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Journal of Biomedicine and Biotechnology
Volume 2012 (2012), Article ID 251364, 11 pages
http://dx.doi.org/10.1155/2012/251364
Review Article

Comparison of Next-Generation Sequencing Systems

NGS Sequencing Department, Beijing Genomics Institute (BGI), 4th Floor, Building 11, Beishan Industrial Zone, Yantian District, Guangdong, Shenzhen 518083, China

Received 11 February 2012; Revised 27 March 2012; Accepted 2 April 2012

Academic Editor: P. J. Oefner

Copyright © 2012 Lin Liu 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.

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  • R. Hitzemann, D. Bottomly, P. Darakjian, N. Walter, O. Iancu, R. Searles, B. Wilmot, and S. McWeeney, “Genes, behavior and next-generation RNA sequencing,” Genes, Brain and Behavior, vol. 12, no. 1, pp. 1–12, 2012. View at Publisher · View at Google Scholar
  • Agnes Dettai, Cyril Gallut, Sophie Brouillet, Joel Pothier, Guillaume Lecointre, and Regis Debruyne, “Conveniently Pre-Tagged and Pre-Packaged: Extended Molecular Identification and Metagenomics Using Complete Metazoan Mitochondrial Genomes,” Plos One, vol. 7, no. 12, 2012. View at Publisher · View at Google Scholar
  • S. Giampaoli, G. Chillemi, F. Valeriani, D. Lazzaro, M. Borro, G. Gentile, M. Simmaco, G. Zanni, A. Berti, and V. Romano Spica, “The SNPs in the human genetic blueprint era,” New Biotechnology, 2012. View at Publisher · View at Google Scholar
  • Mariateresa Volpicella, Claudia Leoni, Alessandra Costanza, Immacolata Fanizza, Antonio Placido, and Luigi R. Ceci, “Genome Walking by Next Generation Sequencing Approaches,” Biology, vol. 1, no. 3, pp. 495–507, 2012. View at Publisher · View at Google Scholar
  • Steffen Kolb, and Astrid Stacheter, “Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment,” Frontiers in Microbiology, vol. 4, 2013. View at Publisher · View at Google Scholar
  • R. Campos-Herrera, J. G. Ali, B. M. Diaz, and L. W. Duncan, “Analyzing spatial patterns linked to the ecology of herbivores and their natural enemies in the soil,” Frontiers in Plant Science, vol. 4, 2013. View at Publisher · View at Google Scholar
  • Philip T. Cagle, Timothy Craig Allen, and Randall J. Olsen, “Lung Cancer Biomarkers: Present Status and Future Developments,” Archives of Pathology & Laboratory Medicine, vol. 137, no. 9, pp. 1191–1198, 2013. View at Publisher · View at Google Scholar
  • Eriko Koshimizu, Satoko Miyatake, Nobuhiko Okamoto, Mitsuko Nakashima, Yoshinori Tsurusaki, Noriko Miyake, Hirotomo Saitsu, and Naomichi Matsumoto, “Performance Comparison of Bench-Top Next Generation Sequencers Using Microdroplet PCR-Based Enrichment for Targeted Sequencing in Patients with Autism Spectrum Disorder,” Plos One, vol. 8, no. 9, 2013. View at Publisher · View at Google Scholar
  • Julia M. Di Bella, Yige Bao, Gregory B. Gloor, Jeremy P. Burton, and Gregor Reid, “High throughput sequencing methods and analysis for microbiome research,” Journal of Microbiological Methods, 2013. View at Publisher · View at Google Scholar
  • Sing Yu Moorcraft, Elizabeth C. Smyth, and David Cunningham, “The role of personalized medicine in metastatic colorectal cancer: An evolving landscape,” Therapeutic Advances in Gastroenterology, vol. 6, no. 5, pp. 381–395, 2013. View at Publisher · View at Google Scholar
  • Sean D. Taylor, Nolan G. Ericson, Joshua N. Burton, Tomas A. Prolla, John R. Silber, Jay Shendure, and Jason H. Bielas, “Targeted Enrichment and High-Resolution Digital Profiling of Mitochondrial DNA Deletions in Human Brain,” Aging Cell, 2013. View at Publisher · View at Google Scholar
  • Zhaochun Ma, Raymond W. Lee, Bin Li, Paul Kenney, Yufang Wang, Jonathan Erikson, Swati Goyal, and Kaiqin Lao, “Isothermal amplification method for next-generation sequencing,” Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 35, pp. 14320–14323, 2013. View at Publisher · View at Google Scholar
  • Brian J. Haas, Matthias Lieber, Matthew D Macmanes, Michael Ott, Joshua Orvis, Nathalie Pochet, Francesco Strozzi, Nathan Weeks, Rick Westerman, Thomas William, Colin N Dewey, Alexie Papanicolaou, Robert Henschel, Richard D Leduc, Nir Friedman, Aviv Regev, Moran Yassour, Manfred Grabherr, Philip D Blood, Joshua Bowden, Matthew Brian Couger, David Eccles, and Bo Li, “De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis,” Nature Protocols, vol. 8, no. 8, pp. 1494–1512, 2013. View at Publisher · View at Google Scholar
