Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data

Authors: Bialy, Nikki, Alber, Frank, Andrews, Brenda, Angelo, Michael, Beliveau, Brian, Bintu, Lacramioara, Boettiger, Alistair, Boehm, Ulrike, Brown, Claire M., Maina, Mahmoud Bukar, Chambers, James J., Cimini, Beth A., Eliceiri, Kevin, Errington, Rachel, Faklaris, Orestis, Gaudreault, Nathalie, Germain, Ronald N., Goscinski, Wojtek, Grunwald, David, Halter, Michael, Hanein, Dorit, Hickey, John W., Lacoste, Judith, Laude, Alex, Lundberg, Emma, Ma, Jian, Malacrida, Leonel, Moore, Josh, Nelson, Glyn, Neumann, Elizabeth Kathleen, Nitschke, Roland, Onami, Shuichi, Pimentel, Jaime A., Plant, Anne L., Radtke, Andrea J., Sabata, Bikash, Schapiro, Denis, Schöneberg, Johannes, Spraggins, Jeffrey M., Sudar, Damir, Vierdag, Wouter-Michiel Adrien Maria, Volkmann, Niels, Wählby, Carolina, Siyuan, Wang, Yaniv, Ziv, Strambio-De-Castillia, Caterina

Subject Terms: Quantitative Biology - Other Quantitative Biology

Access URL: http://arxiv.org/abs/2401.13022

Community-developed checklists for publishing images and image analysis

Authors: Schmied, Christopher, Nelson, Michael, Avilov, Sergiy, Bakker, Gert-Jan, Bertocchi, Cristina, Bischof, Johanna, Boehm, Ulrike, Brocher, Jan, Carvalho, Mariana, Chiritescu, Catalin, Christopher, Jana, Cimini, Beth, Conde-Sousa, Eduardo, Ebner, Michael, Ecker, Rupert, Eliceiri, Kevin, Fernandez-Rodriguez, Julia, Gaudreault, Nathalie, Gelman, Laurent, Grunwald, David, Gu, Tingting, Halidi, Nadia, Hammer, Mathias, Hartley, Matthew, Held, Marie, Jug, Florian, Kapoor, Varun, Koksoy, Ayse Aslihan, Lacoste, Judith, Dévédec, Sylvia Le, Guyader, Sylvie Le, Liu, Penghuan, Martins, Gabriel, Mathur, Aastha, Miura, Kota, Llopis, Paula Montero, Nitschke, Roland, North, Alison, Parslow, Adam, Payne-Dwyer, Alex, Plantard, Laure, Rizwan, Ali, Schroth-Diez, Britta, Schütz, Lucas, Scott, Ryan T., Seitz, Arne, Selchow, Olaf, Sharma, Ved, Spitaler, Martin, Srinivasan, Sathya, De Castillia, Caterina Strambio, Taatjes, Douglas, Tischer, Christian, Jambor, Helena Klara

Subject Terms: Quantitative Biology - Other Quantitative Biology

Access URL: http://arxiv.org/abs/2302.07005

Frequency of targetable genetic alterations in resectable lung adenocarcinoma: Results from the LORD project

Authors: Bossé, Yohan ^{a, b, ⁎}, Boudreau, Dominique K. ^a, Saavedra Armero, Victoria ^a, Li, Zhonglin ^a, Tremblay, Élody ^a, Gaudreault, Nathalie ^a, Gagné, Andréanne ^a, Desmeules, Patrice ^a, Joubert, Philippe ^{a, c}

Source: In Lung Cancer May 2025 203

Clinicopathological Predictors of the Presence of Blood Circulating Tumor DNA in Early-Stage Non–Small Cell Lung Cancers

Authors: Driussi, Arnaud ^a, Lamaze, Fabien C. ^a, Kordahi, Manal ^a, Armero, Victoria Saavedra ^a, Gaudreault, Nathalie ^a, Orain, Michèle ^a, Enlow, William ^a, Abbosh, Chris ^b, Hodgson, Darren ^b, Dasgupta, Abhijit ^c, Gagné, Andréanne ^a, Bossé, Yohan ^{a, d}, Joubert, Philippe ^{a, e, ∗}

Source: In Modern Pathology June 2025 38(6)

A Transcriptomic Approach to Sex Differences in Calcific Aortic Valve Stenosis in Patients with a Tricuspid Aortic Valve

Authors: Le Nezet, Emma ^a, Tam, Rose ^a, Li, Zhonglin ^a, Gaudreault, Nathalie ^a, Mathieu, Patrick ^a, Côté, Nancy ^a, Guisle, Isabelle ^a, Thériault, Sébastien ^a, Bossé, Yohan ^a, Clavel, Marie-Annick ^{a, ∗}

Source: In CJC Open February 2025

Polygenic inheritance and its interplay with smoking history in predicting lung cancer diagnosis: a French-Canadian case-control cohort

