Characterizing and measuring bias in sequence data

[1]  Isaac S. Kohane,et al.  Faculty Opinions recommendation of Characterizing and measuring bias in sequence data. , 2013 .

[2]  T. Tatusova,et al.  Chapter 18 : The Reference Sequence ( RefSeq ) Database , 2013 .

[3]  Barry Merriman,et al.  Progress in Ion Torrent semiconductor chip based sequencing , 2012, Electrophoresis.

[4]  Mauricio O. Carneiro,et al.  Pacific biosciences sequencing technology for genotyping and variation discovery in human data , 2012, BMC Genomics.

[5]  H. Swerdlow,et al.  A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers , 2012, BMC Genomics.

[6]  C. Nusbaum,et al.  Finished bacterial genomes from shotgun sequence data , 2012, Genome research.

[7]  Lin Liu,et al.  Comparison of Next-Generation Sequencing Systems , 2012, Journal of biomedicine & biotechnology.

[8]  James H. Bullard,et al.  A hybrid approach for the automated finishing of bacterial genomes , 2012, Nature Biotechnology.

[9]  M. Schatz,et al.  Hybrid error correction and de novo assembly of single-molecule sequencing reads , 2012, Nature Biotechnology.

[10]  T. Dallman,et al.  Performance comparison of benchtop high-throughput sequencing platforms , 2012, Nature Biotechnology.

[11]  Asaf Levy,et al.  A vast collection of microbial genes that are toxic to bacteria. , 2012, Genome research.

[12]  Jessica C. Ebert,et al.  Computational Techniques for Human Genome Resequencing Using Mated Gapped Reads , 2012, J. Comput. Biol..

[13]  Y. Benjamini,et al.  Summarizing and correcting the GC content bias in high-throughput sequencing , 2012, Nucleic acids research.

[14]  Yuan Hu,et al.  Protection of SH-SY5Y Neuronal Cells from Glutamate-Induced Apoptosis by 3,6′-Disinapoyl Sucrose, a Bioactive Compound Isolated from Radix Polygala , 2011, Journal of biomedicine & biotechnology.

[15]  Euan A Ashley,et al.  Performance comparison of whole-genome sequencing platforms , 2011, Nature Biotechnology.

[16]  D. Kwiatkowski,et al.  Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes , 2012, BMC Genomics.

[17]  Bernard P. Puc,et al.  An integrated semiconductor device enabling non-optical genome sequencing , 2011, Nature.

[18]  Margaret C. Linak,et al.  Sequence-specific error profile of Illumina sequencers , 2011, Nucleic acids research.

[19]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[20]  T. Fennell,et al.  Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries , 2011, Genome Biology.

[21]  Dennis C. Friedrich,et al.  A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries , 2011, Genome Biology.

[22]  A. Gnirke,et al.  High-quality draft assemblies of mammalian genomes from massively parallel sequence data , 2010, Proceedings of the National Academy of Sciences.

[23]  D. Altshuler,et al.  A map of human genome variation from population-scale sequencing , 2010, Nature.

[24]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[25]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[26]  Robert B. Hartlage,et al.  This PDF file includes: Materials and Methods , 2009 .

[27]  D. Mead,et al.  Linear plasmid vector for cloning of repetitive or unstable sequences in Escherichia coli , 2009, Nucleic acids research.

[28]  Taichi E. Takasuka,et al.  Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences? , 2009, Nucleic acids research.

[29]  S. Turner,et al.  Real-time DNA sequencing from single polymerase molecules. , 2010, Methods in enzymology.

[30]  Thomas R. Ioerger,et al.  Genome Analysis of Multi- and Extensively-Drug-Resistant Tuberculosis from KwaZulu-Natal, South Africa , 2009, PloS one.

[31]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[32]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[33]  S. Turner,et al.  Real-Time DNA Sequencing from Single Polymerase Molecules , 2009, Science.

[34]  Timothy B. Stockwell,et al.  Evaluation of next generation sequencing platforms for population targeted sequencing studies , 2009, Genome Biology.

[35]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[36]  Juliane C. Dohm,et al.  Substantial biases in ultra-short read data sets from high-throughput DNA sequencing , 2008, Nucleic acids research.

[37]  Peer Bork,et al.  Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer , 2007, Science.

[38]  Susan M. Huse,et al.  Accuracy and quality of massively parallel DNA pyrosequencing , 2007, Genome Biology.

[39]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[40]  Peter Adams,et al.  Unlocking hidden genomic sequence. , 2004, Nucleic acids research.

[41]  D. Leach,et al.  In vivo loss of supercoiled DNA carrying a palindromic sequence , 1986, Molecular and General Genetics MGG.

[42]  J. Roder,et al.  Neuronal Calcium Sensor 1 and Activity-Dependent Facilitation of P/Q-Type Calcium Currents at Presynaptic Nerve Terminals , 2002, Science.

[43]  G. Glöckner.  Large Scale Sequencing and Analysis of AT Rich Eukaryote Genomes , 2000 .

[44]  Representation of cloned genomic sequences in two sequencing vectors: correlation of DNA sequence and subclone distribution. , 1997, Nucleic acids research.

[45]  J. Braman,et al.  PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. , 1996, Nucleic acids research.

[46]  C. R. Connell,et al.  DNA sequencing with dye-labeled terminators and T7 DNA polymerase: effect of dyes and dNTPs on incorporation of dye-terminators and probability analysis of termination fragments. , 1992, Nucleic acids research.

[47]  T. Skopek,et al.  Fidelity of Thermococcus litoralis DNA polymerase (Vent) in PCR determined by denaturing gradient gel electrophoresis. , 1991, Nucleic acids research.

[48]  W. Thilly,et al.  Fidelity of DNA polymerases in DNA amplification. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[49]  K. Wertman,et al.  Host strains that alleviate underrepresentation of specific sequences: overview. , 1987, Methods in enzymology.

[50]  J. Collins.  Instability of palindromic DNA in Escherichia coli. , 1981, Cold Spring Harbor symposia on quantitative biology.

[51]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.