Applications of next-generation sequencing technologies in functional genomics.

[1]  J. Lis,et al.  Detecting protein-DNA interactions in vivo: distribution of RNA polymerase on specific bacterial genes. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Ryan D. Morin,et al.  Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. , 2008, Genome research.

[3]  Elaine R Mardis,et al.  Anticipating the $1,000 genome , 2006, Genome Biology.

[4]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[5]  S. Nelson,et al.  Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning , 2008, Nature.

[6]  Steven J. M. Jones,et al.  BMC Genomics BioMed Central Methodology article , 2006 .

[7]  B. Haas,et al.  Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology , 2006, BMC Genomics.

[8]  Eugene Berezikov,et al.  Approaches to microRNA discovery , 2006, Nature Genetics.

[9]  V. Ambros,et al.  The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.

[10]  J. M. Prober,et al.  A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. , 1987, Science.

[11]  R. Madabhushi.  Separation of 4-color DNA sequencing extension products in noncovalently coated capillaries using low viscosity polymer solutions. , 1998, Electrophoresis.

[12]  Arthur W. Miller,et al.  DNA sequencing by capillary electrophoresis with replaceable linear polyacrylamide and laser-induced fluorescence detection. , 1993, Analytical chemistry.

[13]  D. Bartel,et al.  A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. , 2006, Genes & development.

[14]  Jason S. Cumbie,et al.  Genome-Wide Profiling and Analysis of Arabidopsis siRNAs , 2007, PLoS biology.

[15]  Jeppe Emmersen,et al.  DeepSAGE—digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples , 2006, Nucleic acids research.

[16]  Manel Esteller,et al.  The necessity of a human epigenome project. , 2006, Carcinogenesis.

[17]  D. Deamer,et al.  Nanopores and nucleic acids: prospects for ultrarapid sequencing. , 2000, Trends in biotechnology.

[18]  Shivakundan Singh Tej,et al.  Elucidation of the Small RNA Component of the Transcriptome , 2005, Science.

[19]  J. Burnside,et al.  Marek's Disease Virus Encodes MicroRNAs That Map to meq and the Latency-Associated Transcript , 2006, Journal of Virology.

[20]  Neil Hall,et al.  Advanced sequencing technologies and their wider impact in microbiology , 2007, Journal of Experimental Biology.

[21]  R. Quatrano.  Genomics , 1998, Plant Cell.

[22]  P. Schnable,et al.  SNP discovery via 454 transcriptome sequencing , 2007, The Plant journal : for cell and molecular biology.

[23]  Yingyin Yao,et al.  Cloning and characterization of microRNAs from wheat (Triticum aestivum L.) , 2007, Genome Biology.

[24]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[25]  D. Panescu,et al.  Emerging Technologies , 2008, IEEE Engineering in Medicine and Biology Magazine.

[26]  Pamela J Green,et al.  Sweating the small stuff: microRNA discovery in plants. , 2006, Current opinion in biotechnology.

[27]  T. Mikkelsen,et al.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.

[28]  W. Gilbert,et al.  A new method for sequencing DNA. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[30]  C. Nusbaum,et al.  Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. , 2006, Genome research.

[31]  E. Petricoin,et al.  Laser Capture Microdissection , 1996, Science.

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

[33]  S. Bennett.  Solexa Ltd. , 2004, Pharmacogenomics.

[34]  John J. Wyrick,et al.  Genome-wide location and function of DNA binding proteins. , 2000, Science.

[35]  Jason S. Cumbie,et al.  High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes , 2007, PloS one.

[36]  J. Leebens-Mack,et al.  Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants. , 2007, The Plant journal : for cell and molecular biology.

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

[38]  Steven M. Johnson,et al.  Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. , 2006, Genome research.

[39]  W Brad Barbazuk,et al.  Gene discovery and annotation using LCM-454 transcriptome sequencing. , 2006, Genome research.

[40]  A. Paulus,et al.  Rapid separation and purification of oligonucleotides by high-performance capillary gel electrophoresis. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

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

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

[43]  N. Lau,et al.  Characterization of the piRNA Complex from Rat Testes , 2006, Science.

