Identification of genetic variants associated with alternative splicing using sQTLseekeR

por Monlong, Jean, Calvo, Miquel, Ferreira, Pedro G., Guigó, Roderic
Publicado 2014

Overdiagnosis from non-progressive cancer detected by screening mammography: stochastic simulation study with calibration to population based registry data

por Seigneurin, Arnaud, François, Olivier, Labarère, José, Oudeville, Pierre, Monlong, Jean, Colonna, Marc
Publicado 2011

Human copy number variants are enriched in regions of low mappability

por Monlong, Jean, Cossette, Patrick, Meloche, Caroline, Rouleau, Guy, Girard, Simon L, Bourque, Guillaume
Publicado 2018

Genotyping structural variants in pangenome graphs using the vg toolkit

por Hickey, Glenn, Heller, David, Monlong, Jean, Sibbesen, Jonas A., Sirén, Jouni, Eizenga, Jordan, Dawson, Eric T., Garrison, Erik, Novak, Adam M., Paten, Benedict
Publicado 2020

Genome-wide microhomologies enable precise template-free editing of biologically relevant deletion mutations

por Grajcarek, Janin, Monlong, Jean, Nishinaka-Arai, Yoko, Nakamura, Michiko, Nagai, Miki, Matsuo, Shiori, Lougheed, David, Sakurai, Hidetoshi, Saito, Megumu K., Bourque, Guillaume, Woltjen, Knut
Publicado 2019

Global characterization of copy number variants in epilepsy patients from whole genome sequencing

por Monlong, Jean, Girard, Simon L., Meloche, Caroline, Cadieux-Dion, Maxime, Andrade, Danielle M., Lafreniere, Ron G., Gravel, Micheline, Spiegelman, Dan, Dionne-Laporte, Alexandre, Boelman, Cyrus, Hamdan, Fadi F., Michaud, Jacques L., Rouleau, Guy, Minassian, Berge A., Bourque, Guillaume, Cossette, Patrick
Publicado 2018

Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy

por Couturier, Charles P., Ayyadhury, Shamini, Le, Phuong U., Nadaf, Javad, Monlong, Jean, Riva, Gabriele, Allache, Redouane, Baig, Salma, Yan, Xiaohua, Bourgey, Mathieu, Lee, Changseok, Wang, Yu Chang David, Wee Yong, V., Guiot, Marie-Christine, Najafabadi, Hamed, Misic, Bratislav, Antel, Jack, Bourque, Guillaume, Ragoussis, Jiannis, Petrecca, Kevin
Publicado 2020

Author Correction: Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy

por Couturier, Charles P., Ayyadhury, Shamini, Le, Phuong U., Nadaf, Javad, Monlong, Jean, Riva, Gabriele, Allache, Redouane, Baig, Salma, Yan, Xiaohua, Bourgey, Mathieu, Lee, Changseok, Wang, Yu Chang David, Yong, V. Wee, Guiot, Marie-Christine, Najafabadi, Hamed, Misic, Bratislav, Antel, Jack, Bourque, Guillaume, Ragoussis, Jiannis, Petrecca, Kevin
Publicado 2020

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

por Lorig-Roach, Ryan, Meredith, Melissa, Monlong, Jean, Jain, Miten, Olsen, Hugh, McNulty, Brandy, Porubsky, David, Montague, Tessa, Lucas, Julian, Condon, Chris, Eizenga, Jordan, Juul, Sissel, McKenzie, Sean, Simmonds, Sara E., Park, Jimin, Asri, Mobin, Koren, Sergey, Eichler, Evan, Axel, Richard, Martin, Bruce, Carnevali, Paolo, Miga, Karen, Paten, Benedict
Publicado 2023

Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression

por Pervouchine, Dmitri D., Djebali, Sarah, Breschi, Alessandra, Davis, Carrie A., Barja, Pablo Prieto, Dobin, Alex, Tanzer, Andrea, Lagarde, Julien, Zaleski, Chris, See, Lei-Hoon, Fastuca, Meagan, Drenkow, Jorg, Wang, Huaien, Bussotti, Giovanni, Pei, Baikang, Balasubramanian, Suganthi, Monlong, Jean, Harmanci, Arif, Gerstein, Mark, Beer, Michael A., Notredame, Cedric, Guigó, Roderic, Gingeras, Thomas R.
Publicado 2015

Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma

por Arseneault, Madeleine, Monlong, Jean, Vasudev, Naveen S., Laskar, Ruhina S., Safisamghabadi, Maryam, Harnden, Patricia, Egevad, Lars, Nourbehesht, Nazanin, Panichnantakul, Pudchalaluck, Holcatova, Ivana, Brisuda, Antonin, Janout, Vladimir, Kollarova, Helena, Foretova, Lenka, Navratilova, Marie, Mates, Dana, Jinga, Viorel, Zaridze, David, Mukeria, Anush, Jandaghi, Pouria, Brennan, Paul, Brazma, Alvis, Tost, Jorg, Scelo, Ghislaine, Banks, Rosamonde E., Lathrop, Mark, Bourque, Guillaume, Riazalhosseini, Yasser
Publicado 2017

