Piero Carninci

All Stories

1. 
   The commitment of the human cell atlas to humanity

   Article • Nature Communications, November 2024, Springer Science + Business Media

   Piero Carninci

2. 
   Challenges in Detecting Somatic Recombination of Repeat Elements: Insights from Short and Long Read Datasets

   Article • August 2024, Cold Spring Harbor Laboratory Press

   Piero Carninci

3. 
   CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing

   Article • Nature Communications, June 2024, Springer Science + Business Media

   Piero Carninci

4. 
   RADIP technology comprehensively identifies H3K27me3-mediated RNA-chromatin interactions

   Article • June 2024, Cold Spring Harbor Laboratory Press

   Piero Carninci

5. 
   Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation

   Article • Nature Communications, February 2024, Springer Science + Business Media

   Piero Carninci

6. 
   CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing

   Article • June 2023, Cold Spring Harbor Laboratory Press

   Piero Carninci

7. 
   Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA–mediated post-transcriptional gene regulation

   Article • May 2023, Cold Spring Harbor Laboratory Press

   Piero Carninci

8. 
   A new layer of complexity in the human genome: Somatic recombination of repeat elements

   Article • Clinical and Translational Medicine, March 2023, Wiley

   Piero Carninci

9. 
   Long non-coding RNAs: definitions, functions, challenges and recommendations

   Article • Nature Reviews Molecular Cell Biology, January 2023, Springer Science + Business Media

   Piero Carninci

10. 
    SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells

    Article • Bioinformatics, September 2022, Oxford University Press (OUP)

    Piero Carninci

11. 
    Distinctive exercise-induced inflammatory response and exerkine induction in skeletal muscle of people with type 2 diabetes

    Article • Science Advances, September 2022, American Association for the Advancement of Science

    Piero Carninci

12. 
    Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

    Article • Nature Genetics, July 2022, Springer Science + Business Media

    Piero Carninci

13. 
    Lessons from the functional characterization of lncRNAs: introduction to mammalian genome special issue

    Article • Mammalian Genome, May 2022, Springer Science + Business Media

    Piero Carninci

14. 
    Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

    Article • Nature Communications, March 2022, Springer Science + Business Media

    Piero Carninci

15. 
    Towards SINEUP-based therapeutics: design of an in vitro synthesized SINEUP RNA

    Article • Molecular Therapy — Nucleic Acids, February 2022, Elsevier

    Piero Carninci

16. 
    Inducing human retinal pigment epithelium-like cells from somatic tissue

    Article • Stem Cell Reports, February 2022, Elsevier

    Piero Carninci

17. 
    Japan: prize diversity, not conformity, to boost research

    Article • Nature, November 2021, Springer Science + Business Media

    Piero Carninci

18. 
    Embryonic LTR retrotransposons supply promoter modules to somatic tissues

    Article • Genome Research, October 2021, Cold Spring Harbor Laboratory Press

    Piero Carninci

19. 
    A field guide to cultivating computational biology

    Article • PLoS Biology, October 2021, PLOS

    Piero Carninci, Dr Anne Carpenter

20. 
    SINEUPs: a novel toolbox for RNA therapeutics

    Article • Essays in Biochemistry, October 2021, Portland Press Ltd.

    Piero Carninci

21. 
    The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background

    Article • BMC Genomic Data, September 2021, Springer Science + Business Media

    Piero Carninci

22. 
    Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

    Article • Nature Communications, June 2021, Springer Science + Business Media

    Piero Carninci

23. 
    Author Correction: RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions

    Article • Nature Communications, May 2021, Springer Science + Business Media

    Piero Carninci

24. 
    Antisense RNAs during early vertebrate development are divided in groups with distinct features

    Article • Genome Research, April 2021, Cold Spring Harbor Laboratory Press

    Piero Carninci

25. 
    Decoding Neuronal Diversification by Multiplexed Single-cell RNA-Seq

    Article • Stem Cell Reports, April 2021, Elsevier

    Piero Carninci

26. 
    LETR1 is a lymphatic endothelial-specific lncRNA governing cell proliferation and migration through KLF4 and SEMA3C

    Article • Nature Communications, February 2021, Springer Science + Business Media

    Piero Carninci

27. 
    FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs

    Article • Nucleic Acids Research, November 2020, Oxford University Press (OUP)

    Piero Carninci

28. 
    Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene

    Article • BMC Genomics, November 2020, Springer Science + Business Media

    Piero Carninci

29. 
    SINEUP long non-coding RNA acts via PTBP1 and HNRNPK to promote translational initiation assemblies

    Article • Nucleic Acids Research, November 2020, Oxford University Press (OUP)

    Piero Carninci

30. 
    Use of Cap Analysis Gene Expression to detect human papillomavirus promoter activity patterns at different disease stages

    Article • Scientific Reports, October 2020, Springer Science + Business Media

    Piero Carninci

31. 
    Synthetic in vitro transcribed lncRNAs (SINEUPs) with chemical modifications enhance target mRNA translation

    Article • FEBS Letters, October 2020, Wiley

    Piero Carninci

32. 
    Safety and efficacy of the Russian COVID-19 vaccine: more information needed

    Article • The Lancet, October 2020, Elsevier

    Piero Carninci

33. 
    Single-cell transcriptomics, scRNA-Seq and C1 CAGE discovered distinct phases of pluripotency during naïve-to-primed conversion in mice

    Article • September 2020, Cold Spring Harbor Laboratory Press

    Piero Carninci

34. 
    Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping

    Article • Genome Research, September 2020, Cold Spring Harbor Laboratory Press

    Piero Carninci

35. 
    Low Quantity single strand CAGE (LQ-ssCAGE) maps regulatory enhancers and promoters

    Article • August 2020, Cold Spring Harbor Laboratory Press

    Piero Carninci

36. 
    Expanded ENCODE delivers invaluable genomic encyclopedia

    Article • Nature, July 2020, Springer Science + Business Media

    Piero Carninci

37. 
    An NMR-based approach reveals the core structure of the functional domain of SINEUP lncRNAs

    Article • Nucleic Acids Research, July 2020, Oxford University Press (OUP)

    Piero Carninci

38. 
    Comparative transcriptomics of primary cells in vertebrates

    Article • Genome Research, July 2020, Cold Spring Harbor Laboratory Press

    Piero Carninci

39. 
    Functional annotation of human long noncoding RNAs via molecular phenotyping

    Article • Genome Research, July 2020, Cold Spring Harbor Laboratory Press

    Piero Carninci

40. 
    Genome-Wide Technologies to Study RNA–Chromatin Interactions

    Article • Non-Coding RNA, May 2020, MDPI AG

    Piero Carninci

41. 
    The Secret Life of lncRNAs: Conserved, yet Not Conserved

    Article • Cell, April 2020, Elsevier

    Piero Carninci

42. 
    Comprehensive Characterization of Transcriptional Activity during Influenza A Virus Infection Reveals Biases in Cap-Snatching of Host RNA Sequences

    Article • Journal of Virology, March 2020, ASM Journals

    Piero Carninci

43. 
    RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions

    Article • Nature Communications, February 2020, Springer Science + Business Media

    Piero Carninci

44. 
    Recounting the FANTOM CAGE-Associated Transcriptome

    Article • Genome Research, February 2020, Cold Spring Harbor Laboratory Press

    Piero Carninci

45. 
    Antisense ncRNAs during early vertebrate development are divided in groups with distinct features

    Article • February 2020, Cold Spring Harbor Laboratory Press

    Piero Carninci

46. 
    Machine-driven parameter screen of biochemical reactions

    Article • Nucleic Acids Research, February 2020, Oxford University Press (OUP)

    Piero Carninci

47. 
    SINEUP Non-coding RNA Targeting GDNF Rescues Motor Deficits and Neurodegeneration in a Mouse Model of Parkinson’s Disease

    Article • Molecular Therapy, February 2020, Elsevier

    Piero Carninci

48. 
    A human minisatellite hosts an alternative transcription start site for NPRL3 driving its expression in a repeat number‐dependent manner

    Article • Human Mutation, January 2020, Wiley

    Piero Carninci

49. 
    Low Quantity single strand CAGE protocol v1

    Article • January 2020, ZappyLab, Inc.

