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2024

Lougheed, David R; Liu, Hanshi; Aracena, Katherine A; Grégoire, Romain; Pacis, Alain; Pastinen, Tomi; Barreiro, Luis B; Joly, Yann; Bujold, David; Bourque, Guillaume

EpiVar browser: advanced exploration of epigenomics data under controlled access Journal Article

In: Bioinformatics, 2024, ISSN: 1367-4811.

Abstract | Links | BibTeX | Tags:

Bhérer, Claude; Eveleigh, Robert; Trajanoska, Katerina; St-Cyr, Janick; Paccard, Antoine; Ravindran, Praveen Nadukkalam; Caron, Elizabeth; Asbah, Nimara Bader; McClelland, Peyton; Wei, Clare; Baumgartner, Iris; Schindewolf, Marc; Döring, Yvonne; Perley, Danielle; Lefebvre, François; Lepage, Pierre; Bourgey, Mathieu; Bourque, Guillaume; Ragoussis, Jiannis; Mooser, Vincent; Taliun, Daniel

A cost-effective sequencing method for genetic studies combining high-depth whole exome and low-depth whole genome Journal Article

In: NPJ Genom Med, vol. 9, no. 1, pp. 8, 2024, ISSN: 2056-7944.

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Aracena, Katherine A; Lin, Yen-Lung; Luo, Kaixuan; Pacis, Alain; Gona, Saideep; Mu, Zepeng; Yotova, Vania; Sindeaux, Renata; Pramatarova, Albena; Simon, Marie-Michelle; Chen, Xun; Groza, Cristian; Lougheed, David; Gregoire, Romain; Brownlee, David; Boye, Carly; Pique-Regi, Roger; Li, Yang; He, Xin; Bujold, David; Pastinen, Tomi; Bourque, Guillaume; Barreiro, Luis B

Epigenetic variation impacts individual differences in the transcriptional response to influenza infection Journal Article

In: Nat Genet, 2024, ISSN: 1546-1718.

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Groza, Cristian; Schwendinger-Schreck, Carl; Cheung, Warren A; Farrow, Emily G; Thiffault, Isabelle; Lake, Juniper; Rizzo, William B; Evrony, Gilad; Curran, Tom; Bourque, Guillaume; Pastinen, Tomi

Pangenome graphs improve the analysis of structural variants in rare genetic diseases Journal Article

In: Nat Commun, vol. 15, no. 1, pp. 657, 2024, ISSN: 2041-1723.

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Gutierrez-Camino, Angela; Caron, Maxime; Richer, Chantal; Fuchs, Claire; Illarregi, Unai; Poncelet, Lucas; St-Onge, Pascal; Bataille, Alain R; Tremblay-Dauphinais, Pascal; Lopez-Lopez, Elixabet; Camos, Mireia; Ramirez-Orellana, Manuel; Astigarraga, Itziar; Lécuyer, Éric; Bourque, Guillaume; Martin-Guerrero, Idoia; Sinnett, Daniel

CircRNAome of Childhood Acute Lymphoblastic Leukemia: Deciphering Subtype-Specific Expression Profiles and Involvement in ALL Journal Article

In: Int J Mol Sci, vol. 25, no. 3, 2024, ISSN: 1422-0067.

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2023

A second update on mapping the human genetic architecture of COVID-19

2023.

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Graham-Paquin, Adda-Lee; Saini, Deepak; Sirois, Jacinthe; Hossain, Ishtiaque; Katz, Megan S; Zhuang, Qinwei Kim-Wee; Kwon, Sin Young; Yamanaka, Yojiro; Bourque, Guillaume; Bouchard, Maxime; Pastor, William A

ZMYM2 is essential for methylation of germline genes and active transposons in embryonic development Journal Article

In: Nucleic Acids Res, vol. 51, no. 14, pp. 7314–7329, 2023, ISSN: 1362-4962.

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Lougheed, David R; Liu, Hanshi; Aracena, Katherine A; Grégoire, Romain; Pacis, Alain; Pastinen, Tomi; Barreiro, Luis B; Joly, Yann; Bujold, David; Bourque, Guillaume

EpiVar Browser: advanced exploration of epigenomics data under controlled access

2023.

