All Stories

  1. Ku limits aberrant mRNA splicing promoted by intronic antisense Alu elements

    Article • November 2025, Cold Spring Harbor Laboratory Press

    Piero Carninci

  2. Evidence of distal regulations orchestrated by RNAs initiating at short tandem repeats

    Article • April 2025, Cold Spring Harbor Laboratory Press

    Piero Carninci

  3. The commitment of the human cell atlas to humanity

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

    Piero Carninci

  4. 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

  5. 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

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

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

    Piero Carninci

  8. Nanopore Long-Read Sequencing Unveils Genomic Disruptions in Alzheimer’s Disease

    Article • February 2024, Cold Spring Harbor Laboratory Press

    Piero Carninci

  9. 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

  10. 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

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

    Article • Clinical and Translational Medicine, March 2023, Wiley

    Piero Carninci

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

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

    Piero Carninci

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

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

    Piero Carninci

  14. 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

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

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

    Piero Carninci

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

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

    Piero Carninci

  17. 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

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

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

    Piero Carninci

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

    Article • Stem Cell Reports, February 2022, Elsevier

    Piero Carninci

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

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

    Piero Carninci

  21. Embryonic LTR retrotransposons supply promoter modules to somatic tissues

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

    Piero Carninci

  22. A field guide to cultivating computational biology

    Article • PLoS Biology, October 2021, PLOS

    Piero Carninci, Dr Anne Carpenter, Professor Casey Greene

  23. SINEUPs: a novel toolbox for RNA therapeutics

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

    Piero Carninci

  24. 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

  25. 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

  26. 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

  27. 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

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

    Article • Stem Cell Reports, April 2021, Elsevier

    Piero Carninci

  29. 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

  30. 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

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

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

    Piero Carninci

  32. 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

  33. 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

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

    Article • FEBS Letters, October 2020, Wiley

    Piero Carninci

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

    Article • The Lancet, October 2020, Elsevier

    Piero Carninci

  36. 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

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

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

    Piero Carninci

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

    Article • August 2020, Cold Spring Harbor Laboratory Press

    Piero Carninci

  39. Expanded ENCODE delivers invaluable genomic encyclopedia

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

    Piero Carninci

  40. 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

  41. Comparative transcriptomics of primary cells in vertebrates

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

    Piero Carninci

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

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

    Piero Carninci

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

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

    Piero Carninci

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

    Article • Cell, April 2020, Elsevier

    Piero Carninci

  45. 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

  46. 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

  47. Recounting the FANTOM CAGE-Associated Transcriptome

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

    Piero Carninci

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

    Article • February 2020, Cold Spring Harbor Laboratory Press

    Piero Carninci

  49. Machine-driven parameter screen of biochemical reactions

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

    Piero Carninci

  50. 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

  51. 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

  52. Low Quantity single strand CAGE protocol v1

    Article • January 2020, ZappyLab, Inc.

    Piero Carninci

  53. 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

  54. 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

  55. 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

  56. Look for methods, not conclusions

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

    Piero Carninci, Professor Pellegrino Conte, Professor Roberto Bassi

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

    Article • The FASEB Journal, December 2019, Wiley

    Piero Carninci

  58. 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

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

    Article • Cell Systems, November 2019, Elsevier

    Piero Carninci

  60. 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

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

    Article • Developmental Cell, October 2019, Elsevier

    Piero Carninci

  62. 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

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

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

    Piero Carninci

  64. 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

  65. Machine-driven parameter optimisation of biochemical reactions

    Article • August 2019, Cold Spring Harbor Laboratory Press

    Piero Carninci

  66. 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

  67. 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

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

    Article • Journal of Molecular Biology, June 2019, Elsevier

    Piero Carninci

  69. 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

  70. 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

  71. 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

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

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

    Piero Carninci

  73. 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

  74. Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases

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

    Piero Carninci

  75. 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, Craig Billington, Dr Alejandro Lazo-Langner, Joan Albiol, MOURAD TAYEBI, Chuang Ma, Christine Toelzer , Dr. Kathrin Karsay, Professor Andrew M Beale, Professor Hugh James Byrne, Dr Ugo Marzocchi, Ana Nordberg, Martin Bartas, Natalia Echeverría, Dr Patricia M Graves, Dr Elvis A F Martis, Dr marco cascella, Dr. Giuseppe Lanza, Dr Michael Boah

