Sequencing technologies — the next generation

[1]  Jessica C. Ebert,et al.  Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays , 2010, Science.

[2]  K. Frazer,et al.  Microdroplet-based PCR amplification for large scale targeted sequencing , 2009, Nature Biotechnology.

[3]  Jeffrey G. Reifenberger,et al.  Direct RNA sequencing , 2009, Nature.

[4]  P. Park.  ChIP–seq: advantages and challenges of a maturing technology , 2009, Nature Reviews Genetics.

[5]  Ken Chen,et al.  Recurring mutations found by sequencing an acute myeloid leukemia genome. , 2009, The New England journal of medicine.

[6]  Dmitry Pushkarev,et al.  Single-molecule sequencing of an individual human genome , 2009, Nature Biotechnology.

[7]  Francisco M. De La Vega,et al.  Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. , 2009, Genome research.

[8]  Thomas D. Wu,et al.  A highly annotated whole-genome sequence of a Korean individual , 2009, Nature.

[9]  Adrian W. Briggs,et al.  Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes , 2009, Science.

[10]  S. Letovsky,et al.  Quantification of the yeast transcriptome by single-molecule sequencing , 2009, Nature Biotechnology.

[11]  Johnf . Thompson,et al.  Virtual Terminator nucleotides for next generation DNA sequencing , 2009, Nature Methods.

[12]  Sangsoo Kim,et al.  The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. , 2009, Genome research.

[13]  Cole Trapnell,et al.  How to map billions of short reads onto genomes , 2009, Nature Biotechnology.

[14]  Jay Shendure,et al.  Massively parallel exon capture and library-free resequencing across 16 genomes , 2009, Nature Methods.

[15]  Ruth Ann Luna,et al.  Metagenomic pyrosequencing and microbial identification. , 2009, Clinical chemistry.

[16]  K. Frazer,et al.  Human genetic variation and its contribution to complex traits , 2009, Nature Reviews Genetics.

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

[18]  E. Sontheimer,et al.  Origins and Mechanisms of miRNAs and siRNAs , 2009, Cell.

[19]  C. Ponting,et al.  Evolution and Functions of Long Noncoding RNAs , 2009, Cell.

[20]  M. Metzker,et al.  A−β− Subtype of Ketosis-Prone Diabetes Is Not Predominantly a Monogenic Diabetic Syndrome , 2009, Diabetes Care.

[21]  M. Metzker.  Sequencing in real time , 2009, Nature Biotechnology.

[22]  N. Moran,et al.  The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria , 2009, Science.

[23]  J. Maguire,et al.  Solution Hybrid Selection with Ultra-long Oligonucleotides for Massively Parallel Targeted Sequencing , 2009, Nature Biotechnology.

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

[25]  Yufeng Shen,et al.  Comparing Platforms for C. elegans Mutant Identification Using High-Throughput Whole-Genome Sequencing , 2008, PloS one.

[26]  J. Poulain,et al.  High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies , 2008, BMC Genomics.

[27]  Richard M. Clark,et al.  Sequencing of natural strains of Arabidopsis thaliana with short reads. , 2008, Genome research.

[28]  Eric S. Lander,et al.  Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing , 2008, Nature Methods.

[29]  Kalim U. Mir,et al.  Sequencing by Cyclic Ligation and Cleavage (CycLiC) directly on a microarray captured template , 2008, Nucleic acids research.

[30]  M. Daly,et al.  Genetic Mapping in Human Disease , 2008, Science.

[31]  Dawei Li,et al.  The diploid genome sequence of an Asian individual , 2008, Nature.

[32]  K. Sanderson.  Personal genomes: Standard and pores , 2008, Nature.

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

[34]  R. Weinshilboum,et al.  Pharmacogenomics: candidate gene identification, functional validation and mechanisms. , 2008, Human molecular genetics.

[35]  Amy E. Hawkins,et al.  DNA sequencing of a cytogenetically normal acute myeloid leukemia genome , 2008, Nature.