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

por Kolmogorov, Mikhail, Billingsley, Kimberley J., Mastoras, Mira, Meredith, Melissa, Monlong, Jean, Lorig-Roach, Ryan, Asri, Mobin, Jerez, Pilar Alvarez, Malik, Laksh, Dewan, Ramita, Reed, Xylena, Genner, Rylee M., Daida, Kensuke, Behera, Sairam, Shafin, Kishwar, Pesout, Trevor, Prabakaran, Jeshuwin, Carnevali, Paolo, Yang, Jianzhi, Rhie, Arang, Scholz, Sonja W., Traynor, Bryan J., Miga, Karen H., Jain, Miten, Timp, Winston, Phillippy, Adam M., Chaisson, Mark, Sedlazeck, Fritz J., Blauwendraat, Cornelis, Paten, Benedict
Publicado 2023

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

por Shafin, Kishwar, Pesout, Trevor, Lorig-Roach, Ryan, Haukness, Marina, Olsen, Hugh E., Bosworth, Colleen, Armstrong, Joel, Tigyi, Kristof, Maurer, Nicholas, Koren, Sergey, Sedlazeck, Fritz J., Marschall, Tobias, Mayes, Simon, Costa, Vania, Zook, Justin M., Liu, Kelvin J., Kilburn, Duncan, Sorensen, Melanie, Munson, Katy M., Vollger, Mitchell R., Monlong, Jean, Garrison, Erik, Eichler, Evan E., Salama, Sofie, Haussler, David, Green, Richard E., Akeson, Mark, Phillippy, Adam, Miga, Karen H., Carnevali, Paolo, Jain, Miten, Paten, Benedict
Publicado 2020

Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing

por Goenka, Sneha D., Gorzynski, John E., Shafin, Kishwar, Fisk, Dianna G., Pesout, Trevor, Jensen, Tanner D., Monlong, Jean, Chang, Pi-Chuan, Baid, Gunjan, Bernstein, Jonathan A., Christle, Jeffrey W., Dalton, Karen P., Garalde, Daniel R., Grove, Megan E., Guillory, Joseph, Kolesnikov, Alexey, Nattestad, Maria, Ruzhnikov, Maura R. Z., Samadi, Mehrzad, Sethia, Ankit, Spiteri, Elizabeth, Wright, Christopher J., Xiong, Katherine, Zhu, Tong, Jain, Miten, Sedlazeck, Fritz J., Carroll, Andrew, Paten, Benedict, Ashley, Euan A.
Publicado 2022

Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

por Ferreira, Pedro G., Jares, Pedro, Rico, Daniel, Gómez-López, Gonzalo, Martínez-Trillos, Alejandra, Villamor, Neus, Ecker, Simone, González-Pérez, Abel, Knowles, David G., Monlong, Jean, Johnson, Rory, Quesada, Victor, Djebali, Sarah, Papasaikas, Panagiotis, López-Guerra, Mónica, Colomer, Dolors, Royo, Cristina, Cazorla, Maite, Pinyol, Magda, Clot, Guillem, Aymerich, Marta, Rozman, Maria, Kulis, Marta, Tamborero, David, Gouin, Anaïs, Blanc, Julie, Gut, Marta, Gut, Ivo, Puente, Xose S., Pisano, David G., Martin-Subero, José Ignacio, López-Bigas, Nuria, López-Guillermo, Armando, Valencia, Alfonso, López-Otín, Carlos, Campo, Elías, Guigó, Roderic
Publicado 2014

A strategy for building and using a human reference pangenome

por Llamas, Bastien, Narzisi, Giuseppe, Schneider, Valerie, Audano, Peter A., Biederstedt, Evan, Blauvelt, Lon, Bradbury, Peter, Chang, Xian, Chin, Chen-Shan, Fungtammasan, Arkarachai, Clarke, Wayne E., Cleary, Alan, Ebler, Jana, Eizenga, Jordan, Sibbesen, Jonas A., Markello, Charles J., Garrison, Erik, Garg, Shilpa, Hickey, Glenn, Lazo, Gerard R., Lin, Michael F., Mahmoud, Medhat, Marschall, Tobias, Minkin, Ilia, Monlong, Jean, Musunuri, Rajeeva L., Sagayaradj, Sagayamary, Novak, Adam M., Rautiainen, Mikko, Regier, Allison, Sedlazeck, Fritz J., Siren, Jouni, Souilmi, Yassine, Wagner, Justin, Wrightsman, Travis, Yokoyama, Toshiyuki T., Zeng, Qiandong, Zook, Justin M., Paten, Benedict, Busby, Ben
Publicado 2021