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

    Article • December 2018, Cold Spring Harbor Laboratory Press

    Piero Carninci

  77. 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

  78. 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

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

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

    Piero Carninci, Dr Michael Schubert

  80. 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

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

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

    Piero Carninci

  82. 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

  83. 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

  84. 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

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

    Article • July 2018, Cold Spring Harbor Laboratory Press

    Piero Carninci

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

    Article • May 2018, Cold Spring Harbor Laboratory Press

    Piero Carninci

  87. Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages

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

    Piero Carninci

  88. 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

  89. 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

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

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

    Piero Carninci

  91. 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

  92. 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

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

    Article • PLOS One, February 2018, PLOS

    Piero Carninci

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

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

    Piero Carninci

  95. 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

  96. The Human Cell Atlas

    Article • eLife, December 2017, eLife

    Professor Fiona M Watt, Piero Carninci

  97. Monitoring transcription initiation activities in rat and dog

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

    Piero Carninci

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

    Article • Nature Communications, November 2017, Nature

    Piero Carninci

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

    Article • Scientific Data, October 2017, Nature

    Piero Carninci

  100. The Human Cell Atlas: Technical approaches and challenges

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

    Piero Carninci

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

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

    Piero Carninci

  102. Linking FANTOM5 CAGE peaks to annotations with CAGEscan

    Article • Scientific Data, October 2017, Nature

    Piero Carninci

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

    Article • EBioMedicine, October 2017, Elsevier

    Piero Carninci

  104. Systematic analysis of transcription start sites in avian development

    Article • PLoS Biology, September 2017, PLOS

    Piero Carninci

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

    Article • Scientific Data, August 2017, Nature

    Piero Carninci

  106. FANTOM5 CAGE profiles of human and mouse samples

    Article • Scientific Data, August 2017, Nature

    Piero Carninci, Professor Antti Sajantila

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

    Article • Scientific Data, August 2017, Nature

    Piero Carninci

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

    Article • Nature Biotechnology, August 2017, Nature

    Piero Carninci

  109. 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

  110. Genomics dissection of the zebrafish heart

    Article • Mechanisms of Development, July 2017, Elsevier

    Piero Carninci

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

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

    Piero Carninci

  112. 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

  113. 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

  114. 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

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

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

    Piero Carninci

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

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

    Piero Carninci

  117. 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

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

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

    Piero Carninci

  119. RNA extraction from sorted neuronal subtypes

    Article • BioTechniques, January 2017, Future Science

    Piero Carninci

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

    Article • January 2017, Springer Science + Business Media

    Piero Carninci

  121. 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

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

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

    Piero Carninci

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

    Article • Diabetes, November 2016, American Diabetes Association

    Piero Carninci

  124. 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

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

    Article • Journal of Neurochemistry, September 2016, Wiley

    Piero Carninci

  126. 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

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

    Article • Scientific Reports, September 2016, Nature

    Piero Carninci

  128. 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

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

