Institute for Systems Biology (ISB) is a Providence-affiliated cross-disciplinary non-profit biomedical research organization based in Seattle. We focus on some of the most pressing issues in human health, including aging, brain health, cancer, COVID-19, the human microbiome, as well as many infectious diseases. ISB’s science is translational, and we champion sound scientific research that results in real-world clinical impacts. Learn more at isbscience.org, and see our published research papers here.

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Submissions from 2022

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Cytoplasmic Sensing in Innate Immunity, Ajay Suresh Akhade and Naeha Subramanian

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A model for the intrinsic limit of cancer therapy: Duality of treatment-induced cell death and treatment-induced stemness., Erin Angelini, Yue Wang, Joseph X Zhou, Hong Qian, and Sui Huang

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Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia coli., Mario L Arrieta-Ortiz, Min Pan, Amardeep Kaur, Evan Pepper-Tunick, Vivek Srinivas, Ananya Dash, Selva Rupa Christinal Immanuel, Aaron N Brooks, Tyson R Shepherd, and Nitin S Baliga

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Multi-Omic analyses characterize the ceramide/sphingomyelin pathway as a therapeutic target in Alzheimer's disease., Priyanka Baloni, Matthias Arnold, Luna Buitrago, Kwangsik Nho, Herman Moreno, Kevin Huynh, Barbara Brauner, Gregory Louie, Alexandra Kueider-Paisley, Karsten Suhre, Andrew J Saykin, Kim Ekroos, Peter J Meikle, Leroy Hood, Nathan D Price, Alzheimer’s Disease Metabolomics Consortium, P Murali Doraiswamy, Cory C Funk, A Iván Hernández, Gabi Kastenmüller, Rebecca Baillie, Xianlin Han, and Rima Kaddurah-Daouk

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Can precision medicine be personal; Can personalized medicine be precise?, Y. Michael Barilan (Ed), Margherita Brusa (Ed), Aaron Ciechanover (Ed), Leroy Hood (Contributing Author), and Nathan D Price (Contributing Author)

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Systematic mutagenesis of TFIIH subunit p52/Tfb2 identifies residues required for XPB/Ssl2 subunit function and genetic interactions with TFB6., Jacob Bassett, Jenna K Rimel, Shrabani Basu, Pratik Basnet, Jie Luo, Krysta L Engel, Michael Nagel, Alexander Woyciehowsky, Christopher C Ebmeier, Craig D Kaplan, Dylan J Taatjes, and Jeffrey A Ranish

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Imputing Missing Observations with Time Sliced Synthetic Minority Oversampling Technique, Andrew M Baumgartner, Sevda Molani, Qi Wei, and Jennifer J Hadlock

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On the Criticality of Adaptive Boolean Network Robots., Michele Braccini, Andrea Roli, Edoardo Barbieri, and Stuart A Kauffman

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MadR mediates acyl CoA-dependent regulation of mycolic acid desaturation in mycobacteria., Charlotte Cooper, Eliza Jr Peterson, Rebeca Bailo, Min Pan, Albel Singh, Patrick Moynihan, Makoto Nakaya, Nagatoshi Fujiwara, Nitin Baliga, and Apoorva Bhatt

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PARK7/DJ-1 promotes pyruvate dehydrogenase activity and maintains T, Egle Danileviciute, Ni Zeng, Christophe M Capelle, Nicole Paczia, Mark A Gillespie, Henry Kurniawan, Mohaned Benzarti, Myriam P Merz, Djalil Coowar, Sabrina Fritah, Daniela Maria Vogt Weisenhorn, Gemma Gomez Giro, Melanie Grusdat, Alexandre Baron, Coralie Guerin, Davide G Franchina, Cathy Léonard, Olivia Domingues, Sylvie Delhalle, Wolfgang Wurst, Jonathan D Turner, Jens Christian Schwamborn, Johannes Meiser, Rejko Krüger, Jeff Ranish, Dirk Brenner, Carole L Linster, Rudi Balling, Markus Ollert, and Feng Q Hefeng

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The ProteomeXchange consortium at 10 years: 2023 update., Eric W Deutsch, Nuno Bandeira, Yasset Perez-Riverol, Vagisha Sharma, Jeremy J Carver, Luis Mendoza, Deepti J Kundu, Shengbo Wang, Chakradhar Bandla, Selvakumar Kamatchinathan, Suresh Hewapathirana, Benjamin S Pullman, Julie Wertz, Zhi Sun, Shin Kawano, Shujiro Okuda, Yu Watanabe, Brendan MacLean, Michael J MacCoss, Yunping Zhu, Yasushi Ishihama, and Juan Antonio Vizcaíno

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Genome-microbiome interplay provides insight into the determinants of the human blood metabolome., Christian Diener, Chengzhen L Dai, Tomasz Wilmanski, Priyanka Baloni, Brett Smith, Noa Rappaport, Leroy Hood, Andrew T Magis, and Sean M Gibbons

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Angiotensin-Converting Enzyme (ACE) Inhibitors May Moderate COVID-19 Hyperinflammatory Response: An Observational Study with Deep Immunophenotyping., Venkata R Duvvuri, Andrew Baumgartner, Sevda Molani, Patricia V Hernandez, Dan Yuan, Ryan T Roper, Wanessa F Matos, Max Robinson, Yapeng Su, Naeha Subramanian, Jason D Goldman, James R Heath, and Jennifer J Hadlock

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What Is a Digital Twin? Experimental Design for a Data-Centric Machine Learning Perspective in Health., Frank Emmert-Streib and Olli Yli-Harja

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ASO Visual Abstract: Epigenetic Signatures Predict Pathologic Nodal Stage in Breast Cancer Patients with Estrogen-Receptor-Positive, Clinically Node-Positive Disease., Miquel Ensenyat-Mendez, Dennis Rünger, Javier I Orozco, Julie Le, Jennifer L Baker, Joanne Weidhaas, Diego M Marzese, and Maggie L DiNome

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Progress toward a universal biomedical data translator., Karamarie Fecho, Anne E Thessen, Sergio E Baranzini, Chris Bizon, Jennifer J Hadlock, Sui Huang, Ryan Roper, Noel Southall, Casey Ta, Paul B Watkins, Mark D Williams, Hao Xu, William Byrd, Vlado Dančík, Marc P Duby, Michel Dumontier, Gustavo Glusman, Nomi L Harris, Eugene W Hinderer, Greg Hyde, Adam Johs, Andrew I Su, Guangrong Qin, and Qian Zhu

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Roadmap on plasticity and epigenetics in cancer., Jasmine Foo, David Basanta, Russell C Rockne, Carly Strelez, Curran Shah, Kimya Ghaffarian, Shannon M Mumenthaler, Kelly Mitchell, Justin D Lathia, David Frankhouser, Sergio Branciamore, Ya-Huei Kuo, Guido Marcucci, Robert Vander Velde, Andriy Marusyk, Sui Huang, Kishore Hari, Mohit Kumar Jolly, Haralampos Hatzikirou, Kamrine Poels, Mary Spilker, Blerta Shtylla, Mark Robertson-Tessi, and Alexander R A Anderson

