| Year |
Citation |
Score |
| 2024 |
Haberman N, Digby H, Faraway R, Cheung R, Chakrabarti AM, Jobbins AM, Parr C, Yasuzawa K, Kasukawa T, Yip CW, Kato M, Takahashi H, Carninci P, Vernia S, Ule J, et al. Widespread 3'UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites. Bmc Biology. 22: 254. PMID 39511645 DOI: 10.1186/s12915-024-02032-7 |
0.317 |
|
| 2024 |
Oguchi A, Suzuki A, Komatsu S, Yoshitomi H, Bhagat S, Son R, Bonnal RJP, Kojima S, Koido M, Takeuchi K, Myouzen K, Inoue G, Hirai T, Sano H, Takegami Y, ... ... Carninci P, et al. An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases. Science (New York, N.Y.). 385: eadd8394. PMID 38963856 DOI: 10.1126/science.add8394 |
0.3 |
|
| 2024 |
Carbonell-Sala S, Perteghella T, 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 sequencing. Nature Communications. 15: 5278. PMID 38937428 DOI: 10.1038/s41467-024-49523-3 |
0.341 |
|
| 2024 |
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 Martinez JM, Hunt T, Lagarde J, Liang CE, ... ... Carninci P, et al. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature Methods. PMID 38849569 DOI: 10.1038/s41592-024-02298-3 |
0.369 |
|
| 2024 |
Agrawal S, Buyan A, Severin J, Koido M, Alam T, Abugessaisa I, Chang HY, Dostie J, Itoh M, Kere J, Kondo N, Li Y, Makeev VJ, Mendez M, Okazaki Y, ... ... Carninci P, et al. Annotation of nuclear lncRNAs based on chromatin interactions. Plos One. 19: e0295971. PMID 38709794 DOI: 10.1371/journal.pone.0295971 |
0.314 |
|
| 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 |
0.356 |
|
| 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 |
0.45 |
|
| 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 |
0.357 |
|
| 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 |
0.472 |
|
| 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 |
0.445 |
|
| 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 |
0.388 |
|
| 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 |
0.424 |
|
| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.426 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.723 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.398 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 2014 |
Carninci P. Genomics: mice in the ENCODE spotlight. Nature. 515: 346-7. PMID 25409821 DOI: 10.1038/515346A |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.437 |
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| 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 |
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| 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 |
0.474 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.422 |
|
| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.435 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.437 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.486 |
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| 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 |
0.414 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.388 |
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| 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 |
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| 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 |
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| 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 |
0.493 |
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| 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 |
0.474 |
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| 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 |
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| 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 |
0.431 |
|
| 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 |
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| 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 |
0.436 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.434 |
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| 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 |
0.454 |
|
| 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 |
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| 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 |
0.354 |
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| 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 |
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| 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 |
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| 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 |
0.356 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.399 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.46 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.455 |
|
| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.446 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.336 |
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| 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 |
0.395 |
|
| 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 |
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| 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 |
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| 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 |
0.438 |
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| 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 |
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| 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 |
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| 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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