Piero Carninci - Publications

Affiliations: 
RIKEN Omics, Yokohama-shi, Kanagawa-ken, Japan 
Area:
genomics, RACE, EST

218 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.32
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  0.56
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  0.32
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  0.32
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  0.32
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  0.32
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2015 Tebbi A, Levillayer F, Jouvion G, Fiette L, Soubigou G, Varet H, Boudjadja N, Cairo S, Hashimoto K, Suzuki AM, Carninci P, Carissimo A, di Bernado D, Wei Y. Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress. Carcinogenesis. PMID 26542370 DOI: 10.1093/carcin/bgv156  0.56
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  0.56
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  0.56
2015 Konno D, Kasukawa T, Hashimoto K, Itoh T, Suetsugu T, Miura I, Wakana S, Carninci P, Matsuzaki F. STAP cells are derived from ES cells. Nature. 525: E4-5. PMID 26399834 DOI: 10.1038/nature15366  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2015 Ramilowski JA, Goldberg T, Harshbarger J, Kloppman E, Lizio M, Satagopam VP, Itoh M, Kawaji H, Carninci P, Rost B, Forrest AR. A draft network of ligand-receptor-mediated multicellular signalling in human. Nature Communications. 6: 7866. PMID 26198319 DOI: 10.1038/ncomms8866  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2015 Schein A, Carninci P. Complexity of mammalian transcriptome analyzed by RNA deep sequencing Long Noncoding Rnas Structures and Functions. 3-22. DOI: 10.1007/978-4-431-55576-6_1  0.56
2015 Bolhuis J, Botelho R, Caetano-Anolles G, Carninci P, Cheah K, Dagan T, Frye M, Goodson H, Gough J, Groth A, Huang S, Isalan M, Kaeberlein M, López-García P, Pei D, et al. In grateful recognition of our Editorial Board Bioessays. 37: 1254-1255. DOI: 10.1002/bies.201570126  0.56
2014 Vitezic M, Bertin N, Andersson R, Lipovich L, Kawaji H, Lassmann T, Sandelin A, Heutink P, Goldowitz D, Ha T, Zhang P, Patrizi A, Fagiolini M, Forrest AR, Carninci P, et al. CAGE-defined promoter regions of the genes implicated in Rett Syndrome. Bmc Genomics. 15: 1177. PMID 25539566 DOI: 10.1186/1471-2164-15-1177  0.56
2014 Carninci P. Genomics: mice in the ENCODE spotlight. Nature. 515: 346-7. PMID 25409821 DOI: 10.1038/515346a  0.56
2014 Kratz A, Carninci P. The devil in the details of RNA-seq. Nature Biotechnology. 32: 882-4. PMID 25203036 DOI: 10.1038/nbt.3015  0.56
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  0.56
2014 Grison A, Zucchelli S, Urzì A, Zamparo I, Lazarevic D, Pascarella G, Roncaglia P, Giorgetti A, Garcia-Esparcia P, Vlachouli C, Simone R, Persichetti F, Forrest AR, Hayashizaki Y, Carloni P, ... ... Carninci P, et al. Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules. Bmc Genomics. 15: 729. PMID 25164183 DOI: 10.1186/1471-2164-15-729  0.56
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  0.56
2014 Verardo R, Piazza S, Klaric E, Ciani Y, Bussadori G, Marzinotto S, Mariuzzi L, Cesselli D, Beltrami AP, Mano M, Itoh M, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, et al. Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer. Stem Cells (Dayton, Ohio). 32: 2998-3011. PMID 25069783 DOI: 10.1002/stem.1791  0.56
2014 Boele J, Persson H, Shin JW, Ishizu Y, Newie IS, Søkilde R, Hawkins SM, Coarfa C, Ikeda K, Takayama K, Horie-Inoue K, Ando Y, Burroughs AM, Sasaki C, Suzuki C, ... ... Carninci P, et al. PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease. Proceedings of the National Academy of Sciences of the United States of America. 111: 11467-72. PMID 25049417 DOI: 10.1073/pnas.1317751111  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2013 Shukla R, Upton KR, Muñoz-Lopez M, Gerhardt DJ, Fisher ME, Nguyen T, Brennan PM, Baillie JK, Collino A, Ghisletti S, Sinha S, Iannelli F, Radaelli E, Dos Santos A, Rapoud D, ... ... Carninci P, et al. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell. 153: 101-11. PMID 23540693 DOI: 10.1016/j.cell.2013.02.032  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2012 Durand S, Patrizi A, Quast KB, Hachigian L, Pavlyuk R, Saxena A, Carninci P, Hensch TK, Fagiolini M. NMDA receptor regulation prevents regression of visual cortical function in the absence of Mecp2. Neuron. 