Piero Carnici (Piero Carninci)

ResearcherID Loop profile Scopus Author ID Scopus Author ID Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 58

Top Venues

Nature communications

Genome research

Nature methods

Nature

RIKEN Center for Integrative Medical Sciences

This page only lists publications with an associated author ORCID identifier.

Affiliation History

RIKEN Center for Integrative Medical Sciences

Japan

Deputy Center Director

Publications

Harshita Sharma, Matthew N Z Valentine, Naoko Toki, Hiromi Nishiyori Sueki, Stefano Gustincich, Hazuki Takahashi, Piero Carnici
Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation. Nature communications 15 (1) (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods 21 (7) (2024)
Akiko Oguchi, Akari Suzuki, Shuichiro Komatsu, Hiroyuki Yoshitomi, Shruti Bhagat, Raku Son, Raoul Jean Pierre Bonnal, Shohei Kojima, Masaru Koido, Kazuhiro Takeuchi, Keiko Myouzen, Gyo Inoue, Tomoya Hirai, Hiromi Sano, Yujiro Takegami, Ai Kanemaru, Itaru Yamaguchi, Yuki Ishikawa, Nao Tanaka, Shigeki Hirabayashi, Riyo Konishi, Sho Sekito, Takahiro Inoue, Juha Kere, Shunichi Takeda, Akifumi Takaori-Kondo, Itraru Endo, Shinpei Kawaoka, Hideya Kawaji, Kazuyoshi Ishigaki, Hideki Ueno, Yoshihide Hayashizaki, Massimiliano Pagani, Piero Carnici, Motoko Yanagita, null null, Nicholas F Parrish, Chikashi C Terao, Kazuhiko Yamamoto, Yasuhiro Murakawa, null null
An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases. Science (New York, N.Y.) 385 (6704) (2024)
Akiko Oguchi, Akari Suzuki, Shuichiro Komatsu, Hiroyuki Yoshitomi, Shruti Bhagat, Raku Son, Raoul Jean Pierre Bonnal, Shohei Kojima, Masaru Koido, Kazuhiro Takeuchi, Keiko Myouzen, Gyo Inoue, Tomoya Hirai, Hiromi Sano, Yujiro Takegami, Ai Kanemaru, Itaru Yamaguchi, Yuki Ishikawa, Nao Tanaka, Shigeki Hirabayashi, Riyo Konishi, Sho Sekito, Takahiro Inoue, Juha Kere, Shunichi Takeda, Akifumi Takaori-Kondo, Itraru Endo, Shinpei Kawaoka, Hideya Kawaji, Kazuyoshi Ishigaki, Hideki Ueno, Yoshihide Hayashizaki, Massimiliano Pagani, Piero Carnici, Motoko Yanagita, null null, Nicholas F Parrish, Chikashi C Terao, Kazuhiko Yamamoto, Yasuhiro Murakawa, null null
An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases. Science (New York, N.Y.) 385 (6704) (2024)
Silvia Carbonell-Sala, Tamara Perteghella, Julien Lagarde, Hiromi Nishiyori-Sueki, Emilio Palumbo, Carme Arnan, Hazuki Takahashi, Piero Carnici, Barbara Uszczynska-Ratajczak, Roderic Guigo
CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing. Nature communications 15 (1) (2024)
Weibin Liu, Yan Li, George P Patrinos, Shuhua Xu, Meow-Keong Thong, Zhengming Chen, Francis P Crawley, Liming Li, Perihan Elif Ekmekci, Radoje Drmanac, Weiyang Cheong, Robert Benamouzig, Quan Nguyen, Pavel Volchkov, Juergen K V Reichardt, Piero Carnici, Partha Majumder, Xin Jin, George M Church, Jian Wang, Xue Liu
The 1% gift to humanity: The Human Genome Project II. Cell research (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods (2024)
