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Piero Carninci - Publications

Affiliations: 
RIKEN Omics, Yokohama-shi, Kanagawa-ken, Japan 
Area:
genomics, RACE, EST
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328 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Amaral P, Carbonell-Sala S, De La Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, ... ... Carninci P, et al. The status of the human gene catalogue. Nature. 622: 41-47. PMID 37794265 DOI: 10.1038/s41586-023-06490-x  0.347
2023 Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez JM, Hunt T, Lagarde J, Liang CE, ... ... Carninci P, et al. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Biorxiv : the Preprint Server For Biology. PMID 37546854 DOI: 10.1101/2023.07.25.550582  0.372
2023 Carbonell-Sala S, Lagarde J, Nishiyori H, Palumbo E, Arnan C, Takahashi H, Carninci P, Uszczynska-Ratajczak B, Guigó R. CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing. Biorxiv : the Preprint Server For Biology. PMID 37398314 DOI: 10.1101/2023.06.16.543444  0.362
2023 Pierattini B, D'Agostino S, Bon C, Peruzzo O, Alendar A, Codino A, Ros G, Persichetti F, Sanges R, Carninci P, Santoro C, Espinoza S, Valentini P, Pandolfini L, Gustincich S. SINEUP non-coding RNA activity depends on specific N6-methyladenosine nucleotides. Molecular Therapy. Nucleic Acids. 32: 402-414. PMID 37187707 DOI: 10.1016/j.omtn.2023.04.002  0.315
2023 Amaral P, Carbonell-Sala S, Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, ... ... Carninci P, et al. The status of the human gene catalogue. Arxiv. PMID 36994150  0.362
2023 Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, et al. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nature Reviews. Molecular Cell Biology. PMID 36596869 DOI: 10.1038/s41580-022-00566-8  0.355
2022 Koido M, Hon CC, Koyama S, Kawaji H, Murakawa Y, Ishigaki K, Ito K, Sese J, Parrish NF, Kamatani Y, Carninci P, Terao C. Prediction of the cell-type-specific transcription of non-coding RNAs from genome sequences via machine learning. Nature Biomedical Engineering. PMID 36411359 DOI: 10.1038/s41551-022-00961-8  0.359
2022 Moody J, Kouno T, Chang JC, Ando Y, Carninci P, Shin JW, Hon CC. SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells. Bioinformatics (Oxford, England). PMID 36173306 DOI: 10.1093/bioinformatics/btac644  0.332
2022 Kouno T, Carninci P, Shin JW. Complete Transcriptome Analysis by 5'-End Single-Cell RNA-Seq with Random Priming. Methods in Molecular Biology (Clifton, N.J.). 2490: 141-156. PMID 35486244 DOI: 10.1007/978-1-0716-2281-0_11  0.331
2021 Hashimoto K, Jouhilahti EM, Töhönen V, Carninci P, Kere J, Katayama S. Embryonic LTR retrotransposons supply promoter modules to somatic tissues. Genome Research. 31: 1983-1993. PMID 34675070 DOI: 10.1101/gr.275354.121  0.332
2021 Espinoza S, Bon C, Valentini P, Pierattini B, Matey AT, Damiani D, Pulcrano S, Sanges R, Persichetti F, Takahashi H, Carninci P, Santoro C, Cotella D, Gustincich S. SINEUPs: a novel toolbox for RNA therapeutics. Essays in Biochemistry. 65: 775-789. PMID 34623427 DOI: 10.1042/EBC20200114  0.301
2021 Ducoli L, Agrawal S, Hon CC, Ramilowski JA, Sibler E, Tagami M, Itoh M, Kondo N, Abugessaisa I, Hasegawa A, Kasukawa T, Suzuki H, Carninci P, Shin JW, de Hoon MJL, et al. The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background. Bmc Genomic Data. 22: 33. PMID 34521352 DOI: 10.1186/s12863-021-00992-1  0.34
2021 Bonetti A, Kwon AT, Arner E, Carninci P. Analysis of Enhancer-Promoter Interactions using CAGE and RADICL-Seq Technologies. Methods in Molecular Biology (Clifton, N.J.). 2351: 201-210. PMID 34382191 DOI: 10.1007/978-1-0716-1597-3_11  0.385
2021 Takahashi H, Nishiyori-Sueki H, Ramilowski JA, Itoh M, Carninci P. Low Quantity Single Strand CAGE (LQ-ssCAGE) Maps Regulatory Enhancers and Promoters. Methods in Molecular Biology (Clifton, N.J.). 2351: 67-90. PMID 34382184 DOI: 10.1007/978-1-0716-1597-3_4  0.391
2021 Grapotte M, Saraswat M, Bessière C, Menichelli C, Ramilowski JA, Severin J, Hayashizaki Y, Itoh M, Tagami M, Murata M, Kojima-Ishiyama M, Noma S, Noguchi S, Kasukawa T, Hasegawa A, ... ... Carninci P, et al. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications. 12: 3297. PMID 34078885 DOI: 10.1038/s41467-021-23143-7  0.388
2021 Pillay S, Takahashi H, Carninci P, Kanhere A. Antisense RNAs during early vertebrate development are divided in groups with distinct features. Genome Research. PMID 33795334 DOI: 10.1101/gr.262964.120  0.316
2021 Ducoli L, Agrawal S, Sibler E, Kouno T, Tacconi C, Hon CC, Berger SD, Müllhaupt D, He Y, Kim J, D'Addio M, Dieterich LC, Carninci P, de Hoon MJL, Shin JW, et al. LETR1 is a lymphatic endothelial-specific lncRNA governing cell proliferation and migration through KLF4 and SEMA3C. Nature Communications. 12: 925. PMID 33568674 DOI: 10.1038/s41467-021-21217-0  0.351
2020 Kajihara D, Hon CC, Abdullah AN, Wosniak J, Moretti AIS, Poloni JF, Bonatto D, Hashimoto K, Carninci P, Laurindo FRM. Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene. Bmc Genomics. 21: 766. PMID 33148170 DOI: 10.1186/s12864-020-07164-y  0.312
2020 Toki N, Takahashi H, Sharma H, Valentine MNZ, Rahman FM, Zucchelli S, Gustincich S, Carninci P. SINEUP long non-coding RNA acts via PTBP1 and HNRNPK to promote translational initiation assemblies. Nucleic Acids Research. PMID 33130894 DOI: 10.1093/nar/gkaa814  0.301
2020 Hon CC, Carninci P. Expanded ENCODE delivers invaluable genomic encyclopedia. Nature. 583: 685-686. PMID 32728235 DOI: 10.1038/D41586-020-02139-1  0.397
2020 Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, ... ... Carninci P, et al. Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Research. PMID 32718982 DOI: 10.1101/Gr.254219.119  0.48
2020 Alam T, Agrawal S, Severin J, Young RS, Andersson R, Arner E, Hasegawa A, Lizio M, Ramilowski JA, Abugessaisa I, Ishizu Y, Noma S, Tarui H, Taylor MS, Lassmann T, ... ... Carninci P, et al. Comparative transcriptomics of primary cells in vertebrates. Genome Research. PMID 32718981 DOI: 10.1101/Gr.255679.119  0.439
2020 Ohyama T, Takahashi H, Sharma H, Yamazaki T, Gustincich S, Ishii Y, Carninci P. An NMR-based approach reveals the core structure of the functional domain of SINEUP lncRNAs. Nucleic Acids Research. PMID 32697302 DOI: 10.1093/Nar/Gkaa598  0.353
2020 Kato M, Carninci P. Genome-Wide Technologies to Study RNA-Chromatin Interactions. Non-Coding Rna. 6. PMID 32471183 DOI: 10.3390/Ncrna6020020  0.42
2020 Sharma H, Carninci P. The Secret Life of lncRNAs: Conserved, yet Not Conserved. Cell. 181: 512-514. PMID 32359433 DOI: 10.1016/J.Cell.2020.04.012  0.344
2020 Clohisey S, Parkinson N, Wang B, Bertin N, Wise H, Tomoiu A, Summers KM, Hendry RW, Carninci P, Forrest ARR, Hayashizaki Y, Digard P, Hume DA, Baillie JK. Comprehensive characterisation of transcriptional activity during influenza A virus infection reveals biases in cap-snatching of host RNA sequences. Journal of Virology. PMID 32161175 DOI: 10.1128/Jvi.01720-19  0.386
2020 Morioka MS, Kawaji H, Nishiyori-Sueki H, Murata M, Kojima-Ishiyama M, Carninci P, Itoh M. Cap Analysis of Gene Expression (CAGE): A Quantitative and Genome-Wide Assay of Transcription Start Sites. Methods in Molecular Biology (Clifton, N.J.). 2120: 277-301. PMID 32124327 DOI: 10.1007/978-1-0716-0327-7_20  0.482
2020 Bonetti A, Agostini F, Suzuki AM, Hashimoto K, Pascarella G, Gimenez J, Roos L, Nash AJ, Ghilotti M, Cameron CJF, Valentine M, Medvedeva YA, Noguchi S, Agirre E, Kashi K, ... ... Carninci P, et al. RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions. Nature Communications. 11: 1018. PMID 32094342 DOI: 10.1038/S41467-020-14337-6  0.473
2020 Imada EL, Sanchez DF, Collado-Torres L, Wilks C, Matam T, Dinalankara W, Stupnikov A, Pereira Lobo FP, Yip CW, Yasuzawa K, Kondo N, Itoh M, Suzuki H, Kasukawa T, Hon CC, ... ... Carninci P, et al. Recounting the FANTOM CAGEAssociated Transcriptome. Genome Research. PMID 32079618 DOI: 10.1101/Gr.254656.119  0.455
2020 Nepal C, Hadzhiev Y, Balwierz P, Tarifeño-Saldivia E, Cardenas R, Wragg JW, Suzuki AM, Carninci P, Peers B, Lenhard B, Andersen JB, Müller F. Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing. Nature Communications. 11: 168. PMID 31924754 DOI: 10.1038/S41467-019-13687-0  0.472
2020 Bertuzzi M, Tang D, Calligaris R, Vlachouli C, Finaurini S, Sanges R, Goldwurm S, Catalan M, Antonutti L, Manganotti P, Pizzolato G, Pezzoli G, Persichetti F, Carninci P, Gustincich S. A human minisatellite hosts an alternative transcription start site for NPRL3 driving its expression in a repeat number-dependent manner. Human Mutation. PMID 31898848 DOI: 10.1002/Humu.23974  0.451
2020 Ramilowski JA, Yip CW, Agrawal S, Chang J, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, ... ... Carninci P, et al. Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping Genome Research. 30: 1377-1-1377-1. DOI: 10.1101/Gr.270330.120  0.356
2019 Shuaib M, Parsi KM, Thimma M, Adroub SA, Hideya K, Seridi L, Ghosheh Y, Fort A, Fallatah B, Ravasi T, Carninci P, Orlando V. Nuclear AGO1 Regulates Gene Expression by Affecting Chromatin Architecture in Human Cells. Cell Systems. PMID 31629687 DOI: 10.1016/J.Cels.2019.09.005  0.489
2019 Bon C, Luffarelli R, Russo R, Fortuni S, Pierattini B, Santulli C, Fimiani C, Persichetti F, Cotella D, Mallamaci A, Santoro C, Carninci P, Espinoza S, Testi R, Zucchelli S, et al. SINEUP non-coding RNAs rescue defective frataxin expression and activity in a cellular model of Friedreich's Ataxia. Nucleic Acids Research. PMID 31584077 DOI: 10.1093/Nar/Gkz798  0.449
2019 Fasolo F, Patrucco L, Volpe M, Bon C, Peano C, Mignone F, Carninci P, Persichetti F, Santoro C, Zucchelli S, Sblattero D, Sanges R, Cotella D, Gustincich S. The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. fj201901618RR. PMID 31570000 DOI: 10.1096/Fj.201901618Rr  0.414
2019 Ha TJ, Zhang PGY, Robert R, Yeung J, Swanson DJ, Mathelier A, Wasserman WW, Im S, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, et al. Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis. Bmc Genomics. 20: 718. PMID 31533632 DOI: 10.1186/S12864-019-6063-9  0.454
2019 Espinoza S, Scarpato M, Damiani D, Managò F, Mereu M, Contestabile A, Peruzzo O, Carninci P, Santoro C, Papaleo F, Mingozzi F, Ronzitti G, Zucchelli S, Gustincich S. SINEUP Non-coding RNA Targeting GDNF Rescues Motor Deficits and Neurodegeneration in a Mouse Model of Parkinson's Disease. Molecular Therapy : the Journal of the American Society of Gene Therapy. PMID 31495777 DOI: 10.1016/J.Ymthe.2019.08.005  0.303
2019 Hirabayashi S, Bhagat S, Matsuki Y, Takegami Y, Uehata T, Kanemaru A, Itoh M, Shirakawa K, Takaori-Kondo A, Takeuchi O, Carninci P, Katayama S, Hayashizaki Y, Kere J, Kawaji H, et al. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Nature Genetics. 51: 1369-1379. PMID 31477927 DOI: 10.1038/S41588-019-0485-9  0.463
2019 Yamanaka S, Nishihara H, Toh H, Eijy Nagai LA, Hashimoto K, Park SJ, Shibuya A, Suzuki AM, Tanaka Y, Nakai K, Carninci P, Sasaki H, Siomi H. Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation. Developmental Cell. PMID 31474564 DOI: 10.1016/J.Devcel.2019.07.023  0.33