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Non-viral precision T cell receptor replacement for personalized cell therapy., Susan P Foy, Kyle Jacoby, Daniela A Bota, Theresa Hunter, Zheng Pan, Eric Stawiski, Yan Ma, William Lu, Songming Peng, Clifford L Wang, Benjamin Yuen, Olivier Dalmas, Katharine Heeringa, Barbara Sennino, Andy Conroy, Michael T Bethune, Ines Mende, William White, Monica Kukreja, Swetha Gunturu, Emily Humphrey, Adeel Hussaini, Duo An, Adam J Litterman, Boi Bryant Quach, Alphonsus H C Ng, Yue Lu, Chad Smith, Katie M Campbell, Daniel Anaya, Lindsey Skrdlant, Eva Yi-Hsuan Huang, Ventura Mendoza, Jyoti Mathur, Luke Dengler, Bhamini Purandare, Robert Moot, Michael C Yi, Roel Funke, Alison Sibley, Todd Stallings-Schmitt, David Y Oh, Bartosz Chmielowski, Mehrdad Abedi, Yuan Yuan, Jeffrey A Sosman, Sylvia M Lee, Adam J Schoenfeld, David Baltimore, James R Heath, Alex Franzusoff, Antoni Ribas, Arati V Rao, and Stefanie J Mandl

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Label-free plasma proteomics for the identification of the putative biomarkers of oral squamous cell carcinoma., Shashyendra Singh Gautam, Raghwendra Pratap Singh, Kajal Karsauliya, Ashish Kumar Sonker, Panga Jaipal Reddy, Divya Mehrotra, Sameer Gupta, Sudhir Singh, Rashmi Kumar, and Sheelendra Pratap Singh

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Perspective: Leveraging the Gut Microbiota to Predict Personalized Responses to Dietary, Prebiotic, and Probiotic Interventions., Sean M Gibbons, Thomas Gurry, Johanna W Lampe, Anirikh Chakrabarti, Veerle Dam, Amandine Everard, Almudena Goas, Gross Gabriele, Michiel Kleerebez, Jonathan Lane, Johanna Maukonen, Ana Lucia Barretto Penna, Bruno Pot, Ana M Valdes, Gemma Walton, Adrienne Weiss, Yoghatama Cindya Zanzer, Naomi V Venlet, and Michela Miani

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Distribution of 54 polygenic risk scores for common diseases in long lived individuals and their offspring., Sophia Gunn, Michael Wainberg, Zeyuan Song, Stacy Andersen, Robert Boudreau, Mary F Feitosa, Qihua Tan, May E Montasser, Jeffrey R O'Connell, Nathan Stitziel, Nathan D Price, Thomas Perls, Nicholas J Schork, and Paola Sebastiani

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Rare variants implicate NMDA receptor signaling and cerebellar gene networks in risk for bipolar disorder., Naushaba Hasin, Lace M Riggs, Tatyana Shekhtman, Justin Ashworth, Robert Lease, Rediet T Oshone, Elizabeth M Humphries, Judith A Badner, Pippa A Thomson, David C Glahn, David W Craig, Howard J Edenberg, Elliot S Gershon, Francis J McMahon, John I Nurnberger, Peter P Zandi, John R Kelsoe, Jared C Roach, Todd D Gould, and Seth A Ament

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P4 Medicine & What 21st Century Medicine Should Be, Leroy Hood

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Autocatalytic Sets Arising in a Combinatorial Model of Chemical Evolution., Wim Hordijk, Mike Steel, and Stuart Kauffman

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From telomere to telomere: The transcriptional and epigenetic state of human repeat elements., Savannah J Hoyt, Jessica Storer, Gabrielle A Hartley, Patrick G S Grady, Ariel Gershman, Leonardo G de Lima, Charles Limouse, Reza Halabian, Luke Wojenski, Matias Rodriguez, Nicolas Altemose, Arang Rhie, Leighton J Core, Jennifer L Gerton, Wojciech Makalowski, Daniel Olson, Jeb Rosen, Arian F A Smit, Aaron F Straight, Mitchell R Vollger, Travis J Wheeler, Michael C Schatz, Evan E Eichler, Adam M Phillippy, Winston Timp, Karen H Miga, and Rachel J O'Neill

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A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling., Hui Hua, Cem Meydan, Evan E Afshin, Loukia N Lili, Christopher R D'Adamo, Nate Rickard, Joel T Dudley, Nathan D Price, Bodi Zhang, and Christopher E Mason

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Towards a unification of the 2 meanings of "epigenetics"., Sui Huang

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Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families., Robert Hubley, Travis J Wheeler, and Arian F A Smit

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Deletion of Abi3/Gngt2 influences age-progressive amyloid β and tau pathologies in distinctive ways., Kristen R Ibanez, Karen N McFarland, Jennifer Phillips, Mariet Allen, Christian B Lessard, Lillian Zobel, Elsa Gonzalez De La Cruz, Shivani Shah, Quan Vo, Xue Wang, Zachary Quicksall, Daniel Ryu, Cory C Funk, Nilüfer Ertekin-Taner, Stefan Prokop, Todd E Golde, and Paramita Chakrabarty

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Protein Catalyzed Capture (PCC) Agents for Antigen Targeting., Matthew N Idso, Bert T Lai, Heather D Agnew, and James R Heath

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Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future., Andrew R Jones, Eric W Deutsch, and Juan Antonio Vizcaíno

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Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation., Anton Kalyuzhnyy, Patrick A Eyers, Claire E Eyers, Emily Bowler-Barnett, Maria J Martin, Zhi Sun, Eric W Deutsch, and Andrew R Jones

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Programmed cell death detection methods: a systematic review and a categorical comparison., Sana Kari, Kumar Subramanian, Ilenia Agata Altomonte, Akshaya Murugesan, Olli Yli-Harja, and Meenakshisundaram Kandhavelu

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A Testable Theory for the Emergence of the Classical World., Stuart Kauffman and Sudip Patra

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Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms., Richard D LeDuc, Eric W Deutsch, Pierre-Alain Binz, Ryan T Fellers, Anthony J Cesnik, Joshua A Klein, Tim Van Den Bossche, Ralf Gabriels, Arshika Yalavarthi, Yasset Perez-Riverol, Jeremy Carver, Wout Bittremieux, Shin Kawano, Benjamin Pullman, Nuno Bandeira, Neil L Kelleher, Paul M Thomas, and Juan Antonio Vizcaíno

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Recent Advances in RNA Therapy and Its Carriers to Treat the Single-Gene Neurological Disorders., Ming-Jen Lee, Inyoul Lee, and Kai Wang