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

    Piero Carninci

  130. Epi-drivers and cancer-testis genes

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

    Piero Carninci

  131. 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

  132. Characterization of piRNAs across postnatal development in mouse brain

    Article • Scientific Reports, April 2016, Nature

    Piero Carninci

  133. 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

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

    Article • Nature Chemical Biology, March 2016, Nature

    Piero Carninci

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

    Article • Nature Communications, February 2016, Nature

    Piero Carninci

  136. 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

  137. 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

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

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

    Piero Carninci

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

    Article • Molecular Systems Biology, December 2015, EMBO

    Piero Carninci

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

    Article • PLoS Biology, December 2015, PLOS

    Piero Carninci, Professor Antti Sajantila

  141. 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

  142. 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

  143. 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

  144. In grateful recognition of our Editorial Board

    Article • BioEssays, November 2015, Wiley

    Piero Carninci

  145. 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

  146. 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

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

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

    Piero Carninci

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

    Article • Cell Reports, November 2015, Elsevier

    Piero Carninci

  149. 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

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

    Article • Gene, September 2015, Elsevier

    Piero Carninci

  151. STAP cells are derived from ES cells

    Article • Nature, September 2015, Nature

    Piero Carninci

  152. Paradigm shifts in genomics through the FANTOM projects

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

    Piero Carninci

  153. 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

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

    Article • Molecular Cell, August 2015, Elsevier

    Piero Carninci

  155. 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

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

    Article • Nature Communications, July 2015, Nature

    Piero Carninci

  157. 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

  158. 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

  159. 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

  160. 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

  161. 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

  162. 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

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

    Article • PLoS Computational Biology, April 2015, PLOS

    Piero Carninci

  164. 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

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

    Article • Journal of Leukocyte Biology, February 2015, Wiley

    Piero Carninci

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

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

    Piero Carninci

  167. 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

  168. 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

  169. Telomerase Reverse Transcriptase Regulates microRNAs

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

    Piero Carninci

  170. Gateways to the FANTOM5 promoter level mammalian expression atlas

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

    Piero Carninci

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

    Article • January 2015, Springer Science + Business Media

    Piero Carninci

  172. Biased Allelic Expression in Human Primary Fibroblast Single Cells

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

    Piero Carninci

  173. Complexity of Mammalian Transcriptome Analyzed by RNA Deep Sequencing

    Article • January 2015, Springer Science + Business Media

    Piero Carninci

  174. 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

  175. Mice in the ENCODE spotlight

    Article • Nature, November 2014, Nature

    Piero Carninci

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

    Article • Stem Cells, October 2014, Wiley

    Piero Carninci

  177. The devil in the details of RNA-seq

    Article • Nature Biotechnology, September 2014, Nature

    Piero Carninci

  178. Widespread genome transcription: New possibilities for RNA therapies

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

    Piero Carninci

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

    Article • PLOS One, July 2014, PLOS

    Piero Carninci

  180. 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

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

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

    Piero Carninci

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

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

    Piero Carninci

  183. 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

  184. 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

  185. 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

  186. 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, Professor Antti Sajantila