2019 Abugessaisa I, Noguchi S, Hasegawa A, Kondo A, Kawaji H, Carninci P, Kasukawa T. refTSS: A Reference Dataset for Human and Mouse Transcription Start Sites. Journal of Molecular Biology. PMID 31075273 DOI: 10.1016/J.Jmb.2019.04.045  0.484
2019 Takahashi H, Sharma H, Carninci P. Cell Based Assays of SINEUP Non-coding RNAs That Can Specifically Enhance mRNA Translation. Journal of Visualized Experiments : Jove. PMID 30774120 DOI: 10.3791/58627  0.462
2019 Pawlak M, Kedzierska KZ, Migdal M, Nahia KA, Ramilowski JA, Bugajski L, Hashimoto K, Marconi A, Piwocka K, Carninci P, Winata CL. Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development. Genome Research. PMID 30760547 DOI: 10.1101/Gr.244491.118  0.348
2019 Kouno T, Moody J, Kwon AT, Shibayama Y, Kato S, Huang Y, Böttcher M, Motakis E, Mendez M, Severin J, Luginbühl J, Abugessaisa I, Hasegawa A, Takizawa S, Arakawa T, ... ... Carninci P, et al. C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution. Nature Communications. 10: 360. PMID 30664627 DOI: 10.1038/S41467-018-08126-5  0.384
2019 Zucchelli S, Fedele S, Vatta P, Calligaris R, Heutink P, Rizzu P, Itoh M, Persichetti F, Santoro C, Kawaji H, Lassmann T, Hayashizaki Y, Carninci P, Forrest ARR, et al. Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases. Molecular Neurobiology. PMID 30610612 DOI: 10.1007/S12035-018-1465-2  0.494
2018 Marlétaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, ... ... Carninci P, et al. Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature. PMID 30464347 DOI: 10.1038/S41586-018-0734-6  0.432
2018 Lizio M, Abugessaisa I, Noguchi S, Kondo A, Hasegawa A, Hon CC, de Hoon M, Severin J, Oki S, Hayashizaki Y, Carninci P, Kasukawa T, Kawaji H. Update of the FANTOM web resource: expansion to provide additional transcriptome atlases. Nucleic Acids Research. PMID 30407557 DOI: 10.1093/Nar/Gky1099  0.471
2018 Cvetesic N, Leitch HG, Borkowska M, Müller F, Carninci P, Hajkova P, Lenhard B. SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA. Genome Research. PMID 30404778 DOI: 10.1101/Gr.235937.118  0.498
2018 Vacca A, Itoh M, Kawaji H, Arner E, Lassmann T, Daub CO, Carninci P, Forrest ARR, Hayashizaki Y, Aitken S, Semple CA. Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli. Open Biology. 8. PMID 30089658 DOI: 10.1098/Rsob.180011  0.446
2018 Roy S, Schmeier S, Kaczkowski B, Arner E, Alam T, Ozturk M, Tamgue O, Parihar SP, Kawaji H, Itoh M, Lassmann T, Carninci P, Hayashizaki Y, Forrest ARR, Guler R, et al. Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages. Scientific Reports. 8: 6758. PMID 29712924 DOI: 10.1038/S41598-018-24509-6  0.358
2018 Michelini F, Jalihal AP, Francia S, Meers C, Neeb ZT, Rossiello F, Gioia U, Aguado J, Jones-Weinert C, Luke B, Biamonti G, Nowacki M, Storici F, Carninci P, Walter NG, et al. From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond. Chemical Reviews. PMID 29600857 DOI: 10.1021/Acs.Chemrev.7B00487  0.387
2018 Nguyen Q, Aguado J, Iannelli F, Suzuki AM, Rossiello F, d'Adda di Fagagna F, Carninci P. Target-enrichment sequencing for detailed characterization of small RNAs. Nature Protocols. 13: 768-786. PMID 29565901 DOI: 10.1038/Nprot.2018.001  0.396
2018 Baillie JK, Bretherick A, Haley CS, Clohisey S, Gray A, Neyton LPA, Barrett J, Stahl EA, Tenesa A, Andersson R, Brown JB, Faulkner GJ, Lizio M, Schaefer U, Daub C, ... ... Carninci P, et al. Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. Plos Computational Biology. 14: e1005934. PMID 29494619 DOI: 10.1371/Journal.Pcbi.1005934  0.373
2018 Podbevšek P, Fasolo F, Bon C, Cimatti L, Reißer S, Carninci P, Bussi G, Zucchelli S, Plavec J, Gustincich S. Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1. Scientific Reports. 8: 3189. PMID 29453387 DOI: 10.1038/S41598-017-14908-6  0.44
2018 Takahashi H, Kozhuharova A, Sharma H, Hirose M, Ohyama T, Fasolo F, Yamazaki T, Cotella D, Santoro C, Zucchelli S, Gustincich S, Carninci P. Identification of functional features of synthetic SINEUPs, antisense lncRNAs that specifically enhance protein translation. Plos One. 13: e0183229. PMID 29414979 DOI: 10.1371/Journal.Pone.0183229  0.366
2018 Zhang P, Dimont E, Ha T, Swanson DJ, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Hayashizaki Y, Forrest ARR, Hide W, Goldowitz D. Correction to: Relatively frequent switching of transcription start sites during cerebellar development. Bmc Genomics. 19: 39. PMID 29325522 DOI: 10.1186/S12864-017-4291-4  0.361
2018 Zhang PGY, Yeung J, Gupta I, Ramirez M, Ha T, Swanson DJ, Nagao-Sato S, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, de Hoon M, Carninci P, et al. Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection. Cerebellum (London, England). PMID 29307116 DOI: 10.1007/S12311-017-0912-3  0.457
2017 Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell PJ, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, et al. Science Forum: The Human Cell Atlas. Elife. 6. PMID 29206104 DOI: 10.7554/Elife.27041  0.342
2017 Lizio M, Mukarram AK, Ohno M, Watanabe S, Itoh M, Hasegawa A, Lassmann T, Severin J, Harshbarger J, Abugessaisa I, Kasukawa T, Hon CC, Carninci P, Hayashizaki Y, Forrest ARR, et al. Monitoring transcription initiation activities in rat and dog. Scientific Data. 4: 170173. PMID 29182598 DOI: 10.1038/Sdata.2017.173  0.43
2017 Garieri M, Delaneau O, Santoni F, Fish RJ, Mull D, Carninci P, Dermitzakis ET, Antonarakis SE, Fort A. The effect of genetic variation on promoter usage and enhancer activity. Nature Communications. 8: 1358. PMID 29116076 DOI: 10.1038/S41467-017-01467-7  0.425
2017 Francescatto M, Lizio M, Philippens I, Bontrop R, Sakai M, Watanabe S, Itoh M, Hasegawa A, Lassmann T, Severin J, Harshbarger J, Abugessaisa I, Kasukawa T, Carninci P, Hayashizaki Y, et al. Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system. Scientific Data. 4: 170163. PMID 29087374 DOI: 10.1038/Sdata.2017.163  0.478
2017 Abugessaisa I, Noguchi S, Böttcher M, Hasegawa A, Kouno T, Kato S, Tada Y, Ura H, Abe K, Shin JW, Plessy C, Carninci P, Kasukawa T. SCPortalen: human and mouse single-cell centric database. Nucleic Acids Research. PMID 29045713 DOI: 10.1093/Nar/Gkx949  0.322
2017 Bertin N, Mendez M, Hasegawa A, Lizio M, Abugessaisa I, Severin J, Sakai-Ohno M, Lassmann T, Kasukawa T, Kawaji H, Hayashizaki Y, Forrest ARR, Carninci P, Plessy C. Linking FANTOM5 CAGE peaks to annotations with CAGEscan. Scientific Data. 4: 170147. PMID 28972578 DOI: 10.1038/Sdata.2017.147  0.494
2017 Qin XY, Hara M, Arner E, Kawaguchi Y, Inoue I, Tatsukawa H, Furutani Y, Nagatsuma K, Matsuura T, Wei F, Kikuchi J, Sone H, Daub C, Kawaji H, Lassmann T, ... ... Carninci P, et al. Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes. Ebiomedicine. PMID 28927749 DOI: 10.1016/J.Ebiom.2017.09.008  0.312
2017 Lizio M, Deviatiiarov R, Nagai H, Galan L, Arner E, Itoh M, Lassmann T, Kasukawa T, Hasegawa A, Ros MA, Hayashizaki Y, Carninci P, Forrest ARR, Kawaji H, Gusev O, et al. Systematic analysis of transcription start sites in avian development. Plos Biology. 15: e2002887. PMID 28873399 DOI: 10.1371/Journal.Pbio.2002887  0.45
2017 Kawaji H, Kasukawa T, Forrest A, Carninci P, Hayashizaki Y. The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types. Scientific Data. 4: 170113. PMID 28850107 DOI: 10.1038/Sdata.2017.113  0.346
2017 Noguchi S, Arakawa T, Fukuda S, Furuno M, Hasegawa A, Hori F, Ishikawa-Kato S, Kaida K, Kaiho A, Kanamori-Katayama M, Kawashima T, Kojima M, Kubosaki A, Manabe RI, Murata M, ... ... Carninci P, et al. FANTOM5 CAGE profiles of human and mouse samples. Scientific Data. 4: 170112. PMID 28850106 DOI: 10.1038/Sdata.2017.112  0.471
2017 Abugessaisa I, Noguchi S, Hasegawa A, Harshbarger J, Kondo A, Lizio M, Severin J, Carninci P, Kawaji H, Kasukawa T. FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies. Scientific Data. 4: 170107. PMID 28850105 DOI: 10.1038/Sdata.2017.107  0.41
2017 de Rie D, Abugessaisa I, Alam T, Arner E, Arner P, Ashoor H, Åström G, Babina M, Bertin N, Burroughs AM, Carlisle AJ, Daub CO, Detmar M, Deviatiiarov R, Fort A, ... ... Carninci P, et al. An integrated expression atlas of miRNAs and their promoters in human and mouse. Nature Biotechnology. PMID 28829439 DOI: 10.1038/Nbt.3947  0.341
2017 Horie M, Kaczkowski B, Ohshima M, Matsuzaki H, Noguchi S, Mikami Y, Lizio M, Itoh M, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest ARR, Takai D, Yamaguchi Y, et al. Integrative CAGE and DNA Methylation Profiling Identify Epigenetically Regulated Genes in NSCLC. Molecular Cancer Research : McR. PMID 28698358 DOI: 10.1158/1541-7786.Mcr-17-0191  0.376
2017 Iannelli F, Galbiati A, Capozzo I, Nguyen Q, Magnuson B, Michelini F, D'Alessandro G, Cabrini M, Roncador M, Francia S, Crosetto N, Ljungman M, Carninci P, d'Adda di Fagagna F. A damaged genome's transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks. Nature Communications. 8: 15656. PMID 28561034 DOI: 10.1038/Ncomms15656  0.452
2017 Abugessaisa I, Noguchi S, Carninci P, Kasukawa T. The FANTOM5 Computation Ecosystem: Genomic Information Hub for Promoters and Active Enhancers. Methods in Molecular Biology (Clifton, N.J.). 1611: 199-217. PMID 28451981 DOI: 10.1007/978-1-4939-7015-5_15  0.482
2017 Baillie JK, Arner E, Daub C, De Hoon M, Itoh M, Kawaji H, Lassmann T, Carninci P, Forrest AR, Hayashizaki Y, Faulkner GJ, Wells CA, Rehli M, Pavli P, et al. Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease. Plos Genetics. 13: e1006641. PMID 28263993 DOI: 10.1371/Journal.Pgen.1006641  0.4
2017 Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J, Lizio M, Kawaji H, Kasukawa T, Itoh M, Burroughs AM, ... ... Carninci P, et al. An atlas of human long non-coding RNAs with accurate 5' ends. Nature. PMID 28241135 DOI: 10.1038/Nature21374  0.486
2017 Rossiello F, Aguado J, Sepe S, Iannelli F, Nguyen Q, Pitchiaya S, Carninci P, d'Adda di Fagagna F. DNA damage response inhibition at dysfunctional telomeres by modulation of telomeric DNA damage response RNAs. Nature Communications. 8: 13980. PMID 28239143 DOI: 10.1038/Ncomms13980  0.319
2017 Harshbarger J, Kratz A, Carninci P. DEIVA: a web application for interactive visual analysis of differential gene expression profiles. Bmc Genomics. 18: 47. PMID 28061742 DOI: 10.1186/S12864-016-3396-5  0.388
2017 Bonetti A, Carninci P. From bench to bedside: The long journey of long non-coding RNAs Current Opinion in Systems Biology. 3: 119-124. DOI: 10.1016/J.Coisb.2017.04.016  0.401
2016 Ienasescu H, Li K, Andersson R, Vitezic M, Rennie S, Chen Y, Vitting-Seerup K, Lagoni E, Boyd M, Bornholdt J, de Hoon MJ, Kawaji H, Lassmann T, Hayashizaki Y, ... ... Carninci P, et al. On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase. Database : the Journal of Biological Databases and Curation. 2016. PMID 28025337 DOI: 10.1093/Database/Baw144  0.432
2016 Chen CY, Shi W, Balaton BP, Matthews AM, Li Y, Arenillas DJ, Mathelier A, Itoh M, Kawaji H, Lassmann T, Hayashizaki Y, Carninci P, Forrest AR, Brown CJ, Wasserman WW. YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses. Scientific Reports. 6: 37324. PMID 27857184 DOI: 10.1038/Srep37324  0.421