    Piero Carninci

50. 
    Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing

    Article • Nature Communications, January 2020, Springer Science + Business Media

    Piero Carninci

51. 
    Cap Analysis of Gene Expression (CAGE): A Quantitative and Genome-Wide Assay of Transcription Start Sites

    Article • January 2020, Springer Science + Business Media

    Piero Carninci

52. 
    Corrigendum: Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development

    Article • Genome Research, January 2020, Cold Spring Harbor Laboratory Press

    Piero Carninci

53. 
    Look for methods, not conclusions

    Article • Cell Death and Disease, December 2019, Springer Science + Business Media

    Piero Carninci, Professor Pellegrino Conte, Professor Roberto Bassi

54. 
    The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs

    Article • The FASEB Journal, December 2019, Wiley

    Piero Carninci

55. 
    Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians

    Article • Proceedings of the National Academy of Sciences, November 2019, Proceedings of the National Academy of Sciences

    Piero Carninci

56. 
    Nuclear AGO1 Regulates Gene Expression by Affecting Chromatin Architecture in Human Cells

    Article • Cell Systems, November 2019, Elsevier

    Piero Carninci

57. 
    SINEUP non-coding RNAs rescue defective frataxin expression and activity in a cellular model of Friedreich's Ataxia

    Article • Nucleic Acids Research, October 2019, Oxford University Press (OUP)

    Piero Carninci

58. 
    Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation

    Article • Developmental Cell, October 2019, Elsevier

    Piero Carninci

59. 
    MicroRNA-27a/b-3p and PPARG regulate SCAMP3 through a feed-forward loop during adipogenesis

    Article • Scientific Reports, September 2019, Springer Science + Business Media

    Piero Carninci

60. 
    Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis

    Article • BMC Genomics, September 2019, Springer Science + Business Media

    Piero Carninci

61. 
    NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements

    Article • Nature Genetics, September 2019, Springer Science + Business Media

    Piero Carninci, Osamu Takeuchi

62. 
    Machine-driven parameter optimisation of biochemical reactions

    Article • August 2019, Cold Spring Harbor Laboratory Press

    Piero Carninci

63. 
    Meeting report: The Human Genome Meeting (HGM) 2019 in Seoul, Korea

    Article • European Journal of Human Genetics, August 2019, Springer Science + Business Media

    Piero Carninci

64. 
    SINEUP long non-coding RNA acts via PTBP1 and HNRNPK to promote translational initiation assemblies

    Article • June 2019, Cold Spring Harbor Laboratory Press

    Piero Carninci

65. 
    refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites

    Article • Journal of Molecular Biology, June 2019, Elsevier

    Piero Carninci

66. 
    Multi-year whole-blood transcriptome data for the study of onset and progression of Parkinson’s Disease

    Article • Scientific Data, April 2019, Springer Science + Business Media

    Piero Carninci

67. 
    Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development

    Article • Genome Research, February 2019, Cold Spring Harbor Laboratory Press

    Piero Carninci

68. 
    Cell Based Assays of SINEUP Non-coding RNAs That Can Specifically Enhance mRNA Translation

    Article • Journal of Visualized Experiments, February 2019, MyJove Corporation

    Piero Carninci

69. 
    C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

    Article • Nature Communications, January 2019, Springer Science + Business Media

    Piero Carninci

70. 
    AGO1 in association with NEAT1 lncRNA contributes to nuclear and 3D chromatin architecture in human cells: Supplemental Data

    Article • January 2019, Cold Spring Harbor Laboratory Press

    Piero Carninci

71. 
    Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases

    Article • Molecular Neurobiology, January 2019, Springer Science + Business Media

    Piero Carninci

72. 
    Large expert-curated database for benchmarking document

    Article • Database, January 2019, Oxford University Press (OUP)

    Dr Daniel Prieto, Associate Professor James A.L. Brown, Professor Amanda G Thrift, Docent Kutty Selva Nandakumar, Professor Miguel Viveiros, MD Diego A. Valera-Cornejo, Dr Soroush Safaei, Dr Carmen San Martín, Piero Carninci, Dr Florian Rehfeldt, Dr Yoichi Watanabe, Kazuki Ide, Mr Alvin Wong, PD Dr. Adrian Meule, Dr Maurizio Petrelli, Dr Christine McGarrigle, Dr Tristan Reddan, Dr Nicola Roberts, Professor Stefan Lorkowski, Dr Cyrille Goarant, Dr Emma C Hobbs, Dr. Saurab Sharma, Ph.D., Dr Farid Rahimi, Prof. Iseult Lynch, Mirella Walker, Dr Luca Galluzzi, Sophie Ohlsson, Professor Tullio Florio, Dr Rabea A Gadelkareem, Dr Azubuike Christian Ukubuiwe, Prof Gajendra PS Raghava, Prof Jun Shen, Lubna Razak, ABHISHEKA BANSAL

73. 
    Dynamics Of Cardiomyocyte Transcriptome And Chromatin Landscape Demarcates Key Events Of Heart Development

    Article • December 2018, Cold Spring Harbor Laboratory Press

    Piero Carninci

74. 
    Intertwined canonical and non-canonical initiation in dual promoters are pervasive and differentially regulate Polymerase II transcription

    Article • December 2018, Cold Spring Harbor Laboratory Press

    Piero Carninci

75. 
    Author Correction: Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

    Article • Scientific Data, December 2018, Springer Science + Business Media

    Piero Carninci

76. 
    Amphioxus functional genomics and the origins of vertebrate gene regulation

    Article • Nature, November 2018, Springer Science + Business Media

    Piero Carninci, Dr Michael Schubert

77. 
    Integration of genetics and miRNA–target gene network identified disease biology implicated in tissue specificity

    Article • Nucleic Acids Research, November 2018, Oxford University Press (OUP)

    Piero Carninci

78. 
    Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

    Article • Nucleic Acids Research, November 2018, Oxford University Press (OUP)

    Piero Carninci

79. 
    SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA

    Article • Genome Research, November 2018, Cold Spring Harbor Laboratory Press

    Piero Carninci

80. 
    Promoter Usage and Dynamics in Vascular Smooth Muscle Cells Exposed to Fibroblast Growth Factor-2 or Interleukin-1β

    Article • Scientific Reports, September 2018, Springer Science + Business Media

    Piero Carninci

81. 
    Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli

    Article • Open Biology, August 2018, Royal Society Publishing

    Piero Carninci

82. 
    SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA

    Article • July 2018, Cold Spring Harbor Laboratory Press

    Piero Carninci

83. 
    C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

    Article • May 2018, Cold Spring Harbor Laboratory Press

    Piero Carninci

84. 
    Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages

    Article • Scientific Reports, April 2018, Springer Science + Business Media

    Piero Carninci

85. 
    Prevention of hepatocellular carcinoma by targeting MYCN-positive liver cancer stem cells with acyclic retinoid

    Article • Proceedings of the National Academy of Sciences, April 2018, Proceedings of the National Academy of Sciences

    Piero Carninci

86. 
    From “Cellular” RNA to “Smart” RNA: Multiple Roles of RNA in Genome Stability and Beyond

    Article • Chemical Reviews, March 2018, American Chemical Society (ACS)

    Piero Carninci

87. 
    Target-enrichment sequencing for detailed characterization of small RNAs

    Article • Nature Protocols, March 2018, Springer Science + Business Media

    Piero Carninci

88. 
    Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease

    Article • PLoS Computational Biology, March 2018, PLOS

    Piero Carninci

89. 
    Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1

    Article • Scientific Reports, February 2018, Springer Science + Business Media

    Piero Carninci

90. 
    Identification of functional features of synthetic SINEUPs, antisense lncRNAs that specifically enhance protein translation

    Article • PLoS ONE, February 2018, PLOS

    Piero Carninci

91. 
    Correction to: Relatively frequent switching of transcription start sites during cerebellar development

    Article • BMC Genomics, January 2018, Springer Science + Business Media

    Piero Carninci

92. 
    Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection

    Article • The Cerebellum, January 2018, Springer Science + Business Media

    Piero Carninci

93. 
    The Human Cell Atlas

    Article • eLife, December 2017, eLife

    Professor Fiona M Watt, Piero Carninci

94. 
    Monitoring transcription initiation activities in rat and dog

    Article • Scientific Data, November 2017, Springer Science + Business Media

    Piero Carninci

95. 
    The effect of genetic variation on promoter usage and enhancer activity

    Article • Nature Communications, November 2017, Nature

    Piero Carninci

96. 
    Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

    Article • Scientific Data, October 2017, Nature

    Piero Carninci

97. 
    The Human Cell Atlas: Technical approaches and challenges

    Article • Briefings in Functional Genomics, October 2017, Oxford University Press (OUP)

    Piero Carninci

98. 
    SCPortalen: human and mouse single-cell centric database

    Article • Nucleic Acids Research, October 2017, Oxford University Press (OUP)