Abstract | Links | BibTeX | Tags:

N'Guessan, Arnaud; Kailasam, Senthilkumar; Mostefai, Fatima; Poujol, Raphaël; Grenier, Jean-Christophe; Ismailova, Nailya; Contini, Paola; Palma, Raffaele De; Haber, Carsten; Stadler, Volker; Bourque, Guillaume; Hussin, Julie G; Shapiro, B Jesse; Fritz, Jörg H; Piccirillo, Ciriaco A

Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping and sequence analysis Journal Article

In: iScience, vol. 26, no. 8, pp. 107394, 2023, ISSN: 2589-0042.

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Lee, HoJoon; Greer, Stephanie U; Pavlichin, Dmitri S; Zhou, Bo; Urban, Alexander E; Weissman, Tsachy; ; Ji, Hanlee P

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

In: Cell Rep Methods, vol. 3, no. 8, pp. 100543, 2023, ISSN: 2667-2375.

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Hickey, Glenn; Monlong, Jean; Ebler, Jana; Novak, Adam M; Eizenga, Jordan M; Gao, Yan; ; Marschall, Tobias; Li, Heng; Paten, Benedict

Pangenome graph construction from genome alignments with Minigraph-Cactus Journal Article

In: Nat Biotechnol, 2023, ISSN: 1546-1696.

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Vollger, Mitchell R; Dishuck, Philip C; Harvey, William T; DeWitt, William S; Guitart, Xavi; Goldberg, Michael E; Rozanski, Allison N; Lucas, Julian; Asri, Mobin; ; Munson, Katherine M; Lewis, Alexandra P; Hoekzema, Kendra; Logsdon, Glennis A; Porubsky, David; Paten, Benedict; Harris, Kelley; Hsieh, PingHsun; Eichler, Evan E

Increased mutation and gene conversion within human segmental duplications Journal Article

In: Nature, vol. 617, no. 7960, pp. 325–334, 2023, ISSN: 1476-4687.

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Guarracino, Andrea; Buonaiuto, Silvia; de Lima, Leonardo Gomes; Potapova, Tamara; Rhie, Arang; Koren, Sergey; Rubinstein, Boris; Fischer, Christian; ; Gerton, Jennifer L; Phillippy, Adam M; Colonna, Vincenza; Garrison, Erik

Recombination between heterologous human acrocentric chromosomes Journal Article

In: Nature, vol. 617, no. 7960, pp. 335–343, 2023, ISSN: 1476-4687.

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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; Tayoun, Ahmad N Abou; 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

A draft human pangenome reference Journal Article

In: Nature, vol. 617, no. 7960, pp. 312–324, 2023, ISSN: 1476-4687.

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Rahimi, Sophia; Shao, Xiaojian; Chan, Donovan; Martel, Josée; Bérard, Anick; Fraser, William D; Simon, Marie-Michelle; Kwan, Tony; Bourque, Guillaume; Trasler, Jacquetta

Capturing sex-specific and hypofertility-linked effects of assisted reproductive technologies on the cord blood DNA methylome Journal Article

In: Clin Epigenetics, vol. 15, no. 1, pp. 82, 2023, ISSN: 1868-7083.

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Groza, Cristian; Chen, Xun; Pacis, Alain; Simon, Marie-Michelle; Pramatarova, Albena; Aracena, Katherine A; Pastinen, Tomi; Barreiro, Luis B; Bourque, Guillaume

Genome graphs detect human polymorphisms in active epigenomic state during influenza infection Journal Article

In: Cell Genom, vol. 3, no. 5, pp. 100294, 2023, ISSN: 2666-979X.

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Chen, Xun; Pacis, Alain; Aracena, Katherine A; Gona, Saideep; Kwan, Tony; Groza, Cristian; Lin, Yen Lung; Sindeaux, Renata; Yotova, Vania; Pramatarova, Albena; Simon, Marie-Michelle; Pastinen, Tomi; Barreiro, Luis B; Bourque, Guillaume

Transposable elements are associated with the variable response to influenza infection Journal Article

In: Cell Genom, vol. 3, no. 5, pp. 100292, 2023, ISSN: 2666-979X.