Authors: Boumtje, Véronique, Manikpurage, Hasanga D., Li, Zhonglin, Gaudreault, Nathalie, Armero, Victoria Saavedra, Boudreau, Dominique K., Renaut, Sébastien, Henry, Cyndi, Racine, Christine, Eslami, Aida, Bougeard, Stéphanie, Vigneau, Evelyne, Morissette, Mathieu, Arsenault, Benoit J., Labbé, Catherine, Laliberté, Anne-Sophie, Martel, Simon, Maltais, François, Couture, Christian, Desmeules, Patrice, Mathieu, Patrick, Thériault, Sébastien, Joubert, Philippe, Bossé, Yohan

Source: In eBioMedicine August 2024 106

Prognostic implication of methylation-based circulating tumor DNA detection prior to surgery in stage I non-small cell lung cancer

Authors: Bossé, Yohan, Dasgupta, Abhijit, Abadier, Michael, Guthrie, Violeta, Song, Florian, Saavedra Armero, Victoria, Gaudreault, Nathalie, Orain, Michèle, Lamaze, Fabien C., Melton, Collin, Nance, Tracy, Hung, Tiffany, Hodgson, Darren, Abbosh, Chris, Joubert, Philippe

Source: In Cancer Letters 10 July 2024 594

QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy

Authors: Nelson, Glyn, Boehm, Ulrike, Bagley, Steve, Bajcsy, Peter, Bischof, Johanna, Brown, Claire M, Dauphin, Aurelien, Dobbie, Ian M, Eriksson, John E, Faklaris, Orestis, Fernandez-Rodriguez, Julia, Ferrand, Alexia, Gelman, Laurent, Gheisari, Ali, Hartmann, Hella, Kukat, Christian, Laude, Alex, Mitkovski, Miso, Munck, Sebastian, North, Alison J, Rasse, Tobias M, Resch-Genger, Ute, Schuetz, Lucas C, Seitz, Arne, Strambio-De-Castillia, Caterina, Swedlow, Jason R, Alexopoulos, Ioannis, Aumayr, Karin, Avilov, Sergiy, Bakker, Gert-Jan, Bammann, Rodrigo R, Bassi, Andrea, Beckert, Hannes, Beer, Sebastian, Belyaev, Yury, Bierwagen, Jakob, Birngruber, Konstantin A, Bosch, Manel, Breitlow, Juergen, Cameron, Lisa A, Chalfoun, Joe, Chambers, James J, Chen, Chieh-Li, Conde-Sousa, Eduardo, Corbett, Alexander D, Cordelieres, Fabrice P, Del Nery, Elaine, Dietzel, Ralf, Eismann, Frank, Fazeli, Elnaz, Felscher, Andreas, Fried, Hans, Gaudreault, Nathalie, Goh, Wah Ing, Guilbert, Thomas, Hadleigh, Roland, Hemmerich, Peter, Holst, Gerhard A, Itano, Michelle S, Jaffe, Claudia B, Jambor, Helena K, Jarvis, Stuart C, Keppler, Antje, Kirchenbuechler, David, Kirchner, Marcel, Kobayashi, Norio, Krens, Gabriel, Kunis, Susanne, Lacoste, Judith, Marcello, Marco, Martins, Gabriel G, Metcalf, Daniel J, Mitchell, Claire A, Moore, Joshua, Mueller, Tobias, Nelson, Michael S, Ogg, Stephen, Onami, Shuichi, Palmer, Alexandra L, Paul-Gilloteaux, Perrine, Pimentel, Jaime A, Plantard, Laure, Podder, Santosh, Rexhepaj, Elton, Royon, Arnaud, Saari, Markku A, Schapman, Damien, Schoonderwoert, Vincent, Schroth-Diez, Britta, Schwartz, Stanley, Shaw, Michael, Spitaler, Martin, Stoeckl, Martin T, Sudar, Damir, Teillon, Jeremie, Terjung, Stefan, Thuenauer, Roland, Wilms, Christian D, Wright, Graham D, Nitschke, Roland

Source: J. Microsc. 2021;1-18

Subject Terms: Quantitative Biology - Other Quantitative Biology, Physics - Instrumentation and Detectors

Access URL: http://arxiv.org/abs/2101.09153

A perspective on Microscopy Metadata: data provenance and quality control

Authors: Huisman, Maximiliaan, Hammer, Mathias, Rigano, Alex, Boehm, Ulrike, Chambers, James J., Gaudreault, Nathalie, North, Alison J., Pimentel, Jaime A., Sudar, Damir, Bajcsy, Peter, Brown, Claire M., Corbett, Alexander D., Faklaris, Orestis, Lacoste, Judith, Laude, Alex, Nelson, Glyn, Nitschke, Roland, Grunwald, David, Strambio-De-Castillia, Caterina

Subject Terms: Quantitative Biology - Quantitative Methods, Computer Science - Databases

Access URL: http://arxiv.org/abs/1910.11370

Reporting reproducible imaging protocols

Authors: Larsen, DeLaine D., Gaudreault, Nathalie, Gibbs, Holly C.

