck of sequence analysis.

A Massively Parallel Computational Method of Reading Index Files for SOAPsnv.

SOAPsnv is the software used for identifying the single nucleotide variation in cancer genes. However, its performance is yet to match the massive amount of data to be processed. Experiments reveal that the main performance bottleneck of SOAPsnv software is the pileup algorithm.

HSPA9 overexpression inhibits apoptin-induced apoptosis in the HepG2 cell line.

Apoptin, a small protein derived from chicken anemia virus, possesses the capacity to specifically kill tumor cells while leaving normal cells intact. Previous studies have indicated that the subcellular localization of apoptin appears to be crucial for this tumor-selective activity. Apoptin resides in the cytoplasm of normal cells; however, in cancer cells it translocates into the nucleus.

[Expression of neutrophil adhesion molecule CD11b as an early diagnostic marker for neonatal sepsis].

Objective: Neonatal sepsis is a common disease and the sepsis-related mortality rate is still high. Until now, there has no ideal diagnostic marker to early identify neonatal sepsis. Expression of neutrophil adhesion molecule CD(11b) was showed as the earlier reaction to the infection/inflammation, and may be applied as an early diagnostic marker for sepsis.