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ChIP-Sequencing / Protein-Nucleic Acid Interactions
Data Analysis
De Novo Sequencing
DNA Methylation Analysis
Histone Analysis
Metagenomics
Method
Targeted Resequencing
Transcriptomics - mRNA
Transcriptomics - Non-Coding RNA
Whole-Genome Resequencing
ChIP-Sequencing / Protein-Nucleic Acid Interactions
Johnson R, Samuel J, Ng CK, Jauch R, Stanton LW, et al.
(2009) Evolution of the vertebrate gene regulatory network controlled by the transcriptional repressor REST. Mol Biol Evol 26:1491-507.
Hurd PJ, Nelson CJ
(2009) Advantages of next-generation sequencing versus the microarray in epigenetic research. Brief Funct Genomic Proteomic Epub ahead of print.
Theo Sijtse Palstra RJ
(2009) Close encounters of the 3C kind: long-range chromatin interactions and transcriptional regulation. Brief Funct Genomic Proteomic Epub ahead of print.
Hurd PJ, Bannister AJ, Halls K, Dawson MA, Vermeulen M, et al.
(2009) Phosphorylation of histone h3 thr-45 is linked to apoptosis. J Biol Chem 284:16575-83.
Zang C, Schones DE, Zeng C, Cui K, Zhao K, et al.
(2009) A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics Epub ahead of print.
Narlikar L, Ovcharenko I
(2009) Identifying regulatory elements in eukaryotic genomes. Brief Funct Genomic Proteomic Epub ahead of print.
Sugano S
(2009) [Second generation sequencer and personal genomics] Nippon Rinsho 67:1164-9.
Siegel TN, Hekstra DR, Kemp LE, Figueiredo LM, Lowell JE, et al.
(2009) Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei. Genes Dev 23:1063-76.
Wang Z, Tollervey J, Briese M, Turner D, Ule J
(2009) CLIP: Construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo. Methods Epub ahead of print.
Ketel C, Wang HS, McClellan M, Bouchonville K, Selmecki A, et al.
(2009) Neocentromeres form efficiently at multiple possible loci in Candida albicans. PLoS Genet 5:e1000400.
Zhu J, Davidson TS, Wei G, Jankovic D, Cui K, et al.
(2009) Down-regulation of Gfi-1 expression by TGF-{beta} is important for differentiation of Th17 and CD103+ inducible regulatory T cells. J Exp Med 206:329-341.
Warren RL, Nelson BH, Holt RA
(2009) Profiling model T-cell metagenomes with short reads. Bioinformatics 25:458-464.
Service RF
(2009) Biochemistry. Taking stock of a cells protein production. Science 323:864.
Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS
(2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324:218-23.
Jiang C, Pugh BF
(2009) Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 10:161-72.
Guttman M, Amit I, Garber M, French C, Lin MF, et al.
(2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223-7.
Barski A, Zhao K
(2009) Genomic location analysis by ChIP-Seq. J Cell Biochem 107:11-8.
Zheng D, Zhao K, Mehler MF
(2009) Profiling RE1/REST-mediated histone modifications in the human genome. Genome Biol 10:R9.
Sasaki S, Mello CC, Shimada A, Nakatani Y, Hashimoto S, et al.
(2009) Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science 323:401-4.
Ribeiro de Almeida C, Heath H, Krpic S, Dingjan GM, van Hamburg JP, et al.
(2009) Critical role for the transcription regulator CCCTC-binding factor in the control of Th2 cytokine expression. J Immunol 182:999-1010.
Hoffman BG, Jones SJ
(2009) Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing. J Endocrinol 201:1-13.
Pauler FM, Sloane MA, Huang R, Regha K, Koerner MV, et al.
(2009) H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Res 19:221-33.
Gargiulo G, Minucci S
(2009) Epigenomic profiling of cancer cells. Int J Biochem Cell Biol 41:127-35.
Vega VB, Cheung E, Palanisamy N, Sung WK
(2009) Inherent signals in sequencing-based Chromatin-ImmunoPrecipitation control libraries. PLoS One 4:e5241.
Wang LY, Abyzov A, Korbel JO, Snyder M, Gerstein M
(2009) MSB: A mean-shift-based approach for the analysis of structural variation in the genome. Genome Res 19:106-17.
Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, et al.
(2008) Divergent transcription from active promoters. Science 322:1849-51.
