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Genome sequencing

LDx: Estimation of Linkage Disequilibrium from High-Throughput Pooled Resequencing Data

Alison F. Feder, Dmitri A. Petrov, Alan O. Bergland

published 09 Nov 2012

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A Streamlined Method for Detecting Structural Variants in Cancer Genomes by Short Read Paired-End Sequencing

Martina Mijušković, Stuart M. Brown, Zuojian Tang, Cory R. Lindsay, Efstratios Efstathiadis, Ludovic Deriano, David B. Roth

published 29 Oct 2012

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COPS: A Sensitive and Accurate Tool for Detecting Somatic Copy Number Alterations Using Short-Read Sequence Data from Paired Samples

Neeraja M. Krishnan, Prakhar Gaur, Rakshit Chaudhary, Arjun A. Rao, Binay Panda

published 22 Oct 2012

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Detecting Identity by Descent and Homozygosity Mapping in Whole-Exome Sequencing Data

Zhong Zhuang, Alexander Gusev, Judy Cho, Itsik Pe'er

published 11 Oct 2012

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Improving PacBio Long Read Accuracy by Short Read Alignment

Kin Fai Au, Jason G. Underwood, Lawrence Lee, Wing Hung Wong

published 04 Oct 2012

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Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons

Fei Yao, Pramila N. Ariyaratne, Axel M. Hillmer, Wah Heng Lee, Guoliang Li, Audrey S. M. Teo, Xing Yi Woo, Zhenshui Zhang, Jieqi P. Chen, Wan Ting Poh, Kelson F. B. Zawack, Chee Seng Chan, See Ting Leong, Say Chuan Neo, Poh Sum D. Choi, Song Gao, Niranjan Nagarajan, Hervé Thoreau, Atif Shahab, Xiaoan Ruan, Valère Cacheux-Rataboul, Chia-Lin Wei, Guillaume Bourque, Wing-Kin Sung, Edison T. Liu, Yijun Ruan

published 28 Sep 2012

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Paired-End Sequencing of Long-Range DNA Fragments for De Novo Assembly of Large, Complex Mammalian Genomes by Direct Intra-Molecule Ligation

Asan, Chunyu Geng, Yan Chen, Kui Wu, Qingle Cai, Yu Wang, Yongshan Lang, Hongzhi Cao, Huangming Yang, Jian Wang, Xiuqing Zhang

published 27 Sep 2012

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Prolonged and Substantial Discordance in Prevalence of Raltegravir-Resistant HIV-1 in Plasma versus PBMC Samples Revealed by 454 “Deep” Sequencing

Guinevere Q. Lee, Luke C. Swenson, Art F. Y. Poon, Jeffrey N. Martin, Hiroyu Hatano, Steven G. Deeks, P. Richard Harrigan

published 26 Sep 2012

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SNP Discovery with EST and NextGen Sequencing in Switchgrass (Panicum virgatum L.)

Elhan S. Ersoz, Mark H. Wright, Jasmyn L. Pangilinan, Moira J. Sheehan, Christian Tobias, Michael D. Casler, Edward S. Buckler, Denise E. Costich

published 25 Sep 2012

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In-Depth Investigation of Archival and Prospectively Collected Samples Reveals No Evidence for XMRV Infection in Prostate Cancer

Deanna Lee, Jaydip Das Gupta, Christina Gaughan, Imke Steffen, Ning Tang, Ka-Cheung Luk, Xiaoxing Qiu, Anatoly Urisman, Nicole Fischer, Ross Molinaro, Miranda Broz, Gerald Schochetman, Eric A. Klein, Don Ganem, Joseph L. DeRisi, Graham Simmons, John Hackett Jr, Robert H. Silverman, Charles Y. Chiu

published 18 Sep 2012

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An Integrated Pipeline for de Novo Assembly of Microbial Genomes

Andrew Tritt, Jonathan A. Eisen, Marc T. Facciotti, Aaron E. Darling

published 13 Sep 2012

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Genetic Characterisation of Malawian Pneumococci Prior to the Roll-Out of the PCV13 Vaccine Using a High-Throughput Whole Genome Sequencing Approach

Dean B. Everett, Jennifer Cornick, Brigitte Denis, Claire Chewapreecha, Nicholas Croucher, Simon Harris, Julian Parkhill, Stephen Gordon, Enitan D. Carrol, Neil French, Robert S. Heyderman, Stephen D. Bentley

published 10 Sep 2012

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Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads

Colin F. Davenport, Jens Neugebauer, Nils Beckmann, Benedikt Friedrich, Burim Kameri, Svea Kokott, Malte Paetow, Björn Siekmann, Matthias Wieding-Drewes, Markus Wienhöfer, Stefan Wolf, Burkhard Tümmler, Volker Ahlers, Frauke Sprengel

published 21 Aug 2012

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