Piero Carninci, Ph.D.


1989 Ph.D, Biological Sciences at University of Trieste

1990 National (Italian) Examination for the profession of Biologist, University of Ferrara, Italy

Career Positions

April 2008 - present Leader of the Functional Genomics Technology Team

Leader of the Omics Resource Development Unit

Deputy Project Director of the LSA Technology Development Group, RIKEN, Yokohama Institute, Japan

April 2006 Adjunctive Professor, Gunma University

April 2003 Senior Scientist at RIKEN, Wako, Genome Science Laboratory (tenure); adjunct appointment as Senior Scientist at RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Japan

Oct 2001 - Mar 2003 Scientist, Genome Science Laboratory (tenure), RIKEN, Wako, Japan

April 1997- Sept 2001 Scientist, RIKEN-Tsukuba Life Science Center, GS-laboratory (tenure), Japan

Oct 1995-March 1997 STA Fellow at RIKEN, Genome Science Laboratory, Wako, Japan

April 1995 - Sept 1995 Genome Science Laboratory research position at RIKEN,

Tsukuba, Japan.

Oct 1990- Mar 1995 Researcher at TALENT srl (http://www.spin.it/talent/).

Sept 1991- Dec 1993 Researcher with Prof. C. Schneider, director of the National Laboratory of Italian Consortium for Biotechnology, Trieste, Italy

Oct 1989 - Sept 1990 Health assistant in military hospital, part-time consultant in TALENT srl, Trieste, Italy

Compulsory Italian army duty as in a military hospital. At the same time, was a part-time consultant in a biotechnology company, TALENT srl, Trieste, Italy, and prepared the National examination.

April 1989-Sept 1989 Research Associate in laboratory of Prof. C. Schneider, ICGEB, Trieste, Italy, where he developed a discontinuous buffer system to increase speed and resolution in sequencing electrophoresis and methods for the rapid purification of Genomic DNA from whole blood and yeast.


  1. First prize of the Biotec Award in Milan, Italy for constructing full-length cDNA encyclopedia,

dedicated to Italian Scientists under 40 in biological research

  1. Yamazaki-Teiichi Award (http://www.mst.or.jp/prize/2007/jushou.html) for the developing

cap-trapper technology and its use for annotating genome output

2009 OSC Award 2009 “Development of the Cap Analysis of Gene Expression (CAGE) Method”

  1. OSC Award 2010 “Successful Completion of FANTOM4 project

Memberships and Chairs

Major Publications

Publications out of a total of over 200 papers, which have been cited 15,613 times (as of June 2011) with an H-index of 46.

  1. Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO, Carninci P, Forrest AR, Hayashizaki Y. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. Epub 2011 May 19.

  2. Salimullah M, Mizuho S, Plessy C, Carninci P. NanoCAGE: A High-Resolution Technique to Discover and Interrogate Cell Transcriptomes. Cold Spring Harb Protoc. 2011 Jan 1

  3. Plessy C, Bertin N, Takahashi H, Salimullah M, LassmannT, Vitezic M, Severin J, Olivarius S, Lazarevic D, Hornig N, Orland V, Bell I, Gao H, Dumais J, Kapranov P, Wang H, Davis CA, Gingeras TR, Kawai J, Daub CO, Hayashizaki Y, Gustincich S, Carninci P. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat. Methods. 7:528-34.2010

  4. Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren WM, Patone G, Petretto E, Plessy C, Rockland KS, Rockland C, Saar K, Zhao Y, Carninci P, Flicek P, Kurtz T, Cuppen E,Pravenec M, Hubner N, Jones SJ, Birney E, Aitman TJ. The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome Res. 20:791-803.2010

  5. Ravasi T. et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell. 140:744-52.2010

  6. Carninci P. Is Sequencing Enlightenment ending the Dark Age of the transcriptome? Nature Methods. 6:711-13.2009

  7. Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest AR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P. The regulated retrotransposon transcriptome of mammalian cells. Nat. Genet. 41:563-71.2009

  8. Taft R, Glazov EA, Cloonan N, Simons S, Stephen S, Faulkner G, Lassmann T, Forrest AR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A Hayashida K, Kawazu C, Murata M, Nishiyori H, Fukuda S, Kawai J, Daub CO, Hume DA, Suzuki H, Orlando V, Carninci P, Hayashizaki Y and Mattick J. Tiny RNAs associated with transcription start sites in animals, Nat. Genet.41:572-8.2009

  9. Suzuki H. et al. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet. 41:553-62. 2009

  10. Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori H, Lazarevic D, Motti D, Marstrand TT, Eric Tang MH, Zhao X, Krogh A, Winther O, Arakawa T, Kawai J, Wells C, Daub C, Harbers M, Hayashizaki Y, Gustincich S, Sandelin A, Carninci P. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res. 19:255-65.2009

  11. Sandelin A, Carninci P, Lenhard B, Ponjavic J. Hayashizaki Y, Hume DA. Mammalian RNA Polymerase II core promoters — insights from genome-wide studies. Nature Rev. Genetics 8:424-36.2007

  12. The ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447:799-816.2007

  13. Carninci P. et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genetics 38:626-35. 2006

  14. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, Wells C, Frith MC, Ravasi T, Pang KC­, Mattick JS, Hume DA, Lipovich L, Engström PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk A, Mottagui-Tabar S, Liang Z, Lenhard B, Wahlestedt C. Antisense transcription in the mammalian transcriptome. Science 309:1564-6. 2005

  15. FANTOM Consortium. The Transcriptional Landscape of the Mammalian Genome. Science. 309:1559-63. 2005