Won KJ, Chepelev I, Ren B, Wang W
(2008) Prediction of regulatory elements in mammalian genomes using chromatin signatures. BMC Bioinformatics 9:547.
Guenther MG, Lawton LN, Rozovskaia T, Frampton GM, Levine SS, et al.
(2008) Aberrant chromatin at genes encoding stem cell regulators in human mixed-lineage leukemia. Genes Dev 22:3403-8.
Krebs A, Frontini M, Tora L
(2008) GPAT: Retrieval of genomic annotation from large genomic position datasets. BMC Bioinformatics 9:533.
Weddington N, Stuy A, Hiratani I, Ryba T, Yokochi T, et al.
(2008) ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data. BMC Bioinformatics 9:530.
Nix DA, Courdy SJ, Boucher KM
(2008) Empirical methods for controlling false positives and estimating confidence in chIP-seq peaks. BMC Bioinformatics 9:523.
Park PJ
(2008) Epigenetics meets next-generation sequencing. Epigenetics 3:318-321.
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 5:829-834.
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.
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.
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.
Maenz B, Hekerman P, Vela EM, Galceran J, Becker W
(2008) Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1. BMC Mol Biol 9:30.
Collas P, Dahl JA
(2008) Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation. Front Biosci 13:929-43.
Yang MQ, Elnitski LL
(2008) Diversity of core promoter elements comprising human bidirectional promoters. BMC Genomics 9 Suppl 2:S3.
Wold B, Myers RM
(2008) Sequence census methods for functional genomics. Nat Methods 5:19-21.
Fu Y, Sinha M, Peterson CL, Weng Z
(2008) The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet 4:e1000138.
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.
Data Analysis
Birol I, Jackman SD, Nielsen C, Qian JQ, Varhol R, et al.
(2009) De novo Transcriptome Assembly with ABySS. Bioinformatics Epub ahead of print.
Daines B, Wang H, Li Y, Han Y, Gibbs R, et al.
(2009) High-throughput Multiplex Sequencing to Discover Copy Number Variants in Drosophila. Genetics Epub ahead of print.
Zang C, Schones DE, Zeng C, Cui K, Zhao K, et al.
(2009) A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics Epub ahead of print.
Chu T, Bunce K, Hogge WA, Peters DG
(2009) Statistical model for whole genome sequencing and its application to minimally invasive diagnosis of fetal genetic disease. Bioinformatics 25:1244-50.
Li C, Vagin VV, Lee S, Xu J, Ma S, et al.
(2009) Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137:509-21.
Fahlgren N, Sullivan CM, Kasschau KD, Chapman EJ, Cumbie JS, et al.
(2009) Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA 15:992-1002.
Xie C, Tammi MT
(2009) CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 10:80.
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, et al.
(2009) ABySS: A parallel assembler for short read sequence data. Genome Res 19:1117-23.
Jiang H, Wong WH
(2009) Statistical inferences for isoform expression in RNA-Seq. Bioinformatics 25:1026-32.
Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, et al.
(2009) PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol 10:R23.
Bateman A, Quackenbush J
(2009) Editorial. Bioinformatics 25:429.
Warren RL, Nelson BH, Holt RA
(2009) Profiling model T-cell metagenomes with short reads. Bioinformatics 25:458-464.
Campagna D, Albiero A, Bilardi A, Caniato E, Forcato C, et al.
(2009) PASS: a program to align short sequences. Bioinformatics 25:967-8.
Vega VB, Cheung E, Palanisamy N, Sung WK
(2009) Inherent signals in sequencing-based Chromatin-ImmunoPrecipitation control libraries. PLoS One 4:e5241.
Wang W, Zhang P, Liu X
(2009) Short read DNA fragment anchoring algorithm. BMC Bioinformatics 10 Suppl 1:S17.
Malhis N, Butterfield YS, Ester M, Jones SJ
(2009) Slider--maximum use of probability information for alignment of short sequence reads and SNP detection. Bioinformatics 25:6-13.
Pomraning KR, Smith KM, Freitag M
(2009) Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods 47:142-50.
Sugawara H, Ikeo K, Fukuchi S, Gojobori T, Tateno Y
(2009) DDBJ dealing with mass data produced by the second generation sequencer. Nucleic Acids Res 37:D16-8.
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.
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 5:829-834.
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.
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.
De Novo Sequencing
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, et al.