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Vasudev, Naveen S; Scelo, Ghislaine; Glennon, Kate I; Wilson, Michelle; Letourneau, Louis; Eveleigh, Robert; Nourbehesht, Nazanin; Arseneault, Madeleine; Paccard, Antoine; Egevad, Lars; Viksna, Juris; Celms, Edgars; Jackson, Sharon M; Abedi-Ardekani, Behnoush; Warren, Anne Y; Selby, Peter J; Trainor, Sebastian; Kimuli, Michael; Cartledge, Jon; Soomro, Naeem; Adeyoju, Adebanji; Patel, Poulam M; Wozniak, Magdalena B; Holcatova, Ivana; Brisuda, Antonin; Janout, Vladimir; Chanudet, Estelle; Zaridze, David; Moukeria, Anush; Shangina, Oxana; Foretova, Lenka; Navratilova, Marie; Mates, Dana; Jinga, Viorel; Bogdanovic, Ljiljana; Kovacevic, Bozidar; Cambon-Thomsen, Anne; Bourque, Guillaume; Brazma, Alvis; Tost, Jörg; Brennan, Paul; Lathrop, Mark; Riazalhosseini, Yasser; Banks, Rosamonde E

Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma Journal Article

In: Clin Cancer Res, vol. 29, no. 7, pp. 1220–1231, 2023, ISSN: 1557-3265.

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Upchurch, Sean; Palumbo, Emilio; Adams, Jeremy; Bujold, David; Bourque, Guillaume; Nedzel, Jared; Graham, Keenan; Kagda, Meenakshi S; Assis, Pedro; Hitz, Benjamin; Righi, Emilio; Guigó, Roderic; and, Barbara J Wold

RNAget: an API to securely retrieve RNA quantifications Journal Article

In: Bioinformatics, vol. 39, no. 4, 2023, ISSN: 1367-4811.

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Duperron, Marie-Gabrielle; Knol, Maria J; Grand, Quentin Le; Evans, Tavia E; Mishra, Aniket; Tsuchida, Ami; Roshchupkin, Gennady; Konuma, Takahiro; Trégouët, David-Alexandre; Romero, Jose Rafael; Frenzel, Stefan; Luciano, Michelle; Hofer, Edith; Bourgey, Mathieu; Dueker, Nicole D; Delgado, Pilar; Hilal, Saima; Tankard, Rick M; Dubost, Florian; Shin, Jean; Saba, Yasaman; Armstrong, Nicola J; Bordes, Constance; Bastin, Mark E; Beiser, Alexa; Brodaty, Henry; Bülow, Robin; Carrera, Caty; Chen, Christopher; Cheng, Ching-Yu; Deary, Ian J; Gampawar, Piyush G; Himali, Jayandra J; Jiang, Jiyang; Kawaguchi, Takahisa; Li, Shuo; Macalli, Melissa; Marquis, Pascale; Morris, Zoe; Maniega, Susana Muñoz; Miyamoto, Susumu; Okawa, Masakazu; Paradise, Matthew; Parva, Pedram; Rundek, Tatjana; Sargurupremraj, Muralidharan; Schilling, Sabrina; Setoh, Kazuya; Soukarieh, Omar; Tabara, Yasuharu; Teumer, Alexander; Thalamuthu, Anbupalam; Trollor, Julian N; Hernández, Maria C Valdés; Vernooij, Meike W; Völker, Uwe; Wittfeld, Katharina; Wong, Tien Yin; Wright, Margaret J; Zhang, Junyi; Zhao, Wanting; Zhu, Yi-Cheng; Schmidt, Helena; Sachdev, Perminder S; Wen, Wei; Yoshida, Kazumichi; Joutel, Anne; Satizabal, Claudia L; Sacco, Ralph L; Bourque, Guillaume; ; Lathrop, Mark; Paus, Tomas; Fernandez-Cadenas, Israel; Yang, Qiong; Mazoyer, Bernard; Boutinaud, Philippe; Okada, Yukinori; Grabe, Hans J; Mather, Karen A; Schmidt, Reinhold; Joliot, Marc; Ikram, M Arfan; Matsuda, Fumihiko; Tzourio, Christophe; Wardlaw, Joanna M; Seshadri, Sudha; Adams, Hieab H H; Debette, Stéphanie

Genomics of perivascular space burden unravels early mechanisms of cerebral small vessel disease Journal Article

In: Nat Med, vol. 29, no. 4, pp. 950–962, 2023, ISSN: 1546-170X.