    Piero Carninci

99. 
    Linking FANTOM5 CAGE peaks to annotations with CAGEscan

    Article • Scientific Data, October 2017, Nature

    Piero Carninci

100. 
     Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes

     Article • EBioMedicine, October 2017, Elsevier

     Piero Carninci

101. 
     Systematic analysis of transcription start sites in avian development

     Article • PLoS Biology, September 2017, PLOS

     Piero Carninci

102. 
     FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies

     Article • Scientific Data, August 2017, Nature

     Piero Carninci

103. 
     FANTOM5 CAGE profiles of human and mouse samples

     Article • Scientific Data, August 2017, Nature

     Piero Carninci

104. 
     The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types

     Article • Scientific Data, August 2017, Nature

     Piero Carninci

105. 
     An integrated expression atlas of miRNAs and their promoters in human and mouse

     Article • Nature Biotechnology, August 2017, Nature

     Piero Carninci

106. 
     Integrative CAGE and DNA Methylation Profiling Identify Epigenetically Regulated Genes in NSCLC

     Article • Molecular Cancer Research, July 2017, American Association for Cancer Research (AACR)

     Piero Carninci

107. 
     Genomics dissection of the zebrafish heart

     Article • Mechanisms of Development, July 2017, Elsevier

     Piero Carninci

108. 
     From bench to bedside: The long journey of long non-coding RNAs

     Article • Current Opinion in Systems Biology, June 2017, Elsevier

     Piero Carninci

109. 
     A damaged genome’s transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks

     Article • Nature Communications, May 2017, Nature

     Piero Carninci

110. 
     Erratum: Corrigendum: DNA damage response inhibition at dysfunctional telomeres by modulation of telomeric DNA damage response RNAs

     Article • Nature Communications, April 2017, Springer Science + Business Media

     Piero Carninci

111. 
     Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease

     Article • PLoS Genetics, March 2017, PLOS

     Piero Carninci

112. 
     A Transcriptional Switch Point During Hematopoietic Stem and Progenitor Cell Ontogeny

     Article • Stem Cells and Development, March 2017, Mary Ann Liebert Inc

     Piero Carninci

113. 
     An atlas of human long non-coding RNAs with accurate 5′ ends

     Article • Nature, March 2017, Springer Science + Business Media

     Piero Carninci

114. 
     DNA damage response inhibition at dysfunctional telomeres by modulation of telomeric DNA damage response RNAs

     Article • Nature Communications, February 2017, Springer Science + Business Media

     Piero Carninci

115. 
     DEIVA: a web application for interactive visual analysis of differential gene expression profiles

     Article • BMC Genomics, January 2017, Springer Science + Business Media

     Piero Carninci

116. 
     RNA extraction from sorted neuronal subtypes

     Article • BioTechniques, January 2017, Future Science

     Piero Carninci

117. 
     The FANTOM5 Computation Ecosystem: Genomic Information Hub for Promoters and Active Enhancers

     Article • January 2017, Springer Science + Business Media

     Piero Carninci

118. 
     YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses

     Article • Scientific Reports, November 2016, Springer Science + Business Media

     Piero Carninci

119. 
     Genome sequence and analysis of the Japanese morning glory Ipomoea nil

     Article • Nature Communications, November 2016, Springer Science + Business Media

     Piero Carninci

120. 
     Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution

     Article • Diabetes, November 2016, American Diabetes Association

     Piero Carninci

121. 
     Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

     Article • Nucleic Acids Research, October 2016, Oxford University Press (OUP)

     Piero Carninci

122. 
     Isoforms of the Erythropoietin receptor in dopaminergic neurons of theSubstantia Nigra

     Article • Journal of Neurochemistry, September 2016, Wiley

     Piero Carninci

123. 
     Single-Nucleotide Resolution Mapping of Hepatitis B Virus Promoters in Infected Human Livers and Hepatocellular Carcinoma

     Article • Journal of Virology, September 2016, ASM Journals

     Dr Marie A Buendia, Piero Carninci

124. 
     Identification of antisense long noncoding RNAs that function as SINEUPs in human cells

     Article • Scientific Reports, September 2016, Nature

     Piero Carninci

125. 
     Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis

     Article • Scientific Reports, September 2016, Nature

     Piero Carninci

126. 
     Abstract 2897: Recurrent transcriptome alterations across multiple cancer types

     Article • Cancer Research, July 2016, American Association for Cancer Research (AACR)

     Piero Carninci

127. 
     Epi-drivers and cancer-testis genes

     Article • Translational Cancer Research, June 2016, AME Publishing Company

     Piero Carninci

128. 
     DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C

     Article • Journal of Cell Science, May 2016, The Company of Biologists

     Piero Carninci

129. 
     Characterization of piRNAs across postnatal development in mouse brain

     Article • Scientific Reports, April 2016, Nature

     Piero Carninci

130. 
     Functional annotation of the vlinc class of non-coding RNAs using systems biology approach

     Article • Nucleic Acids Research, March 2016, Oxford University Press (OUP)

     Piero Carninci

131. 
     The ORFeome Collaboration: a genome-scale human ORF-clone resource

     Article • Nature Chemical Biology, March 2016, Nature

     Piero Carninci

132. 
     Corrigendum: A draft network of ligand-receptor-mediated multicellular signalling in human

     Article • Nature Communications, February 2016, Nature

     Piero Carninci

133. 
     Discovery and functional analysis of lncRNAs: Methodologies to investigate an uncharacterized transcriptome

     Article • Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, January 2016, Elsevier

     Piero Carninci

134. 
     On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase

     Article • Database, January 2016, Oxford University Press (OUP)

     Piero Carninci

135. 
     FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki

     Article • Database, January 2016, Oxford University Press (OUP)

     Piero Carninci

136. 
     Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation

     Article • Molecular Systems Biology, December 2015, EMBO

     Piero Carninci

137. 
     The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

     Article • PLoS Biology, December 2015, PLOS

     Piero Carninci

138. 
     Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs

     Article • Nucleic Acids Research, December 2015, Oxford University Press (OUP)

     Piero Carninci

139. 
     Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage

     Article • PLoS ONE, December 2015, PLOS

     Piero Carninci

140. 
     Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors

     Article • Epigenetics & Chromatin, December 2015, Springer Science + Business Media

     Piero Carninci

141. 
     In grateful recognition of our Editorial Board

     Article • BioEssays, November 2015, Wiley

     Piero Carninci

142. 
     Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line

     Article • Frontiers in Genetics, November 2015, Frontiers

     Piero Carninci

143. 
     Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers

     Article • Cancer Research, November 2015, American Association for Cancer Research (AACR)

     Piero Carninci

144. 
     Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress

     Article • Carcinogenesis, November 2015, Oxford University Press (OUP)

     Piero Carninci

145. 
     DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium

     Article • Cell Reports, November 2015, Elsevier

     Piero Carninci

146. 
     CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors

     Article • Genome Research, October 2015, Cold Spring Harbor Laboratory Press

     Piero Carninci

147. 
     Engineering mammalian cell factories with SINEUP noncoding RNAs to improve translation of secreted proteins

     Article • Gene, September 2015, Elsevier

     Piero Carninci

148. 
     STAP cells are derived from ES cells

     Article • Nature, September 2015, Nature

     Piero Carninci

149. 
     Paradigm shifts in genomics through the FANTOM projects

     Article • Mammalian Genome, August 2015, Springer Science + Business Media

     Piero Carninci

150. 
     SINEUPs: A new class of natural and synthetic antisense long non-coding RNAs that activate translation

     Article • RNA Biology, August 2015, Taylor & Francis

     Piero Carninci

151. 
     Krimper Enforces an Antisense Bias on piRNA Pools by Binding AGO3 in the Drosophila Germline

     Article • Molecular Cell, August 2015, Elsevier

     Piero Carninci

152. 
     The frequent evolutionary birth and death of functional promoters in mouse and human

     Article • Genome Research, July 2015, Cold Spring Harbor Laboratory Press

     Piero Carninci

153. 
     A draft network of ligand–receptor-mediated multicellular signalling in human

     Article • Nature Communications, July 2015, Nature

     Piero Carninci

154. 
     Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells

     Article • Scientific Reports, July 2015, Nature

     Piero Carninci

155. 
     Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium

     Article • Nucleic Acids Research, June 2015, Oxford University Press (OUP)

     Piero Carninci

156. 
     Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics

     Article • Nucleic Acids Research, June 2015, Oxford University Press (OUP)

     Piero Carninci

157. 
     A new approach for screening cervical cancer by characterization of transcripts using CAGE technology.

     Article • Journal of Clinical Oncology, May 2015, American Society of Clinical Oncology (ASCO)