[44]  R A Mathies,et al.  DNA sequencing using capillary array electrophoresis. , 1992, Analytical chemistry.

[45]  Transcript Profiling by 3′-Untranslated Region Sequencing Resolves Expression of Gene Families1[W][OA] , 2007, Plant Physiology.

[46]  Madabhushi Rs,et al.  Separation of 4‐color DNA sequencing extension products in noncovalently coated capillaries using low viscosity polymer solutions , 1998, Electrophoresis.

[47]  E. Mardis,et al.  Generation and analysis of 280,000 human expressed sequence tags. , 1996, Genome research.

[48]  J. Marden,et al.  Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing , 2008, Molecular ecology.

[49]  Stanley Fields,et al.  Site-Seeing by Sequencing , 2007, Science.

[50]  M. Brent.  Steady progress and recent breakthroughs in the accuracy of automated genome annotation , 2008, Nature Reviews Genetics.

[51]  J. Claverie,et al.  The significance of digital gene expression profiles. , 1997, Genome research.

[52]  S. Ness,et al.  Microarray analysis: basic strategies for successful experiments , 2007, Molecular biotechnology.

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

[54]  David Landsman,et al.  High-resolution genome-wide mapping of histone modifications , 2004, Nature Biotechnology.

[55]  F. Chen,et al.  Robust analysis of 5 0 -transcript ends (5 0 -RATE): a novel technique for transcriptome analysis and genome annotation , 2006 .

[56]  K. Akiyama,et al.  Functional Annotation of a Full-Length Arabidopsis cDNA Collection , 2002, Science.

[57]  G. Hannon,et al.  A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. , 2007, Genes & development.

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

[59]  Ji Huang,et al.  [Serial analysis of gene expression]. , 2002, Yi chuan = Hereditas.

[60]  J. Rothberg,et al.  Erratum: Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing , 2006, Nature Medicine.

[61]  Scott A Givan,et al.  Genome-Wide Analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 Pathway in Arabidopsis Reveals Dependency on miRNA- and tasiRNA-Directed Targeting[W][OA] , 2007, The Plant Cell Online.

[62]  Miao Sun,et al.  SAGE is far more sensitive than EST for detecting low-abundance transcripts , 2004, BMC Genomics.

[63]  H. Lipkin.  Where is the ?c? , 1978 .

[64]  Marco A Marra,et al.  From cytogenetics to next-generation sequencing technologies: advances in the detection of genome rearrangements in tumors. , 2008, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[65]  Shivakundan Singh Tej,et al.  MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. , 2006, Genome research.

[66]  I. Albert,et al.  Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome , 2007, Nature.

[67]  Clive Brown,et al.  Toward the 1,000 dollars human genome. , 2005, Pharmacogenomics.

[68]  D. Hanahan,et al.  The Hallmarks of Cancer , 2000, Cell.

[69]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[70]  Jonghwan Kim,et al.  Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). , 2007, Genome research.

[71]  Guo-Liang Wang,et al.  Robust-LongSAGE (RL-SAGE): A Substantially Improved LongSAGE Method for Gene Discovery and Transcriptome Analysis1[w] , 2004, Plant Physiology.

[72]  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 .

[73]  F. Sanger,et al.  A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. , 1975, Journal of molecular biology.

[74]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

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

[76]  S. Wang,et al.  Understanding SAGE data. , 2007, Trends in genetics : TIG.

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

[78]  Thomas de Quincey.  [C] , 2000, The Works of Thomas De Quincey, Vol. 1: Writings, 1799–1820.

[79]  I. Henderson,et al.  Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning , 2006, Nature Genetics.

[80]  Allen D. Delaney,et al.  Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing , 2007, Nature Methods.

[81]  Clive Brown,et al.  Toward the $1000 human genome , 2005 .

[82]  Matthew E Hudson,et al.  Wasp Gene Expression Supports an Evolutionary Link Between Maternal Behavior and Eusociality , 2007, Science.

[83]  E. Mardis.  ChIP-seq: welcome to the new frontier , 2007, Nature Methods.

