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ChIP-Sequencing / Protein-Nucleic Acid Interactions
Cytogenetics
Data Analysis
Genomic Sequencing
Metagenomics
Method
Methylation
Targeted Sequencing
Transcriptomics / Small RNA
ChIP-Sequencing / Protein-Nucleic Acid Interactions
Nielsen R, Pedersen TA, Hagenbeek D, Moulos P, Siersbæk R, et al.
(2008) Genome-wide profiling of PPAR{gamma}:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis. Genes Dev 22:2953-2967.
Boyle AP, Guinney J, Crawford GE, Furey TS
(2008) F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 24:2537-8.
Alekseyenko AA, Peng S, Larschan E, Gorchakov AA, Lee OK, et al.
(2008) A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell 134:599-609.
Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, et al.
(2008) Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods Epub ahead of print.
Marson A, Levine SS, Cole MF, Frampton GM, Brambrink T, et al.
(2008) Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134:521-33.
Jothi R, Cuddapah S, Barski A, Cui K, Zhao K
(2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res Epub ahead of print.
Wederell ED, Bilenky M, Cullum R, Thiessen N, Dagpinar M, et al.
(2008) Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Res 36:4549-64.
Yu H, Zhu S, Zhou B, Xue H, Han JD
(2008) Inferring causal relationships among different histone modifications and gene expression. Genome Res 18:1314-24.
Chen X, Xu H, Yuan P, Fang F, Huss M, et al.
(2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133:1106-17.
Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, et al.
(2008) Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol 6:e65.
Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, et al.
(2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132:887-98.
Schones DE, Zhao K
(2008) Genome-wide approaches to studying chromatin modifications. Nat Rev Genet 9:179-91.
Wold B, Myers RM
(2008) Sequence census methods for functional genomics. Nat Methods 5:19-21.
Schmid CD, Bucher P
(2007) ChIP-Seq data reveal nucleosome architecture of human promoters. Cell 131:831-2; author reply 832-3.
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, et al.
(2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553-60.
Johnson DS, Mortazavi A, Myers RM, Wold B
(2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497-502.
Fields S
(2007) Molecular biology. Site-seeing by sequencing. Science 316:1441-2.
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, et al.
(2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823-37.
Mardis ER
(2007) ChIP-seq: welcome to the new frontier. Nat Methods 4:613-4.
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, et al.
(2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4:651-7.
Cytogenetics
Campbell PJ, Stephens PJ, Pleasance ED, OMeara S, Li H, et al.
(2008) Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 40:722-9.
Chen W, Kalscheuer V, Tzschach A, Menzel C, Ullmann R, et al.
(2008) Mapping translocation breakpoints by next-generation sequencing. Genome Res 18:1143-9.
Data Analysis
Wicker T, Narechania A, Sabot F, Stein J, Vu GT, et al.
(2008) Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC Genomics 9:518.
Malhis N, Butterfield Y, Ester M, Jones SJ
(2008) Slider - Maximum use of probability information for alignment of short sequence reads and SNP detection. Bioinformatics Epub ahead of print.
Pomraning KR, Smith KM, Freitag M
(2008) Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods Epub ahead of print.
Sugawara H, Ikeo K, Fukuchi S, Gojobori T, Tateno Y
(2008) DDBJ dealing with mass data produced by the second generation sequencer. Nucleic Acids Res Epub ahead of print.
Nobuta K, Lu C, Shrivastava R, Pillay M, De Paoli E, et al.
(2008) Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci U S A 105:14958-63.
Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, et al.
(2008) Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods Epub ahead of print.
De Bona F, Ossowski S, Schneeberger K, Rätsch G
(2008) Optimal spliced alignments of short sequence reads. Bioinformatics 24:i174-80.
Jothi R, Cuddapah S, Barski A, Cui K, Zhao K
(2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res Epub ahead of print.
Lin H, Zhang Z, Zhang MQ, Ma B, Li M
(2008) ZOOM! Zillions of oligos mapped. Bioinformatics 24:2431-7.
Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, et al.
(2008) FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24:1729-30.
Sobreira TJ, Gruber A
(2008) Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data. Bioinformatics 24:1676-80.
Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, et al.
(2008) A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 26:779-85.
Hajirasouliha I, Hormozdiari F, Sahinalp SC, Birol I
(2008) Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. Bioinformatics 24:i32-40.
Huang W, Marth GT
(2008) EagleView: a genome assembly viewer for next-generation sequencing technologies. Genome Res Epub ahead of print.
Zerbino DR, Birney E
(2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821-9.
Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, et al.
(2008) ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res 18:810-20.