2016 Sugiyama D, Joshi A, Kulkeaw K, Tan KS, Yokoo-Inoue T, Mizuochi-Yanagi C, Yasuda K, Doi A, Iino T, Itoh M, Nagao-Sato S, Tani K, Akashi K, Hayashizaki Y, Suzuki H, ... ... Carninci P, et al. A Transcriptional switch point during hematopoietic stem and progenitor cell ontogeny. Stem Cells and Development. PMID 27848279 DOI: 10.1089/Scd.2016.0194  0.371
2016 Hoshino A, Jayakumar V, Nitasaka E, Toyoda A, Noguchi H, Itoh T, Shin-I T, Minakuchi Y, Koda Y, Nagano AJ, Yasugi M, Honjo MN, Kudoh H, Seki M, Kamiya A, ... ... Carninci P, et al. Genome sequence and analysis of the Japanese morning glory Ipomoea nil. Nature Communications. 7: 13295. PMID 27824041 DOI: 10.1038/Ncomms13295  0.346
2016 Ehrlund A, Mejhert N, Björk C, Andersson R, Kulyté A, Åström G, Itoh M, Kawaji H, Lassmann T, Daub CO, Carninci P, Forrest AR, Hayashizaki Y, Sandelin A, Ingelsson E, et al. Transcriptional Dynamics During Human Adipogenesis and its Link to Adipose Morphology and Distribution. Diabetes. PMID 27803022 DOI: 10.2337/Db16-0631  0.432
2016 Lizio M, Harshbarger J, Abugessaisa I, Noguchi S, Kondo A, Severin J, Mungall C, Arenillas D, Mathelier A, Medvedeva YA, Lennartsson A, Drabløs F, Ramilowski JA, Rackham O, Gough J, ... ... Carninci P, et al. Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. Nucleic Acids Research. PMID 27794045 DOI: 10.1093/Nar/Gkw995  0.335
2016 Altinel K, Hashimoto K, Wei Y, Neuveut C, Gupta I, Suzuki AM, Dos Santos A, Moreau P, Xia T, Kojima S, Kato S, Takikawa Y, Hidaka I, Shimizu M, Matsuura T, ... ... Carninci P, et al. Single-nucleotide-resolution mapping of HBV promoters in infected human livers and hepatocellular carcinoma. Journal of Virology. PMID 27681123 DOI: 10.1128/Jvi.01625-16  0.312
2016 Schein A, Zucchelli S, Kauppinen S, Gustincich S, Carninci P. Identification of antisense long noncoding RNAs that function as SINEUPs in human cells. Scientific Reports. 6: 33605. PMID 27646849 DOI: 10.1038/Srep33605  0.441
2016 Horie M, Yamaguchi Y, Saito A, Nagase T, Lizio M, Itoh M, Kawaji H, Lassmann T, Carninci P, Forrest AR, Hayashizaki Y, Suzutani T, Kappert K, Micke P, Ohshima M. Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis. Scientific Reports. 6: 33666. PMID 27645561 DOI: 10.1038/Srep33666  0.427
2016 Marcuzzi F, Zucchelli S, Bertuzzi M, Santoro C, Tell G, Carninci P, Gustincich S. Isoforms of the Erythropoietin Receptor in dopaminergic neurons of the Substantia Nigra. Journal of Neurochemistry. PMID 27488413 DOI: 10.1111/Jnc.13757  0.342
2016 Abugessaisa I, Shimoji H, Sahin S, Kondo A, Harshbarger J, Lizio M, Hayashizaki Y, Carninci P, Forrest A, Kasukawa T, Kawaji H. FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki. Database : the Journal of Biological Databases and Curation. 2016. PMID 27402679 DOI: 10.1093/Database/Baw105  0.385
2016 Klein S, Dieterich LC, Mathelier A, Chong C, Sliwa-Primorac A, Hong YK, Shin JW, Lizio M, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, et al. DeepCAGE transcriptomics identify HOXD10 as transcription factor regulating lymphatic endothelial responses to VEGF-C. Journal of Cell Science. PMID 27199372 DOI: 10.1242/Jcs.186767  0.347
2016 Ghosheh Y, Seridi L, Ryu T, Takahashi H, Orlando V, Carninci P, Ravasi T. Characterization of piRNAs across postnatal development in mouse brain. Scientific Reports. 6: 25039. PMID 27112104 DOI: 10.1038/Srep25039  0.379
2016 Laurent GS, Vyatkin Y, Antonets D, Ri M, Qi Y, Saik O, Shtokalo D, de Hoon MJ, Kawaji H, Itoh M, Lassmann T, Arner E, Forrest AR, Nicolas E, ... ... Carninci P, et al. Functional annotation of the vlinc class of non-coding RNAs using systems biology approach. Nucleic Acids Research. PMID 27001520 DOI: 10.1093/Nar/Gkw162  0.47
2016 Kaczkowski B, Hashimoto K, Carninci P. Epi-drivers and cancer-testis genes Translational Cancer Research. 5: 334-336. DOI: 10.21037/8232  0.346
2016 Kaczkowski B, Tanaka Y, Kawaji H, Sandelin A, Andersson R, Itoh M, Lassmann T, Hayashizaki Y, Carninci P, Forrest ARR. Abstract 2897: Recurrent transcriptome alterations across multiple cancer types Cancer Research. 76: 2897-2897. DOI: 10.1158/1538-7445.Am2016-2897  0.383
2016 Wiemann S, Pennacchio C, Hu Y, Hunter P, Harbers M, Amiet A, Bethel G, Busse M, Carninci P, Diekhans M, Dunham I, Hao T, Harper JW, Hayashizaki Y, Heil O, et al. The ORFeome Collaboration: A genome-scale human ORF-clone resource Nature Methods. 13: 191-192. DOI: 10.1038/Nmeth.3776  0.315
2015 Fraser J, Ferrai C, Chiariello AM, Schueler M, Rito T, Laudanno G, Barbieri M, Moore BL, Kraemer DC, Aitken S, Xie SQ, Morris KJ, Itoh M, Kawaji H, Jaeger I, ... ... Carninci P, et al. Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation. Molecular Systems Biology. 11: 852. PMID 26700852 DOI: 10.15252/Msb.20156492  0.344
2015 Lennartsson A, Arner E, Fagiolini M, Saxena A, Andersson R, Takahashi H, Noro Y, Sng J, Sandelin A, Hensch TK, Carninci P. Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors. Epigenetics & Chromatin. 8: 55. PMID 26673794 DOI: 10.1186/S13072-015-0043-3  0.725
2015 Carbajo D, Magi S, Itoh M, Kawaji H, Lassmann T, Arner E, Forrest AR, Carninci P, Hayashizaki Y, Daub CO, Okada-Hatakeyama M, Mar JC. Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. Plos One. 10: e0144176. PMID 26658111 DOI: 10.1371/Journal.Pone.0144176  0.439
2015 Lizio M, Ishizu Y, Itoh M, Lassmann T, Hasegawa A, Kubosaki A, Severin J, Kawaji H, Nakamura Y, Suzuki H, Hayashizaki Y, Carninci P, Forrest AR. Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line. Frontiers in Genetics. 6: 331. PMID 26635867 DOI: 10.3389/Fgene.2015.00331  0.479
2015 Kaczkowski B, Tanaka Y, Kawaji H, Sandelin A, Andersson R, Itoh M, Lassmann T, Hayashizaki Y, Carninci P, Forrest AR. Transcriptome analysis of recurrently deregulated genes across multiple cancers identifies new pan-cancer biomarkers. Cancer Research. PMID 26552699 DOI: 10.1158/0008-5472.Can-15-0484  0.363
2015 Dieterich LC, Klein S, Mathelier A, Sliwa-Primorac A, Ma Q, Hong YK, Shin JW, Hamada M, Lizio M, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, et al. DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium. Cell Reports. PMID 26549461 DOI: 10.1016/J.Celrep.2015.10.002  0.427
2015 Hashimoto K, Suzuki AM, Dos Santos A, Desterke C, Collino A, Ghisletti S, Braun E, Bonetti A, Fort A, Qin XY, Radaelli E, Kaczkowski B, Forrest AR, Kojima S, Samuel D, ... ... Carninci P, et al. CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors. Genome Research. PMID 26510915 DOI: 10.1101/Gr.191031.115  0.323
2015 Kashi K, Henderson L, Bonetti A, Carninci P. Discovery and functional analysis of lncRNAs: Methodologies to investigate an uncharacterized transcriptome. Biochimica Et Biophysica Acta. PMID 26477492 DOI: 10.1016/J.Bbagrm.2015.10.010  0.474
2015 Nguyen Q, Carninci P. Expression Specificity of Disease-Associated lncRNAs: Toward Personalized Medicine. Current Topics in Microbiology and Immunology. PMID 26318140 DOI: 10.1007/82_2015_464  0.466
2015 Zucchelli S, Cotella D, Takahashi H, Carrieri C, Cimatti L, Fasolo F, Jones MH, Sblattero D, Sanges R, Santoro C, Persichetti F, Carninci P, Gustincich S. SINEUPs: A new class of natural and synthetic antisense long non-coding RNAs that activate translation. Rna Biology. 12: 771-9. PMID 26259533 DOI: 10.1080/15476286.2015.1060395  0.445
2015 de Hoon M, Shin JW, Carninci P. Paradigm shifts in genomics through the FANTOM projects. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 26: 391-402. PMID 26253466 DOI: 10.1007/S00335-015-9593-8  0.478
2015 Young RS, Hayashizaki Y, Andersson R, Sandelin A, Kawaji H, Itoh M, Lassmann T, Carninci P, Bickmore WA, Forrest AR, Taylor MS. The frequent evolutionary birth and death of functional promoters in mouse and human. Genome Research. PMID 26228054 DOI: 10.1101/Gr.190546.115  0.461
2015 Sato K, Iwasaki YW, Shibuya A, Carninci P, Tsuchizawa Y, Ishizu H, Siomi MC, Siomi H. Krimper Enforces an Antisense Bias on piRNA Pools by Binding AGO3 in the Drosophila Germline. Molecular Cell. 59: 553-63. PMID 26212455 DOI: 10.1016/J.Molcel.2015.06.024  0.323
2015 Mina M, Magi S, Jurman G, Itoh M, Kawaji H, Lassmann T, Arner E, Forrest AR, Carninci P, Hayashizaki Y, Daub CO, Okada-Hatakeyama M, Furlanello C. Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells. Scientific Reports. 5: 11999. PMID 26179713 DOI: 10.1038/Srep11999  0.307
2015 Roy S, Schmeier S, Arner E, Alam T, Parihar SP, Ozturk M, Tamgue O, Kawaji H, de Hoon MJ, Itoh M, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Bajic VB, et al. Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics. Nucleic Acids Research. 43: 6969-82. PMID 26117544 DOI: 10.1093/Nar/Gkv646  0.38
2015 Patrucco L, Chiesa A, Soluri MF, Fasolo F, Takahashi H, Carninci P, Zucchelli S, Santoro C, Gustincich S, Sblattero D, Cotella D. Engineering mammalian cell factories with SINEUP noncoding RNAs to improve translation of secreted proteins. Gene. 569: 287-93. PMID 26045368 DOI: 10.1016/J.Gene.2015.05.070  0.381
2015 Zucchelli S, Fasolo F, Russo R, Cimatti L, Patrucco L, Takahashi H, Jones MH, Santoro C, Sblattero D, Cotella D, Persichetti F, Carninci P, Gustincich S. SINEUPs are modular antisense long non-coding RNAs that increase synthesis of target proteins in cells. Frontiers in Cellular Neuroscience. 9: 174. PMID 26029048 DOI: 10.3389/Fncel.2015.00174  0.448
2015 Letourneau A, Cobellis G, Fort A, Santoni F, Garieri M, Falconnet E, Ribaux P, Vannier A, Guipponi M, Carninci P, Borel C, Antonarakis SE. HSA21 Single-Minded 2 (Sim2) Binding Sites Co-Localize with Super-Enhancers and Pioneer Transcription Factors in Pluripotent Mouse ES Cells. Plos One. 10: e0126475. PMID 25955728 DOI: 10.1371/Journal.Pone.0126475  0.399
2015 Aitken S, Magi S, Alhendi AM, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Forrest AR, Hayashizaki Y, Khachigian LM, Okada-Hatakeyama M, Semple CA. Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response. Plos Computational Biology. 11: e1004217. PMID 25885578 DOI: 10.1371/Journal.Pcbi.1004217  0.445
2015 Carrieri C, Forrest AR, Santoro C, Persichetti F, Carninci P, Zucchelli S, Gustincich S. Expression analysis of the long non-coding RNA antisense to Uchl1 (AS Uchl1) during dopaminergic cells' differentiation in vitro and in neurochemical models of Parkinson's disease. Frontiers in Cellular Neuroscience. 9: 114. PMID 25883552 DOI: 10.3389/Fncel.2015.00114  0.485
2015 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, Mungall CJ, Arner E, Baillie JK, Bertin N, Bono H, ... ... Carninci P, et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biology. 16: 22. PMID 25723102 DOI: 10.1186/S13059-014-0560-6  0.375
2015 Joshi A, Pooley C, Freeman TC, Lennartsson A, Babina M, Schmidl C, Geijtenbeek T, Michoel T, Severin J, Itoh M, Lassmann T, Kawaji H, Hayashizaki Y, Carninci P, et al. Transcription factor, promoter, and enhancer utilization in human myeloid cells. Journal of Leukocyte Biology. PMID 25717144 DOI: 10.1189/Jlb.6Ta1014-477Rr  0.471
2015 Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, ... ... Carninci P, et al. Gene regulation. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science (New York, N.Y.). 347: 1010-4. PMID 25678556 DOI: 10.1126/Science.1259418  0.457