     Piero Carninci

158. 
     SINEUPs are modular antisense long non-coding RNAs that increase synthesis of target proteins in cells

     Article • Frontiers in Cellular Neuroscience, May 2015, Frontiers

     Piero Carninci

159. 
     HSA21 Single-Minded 2 (Sim2) Binding Sites Co-Localize with Super-Enhancers and Pioneer Transcription Factors in Pluripotent Mouse ES Cells

     Article • PLoS ONE, May 2015, PLOS

     Piero Carninci

160. 
     Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response

     Article • PLoS Computational Biology, April 2015, PLOS

     Piero Carninci

161. 
     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

     Article • Frontiers in Cellular Neuroscience, April 2015, Frontiers

     Piero Carninci

162. 
     Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells

     Article • Journal of Leukocyte Biology, February 2015, Wiley

     Piero Carninci

163. 
     Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

     Article • Science, February 2015, American Association for the Advancement of Science

     Piero Carninci

164. 
     Nuclear transcriptome profiling of induced pluripotent stem cells and embryonic stem cells identify non-coding loci resistant to reprogramming

     Article • Cell Cycle, February 2015, Taylor & Francis

     Piero Carninci

165. 
     CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

     Article • Nucleic Acids Research, February 2015, Oxford University Press (OUP)

     Piero Carninci

166. 
     Telomerase Reverse Transcriptase Regulates microRNAs

     Article • International Journal of Molecular Sciences, January 2015, MDPI AG

     Piero Carninci

167. 
     Gateways to the FANTOM5 promoter level mammalian expression atlas

     Article • Genome Biology, January 2015, Springer Science + Business Media

     Piero Carninci

168. 
     Expression Specificity of Disease-Associated lncRNAs: Toward Personalized Medicine

     Article • January 2015, Springer Science + Business Media

     Piero Carninci

169. 
     Biased Allelic Expression in Human Primary Fibroblast Single Cells

     Article • The American Journal of Human Genetics, January 2015, Elsevier

     Piero Carninci

170. 
     Complexity of Mammalian Transcriptome Analyzed by RNA Deep Sequencing

     Article • January 2015, Springer Science + Business Media

     Piero Carninci

171. 
     Characterization of Novel Transcripts of Human Papillomavirus Type 16 Using Cap Analysis Gene Expression Technology

     Article • Journal of Virology, December 2014, ASM Journals

     Dr Kazunori Nagasaka, Piero Carninci

172. 
     Mice in the ENCODE spotlight

     Article • Nature, November 2014, Nature

     Piero Carninci

173. 
     Specific Mesothelial Signature Marks the Heterogeneity of Mesenchymal Stem Cells From High-Grade Serous Ovarian Cancer

     Article • Stem Cells, October 2014, Wiley

     Piero Carninci

174. 
     The devil in the details of RNA-seq

     Article • Nature Biotechnology, September 2014, Nature

     Piero Carninci

175. 
     Widespread genome transcription: New possibilities for RNA therapies

     Article • Biochemical and Biophysical Research Communications, September 2014, Elsevier

     Piero Carninci

176. 
     Multiplicity of 5′ Cap Structures Present on Short RNAs

     Article • PLoS ONE, July 2014, PLOS

     Piero Carninci

177. 
     PAPD5-mediated 3′ adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease

     Article • Proceedings of the National Academy of Sciences, July 2014, Proceedings of the National Academy of Sciences

     Piero Carninci

178. 
     Comparative validation of the D. melanogaster modENCODE transcriptome annotation

     Article • Genome Research, July 2014, Cold Spring Harbor Laboratory Press

     Piero Carninci

179. 
     Digital expression profiling of the compartmentalized translatome of Purkinje neurons

     Article • Genome Research, June 2014, Cold Spring Harbor Laboratory Press

     Piero Carninci

180. 
     Systemic identification of estrogen-regulated genes in breast cancer cells through cap analysis of gene expression mapping

     Article • Biochemical and Biophysical Research Communications, May 2014, Elsevier

     Piero Carninci

181. 
     Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

     Article • Nature Genetics, April 2014, Nature

     Piero Carninci, Dr Md Salimullah

182. 
     Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing

     Article • Genome Research, March 2014, Cold Spring Harbor Laboratory Press

     Piero Carninci

183. 
     Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation

     Article • Proceedings of the National Academy of Sciences, March 2014, Proceedings of the National Academy of Sciences

     Piero Carninci

184. 
     Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation

     Article • Blood, March 2014, American Society of Hematology

     Piero Carninci

185. 
     Redefinition of the human mast cell transcriptome by deep-CAGE sequencing

     Article • Blood, March 2014, American Society of Hematology

     Piero Carninci

186. 
     The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations

     Article • Blood, March 2014, American Society of Hematology

     Piero Carninci

187. 
     Transcription and enhancer profiling in human monocyte subsets

     Article • Blood, March 2014, American Society of Hematology

     Piero Carninci

188. 
     Diversity and dynamics of the Drosophila transcriptome

     Article • Nature, March 2014, Nature

     Dr James Bentley Brown, Piero Carninci

189. 
     A promoter-level mammalian expression atlas

     Article • Nature, March 2014, Nature

     Piero Carninci

190. 
     An atlas of active enhancers across human cell types and tissues

     Article • Nature, March 2014, Nature

     Piero Carninci

191. 
     Two independent transcription initiation codes overlap on vertebrate core promoters

     Article • Nature, February 2014, Nature

     Altuna A, Piero Carninci, Dr ir Wilfred van IJcken

192. 
     NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements

     Article • Frontiers in Cellular Neuroscience, January 2014, Frontiers

     Altuna A, Piero Carninci

193. 
     CAGE-defined promoter regions of the genes implicated in Rett Syndrome

     Article • BMC Genomics, January 2014, Springer Science + Business Media

     Piero Carninci

194. 
     Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines

     Article • BMC Genomics, January 2014, Springer Science + Business Media

     Piero Carninci

195. 
     Detecting Expressed Genes Using CAGE

     Article • January 2014, Springer Science + Business Media

     Piero Carninci

196. 
     MOIRAI: a compact workflow system for CAGE analysis

     Article • BMC Bioinformatics, January 2014, Springer Science + Business Media

     Piero Carninci

197. 
     Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules

     Article • BMC Genomics, January 2014, Springer Science + Business Media

     Piero Carninci

198. 
     RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE)

     Article • BMC Genomics, January 2014, Springer Science + Business Media

     Piero Carninci

199. 
     Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

     Article • Genome Research, September 2013, Cold Spring Harbor Laboratory Press

     Altuna A, Piero Carninci, Dr ir Wilfred van IJcken

200. 
     Regional differences in gene expression and promoter usage in aged human brains

     Article • Neurobiology of Aging, July 2013, Elsevier

     Piero Carninci

201. 
     Noncoding RNA: The Major Output of Gene Expression

     Article • June 2013, Wiley

     Piero Carninci

202. 
     Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma

     Article • Cell, March 2013, Elsevier

     Dr Serena Ghisletti, Piero Carninci

203. 
     Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA

     Article • Nature Structural & Molecular Biology, January 2013, Nature

     Piero Carninci

204. 
     A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells

     Article • Frontiers in Genetics, January 2013, Frontiers

     Piero Carninci

205. 
     Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation

     Article • BMC Genomics, January 2013, Springer Science + Business Media

     Piero Carninci

206. 
     Temporal dynamics and transcriptional control using single-cell gene expression analysis

     Article • Genome Biology, January 2013, Springer Science + Business Media

     Piero Carninci

207. 
     Population transcriptomics with single-cell resolution: A new field made possible by microfluidics

     Article • BioEssays, December 2012, Wiley

     Piero Carninci

208. 
     NMDA Receptor Regulation Prevents Regression of Visual Cortical Function in the Absence of Mecp2

     Article • Neuron, December 2012, Elsevier

     Piero Carninci

209. 
     Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching

     Article • Nucleic Acids Research, November 2012, Oxford University Press (OUP)

     Piero Carninci, Dr Md Salimullah

210. 
     Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat

     Article • Nature, October 2012, Nature

     Piero Carninci

211. 
     Structure by Sequencing: Discovery of Hidden Messages in the Noncoding RNA Fraction

     Article • Molecular Cell, October 2012, Elsevier

     Piero Carninci

212. 
     An integrated encyclopedia of DNA elements in the human genome

     Article • Nature, September 2012, Springer Science + Business Media

     Dr Daniel Sobral, Piero Carninci

213. 
     Landscape of transcription in human cells

     Article • Nature, September 2012, Nature

     Piero Carninci

214. 
     The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

     Article • Genome Research, September 2012, Cold Spring Harbor Laboratory Press

     Piero Carninci

215. 
     Understanding transcriptional regulation by integrative analysis of transcription factor binding data

     Article • Genome Research, September 2012, Cold Spring Harbor Laboratory Press

     Piero Carninci

216. 
     High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

     Article • Genome Research, August 2012, Cold Spring Harbor Laboratory Press

     Piero Carninci

217. 
     Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain

     Article • BioTechniques, June 2012, Informa UK (Informa Life Sciences)