Hernandez D, François P, Farinelli L, Osterås M, Schrenzel J
(2008) De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res 18:802-9.
Smith AD, Xuan Z, Zhang MQ
(2008) Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics 9:128.
Chaisson MJ, Pevzner PA
(2008) Short read fragment assembly of bacterial genomes. Genome Res 18:324-30.
Li R, Li Y, Kristiansen K, Wang J
(2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24:713-4.
Sharon E, Lubliner S, Segal E
(2008) A feature-based approach to modeling protein-DNA interactions. PLoS Comput Biol 4:e1000154.
Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, et al.
(2008) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 36:D13-21.
Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M
(2008) Modeling ChIP sequencing in silico with applications. PLoS Comput Biol 4:e1000158.
Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, et al.
(2008) Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics 9:431.
Schatz MC, Trapnell C, Delcher AL, Varshney A
(2007) High-throughput sequence alignment using Graphics Processing Units. BMC Bioinformatics 8:474.
Jeck WR, Reinhardt JA, Baltrus DA, Hickenbotham MT, Magrini V, et al.
(2007) Extending assembly of short DNA sequences to handle error. Bioinformatics 23:2942-4.
Warren RL, Sutton GG, Jones SJ, Holt RA
(2007) Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23:500-1.
Dohm JC, Lottaz C, Borodina T, Himmelbauer H
(2007) SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res 17:1697-706.
Whiteford N, Haslam N, Weber G, Prügel-Bennett A, Essex JW, et al.
(2005) An analysis of the feasibility of short read sequencing. Nucleic Acids Res 33:e171.
Genomic Sequencing
Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al.
(2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53-9.
Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, et al.
(2008) DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456:66-72.
Wang J, Wang W, Li R, Li Y, Tian G, et al.
(2008) The diploid genome sequence of an Asian individual. Nature 456:60-5.
Wicker T, Narechania A, Sabot F, Stein J, Vu GT, et al.
(2008) Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC Genomics 9:518.
Bau S, Schracke N, Kränzle M, Wu H, Stähler PF, et al.
(2008) Targeted next-generation sequencing by specific capture of multiple genomic loci using low-volume microfluidic DNA arrays. Anal Bioanal Chem Epub ahead of print.
Sugawara H, Ikeo K, Fukuchi S, Gojobori T, Tateno Y
(2008) DDBJ dealing with mass data produced by the second generation sequencer. Nucleic Acids Res Epub ahead of print.
Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, et al.
(2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res 18:2024-33.
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al.
(2008) Model-based Analysis of ChIP-Seq (MACS). Genome Biol 9:R137.
Craig DW, Pearson JV, Szelinger S, Sekar A, Redman M, et al.
(2008) Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods 5:887-93.
Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, et al.
(2008) Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res 18:1906-17.
Boyle AP, Guinney J, Crawford GE, Furey TS
(2008) F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 24:2537-8.
Cronn R, Liston A, Parks M, Gernandt DS, Shen R, et al.
(2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res 36:e122.
Sarin S, Prabhu S, OMeara MM, Peer I, Hobert O
(2008) Caenorhabditis elegans mutant allele identification by whole-genome sequencing. Nat Methods 5:865-7.
Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX, et al.
(2008) High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet 40:987-93.
Kistler AL, Gancz A, Clubb S, Skewes-Cox P, Fischer K, et al.
(2008) Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent. Virol J 5:88.
Hajirasouliha I, Hormozdiari F, Sahinalp SC, Birol I
(2008) Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. Bioinformatics 24:i32-40.
Graveley BR
(2008) Molecular biology: power sequencing. Nature 453:1197-8.
Batista PJ, Ruby JG, Claycomb JM, Chiang R, Fahlgren N, et al.
(2008) PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Mol Cell 31:67-78.
Campbell PJ, Stephens PJ, Pleasance ED, OMeara S, Li H, et al.
(2008) Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 40:722-9.
Woods IG, Schier AF
(2008) Targeted mutagenesis in zebrafish. Nat Biotechnol 26:650-1.
Holt RA, Jones SJ
(2008) The new paradigm of flow cell sequencing. Genome Res 18:839-46.
Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ
(2008) Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol 18:758-62.
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, et al.
(2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344-9.
Blow MJ, Zhang T, Woyke T, Speller CF, Krivoshapkin A, et al.
(2008) Identification of ancient remains through genomic sequencing. Genome Res 18:1347-53.
Margulies EH, Birney E
(2008) Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes. Nat Rev Genet 9:303-13.
Friedländer MR, Chen W, Adamidi C, Maaskola J, Einspanier R, et al.
(2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 26:407-15.