  • GuangCheng Xie, JieMei Yu, and ZhaoJun Duan, “New strategy for virus discovery: Viruses identified in human feces in the last decade,” Science China Life Sciences, vol. 56, no. 8, pp. 688–696, 2013. View at Publisher · View at Google Scholar
  • Xiaohan Chen, Qiong Yang, Zhenping Liao, Hui Wang, Digang Zeng, Xiuli Chen, Daxiang Xie, Yongzhen Zhao, Chunling Yang, Yongmei Li, Ning Ma, and Ming Li, “Transcriptome Analysis of Litopenaeus vannamei in Response to White Spot Syndrome Virus Infection,” PLoS ONE, vol. 8, no. 8, 2013. View at Publisher · View at Google Scholar
  • Nathan D. Grubaugh, Scott S. McMenamy, Michael J. Turell, and John S. Lee, “Multi-Gene Detection and Identification of Mosquito-Borne RNA Viruses Using an Oligonucleotide Microarray,” PLoS Neglected Tropical Diseases, vol. 7, no. 8, 2013. View at Publisher · View at Google Scholar
  • Matthew T. Laurie, Jessica A. Bertout, Sean D. Taylor, Joshua N. Burton, Jay A. Shendure, and Jason H. Bielas, “Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries,” Biotechniques, vol. 55, no. 2, pp. 61–67, 2013. View at Publisher · View at Google Scholar
  • Lijia Cui, Alison Morris, and Elodie Ghedin, “The human mycobiome in health and disease,” Genome Medicine, vol. 5, no. 7, 2013. View at Publisher · View at Google Scholar
  • Christian Milani, Douwe van Sinderen, Abelardo Margolles, Marco Ventura, Arancha Hevia, Elena Foroni, Sabrina Duranti, Francesca Turroni, Gabriele Andrea Lugli, Borja Sanchez, Rebeca Martín, and Miguel Gueimonde, “Assessing the Fecal Microbiota: An Optimized Ion Torrent 16S rRNA Gene-Based Analysis Protocol,” PLoS ONE, vol. 8, no. 7, 2013. View at Publisher · View at Google Scholar
  • Wei Zhou, Yiyi Hu, Zhenghong Sui, Feng Fu, Jinguo Wang, Lianpeng Chang, Weihua Guo, and Binbin Li, “Genome Survey Sequencing and Genetic Background Characterization of Gracilariopsis lemaneiformis (Rhodophyta) Based on Next-Generation Sequencing,” PLoS ONE, vol. 8, no. 7, 2013. View at Publisher · View at Google Scholar
  • Michael Smith, and Gopinath Rajadinakaran, “The Transcriptomics to Proteomics of Hair Cell Regeneration: Looking for a Hair Cell in a Haystack,” Microarrays, vol. 2, no. 3, pp. 186–207, 2013. View at Publisher · View at Google Scholar
  • Jeff J. Doyle, “The promise of genomics for a “next generation” of advances in higher-level legume molecular systematics,” South African Journal of Botany, 2013. View at Publisher · View at Google Scholar
  • Karen E. Mock, Bryce A. Richardson, and Paul G. Wolf, “Molecular tools and aspen management: A primer and prospectus,” Forest Ecology and Management, vol. 299, pp. 6–13, 2013. View at Publisher · View at Google Scholar
  • Sara Huston Katsanis, and Nicholas Katsanis, “Molecular genetic testing and the future of clinical genomics,” Nature Reviews Genetics, vol. 14, no. 6, pp. 415–426, 2013. View at Publisher · View at Google Scholar
  • Monic Roengvoraphoj, Gregory J. Tsongalis, Konstantin H. Dragnev, and James R. Rigas, “Epidermal growth factor receptor tyrosine kinase inhibitors as initial therapy for non-small cell lung cancer: Focus on epidermal growth factor receptor mutation testing and mutation-positive patients,” Cancer Treatment Reviews, 2013. View at Publisher · View at Google Scholar
  • Sp Daiger, Ls Sullivan, and Sj Bowne, “Genes and mutations causing retinitis pigmentosa,” Clinical Genetics, 2013. View at Publisher · View at Google Scholar
  • Man-Wah Li, Xinpeng Qi, Meng Ni, and Hon-Ming Lam, “Silicon era of carbon-based life: Application of genomics and bioinformatics in crop stress research,” International Journal of Molecular Sciences, vol. 14, no. 6, pp. 11444–11483, 2013. View at Publisher · View at Google Scholar
  • Davit Bzhalava, Bengt Persson, Ola Forslund, Joakim Dillner, Hanna Johansson, Johanna Ekström, Helena Faust, Birgitta Möller, Carina Eklund, Peter Nordin, Bo Stenquist, and John Paoli, “Unbiased Approach for Virus Detection in Skin Lesions,” PLoS ONE, vol. 8, no. 6, 2013. View at Publisher · View at Google Scholar
  • Laura E. MacConaill, “Existing and Emerging Technologies for Tumor Genomic Profiling,” Journal of Clinical Oncology, vol. 31, no. 15, pp. 1815–1824, 2013. View at Publisher · View at Google Scholar
  • Kelly Sillence, Tracey Madgett, Llinos Roberts, Timothy Overton, and Neil Avent, “Non-Invasive Screening Tools for Down’s Syndrome: A Review,” Diagnostics, vol. 3, no. 2, pp. 291–314, 2013. View at Publisher · View at Google Scholar