Silvia Carbonell-Sala, Tamara Perteghella, Julien Lagarde, Hiromi Nishiyori-Sueki, Emilio Palumbo, Carme Arnan, Hazuki Takahashi, Piero Carnici, Barbara Uszczynska-Ratajczak, Roderic Guigo
CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing. Nature communications 15 (1) (2024)
Harshita Sharma, Matthew N Z Valentine, Naoko Toki, Hiromi Nishiyori Sueki, Stefano Gustincich, Hazuki Takahashi, Piero Carnici
Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation. Nature communications 15 (1) (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods 21 (7) (2024)
Harshita Sharma, Matthew N Z Valentine, Naoko Toki, Hiromi Nishiyori Sueki, Stefano Gustincich, Hazuki Takahashi, Piero Carnici
Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation. Nature communications 15 (1) (2024)
Silvia Carbonell-Sala, Tamara Perteghella, Julien Lagarde, Hiromi Nishiyori-Sueki, Emilio Palumbo, Carme Arnan, Hazuki Takahashi, Piero Carnici, Barbara Uszczynska-Ratajczak, Roderic Guigo
CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing. Nature communications 15 (1) (2024)
Silvia Carbonell-Sala, Tamara Perteghella, Julien Lagarde, Hiromi Nishiyori-Sueki, Emilio Palumbo, Carme Arnan, Hazuki Takahashi, Piero Carnici, Barbara Uszczynska-Ratajczak, Roderic Guigo
CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing. Nature communications 15 (1) (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods 21 (7) (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods 21 (7) (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods (2024)
Silvia Carbonell-Sala, Julien Lagarde, Hiromi Nishiyori, Emilio Palumbo, Carme Arnan, Hazuki Takahashi, Piero Carnici, Barbara Uszczynska-Ratajczak, Roderic Guigó
CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing. bioRxiv : the preprint server for biology (2023)
Giovanni Pascarella, Martin C Frith, Piero Carnici
A new layer of complexity in the human genome: Somatic recombination of repeat elements. Clinical and translational medicine 13 (3) (2023)
Tadashi Takeuchi, Tetsuya Kubota, Yumiko Nakanishi, Hiroshi Tsugawa, Wataru Suda, Andrew Tae-Jun Kwon, Junshi Yazaki, Kazutaka Ikeda, Shino Nemoto, Yoshiki Mochizuki, Toshimori Kitami, Katsuyuki Yugi, Yoshiko Mizuno, Nobutake Yamamichi, Tsutomu Yamazaki, Iseki Takamoto, Naoto Kubota, Takashi Kadowaki, Erik Arner, Piero Carnici, Osamu Ohara, Makoto Arita, Masahira Hattori, Shigeo Koyasu, Hiroshi Ohno
Gut microbial carbohydrate metabolism contributes to insulin resistance. Nature (2023)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell-Sala, Brian Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose M Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew Berry, Salvador Capella, Angela N Brooks, Jose M Fernandez-Gonzalez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Goetz, Carles Hernández-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Eric C Rouchka, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid Ashley Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigó, Margaret E Hunter, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. bioRxiv : the preprint server for biology (2023)