Bashir A, Volik S, Collins C, Bafna V, Raphael BJ
(2008) Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput Biol 4:e1000051.
Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, et al.
(2008) Whole-genome sequencing and variant discovery in C. elegans. Nat Methods 5:183-8.
Van Tassell CP, Smith TP, Matukumalli LK, Taylor JF, Schnabel RD, et al.
(2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 5:247-52.
Srivatsan A, Han Y, Peng J, Tehranchi AK, Gibbs R, et al.
(2008) High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet 4:e1000139.
Schuster SC
(2008) Next-generation sequencing transforms todays biology. Nat Methods 5:16-8.
van Ommen GJ
(2008) Popper revisited: GWAS here, last year. Eur J Hum Genet 16:1-2.
Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, et al.
(2008) Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics 9:431.
McCutcheon JP, Moran NA
(2007) Parallel genomic evolution and metabolic interdependence in an ancient symbiosis. Proc Natl Acad Sci U S A 104:19392-7.
Zilberman D, Henikoff S
(2007) Genome-wide analysis of DNA methylation patterns. Development 134:3959-65.
Hutchison CA
(2007) DNA sequencing: bench to bedside and beyond. Nucleic Acids Res 35:6227-37.
Blow N
(2007) Genomics: the personal side of genomics. Nature 449:627-30.
Baker S, Holt K, Whitehead S, Goodhead I, Perkins T, et al.
(2007) A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi. Mol Microbiol 66:1207-18.
Hall N
(2007) Advanced sequencing technologies and their wider impact in microbiology. J Exp Biol 210:1518-25.
Topol EJ, Frazer KA
(2007) The resequencing imperative. Nat Genet 39:439-40.
Mardis ER
(2006) Anticipating the 1,000 dollar genome. Genome Biol 7:112.
Bentley DR
(2006) Whole-genome re-sequencing. Curr Opin Genet Dev 16:545-52.
Bennett ST, Barnes C, Cox A, Davies L, Brown C
(2005) Toward the 1,000 dollars human genome. Pharmacogenomics 6:373-82.
Bennett S
(2004) Solexa Ltd. Pharmacogenomics 5:433-8.
Shendure J, Mitra RD, Varma C, Church GM
(2004) Advanced sequencing technologies: methods and goals. Nat Rev Genet 5:335-44.
Method
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al.
(2008) Model-based Analysis of ChIP-Seq (MACS). Genome Biol 9:R137.
Yu H, Zhu S, Zhou B, Xue H, Han JD
(2008) Inferring causal relationships among different histone modifications and gene expression. Genome Res 18:1314-24.
Wendl MC, Wilson RK
(2008) Aspects of coverage in medical DNA sequencing. BMC Bioinformatics 9:239.
Bashir A, Volik S, Collins C, Bafna V, Raphael BJ
(2008) Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput Biol 4:e1000051.
Edlund CK, Lee WH, Li D, Van Den Berg DJ, Conti DV
(2008) Snagger: a user-friendly program for incorporating additional information for tagSNP selection. BMC Bioinformatics 9:174.
Turcatti G, Romieu A, Fedurco M, Tairi AP
(2008) A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Nucleic Acids Res 36:e25.
Dolan PC, Denver DR
(2008) TileQC: a system for tile-based quality control of Solexa data. BMC Bioinformatics 9:250.
Schmid CD, Sengstag T, Bucher P, Delorenzi M
(2007) MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data. Nucleic Acids Res 35:W201-5.
Methylation
Pomraning KR, Smith KM, Freitag M
(2008) Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods Epub ahead of print.
Bonetta L
(2008) Epigenomics: Detailed analysis. Nature 454:795-8.
Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, et al.
(2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454:766-70.
Lister R, OMalley RC, Tonti-Filippini J, Gregory BD, Berry CC, et al.
(2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523-36.
Beck S, Rakyan VK
(2008) The methylome: approaches for global DNA methylation profiling. Trends Genet 24:231-7.
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, et al.
(2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452:215-9.
Targeted Sequencing
Bau S, Schracke N, Kränzle M, Wu H, Stähler PF, et al.
(2008) Targeted next-generation sequencing by specific capture of multiple genomic loci using low-volume microfluidic DNA arrays. Anal Bioanal Chem Epub ahead of print.
Hajirasouliha I, Hormozdiari F, Sahinalp SC, Birol I
(2008) Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. Bioinformatics 24:i32-40.
Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, et al.
(2007) Genome-wide in situ exon capture for selective resequencing. Nat Genet 39:1522-7.
Olson M
(2007) Enrichment of super-sized resequencing targets from the human genome. Nat Methods 4:891-2.