[36]  D. Rockey,et al.  Identification of Concomitant Infection with Chlamydia trachomatis IncA-Negative Mutant and Wild-Type Strains by Genomic, Transcriptional, and Biological Characterizations , 2008, Infection and Immunity.

[37]  D. Branton,et al.  The potential and challenges of nanopore sequencing , 2008, Nature Biotechnology.

[38]  J. Schloss,et al.  How to get genomes at one ten-thousandth the cost , 2008, Nature Biotechnology.

[39]  K. Garber.  Fixing the front end , 2008, Nature Biotechnology.

[40]  Richard Gibbs,et al.  High-Precision, Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies , 2008, PLoS genetics.

[41]  I. Pe’er,et al.  Caenorhabditis elegans mutant allele identification by whole-genome sequencing , 2008, Nature Methods.

[42]  J. Wain,et al.  High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi , 2008, Nature Genetics.

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

[44]  Jingyue Ju,et al.  Four-color DNA sequencing with 3′-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides , 2008, Proceedings of the National Academy of Sciences.

[45]  Malek Faham,et al.  A comprehensive assay for targeted multiplex amplification of human DNA sequences , 2008, Proceedings of the National Academy of Sciences.

[46]  P. Mitra,et al.  Alta-Cyclic: a self-optimizing base caller for next-generation sequencing , 2008, Nature Methods.

[47]  Steven M. Johnson,et al.  A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. , 2008, Genome research.

[48]  Joshua M. Korn,et al.  Mapping and sequencing of structural variation from eight human genomes , 2008, Nature.

[49]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[50]  C. Nusbaum,et al.  ALLPATHS: de novo assembly of whole-genome shotgun microreads. , 2008, Genome research.

[51]  David Hernández,et al.  De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. , 2008, Genome research.

[52]  J. Lupski,et al.  The complete genome of an individual by massively parallel DNA sequencing , 2008, Nature.

[53]  S. Quake,et al.  Single-Molecule DNA Sequencing of a Viral Genome , 2008, Science.

[54]  S. Salzberg,et al.  Bioinformatics challenges of new sequencing technology. , 2008, Trends in genetics : TIG.

[55]  M. Fedurco,et al.  A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis† , 2008, Nucleic acids research.

[56]  Mark J. P. Chaisson,et al.  Short read fragment assembly of bacterial genomes. , 2008, Genome research.

[57]  Gabor T. Marth,et al.  Whole-genome sequencing and variant discovery in C. elegans , 2008, Nature Methods.

[58]  Z. Xuan,et al.  Genome-wide in situ exon capture for selective resequencing , 2007, Nature Genetics.

[59]  Jay Shendure,et al.  Multiplex amplification of large sets of human exons , 2007, Nature Methods.

[60]  M. Olson.  Enrichment of super-sized resequencing targets from the human genome , 2007, Nature Methods.

[61]  David T. Okou,et al.  Microarray-based genomic selection for high-throughput resequencing , 2007, Nature Methods.

[62]  Philip M. Kim,et al.  Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome , 2007, Science.

[63]  G. Weinstock,et al.  Direct selection of human genomic loci by microarray hybridization , 2007, Nature Methods.

[64]  M. Metzker,et al.  Termination of DNA synthesis by N6-alkylated, not 3′-O-alkylated, photocleavable 2′-deoxyadenosine triphosphates , 2007, Nucleic acids research.

[65]  Timothy B. Stockwell,et al.  The Diploid Genome Sequence of an Individual Human , 2007, PLoS biology.

[66]  C. Hutchison.  DNA sequencing: bench to bedside and beyond , 2007, Nucleic acids research.

[67]  G. Church,et al.  Polony Multiplex Analysis of Gene Expression (PMAGE) in Mouse Hypertrophic Cardiomyopathy , 2007, Science.

[68]  Francis S. Collins,et al.  Mapping the cancer genome , 2007 .

[69]  Francis S Collins,et al.  Mapping the cancer genome. Pinpointing the genes involved in cancer will help chart a new course across the complex landscape of human malignancies. , 2007, Scientific American.

[70]  R. Redon,et al.  Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes , 2007, Science.