(2009) ABySS: A parallel assembler for short read sequence data. Genome Res 19:1117-23.
Moran NA, McLaughlin HJ, Sorek R
(2009) The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 323:379-82.
Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, et al.
(2009) De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res 19:294-305.
Koenig R
(2007) Tuberculosis. Few mutations divide some drug-resistant TB strains. Science 318:901-2.
DNA Methylation Analysis
Hurd PJ, Nelson CJ
(2009) Advantages of next-generation sequencing versus the microarray in epigenetic research. Brief Funct Genomic Proteomic Epub ahead of print.
Kristensen LS, Hansen LL
(2009) PCR-Based Methods for Detecting Single-Locus DNA Methylation Biomarkers in Cancer Diagnostics, Prognostics, and Response to Treatment. Clin Chem Epub ahead of print.
Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, et al.
(2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 27:361-8.
Deng J, Shoemaker R, Xie B, Gore A, LeProust EM, et al.
(2009) Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol 27:353-60.
Brunner AL, Johnson DS, Kim SW, Valouev A, Reddy TE, et al.
(2009) Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res 19:1044-56.
Dudley KJ, Revill K, Clayton RN, Farrell WE
(2009) Pituitary tumours: all silent on the epigenetics front. J Mol Endocrinol 42:461-8.
Muhonen P, Holthofer H
(2009) Epigenetic and microRNA-mediated regulation in diabetes. Nephrol Dial Transplant 24:1088-96.
Li J, Gao F, Li N, Li S, Yin G, et al.
(2009) An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines. BMC Genomics 10:223.
Pomraning KR, Smith KM, Freitag M
(2009) Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods 47:142-50.
Stöger R
(2008) Epigenetics and obesity. Pharmacogenomics 9:1851-60.
Park PJ
(2008) Epigenetics meets next-generation sequencing. Epigenetics 3:318-321.
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.
Jacinto FV, Ballestar E, Esteller M
(2008) Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome. Biotechniques 44:35, 37, 39 passim.
Histone Analysis
Jiang C, Pugh BF
(2009) Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 10:161-72.
Dudley KJ, Revill K, Clayton RN, Farrell WE
(2009) Pituitary tumours: all silent on the epigenetics front. J Mol Endocrinol 42:461-8.
Zheng D, Zhao K, Mehler MF
(2009) Profiling RE1/REST-mediated histone modifications in the human genome. Genome Biol 10:R9.
Fu Y, Sinha M, Peterson CL, Weng Z
(2008) The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet 4:e1000138.
Metagenomics
Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, et al.
(2009) Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 6:283-9.
Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, et al.
(2009) Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nat Methods 6:67-9.
Sorber K, Chiu C, Webster D, Dimon M, Ruby JG, et al.
(2008) The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing. PLoS ONE 3:e3495.
Method
Birol I, Jackman SD, Nielsen C, Qian JQ, Varhol R, et al.
(2009) De novo Transcriptome Assembly with ABySS. Bioinformatics Epub ahead of print.
Daines B, Wang H, Li Y, Han Y, Gibbs R, et al.
(2009) High-throughput Multiplex Sequencing to Discover Copy Number Variants in Drosophila. Genetics Epub ahead of print.
Zang C, Schones DE, Zeng C, Cui K, Zhao K, et al.
(2009) A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics Epub ahead of print.
Chu T, Bunce K, Hogge WA, Peters DG
(2009) Statistical model for whole genome sequencing and its application to minimally invasive diagnosis of fetal genetic disease. Bioinformatics 25:1244-50.
Fahlgren N, Sullivan CM, Kasschau KD, Chapman EJ, Cumbie JS, et al.
(2009) Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA 15:992-1002.
Xie C, Tammi MT
(2009) CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 10:80.
Ebhardt HA, Tsang HH, Dai DC, Liu Y, Bostan B, et al.
(2009) Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Res 37:2461-70.
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, et al.
(2009) ABySS: A parallel assembler for short read sequence data. Genome Res 19:1117-23.
Tsuchihara K, Suzuki Y, Wakaguri H, Irie T, Tanimoto K, et al.
(2009) Massive transcriptional start site analysis of human genes in hypoxia cells. Nucleic Acids Res 37:2249-63.
Beck J, Urnovitz HB, Riggert J, Clerici M, Schütz E
(2009) Profile of the circulating DNA in apparently healthy individuals. Clin Chem 55:730-8.