  187. 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

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

    Article • Blood, March 2014, American Society of Hematology

    Piero Carninci

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

    Article • Blood, March 2014, American Society of Hematology

    Piero Carninci

  190. Transcription and enhancer profiling in human monocyte subsets

    Article • Blood, March 2014, American Society of Hematology

    Piero Carninci

  191. Diversity and dynamics of the Drosophila transcriptome

    Article • Nature, March 2014, Nature

    Dr James Bentley Brown, Piero Carninci

  192. A promoter-level mammalian expression atlas

    Article • Nature, March 2014, Nature

    Piero Carninci, Professor Antti Sajantila

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

    Article • Nature, March 2014, Nature

    Piero Carninci, Professor Antti Sajantila

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

    Article • Nature, February 2014, Nature

    Altuna A, Piero Carninci, Dr ir Wilfred van IJcken

  195. 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

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

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

    Piero Carninci

  197. 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

  198. Detecting Expressed Genes Using CAGE

    Article • January 2014, Springer Science + Business Media

    Piero Carninci

  199. MOIRAI: a compact workflow system for CAGE analysis

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

    Piero Carninci

  200. 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

  201. 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

  202. 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

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

    Article • Neurobiology of Aging, July 2013, Elsevier

    Piero Carninci

  204. Noncoding RNA: The Major Output of Gene Expression

    Article • June 2013, Wiley

    Piero Carninci

  205. Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma

    Article • Cell, March 2013, Elsevier

    Dr Serena Ghisletti, Piero Carninci

  206. 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

  207. 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

  208. 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

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

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

    Piero Carninci

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

    Article • BioEssays, December 2012, Wiley

    Piero Carninci

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

    Article • Neuron, December 2012, Elsevier

    Piero Carninci

  212. 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

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

    Article • Nature, October 2012, Nature

    Piero Carninci

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

    Article • Molecular Cell, October 2012, Elsevier

    Piero Carninci

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

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

    Dr Daniel Sobral, Piero Carninci

  216. Landscape of transcription in human cells

    Article • Nature, September 2012, Nature

    Piero Carninci

  217. 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

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

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

    Piero Carninci

  219. 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

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

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

    Piero Carninci

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

    Article • Nature, May 2012, Nature

    Piero Carninci

  222. 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

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

    Article • Nature Reviews Genetics, March 2012, Nature

    Piero Carninci

  224. 5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing

    Article • Nature Protocols, February 2012, Nature

    Piero Carninci

  225. 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

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

    Article • January 2012, Wiley

    Piero Carninci

  227. Definition of Promotome-Transcriptome Architecture Using CAGEscan

    Article • January 2012, Wiley

    Piero Carninci

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

    Article • Disease Markers, January 2012, Hindawi Publishing Corporation

    Piero Carninci

  229. Promoter architecture of mouse olfactory receptor genes

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

    Altuna A, Piero Carninci

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

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

    Piero Carninci

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

    Article • Nature, November 2011, Nature

    Piero Carninci

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

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

    Piero Carninci

  233. Long non-coding RNA modifies chromatin

    Article • BioEssays, September 2011, Wiley

    Piero Carninci

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

    Article • PLoS Neglected Tropical Diseases, August 2011, PLOS

    Piero Carninci, Daniel Nilsson

  235. 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

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

    Article • PLOS One, August 2011, PLOS

    Piero Carninci

  237. The Reality of Pervasive Transcription

    Article • PLoS Biology, July 2011, PLOS

    Piero Carninci

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

    Article • Nature, July 2011, Nature

    Piero Carninci

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

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

    Piero Carninci

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

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

    Piero Carninci

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

    Article • PLoS Biology, April 2011, PLOS

    Dr Daniel Sobral, Piero Carninci

  242. 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

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

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

    Piero Carninci

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

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

    Piero Carninci

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

    Article • PLOS One, November 2010, PLOS

    Piero Carninci

  246. 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

  247. From identification to validation to gene count

    Article • October 2010, Springer Science + Business Media

    Piero Carninci

  248. 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

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

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

    Piero Carninci

  250. 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

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

    Article • Nature Chemical Biology, June 2010, Nature

    Piero Carninci, Dr Md Salimullah

  252. RNA Dust: Where are the Genes?

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

    Piero Carninci

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

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

    Piero Carninci

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

    Article • Cell, April 2010, Elsevier

    Piero Carninci, Altuna A

  255. RNA Dust: Where are the Genes?

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

    Piero Carninci

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

    Article • Cell, March 2010, Elsevier

    Altuna A, Piero Carninci

  257. 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

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

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

    Piero Carninci

  259. Beyond the FANTOM4

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

    Piero Carninci

  260. Tunable fractionation of nucleic acids

    Article • BioTechniques, December 2009, Future Science

    Piero Carninci, Dr Md Salimullah

  261. Cap-Analysis Gene Expression (CAGE)

    Article • October 2009, Taylor & Francis

    Piero Carninci

  262. Construction of CAGE Libraries

    Article • October 2009, Taylor & Francis

    Piero Carninci

  263. Tagging Transcription Starting Sites with CAGE

    Article • October 2009, Taylor & Francis

    Piero Carninci

  264. Annotating non-coding transcription using functional genomics strategies

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

    Piero Carninci

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

    Article • Nature Chemical Biology, October 2009, Nature

    Piero Carninci

  266. 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

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

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

    Piero Carninci

  268. Small RNAs derived from snoRNAs

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

    Piero Carninci

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

    Article • Genomics, May 2009, Elsevier

    Piero Carninci

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

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

    Piero Carninci

  271. Tiny RNAs associated with transcription start sites in animals

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

    Piero Carninci

  272. The regulated retrotransposon transcriptome of mammalian cells

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

    Piero Carninci

  273. 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, Professor Nikolai Petrovsky