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Porubsky, David; Vollger, Mitchell R; Harvey, William T; Rozanski, Allison N; Ebert, Peter; Hickey, Glenn; Hasenfeld, Patrick; Sanders, Ashley D; Stober, Catherine; ; Korbel, Jan O; Paten, Benedict; Marschall, Tobias; Eichler, Evan E

Gaps and complex structurally variant loci in phased genome assemblies Journal Article

In: Genome Res, vol. 33, no. 4, pp. 496–510, 2023, ISSN: 1549-5469.

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Batdorj, Enkhjin; AlOgayil, Najla; Zhuang, Qinwei Kim-Wee; Galvez, Jose Hector; Bauermeister, Klara; Nagata, Kei; Kimura, Tohru; Ward, Monika A; Taketo, Teruko; Bourque, Guillaume; Naumova, Anna K

Genetic variation in the Y chromosome and sex-biased DNA methylation in somatic cells in the mouse Journal Article

In: Mamm Genome, vol. 34, no. 1, pp. 44–55, 2023, ISSN: 1432-1777.

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Chen, Xun; Bourque, Guillaume; Goubert, Clément

Genotyping of Transposable Element Insertions Segregating in Human Populations Using Short-Read Realignments Journal Article

In: Methods Mol Biol, vol. 2607, pp. 63–83, 2023, ISSN: 1940-6029.

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Groza, Cristian; Bourque, Guillaume; Goubert, Clément

A Pangenome Approach to Detect and Genotype TE Insertion Polymorphisms Journal Article

In: Methods Mol Biol, vol. 2607, pp. 85–94, 2023, ISSN: 1940-6029.

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Tav, Christophe; Fournier, Éric; Fournier, Michèle; Khadangi, Fatemeh; Baguette, Audrey; Côté, Maxime C; Silveira, Maruhen A D; Bérubé-Simard, Félix-Antoine; Bourque, Guillaume; Droit, Arnaud; Bilodeau, Steve

Glucocorticoid stimulation induces regionalized gene responses within topologically associating domains Journal Article

In: Front Genet, vol. 14, pp. 1237092, 2023, ISSN: 1664-8021.

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2022

da Silva, Sabrina Daniela; Morand, Grégoire B; Diesel, Luciana; de Lima, Jefferson Muniz; Bijian, Krikor; Kailasam, Senthilkumar; Lefebvre, Francois; Bourque, Guillaume; Hier, Michael; Alaoui-Jamali, Moulay A

Identification of R-Spondin Gene Signature Predictive of Metastatic Progression in BRAFV-Positive Papillary Thyroid Cancer Journal Article

In: Cells, vol. 12, no. 1, 2022, ISSN: 2073-4409.

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Couturier, Charles P; Nadaf, Javad; Li, Zhaorong; Baig, Salma; Riva, Gabriele; Le, Phuong; Kloosterman, Daan J; Monlong, Jean; Meyong, Andriniaina Nkili; Allache, Redouane; Degenhard, Theresa; Al-Rashid, Mariam; Guiot, Marie-Christine; Bourque, Guillaume; Ragoussis, Jiannis; Akkari, Leila; Quintana, Francisco J; Petrecca, Kevin

Glioblastoma scRNA-seq shows treatment-induced, immune-dependent increase in mesenchymal cancer cells and structural variants in distal neural stem cells Journal Article

In: Neuro Oncol, vol. 24, no. 9, pp. 1494–1508, 2022, ISSN: 1523-5866.

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Farooq, Zeenat; Kusuma, Fedho; Burke, Phillip; Dufour, Catherine R; Lee, Duckgue; Tabatabaei, Negar; Toboz, Phoenix; Radovani, Ernest; Greenblatt, Jack F; Rehman, Jalees; Class, Jacob; Khoutorsky, Arkady; Fonseca, Bruno D; Richner, Justin M; Mercier, Eloi; Bourque, Guillaume; Giguère, Vincent; Subramaniam, Arvind R; Han, Jaeseok; Tahmasebi, Soroush

The amino acid sensor GCN2 suppresses terminal oligopyrimidine (TOP) mRNA translation via La-related protein 1 (LARP1) Journal Article

In: J Biol Chem, vol. 298, no. 9, pp. 102277, 2022, ISSN: 1083-351X.