     Piero Carninci

218. 
     Site-specific DICER and DROSHA RNA products control the DNA-damage response

     Article • Nature, May 2012, Nature

     Piero Carninci

219. 
     Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

     Article • Proceedings of the National Academy of Sciences, March 2012, Proceedings of the National Academy of Sciences

     Altuna A, Piero Carninci

220. 
     Metazoan promoters: emerging characteristics and insights into transcriptional regulation

     Article • Nature Reviews Genetics, March 2012, Nature

     Piero Carninci

221. 
     5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing

     Article • Nature Protocols, February 2012, Nature

     Piero Carninci

222. 
     Automated Workflow for Preparation of cDNA for Cap Analysis of Gene Expression on a Single Molecule Sequencer

     Article • PLoS ONE, January 2012, PLOS

     Piero Carninci

223. 
     DeepCAGE: Genome-Wide Mapping of Transcription Start Sites

     Article • January 2012, Wiley

     Piero Carninci

224. 
     Definition of Promotome-Transcriptome Architecture Using CAGEscan

     Article • January 2012, Wiley

     Piero Carninci

225. 
     piRNAs Warrant Investigation in Rett Syndrome: An Omics Perspective

     Article • Disease Markers, January 2012, Hindawi Publishing Corporation

     Piero Carninci

226. 
     Promoter architecture of mouse olfactory receptor genes

     Article • Genome Research, December 2011, Cold Spring Harbor Laboratory Press

     Altuna A, Piero Carninci

227. 
     Profiling transcription initiation in human aged brain using deep-CAGE

     Article • BMC Bioinformatics, November 2011, Springer Science + Business Media

     Piero Carninci

228. 
     Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila

     Article • Nature, November 2011, Nature

     Piero Carninci

229. 
     Somatic retrotransposition alters the genetic landscape of the human brain

     Article • Nature, October 2011, Springer Science + Business Media

     Piero Carninci

230. 
     Long non-coding RNA modifies chromatin

     Article • BioEssays, September 2011, Wiley

     Piero Carninci

231. 
     The Short Non-Coding Transcriptome of the Protozoan Parasite Trypanosoma cruzi

     Article • PLoS Neglected Tropical Diseases, August 2011, PLOS

     Piero Carninci, Daniel Nilsson

232. 
     CAGE (Cap Analysis of Gene Expression): A Protocol for the Detection of Promoter and Transcriptional Networks

     Article • August 2011, Springer Science + Business Media

     Piero Carninci

233. 
     Nuclear Pore Complex Protein Mediated Nuclear Localization of Dicer Protein in Human Cells

     Article • PLoS ONE, August 2011, PLOS

     Piero Carninci

234. 
     The Reality of Pervasive Transcription

     Article • PLoS Biology, July 2011, PLOS

     Piero Carninci

235. 
     Direct generation of functional dopaminergic neurons from mouse and human fibroblasts

     Article • Nature, July 2011, Nature

     Piero Carninci

236. 
     FXYD6, a Na,K-ATPase Regulator, Is Expressed in Type II Taste Cells

     Article • Bioscience Biotechnology and Biochemistry, June 2011, Taylor & Francis

     Piero Carninci

237. 
     Unamplified cap analysis of gene expression on a single-molecule sequencer

     Article • Genome Research, May 2011, Cold Spring Harbor Laboratory Press

     Piero Carninci

238. 
     A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

     Article • PLoS Biology, April 2011, PLOS

     Dr Daniel Sobral, Piero Carninci

239. 
     NanoCAGE: A High-Resolution Technique to Discover and Interrogate Cell Transcriptomes

     Article • Cold Spring Harbor Protocols, January 2011, Cold Spring Harbor Laboratory Press

     Piero Carninci, Dr Md Salimullah

240. 
     Whole transcriptome analysis: what are we still missing?

     Article • WIREs Systems Biology and Medicine, December 2010, Wiley

     Piero Carninci

241. 
     Genome-wide analysis of promoter architecture in Drosophila melanogaster

     Article • Genome Research, December 2010, Cold Spring Harbor Laboratory Press

     Piero Carninci

242. 
     High Sensitivity TSS Prediction: Estimates of Locations Where TSS Cannot Occur

     Article • PLoS ONE, November 2010, PLOS

     Piero Carninci

243. 
     Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

     Article • Nucleic Acids Research, November 2010, Oxford University Press (OUP)

     Piero Carninci

244. 
     From identification to validation to gene count

     Article • October 2010, Springer Science + Business Media

     Piero Carninci

245. 
     Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing

     Article • BioTechniques, October 2010, Informa UK (Informa Life Sciences)

     Piero Carninci

246. 
     Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE

     Article • Nucleic Acids Research, August 2010, Oxford University Press (OUP)

     Piero Carninci

247. 
     Molecular mechanisms of pituitary organogenesis: In search of novel regulatory genes

     Article • Molecular and Cellular Endocrinology, July 2010, Elsevier

     Piero Carninci, Professor Berenice B Mendonca

248. 
     Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

     Article • Nature Chemical Biology, June 2010, Nature

     Piero Carninci, Dr Md Salimullah

249. 
     RNA Dust: Where are the Genes?

     Article • DNA Research, June 2010, Oxford University Press (OUP)

     Piero Carninci

250. 
     The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance

     Article • Genome Research, April 2010, Cold Spring Harbor Laboratory Press

     Piero Carninci

251. 
     An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

     Article • Cell, April 2010, Elsevier

     Piero Carninci, Altuna A

252. 
     RNA Dust: Where are the Genes?

     Article • DNA Research, March 2010, Oxford University Press (OUP)

     Piero Carninci

253. 
     An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

     Article • Cell, March 2010, Elsevier

     Altuna A, Piero Carninci

254. 
     Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries

     Article • Genome Research, January 2010, Cold Spring Harbor Laboratory Press

     Piero Carninci

255. 
     Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns

     Article • BMC Genomics, January 2010, Springer Science + Business Media

     Piero Carninci

256. 
     Beyond the FANTOM4

     Article • Genome Biology, January 2010, Springer Science + Business Media

     Piero Carninci

257. 
     Tunable fractionation of nucleic acids

     Article • BioTechniques, December 2009, Future Science

     Piero Carninci, Dr Md Salimullah

258. 
     Cap-Analysis Gene Expression (CAGE)

     Article • October 2009, Taylor & Francis

     Piero Carninci

259. 
     Construction of CAGE Libraries

     Article • October 2009, Taylor & Francis

     Piero Carninci

260. 
     Tagging Transcription Starting Sites with CAGE

     Article • October 2009, Taylor & Francis

     Piero Carninci

261. 
     Annotating non-coding transcription using functional genomics strategies

     Article • Briefings in Functional Genomics and Proteomics, October 2009, Oxford University Press (OUP)

     Piero Carninci

262. 
     Is sequencing enlightenment ending the dark age of the transcriptome?

     Article • Nature Chemical Biology, October 2009, Nature

     Piero Carninci

263. 
     Unexpected expression of α- and β-globin in mesencephalic dopaminergic neurons and glial cells

     Article • Proceedings of the National Academy of Sciences, September 2009, Proceedings of the National Academy of Sciences

     Piero Carninci

264. 
     Erratum: Corrigendum: Tiny RNAs associated with transcription start sites in animals

     Article • Nature Genetics, July 2009, Springer Science + Business Media

     Piero Carninci

265. 
     Small RNAs derived from snoRNAs

     Article • RNA, May 2009, Cold Spring Harbor Laboratory Press

     Piero Carninci

266. 
     Discovery of transcriptional regulators and signaling pathways in the developing pituitary gland by bioinformatic and genomic approaches

