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 2021

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DUOX2 variants associate with preclinical disturbances in microbiota-immune homeostasis and increased inflammatory bowel disease risk., Helmut Grasberger, Andrew T Magis, Elisa Sheng, Matthew P Conomos, Min Zhang, Lea S Garzotto, Guoqing Hou, Shrinivas Bishu, Hiroko Nagao-Kitamoto, Mohamad El-Zataari, Sho Kitamoto, Nobuhiko Kamada, Ryan Stidham, Yasutada Akiba, Jonathan Kaunitz, Yael Haberman, Subra Kugathasan, Lee A Denson, Gilbert S Omenn, and John Y Kao

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Elevated rates of horizontal gene transfer in the industrialized human microbiome., Mathieu Groussin, Mathilde Poyet, Ainara Sistiaga, Sean M Kearney, Katya Moniz, Mary Noel, Jeff Hooker, Sean M Gibbons, Laure Segurel, Alain Froment, Rihlat Said Mohamed, Alain Fezeu, Vanessa A Juimo, Sophie Lafosse, Francis E Tabe, Catherine Girard, Deborah Iqaluk, Le Thanh Tu Nguyen, B Jesse Shapiro, Jenni Lehtimäki, Lasse Ruokolainen, Pinja P Kettunen, Tommi Vatanen, Shani Sigwazi, Audax Mabulla, Manuel Domínguez-Rodrigo, Yvonne A Nartey, Adwoa Agyei-Nkansah, Amoako Duah, Yaw A Awuku, Kenneth A Valles, Shadrack O Asibey, Mary Y Afihene, Lewis R Roberts, Amelie Plymoth, Charles A Onyekwere, Roger E Summons, Ramnik J Xavier, and Eric J Alm

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Single-Cell Profiling of Fatty Acid Uptake Using Surface-Immobilized Dendrimers., Zhili Guo, Hanjun Cheng, Zhonghan Li, Shiqun Shao, Priyanka Sarkar, Siwen Wang, Rohit Chaudhuri, Nicole G Perkins, Fei Ji, Wei Wei, and Min Xue

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Debris-stimulated tumor growth: a Pandora's box?, Victoria M Haak, Sui Huang, and Dipak Panigrahy

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MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics., Zachary B Haiman, Daniel C Zielinski, Yuko Koike, James T Yurkovich, and Bernhard O Palsson

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Dissolved Organic Matter in the Global Ocean: A Primer., Dennis A Hansell and Monica V Orellana

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Digital twins for predictive oncology will be a paradigm shift for precision cancer care., Tina Hernandez-Boussard, Paul Macklin, Emily J Greenspan, Amy L Gryshuk, Eric Stahlberg, Tanveer Syeda-Mahmood, and Ilya Shmulevich

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Measuring the Efficacy of Pathology Career Recruitment Strategies in US Medical Students., Patricia V Hernandez, Dana Razzano, Nicole D Riddle, John T Fallon, Humayun K Islam, Kamran M Mirza, Rugved Pattarkine, Tania Platero, Daniela Hermelin, Patricia V Adem, Adam L Booth, Eunice Mbela Nachinga, Kalpana S Reddy, Angelica Mares, and Patrick A Lento

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Op-Ed: How science education can stave off demagogues, Leroy Hood and Matthew D. LaPlante

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Reconciling Non-Genetic Plasticity with Somatic Evolution in Cancer., Sui Huang

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Should biophysics study nonphysical quantities of biological systems? Take Max Delbrück for inspiration., Sui Huang

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Modulation of SETDB1 activity by APQ ameliorates heterochromatin condensation, motor function, and neuropathology in a Huntington's disease mouse model., Yu Jin Hwang, Seung Jae Hyeon, Younghee Kim, Sungsu Lim, Min Young Lee, Jieun Kim, Ashwini M Londhe, Lizaveta Gotina, Yunha Kim, Ae Nim Pae, Yong Seo Cho, Jihye Seong, Hyemyung Seo, Yun Kyung Kim, Hyunah Choo, Hoon Ryu, and Sun-Joon Min

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Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME., Selva Rupa Christinal Immanuel, Mario L Arrieta-Ortiz, Rene A Ruiz, Min Pan, Adrián López García de Lomana, Eliza Jr Peterson, and Nitin S Baliga

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Integrated genetic and metabolic landscapes predict vulnerabilities of temozolomide resistant glioblastoma cells., Selva Rupa Christinal Immanuel, Avinash D Ghanate, Dharmeshkumar S Parmar, Ritu Yadav, Riya Uthup, Venkateswarlu Panchagnula, and Anu Raghunathan

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Chromatin-Associated Protein Complexes Link DNA Base J and Transcription Termination in, Bryan C Jensen, Isabelle Q Phan, Jacquelyn R McDonald, Aakash Sur, Mark A Gillespie, Jeffrey A Ranish, Marilyn Parsons, and Peter J Myler