  • Danilo Ercolini, “High-throughput sequencing and metagenomics: Moving forward in the culture-independent analysis of food microbial ecology,” Applied and Environmental Microbiology, vol. 79, no. 10, pp. 3148–3155, 2013. View at Publisher · View at Google Scholar
  • Elles M. J. Boon, and Brigitte H. W. Faas, “Benefits and limitations of whole genome versus targeted approaches for noninvasive prenatal testing for fetal aneuploidies,” Prenatal Diagnosis, vol. 33, no. 6, pp. 563–568, 2013. View at Publisher · View at Google Scholar
  • Mark John Pallen, “Reply to Updating benchtop sequencing performance comparison,” Nature Biotechnology, vol. 31, no. 4, pp. 296, 2013. View at Publisher · View at Google Scholar
  • Cs Ku, Dn Cooper, B Iacopetta, and Dh Roukos, “Integrating next-generation sequencing into the diagnostic testing of inherited cancer predisposition,” Clinical Genetics, vol. 83, no. 1, pp. 2–6, 2013. View at Publisher · View at Google Scholar
  • Karen Frese, Hugo Katus, and Benjamin Meder, “Next-Generation Sequencing: From Understanding Biology to Personalized Medicine,” Biology, vol. 2, no. 1, pp. 378–398, 2013. View at Publisher · View at Google Scholar
  • Digang Zeng, Zhenping Liao, Hui Wang, Xiaohan Chen, Xiuli Chen, Daxiang Xie, Yongzhen Zhao, Chunling Yang, Yongmei Li, Ning Ma, Min Peng, and Qiong Yang, “Transcriptome Analysis of Pacific White Shrimp (Litopenaeus vannamei) Hepatopancreas in Response to Taura Syndrome Virus (TSV) Experimental Infection,” PLoS ONE, vol. 8, no. 2, 2013. View at Publisher · View at Google Scholar
  • Fei Chen, Mengxing Dong, Meng Ge, Lingxiang Zhu, Lufeng Ren, Guocheng Liu, and Rong Mu, “The History and Advances of Reversible Terminators Used in New Generations of Sequencing Technology,” Genomics, Proteomics & Bioinformatics, vol. 11, no. 1, pp. 34–40, 2013. View at Publisher · View at Google Scholar
  • Nasim Vasli, and Jocelyn Laporte, “Impacts of massively parallel sequencing for genetic diagnosis of neuromuscular disorders,” Acta Neuropathologica, vol. 125, no. 2, pp. 173–185, 2013. View at Publisher · View at Google Scholar
  • Thomas Haselgrübler, Michaela Haider, Bozhi Ji, Kata Juhasz, Alois Sonnleitner, Zsolt Balogi, and Jan Hesse, “High-throughput, multiparameter analysis of single cells,” Analytical and Bioanalytical Chemistry, 2013. View at Publisher · View at Google Scholar
  • Paul Hong, Cindy M. Liu, Lora Nordstrom, and Anil K. Lalwani, “The role of the human microbiome in otolaryngology-head and neck surgery: A contemporary review,” The Laryngoscope, vol. 124, no. 6, pp. 1352–1357, 2013. View at Publisher · View at Google Scholar
  • Takuyo Aita, Norikazu Ichihashi, and Tetsuya Yomo, “Probabilistic model based error correction in a set of various mutant sequences analyzed by next-generation sequencing,” Computational Biology and Chemistry, vol. 47, pp. 221–230, 2013. View at Publisher · View at Google Scholar
  • Claudia Calabrese, Marina Mangiulli, Caterina Manzari, Anna Maria Paluscio, Mariano Francesco Caratozzolo, Flaviana Marzano, Ivana Kurelac, Anna Maria D'Erchia, Domenica D'Elia, Flavio Licciulli, Sabino Liuni, Ernesto Picardi, Marcella Attimonelli, Giuseppe Gasparre, Anna Maria Porcelli, Graziano Pesole, Elisabetta Sbisa, and Apollonia Tullo, “A platform independent RNA-Seq protocol for the detection of transcriptome complexity,” Bmc Genomics, vol. 14, 2013. View at Publisher · View at Google Scholar
  • Andreas O. Tillmar, Barbara Dell'Amico, Jenny Welander, and Gunilla Holmlund, “A Universal Method for Species Identification of Mammals Utilizing Next Generation Sequencing for the Analysis of DNA Mixtures,” Plos One, vol. 8, no. 12, 2013. View at Publisher · View at Google Scholar
  • Sara El-Metwally, Taher Hamza, Magdi Zakaria, and Mohamed Helmy, “Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges,” Plos Computational Biology, vol. 9, no. 12, 2013. View at Publisher · View at Google Scholar
  • Alexandra Dangel, and Hanns-Georg Klein, “Developments and insights into the analysis of the human microbiome,” Laboratoriumsmedizin-Journal of Laboratory Medicine, vol. 37, no. 6, pp. 329–335, 2013. View at Publisher · View at Google Scholar
  • Gous Miah, Mohd Y. Rafii, Mohd R. Ismail, Adam B. Puteh, Harun A. Rahim, Kh. Nurul Islam, and Mohammad Abdul Latif, “A Review of Microsatellite Markers and Their Applications in Rice Breeding Programs to Improve Blast Disease Resistance,” International Journal of Molecular Sciences, vol. 14, no. 11, pp. 22499–22528, 2013. View at Publisher · View at Google Scholar