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Fava, Vinicius M; Bourgey, Mathieu; Nawarathna, Pubudu M; Orlova, Marianna; Cassart, Pauline; Vinh, Donald C; Cheng, Matthew Pellan; Bourque, Guillaume; Schurr, Erwin; Langlais, David

A systems biology approach identifies candidate drugs to reduce mortality in severely ill patients with COVID-19 Journal Article

In: Sci Adv, vol. 8, no. 22, pp. eabm2510, 2022, ISSN: 2375-2548.

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Mendel, Arielle; Colmegna, Ines; Bourque, Guillaume; Rajda, Ewa; Lee, Todd C; Gálvez, José Héctor; Vinet, Évelyne; Cheng, Matthew P

More than a 'Hundred Days War': Persistent SARS-CoV-2 infection in a patient with ANCA-associated vasculitis Journal Article

In: J Assoc Med Microbiol Infect Dis Can, vol. 7, no. 2, pp. 131–134, 2022, ISSN: 2371-0888.

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Olson, Nathan D; Wagner, Justin; McDaniel, Jennifer; Stephens, Sarah H; Westreich, Samuel T; Prasanna, Anish G; Johanson, Elaine; Boja, Emily; Maier, Ezekiel J; Serang, Omar; Jáspez, David; Lorenzo-Salazar, José M; Muñoz-Barrera, Adrián; Rubio-Rodríguez, Luis A; Flores, Carlos; Kyriakidis, Konstantinos; Malousi, Andigoni; Shafin, Kishwar; Pesout, Trevor; Jain, Miten; Paten, Benedict; Chang, Pi-Chuan; Kolesnikov, Alexey; Nattestad, Maria; Baid, Gunjan; Goel, Sidharth; Yang, Howard; Carroll, Andrew; Eveleigh, Robert; Bourgey, Mathieu; Bourque, Guillaume; Li, Gen; Ma, ChouXian; Tang, LinQi; Du, YuanPing; Zhang, ShaoWei; Morata, Jordi; Tonda, Raúl; Parra, Genís; Trotta, Jean-Rémi; Brueffer, Christian; Demirkaya-Budak, Sinem; Kabakci-Zorlu, Duygu; Turgut, Deniz; Kalay, Özem; Budak, Gungor; Narcı, Kübra; Arslan, Elif; Brown, Richard; Johnson, Ivan J; Dolgoborodov, Alexey; Semenyuk, Vladimir; Jain, Amit; Tetikol, H Serhat; Jain, Varun; Ruehle, Mike; Lajoie, Bryan; Roddey, Cooper; Catreux, Severine; Mehio, Rami; Ahsan, Mian Umair; Liu, Qian; Wang, Kai; Sahraeian, Sayed Mohammad Ebrahim; Fang, Li Tai; Mohiyuddin, Marghoob; Hung, Calvin; Jain, Chirag; Feng, Hanying; Li, Zhipan; Chen, Luoqi; Sedlazeck, Fritz J; Zook, Justin M

PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions Journal Article

In: Cell Genom, vol. 2, no. 5, 2022, ISSN: 2666-979X.

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Sahinyan, Korin; Blackburn, Darren M; Simon, Marie-Michelle; Lazure, Felicia; Kwan, Tony; Bourque, Guillaume; Soleimani, Vahab D

Application of ATAC-Seq for genome-wide analysis of the chromatin state at single myofiber resolution Journal Article

In: Elife, vol. 11, 2022, ISSN: 2050-084X.

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Breeze, Charles E; Haugen, Eric; Reynolds, Alex; Teschendorff, Andrew; van Dongen, Jenny; Lan, Qing; Rothman, Nathaniel; Bourque, Guillaume; Dunham, Ian; Beck, Stephan; Stamatoyannopoulos, John; Franceschini, Nora; Berndt, Sonja I

Integrative analysis of 3604 GWAS reveals multiple novel cell type-specific regulatory associations Journal Article

In: Genome Biol, vol. 23, no. 1, pp. 13, 2022, ISSN: 1474-760X.