Paulo Amaral, Silvia Carbonell-Sala, Francisco M De La Vega, Tiago Faial, Adam Frankish, Thomas Gingeras, Roderic Guigo, Jennifer L Harrow, Artemis G Hatzigeorgiou, Rory Johnson, Terence D Murphy, Mihaela Pertea, Kim D Pruitt, Shashikant Pujar, Hazuki Takahashi, Igor Ulitsky, Ales Varabyou, Christine A Wells, Mark Yandell, Piero Carnici, Steven L Salzberg
The status of the human gene catalogue. Nature 622 (7981) (2023)
John S Mattick, Paulo P Amaral, Piero Carnici, Susan Carpenter, Howard Y Chang, Ling-Ling Chen, Runsheng Chen, Caroline Dean, Marcel E Dinger, Katherine A Fitzgerald, Thomas R Gingeras, Mitchell Guttman, Tetsuro Hirose, Maite Huarte, Rory Johnson, Chandrasekhar Kanduri, Philipp Kapranov, Jeanne B Lawrence, Jeannie T Lee, Joshua T Mendell, Timothy R Mercer, Kathryn J Moore, Shinichi Nakagawa, John L Rinn, David L Spector, Igor Ulitsky, Yue Wan, Jeremy E Wilusz, Mian Wu
Long non-coding RNAs: definitions, functions, challenges and recommendations. Nature reviews. Molecular cell biology (2023)
Giovanni Pascarella, Martin C Frith, Piero Carnici
A new layer of complexity in the human genome: Somatic recombination of repeat elements. Clinical and translational medicine 13 (3) (2023)
Caterina Gasperini, Kiril Tuntevski, Silvia Beatini, Roberta Pelizzoli, Amanda Lo Van, Damiano Mangoni, Rosa M Cossu, Giovanni Pascarella, Paolo Bianchini, Pascal Bielefeld, Margherita Scarpato, Meritxell Pons-Espinal, Remo Sanges, Alberto Diaspro, Carlos P Fitzsimons, Piero Carnici, Stefano Gustincich, Davide De Pietri Tonelli
Piwil2 (Mili) sustains neurogenesis and prevents cellular senescence in the postnatal hippocampus. EMBO reports (2022)
Stefano Espinoza, Carlotta Bon, Paola Valentini, Bianca Pierattini, Abraham Tettey Matey, Devid Damiani, Salvatore Pulcrano, Remo Sanges, Francesca Persichetti, Hazuki Takahashi, Piero Carnici, Claudio Santoro, Diego Cotella, Stefano Gustincich
SINEUPs: a novel toolbox for RNA therapeutics. Essays in biochemistry 65 (4) (2022)
Guojun Sheng, Piero Carnici, Mikiko C Siomi, Toshio Suda, Cantas Alev
Japan: prize diversity, not conformity, to boost research. Nature 599 (7884) (2022)
Nicolas J Pillon, Jonathon A B Smith, Petter S Alm, Alexander Valerievich Chibalin, Julia Alhusen, Erik Arner, Piero Carnici, Tomas Fritz, Julia Otten, Tommy Olsson, Sophie van Doorslaer de Ten Ryen, Louise Deldicque, Kenneth Caidahl, Harriet Wallberg-Henriksson, Anna Krook, Juleen R Zierath
Distinctive exercise-induced inflammatory response and exerkine induction in skeletal muscle of people with type 2 diabetes. Science advances 8 (36) (2022)
Jonathan Moody, Tsukasa Kouno, Jen-Chien Chang, Yoshinari Ando, Piero Carnici, Jay W Shin, Chung-Chau Hon
SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells. Bioinformatics (Oxford, England) 38 (22) (2022)
Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli, Jordan A Ramilowski, Jessica Severin, Yoshihide Hayashizaki, Masayoshi Itoh, Michihira Tagami, Mitsuyoshi Murata, Miki Kojima-Ishiyama, Shohei Noma, Shuhei Noguchi, Takeya Kasukawa, Akira Hasegawa, Harukazu Suzuki, Hiromi Nishiyori-Sueki, Martin C Frith, null null, Clément Chatelain, Piero Carnici, Michiel J L de Hoon, Wyeth W Wasserman, Laurent Bréhélin, Charles-Henri Lecellier
Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature communications 13 (1) (2022)
Michiel J L de Hoon, Alessandro Bonetti, Charles Plessy, Yoshinari Ando, Chung-Chau Hon, Yuri Ishizu, Masayoshi Itoh, Sachi Kato, Dongyan Lin, Sho Maekawa, Mitsuyoshi Murata, Hiromi Nishiyori, Jay W Shin, Jens Stolte, Ana Maria Suzuki, Michihira Tagami, Hazuki Takahashi, Supat Thongjuea, Alistair R R Forrest, Yoshihide Hayashizaki, Juha Kere, Piero Carnici
Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs. Genome research (2022)
Damir Baranasic, Matthias Hörtenhuber, Piotr J Balwierz, Tobias Zehnder, Abdul Kadir Mukarram, Chirag Nepal, Csilla Varnai, Yavor Hadzhiev, Ada Jimenez Gonzalez, Nan Li, Joseph Wragg, Fabio M D'Orazio, Dorde Relic, Mikhail Pachkov, Noelia Díaz, Benjamín Hernández-Rodríguez, Zelin Chen, Marcus Stoiber, Michael X Dong, Irene Stevens, Samuel E Ross, Anne Eagle, Ryan Martin, Oluwapelumi Obasaju, Sepand Rastegar, Alison C McGarvey, Wolfgang Kopp, Emily V Chambers, Dennis Wang, Hyejeong R Kim, Rafael D Acemel, Silvia Naranjo, Maciej Łapiński, Vanessa Chong-Morrison, Sinnakaruppan Mathavan, Bernard Peers, Tatjana Sauka-Spengler, Martin Vingron, Piero Carnici, Uwe Ohler, Scott Allen Lacadie, Jason W Sinclair, Cecilia Lanny Winata, Fredericus J M van Eeden, Juan M Vaquerizas, José Luis Gómez-Skarmeta, Daria Onichtchouk, Ben James Brown, Ozren Bogdanovic, Erik van Nimwegen, Monte Westerfield, Fiona C Wardle, Carsten O Daub, Boris Lenhard, Ferenc Müller
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nature genetics 54 (7) (2022)
Masaru Koido, Chung-Chau Hon, Satoshi Koyama, Hideya Kawaji, Yasuhiro Murakawa, Kazuyoshi Ishigaki, Kaoru Ito, Jun Sese, Nicholas F Parrish, Yoichiro Kamatani, Piero Carnici, Chikashi C Terao
Prediction of the cell-type-specific transcription of non-coding RNAs from genome sequences via machine learning. Nature biomedical engineering (2022)
Gregory P Way, Casey S Greene, Piero Carnici, Benilton S Carvalho, Michiel J L de Hoon, Stacey D Finley, Sara J C Gosline, Kim-Anh Lê Cao, Jerry S H Lee, Luigi Marchionni, Nicolas Robine, Suzanne S Sindi, Fabian Joachim Theis, Jean Yee Hwa Yang, Anne E Carpenter, Elana J Fertig
A field guide to cultivating computational biology. PLoS biology 19 (10) (2021)
Sanjana Pillay, Hazuki Takahashi, Piero Carnici, Aditi Kanhere
Antisense RNAs during early vertebrate development are divided in groups with distinct features. Genome research 31 (6) (2021)
Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli, Jordan A Ramilowski, Jessica Severin, Yoshihide Hayashizaki, Masayoshi Itoh, Michihira Tagami, Mitsuyoshi Murata, Miki Kojima-Ishiyama, Shohei Noma, Shuhei Noguchi, Takeya Kasukawa, Akira Hasegawa, Harukazu Suzuki, Hiromi Nishiyori-Sueki, Martin C Frith, null null, Clément Chatelain, Piero Carnici, Michiel J L de Hoon, Wyeth W Wasserman, Laurent Bréhélin, Charles-Henri Lecellier
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature communications 12 (1) (2021)
