Pathogenic variants in KMT2C result in a neurodevelopmental disorder distinct from Kleefstra and Kabuki syndromes

Authors: Rots, Dmitrijs, Choufani, Sanaa, Faundes, Victor, Dingemans, Alexander J.M., Joss, Shelagh, Foulds, Nicola, Jones, Elizabeth A., Stewart, Sarah, Vasudevan, Pradeep, Dabir, Tabib, Park, Soo-Mi, Jewell, Rosalyn, Brown, Natasha, Pais, Lynn, Jacquemont, Sébastien, Jizi, Khadijé, Ravenswaaij-Arts, Conny M.A. van, Kroes, Hester Y., Stumpel, Constance T.R. M., Ockeloen, Charlotte W., Diets, Illja J., Nizon, Mathilde, Vincent, Marie, Cogné, Benjamin, Besnard, Thomas, Kambouris, Marios, Anderson, Emily, Zackai, Elaine H., McDougall, Carey, Donoghue, Sarah, O'Donnell-Luria, Anne, Valivullah, Zaheer, O'Leary, Melanie, Srivastava, Siddharth, Byers, Heather, Leslie, Nancy, Mazzola, Sarah, Tiller, George E., Vera, Moin, Shen, Joseph J., Boles, Richard, Jain, Vani, Brischoux-Boucher, Elise, Kinning, Esther, Simpson, Brittany N., Giltay, Jacques C., Harris, Jacqueline, Keren, Boris, Guimier, Anne, Marijon, Pierre, Vries, Bert B.A. de, Motter, Constance S., Mendelsohn, Bryce A., Coffino, Samantha, Gerkes, Erica H., Afenjar, Alexandra, Visconti, Paola, Bacchelli, Elena, Maestrini, Elena, Delahaye-Duriez, Andree, Gooch, Catherine, Hendriks, Yvonne, Adams, Hieab, Thauvin-Robinet, Christel, Josephi-Taylor, Sarah, Bertoli, Marta, Parker, Michael J., Rutten, Julie W., Caluseriu, Oana, Vernon, Hilary J., Kaziyev, Jonah, Zhu, Jia, Kremen, Jessica, Frazier, Zoe, Osika, Hailey, Breault, David, Nair, Sreelata, Lewis, Suzanne M.E., Ceroni, Fabiola, Viggiano, Marta, Posar, Annio, Brittain, Helen, Giovanna, Traficante, Giulia, Gori, Quteineh, Lina, Ha-Vinh Leuchter, Russia, Zonneveld-Huijssoon, Evelien, Mellado, Cecilia, Marey, Isabelle, Coudert, Alicia, Aracena Alvarez, Mariana Inés, Kennis, Milou G.P., Bouman, Arianne, Roifman, Maian, Amorós Rodríguez, María Inmaculada, Ortigoza-Escobar, Juan Dario, Vernimmen, Vivian, Sinnema, Margje, Pfundt, Rolph, Brunner, Han G., Vissers, Lisenka E.L.M., Kleefstra, Tjitske, Weksberg, Rosanna, Banka, Siddharth

Source: In The American Journal of Human Genetics 8 August 2024 111(8):1626-1642

Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

Authors: Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Chang, Xian H., Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fischer, Christian, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A., Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E., Cornejo, Omar E., Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L., Formenti, Giulio, Frankish, Adam, Gao, Yan, Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Kolesnikov, Alexey, Korbel, Jan O., Kordosky, Jennifer, Lee, HoJoon, Lewis, Alexandra P., Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Olson, Nathan D., Puiu, Daniela, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Sirén, Jouni, Smith, Michael W., Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Wood, Jonathan M.D., Zimin, Aleksey V., Popejoy, Alice B., Bourque, Guillaume, Chaisson, Mark J.P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Jarvis, Erich D., Miga, Karen H., Wang, Ting, Garrison, Erik, Marschall, Tobias, Hall, Ira, Li, Heng, Paten, Benedict, Greer, Stephanie U., Pavlichin, Dmitri S., Zhou, Bo, Urban, Alexander E., Weissman, Tsachy

Source: In Cell Reports Methods 28 August 2023 3(8)

Les voies de l’ovogenèse : quels groupes de gènes candidats dans l’insuffisance ovarienne prématurée ?