2015 Fort A, Yamada D, Hashimoto K, Koseki H, Carninci P. Nuclear transcriptome profiling of induced pluripotent stem cells and embryonic stem cells identify non-coding loci resistant to reprogramming. Cell Cycle (Georgetown, Tex.). 14: 1148-55. PMID 25664506 DOI: 10.4161/15384101.2014.988031  0.455
2015 Haberle V, Forrest AR, Hayashizaki Y, Carninci P, Lenhard B. CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. Nucleic Acids Research. 43: e51. PMID 25653163 DOI: 10.1093/Nar/Gkv054  0.381
2015 Lassmann T, Maida Y, Tomaru Y, Yasukawa M, Ando Y, Kojima M, Kasim V, Simon C, Daub CO, Carninci P, Hayashizaki Y, Masutomi K. Telomerase reverse transcriptase regulates microRNAs. International Journal of Molecular Sciences. 16: 1192-208. PMID 25569094 DOI: 10.3390/Ijms16011192  0.422
2015 Borel C, Ferreira PG, Santoni F, Delaneau O, Fort A, Popadin KY, Garieri M, Falconnet E, Ribaux P, Guipponi M, Padioleau I, Carninci P, Dermitzakis ET, Antonarakis SE. Biased allelic expression in human primary fibroblast single cells. American Journal of Human Genetics. 96: 70-80. PMID 25557783 DOI: 10.1016/J.Ajhg.2014.12.001  0.446
2015 Taguchi A, Nagasaka K, Kawana K, Hashimoto K, Kusumoto-Matsuo R, Plessy C, Thomas M, Nakamura H, Bonetti A, Oda K, Kukimoto I, Carninci P, Banks L, Osuga Y, Fujii T. Characterization of novel transcripts of human papillomavirus type 16 using cap analysis gene expression technology. Journal of Virology. 89: 2448-52. PMID 25505068 DOI: 10.1128/Jvi.03433-14  0.417
2014 Vitezic M, Bertin N, Andersson R, Lipovich L, Kawaji H, Lassmann T, Sandelin A, Heutink P, Goldowitz D, Ha T, Zhang P, Patrizi A, Fagiolini M, Forrest AR, Carninci P, et al. CAGE-defined promoter regions of the genes implicated in Rett Syndrome. Bmc Genomics. 15: 1177. PMID 25539566 DOI: 10.1186/1471-2164-15-1177  0.459
2014 Carninci P. Genomics: mice in the ENCODE spotlight. Nature. 515: 346-7. PMID 25409821 DOI: 10.1038/515346A  0.463
2014 Kratz A, Carninci P. The devil in the details of RNA-seq. Nature Biotechnology. 32: 882-4. PMID 25203036 DOI: 10.1038/Nbt.3015  0.335
2014 Takahashi H, Carninci P. Widespread genome transcription: new possibilities for RNA therapies. Biochemical and Biophysical Research Communications. 452: 294-301. PMID 25193698 DOI: 10.1016/J.Bbrc.2014.08.139  0.422
2014 Abdelhamid RF, Plessy C, Yamauchi Y, Taoka M, de Hoon M, Gingeras TR, Isobe T, Carninci P. Multiplicity of 5' cap structures present on short RNAs. Plos One. 9: e102895. PMID 25079783 DOI: 10.1371/Journal.Pone.0102895  0.385
2014 Verardo R, Piazza S, Klaric E, Ciani Y, Bussadori G, Marzinotto S, Mariuzzi L, Cesselli D, Beltrami AP, Mano M, Itoh M, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, et al. Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer. Stem Cells (Dayton, Ohio). 32: 2998-3011. PMID 25069783 DOI: 10.1002/Stem.1791  0.349
2014 Chen ZX, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, ... ... Carninci P, et al. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Research. 24: 1209-23. PMID 24985915 DOI: 10.1101/Gr.159384.113  0.418
2014 Murata M, Nishiyori-Sueki H, Kojima-Ishiyama M, Carninci P, Hayashizaki Y, Itoh M. Detecting expressed genes using CAGE. Methods in Molecular Biology (Clifton, N.J.). 1164: 67-85. PMID 24927836 DOI: 10.1007/978-1-4939-0805-9_7  0.499
2014 Kratz A, Beguin P, Kaneko M, Chimura T, Suzuki AM, Matsunaga A, Kato S, Bertin N, Lassmann T, Vigot R, Carninci P, Plessy C, Launey T. Digital expression profiling of the compartmentalized translatome of Purkinje neurons. Genome Research. 24: 1396-410. PMID 24904046 DOI: 10.1101/Gr.164095.113  0.352
2014 Hasegawa A, Daub C, Carninci P, Hayashizaki Y, Lassmann T. MOIRAI: a compact workflow system for CAGE analysis. Bmc Bioinformatics. 15: 144. PMID 24884663 DOI: 10.1186/1471-2105-15-144  0.413
2014 Ohmiya H, Vitezic M, Frith MC, Itoh M, Carninci P, Forrest AR, Hayashizaki Y, Lassmann T. RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE). Bmc Genomics. 15: 269. PMID 24779366 DOI: 10.1186/1471-2164-15-269  0.518
2014 Fort A, Hashimoto K, Yamada D, Salimullah M, Keya CA, Saxena A, Bonetti A, Voineagu I, Bertin N, Kratz A, Noro Y, Wong CH, de Hoon M, Andersson R, Sandelin A, ... ... Carninci P, et al. Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nature Genetics. 46: 558-66. PMID 24777452 DOI: 10.1038/Ng.2965  0.41
2014 Yamaga R, Ikeda K, Boele J, Horie-Inoue K, Takayama K, Urano T, Kaida K, Carninci P, Kawai J, Hayashizaki Y, Ouchi Y, de Hoon M, Inoue S. Systemic identification of estrogen-regulated genes in breast cancer cells through cap analysis of gene expression mapping. Biochemical and Biophysical Research Communications. 447: 531-6. PMID 24746470 DOI: 10.1016/J.Bbrc.2014.04.033  0.395
2014 Morikawa H, Ohkura N, Vandenbon A, Itoh M, Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Standley DM, Date H, Sakaguchi S. Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. Proceedings of the National Academy of Sciences of the United States of America. 111: 5289-94. PMID 24706905 DOI: 10.1073/Pnas.1312717110  0.433
2014 Kawaji H, Lizio M, Itoh M, Kanamori-Katayama M, Kaiho A, Nishiyori-Sueki H, Shin JW, Kojima-Ishiyama M, Kawano M, Murata M, Ninomiya-Fukuda N, Ishikawa-Kato S, Nagao-Sato S, Noma S, Hayashizaki Y, ... ... Carninci P, et al. Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing. Genome Research. 24: 708-17. PMID 24676093 DOI: 10.1101/Gr.156232.113  0.488
2014 Schmidl C, Renner K, Peter K, Eder R, Lassmann T, Balwierz PJ, Itoh M, Nagao-Sato S, Kawaji H, Carninci P, Suzuki H, Hayashizaki Y, Andreesen R, Hume DA, Hoffmann P, et al. Transcription and enhancer profiling in human monocyte subsets. Blood. 123: e90-9. PMID 24671955 DOI: 10.1182/Blood-2013-02-484188  0.375
2014 Motakis E, Guhl S, Ishizu Y, Itoh M, Kawaji H, de Hoon M, Lassmann T, Carninci P, Hayashizaki Y, Zuberbier T, Forrest AR, Babina M. Redefinition of the human mast cell transcriptome by deep-CAGE sequencing. Blood. 123: e58-67. PMID 24671954 DOI: 10.1182/Blood-2013-02-483792  0.448
2014 Schmidl C, Hansmann L, Lassmann T, Balwierz PJ, Kawaji H, Itoh M, Kawai J, Nagao-Sato S, Suzuki H, Andreesen R, Hayashizaki Y, Forrest AR, Carninci P, Hoffmann P, Edinger M, et al. The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations. Blood. 123: e68-78. PMID 24671953 DOI: 10.1182/Blood-2013-02-486944  0.395
2014 Rönnerblad M, Andersson R, Olofsson T, Douagi I, Karimi M, Lehmann S, Hoof I, de Hoon M, Itoh M, Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, et al. Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation. Blood. 123: e79-89. PMID 24671952 DOI: 10.1182/Blood-2013-02-482893  0.333
2014 Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, ... ... Carninci P, et al. A promoter-level mammalian expression atlas. Nature. 507: 462-70. PMID 24670764 DOI: 10.1038/Nature13182  0.495
2014 Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, ... ... Carninci P, et al. An atlas of active enhancers across human cell types and tissues. Nature. 507: 455-61. PMID 24670763 DOI: 10.1038/Nature12787  0.441
2014 Brown JB, Boley N, Eisman R, May GE, Stoiber MH, Duff MO, Booth BW, Wen J, Park S, Suzuki AM, Wan KH, Yu C, Zhang D, Carlson JW, Cherbas L, ... ... Carninci P, et al. Diversity and dynamics of the Drosophila transcriptome. Nature. 512: 393-9. PMID 24670639 DOI: 10.1038/Nature12962  0.504
2014 Rye M, Sandve GK, Daub CO, Kawaji H, Carninci P, Forrest AR, Drabløs F. Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines. Bmc Genomics. 15: 120. PMID 24669905 DOI: 10.1186/1471-2164-15-120  0.438
2014 Pascarella G, Lazarevic D, Plessy C, Bertin N, Akalin A, Vlachouli C, Simone R, Faulkner GJ, Zucchelli S, Kawai J, Daub CO, Hayashizaki Y, Lenhard B, Carninci P, Gustincich S. NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements. Frontiers in Cellular Neuroscience. 8: 41. PMID 24600346 DOI: 10.3389/Fncel.2014.00041  0.401
2014 Haberle V, Li N, Hadzhiev Y, Plessy C, Previti C, Nepal C, Gehrig J, Dong X, Akalin A, Suzuki AM, van IJcken WF, Armant O, Ferg M, Strähle U, Carninci P, et al. Two independent transcription initiation codes overlap on vertebrate core promoters. Nature. 507: 381-5. PMID 24531765 DOI: 10.1038/Nature12974  0.475
2013 Sompallae R, Hofmann O, Maher CA, Gedye C, Behren A, Vitezic M, Daub CO, Devalle S, Caballero OL, Carninci P, Hayashizaki Y, Lawlor ER, Cebon J, Hide W. A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells. Frontiers in Genetics. 4: 209. PMID 24194746 DOI: 10.3389/Fgene.2013.00209  0.392
2013 Kouno T, de Hoon M, Mar JC, Tomaru Y, Kawano M, Carninci P, Suzuki H, Hayashizaki Y, Shin JW. Temporal dynamics and transcriptional control using single-cell gene expression analysis. Genome Biology. 14: R118. PMID 24156252 DOI: 10.1186/Gb-2013-14-10-R118  0.397
2013 Harbers M, Kato S, de Hoon M, Hayashizaki Y, Carninci P, Plessy C. Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation. Bmc Genomics. 14: 665. PMID 24079827 DOI: 10.1186/1471-2164-14-665  0.419
2013 Nepal C, Hadzhiev Y, Previti C, Haberle V, Li N, Takahashi H, Suzuki AM, Sheng Y, Abdelhamid RF, Anand S, Gehrig J, Akalin A, Kockx CE, van der Sloot AA, van Ijcken WF, ... ... Carninci P, et al. Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome Research. 23: 1938-50. PMID 24002785 DOI: 10.1101/Gr.153692.112  0.496
2013 Pardo LM, Rizzu P, Francescatto M, Vitezic M, Leday GG, Sanchez JS, Khamis A, Takahashi H, van de Berg WD, Medvedeva YA, van de Wiel MA, Daub CO, Carninci P, Heutink P. Regional differences in gene expression and promoter usage in aged human brains. Neurobiology of Aging. 34: 1825-36. PMID 23428183 DOI: 10.1016/J.Neurobiolaging.2013.01.005  0.441
2013 Fadloun A, Le Gras S, Jost B, Ziegler-Birling C, Takahashi H, Gorab E, Carninci P, Torres-Padilla ME. Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA. Nature Structural & Molecular Biology. 20: 332-8. PMID 23353788 DOI: 10.1038/Nsmb.2495  0.429
2013 Plessy C, Desbois L, Fujii T, Carninci P. Population transcriptomics with single-cell resolution: a new field made possible by microfluidics: a technology for high throughput transcript counting and data-driven definition of cell types. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 35: 131-40. PMID 23281054 DOI: 10.1002/Bies.201200093  0.349
2013 Tang DT, Plessy C, Salimullah M, Suzuki AM, Calligaris R, Gustincich S, Carninci P. Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching. Nucleic Acids Research. 41: e44. PMID 23180801 DOI: 10.1093/Nar/Gks1128  0.396
2013 Batut P, Dobin A, Plessy C, Carninci P, Gingeras TR. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 23: 169-80. PMID 22936248 DOI: 10.1101/Gr.139618.112  0.505
2012 Bonetti A, Carninci P. Structure by sequencing: discovery of hidden messages in the noncoding RNA fraction. Molecular Cell. 48: 153-5. PMID 23102264 DOI: 10.1016/J.Molcel.2012.10.004  0.388
2012 Carrieri C, Cimatti L, Biagioli M, Beugnet A, Zucchelli S, Fedele S, Pesce E, Ferrer I, Collavin L, Santoro C, Forrest AR, Carninci P, Biffo S, Stupka E, Gustincich S. Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature. 491: 454-7. PMID 23064229 DOI: 10.1038/Nature11508  0.482