     Article • Genomics, May 2009, Elsevier

     Piero Carninci

267. 
     Genetics, Gene Expression and Bioinformatics of the Pituitary Gland

     Article • Hormone Research in Paediatrics, April 2009, Karger Publishers

     Piero Carninci

268. 
     Tiny RNAs associated with transcription start sites in animals

     Article • Nature Genetics, April 2009, Springer Science + Business Media

     Piero Carninci

269. 
     The regulated retrotransposon transcriptome of mammalian cells

     Article • Nature Genetics, April 2009, Springer Science + Business Media

     Piero Carninci

270. 
     The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

     Article • Nature Genetics, April 2009, Nature

     Altuna A, Piero Carninci

271. 
     Whole genome transcriptome analysis

     Article • RNA Biology, April 2009, Taylor & Francis

     Piero Carninci

272. 
     High-throughput verification of transcriptional starting sites by Deep-RACE

     Article • BioTechniques, February 2009, Future Science

     Piero Carninci

273. 
     The long and short of RNAs

     Article • Nature, February 2009, Nature

     Piero Carninci

274. 
     FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions

     Article • Genome Biology, January 2009, Springer Science + Business Media

     Piero Carninci

275. 
     Generation of Full-Length cDNA Libraries: Focus on Plants

     Article • January 2009, Springer Science + Business Media

     Piero Carninci

276. 
     Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

     Article • Genome Biology, January 2009, Springer Science + Business Media

     Piero Carninci

277. 
     The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

     Article • Genome Biology, January 2009, Springer Science + Business Media

     Piero Carninci

278. 
     Genome-wide analysis of cancer/testis gene expression

     Article • Proceedings of the National Academy of Sciences, December 2008, Proceedings of the National Academy of Sciences

     Piero Carninci

279. 
     Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

     Article • Genome Research, December 2008, Cold Spring Harbor Laboratory Press

     Piero Carninci

280. 
     Placental expression profiling in preeclampsia: local overproduction of hemoglobin may drive pathological changes

     Article • Fertility and Sterility, November 2008, Elsevier

     Piero Carninci

281. 
     Gα14 is a candidate mediator of sweet/umami signal transduction in the posterior region of the mouse tongue

     Article • Biochemical and Biophysical Research Communications, November 2008, Elsevier

     Piero Carninci

282. 
     Rapidly evolving human promoter regions

     Article • Nature Genetics, November 2008, Nature

     Piero Carninci

283. 
     Non-coding RNA transcription: turning on neighbours

     Article • Nature Cell Biology, September 2008, Nature

     Piero Carninci

284. 
     A Resource for Transcriptomic Analysis in the Mouse Brain

     Article • PLoS ONE, August 2008, PLOS

     Piero Carninci

285. 
     Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer

     Article • BioTechniques, July 2008, Future Science

     Piero Carninci

286. 
     Hunting hidden transcripts

     Article • Nature Chemical Biology, July 2008, Nature

     Piero Carninci

287. 
     Multifaceted mammalian transcriptome

     Article • Current Opinion in Cell Biology, June 2008, Elsevier

     Piero Carninci

288. 
     A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE

     Article • Genomics, March 2008, Elsevier

     Piero Carninci

289. 
     Hidden layers of human small RNAs

     Article • BMC Genomics, January 2008, Springer Science + Business Media

     Piero Carninci

290. 
     Gene Organization in Rice Revealed by Full-Length cDNA Mapping and Gene Expression Analysis through Microarray

     Article • PLoS ONE, November 2007, PLOS

     Piero Carninci

291. 
     A code for transcription initiation in mammalian genomes

     Article • Genome Research, November 2007, Cold Spring Harbor Laboratory Press

     Piero Carninci

292. 
     Splicing bypasses 3′ end formation signals to allow complex gene architectures

     Article • Gene, November 2007, Elsevier

     Piero Carninci

293. 
     Corrigendum: Genome-wide analysis of mammalian promoter architecture and evolution

     Article • Nature Genetics, September 2007, Nature

     Piero Carninci

294. 
     Transcriptomics resources for functional genomics

     Article • Briefings in Functional Genomics and Proteomics, August 2007, Oxford University Press (OUP)

     Piero Carninci

295. 
     Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

     Article • Nature, June 2007, Nature

     Dr Stefan Enroth, Piero Carninci, Sean Davis, Jonghwan Kim

296. 
     Informatic and genomic analysis of melanocyte cDNA libraries as a resource for the study of melanocyte development and function

     Article • Pigment Cell Research, June 2007, Wiley

     Piero Carninci

297. 
     Mammalian RNA polymerase II core promoters: insights from genome-wide studies

     Article • Nature Reviews Genetics, May 2007, Nature

     Piero Carninci

298. 
     Constructing the landscape of the mammalian transcriptome

     Article • Journal of Experimental Biology, May 2007, The Company of Biologists

     Piero Carninci

299. 
     Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality

     Article • Genomics, May 2007, Elsevier

     Piero Carninci

300. 
     Noncoding RNA transcription beyond annotated genes

     Article • Current Opinion in Genetics & Development, April 2007, Elsevier

     Piero Carninci

301. 
     CAGE-TSSchip: promoter-based expression profiling using the 5'-leading label of capped transcripts

     Article • Genome Biology, January 2007, Springer Science + Business Media

     Piero Carninci

302. 
     Diversity of Ca2+-activated K+ channel transcripts in inner ear hair cells

     Article • Gene, January 2007, Elsevier

     Piero Carninci

303. 
     Large-scale clustering of CAGE tag expression data

     Article • BMC Bioinformatics, January 2007, Springer Science + Business Media

     Piero Carninci

304. 
     Simplified ontologies allowing comparison of developmental mammalian gene expression

     Article • Genome Biology, January 2007, Springer Science + Business Media

     Piero Carninci

305. 
     Epigenetic regulation of critical period plasticity in visual cortex

     Article • Neuroscience Research, January 2007, Elsevier

     Piero Carninci

306. 
     Correction for Wada et al., A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes

     Article • Proceedings of the National Academy of Sciences, November 2006, Proceedings of the National Academy of Sciences

     Piero Carninci

307. 
     A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes

     Article • Proceedings of the National Academy of Sciences, October 2006, Proceedings of the National Academy of Sciences

     Piero Carninci

308. 
     Insights into social insects from the genome of the honeybee Apis mellifera

     Article • Nature, October 2006, Springer Science + Business Media

     Prof. H. Michael G. Lattorff, Piero Carninci

309. 
     Tagging mammalian transcription complexity

     Article • Trends in Genetics, September 2006, Elsevier

     Piero Carninci

310. 
     The complexity of the mammalian transcriptome

     Article • The Journal of Physiology, August 2006, Wiley

     Piero Carninci

311. 
     Transcriptional network dynamics in macrophage activation

     Article • Genomics, August 2006, Elsevier

     Piero Carninci

312. 
     Constructing ORFeome resources with removable termination codons

     Article • BioTechniques, July 2006, Future Science

     Piero Carninci

313. 
     Evolutionary turnover of mammalian transcription start sites

     Article • Genome Research, June 2006, Cold Spring Harbor Laboratory Press

     Piero Carninci

314. 
     Genome-wide analysis of mammalian promoter architecture and evolution

     Article • Nature Genetics, April 2006, Nature

     Piero Carninci

315. 
     Subcellular Localization of Mammalian Type II Membrane Proteins

     Article • Traffic, March 2006, Wiley

     Piero Carninci

316. 
     CAGE: cap analysis of gene expression

     Article • Nature Chemical Biology, March 2006, Nature

     Piero Carninci

317. 
     Complex Loci in Human and Mouse Genomes

     Article • PLoS Genetics, January 2006, PLOS

     Altuna A, Piero Carninci

318. 
     A Method for Similarity Search of Genomic Positional Expression Using CAGE

     Article • PLoS Genetics, January 2006, PLOS

     Piero Carninci

319. 
     A Simple Physical Model Predicts Small Exon Length Variations

     Article • PLoS Genetics, January 2006, PLOS

     Piero Carninci

320. 
     Article • Genome Biology, January 2006, Springer Science + Business Media

     Piero Carninci

321. 
     Clusters of Internally Primed Transcripts Reveal Novel Long Noncoding RNAs

     Article • PLoS Genetics, January 2006, PLOS

     Piero Carninci

322. 
     Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes

     Article • BMC Bioinformatics, January 2006, Springer Science + Business Media

     Piero Carninci

323. 
     Differential Use of Signal Peptides and Membrane Domains Is a Common Occurrence in the Protein Output of Transcriptional Units

