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The Scientific World Journal
Volume 2013, Article ID 730210, 10 pages
http://dx.doi.org/10.1155/2013/730210
Review Article

Computational and Bioinformatics Frameworks for Next-Generation Whole Exome and Genome Sequencing

Rare Genomics Institute, 4100 Forest Park Avenue, Suite 204, St. Louis, MO 63108, USA

Received 28 October 2012; Accepted 22 November 2012

Academic Editors: R. Jiang, W. Tian, J. Wan, and X. Zhao

Copyright © 2013 Marisa P. Dolled-Filhart 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.

Citations to this Article [24 citations]

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  • Mattia D'Antonio, Paolo D'Onorio De Meo, Tiziana Castrignano, Giovanni Erbacci, Matteo Pallocca, and Graziano Pesole, “ODESSA: A high performance analysis pipeline for Ultra Deep targeted Exome Sequencing data,” 2014 International Conference on High Performance Computing & Simulation (HPCS), pp. 608–615, . View at Publisher · View at Google Scholar
  • Dongliang Ding, Dongyue Wu, and Fuli Yu, “An overview on cloud computing platform spark for Human Genome mining,” 2016 IEEE International Conference on Mechatronics and Automation, pp. 2605–2610, . View at Publisher · View at Google Scholar
  • Giuseppe Aceto, Antonio Montieri, Valerio Persico, Antonio Pescape, Valeria D'Argenio, Francesco Salvatore, and Lucio Pastore, “A First Look at an Automated Pipeline for NGS-Based Breast-Cancer Diagnosis: The CArDIGAN Approach,” 2016 12th International Conference on Signal-Image Technology & Internet-Based Systems (SITIS), pp. 507–514, . View at Publisher · View at Google Scholar
  • Josefina Lenis, Miquel Angel Senar, Josefina Lenis, and Miquel Angel Senar, “On the Performance of BWA on NUMA Architectures,” 2015 IEEE Trustcom/BigDataSE/ISPA, pp. 236–241, . View at Publisher · View at Google Scholar
  • Anna Benet-Pages, Sebastian H. Eck, Marius Kuhn, Sebastian Vosberg, Philipp A. Greif, Klaus H. Metzeler, Saskia Biskup, Clemens Mueller-Reible, and Hanns-Georg Klein, “Applications and data analysis of next-generation sequencing,” Laboratoriumsmedizin-Journal of Laboratory Medicine, vol. 37, no. 6, pp. 305–315, 2013. View at Publisher · View at Google Scholar
  • Brijesh Singh Yadav, Venkateswarlu Ronda, Dinesh P Vashista, and Bhaskar Sharma, “Sequencing and computational approaches to identification and characterization of microbial organisms.,” Biomedical engineering and computational biology, vol. 5, pp. 43–9, 2013. View at Publisher · View at Google Scholar
  • Alimuddin Zumla, Jaffar A Al-Tawfiq, Virve I Enne, Mike Kidd, Christian Drosten, Judy Breuer, Marcel A Muller, David Hui, Markus Maeurer, Matthew Bates, Peter Mwaba, Rafaat Al-Hakeem, Gregory Gray, Philippe Gautret, Abdullah A Al-Rabeeah, Ziad A Memish, and Vanya Gant, “Rapid point of care diagnostic tests for viral and bacterial respiratory tract infections—needs, advances, and future prospects,” The Lancet Infectious Diseases, 2014. View at Publisher · View at Google Scholar
  • Stefan W. Groetzinger, Intikhab Alam, Wail Ba Alawi, Vladimir B. Bajic, Ulrich Stingl, and Joerg Eppinger, “Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of genefunction prediction using a profile and pattern matching algorithm (PPMA),” Frontiers in Microbiology, vol. 5, 2014. View at Publisher · View at Google Scholar
  • Vahan Simonyan, and Raja Mazumder, “High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis,” Genes, vol. 5, no. 4, pp. 957–981, 2014. View at Publisher · View at Google Scholar
  • Byong H. Lee, “Concepts and Tools for Recombinant DNA Technology,” Fundamentals of Food Biotechnology, pp. 147–192, 2014. View at Publisher · View at Google Scholar
