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

por Tang, Dave T. P., Plessy, Charles, Salimullah, Md, Suzuki, Ana Maria, Calligaris, Raffaella, Gustincich, Stefano, Carninci, Piero
Publicado 2013

Digital expression profiling of the compartmentalized translatome of Purkinje neurons

por Kratz, Anton, Beguin, Pascal, Kaneko, Megumi, Chimura, Takahiko, Suzuki, Ana Maria, Matsunaga, Atsuko, Kato, Sachi, Bertin, Nicolas, Lassmann, Timo, Vigot, Réjan, Carninci, Piero, Plessy, Charles, Launey, Thomas
Publicado 2014

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

por Nepal, Chirag, Hadzhiev, Yavor, Balwierz, Piotr, Tarifeño-Saldivia, Estefanía, Cardenas, Ryan, Wragg, Joseph W., Suzuki, Ana-Maria, Carninci, Piero, Peers, Bernard, Lenhard, Boris, Andersen, Jesper B., Müller, Ferenc
Publicado 2020

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

por Tebbi, Ali, Levillayer, Florence, Jouvion, Grégory, Fiette, Laurence, Soubigou, Guillaume, Varet, Hugo, Boudjadja, Nesrine, Cairo, Stefano, Hashimoto, Kosuke, Suzuki, Ana Maria, Carninci, Piero, Carissimo, Annamaria, di Bernardo, Diego, Wei, Yu
Publicado 2016

Two independent transcription initiation codes overlap on vertebrate core promoters

por Haberle, Vanja, Li, Nan, Hadzhiev, Yavor, Plessy, Charles, Previti, Christopher, Nepal, Chirag, Gehrig, Jochen, Dong, Xianjun, Akalin, Altuna, Suzuki, Ana Maria, van IJcken, Wilfred F.J., Armant, Olivier, Ferg, Marco, Strähle, Uwe, Carninci, Piero, Müller, Ferenc, Lenhard, Boris
Publicado 2014

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

por Hashimoto, Kosuke, Suzuki, Ana Maria, Dos Santos, Alexandre, Desterke, Christophe, Collino, Agnese, Ghisletti, Serena, Braun, Emilie, Bonetti, Alessandro, Fort, Alexandre, Qin, Xian-Yang, Radaelli, Enrico, Kaczkowski, Bogumil, Forrest, Alistair R.R., Kojima, Soichi, Samuel, Didier, Natoli, Gioacchino, Buendia, Marie Annick, Faivre, Jamila, Carninci, Piero
Publicado 2015

Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs

por de Hoon, Michiel, Bonetti, Alessandro, Plessy, Charles, Ando, Yoshinari, Hon, Chung-Chau, Ishizu, Yuri, Itoh, Masayoshi, Kato, Sachi, Lin, Dongyan, Maekawa, Sho, Murata, Mitsuyoshi, Nishiyori, Hiromi, Shin, Jay W., Stolte, Jens, Suzuki, Ana Maria, Tagami, Michihira, Takahashi, Hazuki, Thongjuea, Supat, Forrest, Alistair R.R., Hayashizaki, Yoshihide, Kere, Juha, Carninci, Piero
Publicado 2022

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

por Altinel, Kübra, Hashimoto, Kosuke, Wei, Yu, Neuveut, Christine, Gupta, Ishita, Suzuki, Ana Maria, Dos Santos, Alexandre, Moreau, Pierrick, Xia, Tian, Kojima, Soichi, Kato, Sachi, Takikawa, Yasuhiro, Hidaka, Isao, Shimizu, Masahito, Matsuura, Tomokazu, Tsubota, Akihito, Ikeda, Hitoshi, Nagoshi, Sumiko, Suzuki, Harukazu, Michel, Marie-Louise, Samuel, Didier, Buendia, Marie Annick, Faivre, Jamila, Carninci, Piero
Publicado 2016

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

por Nepal, Chirag, Hadzhiev, Yavor, Previti, Christopher, Haberle, Vanja, Li, Nan, Takahashi, Hazuki, Suzuki, Ana Maria M., Sheng, Ying, Abdelhamid, Rehab F., Anand, Santosh, Gehrig, Jochen, Akalin, Altuna, Kockx, Christel E.M., van der Sloot, Antoine A.J., van IJcken, Wilfred F.J., Armant, Olivier, Rastegar, Sepand, Watson, Craig, Strähle, Uwe, Stupka, Elia, Carninci, Piero, Lenhard, Boris, Müller, Ferenc
Publicado 2013

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

por Bonetti, Alessandro, Agostini, Federico, Suzuki, Ana Maria, Hashimoto, Kosuke, Pascarella, Giovanni, Gimenez, Juliette, Roos, Leonie, Nash, Alex J., Ghilotti, Marco, Cameron, Christopher J.  F., Valentine, Matthew, Medvedeva, Yulia A., Noguchi, Shuhei, Agirre, Eneritz, Kashi, Kaori, Samudyata, Luginbühl, Joachim, Cazzoli, Riccardo, Agrawal, Saumya, Luscombe, Nicholas M., Blanchette, Mathieu, Kasukawa, Takeya, Hoon, Michiel de, Arner, Erik, Lenhard, Boris, Plessy, Charles, Castelo-Branco, Gonçalo, Orlando, Valerio, Carninci, Piero
Publicado 2020