Luca Ducoli, Saumya Agrawal, Eliane Sibler, Tsukasa Kouno, Carlotta Tacconi, Chung-Chau Hon, Simone D Berger, Daniela Müllhaupt, Yuliang He, Jihye Kim, Marco D'Addio, Lothar C Dieterich, Piero Carnici, Michiel J L de Hoon, Jay W Shin, Michael Detmar
LETR1 is a lymphatic endothelial-specific lncRNA governing cell proliferation and migration through KLF4 and SEMA3C. Nature communications 12 (1) (2021)
Kosuke Hashimoto, Eeva-Mari Jouhilahti, Virpi Töhönen, Piero Carnici, Juha Kere, Shintaro Katayama
Embryonic LTR retrotransposons supply promoter modules to somatic tissues. Genome research 31 (11) (2021)
Alessandro Bonetti, Federico Agostini, Ana Maria Suzuki, Kosuke Hashimoto, Giovanni Pascarella, Juliette Gimenez, Leonie Roos, Alex J Nash, Marco Ghilotti, Christopher J F Cameron, Matthew Valentine, Yulia A Medvedeva, Shuhei Noguchi, Eneritz Agirre, Kaori Kashi, null Samudyata, Joachim Luginbühl, Riccardo Cazzoli, Saumya Agrawal, Nicholas M Luscombe, Mathieu Blanchette, Takeya Kasukawa, Michiel de Hoon, Erik Arner, Boris Lenhard, Charles Plessy, Gonçalo Castelo-Branco, Valerio Orlando, Piero Carnici
Author Correction: RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions. Nature communications 12 (1) (2021)
Alessandro Bonetti, Federico Agostini, Ana Maria Suzuki, Kosuke Hashimoto, Giovanni Pascarella, Juliette Gimenez, Leonie Roos, Alex J Nash, Marco Ghilotti, Christopher J F Cameron, Matthew Valentine, Yulia A Medvedeva, Shuhei Noguchi, Eneritz Agirre, Kaori Kashi, null Samudyata, Joachim Luginbühl, Riccardo Cazzoli, Saumya Agrawal, Nicholas M Luscombe, Mathieu Blanchette, Takeya Kasukawa, Michiel de Hoon, Erik Arner, Boris Lenhard, Charles Plessy, Gonçalo Castelo-Branco, Valerio Orlando, Piero Carnici
RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions. Nature communications 11 (1) (2020)
Chirag Nepal, Yavor Hadzhiev, Piotr J Balwierz, Estefanía Tarifeño-Saldivia, Ryan Cardenas, Joseph W Wragg, Ana-Maria Suzuki, Piero Carnici, Bernard Peers, Boris Lenhard, Jesper B Andersen, Ferenc Müller
Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing. Nature communications 11 (1) (2020)
Jordan A Ramilowski, Chi Wai Yip, Saumya Agrawal, Jen-Chien Chang, Yari Ciani, Ivan V Kulakovskiy, Mickaël Mendez, Jasmine Li Ching Ooi, John F Ouyang, Nick Parkinson, Andreas Petri, Leonie Roos, Jessica Severin, Kayoko Yasuzawa, Imad Abugessaisa, Altuna Akalin, Ivan V Antonov, Erik Arner, Alessandro Bonetti, Hidemasa Bono, Beatrice Borsari, Frank Brombacher, Christopher JF Cameron, Carlo Vittorio Cannistraci, Ryan Cardenas, Melissa Cardon, Howard Chang, Josée Dostie, Luca Ducoli, Alexander Favorov, Alexandre Fort, Diego Garrido, Noa Gil, Juliette Gimenez, Reto Guler, Lusy Handoko, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Kosuke Hashimoto, Norihito Hayatsu, Peter Heutink, Tetsuro Hirose, Eddie L Imada, Masayoshi Itoh, Bogumil Kaczkowski, Aditi Kanhere, Emily Kawabata, Hideya Kawaji, Tsugumi Kawashima, S Thomas Kelly, Miki Kojima, Naoto Kondo, Haruhiko Koseki, Tsukasa Kouno, Anton Kratz, Mariola Kurowska-Stolarska, Andrew Tae Jun Kwon, Jeffrey