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Golesworthy, Bryn; Wang, Yifan; Tanti, Amanda; Pacis, Alain; Romero, Joan Miguel; Cuggia, Adeline; Domecq, Celine; Bourdel, Guillaume; Denroche, Robert E; Jang, Gun Ho; Grant, Robert C; Borgida, Ayelet; Grünwald, Barbara T; Dodd, Anna; Wilson, Julie M; Bourque, Guillaume; O'Kane, Grainne M; Fischer, Sandra E; Kron, Chelsea Maedler; Fiset, Pierre-Olivier; Omeroglu, Atilla; Foulkes, William D; Gallinger, Steven; Guiot, Marie-Christine; Gao, Zu-Hua; Zogopoulos, George

Intra-Tumoral CD8+ T-Cell Infiltration and PD-L1 Positivity in Homologous Recombination Deficient Pancreatic Ductal Adenocarcinoma Journal Article

In: Front Oncol, vol. 12, pp. 860767, 2022, ISSN: 2234-943X.

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2021

Yokobayashi, Shihori; Yabuta, Yukihiro; Nakagawa, Masato; Okita, Keisuke; Hu, Bo; Murase, Yusuke; Nakamura, Tomonori; Bourque, Guillaume; Majewski, Jacek; Yamamoto, Takuya; Saitou, Mitinori

Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells Journal Article

In: Cell Rep, vol. 37, no. 5, pp. 109909, 2021, ISSN: 2211-1247.

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Dursi, L Jonathan; Bozoky, Zoltan; de Borja, Richard; Li, Haoyuan; Bujold, David; Lipski, Adam; Rashid, Shaikh Farhan; Sethi, Amanjeev; Memon, Neelam; Naidoo, Dashaylan; Coral-Sasso, Felipe; Wong, Matthew; Quirion, P-O; Lu, Zhibin; Agarwal, Samarth; Pavlov, Yuriy; Ponomarev, Andrew; Husic, Mia; Pace, Krista; Palmer, Samantha; Grover, Stephanie A; Hakgor, Sevan; Siu, Lillian L; Malkin, David; Virtanen, Carl; Pugh, Trevor J; Jacques, Pierre-Étienne; Joly, Yann; Jones, Steven J M; Bourque, Guillaume; Brudno, Michael

CanDIG: Federated network across Canada for multi-omic and health data discovery and analysis

2021.

Abstract | Links | BibTeX | Tags:

Murall, Carmen Lía; Fournier, Eric; Galvez, Jose Hector; N'Guessan, Arnaud; Reiling, Sarah J; Quirion, Pierre-Olivier; Naderi, Sana; Roy, Anne-Marie; Chen, Shu-Huang; Stretenowich, Paul; Bourgey, Mathieu; Bujold, David; Gregoire, Romain; Lepage, Pierre; St-Cyr, Janick; Willet, Patrick; Dion, Réjean; Charest, Hugues; Lathrop, Mark; Roger, Michel; Bourque, Guillaume; Ragoussis, Jiannis; Shapiro, B Jesse; Moreira, Sandrine

A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada Journal Article

In: Genome Med, vol. 13, no. 1, pp. 169, 2021, ISSN: 1756-994X.

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Dankner, Matthew; Caron, Maxime; Al-Saadi, Tariq; Yu, WenQing; Ouellet, Véronique; Ezzeddine, Rima; Maritan, Sarah M; Annis, Matthew G; Le, Phuong Uyen; Nadaf, Javad; Neubarth, Noah S; Savage, Paul; Zuo, Dongmei; Couturier, Charles P; Monlong, Jean; Djambazian, Haig; Altoukhi, Huda; Bourque, Guillaume; Ragoussis, Jiannis; Diaz, Roberto J; Park, Morag; Guiot, Marie-Christine; Lam, Stephanie; Petrecca, Kevin; Siegel, Peter M

Invasive growth associated with cold-inducible RNA-binding protein expression drives recurrence of surgically resected brain metastases Journal Article

In: Neuro Oncol, vol. 23, no. 9, pp. 1470–1480, 2021, ISSN: 1523-5866.