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Decompression only versus fusion in octogenarians with spinal epidural abscesses: early complications, clinical and radiological outcome with 2-year follow-up., Pavlina Lenga, Gelo Gülec, Awais Akbar Bajwa, Mohammed Issa, Rod J Oskouian, Jens R Chapman, Karl Kiening, Andreas W Unterberg, and Basem Ishak

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KIR + CD8 + T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19, Jing Li, Maxim Zaslavsky, Yapeng Su, Jing Guo, Michael J Sikora, Vincent van Unen, Asbjørn Christophersen, Shin-Heng Chiou, Liang Chen, Jiefu Li, Xuhuai Ji, Julie Wilhelmy, Alana M McSween, Brad A Palanski, Venkata Vamsee Aditya Mallajosyula, Nathan A Bracey, Gopal Krishna R Dhondalay, Kartik Bhamidipati, Joy Pai, Lucas B Kipp, Jeffrey E Dunn, Stephen L Hauser, Jorge R Oksenberg, Ansuman T Satpathy, William H Robinson, Cornelia L Dekker, Lars M Steinmetz, Chaitan Khosla, Paul J Utz, Ludvig M Sollid, Yueh-Hsiu Chien, James R Heath, Nielsen Q Fernandez-Becker, Kari C Nadeau, Naresha Saligrama, and Mark M Davis

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Addendum: Transcriptomics and proteomics reveal two waves of translational repression during the maturation of malaria parasite sporozoites., Scott E Lindner, Kristian E Swearingen, Melanie J Shears, Aswathy Sebastian, Michael P Walker, Erin N Vrana, Kevin J Hart, Allen M Minns, Istvan Albert, Photini Sinnis, Robert L Moritz, and Stefan H I Kappe

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Author Correction: Comparative and demographic analysis of orang-utan genomes., Devin P Locke, LaDeana W Hillier, Wesley C Warren, Kim C Worley, Lynne V Nazareth, Donna M Muzny, Shiaw-Pyng Yang, Zhengyuan Wang, Asif T Chinwalla, Pat Minx, Makedonka Mitreva, Lisa Cook, Kim D Delehaunty, Catrina Fronick, Heather Schmidt, Lucinda A Fulton, Robert S Fulton, Joanne O Nelson, Vincent Magrini, Craig Pohl, Tina A Graves, Chris Markovic, Andy Cree, Huyen H Dinh, Jennifer Hume, Christie L Kovar, Gerald R Fowler, Gerton Lunter, Stephen Meader, Andreas Heger, Chris P Ponting, Tomas Marques-Bonet, Can Alkan, Lin Chen, Ze Cheng, Jeffrey M Kidd, Evan E Eichler, Simon White, Stephen Searle, Albert J Vilella, Yuan Chen, Paul Flicek, Jian Ma, Brian Raney, Bernard Suh, Richard Burhans, Javier Herrero, David Haussler, Rui Faria, Olga Fernando, Fleur Darré, Domènec Farré, Elodie Gazave, Meritxell Oliva, Arcadi Navarro, Roberta Roberto, Oronzo Capozzi, Nicoletta Archidiacono, Giuliano Della Valle, Stefania Purgato, Mariano Rocchi, Miriam K Konkel, Jerilyn A Walker, Brygg Ullmer, Mark A Batzer, Arian F A Smit, Robert Hubley, Claudio Casola, Daniel R Schrider, Matthew W Hahn, Victor Quesada, Xose S Puente, Gonzalo R Ordoñez, Carlos López-Otín, Tomas Vinar, Brona Brejova, Aakrosh Ratan, Robert S Harris, Webb Miller, Carolin Kosiol, Heather A Lawson, Vikas Taliwal, André L Martins, Adam Siepel, Arindam RoyChoudhury, Xin Ma, Jeremiah Degenhardt, Carlos D Bustamante, Ryan N Gutenkunst, Thomas Mailund, Julien Y Dutheil, Asger Hobolth, Mikkel H Schierup, Oliver A Ryder, Yuko Yoshinaga, Pieter J de Jong, George M Weinstock, Jeffrey Rogers, Elaine R Mardis, Richard A Gibbs, and Richard K Wilson

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A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics., Xiyang Luo, Wout Bittremieux, Johannes Griss, Eric W Deutsch, Timo Sachsenberg, Lev I Levitsky, Mark V Ivanov, Julia A Bubis, Ralf Gabriels, Henry Webel, Aniel Sanchez, Mingze Bai, Lukas Käll, and Yasset Perez-Riverol

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The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies., Jérémy Manry, Paul Bastard, Adrian Gervais, Tom Le Voyer, Jérémie Rosain, Quentin Philippot, Eleftherios Michailidis, Hans-Heinrich Hoffmann, Shohei Eto, Marina Garcia-Prat, Lucy Bizien, Alba Parra-Martínez, Rui Yang, Liis Haljasmägi, Mélanie Migaud, Karita Särekannu, Julia Maslovskaja, Nicolas de Prost, Yacine Tandjaoui-Lambiotte, Charles-Edouard Luyt, Blanca Amador-Borrero, Alexandre Gaudet, Julien Poissy, Pascal Morel, Pascale Richard, Fabrice Cognasse, Jesús Troya, Sophie Trouillet-Assant, Alexandre Belot, Kahina Saker, Pierre Garçon, Jacques G Rivière, Jean-Christophe Lagier, Stéphanie Gentile, Lindsey B Rosen, Elana Shaw, Tomohiro Morio, Junko Tanaka, David Dalmau, Pierre-Louis Tharaux, Damien Sene, Alain Stepanian, Bruno Mégarbane, Vasiliki Triantafyllia, Arnaud Fekkar, James R Heath, José Luis Franco, Juan-Manuel Anaya, Jordi Solé-Violán, Luisa Imberti, Andrea Biondi, Paolo Bonfanti, Riccardo Castagnoli, Ottavia M Delmonte, Yu Zhang, Andrew L Snow, Steven M Holland, Catherine M Biggs, Marcela Moncada-Vélez, Andrés Augusto Arias, Lazaro Lorenzo, Soraya Boucherit, Dany Anglicheau, Anna M Planas, Filomeen Haerynck, Sotirija Duvlis, Tayfun Ozcelik, Sevgi Keles, Ahmed A Bousfiha, Jalila El Bakkouri, Carolina Ramirez-Santana, Stéphane Paul, Qiang Pan-Hammarström, Lennart Hammarström, Annabelle Dupont, Alina Kurolap, Christine N Metz, Alessandro Aiuti, Giorgio Casari, Vito Lampasona, Fabio Ciceri, Lucila A Barreiros, Elena Dominguez-Garrido, Mateus Vidigal, Mayana Zatz, Diederik van de Beek, Sabina Sahanic, Ivan Tancevski, Yurii Stepanovskyy, Oksana Boyarchuk, Yoko Nukui, Miyuki Tsumura, Loreto Vidaur, Stuart G Tangye, Sonia Burrel, Darragh Duffy, Lluis Quintana-Murci, Adam Klocperk, Nelli Y Kann, Anna Shcherbina, Yu-Lung Lau, Daniel Leung, Matthieu Coulongeat, Julien Marlet, Rutger Koning, Luis Felipe Reyes, Angélique Chauvineau-Grenier, Fabienne Venet, Guillaume Monneret, Michel C Nussenzweig, Romain Arrestier, Idris Boudhabhay, Hagit Baris-Feldman, David Hagin, Joost Wauters, Isabelle Meyts, Adam H Dyer, Sean P Kennelly, Nollaig M Bourke, Rabih Halwani, Fatemeh Saheb Sharif-Askari, Karim Dorgham, Jérôme Sallette, Souad Mehlal Sedkaoui, Suzan AlKhater, Raúl Rigo-Bonnin, Francisco Morandeira, Lucie Roussel, Donald C Vinh, Christian Erikstrup, Antonio Condino-Neto, Carolina Prando, Anastasiia Bondarenko, András N Spaan, Laurent Gilardin, Jacques Fellay, Stanislas Lyonnet, Kaya Bilguvar, Richard P Lifton, Shrikant Mane, Mark S Anderson, Bertrand Boisson, Vivien Béziat, Shen-Ying Zhang, Evangelos Andreakos, Olivier Hermine, Aurora Pujol, Pärt Peterson, Trine H Mogensen, Lee Rowen, James Mond, Stéphanie Debette, Xavier de Lamballerie, Charles Burdet, Lila Bouadma, Marie Zins, Pere Soler-Palacin, Roger Colobran, Guy Gorochov, Xavier Solanich, Sophie Susen, Javier Martinez-Picado, Didier Raoult, Marc Vasse, Peter K Gregersen, Lorenzo Piemonti, Carlos Rodríguez-Gallego, Luigi D Notarangelo, Helen C Su, Kai Kisand, Satoshi Okada, Anne Puel, Emmanuelle Jouanguy, Charles M Rice, Pierre Tiberghien, Qian Zhang, Jean-Laurent Casanova, Laurent Abel, and Aurélie Cobat