Vega VB, Cheung E, Palanisamy N, Sung WK
(2009) Inherent signals in sequencing-based Chromatin-ImmunoPrecipitation control libraries. PLoS One 4:e5241.
Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, et al.
(2009) Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nat Methods 6:67-9.
Nix DA, Courdy SJ, Boucher KM
(2008) Empirical methods for controlling false positives and estimating confidence in chIP-seq peaks. BMC Bioinformatics 9:523.
Sorber K, Chiu C, Webster D, Dimon M, Ruby JG, et al.
(2008) The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing. PLoS ONE 3:e3495.
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.
Richter DC, Ott F, Auch AF, Schmid R, Huson DH
(2008) MetaSim: a sequencing simulator for genomics and metagenomics. PLoS ONE 3:e3373.
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.
Targeted Resequencing
Brkanac Z, Spencer D, Shendure J, Robertson PD, Matsushita M, et al.
(2009) IFRD1 is a candidate gene for SMNA on chromosome 7q22-q23. Am J Hum Genet 84:692-7.
Guryev V, Cuppen E
(2009) Next-generation sequencing approaches in genetic rodent model systems to study functional effects of human genetic variation. FEBS Lett 583:1668-73.
Turner EH, Lee C, Ng SB, Nickerson DA, Shendure J
(2009) Massively parallel exon capture and library-free resequencing across 16 genomes. Nat Methods 6:315-6.
Hasin-Brumshtein Y, Lancet D, Olender T
(2009) Human olfaction: from genomic variation to phenotypic diversity. Trends Genet 25:178-84.
Voelkerding KV, Dames SA, Durtschi JD
(2009) Next-generation sequencing: from basic research to diagnostics. Clin Chem 55:641-58.
Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, et al.
(2009) PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol 10:R23.
Lo YM, Chiu RW
(2009) Next-generation sequencing of plasma/serum DNA: an emerging research and molecular diagnostic tool. Clin Chem 55:607-8.
Beck J, Urnovitz HB, Riggert J, Clerici M, Schütz E
(2009) Profile of the circulating DNA in apparently healthy individuals. Clin Chem 55:730-8.
Rodriguez JA, Guiteau JJ, Nazareth L, Reid JG, Goss JA, et al.
(2009) Sequencing the full-length of the phosphatase and tensin homolog (PTEN) gene in hepatocellular carcinoma (HCC) using the 454 GS20 and Illumina GA DNA sequencing platforms. World J Surg 33:647-52.
Jao LE, Maddison L, Chen W, Burgess SM
(2008) Using retroviruses as a mutagenesis tool to explore the zebrafish genome. Brief Funct Genomic Proteomic 7:427-43.
Transcriptomics - mRNA
Morrissy AS, Morin RD, Delaney A, Zeng T, McDonald H, et al.
(2009) Next-generation tag sequencing for cancer gene expression profiling. Genome Res Epub ahead of print.
Theo Sijtse Palstra RJ
(2009) Close encounters of the 3C kind: long-range chromatin interactions and transcriptional regulation. Brief Funct Genomic Proteomic Epub ahead of print.
Philippe N, Boureux A, Bréhélin L, Tarhio J, Commes T, et al.
(2009) Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity. Nucleic Acids Res Epub ahead of print.
Blencowe BJ, Ahmad S, Lee LJ
(2009) Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes Dev 23:1379-86.
Birol I, Jackman SD, Nielsen C, Qian JQ, Varhol R, et al.
(2009) De novo Transcriptome Assembly with ABySS. Bioinformatics Epub ahead of print.
Chepelev I, Wei G, Tang Q, Zhao K
(2009) Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq. Nucleic Acids Res Epub ahead of print.
Gaidatzis D, Jacobeit K, Oakeley EJ, Stadler MB
(2009) Overestimation of alternative splicing caused by variable probe characteristics in exon arrays. Nucleic Acids Res Epub ahead of print.
Sackton TB, Clark AG
(2009) Comparative profiling of the transcriptional response to infection in two species of Drosophila by short-read cDNA sequencing. BMC Genomics 10:259.
Sugano S
(2009) [Second generation sequencer and personal genomics] Nippon Rinsho 67:1164-9.
Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, Rubin EM, et al.
(2009) Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci U S A 106:3976-81.
Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, et al.
(2009) Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A 106:3264-9.