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Povysil, Gundula; Butler-Laporte, Guillaume; Shang, Ning; Wang, Chen; Khan, Atlas; Alaamery, Manal; Nakanishi, Tomoko; Zhou, Sirui; Forgetta, Vincenzo; Eveleigh, Robert Jm; Bourgey, Mathieu; Aziz, Naveed; Jones, Steven Jm; Knoppers, Bartha; Scherer, Stephen W; Strug, Lisa J; Lepage, Pierre; Ragoussis, Jiannis; Bourque, Guillaume; Alghamdi, Jahad; Aljawini, Nora; Albes, Nour; Al-Afghani, Hani M; Alghamdi, Bader; Almutairi, Mansour S; Mahmoud, Ebrahim Sabri; Abu-Safieh, Leen; Bardisy, Hadeel El; Harthi, Fawz S Al; Alshareef, Abdulraheem; Suliman, Bandar Ali; Alqahtani, Saleh A; Almalik, Abdulaziz; Alrashed, May M; Massadeh, Salam; Mooser, Vincent; Lathrop, Mark; Fawzy, Mohamed; Arabi, Yaseen M; Mbarek, Hamdi; Saad, Chadi; Al-Muftah, Wadha; Jung, Junghyun; Mangul, Serghei; Badji, Radja; Thani, Asma Al; Ismail, Said I; Gharavi, Ali G; Abedalthagafi, Malak S; Richards, J Brent; Goldstein, David B; Kiryluk, Krzysztof

Rare loss-of-function variants in type I IFN immunity genes are not associated with severe COVID-19 Journal Article

In: J Clin Invest, vol. 131, no. 14, 2021, ISSN: 1558-8238.

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AlOgayil, Najla; Bauermeister, Klara; Galvez, Jose Hector; Venkatesh, Varun S; Zhuang, Qinwei Kim-Wee; Chang, Matthew L; Davey, Rachel A; Zajac, Jeffrey D; Ida, Kinuyo; Kamiya, Akihide; Taketo, Teruko; Bourque, Guillaume; Naumova, Anna K

Distinct roles of androgen receptor, estrogen receptor alpha, and BCL6 in the establishment of sex-biased DNA methylation in mouse liver Journal Article

In: Sci Rep, vol. 11, no. 1, pp. 13766, 2021, ISSN: 2045-2322.

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Lambrot, Romain; Chan, Donovan; Shao, Xiaojian; Aarabi, Mahmoud; Kwan, Tony; Bourque, Guillaume; Moskovtsev, Sergey; Librach, Clifford; Trasler, Jacquetta; Dumeaux, Vanessa; Kimmins, Sarah

Whole-genome sequencing of H3K4me3 and DNA methylation in human sperm reveals regions of overlap linked to fertility and development Journal Article

In: Cell Rep, vol. 36, no. 3, pp. 109418, 2021, ISSN: 2211-1247.

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Sanchez-Ferras, Oraly; Pacis, Alain; Sotiropoulou, Maria; Zhang, Yuhong; Wang, Yu Chang; Bourgey, Mathieu; Bourque, Guillaume; Ragoussis, Jiannis; Bouchard, Maxime

A coordinated progression of progenitor cell states initiates urinary tract development Journal Article

In: Nat Commun, vol. 12, no. 1, pp. 2627, 2021, ISSN: 2041-1723.

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Cheng, Alexandre Pellan; Cheng, Matthew Pellan; Gu, Wei; Lenz, Joan Sesing; Hsu, Elaine; Schurr, Erwin; Bourque, Guillaume; Bourgey, Mathieu; Ritz, Jerome; Marty, Francisco M; Chiu, Charles Y; Vinh, Donald C; Vlaminck, Iwijn De

Cell-free DNA tissues of origin by methylation profiling reveals significant cell, tissue, and organ-specific injury related to COVID-19 severity Journal Article

In: Med, vol. 2, no. 4, pp. 411–422.e5, 2021, ISSN: 2666-6340.