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Physical and in silico immunopeptidomic profiling of a cancer antigen prostatic acid phosphatase reveals targets enabling TCR isolation., Zhiyuan Mao, Pavlo A Nesterenko, Jami McLaughlin, Weixian Deng, Giselle Burton Sojo, Donghui Cheng, Miyako Noguchi, William Chour, Diana C DeLucia, Kathryn A Finton, Yu Qin, Matthew B Obusan, Wendy Tran, Liang Wang, Nathanael J Bangayan, Lisa Ta, Chia-Chun Chen, Christopher S Seet, Gay M Crooks, John W Phillips, James R Heath, Roland K Strong, John K Lee, James A Wohlschlegel, and Owen N Witte

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Engineered SH2 Domains for Targeted Phosphoproteomics., Gregory D Martyn, Gianluca Veggiani, Ulrike Kusebauch, Seamus R Morrone, Bradley P Yates, Alex U Singer, Jiefei Tong, Noah Manczyk, Gerald Gish, Zhi Sun, Igor Kurinov, Frank Sicheri, Michael F Moran, Robert L Moritz, and Sachdev S Sidhu

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More Thumbs Than Rules: Is Rationality an Exaptation?, Antonio Mastrogiorgio, Teppo Felin, Stuart Kauffman, and Mariano Mastrogiorgio

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Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research., Bogdan Mateescu, Jennifer C Jones, Roger P Alexander, Eric Alsop, Ji Yeong An, Mohammad Asghari, Alex Boomgarden, Laura Bouchareychas, Alfonso Cayota, Hsueh-Chia Chang, Al Charest, Daniel T Chiu, Robert J Coffey, Saumya Das, Peter De Hoff, Andrew deMello, Crislyn D'Souza-Schorey, David Elashoff, Kiarash R Eliato, Jeffrey L Franklin, David J Galas, Mark B Gerstein, Ionita H Ghiran, David B Go, Stephen Gould, Tristan R Grogan, James N Higginbotham, Florian Hladik, Tony Jun Huang, Xiaoye Huo, Elizabeth Hutchins, Dennis K Jeppesen, Tijana Jovanovic-Talisman, Betty Y S Kim, Sung Kim, Kyoung-Mee Kim, Yong Kim, Robert R Kitchen, Vaughan Knouse, Emily L LaPlante, Carlito B Lebrilla, L James Lee, Kathleen M Lennon, Guoping Li, Feng Li, Tieyi Li, Tao Liu, Zirui Liu, Adam L Maddox, Kyle McCarthy, Bessie Meechoovet, Nalin Maniya, Yingchao Meng, Aleksandar Milosavljevic, Byoung-Hoon Min, Amber Morey, Martin Ng, John Nolan, Getulio P De Oliveira Junior, Michael E Paulaitis, Tuan Anh Phu, Robert L Raffai, Eduardo Reátegui, Matthew E Roth, David A Routenberg, Joel Rozowsky, Joseph Rufo, Satyajyoti Senapati, Sigal Shachar, Himani Sharma, Anil K Sood, Stavros Stavrakis, Alessandra Stürchler, Muneesh Tewari, Juan P Tosar, Alexander K Tucker-Schwartz, Andrey Turchinovich, Nedyalka Valkov, Kendall Van Keuren-Jensen, Kasey C Vickers, Lucia Vojtech, Wyatt N Vreeland, Ceming Wang, Kai Wang, ZeYu Wang, Joshua A Welsh, Kenneth W Witwer, David T W Wong, Jianping Xia, Ya-Hong Xie, Kaichun Yang, Mikołaj P Zaborowski, Chenguang Zhang, Qin Zhang, Angela M Zivkovic, and Louise C Laurent

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Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class., Paula Montaña-Lozano, Manuela Moreno-Carmona, Mauricio Ochoa-Capera, Natalia S Medina, Jeffrey L Boore, and Carlos F Prada

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Synthetic lethal kinases in Ras/p53 mutant squamous cell carcinoma., Russell Moser, Kay E Gurley, Olga Nikolova, Guangrong Qin, Rashmi Joshi, Eduardo Mendez, Ilya Shmulevich, Amanda Ashley, Carla Grandori, and Christopher J Kemp

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Standardized annotation of translated open reading frames., Jonathan M Mudge, Jorge Ruiz-Orera, John R Prensner, Marie A Brunet, Ferriol Calvet, Irwin Jungreis, Jose Manuel Gonzalez, Michele Magrane, Thomas F Martinez, Jana Felicitas Schulz, Yucheng T Yang, M Mar Albà, Julie L Aspden, Pavel V Baranov, Ariel A Bazzini, Elspeth Bruford, Maria Jesus Martin, Lorenzo Calviello, Anne-Ruxandra Carvunis, Jin Chen, Juan Pablo Couso, Eric W Deutsch, Paul Flicek, Adam Frankish, Mark Gerstein, Norbert Hubner, Nicholas T Ingolia, Manolis Kellis, Gerben Menschaert, Robert L Moritz, Uwe Ohler, Xavier Roucou, Alan Saghatelian, Jonathan S Weissman, and Sebastiaan van Heesch