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

por Bonetti, Alessandro, Agostini, Federico, Suzuki, Ana Maria, Hashimoto, Kosuke, Pascarella, Giovanni, Gimenez, Juliette, Roos, Leonie, Nash, Alex J., Ghilotti, Marco, Cameron, Christopher J. F., Valentine, Matthew, Medvedeva, Yulia A., Noguchi, Shuhei, Agirre, Eneritz, Kashi, Kaori, Samudyata, Luginbühl, Joachim, Cazzoli, Riccardo, Agrawal, Saumya, Luscombe, Nicholas M., Blanchette, Mathieu, Kasukawa, Takeya, de Hoon, Michiel, Arner, Erik, Lenhard, Boris, Plessy, Charles, Castelo-Branco, Gonçalo, Orlando, Valerio, Carninci, Piero
Publicado 2021

Diversity and dynamics of the Drosophila transcriptome

por Brown, James B., Boley, Nathan, Eisman, Robert, May, Gemma E., Stoiber, Marcus H., Duff, Michael O., Booth, Ben W., Wen, Jiayu, Park, Soo, Suzuki, Ana Maria, Wan, Kenneth H., Yu, Charles, Zhang, Dayu, Carlson, Joseph W., Cherbas, Lucy, Eads, Brian D., Miller, David, Mockaitis, Keithanne, Roberts, Johnny, Davis, Carrie A., Frise, Erwin, Hammonds, Ann S., Olson, Sara, Shenker, Sol, Sturgill, David, Samsonova, Anastasia A., Weiszmann, Richard, Robinson, Garret, Hernandez, Juan, Andrews, Justen, Bickel, Peter J., Carninci, Piero, Cherbas, Peter, Gingeras, Thomas R., Hoskins, Roger A., Kaufman, Thomas C., Lai, Eric C., Oliver, Brian, Perrimon, Norbert, Graveley, Brenton R., Celniker, Susan E.
Publicado 2014

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

por Chen, Zhen-Xia, Sturgill, David, Qu, Jiaxin, Jiang, Huaiyang, Park, Soo, Boley, Nathan, Suzuki, Ana Maria, Fletcher, Anthony R., Plachetzki, David C., FitzGerald, Peter C., Artieri, Carlo G., Atallah, Joel, Barmina, Olga, Brown, James B., Blankenburg, Kerstin P., Clough, Emily, Dasgupta, Abhijit, Gubbala, Sai, Han, Yi, Jayaseelan, Joy C., Kalra, Divya, Kim, Yoo-Ah, Kovar, Christie L., Lee, Sandra L., Li, Mingmei, Malley, James D., Malone, John H., Mathew, Tittu, Mattiuzzo, Nicolas R., Munidasa, Mala, Muzny, Donna M., Ongeri, Fiona, Perales, Lora, Przytycka, Teresa M., Pu, Ling-Ling, Robinson, Garrett, Thornton, Rebecca L., Saada, Nehad, Scherer, Steven E., Smith, Harold E., Vinson, Charles, Warner, Crystal B., Worley, Kim C., Wu, Yuan-Qing, Zou, Xiaoyan, Cherbas, Peter, Kellis, Manolis, Eisen, Michael B., Piano, Fabio, Kionte, Karin, Fitch, David H., Sternberg, Paul W., Cutter, Asher D., Duff, Michael O., Hoskins, Roger A., Graveley, Brenton R., Gibbs, Richard A., Bickel, Peter J., Kopp, Artyom, Carninci, Piero, Celniker, Susan E., Oliver, Brian, Richards, Stephen
Publicado 2014

Landscape of transcription in human cells

por Djebali, Sarah, Davis, Carrie A., Merkel, Angelika, Dobin, Alex, Lassmann, Timo, Mortazavi, Ali M., Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Schlesinger, Felix, Xue, Chenghai, Marinov, Georgi K., Khatun, Jainab, Williams, Brian A., Zaleski, Chris, Rozowsky, Joel, Röder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F., Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T., Bar, Nadav S., Batut, Philippe, Bell, Kimberly, Bell, Ian, Chakrabortty, Sudipto, Chen, Xian, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jacqueline, Duttagupta, Radha, Falconnet, Emilie, Fastuca, Meagan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J., Gao, Hui, Gonzalez, David, Gordon, Assaf, Gunawardena, Harsha, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Luo, Oscar J., Park, Eddie, Persaud, Kimberly, Preall, Jonathan B., Ribeca, Paolo, Risk, Brian, Robyr, Daniel, Sammeth, Michael, Schaffer, Lorian, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Wrobel, John, Yu, Yanbao, Ruan, Xiaoan, Hayashizaki, Yoshihide, Harrow, Jennifer, Gerstein, Mark, Hubbard, Tim, Reymond, Alexandre, Antonarakis, Stylianos E., Hannon, Gregory, Giddings, Morgan C., Ruan, Yijun, Wold, Barbara, Carninci, Piero, Guigó, Roderic, Gingeras, Thomas R.
Publicado 2012