Porreca GJ, Zhang K, Li JB, Xie B, Austin D, et al.
(2007) Multiplex amplification of large sets of human exons. Nat Methods 4:931-6.
Transcriptomics / Small RNA
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, et al.
(2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470-6.
Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ
(2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40:1413-5.
t Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, et al.
(2008) Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res 36:e141.
Ahsan B, Saito TL, Hashimoto SI, Muramatsu K, Tsuda M, et al.
(2008) MachiBase: a Drosophila melanogaster 5-end mRNA transcription database. Nucleic Acids Res Epub ahead of print.
Chen X, Ba Y, Ma L, Cai X, Yin Y, et al.
(2008) Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res 18:997-1006.
Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, et al.
(2008) Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 455:1193-7.
Nobuta K, Lu C, Shrivastava R, Pillay M, De Paoli E, et al.
(2008) Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci U S A 105:14958-63.
Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, et al.
(2008) A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res 18:1456-65.
Marson A, Levine SS, Cole MF, Frampton GM, Brambrink T, et al.
(2008) Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134:521-33.
Rosenkranz R, Borodina T, Lehrach H, Himmelbauer H
(2008) Characterizing the mouse ES cell transcriptome with Illumina sequencing. Genomics 92:187-94.
Das PP, Bagijn MP, Goldstein LD, Woolford JR, Lehrbach NJ, et al.
(2008) Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Mol Cell 31:79-90.
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B
(2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621-8.
Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, et al.
(2008) Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques 45:81-94.
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y
(2008) RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res Epub ahead of print.
German MA, Pillay M, Jeong DH, Hetawal A, Luo S, et al.
(2008) Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 26:941-6.
Gregory BD, OMalley RC, Lister R, Urich MA, Tonti-Filippini J, et al.
(2008) A link between RNA metabolism and silencing affecting Arabidopsis development. Dev Cell 14:854-66.
Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, et al.
(2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453:1239-43.
Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, et al.
(2008) A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res 18:957-64.
Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C, et al.
(2008) An endogenous small interfering RNA pathway in Drosophila. Nature 453:798-802.
Lister R, OMalley RC, Tonti-Filippini J, Gregory BD, Berry CC, et al.
(2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523-36.
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, et al.
(2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344-9.
Ghildiyal M, Seitz H, Horwich MD, Li C, Du T, et al.
(2008) Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science 320:1077-81.
Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, et al.
(2008) Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453:534-8.
Massie CE, Mills IG
(2008) ChIPping away at gene regulation. EMBO Rep 9:337-43.
de Hoon M, Hayashizaki Y
(2008) Deep cap analysis gene expression (CAGE): genome-wide identification of promoters, quantification of their expression, and network inference. Biotechniques 44:627-8, 630, 632.
Mi S, Cai T, Hu Y, Chen Y, Hodges E, et al.
(2008) Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5 terminal nucleotide. Cell 133:116-27.
Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE, et al.
(2008) Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133:128-41.
Chen W, Kalscheuer V, Tzschach A, Menzel C, Ullmann R, et al.
(2008) Mapping translocation breakpoints by next-generation sequencing. Genome Res 18:1143-9.
Morin RD, OConnor MD, Griffith M, Kuchenbauer F, Delaney A, et al.
(2008) Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 18:610-21.
Stark A, Bushati N, Jan CH, Kheradpour P, Hodges E, et al.
(2008) A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev 22:8-13.
Tyler DM, Okamura K, Chung WJ, Hagen JW, Berezikov E, et al.
(2008) Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. Genes Dev 22:26-36.
Mudge J, Miller NA, Khrebtukova I, Lindquist IE, May GD, et al.
(2008) Genomic convergence analysis of schizophrenia: mRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum. PLoS ONE 3:e3625.
Hafner M, Landgraf P, Ludwig J, Rice A, Ojo T, et al.
(2008) Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods 44:3-12.
Wold B, Myers RM
(2008) Sequence census methods for functional genomics. Nat Methods 5:19-21.
Wakaguri H, Yamashita R, Suzuki Y, Sugano S, Nakai K
(2008) DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res 36:D97-101.
Ibarra I, Erlich Y, Muthuswamy SK, Sachidanandam R, Hannon GJ
(2007) A role for microRNAs in maintenance of mouse mammary epithelial progenitor cells. Genes Dev 21:3238-43.
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, et al.
(2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450:219-32.
Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, et al.
(2007) Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res 17:1865-79.
Yamashita R, Suzuki Y, Wakaguri H, Tsuritani K, Nakai K, et al.
(2006) DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. Nucleic Acids Res 34:D86-9.
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