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Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer., Rachel H Ng, Jihoon W Lee, Priyanka Baloni, Christian Diener, James R Heath, and Yapeng Su

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GPR17 Signaling Activation by CHBC Agonist Induced Cell Death via Modulation of MAPK Pathway in Glioblastoma., Phung Nguyen, Phuong Doan, Akshaya Murugesan, Thiyagarajan Ramesh, Tatu Rimpilainen, Nuno R Candeias, Olli Yli-Harja, and Meenakshisundaram Kandhavelu

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Organ-Based Proteome and Post-Translational Modification Profiling of a Widely Cultivated Tropical Water Fish, Labeo rohita, Mehar Un Nissa, Nevil Pinto, Arijit Mukherjee, Panga Jaipal Reddy, Biplab Ghosh, Zhi Sun, Saicharan Ghantasala, Chetanya Chetanya, Sanjyot Vinayak Shenoy, Robert L Moritz, Mukunda Goswami, and Sanjeeva Srivastava

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The PeptideAtlas of a widely cultivated fish Labeo rohita: A resource for the Aquaculture Community., Mehar Un Nissa, Panga Jaipal Reddy, Nevil Pinto, Zhi Sun, Biplab Ghosh, Robert L Moritz, Mukunda Goswami, and Sanjeeva Srivastava

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The complete sequence of a human genome., Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V Bzikadze, Alla Mikheenko, Mitchell R Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman, Sergey Aganezov, Savannah J Hoyt, Mark Diekhans, Glennis A Logsdon, Michael Alonge, Stylianos E Antonarakis, Matthew Borchers, Gerard G Bouffard, Shelise Y Brooks, Gina V Caldas, Nae-Chyun Chen, Haoyu Cheng, Chen-Shan Chin, William Chow, Leonardo G de Lima, Philip C Dishuck, Richard Durbin, Tatiana Dvorkina, Ian T Fiddes, Giulio Formenti, Robert S Fulton, Arkarachai Fungtammasan, Erik Garrison, Patrick G S Grady, Tina A Graves-Lindsay, Ira M Hall, Nancy F Hansen, Gabrielle A Hartley, Marina Haukness, Kerstin Howe, Michael W Hunkapiller, Chirag Jain, Miten Jain, Erich D Jarvis, Peter Kerpedjiev, Melanie Kirsche, Mikhail Kolmogorov, Jonas Korlach, Milinn Kremitzki, Heng Li, Valerie V Maduro, Tobias Marschall, Ann M McCartney, Jennifer McDaniel, Danny E Miller, James C Mullikin, Eugene W Myers, Nathan D Olson, Benedict Paten, Paul Peluso, Pavel A Pevzner, David Porubsky, Tamara Potapova, Evgeny I Rogaev, Jeffrey A Rosenfeld, Steven L Salzberg, Valerie A Schneider, Fritz J Sedlazeck, Kishwar Shafin, Colin J Shew, Alaina Shumate, Ying Sims, Arian F A Smit, Daniela C Soto, Ivan Sović, Jessica Storer, Aaron Streets, Beth A Sullivan, Françoise Thibaud-Nissen, James Torrance, Justin Wagner, Brian P Walenz, Aaron Wenger, Jonathan M D Wood, Chunlin Xiao, Stephanie M Yan, Alice C Young, Samantha Zarate, Urvashi Surti, Rajiv C McCoy, Megan Y Dennis, Ivan A Alexandrov, Jennifer L Gerton, Rachel J O'Neill, Winston Timp, Justin M Zook, Michael C Schatz, Evan E Eichler, Karen H Miga, and Adam M Phillippy

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The 2022 Report on the Human Proteome from the HUPO Human Proteome Project., Gilbert S Omenn, Lydie Lane, Christopher M Overall, Charles Pineau, Nicolle H Packer, Ileana M Cristea, Cecilia Lindskog, Susan T Weintraub, Sandra Orchard, Michael H A Roehrl, Edouard Nice, Siqi Liu, Nuno Bandeira, Yu-Ju Chen, Tiannan Guo, Ruedi Aebersold, Robert L Moritz, and Eric W Deutsch

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Personal Dense Dynamic Data Clouds Connect Systems Biomedicine to Scientific Wellness., Gilbert S Omenn, Andrew T Magis, Nathan D Price, and Leroy Hood

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ToPP: Tumor online prognostic analysis platform for prognostic feature selection and clinical patient subgroup selection., Jian Ouyang, Guangrong Qin, Zhenhao Liu, Xingxing Jian, Tieliu Shi, and Lu Xie

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A single-cell based precision medicine approach using glioblastoma patient-specific models., James H Park, Abdullah H Feroze, Samuel N Emerson, Anca B Mihalas, C Dirk Keene, Patrick J Cimino, Adrian Lopez Garcia de Lomana, Kavya Kannan, Wei-Ju Wu, Serdar Turkarslan, Nitin S Baliga, and Anoop P Patel

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Reconsidering the in vivo functions of Clostridial Stickland amino acid fermentations., Aidan Pavao, Madeline Graham, Mario L Arrieta-Ortiz, Selva Rupa Christinal Immanuel, Nitin S Baliga, and Lynn Bry

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The effect of COVID-19 vaccination and booster on maternal-fetal outcomes: a retrospective multicenter cohort study., Samantha N Piekos, Yeon Mi Hwang, Ryan Roper, Tanya K Sorensen, Nathan D Price, Leroy Hood, and Jennifer J Hadlock

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The impact of maternal SARS-CoV-2 infection and COVID-19 vaccination on maternal-fetal outcomes., Samantha N Piekos, Nathan D Price, Leroy Hood, and Jennifer J Hadlock

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The effect of race on treatment patterns and subsequent health-related quality of life outcomes in men undergoing treatment for localized prostate cancer., Natasza M Posielski, Santosh Shanmuga, On Ho, Jiji Jiang, Sally Elsamanoudi, Ryan Speir, Sean Stroup, John Musser, Alexander Ernest, Gregory T Chesnut, Timothy Tausch, John Paul Flores, and Christopher Porter

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A Functional Module States Framework Reveals Transcriptional States for Drug and Target Prediction., Guangrong Qin, Theo A Knijnenburg, David L Gibbs, Russell Moser, Raymond J Monnat, Christopher J Kemp, and Ilya Shmulevich

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Method for Independent Estimation of the False Localization Rate for Phosphoproteomics., Kerry A Ramsbottom, Ananth Prakash, Yasset Perez Riverol, Oscar Martin Camacho, Maria-Jesus Martin, Juan Antonio Vizcaíno, Eric W Deutsch, and Andrew R Jones