Authors: Lokchine, Anna, Christin-Maitre, Sophie, Akloul, Linda, Cluzeau, Laurence, Le Page, Lorrie, Mary, Laura, Launay, Erika, Planes, Marc, Dubourg, Christèle, Domin-Bernhard, Mathilde, Nouyou, Bénédicte, Duros, Solène, Carré, Wilfrid, Detivaud, Leniack, Metayer-Amelot, Laure, Krieger, Sophie, Goardon, Nicolas, Marijon, Pierre, Blanc, Pierre, Chalmel, Frédéric, Odent, Sylvie, Rotureau, Marc-Antoine Belaud, Schluth-Bolard, Caroline, Coutton, Charles, Vialard, François, Tucker, Elena, Jaillard, Sylvie

Source: In Morphologie December 2024 108(363) Supplement

Targeted RNAseq from patients’ urinary cells to validate pathogenic noncoding variants in autosomal dominant polycystic kidney disease genes: a proof of concept

Authors: Dorval, Guillaume, Le Gac, Gérald, Morinière, Vincent, Ka, Chandran, Goursaud, Claire, Knebelmann, Bertrand, Marijon, Pierre, Nambot, Sophie, Cagnard, Nicolas, Nitschké, Patrick, Michel-Calemard, Laurence, Audrézet, Marie-Pierre, Heidet, Laurence

Source: In Kidney International September 2024 106(3):532-535

A draft human pangenome reference

Authors: Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Chang, Xian H., Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fischer, Christian, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A., Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E., Cook-Deegan, Robert M., Cornejo, Omar E., Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L., Formenti, Giulio, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A., Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Kenny, Eimear E., Koenig, Barbara A., Kolesnikov, Alexey, Korbel, Jan O., Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Lewis, Alexandra P., Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D., Popejoy, Alice B., Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Smith, Michael W., Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Walenz, Brian, Wood, Jonathan M. D., Zimin, Aleksey V., Bourque, Guillaume, Chaisson, Mark J. P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Wang, Ting, Jarvis, Erich D., Miga, Karen H., Garrison, Erik, Marschall, Tobias, Hall, Ira M., Li, Heng, Paten, Benedict

Source: Nature; May 2023, Vol. 617 Issue: 7960 p312-324, 13p

K-mer File Format: a standardized and compact disk representation of sets of k-mers.

Authors: Dufresne, Yoann, Lemane, Teo, Marijon, Pierre, Peterlongo, Pierre, Rahman, Amatur, Kokot, Marek, Medvedev, Paul, Deorowicz, Sebastian, Chikhi, Rayan