  274. Whole genome transcriptome analysis

    Article • RNA Biology, April 2009, Taylor & Francis

    Piero Carninci

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

    Article • BioTechniques, February 2009, Future Science

    Piero Carninci

  276. The long and short of RNAs

    Article • Nature, February 2009, Nature

    Piero Carninci

  277. 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

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

    Article • January 2009, Springer Science + Business Media

    Piero Carninci

  279. 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

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

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

    Piero Carninci

  281. 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

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

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

    Piero Carninci

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

    Article • Fertility and Sterility, November 2008, Elsevier

    Piero Carninci

  284. 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

  285. Rapidly evolving human promoter regions

    Article • Nature Genetics, November 2008, Nature

    Piero Carninci

  286. Non-coding RNA transcription: turning on neighbours

    Article • Nature Cell Biology, September 2008, Nature

    Piero Carninci

  287. A Resource for Transcriptomic Analysis in the Mouse Brain

    Article • PLOS One, August 2008, PLOS

    Piero Carninci

  288. 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

  289. Hunting hidden transcripts

    Article • Nature Chemical Biology, July 2008, Nature

    Piero Carninci

  290. Multifaceted mammalian transcriptome

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

    Piero Carninci

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

    Article • Genomics, March 2008, Elsevier

    Piero Carninci

  292. Hidden layers of human small RNAs

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

    Piero Carninci

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

    Article • PLOS One, November 2007, PLOS

    Piero Carninci

  294. A code for transcription initiation in mammalian genomes

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

    Piero Carninci

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

    Article • Gene, November 2007, Elsevier

    Piero Carninci

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

    Article • Nature Genetics, September 2007, Nature

    Piero Carninci

  297. Transcriptomics resources for functional genomics

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

    Piero Carninci

  298. 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

  299. 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

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

    Article • Nature Reviews Genetics, May 2007, Nature

    Piero Carninci

  301. Constructing the landscape of the mammalian transcriptome

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

    Piero Carninci

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

    Article • Genomics, May 2007, Elsevier

    Piero Carninci

  303. Noncoding RNA transcription beyond annotated genes

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

    Piero Carninci

  304. 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

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

    Article • Gene, January 2007, Elsevier

    Piero Carninci

  306. Large-scale clustering of CAGE tag expression data

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

    Piero Carninci

  307. Simplified ontologies allowing comparison of developmental mammalian gene expression

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

    Piero Carninci

  308. Epigenetic regulation of critical period plasticity in visual cortex

    Article • Neuroscience Research, January 2007, Elsevier

    Piero Carninci

  309. 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

  310. 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

  311. 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

  312. Tagging mammalian transcription complexity

    Article • Trends in Genetics, September 2006, Elsevier

    Piero Carninci

  313. The complexity of the mammalian transcriptome

    Article • The Journal of Physiology, August 2006, Wiley

    Piero Carninci

  314. Transcriptional network dynamics in macrophage activation

    Article • Genomics, August 2006, Elsevier

    Piero Carninci

  315. Constructing ORFeome resources with removable termination codons

    Article • BioTechniques, July 2006, Future Science

    Piero Carninci

  316. Evolutionary turnover of mammalian transcription start sites

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

    Piero Carninci

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

    Article • Nature Genetics, April 2006, Nature

    Piero Carninci

  318. Subcellular Localization of Mammalian Type II Membrane Proteins

    Article • Traffic, March 2006, Wiley

    Piero Carninci

  319. CAGE: cap analysis of gene expression

    Article • Nature Chemical Biology, March 2006, Nature

    Piero Carninci

  320. Complex Loci in Human and Mouse Genomes

    Article • PLoS Genetics, January 2006, PLOS

    Altuna A, Piero Carninci

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

    Article • PLoS Genetics, January 2006, PLOS

    Piero Carninci

  322. A Simple Physical Model Predicts Small Exon Length Variations

    Article • PLoS Genetics, January 2006, PLOS

    Piero Carninci

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

    Piero Carninci

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

    Article • PLoS Genetics, January 2006, PLOS

    Piero Carninci

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

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

    Piero Carninci

  326. 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

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

    Piero Carninci

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

    Article • PLoS Genetics, January 2006, PLOS

    Piero Carninci

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

    Piero Carninci

  330. Heterotachy in Mammalian Promoter Evolution

    Article • PLoS Genetics, January 2006, PLOS

    Piero Carninci

  331. Mice and Men: Their Promoter Properties

    Article • PLoS Genetics, January 2006, PLOS

    Piero Carninci

  332. Pseudo–Messenger RNA: Phantoms of the Transcriptome

    Article • PLoS Genetics, January 2006, PLOS

    Piero Carninci

  333. The Abundance of Short Proteins in the Mammalian Proteome

    Article • PLoS Genetics, January 2006, PLOS

    Piero Carninci

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

    Article • PLoS Genetics, January 2006, PLOS

    Piero Carninci

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

    Piero Carninci

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

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

    Piero Carninci

  337. LOCATE: a mouse protein subcellular localization database

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

    Piero Carninci

  338. Antisense Transcription in the Mammalian Transcriptome

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

    Dr Hiromi Nishida, Piero Carninci

  339. The Transcriptional Landscape of the Mammalian Genome

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

    Piero Carninci, Professor Nikolai Petrovsky

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

    Article • Nature Chemical Biology, July 2005, Nature

    Piero Carninci

  341. 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

  342. 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

  343. 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

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

    Article • PLoS Genetics, January 2005, PLOS

    Piero Carninci

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

    Article • PLoS Genetics, January 2005, PLOS

    Piero Carninci

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

    Piero Carninci

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

    Article • Nature Chemical Biology, November 2004, Nature

    Piero Carninci

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

    Article • Protein Science, August 2004, Wiley

    Piero Carninci, Dr. Akiko Tanaka