  • Ying Yang, Meng Xu, Qunfeng Luo, Jie Wang, and Huogen Li, “De novo transcriptome analysis of Liriodendron chinense petals and leaves by Illumina sequencing,” Gene, 2013. View at Publisher · View at Google Scholar
  • Roshan Padmanabhan, Ajay Kumar Mishra, Didier Raoult, and Pierre-Edouard Fournier, “Genomics and Metagenomics in Medical Microbiology,” Journal of Microbiological Methods, 2013. View at Publisher · View at Google Scholar
  • Agnese Lupo, Krisztina M. Papp-Wallace, Parham Sendi, Robert A. Bonomo, and Andrea Endimiani, “Non-phenotypic tests to detect and characterize antibiotic resistance mechanisms in Enterobacteriaceae,” Diagnostic Microbiology and Infectious Disease, 2013. View at Publisher · View at Google Scholar
  • Fengqi Chang, and Marilyn M. Li, “Clinical Application of Amplicon-based Next-Generation Sequencing in Cancer,” Cancer Genetics, 2013. View at Publisher · View at Google Scholar
  • Shawna Miles, Lihong Li, Jerry Davison, and Linda L. Breeden, “Xbp1 Directs Global Repression of Budding Yeast Transcription during the Transition to Quiescence and Is Important for the Longevity and Reversibility of the Quiescent State,” Plos Genetics, vol. 9, no. 10, 2013. View at Publisher · View at Google Scholar
  • Marco Ferrarini, Marco Moretto, Judson A. Ward, Nada Surbanovski, Vladimir Stevanovic, Lara Giongo, Roberto Viola, Duccio Cavalieri, Riccardo Velasco, Alessandro Cestaro, and Daniel J. Sargent, “An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome,” Bmc Genomics, vol. 14, 2013. View at Publisher · View at Google Scholar
  • Deirdre L. Church, “Principles of Capillary-Based Sequencing for Clinical Microbiologists,” Clinical Microbiology Newsletter, vol. 35, no. 2, pp. 11–18, 2013. View at Publisher · View at Google Scholar
  • M.R. Capobianchi, E. Giombini, and G. Rozera, “Next-generation sequencing technology in clinical virology,” Clinical Microbiology and Infection, vol. 19, no. 1, pp. 15–22, 2013. View at Publisher · View at Google Scholar
  • Manfred Kunz, Michael Dannemann, and Janet Kelso, “High-throughput sequencing of the melanoma genome,” Experimental Dermatology, vol. 22, no. 1, pp. 10–17, 2013. View at Publisher · View at Google Scholar
  • Martin Dragosits, and Diethard Mattanovich, “Adaptive laboratory evolution – principles and applications for biotechnology,” Microbial Cell Factories, vol. 12, no. 1, pp. 64, 2013. View at Publisher · View at Google Scholar
  • Madhugiri Nageswara-Rao, Jaya R Soneji, Charles Kwit, and C Stewart, “Advances in biotechnology and genomics of switchgrass,” Biotechnology for Biofuels, vol. 6, no. 1, pp. 77, 2013. View at Publisher · View at Google Scholar
  • Georgios A Pavlopoulos, Anastasis Oulas, Ernesto Iacucci, Alejandro Sifrim, Yves Moreau, Reinhard Schneider, Jan Aerts, and Ioannis Iliopoulos, “Unraveling genomic variation from next generation sequencing data,” BioData Mining, vol. 6, no. 1, 2013. View at Publisher · View at Google Scholar
  • Ying-Chih Lin, Chin-Sheng Yu, and Yen-Jen Lin, “Enabling Large-Scale Biomedical Analysis in the Cloud,” BioMed Research International, vol. 2013, pp. 1–6, 2013. View at Publisher · View at Google Scholar
  • Chun-Hung Richard Lin, Chun-Hao Wen, Ying-Chih Lin, Kuang-Yuan Tung, Rung-Wei Lin, and Chun-Yuan Lin, “A P2P Framework for Developing Bioinformatics Applications in Dynamic Cloud Environments,” International Journal of Genomics, vol. 2013, pp. 1–9, 2013. View at Publisher · View at Google Scholar
  • Jorge L. Cervantes, and Bo-Young Hong, “Role of Next-Generation Sequencing in Understanding the Interactions between Human Papillomavirus and the Cervicovaginal Microbiome,” Gynecologic and Obstetric Investigation, vol. 76, no. 4, pp. 195–202, 2013. View at Publisher · View at Google Scholar
  • Jacques Zaneveld, Feng Wang, Xia Wang, and Rui Chen, “Dawn of ocular gene therapy: Implications for molecular diagnosis in retinal disease,” Science China Life Sciences, vol. 56, no. 2, pp. 125–133, 2013. View at Publisher · View at Google Scholar
  • Rabab Khairat, Carsten M. Pusch, Raffaella Bianucci, Gamila M. L. Shanab, Amr M. Karim, Markus Ball, Chun-Chi Hsieh Chang, Andreas G. Nerlich, Martin Trautmann, Yehia Z. Gad, and Somaia Ismail, “First insights into the metagenome of Egyptian mummies using next-generation sequencing,” Journal Of Applied Genetics, vol. 54, no. 3, pp. 309–325, 2013. View at Publisher · View at Google Scholar