  • T. J. Ow, K. Upadhyay, T. J. Belbin, M. B. Prystowsky, H. Ostrer, and R. V. Smith, “Bioinformatics in otolaryngology research. Part one: concepts in DNA sequencing and gene expression analysis,” Journal of Laryngology and Otology, vol. 128, no. 10, pp. 848–858, 2014. View at Publisher · View at Google Scholar
  • Darren A Abbey, Jason Funt, Mor N Lurie-Weinberger, Dawn A Thompson, Aviv Regev, Chad L Myers, and Judith Berman, “YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens,” Genome Medicine, vol. 6, no. 11, pp. 100, 2014. View at Publisher · View at Google Scholar
  • Diana Mandelker, Bruce A Beckwith, Jason M Baron, David S McClintock, Frank C Kuo, Matthew S Lebo, John R Gilbertson, Roy E Lee, Mia Y Platt, Gregory Riedlinger, Andrew Quinn, Luigi K F Rao, Veronica E Klepeis, Michael Mahowald, and William J Lane, “Pathology informatics fellowship training: Focus on molecular pathology.,” Journal of pathology informatics, vol. 5, no. 1, pp. 11, 2014. View at Publisher · View at Google Scholar
  • Daoud Meerzaman, Barbara K. Dunn, Maxwell Lee, Qingrong Chen, Chunhua Yan, and Sharon Ross, “The promise of omics-based approaches to cancer prevention,” Seminars in Oncology, 2015. View at Publisher · View at Google Scholar
  • Byong H. Leepp. 1–518, 2015. View at Publisher · View at Google Scholar
  • Rong Chen, Jiaming Luo, and Dingding Zhang, “Progress of molecular genetics research on rheumatoid arthritis,” Chinese Journal of Medical Genetics, vol. 32, no. 5, pp. 728–733, 2015. View at Publisher · View at Google Scholar
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  • Kewal K. Jain, “An overview of methods used in neurogenomics and their applications,” Neuromethods, vol. 97, pp. 1–59, 2015. View at Publisher · View at Google Scholar
  • Ariel Lee, Carol Shen, Tony Shen, and C Jimmy Lin, “The long tail and rare disease research: the impact of next-generation sequencing for rare Mendelian disorders,” Genetics research, vol. 97, pp. e15, 2015. View at Publisher · View at Google Scholar
  • Lay Kek Teh, Vinothini Subramaniam, Tuan Azlin Tuan Abdu Aziz, Lian Shien Lee, Mohamed Izwan Ismail, Choo Yee Yu, Geik Yong Ang, Mohammad Richard James Johari, Rose Iszati Ismet, Noor Saadah Sahak, Aminuddin Ahmad, Thuhairah Abdul Rahman, Fadzilah Mohd Nor @ Ghazali, SyahrulAzlin Shaari, Mustaffa Omar, Adzrool Idzwan Ismail, Kamarudzaman Md. Isa, Hood Salleh, and Mohd Zaki Salleh, “Systematic characterization and comparison of the CYP2C9 variability of the Orang Asli in Malaysia with 12 populations,” Drug Metabolism and Pharmacokinetics, 2016. View at Publisher · View at Google Scholar
  • Bahareh Rabbani, Hirofumi Nakaoka, Shahin Akhondzadeh, Mustafa Tekin, and Nejat Mahdieh, “Next generation sequencing: implications in personalized medicine and pharmacogenomics,” Mol. BioSyst., 2016. View at Publisher · View at Google Scholar
  • Andriniaina Andy Nkili-Meyong, Laurent Bigarré, Ingrid Labouba, Tatiana Vallaeys, Jean-Christophe Avarre, and Nicolas Berthet, “Contribution of Next-Generation Sequencing to Aquatic and Fish Virology,” Intervirology, pp. 285–300, 2017. View at Publisher · View at Google Scholar
  • Nina Pirih, and Tanja Kunej, “Toward a taxonomy for multi-omics science? Terminology development for whole genome study approaches by omics technology and hierarchy,” OMICS A Journal of Integrative Biology, vol. 21, no. 1, pp. 1–16, 2017. View at Publisher · View at Google Scholar
  • D.L. Duncan, and N.M. Patel, “Next-Generation Sequencing in the Clinical Laboratory,” Diagnostic Molecular Pathology, pp. 25–33, 2017. View at Publisher · View at Google Scholar