Leek, Andreas Lennartsson, Marina Lizio, Fernando López-Redondo, Joachim Luginbühl, Shiori Maeda, Vsevolod J Makeev, Luigi Marchionni, Yulia A Medvedeva, Aki Minoda, Ferenc Müller, Manuel Muñoz-Aguirre, Mitsuyoshi Murata, Hiromi Nishiyori, Kazuhiro R Nitta, Shuhei Noguchi, Yukihiko Noro, Ramil Nurtdinov, Yasushi Okazaki, Valerio Orlando, Denis Paquette, Callum J C Parr, Owen J L Rackham, Patrizia Rizzu, Diego Fernando Sánchez Martinez, Albin Sandelin, Pillay Sanjana, Colin A M Semple, Youtaro Shibayama, Divya M Sivaraman, Takahiro Suzuki, Suzannah C Szumowski, Michihira Tagami, Martin S Taylor, Chikashi Terao, Malte Thodberg, Supat Thongjuea, Vidisha Tripathi, Igor Ulitsky, Roberto Verardo, Ilya E Vorontsov, Chinatsu Yamamoto, Robert S Young, John Kenneth Baillie, Alistair R R Forrest, Roderic Guigó, Michael M Hoffman, Chung Chau Hon, Takeya Kasukawa, Sakari Kauppinen, Juha Kere, Boris Lenhard, Claudio Schneider, Harukazu Suzuki, Ken Yagi, Michiel J L de Hoon, Jay W Shin, Piero Carnici
Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome research 30 (7) (2020)
Tanvir Alam, Saumya Agrawal, Jessica Severin, Robert S Young, Robin Andersson, Erik Arner, Akira Hasegawa, Marina Lizio, Jordan A Ramilowski, Imad Abugessaisa, Yuri Ishizu, Shohei Noma, Hiroshi Tarui, Martin S Taylor, Timo Lassmann, Masayoshi Itoh, Takeya Kasukawa, Hideya Kawaji, Luigi Marchionni, Guojun Sheng, Alistair R R Forrest, Levon Michael Khachigian, Yoshihide Hayashizaki, Piero Carnici, Michiel J L de Hoon
Comparative transcriptomics of primary cells in vertebrates. Genome research 30 (7) (2020)
Eddie Luidy Imada, Diego Fernando Sanchez, Leonardo Collado-Torres, Christopher Wilks, Tejasvi Matam, Wikum Dinalankara, Aleksey Stupnikov, Francisco Pereira Lobo, Chi-Wai Yip, Kayoko Yasuzawa, Naoto Kondo, Masayoshi Itoh, Harukazu Suzuki, Takeya Kasukawa, Chung-Chau Hon, Michiel J L de Hoon, Jay W Shin, Piero Carnici, Andrew E Jaffe, Jeffery T Leek, Alexander V Favorov, Gloria R Franco, Ben Langmead, Luigi Marchionni
Recounting the FANTOM CAGE-Associated Transcriptome. Genome research 30 (7) (2020)
Naoko Toki, Hazuki Takahashi, Silvia Zucchelli, Stefano Gustincich, Piero Carnici
Synthetic in vitro transcribed lncRNAs (SINEUPs) with chemical modifications enhance target mRNA translation. FEBS letters 594 (24) (2020)
Roberto Bassi, Enrico M Bucci, Raffaele A Calogero, Piero Carnici, Gennaro Ciliberto, Pellegrino Conte, Michele De Luca, Gilberto Corbellini, Antonio Giordano, Luigi Marchionni, Giacomina Massaro Giordano, Angelo Parini, Gianluca Sbardella
Look for methods, not conclusions. Cell death & disease 10 (12) (2019)
Angela Solano, Giuseppe Novelli, Shruti Baghat, Piero Carnici, Gert-Jan van Ommen, Juergen K V Reichardt
Meeting report: The Human Genome Meeting (HGM) 2019 in Seoul, Korea. European journal of human genetics : EJHG 28 (1) (2019)
Shigeki Hirabayashi, Shruti Bhagat, Yu Matsuki, Yujiro Takegami, Takuya Uehata, Ai Kanemaru, Masayoshi Itoh, Kotaro Shirakawa, Akifumi Takaori-Kondo, Osamu Takeuchi, Piero Carnici, Shintaro Katayama, Yoshihide Hayashizaki, Juha Kere, Hideya Kawaji, Yasuhiro Murakawa
NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Nature genetics 51 (9) (2019)
Tsukasa Kouno, Jonathan Moody, Andrew Tae-Jun Kwon, Youtaro Shibayama, Sachi Kato, Yi Huang, Michael Böttcher, Efthymios Motakis, Mickaël Mendez, Jessica Severin, Joachim Luginbühl, Imad Abugessaisa, Akira Hasegawa, Satoshi Takizawa, Takahiro Arakawa, Masaaki Furuno, Naveen Ramalingam, Jay West, Harukazu Suzuki, Takeya Kasukawa, Timo Lassmann, Chung-Chau Hon, Erik Arner, Piero Carnici, Charles Plessy, Jay W Shin
C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution. Nature communications 10 (1) (2019)
Kosuke Hashimoto, Tsukasa Kouno, Tomokatsu Ikawa, Norihito Hayatsu, Yurina Miyajima, Haruka Yabukami, Tommy Terooatea, Takashi Sasaki, Takahiro Suzuki, Matthew Valentine, Giovanni Pascarella, Yasushi Okazaki, Harukazu Suzuki, Jay W Shin, Aki Minoda, Ichiro Taniuchi, Hideyuki Okano, Yasumichi Arai, Nobuyoshi Hirose, Piero Carnici
Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians. Proceedings of the National Academy of Sciences of the United States of America 116 (48) (2019)
Quan Nguyen, Julio Aguado, Fabio Iannelli, Ana Maria Suzuki, Francesca Rossiello, Fabrizio d'Adda di Fagagna, Piero Carnici
Target-enrichment sequencing for detailed characterization of small RNAs. Nature protocols 13 (4) (2018)
John Kenneth Baillie, Andrew D Bretherick, Christopher S Haley, Sara Clohisey Hendry, Alan Gray, Lucile P A Neyton, Jeffrey Barrett, Eli A Stahl, Albert Tenesa, Robin Andersson, J Ben Brown, Geoffrey J Faulkner, Marina Lizio, Ulf Schaefer, Carsten Daub, Masayoshi Itoh, Naoto Kondo, Timo Lassmann, Jun Kawai, null null, Damian J Mole, Vladimir B Bajic, Peter Heutink, Michael Rehli, Hideya Kawaji, Albin Sandelin, Harukazu Suzuki, Jack Satsangi, Christine A Wells, Nir Hacohen, Thomas C Freeman, Yoshihide Hayashizaki, Piero Carnici, Alistair R R Forrest, David A Hume
Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. PLoS computational biology 14 (3) (2018)
Jayson Harshbarger, Anton Kratz, Piero Carnici
DEIVA: a web application for interactive visual analysis of differential gene expression profiles. BMC genomics 18 (1) (2017)
Fabio Iannelli, Alessandro Galbiati, Ilaria Capozzo, Quan Nguyen, Brian Magnuson, Flavia Michelini, Giuseppina D'Alessandro, Matteo Cabrini, Marco Roncador, Sofia Francia, Nicola Crosetto, Mats Ljungman, Piero Carnici, Fabrizio d'Adda di Fagagna
A damaged genome's transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks. Nature communications 8 (2017)
Derek de Rie, Imad Abugessaisa, Tanvir Alam, Erik Arner, Peter Arner, Haitham Ashoor, Gaby Åström, Magda Babina, Nicolas Bertin, A Maxwell Burroughs, Ailsa J Carlisle, Carsten O Daub, Michael Detmar, Ruslan Deviatiiarov, Alexandre Fort, Claudia Gebhard, Daniel Goldowitz, Sven Guhl, Thomas J Ha, Jayson Harshbarger, Akira Hasegawa, Kosuke Hashimoto, Meenhard Herlyn, Peter Heutink, Kelly J Hitchens, Chung-Chau Hon, Edward Huang, Yuri Ishizu, Chieko Kai, Takeya Kasukawa, Peter Klinken, Timo Lassmann, Charles-Henri Lecellier, Weonju Lee, Marina Lizio, Vsevolod