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Bioinformatics Methods and Biological Interpretation for Next-Generation Sequencing Data BioMed Research International Bioinformatics Methods and Biological Interpretation for Next-Generation Sequencing Data Guest Editors: Guohua Wang, Yunlong Liu, Dongxiao Zhu, Gunnar W. Klau, and Weixing Feng Bioinformatics Methods and Biological Interpretation for Next-Generation Sequencing Data BioMed Research International Bioinformatics Methods and Biological Interpretation for Next-Generation Sequencing Data Guest Editors: Guohua Wang, Yunlong Liu, Dongxiao Zhu, Gunnar W. Klau, and Weixing Feng Copyright © 2015 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in “BioMed Research International.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Contents Bioinformatics Methods and Biological Interpretation for Next-Generation Sequencing Data, Guohua Wang, Yunlong Liu, Dongxiao Zhu, Gunnar W. Klau, and Weixing Feng Volume 2015, Article ID 690873, 2 pages MicroRNA Promoter Identification in Arabidopsis Using Multiple Histone Markers,YumingZhao, Fang Wang, and Liran Juan Volume 2015, Article ID 861402, 10 pages Constructing a Genome-Wide LD Map of Wild A. gambiae Using Next-Generation Sequencing, Xiaohong Wang, Yaw A. Afrane, Guiyun Yan, and Jun Li Volume 2015, Article ID 238139, 8 pages Survey of Programs Used to Detect Alternative Splicing Isoforms from Deep Sequencing Data In Silico, Feng Min, Sumei Wang, and Li Zhang Volume 2015, Article ID 831352, 9 pages Understanding Transcription Factor Regulation by Integrating Gene Expression and DNase I Hypersensitive Sites, Guohua Wang, Fang Wang, Qian Huang, Yu Li, Yunlong Liu, and Yadong Wang Volume 2015, Article ID 757530, 7 pages Active Microbial Communities Inhabit Sulphate-Methane Interphase in Deep Bedrock Fracture Fluids in Olkiluoto, Finland,MalinBomberg,MariNyyssonen,¨ Petteri Pitkanen,¨ Anne Lehtinen, and Merja Itavaara¨ Volume 2015, Article ID 979530, 17 pages 454-Pyrosequencing Analysis of Bacterial Communities from Autotrophic Nitrogen Removal Bioreactors Utilizing Universal Primers: Effect of Annealing Temperature, Alejandro Gonzalez-Martinez, Alejandro Rodriguez-Sanchez, Belen´ Rodelas, Ben A. Abbas, Maria Victoria Martinez-Toledo, Mark C. M. van Loosdrecht, F. Osorio, and Jesus Gonzalez-Lopez Volume 2015, Article ID 892013, 12 pages mmnet: An R Package for Metagenomics Systems Biology Analysis, Yang Cao, Xiaofei Zheng, Fei Li, and Xiaochen Bo Volume 2015, Article ID 167249, 5 pages Genetic Interactions Explain Variance in Cingulate Amyloid Burden: An AV-45 PET Genome-Wide Association and Interaction Study in the ADNI Cohort, Jin Li, Qiushi Zhang, Feng Chen, Jingwen Yan, Sungeun Kim, Lei Wang, Weixing Feng, Andrew J. Saykin, Hong Liang, and Li Shen Volume 2015, Article ID 647389, 11 pages How to Isolate a Plant’s Hypomethylome in One Shot, Elisabeth Wischnitzki, Eva Maria Sehr, Karin Hansel-Hohl, Maria Berenyi, Kornel Burg, and Silvia Fluch Volume 2015, Article ID 570568, 12 pages Hindawi Publishing Corporation BioMed Research International Volume 2015, Article ID 690873, 2 pages http://dx.doi.org/10.1155/2015/690873 Editorial Bioinformatics Methods and Biological Interpretation for Next-Generation Sequencing Data Guohua Wang,1 Yunlong Liu,2 Dongxiao Zhu,3 Gunnar W. Klau,4 and Weixing Feng5 1 School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China 2Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA 3Department of Computer Science, Wayne State University, Detroit, MI 48202, USA 4Life Sciences, Centrum Wiskunde & Informatica, Science Park 123, 1098 XG Amsterdam, Netherlands 5Pattern Recognition and Intelligent System Institute, Automation College, Harbin Engineering University, Harbin, Heilongjiang 150001, China Correspondence should be addressed to Guohua Wang; [email protected] Received 24 June 2015; Accepted 24 June 2015 Copyright © 2015 Guohua Wang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Next-generation sequencing (NGS) technologies have revo- In “mmnet: An R Package for Metagenomics Systems lutionarily reshaped the landscape of “-omics” research areas Biology Analysis,” the authors developed R package, mmnet, and their effects are becoming increasingly widespread. With to implement community-level metabolic network recon- its significantly lower costs and higher throughput, NGS struction and also implement a set of functions for automatic has been applied to genome, transcriptome, and epigenome analysis pipeline construction. The package has substantial research. The plethora of information that emerges from potentials