Jiang H, Wong WH
(2009) Statistical inferences for isoform expression in RNA-Seq. Bioinformatics 25:1026-32.
Tsuchihara K, Suzuki Y, Wakaguri H, Irie T, Tanimoto K, et al.
(2009) Massive transcriptional start site analysis of human genes in hypoxia cells. Nucleic Acids Res 37:2249-63.
Service RF
(2009) Biochemistry. Taking stock of a cells protein production. Science 323:864.
Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS
(2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324:218-23.
Guttman M, Amit I, Garber M, French C, Lin MF, et al.
(2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223-7.
Hillier LW, Reinke V, Green P, Hirst M, Marra MA, et al.
(2009) Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res 19:657-66.
,
(2009) Post-transcriptional processing generates a diversity of 5-modified long and short RNAs. Nature 457:1028-32.
Kutlu B, Burdick D, Baxter D, Rasschaert J, Flamez D, et al.
(2009) Detailed transcriptome atlas of the pancreatic beta cell. BMC Med Genomics 2:3.
Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, et al.
(2009) Transcriptome sequencing to detect gene fusions in cancer. Nature 458:97-101.
Simon SA, Zhai J, Nandety RS, McCormick KP, Zeng J, et al.
(2009) Short-Read Sequencing Technologies for Transcriptional Analyses. Annu Rev Plant Biol Epub ahead of print.
Fu X, Fu N, Guo S, Yan Z, Xu Y, et al.
(2009) Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics 10:161.
McGhee JD, Fukushige T, Krause MW, Minnema SE, Goszczynski B, et al.
(2009) ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult. Dev Biol 327:551-65.
Ahsan B, Saito TL, Hashimoto S, Muramatsu K, Tsuda M, et al.
(2009) MachiBase: a Drosophila melanogaster 5-end mRNA transcription database. Nucleic Acids Res 37:D49-53.
Li H, Lovci MT, Kwon YS, Rosenfeld MG, Fu XD, et al.
(2008) Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Proc Natl Acad Sci U S A 105:20179-84.
Myles KM, Wiley MR, Morazzani EM, Adelman ZN
(2008) Alphavirus-derived small RNAs modulate pathogenesis in disease vector mosquitoes. Proc Natl Acad Sci U S A 105:19938-43.
Denoeud F, Aury JM, Da Silva C, Noel B, Rogier O, et al.
(2008) Annotating genomes with massive-scale RNA sequencing. Genome Biol 9:R175.
The International Silkworm Genome Consortium
(2008) The genome of a lepidopteran model insect, the silkworm Bombyx mori. Insect Biochem Mol Biol 38:1036-45.
Core LJ, Waterfall JJ, Lis JT
(2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322:1845-8.
He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW
(2008) The antisense transcriptomes of human cells. Science 322:1855-7.
Lee A, Hansen KD, Bullard J, Dudoit S, Sherlock G
(2008) Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species. PLoS Genet 4:e1000299.
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.
Rosenkranz R, Borodina T, Lehrach H, Himmelbauer H
(2008) Characterizing the mouse ES cell transcriptome with Illumina sequencing. Genomics 92:187-94.
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.
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.
Efroni S, Duttagupta R, Cheng J, Dehghani H, Hoeppner DJ, et al.
(2008) Global transcription in pluripotent embryonic stem cells. Cell Stem Cell 2:437-47.
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.
Yang MQ, Elnitski LL
(2008) Diversity of core promoter elements comprising human bidirectional promoters. BMC Genomics 9 Suppl 2:S3.
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.
Wold B, Myers RM
(2008) Sequence census methods for functional genomics. Nat Methods 5:19-21.
Wang X, Sun Q, McGrath SD, Mardis ER, Soloway PD, et al.
(2008) Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS ONE 3:e3839.
Shaw MW, Ablin RJ, Guinan PD, Bhatti RA
(1985) Effect of transfer factor on tumor-associated immunity and tumor growth of the Dunning R-3327G rat prostate adenocarcinoma. Am J Reprod Immunol Microbiol 8:80-3.
Transcriptomics - Non-Coding RNA
Wei B, Cai T, Zhang R, Li A, Huo N, et al.
(2009) Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv. Funct Integr Genomics Epub ahead of print.
Kato M, de Lencastre A, Pincus Z, Slack FJ
(2009) Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development. Genome Biol 10:R54.