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PTPRD and CNTNAP2 as markers of tumor aggressiveness in oligodendrogliomas., Kirsi J Rautajoki, Serafiina Jaatinen, Aliisa M Tiihonen, Matti Annala, Elisa M Vuorinen, Anni Kivinen, Minna J Rauhala, Kendra K Maass, Kristian W Pajtler, Olli Yli-Harja, Pauli Helén, Joonas Haapasalo, Hannu Haapasalo, Wei Zhang, and Matti Nykter

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Discovery and Visualization of Uncharacterized Drug-Protein Adducts Using Mass Spectrometry., Michael Riffle, Michael R Hoopmann, Daniel Jaschob, Guo Zhong, Robert L Moritz, Michael J MacCoss, Trisha N Davis, Nina Isoherranen, and Alex Zelter

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Quality control of large genome datasets., Max Robinson, Arpita Joshi, Ansh Vidyarthi, Mary Maccoun, Sanjay Rangavajjhala, and Gustavo Glusman

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The hiatus between organism and machine evolution: Contrasting mixed microbial communities with robots., Andrea Roli and Stuart A Kauffman

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Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors., Rosalyn W Sayaman, Mohamad Saad, Carolina Heimann, Donglei Hu, Khalid Kunji, Jessica Roelands, Denise M Wolf, Scott Huntsman, Michele Ceccarelli, Vésteinn Thorsson, Elad Ziv, and Davide Bedognetti

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MITI minimum information guidelines for highly multiplexed tissue images., Denis Schapiro, Clarence Yapp, Artem Sokolov, Sheila Reynolds, Yu-An Chen, Damir Sudar, Yubin Xie, Jeremy Muhlich, Raquel Arias-Camison, Sarah Arena, Adam J Taylor, Milen Nikolov, Madison Tyler, Jia-Ren Lin, Erik A Burlingame, Human Tumor Atlas Network, Young H Chang, Samouil L Farhi, Vésteinn Thorsson, Nithya Venkatamohan, Julia L Drewes, Dana Pe'er, David A Gutman, Markus D Herrmann, Nils Gehlenborg, Peter Bankhead, Joseph T Roland, John M Herndon, Michael P Snyder, Michael Angelo, Garry Nolan, Jason R Swedlow, Nikolaus Schultz, Daniel T Merrick, Sarah A Mazzili, Ethan Cerami, Scott J Rodig, Sandro Santagata, and Peter K Sorger

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A metabolomic signature of the APOE2 allele., Paola Sebastiani, Zeyuan Song, Dylan Ellis, Qu Tian, Michaela Schwaiger-Haber, Ethan Stancliffe, Michael S Lustgarten, Cory C Funk, Priyanka Baloni, Cong-Hui Yao, Shakchhi Joshi, Megan M Marron, Anastasia Gurinovich, Mengze Li, Anastasia Leshchyk, Qingyan Xiang, Stacy L Andersen, Mary F Feitosa, Svetlana Ukraintseva, Mette Soerensen, Oliver Fiehn, Jose M Ordovas, Marcia Haigis, Stefano Monti, Nir Barzilai, Sofiya Milman, Luigi Ferrucci, Noa Rappaport, Gary J Patti, and Thomas T Perls

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Diminished cell proliferation promotes natural killer cell adaptive-like phenotype by limiting FcεRIγ expression., Avishai Shemesh, Yapeng Su, Daniel R Calabrese, Daniel Chen, Janice Arakawa-Hoyt, Kole T Roybal, James R Heath, John R Greenland, and Lewis L Lanier

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The immune landscape of solid pediatric tumors., Shimaa Sherif, Jessica Roelands, William Mifsud, Eiman I Ahmed, Christophe M Raynaud, Darawan Rinchai, Abbirami Sathappan, Ata Maaz, Ayman Saleh, Erdener Ozer, Khalid A Fakhro, Borbala Mifsud, Vésteinn Thorsson, Davide Bedognetti, and Wouter R L Hendrickx

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Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation., Eric A Stahlberg, Mohamed Abdel-Rahman, Boris Aguilar, Alireza Asadpoure, Robert A Beckman, Lynn L Borkon, Jeffrey N Bryan, Colleen M Cebulla, Young Hwan Chang, Ansu Chatterjee, Jun Deng, Sepideh Dolatshahi, Olivier Gevaert, Emily J Greenspan, Wenrui Hao, Tina Hernandez-Boussard, Pamela R Jackson, Marieke Kuijjer, Adrian Lee, Paul Macklin, Subha Madhavan, Matthew D McCoy, Navid Mohammad Mirzaei, Talayeh Razzaghi, Heber L Rocha, Leili Shahriyari, Ilya Shmulevich, Daniel G Stover, Yi Sun, Tanveer Syeda-Mahmood, Jinhua Wang, Qi Wang, and Ioannis Zervantonakis

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Methodologies for the De novo Discovery of Transposable Element Families, Jessica Storer, Robert Hubley, Jeb Rosen, and Arian F A Smit

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Cebidae, Jessica M Storer, Jerilyn A Walker, Morgan A Brown, and Mark A Batzer

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Owl Monkey, Jessica Storer, Jerilyn A Walker, Lydia C Rewerts, Morgan A Brown, Thomas O Beckstrom, Scott W Herke, Christian Roos, and Mark A Batzer

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Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus/ Sapajus Genomics, Jessica Storer, Jerilyn A Walker, Catherine E Rockwell, Grayce Mores, Thomas O Beckstrom, Joseph D Orkin, Amanda D Melin, Kimberley A Phillips, Christian Roos, and Mark A Batzer

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Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases., Kevin M Sullivan, Xiuyun Jiang, Prajna Guha, Christopher Lausted, Jason A Carter, Cynthia Hsu, Kevin P Labadie, Karan Kohli, Heidi L Kenerson, Sara K Daniel, Xiaowei Yan, Changting Meng, Arezou Abbasi, Marina Chan, Y David Seo, James O Park, Ian Nicholas Crispe, Raymond S Yeung, Teresa S Kim, Taranjit S Gujral, Qiang Tian, Steven C Katz, and Venu G Pillarisetty