in metagenomic studies that focus on identifying large-scale next-generation sequencing experiments has trig- system-level variations of human microbiome associated gered the development of bioinformatics tools and method with disease. for efficient analysis, interpretation, and visualization of NGS The paper “Constructing a Genome-Wide LD Map data. Such methods and tools will substantially promote of Wild A. gambiae Using Next-Generation Sequencing” the life-science community to better and efficiently help sequenced the genomes of nine individual wild A. gambiae understand the underlying biological principles and mech- mosquitoes using next-generation sequencing technologies. anisms. This special issue mainly focuses on the original And 2,219,815 common single nucleotide polymorphisms research articles as well as review articles that develop (SNPs) were detected. Nearly one million SNPs that were new bioinformatics approaches, present novel platforms and genotyped with 99.6% confidence were extracted from these systems, and describe concise models well explaining the high-throughput sequencing data. Based on these SNP biological context and application in relation to genetics, genotypes, the authors constructed a genome-wide linkage metagenomics, and clinical study from NGS data. disequilibrium (LD) map for wild A. gambiae mosquitoes This special issue contains nine papers. Two papers from malaria-endemic areas in Kenya and made it available discuss the application of NGS data analysis in metagenomics through a public website. and one paper presents R package for metagenomic systems The paper entitled “How to Isolate a Plant’s Hypomethy- biology analysis. One review paper discusses the software lome in One Shot” provided an easy, fast, and cost-effective to detect alternative splicing isoforms from deep sequencing tool to obtain a plant’s hypomethylome (the nonmethylated data. The other five papers are related to application of NGS part of the genome) by an optimized methyl filtration proto- data integration in genomics, genetics, and epigenetics. col with subsequent next-generation sequencing, in essence 2 BioMed Research International a variant of MRE-seq. The hypomethylomes which were two bench-scale (MBR and low temperature CANON) and identified in three plant species, Oryza sativa, Picea abies, threefull-scale(Anammox,CANON,andDEMON),by and Crocus sativus, showed clear enrichment in genes and optimization of primer selection and PCR conditions. The their flanking regions. This method is extremely conducive pyrosequencing data showed that annealing temperature of ∘ to studying and understanding the genomes of nonmodel 45 C yielded the best results in terms of species richness and organisms. diversity for all bioreactors analyzed. In “Genetic Interactions Explain Variance in Cingulate The paper entitled “Active Microbial Communities Amyloid Burden: An AV-45 PET Genome-Wide Association Inhabit Sulphate-Methane Interphase in Deep Bedrock Frac- andInteractionStudyintheADNICohort,”theauthors ture Fluids in Olkiluoto, Finland” investigated active micro- performed a genome-wide association study (GWAS) and a bial communities of deep crystalline bedrock fracture water genome-wide interaction study (GWIS) of an amyloid imag- from seven different boreholes in Olkiluoto (Western Fin- ing phenotype, using the data from Alzheimer’s Disease land), using bacterial and archaeal 16S rRNA, dsrB, and mcrA (AD) Neuroimaging Initiative. The GWAS analysis revealed gene transcript targeted 454 pyrosequencing. The results significant hits within or proximal to APOE, APOC1, and demonstrated that active and highly diverse but sparse and TOMM40 genes. The GWIS analysis yielded 8 novel SNP- stratified microbial communities inhabited the Fennoscan- SNP interaction findings that warrant replication and further dian deep bedrock ecosystems. investigation. The paper “Understanding Transcription Factor Regula- Acknowledgments tion by Integrating Gene Expression and DNase I Hyper- sensitive Sites” identified the functional transcription factor The guest editors heartily thank all authors for their excellent binding sites in gene regulatory region by integrating the contributions and patience in undertaking revisions of their DNase I hypersensitive sites with known position weight manuscripts.Wewouldliketoacknowledgethenumerous matrices. The authors present a model-based computational reviewers for their professional effort that helped to improve approach to predict a set of transcription factors that poten- the quality
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