76: 1078-90. PMID 23259945 DOI: 10.1016/j.neuron.2012.12.004  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2012 Saxena A, Wagatsuma A, Noro Y, Kuji T, Asaka-Oba A, Watahiki A, Gurnot C, Fagiolini M, Hensch TK, Carninci P. Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain. Biotechniques. 52: 381-5. PMID 22668417 DOI: 10.2144/0000113878  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2012 Bertin N, Plessy C, Carninci P, Harbers M. Definition of Promotome-Transcriptome Architecture Using CAGEscan Tag-Based Next Generation Sequencing. 47-61. DOI: 10.1002/9783527644582.ch3  0.56
2012 Harbers M, Dushay MS, Carninci P. DeepCAGE: Genome-Wide Mapping of Transcription Start Sites Tag-Based Next Generation Sequencing. 23-46. DOI: 10.1002/9783527644582.ch2  0.56
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  0.56
2011 Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan PM, Rizzu P, Smith S, Fell M, Talbot RT, Gustincich S, Freeman TC, Mattick JS, Hume DA, ... ... Carninci P, et al. Somatic retrotransposition alters the genetic landscape of the human brain. Nature. 479: 534-7. PMID 22037309 DOI: 10.1038/nature10531  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2011 Caiazzo M, Dell'Anno MT, Dvoretskova E, Lazarevic D, Taverna S, Leo D, Sotnikova TD, Menegon A, Roncaglia P, Colciago G, Russo G, Carninci P, Pezzoli G, Gainetdinov RR, Gustincich S, et al. Direct generation of functional dopaminergic neurons from mouse and human fibroblasts. Nature. 476: 224-7. PMID 21725324 DOI: 10.1038/nature10284  0.56
2011 Shindo Y, Morishita K, Kotake E, Miura H, Carninci P, Kawai J, Hayashizaki Y, Hino A, Kanda T, Kusakabe Y. FXYD6, a Na,K-ATPase regulator, is expressed in type II taste cells. Bioscience, Biotechnology, and Biochemistry. 75: 1061-6. PMID 21670532 DOI: 10.1271/bbb.100718  0.56
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  0.56
2011 . A user's guide to the encyclopedia of DNA elements (ENCODE). Plos Biology. 9: e1001046. PMID 21526222 DOI: 10.1371/journal.pbio.1001046  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2010 Kratz A, Arner E, Saito R, Kubosaki A, Kawai J, Suzuki H, Carninci P, Arakawa T, Tomita M, Hayashizaki Y, Daub CO. Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns. Bmc Genomics. 11: 257. PMID 20409305 DOI: 10.1186/1471-2164-11-257  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2009 Salimullah M, Kato S, Murata M, Kawazu C, Plessy C, Carninci P. Tunable fractionation of nucleic acids. Biotechniques. 47: 1041-3. PMID 20041857 DOI: 10.2144/000113249  0.56
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  0.56
2009 Forrest AR, Carninci P. Whole genome transcriptome analysis. Rna Biology. 6: 107-12. PMID 19875928 DOI: 10.4161/rna.6.2.7931  0.56
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  0.56
2009 Faulkner GJ, Carninci P. Altruistic functions for selfish DNA. Cell Cycle (Georgetown, Tex.). 8: 2895-900. PMID 19736519  0.56
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  0.56
2009 Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen E. Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biology. 10: R79. PMID 19624849 DOI: 10.1186/gb-2009-10-7-r79  0.56
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  0.56
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  0.56
2009 Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest AR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A, Hayashida K, ... ... Carninci P, et al. Tiny RNAs associated with transcription start sites in animals. Nature Genetics. 41: 572-8. PMID 19377478 DOI: 10.1038/ng.312  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2009 Carninci P. Molecular biology: The long and short of RNAs. Nature. 457: 974-5. PMID 19225515 DOI: 10.1038/457974b  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2008 Shindo Y, Miura H, Carninci P, Kawai J, Hayashizaki Y, Ninomiya Y, Hino A, Kanda T, Kusakabe Y. G alpha14 is a candidate mediator of sweet/umami signal transduction in the posterior region of the mouse tongue. Biochemical and Biophysical Research Communications. 376: 504-8. PMID 18801333 DOI: 10.1016/j.bbrc.2008.09.035  0.56