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Liu, Peng; Ewald, Jessica; Galvez, Jose Hector; Head, Jessica; Crump, Doug; Bourque, Guillaume; Basu, Niladri; Xia, Jianguo

Ultrafast functional profiling of RNA-seq data for nonmodel organisms Journal Article

In: Genome Res, vol. 31, no. 4, pp. 713–720, 2021, ISSN: 1549-5469.

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Ferreira-Neto, José Ribamar Costa; da Costa Borges, Artemisa Nazaré; da Silva, Manassés Daniel; de Lima Morais, David Anderson; Bezerra-Neto, João Pacífico; Bourque, Guillaume; Kido, Ederson Akio; Benko-Iseppon, Ana Maria

The Cowpea Kinome: Genomic and Transcriptomic Analysis Under Biotic and Abiotic Stresses Journal Article

In: Front Plant Sci, vol. 12, pp. 667013, 2021, ISSN: 1664-462X.

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MacDonald, Adam; Lu, Brianna; Caron, Maxime; Caporicci-Dinucci, Nina; Hatrock, Dale; Petrecca, Kevin; Bourque, Guillaume; Stratton, Jo Anne

Single Cell Transcriptomics of Ependymal Cells Across Age, Region and Species Reveals Cilia-Related and Metal Ion Regulatory Roles as Major Conserved Ependymal Cell Functions Journal Article

In: Front Cell Neurosci, vol. 15, pp. 703951, 2021, ISSN: 1662-5102.

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Kuzmin, Elena; Monlong, Jean; Martinez, Constanza; Kuasne, Hellen; Kleinman, Claudia L; Ragoussis, Jiannis; Bourque, Guillaume; Park, Morag

Inferring Copy Number from Triple-Negative Breast Cancer Patient Derived Xenograft scRNAseq Data Using scCNA Journal Article

In: Methods Mol Biol, vol. 2381, pp. 285–303, 2021, ISSN: 1940-6029.

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Brereton, N J B; Pitre, F E; Gonzalez, E

Reanalysis of the Mars500 experiment reveals common gut microbiome alterations in astronauts induced by long-duration confinement Journal Article

In: Computational and Structural Biotechnology Journal, vol. 19, pp. 2223–2235, 2021, ISSN: 2001-0370.

Abstract | Links | BibTeX | Tags: 16S rRNA gene, Astronaut health, Mars, Microbiome, Space science

El-Far, Mohamed; Durand, Madeleine; Turcotte, Isabelle; Larouche-Anctil, Etienne; Sylla, Mohamed; Zaidan, Sarah; Chartrand-Lefebvre, Carl; Bunet, Rémi; Ramani, Hardik; Sadouni, Manel; Boldeanu, Irina; Chamberland, Annie; Lesage, Sylvie; Baril, Jean-Guy; Trottier, Benoit; Thomas, Réjean; Gonzalez, Emmanuel; Filali-Mouhim, Ali; Goulet, Jean-Philippe; Martinson, Jeffrey A; Kassaye, Seble; Karim, Roksana; Kizer, Jorge R; French, Audrey L; Gange, Stephen J; Ancuta, Petronela; Routy, Jean-Pierre; Hanna, David B; Kaplan, Robert C; Chomont, Nicolas; Landay, Alan L; Tremblay, Cécile L

Upregulated IL-32 Expression And Reduced Gut Short Chain Fatty Acid Caproic Acid in People Living With HIV With Subclinical Atherosclerosis Journal Article

In: Frontiers in Immunology, vol. 12, 2021, ISSN: 1664-3224, (Publisher: Frontiers).

Abstract | Links | BibTeX | Tags: Atherosclerosis, CVD (cardio vascular disease), gut microbiome, HIV, IL-32, Inflammation, short-chain fatty acids

Lopez Leyva, Lilian; Gonzalez, Emmanuel; Li, Chen; Ajeeb, Tamara; Solomons, Noel W; Agellon, Luis B; Scott, Marilyn E; Koski, Kristine G

Human Milk Microbiota in an Indigenous Population Is Associated with Maternal Factors, Stage of Lactation, and Breastfeeding Practices Journal Article

In: Current Developments in Nutrition, vol. 5, no. nzab013, 2021, ISSN: 2475-2991.

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