2012 Saxena A, Tang D, Carninci P. piRNAs warrant investigation in Rett Syndrome: an omics perspective. Disease Markers. 33: 261-75. PMID 22976001 DOI: 10.3233/Dma-2012-0932  0.423
2012 Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, ... Carninci P, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Research. 22: 1775-89. PMID 22955988 DOI: 10.1101/Gr.132159.111  0.507
2012 Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, et al. Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Research. 22: 1658-67. PMID 22955978 DOI: 10.1101/Gr.136838.111  0.432
2012 Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, ... ... Carninci P, et al. Landscape of transcription in human cells. Nature. 489: 101-8. PMID 22955620 DOI: 10.1038/Nature11233  0.459
2012 Francia S, Michelini F, Saxena A, Tang D, de Hoon M, Anelli V, Mione M, Carninci P, d'Adda di Fagagna F. Site-specific DICER and DROSHA RNA products control the DNA-damage response. Nature. 488: 231-5. PMID 22722852 DOI: 10.1038/Nature11179  0.364
2012 Schroder K, Irvine KM, Taylor MS, Bokil NJ, Le Cao KA, Masterman KA, Labzin LI, Semple CA, Kapetanovic R, Fairbairn L, Akalin A, Faulkner GJ, Baillie JK, Gongora M, Daub CO, ... ... Carninci P, et al. Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. Proceedings of the National Academy of Sciences of the United States of America. 109: E944-53. PMID 22451944 DOI: 10.1073/Pnas.1110156109  0.405
2012 Lenhard B, Sandelin A, Carninci P. Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nature Reviews. Genetics. 13: 233-45. PMID 22392219 DOI: 10.1038/Nrg3163  0.472
2012 Takahashi H, Lassmann T, Murata M, Carninci P. 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nature Protocols. 7: 542-61. PMID 22362160 DOI: 10.1038/Nprot.2012.005  0.51
2012 Itoh M, Kojima M, Nagao-Sato S, Saijo E, Lassmann T, Kanamori-Katayama M, Kaiho A, Lizio M, Kawaji H, Carninci P, Forrest AR, Hayashizaki Y. Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer. Plos One. 7: e30809. PMID 22303458 DOI: 10.1371/Journal.Pone.0030809  0.463
2012 Plessy C, Pascarella G, Bertin N, Akalin A, Carrieri C, Vassalli A, Lazarevic D, Severin J, Vlachouli C, Simone R, Faulkner GJ, Kawai J, Daub CO, Zucchelli S, Hayashizaki Y, ... ... Carninci P, et al. Promoter architecture of mouse olfactory receptor genes. Genome Research. 22: 486-97. PMID 22194471 DOI: 10.1101/Gr.126201.111  0.466
2012 Takahashi H, Kato S, Murata M, Carninci P. CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks. Methods in Molecular Biology (Clifton, N.J.). 786: 181-200. PMID 21938627 DOI: 10.1007/978-1-61779-292-2_11  0.458
2011 Cernilogar FM, Onorati MC, Kothe GO, Burroughs AM, Parsi KM, Breiling A, Lo Sardo F, Saxena A, Miyoshi K, Siomi H, Siomi MC, Carninci P, Gilmour DS, Corona DF, Orlando V. Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature. 480: 391-5. PMID 22056986 DOI: 10.1038/Nature10492  0.434
2011 Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan PM, Rizzu P, Smith S, Fell M, Talbot RT, Gustincich S, Freeman TC, Mattick JS, Hume DA, ... ... Carninci P, et al. Somatic retrotransposition alters the genetic landscape of the human brain. Nature. 479: 534-7. PMID 22037309 DOI: 10.1038/Nature10531  0.372
2011 Saxena A, Carninci P. Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 33: 830-9. PMID 21915889 DOI: 10.1002/Bies.201100084  0.419
2011 Franzén O, Arner E, Ferella M, Nilsson D, Respuela P, Carninci P, Hayashizaki Y, Aslund L, Andersson B, Daub CO. The short non-coding transcriptome of the protozoan parasite Trypanosoma cruzi. Plos Neglected Tropical Diseases. 5: e1283. PMID 21912713 DOI: 10.1371/Journal.Pntd.0001283  0.435
2011 Ando Y, Tomaru Y, Morinaga A, Burroughs AM, Kawaji H, Kubosaki A, Kimura R, Tagata M, Ino Y, Hirano H, Chiba J, Suzuki H, Carninci P, Hayashizaki Y. Nuclear pore complex protein mediated nuclear localization of dicer protein in human cells. Plos One. 6: e23385. PMID 21858095 DOI: 10.1371/Journal.Pone.0023385  0.336
2011 Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A, Rozowsky JS, Gerstein MB, Wahlestedt C, Hayashizaki Y, Carninci P, et al. The reality of pervasive transcription. Plos Biology. 9: e1000625; discussion. PMID 21765801 DOI: 10.1371/Journal.Pbio.1000625  0.436
2011 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO, Carninci P, Forrest AR, Hayashizaki Y. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Research. 21: 1150-9. PMID 21596820 DOI: 10.1101/Gr.115469.110  0.489
2011 Salimullah M, Sakai M, Mizuho S, Plessy C, Carninci P. NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes. Cold Spring Harbor Protocols. 2011: pdb.prot5559. PMID 21205859 DOI: 10.1101/Pdb.Prot5559  0.515
2011 Saxena A, Carninci P. Whole transcriptome analysis: what are we still missing? Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 3: 527-43. PMID 21197667 DOI: 10.1002/Wsbm.135  0.372
2011 Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH, Yang L, Boley N, Andrews J, Kaufman TC, Graveley BR, ... ... Carninci P, et al. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Research. 21: 182-92. PMID 21177961 DOI: 10.1101/Gr.112466.110  0.513
2011 Kawaji H, Severin J, Lizio M, Forrest AR, van Nimwegen E, Rehli M, Schroder K, Irvine K, Suzuki H, Carninci P, Hayashizaki Y, Daub CO. Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Research. 39: D856-60. PMID 21075797 DOI: 10.1093/Nar/Gkq1112  0.521
2011 Francescatto M, Pardo L, Rizzu P, Vitezic M, Simón-Sánchez J, Takahashi H, Daub C, Carninci P, Heutink P. Profiling transcription initiation in human aged brain using deep-CAGE Bmc Bioinformatics. 12. DOI: 10.1186/1471-2105-12-S11-A8  0.494
2011 Brinkmeier ML, Davis SW, Carninci P, MacDonald JW, Kawai J, Ghosh D, Hayashizaki Y, Lyons RH, Camper SA. Retraction notice to “Discovery of transcriptional regulators and signaling pathways in the developing pituitary gland by bioinformatic and genomic approaches” [Genomics 93 (2009) 449–460] Genomics. DOI: 10.1016/J.Ygeno.2011.03.004  0.309
2010 Schaefer U, Kodzius R, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bajic VB. High sensitivity TSS prediction: estimates of locations where TSS cannot occur. Plos One. 5: e13934. PMID 21085627 DOI: 10.1371/Journal.Pone.0013934  0.46
2010 Kawano M, Kawazu C, Lizio M, Kawaji H, Carninci P, Suzuki H, Hayashizaki Y. Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing. Biotechniques. 49: 751-5. PMID 20964636 DOI: 10.2144/000113516  0.414
2010 Vitezic M, Lassmann T, Forrest AR, Suzuki M, Tomaru Y, Kawai J, Carninci P, Suzuki H, Hayashizaki Y, Daub CO. Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE. Nucleic Acids Research. 38: 8141-8. PMID 20724440 DOI: 10.1093/Nar/Gkq729  0.452
2010 Plessy C, Bertin N, Takahashi H, Simone R, Salimullah M, Lassmann T, Vitezic M, Severin J, Olivarius S, Lazarevic D, Hornig N, Orlando V, Bell I, Gao H, Dumais J, ... ... Carninci P, et al. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nature Methods. 7: 528-34. PMID 20543846 DOI: 10.1038/Nmeth.1470  0.493
2010 Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren WM, Patone G, Petretto E, Plessy C, Rockland KS, Rockland C, ... ... Carninci P, et al. The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome Research. 20: 791-803. PMID 20430781 DOI: 10.1101/Gr.103499.109  0.42
2010 Kratz A, Arner E, Saito R, Kubosaki A, Kawai J, Suzuki H, Carninci P, Arakawa T, Tomita M, Hayashizaki Y, Daub CO. Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns. Bmc Genomics. 11: 257. PMID 20409305 DOI: 10.1186/1471-2164-11-257  0.432
2010 Carninci P. RNA dust: where are the genes? Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 17: 51-9. PMID 20211845 DOI: 10.1093/Dnares/Dsq006  0.485
2010 Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell. 140: 744-52. PMID 20211142 DOI: 10.1016/J.Cell.2010.01.044  0.415
2010 de Hoon MJ, Taft RJ, Hashimoto T, Kanamori-Katayama M, Kawaji H, Kawano M, Kishima M, Lassmann T, Faulkner GJ, Mattick JS, Daub CO, Carninci P, Kawai J, Suzuki H, Hayashizaki Y. Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Research. 20: 257-64. PMID 20051556 DOI: 10.1101/Gr.095273.109  0.402
2010 Davis SW, Castinetti F, Carvalho LR, Ellsworth BS, Potok MA, Lyons RH, Brinkmeier ML, Raetzman LT, Carninci P, Mortensen AH, Hayashizaki Y, Arnhold IJ, Mendonça BB, Brue T, Camper SA. Molecular mechanisms of pituitary organogenesis: In search of novel regulatory genes. Molecular and Cellular Endocrinology. 323: 4-19. PMID 20025935 DOI: 10.1016/J.Mce.2009.12.012  0.336
2010 Suzuki H, Carninci P, Daub C, Kawai J, Hayashizaki Y. Beyond the FANTOM4 Genome Biology. 11: O11. DOI: 10.1186/Gb-2010-11-S1-O11  0.524
2010 Amid C, Frankish A, Aken B, Ezkurdia I, Kokocinsk F, Gilbert J, White S, Carninci P, Gingeras T, Guigo R, Searle S, Tress ML, Harrow J, Hubbard T. From identification to validation to gene count. Genome Biology. 11: 1-1. DOI: 10.1186/Gb-2010-11-S1-O1  0.45
2009 Carninci P. Is sequencing enlightenment ending the dark age of the transcriptome? Nature Methods. 6: 711-13. PMID 19953680 DOI: 10.1038/Nmeth1009-711  0.388
2009 Forrest AR, Carninci P. Whole genome transcriptome analysis. Rna Biology. 6: 107-12. PMID 19875928 DOI: 10.4161/Rna.6.2.7931  0.504
2009 Forrest AR, Abdelhamid RF, Carninci P. Annotating non-coding transcription using functional genomics strategies. Briefings in Functional Genomics & Proteomics. 8: 437-43. PMID 19833699 DOI: 10.1093/Bfgp/Elp041  0.49
2009 Faulkner GJ, Carninci P. Altruistic functions for selfish DNA. Cell Cycle (Georgetown, Tex.). 8: 2895-900. PMID 19736519 DOI: 10.4161/Cc.8.18.9536  0.467
2009 Biagioli M, Pinto M, Cesselli D, Zaninello M, Lazarevic D, Roncaglia P, Simone R, Vlachouli C, Plessy C, Bertin N, Beltrami A, Kobayashi K, Gallo V, Santoro C, Ferrer I, ... ... Carninci P, et al. Unexpected expression of alpha- and beta-globin in mesencephalic dopaminergic neurons and glial cells. Proceedings of the National Academy of Sciences of the United States of America. 106: 15454-9. PMID 19717439 DOI: 10.1073/Pnas.0813216106  0.302
2009 Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen E. Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biology. 10: R79. PMID 19624849 DOI: 10.1186/Gb-2009-10-7-R79  0.492
2009 Taft RJ, Glazov EA, Lassmann T, Hayashizaki Y, Carninci P, Mattick JS. Small RNAs derived from snoRNAs. Rna (New York, N.Y.). 15: 1233-40. PMID 19474147 DOI: 10.1261/Rna.1528909  0.369
2009 Davis SW, Potok MA, Brinkmeier ML, Carninci P, Lyons RH, MacDonald JW, Fleming MT, Mortensen AH, Egashira N, Ghosh D, Steel KP, Osamura RY, Hayashizaki Y, Camper SA. Genetics, gene expression and bioinformatics of the pituitary gland. Hormone Research. 71: 101-15. PMID 19407506 DOI: 10.1159/000192447  0.404
2009 Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest AR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A, Hayashida K, ... ... Carninci P, et al. Tiny RNAs associated with transcription start sites in animals. Nature Genetics. 41: 572-8. PMID 19377478 DOI: 10.1038/Ng.312  0.468