[84]  M. Uhlén,et al.  Solid phase DNA minisequencing by an enzymatic luminometric inorganic pyrophosphate detection assay. , 1993, Analytical biochemistry.

[85]  Stanley Fields.  Molecular biology. Site-seeing by sequencing. , 2007, Science.

[86]  Eugene Berezikov,et al.  A Role for Piwi and piRNAs in Germ Cell Maintenance and Transposon Silencing in Zebrafish , 2007, Cell.

[87]  Dong Xu,et al.  Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. , 2007, Cancer research.

[88]  Dustin E. Schones,et al.  Genome-wide approaches to studying chromatin modifications , 2008, Nature Reviews Genetics.

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

[90]  J Seth Strattan,et al.  Nucleosomes unfold completely at a transcriptionally active promoter. , 2003, Molecular cell.

[91]  W. Filipowicz,et al.  Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? , 2008, Nature Reviews Genetics.

[92]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

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

[94]  Thomas LaFramboise,et al.  Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing , 2006, Nature Medicine.

[95]  C. Allis,et al.  In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment. , 1999, Methods.

[96]  A. Sparks,et al.  Using the transcriptome to annotate the genome , 2002, Nature Biotechnology.

[97]  Christian Schlötterer,et al.  Gene expression profiling by massively parallel sequencing. , 2007, Genome research.

[98]  A. Mortazavi,et al.  Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.

[99]  Adam M. Gustafson,et al.  Genetic and Functional Diversification of Small RNA Pathways in Plants , 2004, PLoS biology.

[100]  Atif Shahab,et al.  Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). , 2007, Genome research.

[101]  J. Ohlrogge,et al.  Sampling the Arabidopsis Transcriptome with Massively Parallel Pyrosequencing1[W][OA] , 2007, Plant Physiology.

[102]  David P. Bartel,et al.  A Two-Hit Trigger for siRNA Biogenesis in Plants , 2006, Cell.

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

[104]  Justin O Borevitz,et al.  Genome-Wide Expression Profiling of the Arabidopsis Female Gametophyte Identifies Families of Small, Secreted Proteins , 2007, PLoS genetics.

[105]  C. Nusbaum,et al.  Quality scores and SNP detection in sequencing-by-synthesis systems. , 2008, Genome research.

[106]  A. Feinberg,et al.  The emerging science of epigenomics. , 2006, Human molecular genetics.

[107]  Rithy K. Roth,et al.  Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays , 2000, Nature Biotechnology.

[108]  Edwin Cuppen,et al.  Diversity of microRNAs in human and chimpanzee brain , 2006, Nature Genetics.

[109]  L. Du,et al.  Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes , 2006, Nucleic acids research.

[110]  E. Carrilho,et al.  DNA sequencing by capillary array electrophoresis and microfabricated array systems , 2000, Electrophoresis.

[111]  M. Adams,et al.  Caenorhabditis elegans expressed sequence tags identify gene families and potential disease gene homologues , 1992, Nature Genetics.

[112]  G. Crawford,et al.  Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1. , 2007, Cancer research.

[113]  J. Rogers,et al.  DNA methylation profiling of human chromosomes 6, 20 and 22 , 2006, Nature Genetics.

[114]  Taking a census of mRNA populations with microbeads , 2000, Nature Biotechnology.

[115]  D. Bentley,et al.  Whole-genome re-sequencing. , 2006, Current opinion in genetics & development.

[116]  International Human Genome Sequencing Consortium.  Finishing the euchromatic sequence of the human genome , 2004 .

[117]  Lloyd M. Smith,et al.  Fluorescence detection in automated DNA sequence analysis , 1986, Nature.

[118]  Ravi Sachidanandam,et al.  A germline-specific class of small RNAs binds mammalian Piwi proteins , 2006, Nature.

[119]  Dan Nettleton,et al.  Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.) , 2007, The Plant journal : for cell and molecular biology.

[120]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[121]  Dan S. Tawfik,et al.  Man-made cell-like compartments for molecular evolution , 1998, Nature Biotechnology.

[122]  Philipp Bucher,et al.  ChIP-Seq Data Reveal Nucleosome Architecture of Human Promoters , 2007, Cell.