Kawaoka S, Hayashi N, Suzuki Y, Abe H, Sugano S, et al.
(2009) The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes. RNA 15:1258-64.
Kirino Y, Kim N, de Planell-Saguer M, Khandros E, Chiorean S, et al.
(2009) Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability. Nat Cell Biol 11:652-8.
Li C, Vagin VV, Lee S, Xu J, Ma S, et al.
(2009) Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137:509-21.
Fahlgren N, Sullivan CM, Kasschau KD, Chapman EJ, Cumbie JS, et al.
(2009) Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA 15:992-1002.
Wang X, Elling AA, Li X, Li N, Peng Z, et al.
(2009) Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 21:1053-69.
Gingeras T
(2009) Missing lincs in the transcriptome. Nat Biotechnol 27:346-7.
Flynt A, Liu N, Martin R, Lai EC
(2009) Dicing of viral replication intermediates during silencing of latent Drosophila viruses. Proc Natl Acad Sci U S A 106:5270-5.
Rathjen T, Pais H, Sweetman D, Moulton V, Munsterberg A, et al.
(2009) High throughput sequencing of microRNAs in chicken somites. FEBS Lett 583:1422-6.
Ebhardt HA, Tsang HH, Dai DC, Liu Y, Bostan B, et al.
(2009) Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Res 37:2461-70.
Lord CJ, Martin SA, Ashworth A
(2009) RNA interference screening demystified. J Clin Pathol 62:195-200.
Guttman M, Amit I, Garber M, French C, Lin MF, et al.
(2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223-7.
,
(2009) Post-transcriptional processing generates a diversity of 5-modified long and short RNAs. Nature 457:1028-32.
Wei Y, Chen S, Yang P, Ma Z, Kang L
(2009) Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust. Genome Biol 10:R6.
Wei Y, Chen S, Yang P, Ma Z, Kang L
(2009) Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust. Genome Biol 10:R6.
Yi R, Pasolli HA, Landthaler M, Hafner M, Ojo T, et al.
(2009) DGCR8-dependent microRNA biogenesis is essential for skin development. Proc Natl Acad Sci U S A 106:498-502.
Ben-Ami O, Pencovich N, Lotem J, Levanon D, Groner Y
(2009) A regulatory interplay between miR-27a and Runx1 during megakaryopoiesis. Proc Natl Acad Sci U S A 106:238-43.
Chellappan P, Jin H
(2009) Discovery of Plant MicroRNAs and Short-Interfering RNAs by Deep Parallel Sequencing. Methods Mol Biol 495:1-12.
Qi X, Bao FS, Xie Z
(2009) Small RNA deep sequencing reveals role for Arabidopsis thaliana RNA-dependent RNA polymerases in viral siRNA biogenesis. PLoS ONE 4:e4971.
Montgomery TA, Yoo SJ, Fahlgren N, Gilbert SD, Howell MD, et al.
(2008) AGO1-miR173 complex initiates phased siRNA formation in plants. Proc Natl Acad Sci U S A 105:20055-62.
Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, et al.
(2008) Divergent transcription from active promoters. Science 322:1849-51.
Buratowski S
(2008) Transcription. Gene expression--where to start? Science 322:1804-5.
Myles KM, Wiley MR, Morazzani EM, Adelman ZN
(2008) Alphavirus-derived small RNAs modulate pathogenesis in disease vector mosquitoes. Proc Natl Acad Sci U S A 105:19938-43.
He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW
(2008) The antisense transcriptomes of human cells. Science 322:1855-7.
Nelson KM, Weiss GJ
(2008) MicroRNAs and cancer: past, present, and potential future. Mol Cancer Ther 7:3655-60.
Nelson KM, Weiss GJ
(2008) MicroRNAs and cancer: past, present, and potential future. Mol Cancer Ther 7:3655-60.
Brennecke J, Malone CD, Aravin AA, Sachidanandam R, Stark A, et al.
(2008) An epigenetic role for maternally inherited piRNAs in transposon silencing. Science 322:1387-92.
Brennecke J, Malone CD, Aravin AA, Sachidanandam R, Stark A, et al.
(2008) An epigenetic role for maternally inherited piRNAs in transposon silencing. Science 322:1387-92.
Ender C, Krek A, Friedländer MR, Beitzinger M, Weinmann L, et al.
(2008) A human snoRNA with microRNA-like functions. Mol Cell 32:519-28.