     Article • PLoS Genetics, January 2006, PLOS

     Piero Carninci

324. 
     Article • Genome Biology, January 2006, Springer Science + Business Media

     Piero Carninci

325. 
     Genome Network and FANTOM3: Assessing the Complexity of the Transcriptome

     Article • PLoS Genetics, January 2006, PLOS

     Piero Carninci

326. 
     Article • Genome Biology, January 2006, Springer Science + Business Media

     Piero Carninci

327. 
     Heterotachy in Mammalian Promoter Evolution

     Article • PLoS Genetics, January 2006, PLOS

     Piero Carninci

328. 
     Mice and Men: Their Promoter Properties

     Article • PLoS Genetics, January 2006, PLOS

     Piero Carninci

329. 
     Pseudo–Messenger RNA: Phantoms of the Transcriptome

     Article • PLoS Genetics, January 2006, PLOS

     Piero Carninci

330. 
     The Abundance of Short Proteins in the Mammalian Proteome

     Article • PLoS Genetics, January 2006, PLOS

     Piero Carninci

331. 
     Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs

     Article • PLoS Genetics, January 2006, PLOS

     Piero Carninci

332. 
     Article • Genome Biology, January 2006, Springer Science + Business Media

     Piero Carninci

333. 
     CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis

     Article • Nucleic Acids Research, January 2006, Oxford University Press (OUP)

     Piero Carninci

334. 
     LOCATE: a mouse protein subcellular localization database

     Article • Nucleic Acids Research, January 2006, Oxford University Press (OUP)

     Piero Carninci

335. 
     Antisense Transcription in the Mammalian Transcriptome

     Article • Science, September 2005, American Association for the Advancement of Science

     Dr Hiromi Nishida, Piero Carninci

336. 
     The Transcriptional Landscape of the Mammalian Genome

     Article • Science, September 2005, American Association for the Advancement of Science

     Piero Carninci

337. 
     Tag-based approaches for transcriptome research and genome annotation

     Article • Nature Chemical Biology, July 2005, Nature

     Piero Carninci

338. 
     Transcriptome analysis of the aphid bacteriocyte, the symbiotic host cell that harbors an endocellular mutualistic bacterium, Buchnera

     Article • Proceedings of the National Academy of Sciences, March 2005, Proceedings of the National Academy of Sciences

     Piero Carninci

339. 
     Differential Expression of Genes within the Cochlea as Defined by a Custom Mouse Inner Ear Microarray

     Article • Journal of the Association for Research in Otolaryngology, March 2005, Springer Science + Business Media

     Piero Carninci

340. 
     Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa)

     Article • Bioinformatics, January 2005, Oxford University Press (OUP)

     Piero Carninci

341. 
     Cytoskeletal Rearrangements in Synovial Fibroblasts as a Novel Pathophysiological Determinant of Modeled Rheumatoid Arthritis

     Article • PLoS Genetics, January 2005, PLOS

     Piero Carninci

342. 
     Correction: Cytoskeletal Rearrangements in Synovial Fibroblasts as a Novel Pathophysiological Determinant of Modeled Rheumatoid Arthritis

     Article • PLoS Genetics, January 2005, PLOS

     Piero Carninci

343. 
     Article • Genome Biology, January 2005, Springer Science + Business Media

     Piero Carninci

344. 
     Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas

     Article • Nature Chemical Biology, November 2004, Nature

     Piero Carninci

345. 
     Solution structure of the RWD domain of the mouse GCN2 protein

     Article • Protein Science, August 2004, Wiley

     Piero Carninci

346. 
     Comparative Analysis of Plant and Animal Calcium Signal Transduction Element Using Plant Full-Length cDNA Data

     Article • Molecular Biology and Evolution, June 2004, Oxford University Press (OUP)

     Piero Carninci

347. 
     CTAB-Urea Method Purifies RNA from Melanin for cDNA Microarray Analysis

     Article • Pigment Cell Research, June 2004, Wiley

     Piero Carninci

348. 
     Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library

     Article • Genomics, June 2004, Elsevier

     Piero Carninci

349. 
     Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

     Article • PLoS Biology, April 2004, PLOS

     Piero Carninci

350. 
     Gene discovery in genetically labeled single dopaminergic neurons of the retina

     Article • Proceedings of the National Academy of Sciences, March 2004, Proceedings of the National Academy of Sciences

     Piero Carninci

351. 
     Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice andArabidopsis

     Article • Physiological Genomics, February 2004, American Physiological Society

     Junshi Yazaki, Piero Carninci

352. 
     Solution Structure of the SEA Domain from the Murine Homologue of Ovarian Cancer Antigen CA125 (MUC16)

     Article • Journal of Biological Chemistry, February 2004, American Society for Biochemistry & Molecular Biology (ASBMB)

     Piero Carninci

353. 
     Solution structure of a BolA-like protein from Mus musculus

     Article • Protein Science, February 2004, Wiley

     Piero Carninci

354. 
     Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags

     Article • FEBS Letters, January 2004, Wiley

     Piero Carninci

355. 
     Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags

     Article • Genes & Genetic Systems, January 2004, Genetics Society of Japan

     Piero Carninci

356. 
     Article • Genome Biology, January 2004, Springer Science + Business Media

     Piero Carninci

357. 
     Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

     Article • Proceedings of the National Academy of Sciences, December 2003, Proceedings of the National Academy of Sciences

     Piero Carninci

358. 
     Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome

     Article • Science, October 2003, American Association for the Advancement of Science

     Piero Carninci, Dr Joseph R Ecker

359. 
     A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription

     Article • FEBS Letters, October 2003, Wiley

     Piero Carninci

360. 
     Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts

     Article • BioTechniques, September 2003, Future Science

     Piero Carninci

361. 
     Collection, Mapping, and Annotation of Over 28,000 cDNA Clones from japonica Rice

     Article • Science, July 2003, American Association for the Advancement of Science

     Junshi Yazaki, Piero Carninci

362. 
     Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana : Implication for land plant evolution

     Article • Proceedings of the National Academy of Sciences, June 2003, Proceedings of the National Academy of Sciences

     Piero Carninci

363. 
     A Comprehensive Transcript Map of the Mouse Gnas Imprinted Complex

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

364. 
     Analysis of the Mouse Transcriptome for Genes Involved in the Function of the Nervous System

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

365. 
     Antisense Transcripts With FANTOM2 Clone Set and Their Implications for Gene Regulation

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

366. 
     Comparative Analysis of Apoptosis and Inflammation Genes of Mice and Humans

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

367. 
     Comprehensive Analysis of the Mouse Metabolome Based on the Transcriptome

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

368. 
     Continued Discovery of Transcriptional Units Expressed in Cells of the Mouse Mononuclear Phagocyte Lineage

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

369. 
     Cytokine-Related Genes Identified From the RIKEN Full-Length Mouse cDNA Data Set

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

370. 
     Discovery of Imprinted Transcripts in the Mouse Transcriptome Using Large-Scale Expression Profiling

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

371. 
     Exploration of the Cell-Cycle Genes Found Within the RIKEN FANTOM2 Data Set

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

372. 
     G Protein-Coupled Receptor Genes in the FANTOM2 Database

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

373. 
     Human Disease Genes and Their Cloned Mouse Orthologs: Exploration of the FANTOM2 cDNA Sequence Data Set

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

374. 
     Identification and Analysis of Chromodomain-Containing Proteins Encoded in the Mouse Transcriptome

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

375. 
     Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA Collection

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

376. 
     Impact of Alternative Initiation, Splicing, and Termination on the Diversity of the mRNA Transcripts Encoded by the Mouse Transcriptome

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

377. 
     Kinesin Superfamily Proteins (KIFs) in the Mouse Transcriptome

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

378. 
     Mouse Proteome Analysis

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

379. 
     Phosphoregulators: Protein Kinases and Protein Phosphatases of Mouse

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

380. 
     Systematic Characterization of the Zinc-Finger-Containing Proteins in the Mouse Transcriptome

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

381. 
     Systematic Expression Profiling of the Mouse Transcriptome Using RIKEN cDNA Microarrays

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

382. 
     Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

383. 
     The Mouse Secretome: Functional Classification of the Proteins Secreted Into the Extracellular Environment

     Article • Genome Research, June 2003, Cold Spring Harbor Laboratory Press

     Piero Carninci

384. 
     Multiple tissue-specific promoters control expression of the murine tartrate-resistant acid phosphatase gene

     Article • Gene, March 2003, Elsevier

     Piero Carninci

385. 
     Genomics Approach to Abscisic Acid- and Gibberellin-responsive Genes in Rice

     Article • DNA Research, January 2003, Oxford University Press (OUP)

     Junshi Yazaki, Piero Carninci

386. 
     Comprehensive Analysis of NAC Family Genes in Oryza sativa and Arabidopsis thaliana

     Article • DNA Research, January 2003, Oxford University Press (OUP)

     Piero Carninci

387. 
     Article • BMC Immunology, January 2003, Springer Science + Business Media

     Piero Carninci

388. 
     Article • Genome Biology, January 2003, Springer Science + Business Media

     Piero Carninci

389. 
     Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences

     Article • Proceedings of the National Academy of Sciences, December 2002, Proceedings of the National Academy of Sciences