Stalled developmental programs at the root of pediatric brain tumors

por Jessa, Selin, Blanchet-Cohen, Alexis, Krug, Brian, Vladoiu, Maria, Coutelier, Marie, Faury, Damien, Poreau, Brice, De Jay, Nicolas, Hébert, Steven, Monlong, Jean, Farmer, W. Todd, Donovan, Laura K., Hu, Yixing, McConechy, Melissa K., Cavalli, Florence M. G., Mikael, Leonie G., Ellezam, Benjamin, Richer, Maxime, Allaire, Andréa, Weil, Alexander G., Atkinson, Jeffrey, Farmer, Jean-Pierre, Dudley, Roy W. R., Larouche, Valerie, Crevier, Louis, Albrecht, Steffen, Filbin, Mariella G., Sartelet, Hervé, Lutz, Pierre-Eric, Nagy, Corina, Turecki, Gustavo, Costantino, Santiago, Dirks, Peter B., Murai, Keith K., Bourque, Guillaume, Ragoussis, Jiannis, Garzia, Livia, Taylor, Michael D., Jabado, Nada, Kleinman, Claudia L.
Publicado 2019

Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

por Rodriguez-Martin, Bernardo, Alvarez, Eva G., Baez-Ortega, Adrian, Zamora, Jorge, Supek, Fran, Demeulemeester, Jonas, Santamarina, Martin, Ju, Young Seok, Temes, Javier, Garcia-Souto, Daniel, Detering, Harald, Li, Yilong, Rodriguez-Castro, Jorge, Dueso-Barroso, Ana, Bruzos, Alicia L., Dentro, Stefan C., Blanco, Miguel G., Contino, Gianmarco, Ardeljan, Daniel, Tojo, Marta, Roberts, Nicola D., Zumalave, Sonia, Edwards, Paul A., Weischenfeldt, Joachim, Puiggròs, Montserrat, Chong, Zechen, Chen, Ken, Lee, Eunjung Alice, Wala, Jeremiah A., Raine, Keiran M., Butler, Adam, Waszak, Sebastian M., Navarro, Fabio C. P., Schumacher, Steven E., Monlong, Jean, Maura, Francesco, Bolli, Niccolo, Bourque, Guillaume, Gerstein, Mark, Park, Peter J., Wedge, David C., Beroukhim, Rameen, Torrents, David, Korbel, Jan O., Martincorena, Iñigo, Fitzgerald, Rebecca C., Van Loo, Peter, Kazazian, Haig H., Burns, Kathleen H., Campbell, Peter J., Tubio, Jose M. C.
Publicado 2023

Transcriptome and genome sequencing uncovers functional variation in humans

por Lappalainen, Tuuli, Sammeth, Michael, Friedländer, Marc R, ‘t Hoen, Peter AC, Monlong, Jean, Rivas, Manuel A, Gonzàlez-Porta, Mar, Kurbatova, Natalja, Griebel, Thasso, Ferreira, Pedro G, Barann, Matthias, Wieland, Thomas, Greger, Liliana, van Iterson, Maarten, Almlöf, Jonas, Ribeca, Paolo, Pulyakhina, Irina, Esser, Daniela, Giger, Thomas, Tikhonov, Andrew, Sultan, Marc, Bertier, Gabrielle, MacArthur, Daniel G, Lek, Monkol, Lizano, Esther, Buermans, Henk PJ, Padioleau, Ismael, Schwarzmayr, Thomas, Karlberg, Olof, Ongen, Halit, Kilpinen, Helena, Beltran, Sergi, Gut, Marta, Kahlem, Katja, Amstislavskiy, Vyacheslav, Stegle, Oliver, Pirinen, Matti, Montgomery, Stephen B, Donnelly, Peter, McCarthy, Mark I, Flicek, Paul, Strom, Tim M, Lehrach, Hans, Schreiber, Stefan, Sudbrak, Ralf, Carracedo, Ángel, Antonarakis, Stylianos E, Häsler, Robert, Syvänen, Ann-Christine, van Ommen, Gert-Jan, Brazma, Alvis, Meitinger, Thomas, Rosenstiel, Philip, Guigó, Roderic, Gut, Ivo G, Estivill, Xavier, Dermitzakis, Emmanouil T
Publicado 2013

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

por Rodriguez-Martin, Bernardo, Alvarez, Eva G., Baez-Ortega, Adrian, Zamora, Jorge, Supek, Fran, Demeulemeester, Jonas, Santamarina, Martin, Ju, Young Seok, Temes, Javier, Garcia-Souto, Daniel, Detering, Harald, Li, Yilong, Rodriguez-Castro, Jorge, Dueso-Barroso, Ana, Bruzos, Alicia L., Dentro, Stefan C., Blanco, Miguel G., Contino, Gianmarco, Ardeljan, Daniel, Tojo, Marta, Roberts, Nicola D., Zumalave, Sonia, Edwards, Paul A., Weischenfeldt, Joachim, Puiggròs, Montserrat, Chong, Zechen, Chen, Ken, Lee, Eunjung Alice, Wala, Jeremiah A., Raine, Keiran M., Butler, Adam, Waszak, Sebastian M., Navarro, Fabio C. P., Schumacher, Steven E., Monlong, Jean, Maura, Francesco, Bolli, Niccolo, Bourque, Guillaume, Gerstein, Mark, Park, Peter J., Wedge, David C., Beroukhim, Rameen, Torrents, David, Korbel, Jan O., Martincorena, Iñigo, Fitzgerald, Rebecca C., Van Loo, Peter, Kazazian, Haig H., Burns, Kathleen H., Campbell, Peter J., Tubio, Jose M. C.
Publicado 2020