  349. 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

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

    Article • Pigment Cell Research, June 2004, Wiley

    Piero Carninci

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

    Article • Genomics, June 2004, Elsevier

    Piero Carninci

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

    Article • PLoS Biology, April 2004, PLOS

    Piero Carninci

  353. 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

  354. 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

  355. 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

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

    Article • Protein Science, February 2004, Wiley

    Piero Carninci

  357. 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

  358. 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

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

    Piero Carninci

  360. 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

  361. 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

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

    Article • FEBS Letters, October 2003, Wiley

    Piero Carninci

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

    Article • BioTechniques, September 2003, Future Science

    Piero Carninci

  364. 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

  365. 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

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

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

    Piero Carninci

  367. 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

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

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

    Piero Carninci

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

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

    Piero Carninci

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

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

    Piero Carninci

  371. 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

  372. 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, Professor Nikolai Petrovsky

  373. 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

  374. 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

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

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

    Piero Carninci

  376. 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

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

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

    Piero Carninci

  378. 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

  379. 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

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

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

    Piero Carninci

  381. Mouse Proteome Analysis

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

    Piero Carninci

  382. Phosphoregulators: Protein Kinases and Protein Phosphatases of Mouse

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

    Piero Carninci

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

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

    Piero Carninci

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

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

    Piero Carninci

  385. 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

  386. 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

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

    Article • Gene, March 2003, Elsevier

    Piero Carninci

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

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

    Junshi Yazaki, Piero Carninci

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

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

    Piero Carninci

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

    Piero Carninci

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

    Piero Carninci

  392. 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

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

    Article • Nature, December 2002, Nature

    Piero Carninci, Professor Nikolai Petrovsky

  394. Initial sequencing and comparative analysis of the mouse genome

    Article • Nature, December 2002, Nature

    Piero Carninci

  395. 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

  396. 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

  397. 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

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

    Article • Gene, October 2002, Elsevier

    Piero Carninci

  399. On biased distribution of introns in various eukaryotes

    Article • Gene, October 2002, Elsevier

    Piero Carninci

  400. 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

  401. 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

  402. Cytoplasmic RNA Extraction from Fresh and Frozen Mammalian Tissues

    Article • BioTechniques, August 2002, Future Science

    Piero Carninci

  403. 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

  404. 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

  405. Extra-Long First-Strand cDNA Synthesis

    Article • BioTechniques, May 2002, Future Science

    Piero Carninci

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

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

    Piero Carninci

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

    Piero Carninci

  408. 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

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

    Article • BioTechniques, November 2001, Future Science

    Piero Carninci

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

    Article • Gene, October 2001, Elsevier

    Piero Carninci

  411. 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

  412. Meeting Report: 14th International Mouse Genome Conference

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

    Piero Carninci

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

    Article • BioTechniques, June 2001, Future Science

    Piero Carninci

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

    Article • Plant Physiology and Biochemistry, March 2001, Elsevier

    Piero Carninci

  415. 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

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

    Article • Nature, February 2001, Nature

    Piero Carninci, Kazuhito Toyooka

  417. 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

  418. 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

  419. 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

  420. 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

  421. 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

  422. 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

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

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

    Piero Carninci

  424. 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

  425. [2] High-efficiency full-length cDNA cloning

    Article • January 1999, Elsevier

    Piero Carninci

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

    Article • Genomics, December 1998, Elsevier

    Piero Carninci

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

    Article • The Plant Journal, September 1998, Wiley

    Piero Carninci

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

    Article • Genomics, April 1998, Elsevier

    Piero Carninci

  429. 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

  430. 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

  431. 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

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

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

    Piero Carninci

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

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

    Piero Carninci

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

    Article • Genomics, November 1996, Elsevier

    Piero Carninci

  435. 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

  436. 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

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

    Article • Wiley

    Piero Carninci

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

    Article • Institute of Electrical & Electronics Engineers (IEEE)

    Piero Carninci