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Angiotensin II receptor I auto-antibodies following SARS-CoV-2 infection., Yonghou Jiang, Fergal Duffy, Jennifer J Hadlock, Andrew Raappana, Sheila Styrchak, Ingrid Beck, Fred D Mast, Leslie R Miller, William Chour, John Houck, Blair Armistead, Venkata R Duvvuri, Winnie Yeung, Micaela Haglund, Jackson Wallner, Julie A Wallick, Samantha Hardy, Alyssa Oldroyd, Daisy Ko, Ana Gervassi, Kim M Murray, Henry G Kaplan, John D Aitchison, James R Heath, D Noah Sather, Jason D Goldman, Lisa Frenkel, and Whitney E Harrington

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SPACEPro: A Software Tool for Analysis of Protein Sample Cleavage for Tandem Mass Spectrometry., Vidur Kailash, Luis Mendoza, Robert L Moritz, and Michael R Hoopmann

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The World Is Not a Theorem., Stuart Kauffman and Andrea Roli

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Genomic and functional characterization of a mucosal symbiont involved in early-stage colorectal cancer., Melissa C Kordahi, Ian B Stanaway, Marion Avril, Denise Chac, Marie-Pierre Blanc, Benjamin Ross, Christian Diener, Sumita Jain, Paul McCleary, Ana Parker, Vincent Friedman, Jennifer Huang, Wynn Burke, Sean M Gibbons, Amy D Willis, Richard P Darveau, William M Grady, Cynthia W Ko, and R William DePaolo

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Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19., Benjamin Krämer, Rainer Knoll, Lorenzo Bonaguro, Michael ToVinh, Jan Raabe, Rosario Astaburuaga-García, Jonas Schulte-Schrepping, Kim Melanie Kaiser, Gereon J Rieke, Jenny Bischoff, Malte B Monin, Christoph Hoffmeister, Stefan Schlabe, Elena De Domenico, Nico Reusch, Kristian Händler, Gary Reynolds, Nils Blüthgen, Gudrun Hack, Claudia Finnemann, Hans D Nischalke, Christian P Strassburg, Emily Stephenson, Yapeng Su, Louis Gardner, Dan Yuan, Daniel Chen, Jason D Goldman, Philipp Rosenstiel, Susanne V Schmidt, Eicke Latz, Kevin Hrusovsky, Andrew J Ball, Joe M Johnson, Paul-Albert Koenig, Florian I Schmidt, Muzlifah Haniffa, James R Heath, Beate M Kümmerer, Verena Keitel, Björn Jensen, Paula Stubbemann, Florian Kurth, Leif E Sander, Birgit Sawitzki, Deutsche COVID-19 OMICS Initiative (DeCOI), Anna C Aschenbrenner, Joachim L Schultze, and Jacob Nattermann

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THP1 proteomics in response to mycobacterium tuberculosis infection, Ajay Kumar, Mukul K Midha, and Kanury Vs Rao

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Plasmodium falciparum Calcium-Dependent Protein Kinase 4 is Critical for Male Gametogenesis and Transmission to the Mosquito Vector., Sudhir Kumar, Meseret T Haile, Michael R Hoopmann, Linh T Tran, Samantha A Michaels, Seamus R Morrone, Kayode K Ojo, Laura M Reynolds, Ulrike Kusebauch, Ashley M Vaughan, Robert L Moritz, Stefan H I Kappe, and Kristian E Swearingen

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Ambulatory risk models for long-term prevention of sepsis: Retrospective Analysis and Predictive Model., Jewel Y Lee, Sevda Molani, Chen Fang, Kathleen Jade, Shane O'Mahony, Sergey A Kornilov, Lindsay T Mico, and Jennifer J Hadlock

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Cordycepin inhibits the proliferation of malignant peripheral nerve sheath tumor cells through the p53/Sp1/tubulin pathway., Ming-Jen Lee, Jen-Chieh Lee, Jung-Hsien Hsieh, May-Yao Lin, I-An Shih, Huey-Ling You, and Kai Wang

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Molecular interaction of HIC, an agonist of P2Y1 receptor, and its role in prostate cancer apoptosis., Hien Thi Thu Le, Akshaya Murugesan, Thiyagarajan Ramesh, Olli Yli-Harja, Saravanan Konda Mani, and Meenakshisundaram Kandhavelu

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Constraint Closure Drove Major Transitions in the Origins of Life., Niles E Lehman and Stuart A Kauffman

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Modulating innate immune activation states impacts the efficacy of specific Aβ immunotherapy., Yona Levites, Cory Funk, Xue Wang, Paramita Chakrabarty, Karen N McFarland, Baxter Bramblett, Veronica O'Neal, Xufei Liu, Thomas Ladd, Max Robinson, Mariet Allen, Minerva M Carrasquillo, Dennis Dickson, Pedro Cruz, Danny Ryu, Hong-Dong Li, Nathan D Price, NIlüfer Ertekin-Taner, and Todd E Golde

