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Detecting genome-wide epistases based on the clustering of relatively frequent items

Motivation: In genome-wide association studies (GWAS), up to millions of single nucleotide polymorphisms (SNPs) are genotyped for thousands of individuals. However, conventional single locus-based approaches are usually unable to detect gene–gene interactions underlying complex diseases. Due to the huge search space for complicated high order interactions, many existing multi...

Constructing Novel Fiber Reinforced Plastic (FRP) Composites through a Biomimetic Approach: Connecting Glass Fiber with Nanosized Boron Nitride by Polydopamine Coating

 Tao Jiang,1 Jian Li,1 Wei Zhang,1 Lei Zhang,1,3 and Huaiqi Shao1 1School of Material Science and Chemical Engineering, Tianjin University of Science and Technology, Tianjin 300457, China 2Tianjin

Low c-Met expression levels are prognostic for and predict the benefits of temozolomide chemotherapy in malignant gliomas

• PubMed • Google ScholarSearch for Tao Jiang in:Nature Research journals • PubMed • Google Scholar Contributions M.Y.L. and P.Y. provided equal contributions to the data analysis, performed the experiments ... Wang or Tao Jiang. Supplementary information PDF files1.Supplementary Information Excel files1.Supplementary dataset 1 Rights and permissions This work is licensed under a Creative Commons

Indian-Ink Perfusion Based Method for Reconstructing Continuous Vascular Networks in Whole Mouse Brain

The topology of the cerebral vasculature, which is the energy transport corridor of the brain, can be used to study cerebral circulatory pathways. Limited by the restrictions of the vascular markers and imaging methods, studies on cerebral vascular structure now mainly focus on either observation of the macro vessels in a whole brain or imaging of the micro vessels in a small...

Genetically shaping morphology of the filamentous fungus Aspergillus glaucus for production of antitumor polyketide aspergiolide A

Zhenzhong Yu Weiqiang Zhou Tao Jiang Xiangshan Zhou Yuanxing Zhang 0 Equal contributors State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai 200237

Revealing an outward-facing open conformational state in a CLC Cl-/H+ exchange transporter

CLC secondary active transporters exchange Cl- for H+. Crystal structures have suggested that the conformational change from occluded to outward-facing states is unusually simple, involving only the rotation of a conserved glutamate (Gluex) upon its protonation. Using 19F NMR, we show that as [H+] is increased to protonate Gluex and enrich the outward-facing state, a residue ~20...

Uncover disease genes by maximizing information flow in the phenome–interactome network

Motivation: Pinpointing genes that underlie human inherited diseases among candidate genes in susceptibility genetic regions is the primary step towards the understanding of pathogenesis of diseases. Although several probabilistic models have been proposed to prioritize candidate genes using phenotype similarities and protein–protein interactions, no combinatorial approaches have...

A linear-time algorithm for reconstructing zero-recombinant haplotype configuration on a pedigree

Background When studying genetic diseases in which genetic variations are passed on to offspring, the ability to distinguish between paternal and maternal alleles is essential. Determining haplotypes from genotype data is called haplotype inference. Most existing computational algorithms for haplotype inference have been designed to use genotype data collected from individuals in...

Recognition and processing of double-stranded DNA by ExoX, a distributive 3′–5′ exonuclease

Members of the DnaQ superfamily are major 3′–5′ exonucleases that degrade either only single-stranded DNA (ssDNA) or both ssDNA and double-stranded DNA (dsDNA). However, the mechanism by which dsDNA is recognized and digested remains unclear. Exonuclease X (ExoX) is a distributive DnaQ exonuclease that cleaves both ssDNA and dsDNA substrates. Here, we report the crystal...

Oncogene addiction in gliomas: Implications for molecular targeted therapy

Oncogene addiction is a phenomenon that the survival of cancer cells depends on an activated oncogene or inactivation of tumor suppressor gene, and is regarded as the 'Achilles heel' of the successful molecular targeted therapies in cancer. However, the role of oncogene addiction in gliomas has not been elucidated systematically. In this review, we summarize the current...

Genetic Characterization of Human-Derived Hydatid Cysts of Echinococcus granulosus Sensu Lato in Heilongjiang Province and the First Report of G7 Genotype of E. canadensis in Humans in China

Cystic echinococcosis (CE) caused by the larval stage of Echinococcus granulosus sensu lato (s.l.) is one of the most important zoonotic parasitic diseases worldwide and 10 genotypes (G1–G10) have been reported. In China, almost all the epidemiological and genotyping studies of E. granulosus s.l. are from the west and northwest pasturing areas. However, in Heilongjiang Province...

Analysis of the Maternal and Child Health Care Status in Suizhou City, Hubei Province, China, from 2005 to 2011

BackgroundImproving the health and well-being of women and children has long been a common goal throughout the world. From 2005 to 2011, Suizhou City had an annual average of 22,405 pregnant and parturient women (1.04% of the population) and 98,811 children under 5 years old (4.57% of the population). Understanding the status of maternal and child health care in Suizhou City...

Visual Working Memory Load-Related Changes in Neural Activity and Functional Connectivity

Background Visual working memory (VWM) helps us store visual information to prepare for subsequent behavior. The neuronal mechanisms for sustaining coherent visual information and the mechanisms for limited VWM capacity have remained uncharacterized. Although numerous studies have utilized behavioral accuracy, neural activity, and connectivity to explore the mechanism of VWM...

MultiMSOAR 2.0: An Accurate Tool to Identify Ortholog Groups among Multiple Genomes

The identification of orthologous genes shared by multiple genomes plays an important role in evolutionary studies and gene functional analyses. Based on a recently developed accurate tool, called MSOAR 2.0, for ortholog assignment between a pair of closely related genomes based on genome rearrangement, we present a new system MultiMSOAR 2.0, to identify ortholog groups among...

Genetic polymorphisms of DNA double-strand break repair pathway genes and glioma susceptibility

Background Genetic variations in DNA double-strand break repair genes can influence the ability of a cell to repair damaged DNA and alter an individual’s susceptibility to cancer. We studied whether polymorphisms in DNA double-strand break repair genes are associated with an increased risk of glioma development. Methods We genotyped 10 potentially functional single nucleotide...

Comparison of microbial diversity determined with the same variable tag sequence extracted from two different PCR amplicons

Background Deep sequencing of the variable region of 16S rRNA genes has become the predominant tool for studying microbial ecology. As sequencing datasets have accumulated, meta-analysis of sequences obtained with different variable 16S rRNA gene targets and by different sequencing methods has become an intriguing prospect that remains to be evaluated experimentally. Results We...

MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement

Background Ortholog assignment is a critical and fundamental problem in comparative genomics, since orthologs are considered to be functional counterparts in different species and can be used to infer molecular functions of one species from those of other species. MSOAR is a recently developed high-throughput system for assigning one-to-one orthologs between closely related...

BMP4, a strong better prognosis predictor, has a subtype preference and cell development association in gliomas

Background The bone morphogenetic family proteins (BMP) are phytogenetically conserved proteins, which are essential for embryonic development. The key regulatory subunit, the bone morphogenetic protein 4 (BMP4), is overexpressed and associated with tumor metastasis in a variety of cancers. However, the prognostic and molecular features of gliomas with BMP4 expression is still...

SEED: efficient clustering of next-generation sequences

Motivation: Similarity clustering of next-generation sequences (NGS) is an important computational problem to study the population sizes of DNA/RNA molecules and to reduce the redundancies in NGS data. Currently, most sequence clustering algorithms are limited by their speed and scalability, and thus cannot handle data with tens of millions of reads. Results: Here, we introduce...