2008 Carninci P. Non-coding RNA transcription: turning on neighbours. Nature Cell Biology. 10: 1023-4. PMID 18758492 DOI: 10.1038/ncb0908-1023  0.56
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  0.56
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  0.56
2008 Carninci P. Hunting hidden transcripts. Nature Methods. 5: 587-9. PMID 18587315 DOI: 10.1038/nmeth0708-587  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2008 Harbers M, Werner T, Carninci P. From CAGE to DeepCAGE: High-Throughput Transcription Start Site and Promoter Identification for Gene Network Analysis The Handbook of Plant Functional Genomics: Concepts and Protocols. 55-75. DOI: 10.1002/9783527622542.ch4  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2006 . Insights into social insects from the genome of the honeybee Apis mellifera. Nature. 443: 931-49. PMID 17073008 DOI: 10.1038/nature05260  0.56
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  0.56
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  0.56
2006 Itoh M, Yasunishi A, Imamura K, Kanamori-Katayama M, Suzuki H, Suzuki M, Carninci P, Kawai J, Hayashizaki Y. Constructing ORFeome resources with removable termination codons. Biotechniques. 41: 44, 46, 48 passim. PMID 16869512 DOI: 10.2144/000112209  0.56
2006 Carninci P. Tagging mammalian transcription complexity. Trends in Genetics : Tig. 22: 501-10. PMID 16859803 DOI: 10.1016/j.tig.2006.07.003  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2006 Frith MC, Forrest AR, Nourbakhsh E, Pang KC, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bailey TL, Grimmond SM. The abundance of short proteins in the mammalian proteome. Plos Genetics. 2: e52. PMID 16683031 DOI: 10.1371/journal.pgen.0020052  0.56
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  0.56
2006 Davis MJ, Hanson KA, Clark F, Fink JL, Zhang F, Kasukawa T, Kai C, Kawai J, Carninci P, Hayashizaki Y, Teasdale RD. Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units. Plos Genetics. 2: e46. PMID 16683029 DOI: 10.1371/journal.pgen.0020046  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2006 Aturaliya RN, Fink JL, Davis MJ, Teasdale MS, Hanson KA, Miranda KC, Forrest AR, Grimmond SM, Suzuki H, Kanamori M, Kai C, Kawai J, Carninci P, Hayashizaki Y, Teasdale RD. Subcellular localization of mammalian type II membrane proteins. Traffic (Copenhagen, Denmark). 7: 613-25. PMID 16643283 DOI: 10.1111/j.1600-0854.2006.00407.x  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2006 Carninci P, Gough J, Kasukawa T, Hayashizaki Y. Response [2] Science. 311: 1709-1711.  0.56
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  0.56
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  0.56
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  0.56
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  0.52
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2004 Nagashima T, Matsuda H, Silva DG, Petrovsky N, Konagaya A, Schönbach C, Kasukawa T, Arakawa T, Carninci P, Kawai J, Hayashizaki Y. FREP: a database of functional repeats in mouse cDNAs. Nucleic Acids Research. 32: D471-5. PMID 14681460 DOI: 10.1093/nar/gkh123  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2002 Jarvis ED, Smith VA, Wada K, Rivas MV, McElroy M, Smulders TV, Carninci P, Hayashizaki Y, Dietrich F, Wu X, McConnell P, Yu J, Wang PP, Hartemink AJ, Lin S. A framework for integrating the songbird brain. Journal of Comparative Physiology. a, Neuroethology, Sensory, Neural, and Behavioral Physiology. 188: 961-80. PMID 12471494 DOI: 10.1007/s00359-002-0358-y  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2002 Buerstedde JM, Arakawa H, Watahiki A, Carninci PP, Hayashizaki YY, Korn B, Plachy J. The DT40 web site: sampling and connecting the genes of a B cell line. Nucleic Acids Research. 30: 230-1. PMID 11752301  0.52
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  0.52
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  0.52
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  0.56
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  0.56
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