Source: Bioinformatics; 9/15/2022, Vol. 38 Issue 18, p4423-4425, 3p

Subject Terms: COMPACT discs, DE Bruijn graph

Critical Assessment of Metagenome Interpretation: the second round of challenges

Authors: Meyer, Fernando, Fritz, Adrian, Deng, Zhi-Luo, Koslicki, David, Lesker, Till Robin, Gurevich, Alexey, Robertson, Gary, Alser, Mohammed, Antipov, Dmitry, Beghini, Francesco, Bertrand, Denis, Brito, Jaqueline J., Brown, C. Titus, Buchmann, Jan, Buluç, Aydin, Chen, Bo, Chikhi, Rayan, Clausen, Philip T. L. C., Cristian, Alexandru, Dabrowski, Piotr Wojciech, Darling, Aaron E., Egan, Rob, Eskin, Eleazar, Georganas, Evangelos, Goltsman, Eugene, Gray, Melissa A., Hansen, Lars Hestbjerg, Hofmeyr, Steven, Huang, Pingqin, Irber, Luiz, Jia, Huijue, Jørgensen, Tue Sparholt, Kieser, Silas D., Klemetsen, Terje, Kola, Axel, Kolmogorov, Mikhail, Korobeynikov, Anton, Kwan, Jason, LaPierre, Nathan, Lemaitre, Claire, Li, Chenhao, Limasset, Antoine, Malcher-Miranda, Fabio, Mangul, Serghei, Marcelino, Vanessa R., Marchet, Camille, Marijon, Pierre, Meleshko, Dmitry, Mende, Daniel R., Milanese, Alessio, Nagarajan, Niranjan, Nissen, Jakob, Nurk, Sergey, Oliker, Leonid, Paoli, Lucas, Peterlongo, Pierre, Piro, Vitor C., Porter, Jacob S., Rasmussen, Simon, Rees, Evan R., Reinert, Knut, Renard, Bernhard, Robertsen, Espen Mikal, Rosen, Gail L., Ruscheweyh, Hans-Joachim, Sarwal, Varuni, Segata, Nicola, Seiler, Enrico, Shi, Lizhen, Sun, Fengzhu, Sunagawa, Shinichi, Sørensen, Søren Johannes, Thomas, Ashleigh, Tong, Chengxuan, Trajkovski, Mirko, Tremblay, Julien, Uritskiy, Gherman, Vicedomini, Riccardo, Wang, Zhengyang, Wang, Ziye, Wang, Zhong, Warren, Andrew, Willassen, Nils Peder, Yelick, Katherine, You, Ronghui, Zeller, Georg, Zhao, Zhengqiao, Zhu, Shanfeng, Zhu, Jie, Garrido-Oter, Ruben, Gastmeier, Petra, Hacquard, Stephane, Häußler, Susanne, Khaledi, Ariane, Maechler, Friederike, Mesny, Fantin, Radutoiu, Simona, Schulze-Lefert, Paul, Smit, Nathiana, Strowig, Till, Bremges, Andreas, Sczyrba, Alexander, McHardy, Alice Carolyn

Source: Nature Methods; 20220101, Issue: Preprints p1-12, 12p

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads.

Authors: Porubsky, David, Ebert, Peter, Audano, Peter A., Vollger, Mitchell R., Harvey, William T., Marijon, Pierre, Ebler, Jana, Munson, Katherine M., Sorensen, Melanie, Sulovari, Arvis, Haukness, Marina, Ghareghani, Maryam, Human Genome Structural Variation Consortium, Lansdorp, Peter M., Paten, Benedict, Devine, Scott E., Sanders, Ashley D., Lee, Charles, Chaisson, Mark J. P., Korbel, Jan O.

Source: Nature Biotechnology; Mar2021, Vol. 39 Issue 3, p302-308, 7p

Cutevariant: a standalone GUI-based desktop application to explore genetic variations from an annotated VCF file.

Authors: Schutz, Sacha, Monod-Broca, Charles, Bourneuf, Lucas, Marijon, Pierre, Montier, Tristan

Source: Bioinformatics Advances; 2022, Vol. 2 Issue 1, p1-3, 3p

Subject Terms: GRAPHICAL user interfaces, QUERY languages (Computer science), OPEN source software, COMPUTER software, DATA analysis

Graph analysis of fragmented long-read bacterial genome assemblies.

Authors: Marijon, Pierre¹ (AUTHOR) pierre.marijon@inria.fr, Chikhi, Rayan² (AUTHOR), Varré, Jean-Stéphane³ (AUTHOR)

Source: Bioinformatics. 11/01/2019, Vol. 35 Issue 21, p4239-4246. 8p.

Subject Terms: *BACTERIAL genomes, *GENOMES

yacrd and fpa: upstream tools for long-read genome assembly.

Authors: Marijon, Pierre¹ (AUTHOR) pierre.marijon@inria.fr, Chikhi, Rayan² (AUTHOR), Varré, Jean-Stéphane³ (AUTHOR)

Source: Bioinformatics. 6/15/2020, Vol. 36 Issue 12, p3894-3896. 3p.

Subject Terms: *GENOMES, *BIOINFORMATICS, *STORAGE

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