  • M. Thanigasalam, and P. Dananjayan, “BER Analysis of OFDM Receiver Using MMSE Channel Estimation Method with PTS for Different Subblocks,” International Journal of Computer and Electrical Engineering, pp. 602–605, 2013. View at Publisher · View at Google Scholar
  • Gudrun Schleiermacher, Niloufar Javanmardi, Virginie Bernard, Quentin Leroy, Julie Cappo, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, Valerie Combaret, Frank Speleman, Bram de Wilde, Anna Djos, Ingrid Ora, Fredrik Hedborg, Catarina Traeger, Britt-Marie Holmqvist, Jonas Abrahamsson, Michel Peuchmaur, Jean Michon, Isabelle Janoueix-Lerosey, Per Kogner, Olivier Delattre, and Tommy Martinsson, “Emergence of New ALK Mutations at Relapse of Neuroblastoma,” Journal of Clinical Oncology, vol. 32, no. 25, pp. 2727–+, 2014. View at Publisher · View at Google Scholar
  • Kang Wei, Li-Yuan Wang, Li-Yun Wu, Cheng-Cai Zhang, Hai-Lin Li, Li-Qiang Tan, Hong-Li Cao, and Hao Cheng, “Transcriptome Analysis of Indole-3-Butyric Acid-Induced Adventitious Root Formation in Nodal Cuttings of Camellia sinensis (L.),” Plos One, vol. 9, no. 9, 2014. View at Publisher · View at Google Scholar
  • Bryan C. Runck, Michael B. Kantar, Nicholas R. Jordan, James A. Anderson, Donald L. Wyse, James O. Eckberg, Richard J. Barnes, Clarence L. Lehman, Lee R. DeHaan, Robert M. Stupar, Craig C. Sheaffer, and Paul M. Porter, “The Reflective Plant Breeding Paradigm: A Robust System of Germplasm Development to Support Strategic Diversification of Agroecosystems,” Crop Science, vol. 54, no. 5, pp. 1939–1948, 2014. View at Publisher · View at Google Scholar
  • Philippe Leprohon, Christopher Fernandez-Prada, Élodie Gazanion, Rubens Monte-Neto, and Marc Ouellette, “Drug resistance analysis by next generation sequencing in Leishmania,” International Journal for Parasitology: Drugs and Drug Resistance, 2014. View at Publisher · View at Google Scholar
  • Miguel E. Quinones-Mateu, Santiago Avila, Gustavo Reyes-Teran, and Miguel A. Martinez, “Deep sequencing: Becoming a critical tool in clinical virology,” Journal of Clinical Virology, vol. 61, no. 1, pp. 9–19, 2014. View at Publisher · View at Google Scholar
  • Sheng Li, Scull W. Tighe, Charles M. Nicolet, Deborah Grove, Shawn Levy, William Farmerie, Agnes Viale, Chris Wright, Peter A. Schweitzer, Yuan Gao, Dewey Kim, Joe Boland, Belynda Hicks, Ryan Kim, Sagar Chhangawala, Nadereh Jafari, Nalini Raghavachari, Jorge Gandara, Natalia Garcia-Reyero, Cynthia Hendrickson, David Roberson, Jeffrey Rosenfeldr, Todd Smith, Jason G. Underwood, May Wang, Paul Zumbo, Don A. Baldwin, George S. Grills, and Christopher E. Mason, “Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study,” Nature Biotechnology, vol. 32, no. 9, pp. 915–925, 2014. View at Publisher · View at Google Scholar
  • Christian Milani, Gabriele A. Lugli, Francesca Turroni, Leonardo Mancabelli, Sabrina Duranti, Alice Viappiani, Marta Mangifesta, Nicola Segata, Douwe van Sinderen, and Marco Ventura, “Evaluation of bifidobacterial community composition in the human gut by means of a targeted amplicon sequencing (ITS) protocol,” FEMS Microbiology Ecology, 2014. View at Publisher · View at Google Scholar
  • Rolf Hilker, Kai Bernd Stadermann, Daniel Doppmeier, Joern Kalinowski, Jens Stoye, Jasmin Straube, Joern Winnebald, and Alexander Goesmann, “ReadXplorer-visualization and analysis of mapped sequences,” Bioinformatics, vol. 30, no. 16, pp. 2247–2254, 2014. View at Publisher · View at Google Scholar
  • M. Olejnik, M. Steuwer, S. Gorlatch, and D. Heider, “gCUP: rapid GPU-based HIV-1 co-receptor usage prediction for next-generation sequencing,” Bioinformatics, 2014. View at Publisher · View at Google Scholar
  • Y. Xu, Y. Liu, S. Yao, J. Li, and C. Cheng, “Genome Sequence of Paenibacillus polymyxa Strain CICC 10580, Isolated from the Fruit of Noni (Morinda citrifolia L.) Grown in the Paracel Islands,” Genome Announcements, vol. 2, no. 4, pp. e00854-14–e00854-14, 2014. View at Publisher · View at Google Scholar
  • Erwin L. van Dijk, Hélène Auger, Yan Jaszczyszyn, and Claude Thermes, “Ten years of next-generation sequencing technology,” Trends in Genetics, 2014. View at Publisher · View at Google Scholar
  • R. Daniel, C. Santos, C. Phillips, M. Fondevila, R.A.H. van Oorschot, Á. Carracedo, M.V. Lareu, and D. McNevin, “A SNaPshot of next generation sequencing for forensic SNP analysis,” Forensic Science International: Genetics, 2014. View at Publisher · View at Google Scholar