[71]  L. Du,et al.  Unique Features of a Highly Pathogenic Campylobacter jejuni Strain , 2007, Infection and Immunity.

[72]  Nicholas J. Turro,et al.  Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators , 2006, Proceedings of the National Academy of Sciences.

[73]  René L. Warren,et al.  Assembling millions of short DNA sequences using SSAKE , 2006, Bioinform..

[74]  Adrian W. Briggs,et al.  Analysis of one million base pairs of Neanderthal DNA , 2006, Nature.

[75]  Kevin L. Gunderson,et al.  Highly parallel genomic assays , 2006, Nature Reviews Genetics.

[76]  M. Fedurco,et al.  BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies , 2006, Nucleic acids research.

[77]  A. Tomkinson,et al.  DNA ligases: structure, reaction mechanism, and function. , 2006, Chemical reviews.

[78]  M. Metzker.  Emerging technologies in DNA sequencing. , 2005, Genome research.

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

[80]  E. Eichler,et al.  Fine-scale structural variation of the human genome , 2005, Nature Genetics.

[81]  C. Fuller,et al.  TERMINAL PHOSPHATE LABELED NUCLEOTIDES: SYNTHESIS, APPLICATIONS, AND LINKER EFFECT ON INCORPORATION BY DNA POLYMERASES , 2005, Nucleosides, nucleotides & nucleic acids.

[82]  E. Lander,et al.  Finishing the euchromatic sequence of the human genome , 2004 .

[83]  J. Bonfield,et al.  Finishing the euchromatic sequence of the human genome , 2004, Nature.

[84]  L. Feuk,et al.  Detection of large-scale variation in the human genome , 2004, Nature Genetics.

[85]  Kenny Q. Ye,et al.  Large-Scale Copy Number Polymorphism in the Human Genome , 2004, Science.

[86]  Jan Berka,et al.  A massively parallel PicoTiterPlate™ based platform for discrete picoliter‐scale polymerase chain reactions , 2003, Electrophoresis.

[87]  Jay Shendure,et al.  Fluorescent in situ sequencing on polymerase colonies. , 2003, Analytical biochemistry.

[88]  D. Dressman,et al.  Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[89]  S. Quake,et al.  Sequence information can be obtained from single DNA molecules , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[90]  S. Turner,et al.  Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations , 2003, Science.

[91]  M. Sussman,et al.  Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array , 1999, Nature Biotechnology.

[92]  M. Ronaghi,et al.  A Sequencing Method Based on Real-Time Pyrophosphate , 1998, Science.

[93]  S. Macevicz.  DNA sequencing by parallel oligonucleotide extensions , 1997 .

[94]  M. Ronaghi,et al.  Real-time DNA sequencing using detection of pyrophosphate release. , 1996, Analytical biochemistry.

[95]  R A Gibbs,et al.  Termination of DNA synthesis by novel 3'-modified-deoxyribonucleoside 5'-triphosphates. , 1994, Nucleic acids research.

[96]  B. Canard,et al.  DNA polymerase fluorescent substrates with reversible 3'-tags. , 1994, Gene.

[97]  U Landegren,et al.  A ligase-mediated gene detection technique. , 1988, Science.

[98]  L. Yarbrough,et al.  Synthesis and properties of fluorescent nucleotide substrates for DNA-dependent RNA polymerases. , 1979, The Journal of biological chemistry.

[99]  Magdalena A. Jonikas,et al.  knowledge-based potentials and structural filters Coarse-grained modeling of large RNA molecules with Material Supplemental , 2009 .

[100]  Mark J. P. Chaisson,et al.  De novo fragment assembly with short mate-paired reads: Does the read length matter? , 2009, Genome research.

[101]  Josephine A. Reinhardt,et al.  De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. , 2009, Genome research.

[102]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[103]  K. Sanderson.  STANDARD AND PORES , 2008 .

[104]  B. Wold,et al.  Sequence census methods for functional genomics , 2008, Nature Methods.

[105]  J. Shendure,et al.  Materials and Methods Som Text Figs. S1 and S2 Tables S1 to S4 References Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome , 2022 .