     Piero Carninci

390. 
     Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

     Article • Nature, December 2002, Nature

     Piero Carninci

391. 
     Initial sequencing and comparative analysis of the mouse genome

     Article • Nature, December 2002, Nature

     Piero Carninci

392. 
     A framework for integrating the songbird brain

     Article • Journal of Comparative Physiology A, December 2002, Springer Science + Business Media

     Dr Tom V. Smulders, Piero Carninci

393. 
     Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray

     Article • Functional & Integrative Genomics, November 2002, Springer Science + Business Media

     Piero Carninci

394. 
     Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray

     Article • Functional & Integrative Genomics, November 2002, Springer Science + Business Media

     Piero Carninci

395. 
     Comprehensive sequence analysis of translation termination sites in various eukaryotes

     Article • Gene, October 2002, Elsevier

     Piero Carninci

396. 
     On biased distribution of introns in various eukaryotes

     Article • Gene, October 2002, Elsevier

     Piero Carninci

397. 
     Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray

     Article • The Plant Journal, August 2002, Wiley

     Piero Carninci

398. 
     The Drosophila Gene Collection: Identification of Putative Full-Length cDNAs for 70% of D. melanogaster Genes

     Article • Genome Research, August 2002, Cold Spring Harbor Laboratory Press

     Piero Carninci

399. 
     Cytoplasmic RNA Extraction from Fresh and Frozen Mammalian Tissues

     Article • BioTechniques, August 2002, Future Science

     Piero Carninci

400. 
     Inferring Alternative Splicing Patterns in Mouse from a Full-Length cDNA Library and Microarray Data

     Article • Genome Research, July 2002, Cold Spring Harbor Laboratory Press

     Piero Carninci

401. 
     A Computer-Based Method of Selecting Clones for a Full-Length cDNA Project: Simultaneous Collection of Negligibly Redundant and Variant cDNAs

     Article • Genome Research, June 2002, Cold Spring Harbor Laboratory Press

     Piero Carninci

402. 
     Extra-Long First-Strand cDNA Synthesis

     Article • BioTechniques, May 2002, Future Science

     Piero Carninci

403. 
     Functional Annotation of a Full-Length Arabidopsis cDNA Collection

     Article • Science, March 2002, American Association for the Advancement of Science

     Piero Carninci

404. 
     Article • Journal of Structural and Functional Genomics, January 2002, Springer Science + Business Media

     Piero Carninci

405. 
     The DT40 web site: sampling and connecting the genes of a B cell line

     Article • Nucleic Acids Research, January 2002, Oxford University Press (OUP)

     Piero Carninci

406. 
     Removal of PolyA Tails from Full-Length cDNA Libraries for High-Efficiency Sequencing

     Article • BioTechniques, November 2001, Future Science

     Piero Carninci

407. 
     Correlation between sequence conservation of the 5′ untranslated region and codon usage bias in Mus musculus genes

     Article • Gene, October 2001, Elsevier

     Piero Carninci

408. 
     Balanced-Size and Long-Size Cloning of Full-Length, Cap-Trapped cDNAs into Vectors of the Novel λ-FLC Family Allows Enhanced Gene Discovery Rate and Functional Analysis

     Article • Genomics, September 2001, Elsevier

     Piero Carninci

409. 
     Meeting Report: 14th International Mouse Genome Conference

     Article • Mammalian Genome, June 2001, Springer Science + Business Media

     Piero Carninci

410. 
     Cloning Full-Length, Cap-Trapper-Selected cDNAs by Using the Single-Strand Linker Ligation Method

     Article • BioTechniques, June 2001, Future Science

     Piero Carninci

411. 
     Arabidopsis encyclopedia using full-length cDNAs and its application

     Article • Plant Physiology and Biochemistry, March 2001, Elsevier

     Piero Carninci

412. 
     Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays

     Article • Proceedings of the National Academy of Sciences, February 2001, Proceedings of the National Academy of Sciences

     Piero Carninci

413. 
     Functional annotation of a full-length mouse cDNA collection

     Article • Nature, February 2001, Nature

     Piero Carninci, Kazuhito Toyooka

414. 
     Computer-Based Methods for the Mouse Full-Length cDNA Encyclopedia: Real-Time Sequence Clustering for Construction of a Nonredundant cDNA Library

     Article • Genome Research, January 2001, Cold Spring Harbor Laboratory Press

     Piero Carninci

415. 
     Comparative evaluation of 5′-end-sequence quality of clones in CAP trapper and other full-length-cDNA libraries

     Article • Gene, January 2001, Elsevier

     Piero Carninci

416. 
     Monitoring the Expression Pattern of 1300 Arabidopsis Genes under Drought and Cold Stresses by Using a Full-Length cDNA Microarray

     Article • The Plant Cell, January 2001, American Society of Plant Biologists (ASPB)

     Piero Carninci

417. 
     Monitoring the Expression Pattern of 1300 Arabidopsis Genes under Drought and Cold Stresses by Using a Full-Length cDNA Microarray

     Article • The Plant Cell, January 2001, JSTOR

     Piero Carninci

418. 
     RIKEN Integrated Sequence Analysis (RISA) System---384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

     Article • Genome Research, November 2000, Cold Spring Harbor Laboratory Press

     Piero Carninci

419. 
     Normalization and Subtraction of Cap-Trapper-Selected cDNAs to Prepare Full-Length cDNA Libraries for Rapid Discovery of New Genes

     Article • Genome Research, October 2000, Cold Spring Harbor Laboratory Press

     Piero Carninci

420. 
     Automated Filtration-Based High-Throughput Plasmid Preparation System

     Article • Genome Research, May 1999, Cold Spring Harbor Laboratory Press

     Piero Carninci

421. 
     Increased specificity of reverse transcription priming by trehalose and oligo-blockers allows high-efficiency window separation of mRNA display

     Article • Nucleic Acids Research, March 1999, Oxford University Press (OUP)

     Piero Carninci

422. 
     [2] High-efficiency full-length cDNA cloning

     Article • January 1999, Elsevier

     Piero Carninci

423. 
     Characterization of Gene Expression in Mouse Blastocyst Using Single-Pass Sequencing of 3995 Clones

     Article • Genomics, December 1998, Elsevier

     Piero Carninci

424. 
     High-efficiency cloning ofArabidopsisfull-length cDNA by biotinylated CAP trapper

     Article • The Plant Journal, September 1998, Wiley

     Piero Carninci

425. 
     Characterization of Gene Expression in Mouse Blastocyst Using Single-Pass Sequencing of 3995 Clones

     Article • Genomics, April 1998, Elsevier

     Piero Carninci

426. 
     Transcriptional sequencing: A method for DNA sequencing using RNA polymerase

     Article • Proceedings of the National Academy of Sciences, March 1998, Proceedings of the National Academy of Sciences

     Piero Carninci

427. 
     Thermostabilization and thermoactivation of thermolabile enzymes by trehalose and its application for the synthesis of full length cDNA

     Article • Proceedings of the National Academy of Sciences, January 1998, Proceedings of the National Academy of Sciences

     Piero Carninci

428. 
     Simple and rapid preparation of plasmid template by a filtration method using microtiter filter plates

     Article • Nucleic Acids Research, March 1997, Oxford University Press (OUP)

     Piero Carninci

429. 
     A Novel Control System for Polymerase Chain Reaction Using a RIKEN GS384 Thermalcycler

     Article • DNA Research, January 1997, Oxford University Press (OUP)

     Piero Carninci

430. 
     High Efficiency Selection of Full-length cDNA by Improved Biotinylated Cap Trapper

     Article • DNA Research, January 1997, Oxford University Press (OUP)

     Piero Carninci

431. 
     High-Efficiency Full-Length cDNA Cloning by Biotinylated CAP Trapper

     Article • Genomics, November 1996, Elsevier

     Piero Carninci

432. 
     A discontinuous buffer system increasing resolution and reproducibility in DNA sequencing on high voltage horizontal ultrathin-layer electrophoresis

     Article • Electrophoresis, January 1995, Wiley

     Piero Carninci

433. 
     A simple discontinuous buffer system for increased resolution and speed in gel electrophoretic analysis of DNA sequence

     Article • Nucleic Acids Research, January 1990, Oxford University Press (OUP)

     Piero Carninci

434. 
     From CAGE to DeepCAGE: High-Throughput Transcription Start Site and Promoter Identification for Gene Network Analysis

     Article • Wiley

     Piero Carninci

435. 
     Wavelet profiles: their application in Oryza sativa DNA sequence analysis

     Article • Institute of Electrical & Electronics Engineers (IEEE)

     Piero Carninci