  • Ting Tang, Xiang Li, Xue Yang, Xue Yu, Jianhui Wang, Fengsong Liu, and Dawei Huang, “Transcriptional Response of Musca domestica Larvae to Bacterial Infection,” Plos One, vol. 9, no. 8, 2014. View at Publisher · View at Google Scholar
  • Andrea Mafficini, Eliana Amato, Matteo Fassan, Michele Simbolo, Davide Antonello, Caterina Vicentini, Maria Scardoni, Samantha Bersani, Marisa Gottardi, Borislav Rusev, Giorgio Malpeli, Vincenzo Corbo, Stefano Barbi, Katarzyna O. Sikora, Rita T. Lawlor, Giampaolo Tortora, and Aldo Scarpa, “Reporting Tumor Molecular Heterogeneity in Histopathological Diagnosis,” Plos One, vol. 9, no. 8, 2014. View at Publisher · View at Google Scholar
  • Gabriel de la Fuente, Alejandro Belanche, Susan E. Girwood, Eric Pinloche, Toby Wilkinson, and C. Jamie Newbold, “Pros and Cons of Ion-Torrent Next Generation Sequencing versus Terminal Restriction Fragment Length Polymorphism T-RFLP for Studying the Rumen Bacterial Community,” Plos One, vol. 9, no. 7, 2014. View at Publisher · View at Google Scholar
  • Miguel A. Hernández-Prieto, Trudi A. Semeniuk, and Matthias E. Futschik, “Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria,” Frontiers in Genetics, vol. 5, 2014. View at Publisher · View at Google Scholar
  • Toni I. Gossmann, and Mathias Ziegler, “Sequence divergence and diversity suggests ongoing functional diversification of vertebrate NAD metabolism,” DNA Repair, 2014. View at Publisher · View at Google Scholar
  • Nguyen Minh Thanh, Hyungtaek Jung, Russell E. Lyons, Vincent Chand, Nguyen Viet Tuan, Vo Thi Minh Thu, and Peter Mather, “A transcriptomic analysis of striped catfish (Pangasianodon hypophthalmus) in response to salinity adaptation: De novo assembly, gene annotation and marker discovery,” Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, vol. 10, pp. 52–63, 2014. View at Publisher · View at Google Scholar
  • Xiaohui Wu, Lina Xu, Wei Gu, Qian Xu, Qing-Yu He, Xuesong Sun, and Gong Zhang, “Iterative Genome Correction Largely Improves Proteomic Analysis of Nonmodel Organisms,” Journal of Proteome Research, vol. 13, no. 6, pp. 2724–2734, 2014. View at Publisher · View at Google Scholar
  • S. M. Utturkar, D. M. Klingeman, M. L. Land, C. W. Schadt, M. J. Doktycz, D. A. Pelletier, and S. D. Brown, “Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences,” Bioinformatics, 2014. View at Publisher · View at Google Scholar
  • H. Budak, Z. Khan, and M. Kantar, “History and current status of wheat miRNAs using next-generation sequencing and their roles in development and stress,” Briefings in Functional Genomics, 2014. View at Publisher · View at Google Scholar
  • Bryan Utter, Douglas R. Deutsch, Raymond Schuch, Benjamin Y. Winer, Kathleen Verratti, Kim Bishop-Lilly, Shanmuga Sozhamannan, and Vincent A. Fischetti, “Beyond the Chromosome: The Prevalence of Unique Extra-Chromosomal Bacteriophages with Integrated Virulence Genes in Pathogenic Staphylococcus aureus,” Plos One, vol. 9, no. 6, 2014. View at Publisher · View at Google Scholar
  • Yiya Zhang, Yong Huang, Quanze He, Jinyan Liu, Ji Luo, Li Zhu, Shanshan Lu, Pengfei Huang, Xinyi Chen, Xiongzhi Zeng, and Songping Liang, “Toxin Diversity Revealed by a Transcriptomic Study of Ornithoctonus huwena,” Plos One, vol. 9, no. 6, 2014. View at Publisher · View at Google Scholar
  • Xin Yi, Jing Zou, Jiajia Xu, Tao Liu, Tengfei Liu, Sang Hua, Feng Xi, Xifang Nie, Lili Ye, Yufen Luo, Lin Xu, Hui Du, Ruifang Wu, Ling Yang, Ren Liu, Bin Yang, Jian Wang, and Jerome L. Belinson, “Development and Validation of a New HPV Genotyping Assay Based on Next-Generation Sequencing,” American Journal of Clinical Pathology, vol. 141, no. 6, pp. 796–804, 2014. View at Publisher · View at Google Scholar
  • David Roy Smith, “Last-gen nostalgia: a lighthearted rant and reflection on genome sequencing culture,” Frontiers in Genetics, vol. 5, 2014. View at Publisher · View at Google Scholar
  • Claudia Knief, “Analysis of plant microbe interactions in the era of next generation sequencing technologies,” Frontiers in Plant Science, vol. 5, 2014. View at Publisher · View at Google Scholar
  • M. Jessri, and C. S. Farah, “Harnessing Massively Parallel Sequencing in Personalized Head and Neck Oncology,” Journal of Dental Research, vol. 93, no. 5, pp. 437–444, 2014. View at Publisher · View at Google Scholar
  • Clícia Grativol, Michael Regulski, Marcelo Bertalan, W. Richard McCombie, Felipe Rodrigues da Silva, Adhemar Zerlotini Neto, Renato Vicentini, Laurent Farinelli, Adriana Silva Hemerly, Robert A. Martienssen, and Paulo Cavalcanti Gomes Ferreira, “ Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum ,” The Plant Journal, 2014. View at Publisher · View at Google Scholar