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Multiple Early Factors Anticipate Post-Acute COVID-19 Sequelae, Yapeng Su, Dan Yuan, Daniel G. Chen, Rachel H. Ng, Kai Wang, Jongchan Choi, Sarah Li, Sunga Hong, Rongyu Zhang, Jingyi Xie, Sergey A Kornilov, Kelsey Scherler, Ana Jimena Pavlovitch-Bedzyk, Shen Dong, Christopher Lausted, Inyoul Lee, Shannon Fallen, Chengzhen L Dai, Priyanka Baloni, Brett Smith, Venkata R Duvvuri, Kristin G. Anderson, Jing Li, Fan Yang, Caroline J. Duncombe, Denise J. McCulloch, Clifford Rostomily, Pamela Troisch, Jing Zhou, Sean Mackay, Quinn DeGottardi, Damon H. May, Ruth Taniguchi, Rachel M. Gittelman, Mark Klinger, Thomas M. Snyder, Ryan Roper, Gladys Wojciechowska, Kim Murray, Rick Edmark, Simon Evans, Lesley Jones, Yong Zhou, Lee Rowen, Rachel Liu, William Chour, Heather A Algren, William R Berrington, Julie A Wallick, Rebecca A. Cochran, Mary Micikas, ISB-Swedish COVID19 Biobanking Unit, Terri Wrin, Christos J. Petropoulos, Hunter R. Cole, Trevan D Fischer, Wei Wei, Dave SB Hoon, Nathan D Price, Naeha Subramanian, Joshua A. Hill, Jennifer J Hadlock, Andrew T. Magis, Antoni Ribas, Lewis L. Lanier, Scott D. Boyd, Jeffrey A. Bluestone, Helen Chu, Leroy Hood, Raphael Gottardo, Philip D. Greenberg, Mark M. Davis, Jason D Goldman, and James R. Heath

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Multiple early factors anticipate post-acute COVID-19 sequelae., Yapeng Su, Dan Yuan, Daniel G Chen, Rachel H Ng, Kai Wang, Jongchan Choi, Sarah Li, Sunga Hong, Rongyu Zhang, Jingyi Xie, Sergey A Kornilov, Kelsey Scherler, Ana Jimena Pavlovitch-Bedzyk, Shen Dong, Christopher Lausted, Inyoul Lee, Shannon Fallen, Chengzhen L Dai, Priyanka Baloni, Brett Smith, Venkata R Duvvuri, Kristin G Anderson, Jing Li, Fan Yang, Caroline J Duncombe, Denise J McCulloch, Clifford Rostomily, Pamela Troisch, Jing Zhou, Sean Mackay, Quinn DeGottardi, Damon H May, Ruth Taniguchi, Rachel M Gittelman, Mark Klinger, Thomas M Snyder, Ryan Roper, Gladys Wojciechowska, Kim Murray, Rick Edmark, Simon Evans, Lesley Jones, Yong Zhou, Lee Rowen, Rachel Liu, William Chour, Heather A Algren, William R Berrington, Julie A Wallick, Rebecca A. Cochran, Mary Micikas, ISB-Swedish COVID-19 Biobanking Unit, Terri Wrin, Christos J Petropoulos, Hunter R Cole, Trevan Fischer, Wei Wei, Dave Hoon, Nathan D Price, Naeha Subramanian, Joshua A Hill, Jennifer J Hadlock, Andrew T Magis, Antoni Ribas, Lewis L Lanier, Scott D Boyd, Jeffrey A Bluestone, Helen Chu, Leroy Hood, Raphael Gottardo, Philip D Greenberg, Mark M Davis, Jason D Goldman, and James R Heath

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Probabilistic boolean networks predict transcription factor targets to induce transdifferentiation., Bahar Tercan, Boris Aguilar, Sui Huang, Edward R Dougherty, and Ilya Shmulevich

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Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science., Deepak R Unni, Sierra A T Moxon, Michael Bada, Matthew Brush, Richard Bruskiewich, J Harry Caufield, Paul A Clemons, Vlado Dancik, Michel Dumontier, Karamarie Fecho, Gustavo Glusman, Jennifer J Hadlock, Nomi L Harris, Arpita Joshi, Tim Putman, Guangrong Qin, Stephen A Ramsey, Kent A Shefchek, Harold Solbrig, Karthik Soman, Anne E Thessen, Melissa A Haendel, Chris Bizon, Christopher J Mungall, and Biomedical Data Translator Consortium

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Attractor-Specific and Common Expression Values in Random Boolean Network Models (with a Preliminary Look at Single-Cell Data)., Marco Villani, Gianluca D'Addese, Stuart A Kauffman, and Roberto Serra

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Design and Validation of a Whole-Genome Sequencing- Based Assay for Population Health, John Welle, Brian D. Piening, Josiah T Wagner, Isabelle Lucas-Beckett, T Ward, Benjamin Cosgrove, Eric Shull, R Rattray, Marina Pukay, M Ricks, Kimberly K Childers, Jennifer M Linehan, Mary Campbell, Ora K Gordon, and Carlo Bifulco

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Healthy aging and the human gut microbiome: why we cannot just turn back the clock., Tomasz Wilmanski, Sean M Gibbons, and Nathan D Price

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RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine., E C Wood, Amy K Glen, Lindsey G Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S Yoon, Chunyu Ma, Veronica Flores, Meghamala Sinha, Yodsawalai Chodpathumwan, Arash Termehchy, Jared C Roach, Luis Mendoza, Andrew S Hoffman, Eric W Deutsch, David Koslicki, and Stephen A Ramsey

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Small-molecule autocatalytic networks are universal metabolic fossils., Joana C Xavier and Stuart Kauffman

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Small-molecule autocatalytic networks are universal metabolic fossils., Joana C Xavier and Stuart Kauffman

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Mathematical models to study the biology of pathogens and the infectious diseases they cause., Joao B Xavier, Jonathan M Monk, Saugat Poudel, Charles J Norsigian, Anand V Sastry, Chen Liao, Jose Bento, Marc A Suchard, Mario L Arrieta-Ortiz, Eliza Jr Peterson, Nitin Baliga, Thomas Stoeger, Felicia Ruffin, Reese A K Richardson, Catherine A Gao, Thomas D Horvath, Anthony M Haag, Qinglong Wu, Tor Savidge, and Michael R Yeaman

Submissions from 2021

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Transition Therapy: Tackling the Ecology of Tumor Phenotypic Plasticity., Guim Aguadé-Gorgorió, Stuart Kauffman, and Ricard Solé

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The quantitative metabolome is shaped by abiotic constraints., Amir Akbari, James T Yurkovich, Daniel C Zielinski, and Bernhard O Palsson

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iNetModels 2.0: an interactive visualization and database of multi-omics data., Muhammad Arif, Cheng Zhang, Xiangyu Li, Cem Güngör, Buğra Çakmak, Metin Arslantürk, Abdellah Tebani, Berkay Özcan, Oğuzhan Subaş, Wenyu Zhou, Brian Piening, Hasan Turkez, Linn Fagerberg, Nathan Price, Leroy Hood, Michael Snyder, Jens Nielsen, Mathias Uhlen, and Adil Mardinoglu

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Predictive regulatory and metabolic network models for systems analysis of Clostridioides difficile., Mario L Arrieta-Ortiz, Selva Rupa Christinal Immanuel, Serdar Turkarslan, Wei-Ju Wu, Brintha P Girinathan, Jay N Worley, Nicholas DiBenedetto, Olga Soutourina, Johann Peltier, Bruno Dupuy, Lynn Bry, and Nitin S Baliga