2009 Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, ... ... Carninci P, et al. The regulated retrotransposon transcriptome of mammalian cells. Nature Genetics. 41: 563-71. PMID 19377475 DOI: 10.1038/Ng.368  0.53
2009 Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, et al. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics. 41: 553-62. PMID 19377474 DOI: 10.1038/Ng.375  0.432
2009 Kawaji H, Severin J, Lizio M, Waterhouse A, Katayama S, Irvine KM, Hume DA, Forrest AR, Suzuki H, Carninci P, Hayashizaki Y, Daub CO. The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Genome Biology. 10: R40. PMID 19374775 DOI: 10.1186/Gb-2009-10-4-R40  0.413
2009 Severin J, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ, de Hoon MJ, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, Forrest AR. FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. Genome Biology. 10: R39. PMID 19374773 DOI: 10.1186/Gb-2009-10-4-R39  0.434
2009 Olivarius S, Plessy C, Carninci P. High-throughput verification of transcriptional starting sites by Deep-RACE. Biotechniques. 46: 130-2. PMID 19317658 DOI: 10.2144/000113066  0.44
2009 Seki M, Kamiya A, Carninci P, Hayashizaki Y, Shinozaki K. Generation of full-length cDNA libraries: focus on plants. Methods in Molecular Biology (Clifton, N.J.). 533: 49-68. PMID 19277562 DOI: 10.1007/978-1-60327-136-3_4  0.403
2009 Carninci P. Molecular biology: The long and short of RNAs. Nature. 457: 974-5. PMID 19225515 DOI: 10.1038/457974B  0.368
2009 Brinkmeier ML, Davis SW, Carninci P, MacDonald JW, Kawai J, Ghosh D, Hayashizaki Y, Lyons RH, Camper SA. Discovery of transcriptional regulators and signaling pathways in the developing pituitary gland by bioinformatic and genomic approaches. Genomics. 93: 449-60. PMID 19121383 DOI: 10.1016/J.Ygeno.2008.11.010  0.416
2009 Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori H, Lazarevic D, Motti D, Marstrand TT, Tang MH, Zhao X, Krogh A, Winther O, ... ... Carninci P, et al. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Research. 19: 255-65. PMID 19074369 DOI: 10.1101/Gr.084541.108  0.489
2009 Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest ARR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A, Hayashida K, ... ... Carninci P, et al. Erratum: Corrigendum: Tiny RNAs associated with transcription start sites in animals Nature Genetics. 41: 859-859. DOI: 10.1038/Ng0709-859A  0.384
2008 Hofmann O, Caballero OL, Stevenson BJ, Chen YT, Cohen T, Chua R, Maher CA, Panji S, Schaefer U, Kruger A, Lehvaslaiho M, Carninci P, Hayashizaki Y, Jongeneel CV, Simpson AJ, et al. Genome-wide analysis of cancer/testis gene expression. Proceedings of the National Academy of Sciences of the United States of America. 105: 20422-7. PMID 19088187 DOI: 10.1073/Pnas.0810777105  0.401
2008 Taylor MS, Massingham T, Hayashizaki Y, Carninci P, Goldman N, Semple CA. Rapidly evolving human promoter regions. Nature Genetics. 40: 1262-3; author reply. PMID 18957975 DOI: 10.1038/Ng1108-1262  0.303
2008 Carninci P. Non-coding RNA transcription: turning on neighbours. Nature Cell Biology. 10: 1023-4. PMID 18758492 DOI: 10.1038/Ncb0908-1023  0.427
2008 Plessy C, Fagiolini M, Wagatsuma A, Harasawa N, Kuji T, Asaka-Oba A, Kanzaki Y, Fujishima S, Waki K, Nakahara H, Hensch TK, Carninci P. A resource for transcriptomic analysis in the mouse brain. Plos One. 3: e3012. PMID 18714383 DOI: 10.1371/Journal.Pone.0003012  0.379
2008 Maeda N, Nishiyori H, Nakamura M, Kawazu C, Murata M, Sano H, Hayashida K, Fukuda S, Tagami M, Hasegawa A, Murakami K, Schroder K, Irvine K, Hume D, Hayashizaki Y, ... Carninci P, et al. Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer. Biotechniques. 45: 95-7. PMID 18611171 DOI: 10.2144/000112814  0.476
2008 Carninci P. Hunting hidden transcripts. Nature Methods. 5: 587-9. PMID 18587315 DOI: 10.1038/Nmeth0708-587  0.428
2008 Carninci P, Yasuda J, Hayashizaki Y. Multifaceted mammalian transcriptome. Current Opinion in Cell Biology. 20: 274-80. PMID 18468878 DOI: 10.1016/J.Ceb.2008.03.008  0.41
2008 Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub CO, Kai C, Kawai J, Yasuda J, Carninci P, Hayashizaki Y. Hidden layers of human small RNAs. Bmc Genomics. 9: 157. PMID 18402656 DOI: 10.1186/1471-2164-9-157  0.38
2008 Faulkner GJ, Forrest AR, Chalk AM, Schroder K, Hayashizaki Y, Carninci P, Hume DA, Grimmond SM. A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics. 91: 281-8. PMID 18178374 DOI: 10.1016/J.Ygeno.2007.11.003  0.479
2008 Centlow M, Carninci P, Nemeth K, Mezey E, Brownstein M, Hansson SR. Placental expression profiling in preeclampsia: local overproduction of hemoglobin may drive pathological changes. Fertility and Sterility. 90: 1834-43. PMID 18166190 DOI: 10.1016/J.Fertnstert.2007.09.030  0.365
2008 Frith MC, Valen E, Krogh A, Hayashizaki Y, Carninci P, Sandelin A. A code for transcription initiation in mammalian genomes. Genome Research. 18: 1-12. PMID 18032727 DOI: 10.1101/Gr.6831208  0.454
2007 Satoh K, Doi K, Nagata T, Kishimoto N, Suzuki K, Otomo Y, Kawai J, Nakamura M, Hirozane-Kishikawa T, Kanagawa S, Arakawa T, Takahashi-Iida J, Murata M, Ninomiya N, Sasaki D, ... ... Carninci P, et al. Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. Plos One. 2: e1235. PMID 18043742 DOI: 10.1371/Journal.Pone.0001235  0.453
2007 Kawai J, Carninci P, Hayashizaki Y. Transcriptomics resources for functional genomics. Briefings in Functional Genomics & Proteomics. 6: 171-9. PMID 18029381 DOI: 10.1093/Bfgp/Elm024  0.387
2007 Kruger A, Hofmann O, Carninci P, Hayashizaki Y, Hide W. Simplified ontologies allowing comparison of developmental mammalian gene expression. Genome Biology. 8: R229. PMID 17961239 DOI: 10.1186/Gb-2007-8-10-R229  0.371
2007 Frith MC, Carninci P, Kai C, Kawai J, Bailey TL, Hayashizaki Y, Mattick JS. Splicing bypasses 3' end formation signals to allow complex gene architectures. Gene. 403: 188-93. PMID 17897791 DOI: 10.1016/J.Gene.2007.08.012  0.464
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Carninci P, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.451
2007 Shimokawa K, Okamura-Oho Y, Kurita T, Frith MC, Kawai J, Carninci P, Hayashizaki Y. Large-scale clustering of CAGE tag expression data. Bmc Bioinformatics. 8: 161. PMID 17517134 DOI: 10.1186/1471-2105-8-161  0.386
2007 Baxter LL, Hsu BJ, Umayam L, Wolfsberg TG, Larson DM, Frith MC, Kawai J, Hayashizaki Y, Carninci P, Pavan WJ. Informatic and genomic analysis of melanocyte cDNA libraries as a resource for the study of melanocyte development and function. Pigment Cell Research / Sponsored by the European Society For Pigment Cell Research and the International Pigment Cell Society. 20: 201-9. PMID 17516927 DOI: 10.1111/J.1600-0749.2007.00372.X  0.494
2007 Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, Hume DA. Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nature Reviews. Genetics. 8: 424-36. PMID 17486122 DOI: 10.1038/Nrg2026  0.489
2007 Carninci P. Constructing the landscape of the mammalian transcriptome. The Journal of Experimental Biology. 210: 1497-506. PMID 17449815 DOI: 10.1242/Jeb.000406  0.473
2007 Purmann A, Toedling J, Schueler M, Carninci P, Lehrach H, Hayashizaki Y, Huber W, Sperling S. Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality. Genomics. 89: 580-7. PMID 17369017 DOI: 10.1016/J.Ygeno.2007.01.010  0.423
2007 Carninci P, Hayashizaki Y. Noncoding RNA transcription beyond annotated genes. Current Opinion in Genetics & Development. 17: 139-44. PMID 17317145 DOI: 10.1016/J.Gde.2007.02.008  0.43
2007 Beisel KW, Rocha-Sanchez SM, Ziegenbein SJ, Morris KA, Kai C, Kawai J, Carninci P, Hayashizaki Y, Davis RL. Diversity of Ca2+-activated K+ channel transcripts in inner ear hair cells. Gene. 386: 11-23. PMID 17097837 DOI: 10.1016/J.Gene.2006.07.023  0.419
2007 Katayama S, Kanamori-Katayama M, Yamaguchi K, Carninci P, Hayashizaki Y. CAGE-TSSchip: Promoter-based expression profiling using the 5′-leading label of capped transcripts Genome Biology. 8. DOI: 10.1186/Gb-2007-8-3-R42  0.441
2007 Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CAM, Taylor MS, Engström G PG, Frith MC, Forrest ARR, Alkema WB, Tan SL, Plessy C, Kodzius R, et al. Erratum: Corrigendum: Genome-wide analysis of mammalian promoter architecture and evolution Nature Genetics. 39: 1174-1174. DOI: 10.1038/Ng0907-1174B  0.322
2006 Brahmachary M, Schönbach C, Yang L, Huang E, Tan SL, Chowdhary R, Krishnan SP, Lin CY, Hume DA, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bajic VB. Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes. Bmc Bioinformatics. 7: S8. PMID 17254313 DOI: 10.1186/1471-2105-7-S5-S8  0.437
2006 Kawaji H, Frith MC, Katayama S, Sandelin A, Kai C, Kawai J, Carninci P, Hayashizaki Y. Dynamic usage of transcription start sites within core promoters. Genome Biology. 7: R118. PMID 17156492 DOI: 10.1186/Gb-2006-7-12-R118  0.401
2006 Frith MC, Bailey TL, Kasukawa T, Mignone F, Kummerfeld SK, Madera M, Sunkara S, Furuno M, Bult CJ, Quackenbush J, Kai C, Kawai J, Carninci P, Hayashizaki Y, Pesole G, et al. Discrimination of non-protein-coding transcripts from protein-coding mRNA. Rna Biology. 3: 40-8. PMID 17114936 DOI: 10.4161/Rna.3.1.2789  0.383
2006 Wada K, Howard JT, McConnell P, Whitney O, Lints T, Rivas MV, Horita H, Patterson MA, White SA, Scharff C, Haesler S, Zhao S, Sakaguchi H, Hagiwara M, Shiraki T, ... ... Carninci P, et al. A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes. Proceedings of the National Academy of Sciences of the United States of America. 103: 15212-7. PMID 17018643 DOI: 10.1073/Pnas.0607098103  0.392
2006 Ponjavic J, Lenhard B, Kai C, Kawai J, Carninci P, Hayashizaki Y, Sandelin A. Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters. Genome Biology. 7: R78. PMID 16916456 DOI: 10.1186/Gb-2006-7-8-R78  0.399
2006 Carninci P. Tagging mammalian transcription complexity. Trends in Genetics : Tig. 22: 501-10. PMID 16859803 DOI: 10.1016/J.Tig.2006.07.003  0.473
2006 Gustincich S, Sandelin A, Plessy C, Katayama S, Simone R, Lazarevic D, Hayashizaki Y, Carninci P. The complexity of the mammalian transcriptome. The Journal of Physiology. 575: 321-32. PMID 16857706 DOI: 10.1113/Jphysiol.2006.115568  0.513
2006 Nilsson R, Bajic VB, Suzuki H, di Bernardo D, Björkegren J, Katayama S, Reid JF, Sweet MJ, Gariboldi M, Carninci P, Hayashizaki Y, Hume DA, Tegner J, Ravasi T. Transcriptional network dynamics in macrophage activation. Genomics. 88: 133-42. PMID 16698233 DOI: 10.1016/J.Ygeno.2006.03.022  0.379
2006 Frith MC, Ponjavic J, Fredman D, Kai C, Kawai J, Carninci P, Hayashizaki Y, Hayshizaki Y, Sandelin A. Evolutionary turnover of mammalian transcription start sites. Genome Research. 16: 713-22. PMID 16687732 DOI: 10.1101/Gr.5031006  0.456
2006 Hayashizaki Y, Carninci P. Genome Network and FANTOM3: assessing the complexity of the transcriptome. Plos Genetics. 2: e63. PMID 16683037 DOI: 10.1371/Journal.Pgen.0020063  0.459
2006 Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engström PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, Bult CJ, Fletcher CF, Forrest AR, Furuno M, Hill D, ... ... Carninci P, et al. Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. Plos Genetics. 2: e62. PMID 16683036 DOI: 10.1371/Journal.Pgen.0020062  0.454
