2016
The time-resolved transcriptome of C. elegans
Boeck ME, Huynh C, Gevirtzman L, Thompson OA, Wang G, Kasper DM, Reinke V, Hillier LW, Waterston RH. The time-resolved transcriptome of C. elegans. Genome Research 2016, 26: 1441-1450. PMID: 27531719, PMCID: PMC5052054, DOI: 10.1101/gr.202663.115.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCaenorhabditis elegansGene Expression Regulation, DevelopmentalMolecular Sequence AnnotationTranscriptomeConceptsTime-resolved transcriptomeAlternative splice formsPost-embryonic stagesRNA-seq dataLife cycleC. elegansNematode CaenorhabditisHistone mRNATranscriptional programsLate embryogenesisRNA-seqSplice formsPromoter usageSplice junctionsDifferential usageDetailed annotationGenesExpression correlatesCaenorhabditisElegansTranscriptomeOperonWormBaseEmbryogenesisSL1
2014
Comparative analysis of the transcriptome across distant species
Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R. Comparative analysis of the transcriptome across distant species. Nature 2014, 512: 445-448. PMID: 25164755, PMCID: PMC4155737, DOI: 10.1038/nature13424.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCaenorhabditis elegansChromatinCluster AnalysisDrosophila melanogasterGene Expression ProfilingGene Expression Regulation, DevelopmentalHistonesHumansLarvaModels, GeneticMolecular Sequence AnnotationPromoter Regions, GeneticPupaRNA, UntranslatedSequence Analysis, RNATranscriptome
2010
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data
Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, Reinke V, Gerstein MB. Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Research 2010, 21: 276-285. PMID: 21177971, PMCID: PMC3032931, DOI: 10.1101/gr.110189.110.Peer-Reviewed Original ResearchConceptsNovel ncRNA candidatesNcRNA candidatesC. elegansC. elegans genomeWhole-genome identificationSpecific transcription factorsHigh-throughput sequencingDistinct expression patternsSecondary structure stabilityEvolutionary conservationGenomic elementsModENCODE consortiumNucleic acid levelIntergenic regionTranscription factorsPotential ncRNAsExpression patternsExpression dataDevelopmental stagesSecondary structureElegansNcRNAsRNAsStructural familyArray data