J Makeev, Anthony Mathelier, Yulia A Medvedeva, Niklas Mejhert, Christopher J Mungall, Shohei Noma, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Helena Persson, Patrizia Rizzu, Filip Roudnicky, Pål Saetrom, Hiroki Sato, Jessica Severin, Jay W Shin, Rolf K Swoboda, Hiroshi Tarui, Hiroo Toyoda, Kristoffer Vitting-Seerup, Louise Winteringham, Yoko Yamaguchi, Kayoko Yasuzawa, Misako Yoneda, Noriko Yumoto, Susan Zabierowski, Peter G Zhang, Christine A Wells, Kim M Summers, Hideya Kawaji, Albin Sandelin, Michael Rehli, null null, Yoshihide Hayashizaki, Piero Carnici, Alistair R R Forrest, Michiel J L de Hoon
An integrated expression atlas of miRNAs and their promoters in human and mouse. Nature biotechnology 35 (9) (2017)
Aviv Regev, Sarah A Teichmann, Eric S Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, Peter Campbell, Piero Carnici, Menna Clatworthy, Hans Clevers, Bart Deplancke, Ian Dunham, James Eberwine, Roland Eils, Wolfgang Enard, Andrew Farmer, Lars Fugger, Berthold Göttgens, Nir Hacohen, Muzlifah A Haniffa, Martin Hemberg, Seung Kim, Paul Klenerman, Arnold Kriegstein, Ed S Lein, Sten Linnarsson, Emma Lundberg, Joakim Lundeberg, Partha Majumder, John C Marioni, Miriam Merad, Musa Mhlanga, Martijn Nawijn, Mihai Netea, Garry Nolan, Dana Pe'er, Anthony Phillipakis, Chris Paul Ponting, Stephen Quake, Wolf Reik, Orit Rozenblatt-Rosen, Joshua R Sanes, Rahul Satija, Ton N Schumacher, Alex Shalek, Ehud Shapiro, Padmanee Sharma, Jay W Shin, Oliver Stegle, Michael Stratton, Michael J T Stubbington, Fabian J Theis, Matthias Uhlen, Alexander van Oudenaarden, Allon Wagner, Fiona M Watt, Jonathan S Weissman, Barbara Wold, Ramnik Xavier, Nir Yosef, null null
The Human Cell Atlas. eLife 6 (2017)
Marco Garieri, Olivier Delaneau, Federico Santoni, Richard J Fish, David Mull, Piero Carnici, Emmanouil T Dermitzakis, Stylianos E Antonarakis, Alexandre Fort
The effect of genetic variation on promoter usage and enhancer activity. Nature communications 8 (1) (2017)
Francesca Rossiello, Julio Aguado, Sara Sepe, Fabio Iannelli, Quan Nguyen, Sethuramasundaram Pitchiaya, Piero Carnici, Fabrizio d'Adda di Fagagna
DNA damage response inhibition at dysfunctional telomeres by modulation of telomeric DNA damage response RNAs. Nature communications 8 (2017)
Atsushi Hoshino, Vasanthan Jayakumar, Eiji Nitasaka, Atsushi Toyoda, Hideki Noguchi, Takehiko Itoh, Tadasu Shin-I, Yohei Minakuchi, Yuki Koda, Atsushi J Nagano, Masaki Yasugi, Mie N Honjo, Hiroshi Kudoh, Motoaki Seki, Asako Kamiya, Toshiyuki Shiraki, Piero Carnici, Erika Asamizu, Hiroyo Nishide, Sachiko Tanaka, Kyeung-Il Park, Yasumasa Morita, Kohei Yokoyama, Ikuo Uchiyama, Yoshikazu Tanaka, Satoshi Tabata, Kazuo Shinozaki, Yoshihide Hayashizaki, Yuji Kohara, Yutaka Suzuki, Sumio Sugano, Asao Fujiyama, Shigeru Iida, Yasubumi Sakakibara
Genome sequence and analysis of the Japanese morning glory Ipomoea nil. Nature communications 7 (2016)

Piero Carnici.css-eqlu8i{font-size:small;padding-left:4px;} (Piero Carninci)

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Piero Carnici (Piero Carninci)