  • Segolene Caboche, Christophe Audebert, Yves Lemoine, and David Hot, “Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data,” Bmc Genomics, vol. 15, 2014. View at Publisher · View at Google Scholar
  • Jiayan Wu, Jingfa Xiao, Zhang Zhang, Xumin Wang, Songnian Hu, and Jun Yu, “Ribogenomics: The Science and Knowledge of RNA,” Genomics, Proteomics & Bioinformatics, 2014. View at Publisher · View at Google Scholar
  • Charlotte A. Hobbs, Shimul Chowdhury, Mario A. Cleves, Stephen Erickson, Stewart L. MacLeod, Gary M. Shaw, Sanjay Shete, John S. Witte, and Benjamin Tycko, “Genetic Epidemiology and Nonsyndromic Structural Birth Defects From Candidate Genes to Epigenetics,” Jama Pediatrics, vol. 168, no. 4, pp. 371–377, 2014. View at Publisher · View at Google Scholar
  • Pugacheva Valentina, Frenkel Felix, and Korotkov Eugene, “Investigation of phase shifts for different period lengths in the genomes of C.elegans, D.melanogaster and S.cerevisiae,” Computational Biology and Chemistry, 2014. View at Publisher · View at Google Scholar
  • Michael E. Pyne, Mark Bruder, Murray Moo-Young, Duane A. Chung, and C. Perry Chou, “Technical guide for genetic advancement of underdeveloped and intractable Clostridium,” Biotechnology Advances, 2014. View at Publisher · View at Google Scholar
  • Eamonn P Culligan, Roy D Sleator, Julian R Marchesi, and Colin Hill, “Metagenomics and novel gene discovery: Promise and potential for novel therapeutics,” Virulence, vol. 5, no. 3, pp. 399–412, 2014. View at Publisher · View at Google Scholar
  • Richard M. Kliman, “Evidence that Natural Selection on Codon Usage in Drosophila pseudoobscura Varies Across Codons,” G3-Genes Genomes Genetics, vol. 4, no. 4, pp. 681–692, 2014. View at Publisher · View at Google Scholar
  • Wataru Yoshida, and Koichi Abe, “Emerging techniques employed in aptamer-based diagnostic tests,” Expert Review of Molecular Diagnostics, vol. 14, no. 2, pp. 143–151, 2014. View at Publisher · View at Google Scholar
  • Rajyalakshmi Luthra, Keyur P. Patel, Neelima G. Reddy, Varan Haghshenas, Mark J. Routbort, Michael A. Harmon, Bedia A. Barkoh, Rashmi Kanagal-Shamanna, Farhad Ravandi, Jorge E. Cortes, Hagop M. Kantarjian, L. Jeffrey Medeiros, and Rajesh R. Singh, “Next-generation sequencing-based multigene mutational screening for acute myeloid leukemia using MiSeq: applicability for diagnostics and disease monitoring,” Haematologica, vol. 99, no. 3, pp. 465–473, 2014. View at Publisher · View at Google Scholar
  • Zsofia K. Stadler, Kasmintan A. Schrader, Joseph Vijai, and Mark E. Robson, “Cancer Genomics and Inherited Risk,” Journal of Clinical Oncology, vol. 32, no. 7, pp. 687–+, 2014. View at Publisher · View at Google Scholar
  • Lori Lowes, and Alison Allan, “Recent Advances in the Molecular Characterization of Circulating Tumor Cells,” Cancers, vol. 6, no. 1, pp. 595–624, 2014. View at Publisher · View at Google Scholar
  • Y. Liu, S. Yao, Y. Liu, Y. Xu, and C. Cheng, “Genome Sequence of Luteimonas huabeiensis HB-2, a Novel Species of Luteimonas with High Oil Displacement Efficiency,” Genome Announcements, vol. 2, no. 2, pp. e00152-14–e00152-14, 2014. View at Publisher · View at Google Scholar
  • Tao Xu, Yongchao Li, Joy D. Van Nostrand, and Zhili He, “Cas9-Based Tools for Targeted Genome Editing and Transcriptional Control,” Applied and Environmental Microbiology, vol. 80, no. 5, pp. 1544–1552, 2014. View at Publisher · View at Google Scholar
  • Tam P. Sneddon, Xiao Si Zhe, Scott C. Edmunds, Peter Li, and Laurie Goodman, “GigaDB: promoting data dissemination and reproducibility,” Database-The Journal of Biological Databases and Curation, 2014. View at Publisher · View at Google Scholar
  • J. P. Meier-Kolthoff, H.-P. Klenk, and M. Goker, “Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age,” International Journal Of Systematic And Evolutionary Microbiology, vol. 64, no. Pt2, pp. 352–356, 2014. View at Publisher · View at Google Scholar
  • Xi Qian, Yi Ba, Qianfeng Zhuang, and Guofang Zhong, “RNA-Seq Technology and Its Application in Fish Transcriptomics,” OMICS: A Journal of Integrative Biology, vol. 18, no. 2, pp. 98–110, 2014. View at Publisher · View at Google Scholar