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.
Technau U
(2008) Evolutionary biology: Small regulatory RNAs pitch in. Nature 455:1184-5.
Technau U
(2008) Evolutionary biology: Small regulatory RNAs pitch in. Nature 455:1184-5.
Babiarz JE, Ruby JG, Wang Y, Bartel DP, Blelloch R
(2008) Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev 22:2773-85.
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.
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.
Nagaraja AK, Andreu-Vieyra C, Franco HL, Ma L, Chen R, et al.
(2008) Deletion of Dicer in somatic cells of the female reproductive tract causes sterility. Mol Endocrinol 22:2336-52.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Szittya G, Moxon S, Santos DM, Jing R, Fevereiro MP, et al.
(2008) High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics 9:593.
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.
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.
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.
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, 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.
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.
Whole-Genome Resequencing
Philippe N, Boureux A, Bréhélin L, Tarhio J, Commes T, et al.
(2009) Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity. Nucleic Acids Res Epub ahead of print.
Chepelev I, Wei G, Tang Q, Zhao K
(2009) Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq. Nucleic Acids Res Epub ahead of print.
Daines B, Wang H, Li Y, Han Y, Gibbs R, et al.
(2009) High-throughput Multiplex Sequencing to Discover Copy Number Variants in Drosophila. Genetics Epub ahead of print.
Sugano S
(2009) [Second generation sequencer and personal genomics] Nippon Rinsho 67:1164-9.
Ahn SM, Kim TH, Lee S, Kim D, Ghang H, et al.
(2009) The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group. Genome Res Epub ahead of print.
Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC
(2009) Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res Epub ahead of print.
Chu T, Bunce K, Hogge WA, Peters DG
(2009) Statistical model for whole genome sequencing and its application to minimally invasive diagnosis of fetal genetic disease. Bioinformatics 25:1244-50.
Brkanac Z, Spencer D, Shendure J, Robertson PD, Matsushita M, et al.
(2009) IFRD1 is a candidate gene for SMNA on chromosome 7q22-q23. Am J Hum Genet 84:692-7.
Guryev V, Cuppen E
(2009) Next-generation sequencing approaches in genetic rodent model systems to study functional effects of human genetic variation. FEBS Lett 583:1668-73.
Hasin-Brumshtein Y, Lancet D, Olender T
(2009) Human olfaction: from genomic variation to phenotypic diversity. Trends Genet 25:178-84.
Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, et al.
(2009) Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods 6:291-5.
Xie C, Tammi MT
(2009) CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 10:80.
Harismendy O, Frazer K
(2009) Method for improving sequence coverage uniformity of targeted genomic intervals amplified by LR-PCR using Illumina GA sequencing-by-synthesis technology. Biotechniques 46:229-31.
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, et al.
(2009) ABySS: A parallel assembler for short read sequence data. Genome Res 19:1117-23.
Voelkerding KV, Dames SA, Durtschi JD
(2009) Next-generation sequencing: from basic research to diagnostics. Clin Chem 55:641-58.
Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, et al.
(2009) PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol 10:R23.
Lo YM, Chiu RW
(2009) Next-generation sequencing of plasma/serum DNA: an emerging research and molecular diagnostic tool. Clin Chem 55:607-8.
Pennisi E
(2009) Neandertal genomics. Tales of a prehistoric human genome. Science 323:866-71.
Farrer RA, Kemen E, Jones JD, Studholme DJ
(2009) De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. FEMS Microbiol Lett 291:103-11.
Beck J, Urnovitz HB, Riggert J, Clerici M, Schütz E
(2009) Profile of the circulating DNA in apparently healthy individuals. Clin Chem 55:730-8.
Moran NA, McLaughlin HJ, Sorek R
(2009) The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 323:379-82.
Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, et al.
(2009) De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res 19:294-305.
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW
(2009) GenBank. Nucleic Acids Res 37:D26-31.
Snyder LA, Loman N, Pallen MJ, Penn CW
(2009) Next-Generation Sequencing-the Promise and Perils of Charting the Great Microbial Unknown. Microb Ecol 57:1-3.
Jiang Z, Rokhsar DS, Harland RM
(2009) Old can be new again: HAPPY whole genome sequencing, mapping and assembly. Int J Biol Sci 5:298-303.
Cochrane G, Akhtar R, Bonfield J, Bower L, Demiralp F, et al.