2006 Bajic VB, Tan SL, Christoffels A, Schönbach C, Lipovich L, Yang L, Hofmann O, Kruger A, Hide W, Kai C, Kawai J, Hume DA, Carninci P, Hayashizaki Y. Mice and men: their promoter properties. Plos Genetics. 2: e54. PMID 16683032 DOI: 10.1371/Journal.Pgen.0020054  0.448
2006 Engström PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, Lavorgna G, Brozzi A, Luzi L, Tan SL, Yang L, Kunarso G, Ng EL, Batalov S, Wahlestedt C, Kai C, ... ... Carninci P, et al. Complex Loci in human and mouse genomes. Plos Genetics. 2: e47. PMID 16683030 DOI: 10.1371/Journal.Pgen.0020047  0.471
2006 Chern TM, van Nimwegen E, Kai C, Kawai J, Carninci P, Hayashizaki Y, Zavolan M. A simple physical model predicts small exon length variations. Plos Genetics. 2: e45. PMID 16683028 DOI: 10.1371/Journal.Pgen.0020045  0.34
2006 Seno S, Takenaka Y, Kai C, Kawai J, Carninci P, Hayashizaki Y, Matsuda H. A method for similarity search of genomic positional expression using CAGE. Plos Genetics. 2: e44. PMID 16683027 DOI: 10.1371/Journal.Pgen.0020044  0.446
2006 Furuno M, Pang KC, Ninomiya N, Fukuda S, Frith MC, Bult C, Kai C, Kawai J, Carninci P, Hayashizaki Y, Mattick JS, Suzuki H. Clusters of internally primed transcripts reveal novel long noncoding RNAs. Plos Genetics. 2: e37. PMID 16683026 DOI: 10.1371/Journal.Pgen.0020037  0.454
2006 Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Semple CA. Heterotachy in mammalian promoter evolution. Plos Genetics. 2: e30. PMID 16683025 DOI: 10.1371/Journal.Pgen.0020030  0.425
2006 Frith MC, Wilming LG, Forrest A, Kawaji H, Tan SL, Wahlestedt C, Bajic VB, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bailey TL, Huminiecki L. Pseudo-messenger RNA: phantoms of the transcriptome. Plos Genetics. 2: e23. PMID 16683022 DOI: 10.1371/Journal.Pgen.0020023  0.494
2006 Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engström PG, Frith MC, Forrest AR, Alkema WB, Tan SL, Plessy C, Kodzius R, et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nature Genetics. 38: 626-35. PMID 16645617 DOI: 10.1038/Ng1789  0.473
2006 Wells CA, Chalk AM, Forrest A, Taylor D, Waddell N, Schroder K, Himes SR, Faulkner G, Lo S, Kasukawa T, Kawaji H, Kai C, Kawai J, Katayama S, Carninci P, et al. Alternate transcription of the Toll-like receptor signaling cascade. Genome Biology. 7: R10. PMID 16507160 DOI: 10.1186/Gb-2006-7-2-R10  0.36
2006 Forrest AR, Taylor DF, Crowe ML, Chalk AM, Waddell NJ, Kolle G, Faulkner GJ, Kodzius R, Katayama S, Wells C, Kai C, Kawai J, Carninci P, Hayashizaki Y, Grimmond SM. Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases. Genome Biology. 7: R5. PMID 16507138 DOI: 10.1186/Gb-2006-7-1-R5  0.369
2006 Kodzius R, Kojima M, Nishiyori H, Nakamura M, Fukuda S, Tagami M, Sasaki D, Imamura K, Kai C, Harbers M, Hayashizaki Y, Carninci P. CAGE: cap analysis of gene expression. Nature Methods. 3: 211-22. PMID 16489339 DOI: 10.1038/Nmeth0306-211  0.387
2006 Kawaji H, Kasukawa T, Fukuda S, Katayama S, Kai C, Kawai J, Carninci P, Hayashizaki Y. CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. Nucleic Acids Research. 34: D632-6. PMID 16381948 DOI: 10.1093/Nar/Gkj034  0.503
2006 Frith MC, Kawaji H, Sandelin A, Ponjavic J, Carninci P, Hayashizaki Y. S2d2-4 New complexities of transcription start site usage in mammals(S2-d2: "Bioinformatics of Transcriptional Regulation",Symposia,Abstract,Meeting Program of EABS & BSJ 2006) Seibutsu Butsuri. 46: S129. DOI: 10.2142/Biophys.46.S129_4  0.345
2005 Aidinis V, Carninci P, Armaka M, Witke W, Harokopos V, Pavelka N, Koczan D, Argyropoulos C, Thwin MM, Möller S, Waki K, Kazunori W, Gopalakrishnakone P, Ricciardi-Castagnoli P, Thiesen HJ, et al. Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis. Plos Genetics. 1: e48. PMID 16254600 DOI: 10.1371/Journal.Pgen.0010048  0.326
2005 Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, Wells C, Frith M, et al. Antisense transcription in the mammalian transcriptome. Science (New York, N.Y.). 309: 1564-6. PMID 16141073 DOI: 10.1126/Science.1112009  0.501
2005 Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, et al. The transcriptional landscape of the mammalian genome. Science (New York, N.Y.). 309: 1559-63. PMID 16141072 DOI: 10.1126/Science.1112014  0.482
2005 Harbers M, Carninci P. Tag-based approaches for transcriptome research and genome annotation. Nature Methods. 2: 495-502. PMID 15973418 DOI: 10.1038/Nmeth768  0.485
2005 Nakabachi A, Shigenobu S, Sakazume N, Shiraki T, Hayashizaki Y, Carninci P, Ishikawa H, Kudo T, Fukatsu T. Transcriptome analysis of the aphid bacteriocyte, the symbiotic host cell that harbors an endocellular mutualistic bacterium, Buchnera. Proceedings of the National Academy of Sciences of the United States of America. 102: 5477-82. PMID 15800043 DOI: 10.1073/Pnas.0409034102  0.363
2005 Morris KA, Snir E, Pompeia C, Koroleva IV, Kachar B, Hayashizaki Y, Carninci P, Soares MB, Beisel KW. Differential expression of genes within the cochlea as defined by a custom mouse inner ear microarray. Journal of the Association For Research in Otolaryngology : Jaro. 6: 75-89. PMID 15735932 DOI: 10.1007/S10162-004-5046-X  0.449
2005 Kitagawa N, Washio T, Kosugi S, Yamashita T, Higashi K, Yanagawa H, Higo K, Satoh K, Ohtomo Y, Sunako T, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, et al. Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). Bioinformatics (Oxford, England). 21: 1758-63. PMID 15647298 DOI: 10.1093/Bioinformatics/Bti253  0.463
2005 Caldwell RB, Kierzek AM, Arakawa H, Bezzubov Y, Zaim J, Fiedler P, Kutter S, Blagodatski A, Kostovska D, Koter M, Plachy J, Carninci P, Hayashizaki Y, Buerstedde JM. Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis. Genome Biology. 6: R6. PMID 15642098 DOI: 10.1186/Gb-2004-6-1-R6  0.435
2004 Watahiki A, Waki K, Hayatsu N, Shiraki T, Kondo S, Nakamura M, Sasaki D, Arakawa T, Kawai J, Harbers M, Hayashizaki Y, Carninci P. Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Nature Methods. 1: 233-9. PMID 15782199 DOI: 10.1038/Nmeth719  0.455
2004 Ogihara Y, Mochida K, Kawaura K, Murai K, Seki M, Kamiya A, Shinozaki K, Carninci P, Hayashizaki Y, Shin-I T, Kohara Y, Yamazaki Y. Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags. Genes & Genetic Systems. 79: 227-32. PMID 15514442 DOI: 10.1266/Ggs.79.227  0.433
2004 Suzuki Y, Yamashita R, Shirota M, Sakakibara Y, Chiba J, Mizushima-Sugano J, Kel AE, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Takagi T, Nakai K, Sugano S. Large-scale collection and characterization of promoters of human and mouse genes. In Silico Biology. 4: 429-44. PMID 15506993  0.355
2004 Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, ... ... Carninci P, et al. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Research. 14: 2121-7. PMID 15489334 DOI: 10.1101/Gr.2596504  0.414
2004 Beisel KW, Shiraki T, Morris KA, Pompeia C, Kachar B, Arakawa T, Bono H, Kawai J, Hayashizaki Y, Carninci P. Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library. Genomics. 83: 1012-23. PMID 15177555 DOI: 10.1016/J.Ygeno.2004.01.006  0.346
2004 Lagonigro MS, De Cecco L, Carninci P, Di Stasi D, Ranzani T, Rodolfo M, Gariboldi M. CTAB-urea method purifies RNA from melanin for cDNA microarray analysis. Pigment Cell Research / Sponsored by the European Society For Pigment Cell Research and the International Pigment Cell Society. 17: 312-5. PMID 15140079 DOI: 10.1111/J.1600-0749.2004.00155.X  0.355
2004 Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, ... ... Carninci P, et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. Plos Biology. 2: e162. PMID 15103394 DOI: 10.1371/Journal.Pbio.0020162  0.457
2004 Gustincich S, Contini M, Gariboldi M, Puopolo M, Kadota K, Bono H, LeMieux J, Walsh P, Carninci P, Hayashizaki Y, Okazaki Y, Raviola E. Gene discovery in genetically labeled single dopaminergic neurons of the retina. Proceedings of the National Academy of Sciences of the United States of America. 101: 5069-74. PMID 15047890 DOI: 10.1073/Pnas.0400913101  0.418
2004 Yazaki J, Shimatani Z, Hashimoto A, Nagata Y, Fujii F, Kojima K, Suzuki K, Taya T, Tonouchi M, Nelson C, Nakagawa A, Otomo Y, Murakami K, Matsubara K, Kawai J, ... Carninci P, et al. Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis. Physiological Genomics. 17: 87-100. PMID 14982972 DOI: 10.1152/Physiolgenomics.00201.2003  0.396
2004 Kodzius R, Matsumura Y, Kasukawa T, Shimokawa K, Fukuda S, Shiraki T, Nakamura M, Arakawa T, Sasaki D, Kawai J, Harbers M, Carninci P, Hayashizaki Y. Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags. Febs Letters. 559: 22-6. PMID 14960301 DOI: 10.1016/S0014-5793(04)00018-3  0.424
2003 Yazaki J, Kishimoto N, Nagata Y, Ishikawa M, Fujii F, Hashimoto A, Shimbo K, Shimatani Z, Kojima K, Suzuki K, Yamamoto M, Honda S, Endo A, Yoshida Y, Sato Y, ... ... Carninci P, et al. Genomics approach to abscisic acid- and gibberellin-responsive genes in rice. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 10: 249-61. PMID 15029956 DOI: 10.1093/Dnares/10.6.249  0.413
2003 Ooka H, Satoh K, Doi K, Nagata T, Otomo Y, Murakami K, Matsubara K, Osato N, Kawai J, Carninci P, Hayashizaki Y, Suzuki K, Kojima K, Takahara Y, Yamamoto K, et al. Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 10: 239-47. PMID 15029955 DOI: 10.1093/Dnares/10.6.239  0.4
2003 Osato N, Yamada H, Satoh K, Ooka H, Yamamoto M, Suzuki K, Kawai J, Carninci P, Ohtomo Y, Murakami K, Matsubara K, Kikuchi S, Hayashizaki Y. Antisense transcripts with rice full-length cDNAs. Genome Biology. 5: R5. PMID 14709177 DOI: 10.1186/Gb-2003-5-1-R5  0.49
2003 Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, Kodzius R, Watahiki A, Nakamura M, Arakawa T, Fukuda S, Sasaki D, Podhajska A, Harbers M, Kawai J, ... Carninci P, et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proceedings of the National Academy of Sciences of the United States of America. 100: 15776-81. PMID 14663149 DOI: 10.1073/Pnas.2136655100  0.486
2003 Fujimori S, Washio T, Higo K, Ohtomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Tomita M. A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription. Febs Letters. 554: 17-22. PMID 14596907 DOI: 10.1016/S0014-5793(03)01041-X  0.379
2003 Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, Pham P, Cheuk R, Karlin-Newmann G, Liu SX, Lam B, ... ... Carninci P, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (New York, N.Y.). 302: 842-6. PMID 14593172 DOI: 10.1126/Science.1088305  0.486
2003 Hirozane-Kishikawa T, Shiraki T, Waki K, Nakamura M, Arakawa T, Kawai J, Fagiolini M, Hensch TK, Hayashizaki Y, Carninci P. Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts. Biotechniques. 35: 510-6, 518. PMID 14513556 DOI: 10.2144/03353St04  0.454
2003 Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, Hotta I, Kojima K, Namiki T, ... ... Carninci P, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science (New York, N.Y.). 301: 376-9. PMID 12869764 DOI: 10.1126/Science.1081288  0.387