Source: In STAR Protocols 17 March 2023 4(1)

Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes

Authors: Gerbin, Kaytlyn A., Grancharova, Tanya, Donovan-Maiye, Rory M., Hendershott, Melissa C., Anderson, Helen G., Brown, Jackson M., Chen, Jianxu, Dinh, Stephanie Q., Gehring, Jamie L., Johnson, Gregory R., Lee, HyeonWoo, Nath, Aditya, Nelson, Angelique M., Sluzewski, M. Filip, Viana, Matheus P., Yan, Calysta, Zaunbrecher, Rebecca J., Cordes Metzler, Kimberly R., Gaudreault, Nathalie, Knijnenburg, Theo A., Rafelski, Susanne M., Theriot, Julie A., Gunawardane, Ruwanthi N.

Source: In Cell Systems 16 June 2021 12(6):670-687

Enhancer-associated aortic valve stenosis risk locus 1p21.2 alters NFATC2 binding site and promotes fibrogenesis

Authors: Chignon, Arnaud, Rosa, Mickael, Boulanger, Marie-Chloé, Argaud, Déborah, Devillers, Romain, Bon-Baret, Valentin, Mkannez, Ghada, Li, Zhonglin, Rufiange, Anne, Gaudreault, Nathalie, Gosselin, David, Thériault, Sébastien, Bossé, Yohan, Mathieu, Patrick

Source: In iScience 19 March 2021 24(3)

Circulating Autoantibodies Targeting TREK-1 in Patients With Short-Coupled Ventricular Fibrillation.

Authors: Li, Jin, Janin, Alexandre, Patoughi, Mona, Gaudreault, Nathalie, Kis, Lenke, Moha Ou Maati, Hamid, Bossé, Yohan, Steinberg, Christian

Source: Circulation; 12/10/2024, Vol. 150 Issue 24, p1944-1954, 11p

Transcriptomic data helps refining classification of pulmonary carcinoid tumors with increased mitotic counts

Authors: Sazonova, Olga, Manem, Venkata, Orain, Michèle, Khoshkrood-Mansoori, Babak, Gaudreault, Nathalie, Desmeules, Patrice, Bossé, Yohan, Joubert, Philippe

Source: In Modern Pathology September 2020 33(9):1712-1721

Single-cell and single-nucleus RNA-sequencing from paired normal-adenocarcinoma lung samples provide both common and discordant biological insights.

Authors: Renaut, Sébastien¹, Armero, Victoria Saavedra¹, Boudreau, Dominique K.¹, Gaudreault, Nathalie¹, Desmeules, Patrice¹, Thériault, Sébastien¹, Mathieu, Patrick¹, Joubert, Philippe¹, Bossé, Yohan^1,2, yohan.bosse@criucpq.ulaval.ca

Source: PLoS Genetics; 5/30/2024, Vol. 20 Issue 5, p1-26, 26p

Early-onset emphysema in a large French-Canadian family: a genetic investigation

Authors: Bossé, Yohan, Lamontagne, Maxime, Gaudreault, Nathalie, Racine, Christine, Levesque, Marie-Hélène, Smith, Benjamin M, Auger, Dominique, Clemenceau, Alisson, Paré, Marie-Ève, Laviolette, Louis, Tremblay, Victor, Maranda, Bruno, Morissette, Mathieu C, Maltais, François

Source: In The Lancet Respiratory Medicine May 2019 7(5):427-436

Identification of aortic valve-specific genes dysregulated in calcific aortic valve stenosis

Authors: Zamani, Pardis, Purage, Hasanga Manik, Houessou, Ursula, Dahmene, Manel, Li, Zhonglin, Gaudreault, Nathalie, Mathieu, Patrick, Bossé, Yohan, Thériault, Sébastien

Source: In Atherosclerosis August 2024 395 Supplement 1

Transcriptome-wide profiling of the aortic valve in patients with calcified aortic valve stenosis at different levels of hemodynamic severity

Authors: Houessou, Ursula, Zamani, Pardis, Purage, Hasanga Manik, Li, Zhonglin, Gaudreault, Nathalie, Dahmene, Manel, Mathieu, Patrick, Bossé, Yohan, Thériault, Sébastien

Source: In Atherosclerosis August 2024 395 Supplement 1

A Test to Comprehensively Capture the Known Genetic Component of Familial Pulmonary Fibrosis.

Authors: Villeneuve, Judith, Tremblay, Élody, Gaudreault, Nathalie, Saavedra Armero, Victoria, Boudreau, Dominique K., Li, Zhonglin, Renaut, Sébastien, Dion, Geneviève, Bossé, Yohan

Source: American Journal of Respiratory Cell & Molecular Biology; Jun2024, Vol. 70 Issue 6, p437-445, 9p

Subject Terms: PULMONARY fibrosis, IDIOPATHIC pulmonary fibrosis, GENETIC testing, GENETIC variation, CONCRETE testing, EXOMES

Influence of Alkyltransferase Activity and Chromosomal Locus on Mutational Hotspots in Chinese Hamster Ovary Cells

Authors: Belouchi, Abdelmajid, Ouimet, Manon, Dion, Patrick, Gaudreault, Nathalie

Source: Proceedings of the National Academy of Sciences of the United States of America, 1996 Jan 01. 93(1), 121-125.

Access URL: https://www.jstor.org/stable/38322