  • Gaurav Sablok, Yuan Fu, Valentina Bobbio, Marina Laura, Giuseppe L. Rotino, Paolo Bagnaresi, Andrea Allavena, Violeta Velikova, Roberto Viola, Francesco Loreto, Mingai Li, and Claudio Varotto, “ Fuelling genetic and metabolic exploration of C 3 bioenergy crops through the first reference transcriptome of Arundo donax L. ,” Plant Biotechnology Journal, 2014. View at Publisher · View at Google Scholar
  • Hannah V. Carey, and Khrystyne N. Duddleston, “Animal-Microbial Symbioses in Changing Environments,” Journal of Thermal Biology, 2014. View at Publisher · View at Google Scholar
  • Arti Tripathi, and Raghavan Varadarajan, “Residue specific contributions to stability and activity inferred from saturation mutagenesis and deep sequencing,” Current Opinion in Structural Biology, vol. 24, pp. 63–71, 2014. View at Publisher · View at Google Scholar
  • Mariana Rosenthal, Allison E. Aiello, Carol Chenoweth, Deborah Goldberg, Elaine Larson, Gregory Gloor, and Betsy Foxman, “Impact of Technical Sources of Variation on the Hand Microbiome Dynamics of Healthcare Workers,” Plos One, vol. 9, no. 2, 2014. View at Publisher · View at Google Scholar
  • Yong E Zhang, and Manyuan Long, “New genes contribute to genetic and phenotypic novelties in human evolution,” Current Opinion in Genetics & Development, vol. 29, pp. 90–96, 2014. View at Publisher · View at Google Scholar
  • Blake W. Buchan, and Nathan A. Ledeboer, “Emerging Technologies for the Clinical Microbiology Laboratory,” Clinical Microbiology Reviews, vol. 27, no. 4, pp. 783–822, 2014. View at Publisher · View at Google Scholar
  • C. Thomas Caskey, Manuel L. Gonzalez-Garay, Stacey Pereira, and Amy L. McGuire, “Adult Genetic Risk Screening,” Annual Review of Medicine, vol. 65, no. 1, pp. 1–17, 2014. View at Publisher · View at Google Scholar
  • Wentian Li, Jan Freudenberg, and Pedro Miramontes, “Diminishing return for increased Mappability with longer sequencing reads: implications of the k-mer distributions in the human genome,” Bmc Bioinformatics, vol. 15, 2014. View at Publisher · View at Google Scholar
  • C. Gabriel, D. Fürst, I. Faé, S. Wenda, C. Zollikofer, J. Mytilineos, and G. F. Fischer, “HLA typing by next-generation sequencing - getting closer to reality,” Tissue Antigens, vol. 83, no. 2, pp. 65–75, 2014. View at Publisher · View at Google Scholar
  • Maren F. Hansen, Ulrike Neckmann, Liss A. S. Lavik, Trine Vold, Bodil Gilde, Ragnhild K. Toft, and Wenche Sjursen, “A massive parallel sequencing workflow for diagnostic genetic testing of mismatch repair genes,” Molecular Genetics & Genomic Medicine, 2014. View at Publisher · View at Google Scholar
  • Sergio Callejas, Rebeca Alvarez, Alberto Benguria, and Ana Dopazo, “AG-NGS: A powerful and user-friendly computing application for the semi-automated preparation of next-generation sequencing libraries using open liquid handling platforms,” Biotechniques, vol. 56, no. 1, pp. 28–+, 2014. View at Publisher · View at Google Scholar
  • Wayne I. L. Davies, “Challenges using diagnostic next-generation sequencing in the clinical environment for inherited retinal disorders,” Personalized Medicine, vol. 11, no. 1, pp. 99–111, 2014. View at Publisher · View at Google Scholar
  • Branka Zukic, and Maja Stojiljkovic Petrovic, “Molecular Genetic Markers As A Basis For Personalized Medicine,” Journal of Medical Biochemistry, vol. 33, no. 1, pp. 8–21, 2014. View at Publisher · View at Google Scholar
  • Marina Barba, Henryk Czosnek, and Ahmed Hadidi, “Historical Perspective, Development and Applications of Next-Generation Sequencing in Plant Virology,” Viruses, vol. 6, no. 1, pp. 106–136, 2014. View at Publisher · View at Google Scholar
  • D. A. Willette, F. W. Allendorf, P. H. Barber, D. J. Barshis, K. E. Carpenter, E. D. Crandall, W. A. Cresko, I. Fernandez-Silva, M. V. Matz, E. Meyer, M. D. Santos, L. W. Seeb, and J. E. Seeb, “So, you want to use next-generation sequencing in marine systems? Insight from the Pan-Pacific Advanced Studies Institute,” Bulletin of Marine Science, vol. 90, no. 1, pp. 79–122, 2014. View at Publisher · View at Google Scholar
  • Jan Haas, Ioana Barb, Hugo A. Katus, and Benjamin Meder, “Targeted next-generation sequencing: the clinician's stethoscope for genetic disorders,” Personalized Medicine, vol. 11, no. 6, pp. 581–592, 2014. View at Publisher · View at Google Scholar
  • Lauren C. White, Alan Horsup, Andrea C. Taylor, and Jeremy J. Austin, “Improving genetic monitoring of the northern hairy-nosed wombat (Lasiorhinus krefftii),” Australian Journal of Zoology, vol. 62, no. 3, pp. 246–250, 2014. View at Publisher · View at Google Scholar