2003 Gustincich S, Batalov S, Beisel KW, Bono H, Carninci P, Fletcher CF, Grimmond S, Hirokawa N, Jarvis ED, Jegla T, Kawasawa Y, LeMieux J, Miki H, Raviola E, Teasdale RD, et al. Analysis of the mouse transcriptome for genes involved in the function of the nervous system. Genome Research. 13: 1395-401. PMID 12819138 DOI: 10.1101/Gr.1135303  0.368
2003 Wells CA, Ravasi T, Sultana R, Yagi K, Carninci P, Bono H, Faulkner G, Okazaki Y, Quackenbush J, Hume DA, Lyons PA. Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage. Genome Research. 13: 1360-5. PMID 12819134 DOI: 10.1101/Gr.1056103  0.44
2003 Carninci P, Waki K, Shiraki T, Konno H, Shibata K, Itoh M, Aizawa K, Arakawa T, Ishii Y, Sasaki D, Bono H, Kondo S, Sugahara Y, Saito R, Osato N, et al. Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Research. 13: 1273-89. PMID 12819125 DOI: 10.1101/Gr.1119703  0.429
2003 Nishiyama T, Fujita T, Shin-I T, Seki M, Nishide H, Uchiyama I, Kamiya A, Carninci P, Hayashizaki Y, Shinozaki K, Kohara Y, Hasebe M. Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution. Proceedings of the National Academy of Sciences of the United States of America. 100: 8007-12. PMID 12808149 DOI: 10.1073/Pnas.0932694100  0.392
2003 Walsh NC, Cahill M, Carninci P, Kawai J, Okazaki Y, Hayashizaki Y, Hume DA, Cassady AI. Multiple tissue-specific promoters control expression of the murine tartrate-resistant acid phosphatase gene. Gene. 307: 111-23. PMID 12706893 DOI: 10.1016/S0378-1119(03)00449-9  0.461
2002 Yamanaka I, Kiyosawa H, Kondo S, Saito T, Carninci P, Shinagawa A, Aizawa K, Fukuda S, Hara A, Itoh M, Kawai J, Shibata K, Arakawa T, Ishii Y, Hayashizaki Y. Mapping of 19032 mouse cDNAs on mouse chromosomes. Journal of Structural and Functional Genomics. 2: 23-8. PMID 12836671 DOI: 10.1023/A:1013203019444  0.31
2002 Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer CF, Bhat NK, Hopkins RF, ... ... Carninci P, et al. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America. 99: 16899-903. PMID 12477932 DOI: 10.1073/Pnas.242603899  0.416
2002 Sakurai A, Fujimori S, Kochiwa H, Kitamura-Abe S, Washio T, Saito R, Carninci P, Hayashizaki Y, Tomita M. On biased distribution of introns in various eukaryotes. Gene. 300: 89-95. PMID 12468090 DOI: 10.1016/S0378-1119(02)01035-1  0.455
2002 Ozawa Y, Hanaoka S, Saito R, Washio T, Nakano S, Shinagawa A, Itoh M, Shibata K, Carninci P, Konno H, Kawai J, Hayashizaki Y, Tomita M. Comprehensive sequence analysis of translation termination sites in various eukaryotes. Gene. 300: 79-87. PMID 12468089 DOI: 10.1016/S0378-1119(02)01042-9  0.379
2002 Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, ... ... Carninci P, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 420: 563-73. PMID 12466851 DOI: 10.1038/Nature01266  0.491
2002 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Carninci P, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/Nature01262  0.398
2002 Seki M, Ishida J, Narusaka M, Fujita M, Nanjo T, Umezawa T, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Yamaguchi-Shinozaki K, Carninci P, Kawai J, et al. Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray. Functional & Integrative Genomics. 2: 282-91. PMID 12444421 DOI: 10.1007/S10142-002-0070-6  0.421
2002 Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 33: 306-9. PMID 12188181 DOI: 10.2144/02332St01  0.387
2002 Stapleton M, Liao G, Brokstein P, Hong L, Carninci P, Shiraki T, Hayashizaki Y, Champe M, Pacleb J, Wan K, Yu C, Carlson J, George R, Celniker S, Rubin GM. The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes. Genome Research. 12: 1294-300. PMID 12176937 DOI: 10.1101/Gr.269102  0.443
2002 Kochiwa H, Suzuki R, Washio T, Saito R, Bono H, Carninci P, Okazaki Y, Miki R, Hayashizaki Y, Tomita M. Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data. Genome Research. 12: 1286-93. PMID 12176936 DOI: 10.1101/Gr.220302  0.457
2002 Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Taji T, Yamaguchi-Shinozaki K, Carninci P, et al. Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. The Plant Journal : For Cell and Molecular Biology. 31: 279-92. PMID 12164808 DOI: 10.1046/J.1365-313X.2002.01359.X  0.397
2002 Osato N, Itoh M, Konno H, Kondo S, Shibata K, Carninci P, Shiraki T, Shinagawa A, Arakawa T, Kikuchi S, Sato K, Kawai J, Hayashizaki Y. A computer-based method of selecting clones for a full-length cDNA project: simultaneous collection of negligibly redundant and variant cDNAs. Genome Research. 12: 1127-34. PMID 12097351 DOI: 10.1101/Gr.75202  0.37
2002 Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T, Nakajima M, Enju A, Akiyama K, Oono Y, Muramatsu M, Hayashizaki Y, Kawai J, Carninci P, Itoh M, et al. Functional annotation of a full-length Arabidopsis cDNA collection. Science (New York, N.Y.). 296: 141-5. PMID 11910074 DOI: 10.1126/Science.1071006  0.456
2001 Shibata Y, Carninci P, Sato K, Hayatsu N, Shiraki T, Ishii Y, Arakawa T, Hara A, Ohsato N, Izawa M, Aizawa K, Itoh M, Shibata K, Shinagawa A, Kawai J, et al. Removal of polyA tails from full-length cDNA libraries for high-efficiency sequencing. Biotechniques. 31: 1042, 1044, 1048-9. PMID 11730011 DOI: 10.2144/01315St04  0.323
2001 Sakai H, Washio T, Saito R, Shinagawa A, Itoh M, Shibata K, Carninci P, Konno H, Kawai J, Hayashizaki Y, Tomita M. Correlation between sequence conservation of the 5' untranslated region and codon usage bias in Mus musculus genes. Gene. 276: 101-5. PMID 11591476 DOI: 10.1016/S0378-1119(01)00671-0  0.373
2001 Carninci P, Shibata Y, Hayatsu N, Itoh M, Shiraki T, Hirozane T, Watahiki A, Shibata K, Konno H, Muramatsu M, Hayashizaki Y. Balanced-size and long-size cloning of full-length, cap-trapped cDNAs into vectors of the novel lambda-FLC family allows enhanced gene discovery rate and functional analysis. Genomics. 77: 79-90. PMID 11543636 DOI: 10.1006/Geno.2001.6601  0.321
2001 Shibata Y, Carninci P, Watahiki A, Shiraki T, Konno H, Muramatsu M, Hayashizaki Y. Cloning full-length, cap-trapper-selected cDNAs by using the single-strand linker ligation method. Biotechniques. 30: 1250-4. PMID 11414214 DOI: 10.2144/01306St01  0.372
2001 Miki R, Kadota K, Bono H, Mizuno Y, Tomaru Y, Carninci P, Itoh M, Shibata K, Kawai J, Konno H, Watanabe S, Sato K, Tokusumi Y, Kikuchi N, Ishii Y, et al. Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proceedings of the National Academy of Sciences of the United States of America. 98: 2199-204. PMID 11226216 DOI: 10.1073/Pnas.041605498  0.378
2001 Sugahara Y, Carninci P, Itoh M, Shibata K, Konno H, Endo T, Muramatsu M, Hayashizaki Y. Comparative evaluation of 5'-end-sequence quality of clones in CAP trapper and other full-length-cDNA libraries. Gene. 263: 93-102. PMID 11223247 DOI: 10.1016/S0378-1119(00)00557-6  0.388
2001 Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, ... ... Carninci P, et al. Functional annotation of a full-length mouse cDNA collection. Nature. 409: 685-90. PMID 11217851 DOI: 10.1038/35055500  0.436
2001 Seki M, Narusaka M, Abe H, Kasuga M, Yamaguchi-Shinozaki K, Carninci P, Hayashizaki Y, Shinozaki K. Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. The Plant Cell. 13: 61-72. PMID 11158529 DOI: 10.1105/Tpc.13.1.61  0.431
2001 Kawagashira N, Ohtomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Higo K. Multiple Zinc Finger Motifs with Comparison of Plant and Insect Genome Informatics. 12: 368-369. DOI: 10.11234/Gi1990.12.368  0.349
2001 Seki M, Narusaka M, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K. Arabidopsis encyclopedia using full-length cDNAs and its application Plant Physiology and Biochemistry. 39: 211-220. DOI: 10.1016/S0981-9428(01)01244-X  0.447
2001 Hagiwara N, Carninci P, Kozak CA, Brilliant MH. Meeting report: 14th international mouse genome conference Mammalian Genome. 12: 401-405. DOI: 10.1007/S003350040004  0.302
2000 Shibata K, Itoh M, Aizawa K, Nagaoka S, Sasaki N, Carninci P, Konno H, Akiyama J, Nishi K, Kitsunai T, Tashiro H, Itoh M, Sumi N, Ishii Y, Nakamura S, et al. RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer. Genome Research. 10: 1757-71. PMID 11076861 DOI: 10.1101/Gr.152600  0.364
2000 Carninci P, Shibata Y, Hayatsu N, Sugahara Y, Shibata K, Itoh M, Konno H, Okazaki Y, Muramatsu M, Hayashizaki Y. Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Research. 10: 1617-30. PMID 11042159 DOI: 10.1101/Gr.145100  0.428
2000 Konno H, Fukunishi Y, Carninci P, Hayashizaki Y. Assessment of Redundancy and Full-Length Rate of Full-Length Enriched cDNA Libraries Genome Informatics. 11: 372-373. DOI: 10.11234/Gi1990.11.372  0.392
2000 Sakai H, Ohkuma Y, Imamura C, Shinagawa A, Itoh M, Shibata K, Carninci P, Konno H, Kawai J, Fukunishi Y, Hayashizaki Y, Tomita M. Correlation between Sequence Conservation of 5' UTR and Codon Usage Bias Genome Informatics. 11: 313-314. DOI: 10.11234/Gi1990.11.313  0.321
1999 Carninci P, Hayashizaki Y. High-efficiency full-length cDNA cloning. Methods in Enzymology. 303: 19-44. PMID 10349636 DOI: 10.1016/S0076-6879(99)03004-9  0.337
1999 Mizuno Y, Carninci P, Okazaki Y, Tateno M, Kawai J, Amanuma H, Muramatsu M, Hayashizaki Y. Increased specificity of reverse transcription priming by trehalose and oligo-blockers allows high-efficiency window separation of mRNA display. Nucleic Acids Research. 27: 1345-9. PMID 9973624 DOI: 10.1093/Nar/27.5.1345  0.396
1999 Okazaki Y, Miki R, Mizuno Y, Tomaru Y, Kadota K, Carninci P, Shibata K, Itoh M, Ozawa Y, Kawai J, Konno H, Fukunishi Y, Kusumi T, Goto H, Nitanda H, et al. Gene expression profiling using a mouse full-length 20 K cDNA microarray Nature Genetics. 23: 66-67. DOI: 10.1038/14379  0.438
1998 Seki M, Carninci P, Nishiyama Y, Hayashizaki Y, Shinozaki K. High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper. The Plant Journal : For Cell and Molecular Biology. 15: 707-20. PMID 9778851 DOI: 10.1046/J.1365-313X.1998.00237.X  0.389
1998 Sasaki N, Nagaoka S, Itoh M, Izawa M, Konno H, Carninci P, Yoshiki A, Kusakabe M, Moriuchi T, Muramatsu M, Okazaki Y, Hayashizaki Y. Characterization of gene expression in mouse blastocyst using single-pass sequencing of 3995 clones. Genomics. 49: 167-79. PMID 9598303 DOI: 10.1006/Geno.1998.5209  0.439
1998 Sasaki N, Izawa M, Watahiki M, Ozawa K, Tanaka T, Yoneda Y, Matsuura S, Carninci P, Muramatsu M, Okazaki Y, Hayashizaki Y. Transcriptional sequencing: A method for DNA sequencing using RNA polymerase. Proceedings of the National Academy of Sciences of the United States of America. 95: 3455-60. PMID 9520387 DOI: 10.1073/Pnas.95.7.3455  0.391
1997 Carninci P, Westover A, Nishiyama Y, Ohsumi T, Itoh M, Nagaoka S, Sasaki N, Okazaki Y, Muramatsu M, Schneider C, Hayashizaki Y. High efficiency selection of full-length cDNA by improved biotinylated cap trapper. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 4: 61-6. PMID 9179497 DOI: 10.1093/Dnares/4.1.61  0.329
1996 Carninci P, Kvam C, Kitamura A, Ohsumi T, Okazaki Y, Itoh M, Kamiya M, Shibata K, Sasaki N, Izawa M, Muramatsu M, Hayashizaki Y, Schneider C. High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics. 37: 327-36. PMID 8938445 DOI: 10.1006/Geno.1996.0567  0.318
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