(2009) Petabyte-scale innovations at the European Nucleotide Archive. Nucleic Acids Res 37:D19-25.
Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, et al.
(2009) Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nat Methods 6:67-9.
Wang W, Zhang P, Liu X
(2009) Short read DNA fragment anchoring algorithm. BMC Bioinformatics 10 Suppl 1:S17.
Messing J
(2009) Synergy of two reference genomes for the grass family. Plant Physiol 149:117-24.
Li G, Ma L, Song C, Yang Z, Wang X, et al.
(2009) The YH database: the first Asian diploid genome database. Nucleic Acids Res 37:D1025-8.
Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, et al.
(2009) VectorBase: a data resource for invertebrate vector genomics. Nucleic Acids Res 37:D583-7.
Chiang DY, Getz G, Jaffe DB, OKelly MJ, Zhao X, et al.
(2009) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods 6:99-103.
Sugawara H, Ikeo K, Fukuchi S, Gojobori T, Tateno Y
(2009) DDBJ dealing with mass data produced by the second generation sequencer. Nucleic Acids Res 37:D16-8.
Chiu RW, Chan KC, Gao Y, Lau VY, Zheng W, et al.
(2008) Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc Natl Acad Sci U S A 105:20458-63.
Aury JM, Cruaud C, Barbe V, Rogier O, Mangenot S, et al.
(2008) High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies. BMC Genomics 9:603.
The International Silkworm Genome Consortium
(2008) The genome of a lepidopteran model insect, the silkworm Bombyx mori. Insect Biochem Mol Biol 38:1036-45.
Hert DG, Fredlake CP, Barron AE
(2008) Advantages and limitations of next-generation sequencing technologies: a comparison of electrophoresis and non-electrophoresis methods. Electrophoresis 29:4618-26.
Suchland RJ, Jeffrey BM, Xia M, Bhatia A, Chu HG, et al.
(2008) Identification of concomitant infection with Chlamydia trachomatis IncA-negative mutant and wild-type strains by genomic, transcriptional, and biological characterizations. Infect Immun 76:5438-46.
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.
Maher B
(2008) Personal genomes: The case of the missing heritability. Nature 456:18-21.
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.
Hayton K, Su XZ
(2008) Drug resistance and genetic mapping in Plasmodium falciparum. Curr Genet 54:223-39.
Amacher SL
(2008) Emerging gene knockout technology in zebrafish: zinc-finger nucleases. Brief Funct Genomic Proteomic 7:460-4.
Darby AC, Hall N
(2008) Fast forward genetics. Nat Biotechnol 26:1248-9.
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.
Sorber K, Chiu C, Webster D, Dimon M, Ruby JG, et al.
(2008) The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing. PLoS ONE 3:e3495.
Fay DS
(2008) Classical genetics goes high-tech. Nat Methods 5:863-4.
Marguerat S, Wilhelm BT, Bähler J
(2008) Next-generation sequencing: applications beyond genomes. Biochem Soc Trans 36:1091-6.
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.
Clark AG
(2008) Genome sequences from extinct relatives. Cell 134:388-9.
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.
Lang L
(2008) Three sequencing companies join the 1000 genomes project. Gastroenterology 135:336-7.
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.
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.
Enserink M
(2008) Genomics. Read all about it--the first female genome! Or is it? Science 320:1274.
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.
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.
Moerman DG, Barstead RJ
(2008) Towards a mutation in every gene in Caenorhabditis elegans. Brief Funct Genomic Proteomic 7:195-204.
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.
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.
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.
Shen Y, Sarin S, Liu Y, Hobert O, Peer I
(2008) Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing. PLoS ONE 3:e4012.
Yosef N, Käll L
(2008) From sequence to structure to networks. Genome Biol 9:326.
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.
Sellner EM, Kim JW, McClure MC, Taylor KH, Schnabel RD, et al.
(2007) Board-invited review: Applications of genomic information in livestock. J Anim Sci 85:3148-58.
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.
Koenig R
(2007) Tuberculosis. Few mutations divide some drug-resistant TB strains. Science 318:901-2.
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.
Lamour KH, Win J, Kamoun S
(2007) Oomycete genomics: new insights and future directions. FEMS Microbiol Lett 274:1-8.
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.
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.
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.
Service RF
(2006) Gene sequencing. The race for the $1000 genome. Science 311:1544-6.
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.
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