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History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications., Karim Azer, Chanchala D Kaddi, Jeffrey S Barrett, Jane P F Bai, Sean T McQuade, Nathaniel J Merrill, Benedetto Piccoli, Susana Neves-Zaph, Luca Marchetti, Rosario Lombardo, Silvia Parolo, Selva Rupa Christinal Immanuel, and Nitin S Baliga

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Systems modeling of metabolic dysregulation in neurodegenerative diseases., Priyanka Baloni, Cory C Funk, Ben Readhead, and Nathan D Price

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Data management of sensitive human proteomics data: current practices, recommendations and perspectives for the future., Nuno Bandeira, Eric W Deutsch, Oliver Kohlbacher, Lennart Martens, and Juan Antonio Vizcaíno

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Autoantibodies neutralizing type I IFNs are present in, Paul Bastard, Adrian Gervais, Tom Le Voyer, Jérémie Rosain, Quentin Philippot, Jérémy Manry, Eleftherios Michailidis, Hans-Heinrich Hoffmann, Shohei Eto, Marina Garcia-Prat, Lucy Bizien, Alba Parra-Martínez, Rui Yang, Liis Haljasmägi, Mélanie Migaud, Karita Särekannu, Julia Maslovskaja, Nicolas de Prost, Yacine Tandjaoui-Lambiotte, Charles-Edouard Luyt, Blanca Amador-Borrero, Alexandre Gaudet, Julien Poissy, Pascal Morel, Pascale Richard, Fabrice Cognasse, Jesus Troya, Sophie Trouillet-Assant, Alexandre Belot, Kahina Saker, Pierre Garçon, Jacques G Rivière, Jean-Christophe Lagier, Stéphanie Gentile, Lindsey B Rosen, Elana Shaw, Tomohiro Morio, Junko Tanaka, David Dalmau, Pierre-Louis Tharaux, Damien Sene, Alain Stepanian, Bruno Megarbane, Vasiliki Triantafyllia, Arnaud Fekkar, James R Heath, José Luis Franco, Juan-Manuel Anaya, Jordi Solé-Violán, Luisa Imberti, Andrea Biondi, Paolo Bonfanti, Riccardo Castagnoli, Ottavia M Delmonte, Yu Zhang, Andrew L Snow, Steven M Holland, Catherine Biggs, Marcela Moncada-Vélez, Andrés Augusto Arias, Lazaro Lorenzo, Soraya Boucherit, Boubacar Coulibaly, Dany Anglicheau, Anna M Planas, Filomeen Haerynck, Sotirija Duvlis, Robert L Nussbaum, Tayfun Ozcelik, Sevgi Keles, Ahmed A Bousfiha, Jalila El Bakkouri, Carolina Ramirez-Santana, Stéphane Paul, Qiang Pan-Hammarström, Lennart Hammarström, Annabelle Dupont, Alina Kurolap, Christine N Metz, Alessandro Aiuti, Giorgio Casari, Vito Lampasona, Fabio Ciceri, Lucila A Barreiros, Elena Dominguez-Garrido, Mateus Vidigal, Mayana Zatz, Diederik van de Beek, Sabina Sahanic, Ivan Tancevski, Yurii Stepanovskyy, Oksana Boyarchuk, Yoko Nukui, Miyuki Tsumura, Loreto Vidaur, Stuart G Tangye, Sonia Burrel, Darragh Duffy, Lluis Quintana-Murci, Adam Klocperk, Nelli Y Kann, Anna Shcherbina, Yu-Lung Lau, Daniel Leung, Matthieu Coulongeat, Julien Marlet, Rutger Koning, Luis Felipe Reyes, Angélique Chauvineau-Grenier, Fabienne Venet, Guillaume Monneret, Michel C Nussenzweig, Romain Arrestier, Idris Boudhabhay, Hagit Baris-Feldman, David Hagin, Joost Wauters, Isabelle Meyts, Adam H Dyer, Sean P Kennelly, Nollaig M Bourke, Rabih Halwani, Narjes Saheb Sharif-Askari, Karim Dorgham, Jérome Sallette, Souad Mehlal Sedkaoui, Suzan AlKhater, Raúl Rigo-Bonnin, Francisco Morandeira, Lucie Roussel, Donald C Vinh, Sisse Rye Ostrowski, Antonio Condino-Neto, Carolina Prando, Anastasiia Bonradenko, András N Spaan, Laurent Gilardin, Jacques Fellay, Stanislas Lyonnet, Kaya Bilguvar, Richard P Lifton, Shrikant Mane, HGID Lab, COVID Clinicians, COVID-STORM Clinicians, NIAID Immune Response to COVID Group, NH-COVAIR Study Group, Danish CHGE, Danish Blood Donor Study, St. James's Hospital, SARS CoV2 Interest group, French COVID Cohort Study Group, Imagine COVID-Group, Milieu Intérieur Consortium, CoV-Contact Cohort, Amsterdam UMC Covid-19, Biobank Investigators, COVID Human Genetic Effort, CONSTANCES cohort, 3C-Dijon Study, Cerba Health-Care, Etablissement du Sang study group, Mark S Anderson, Bertrand Boisson, Vivien Béziat, Shen-Ying Zhang, Evangelos Vandreakos, Olivier Hermine, Aurora Pujol, Pärt Peterson, Trine H Mogensen, Lee Rowen, James Mond, Stéphanie Debette, Xavier de Lamballerie, Xavier Duval, France Mentré, Marie Zins, Pere Soler-Palacin, Roger Colobran, Guy Gorochov, Xavier Solanich, Sophie Susen, Javier Martinez-Picado, Didier Raoult, Marc Vasse, Peter K Gregersen, Lorenzo Piemonti, Carlos Rodríguez-Gallego, Luigi D Notarangelo, Helen C Su, Kai Kisand, Satoshi Okada, Anne Puel, Emmanuelle Jouanguy, Charles M Rice, Pierre Tiberghien, Qian Zhang, Aurélie Cobat, Laurent Abel, and Jean-Laurent Casanova

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mzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant mzML and Optimized for Speed and Storage Requirements., Ranjeet S Bhamber, Andris Jankevics, Eric W Deutsch, Andrew R Jones, and Andrew W Dowsey

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Recent Progress in Lyme Disease and Remaining Challenges., Jason R Bobe, Brandon L Jutras, Elizabeth J Horn, Monica E Embers, Allison Bailey, Robert L Moritz, Ying Zhang, Mark J Soloski, Richard S Ostfeld, Richard T Marconi, John Aucott, Avi Ma'ayan, Felicia Keesing, Kim Lewis, Choukri Ben Mamoun, Alison W Rebman, Mecaila E McClune, Edward B Breitschwerdt, Panga Jaipal Reddy, Ricardo Maggi, Frank Yang, Bennett Nemser, Aydogan Ozcan, Omai Garner, Dino Di Carlo, Zachary Ballard, Hyou-Arm Joung, Albert Garcia-Romeu, Roland R Griffiths, Nicole Baumgarth, and Brian A Fallon