Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers by Jüri Reimand, Gary D Bader

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RETINA: Reconstruction-based pre-trained enhanced TransUNet for electron microscopy segmentation on the CEM500K dataset. by Cheng Xing, Ronald Xie, Gary D Bader

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Interpretable single-cell factor decomposition using sciRED by Delaram Pouyabahar, Tallulah Andrews, Gary D. Bader

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netDx: interpretable patient classification using integrated patient similarity networks by Shraddha Pai, Shirley Hui, Ruth Isserlin, Muhammad A Shah, Hussam Kaka, Gary D Bader

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Dynamic interaction networks in a hierarchically organized tissue by Daniel C Kirouac, Caryn Ito, Elizabeth Csaszar, Aline Roch, Mei Yu, Edward A Sykes, Gary D Bader, Peter W Zandstra

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Intercellular network structure and regulatory motifs in the human hematopoietic system by Wenlian Qiao, Weijia Wang, Elisa Laurenti, Andrei L Turinsky, Shoshana J Wodak, Gary D Bader, John E Dick, Peter W Zandstra

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Approaches to identify scenarios for data science implementations within healthcare settings: recommendations based on experiences at multiple academic institutions by Lillian Sung, Michael Brudno, Michael C. W. Caesar, Amol A. Verma, Brad Buchsbaum, Ravi Retnakaran, Vasily Giannakeas, Azadeh Kushki, Gary D. Bader, Helen Lasthiotakis, Muhammad Mamdani, Lisa Strug

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Combined deletion of Pten and p53 in mammary epithelium accelerates triple‐negative breast cancer with dependency on eEF2K by Jeff C Liu, Veronique Voisin, Sharon Wang, Dong‐Yu Wang, Robert A Jones, Alessandro Datti, David Uehling, Rima Al‐awar, Sean E Egan, Gary D Bader, Ming Tsao, Tak W Mak, Eldad Zacksenhaus

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Large‐scale survey and database of high affinity ligands for peptide recognition modules by Joan Teyra, Abdellali Kelil, Shobhit Jain, Mohamed Helmy, Raghav Jajodia, Yogesh Hooda, Jun Gu, Akshay A D’Cruz, Sandra E Nicholson, Jinrong Min, Marius Sudol, Philip M Kim, Gary D Bader, Sachdev S Sidhu

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Single-cell transcriptome analysis reveals CD34 as a marker of human sinoatrial node pacemaker cardiomyocytes by Amos A. Lim, Delaram Pouyabahar, Mishal Ashraf, Kate Huang, Michelle Lohbihler, Brandon M. Murareanu, Matthew L. Chang, Maggie Kwan, Faisal J. Alibhai, Thinh Tran, Amine Mazine, Michael A. Laflamme, Gary D. Bader, Zachary Laksman, Stephanie Protze

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Elevated mitochondrial membrane potential is a therapeutic vulnerability in Dnmt3a-mutant clonal hematopoiesis by Kira A. Young, Mohsen Hosseini, Jayna J. Mistry, Claudia Morganti, Taylor S. Mills, Xiurong Cai, Brandon T. James, Griffin J. Nye, Natalie R. Fournier, Veronique Voisin, Ali Chegini, Aaron D. Schimmer, Gary D. Bader, Grace Egan, Marc R. Mansour, Grant A. Challen, Eric M. Pietras, Kelsey H. Fisher-Wellman, Keisuke Ito, Steven M. Chan, Jennifer J. Trowbridge

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SH3 interactome conserves general function over specific form by Xiaofeng Xin, David Gfeller, Jackie Cheng, Raffi Tonikian, Lin Sun, Ailan Guo, Lianet Lopez, Alevtina Pavlenco, Adenrele Akintobi, Yingnan Zhang, Jean‐François Rual, Bridget Currell, Somasekar Seshagiri, Tong Hao, Xinping Yang, Yun A Shen, Kourosh Salehi‐Ashtiani, Jingjing Li, Aaron T Cheng, Dryden Bouamalay, Adrien Lugari, David E Hill, Mark L Grimes, David G Drubin, Barth D Grant, Marc Vidal, Charles Boone, Sachdev S Sidhu, Gary D Bader

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SBML Level 3: an extensible format for the exchange and reuse of biological models by Sarah M Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T Bergmann, Andrew Finney, Colin S Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman S Malik‐Sheriff, Stuart L Moodie, Ion I Moraru, Chris J Myers, Aurélien Naldi, Brett G Olivier, Sven Sahle, James C Schaff, Lucian P Smith, Maciej J Swat, Denis Thieffry, Leandro Watanabe, Darren J Wilkinson, Michael L Blinov, Kimberly Begley, James R Faeder, Harold F Gómez, Thomas M Hamm, Yuichiro Inagaki, Wolfram Liebermeister, Allyson L Lister, Daniel Lucio, Eric Mjolsness, Carole J Proctor, Karthik Raman, Nicolas Rodriguez, Clifford A Shaffer, Bruce E Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Wagner, Martin Meier‐Schellersheim, Herbert M Sauro, Bernhard Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C Doyle, Michael Hucka, SBML Level 3 Community members, Richard R Adams, Nicholas A Allen, Bastian R Angermann, Marco Antoniotti, Gary D Bader, Jan Červený, Mélanie Courtot, Chris D Cox, Piero Dalle Pezze, Emek Demir, William S Denney, Harish Dharuri, Julien Dorier, Dirk Drasdo, Ali Ebrahim, Johannes Eichner, Johan Elf, Lukas Endler, Chris T Evelo, Christoph Flamm, Ronan MT Fleming, Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Martin Golebiewski, Hovakim Grabski, Alex Gutteridge, Damon Hachmeister, Leonard A Harris, Benjamin D Heavner, Ron Henkel, William S Hlavacek, Bin Hu, Daniel R Hyduke, Hidde de Jong, Nick Juty, Peter D Karp, Jonathan R Karr, Douglas B Kell, Roland Keller, Ilya Kiselev, Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause, Martina Kutmon, Camille Laibe, Conor Lawless, Lu Li, Leslie M Loew, Rainer Machne, Yukiko Matsuoka, Pedro Mendes, Huaiyu Mi, Florian Mittag, Pedro T Monteiro, Kedar Nath Natarajan, Poul MF Nielsen, Tramy Nguyen, Alida Palmisano, Jean‐Baptiste Pettit, Thomas Pfau, Robert D Phair, Tomas Radivoyevitch, Johann M Rohwer, Oliver A Ruebenacker, Julio Saez‐Rodriguez, Martin Scharm, Henning Schmidt, Falk Schreiber, Michael Schubert, Roman Schulte, Stuart C Sealfon, Kieran Smallbone, Sylvain Soliman, Melanie I Stefan, Devin P Sullivan, Koichi Takahashi, Bas Teusink, David Tolnay, Ibrahim Vazirabad, Axel von Kamp, Ulrike Wittig, Clemens Wrzodek, Finja Wrzodek, Ioannis Xenarios, Anna Zhukova, Jeremy Zucker

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