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Integrative functional genomic analysis of intron retention in human and mouse brain with Alzheimer's disease., Hong-Dong Li, Cory C Funk, Karen McFarland, Eric B Dammer, Mariet Allen, Minerva M Carrasquillo, Yona Levites, Paramita Chakrabarty, Jeremy D Burgess, Xue Wang, Dennis Dickson, Nicholas T Seyfried, Duc M Duong, James J Lah, Steven G Younkin, Allan I Levey, Gilbert S Omenn, Nilüfer Ertekin-Taner, Todd E Golde, and Nathan D Price

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A CRISPR/Cas9-engineered ARID1A-deficient human gastric cancer organoid model reveals essential and non-essential modes of oncogenic transformation., Yuan-Hung Lo, Kevin S Kolahi, Yuhong Du, Chiung-Ying Chang, Andrey Krokhotin, Ajay Nair, Walter D Sobba, Kasper Karlsson, Sunny J Jones, Teri A Longacre, Amanda T Mah, Bahar Tercan, Alexandra Sockell, Hang Xu, Jose A Seoane, Jin Chen, Ilya Shmulevich, Jonathan S Weissman, Christina Curtis, Andrea Califano, Haian Fu, Gerald R Crabtree, and Calvin J Kuo

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Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology., Lauren M Lui, Erica L-W Majumder, Heidi J Smith, Hans K Carlson, Frederick von Netzer, Matthew W Fields, David A Stahl, Jizhong Zhou, Terry C Hazen, Nitin S Baliga, Paul D Adams, and Adam P Arkin

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Resolution of tissue signatures of therapy response in patients with recurrent GBM treated with neoadjuvant anti-PD1., Yue Lu, Alphonsus H C Ng, Frances E Chow, Richard G Everson, Beth A Helmink, Michael T Tetzlaff, Rohit Thakur, Jennifer A Wargo, Timothy F Cloughesy, Robert M Prins, and James R Heath

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Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period., Frank Maixner, Mohamed S Sarhan, Kun D Huang, Adrian Tett, Alexander Schoenafinger, Stefania Zingale, Aitor Blanco-Míguez, Paolo Manghi, Jan Cemper-Kiesslich, Wilfried Rosendahl, Ulrike Kusebauch, Seamus R Morrone, Michael R Hoopmann, Omar Rota-Stabelli, Thomas Rattei, Robert L Moritz, Klaus Oeggl, Nicola Segata, Albert Zink, Hans Reschreiter, and Kerstin Kowarik

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Prognostic gene expression signatures of breast cancer are lacking a sensible biological meaning., Kalifa Manjang, Shailesh Tripathi, Olli Yli-Harja, Matthias Dehmer, Galina Glazko, and Frank Emmert-Streib

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Limitations of Explainability for Established Prognostic Biomarkers of Prostate Cancer., Kalifa Manjang, Olli Yli-Harja, Matthias Dehmer, and Frank Emmert-Streib

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A high-quality bonobo genome refines the analysis of hominid evolution., Yafei Mao, Claudia R Catacchio, LaDeana W Hillier, David Porubsky, Ruiyang Li, Arvis Sulovari, Jason D Fernandes, Francesco Montinaro, David S Gordon, Jessica M Storer, Marina Haukness, Ian T Fiddes, Shwetha Canchi Murali, Philip C Dishuck, PingHsun Hsieh, William T Harvey, Peter A Audano, Ludovica Mercuri, Ilaria Piccolo, Francesca Antonacci, Katherine M Munson, Alexandra P Lewis, Carl Baker, Jason G Underwood, Kendra Hoekzema, Tzu-Hsueh Huang, Melanie Sorensen, Jerilyn A Walker, Jinna Hoffman, Françoise Thibaud-Nissen, Sofie R Salama, Andy W C Pang, Joyce Lee, Alex R Hastie, Benedict Paten, Mark A Batzer, Mark Diekhans, Mario Ventura, and Evan E Eichler

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Asexuality associated with marked genomic expansion of tandemly repeated rRNA and histone genes., Kyle E McElroy, Stefan Müller, Dunja Lamatsch, Laura Bankers, Peter D Fields, Joseph R Jalinsky, Joel Sharbrough, Jeffrey L Boore, John M Logsdon, and Maurine Neiman

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A systems-biology clinical trial of a personalized multimodal lifestyle intervention for early Alzheimer's disease., Sarah C McEwen, David A Merrill, Jennifer Bramen, Verna Porter, Stella Panos, Scott Kaiser, John Hodes, Aarthi Ganapathi, Lesley Bell, Tess Bookheimer, Ryan Glatt, Molly Rapozo, Mary Kay Ross, Nathan D Price, Daniel Kelly, Cory C Funk, Leroy Hood, and Jared C Roach

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Microglia show differential transcriptomic response to Aβ peptide aggregates ex vivo and in vivo., Karen N McFarland, Carolina Ceballos, Awilda Rosario, Thomas Ladd, Brenda Moore, Griffin Golde, Xue Wang, Mariet Allen, Nilüfer Ertekin-Taner, Cory C Funk, Max Robinson, Priyanka Baloni, Noa Rappaport, Paramita Chakrabarty, and Todd E Golde

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The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility., Nathaly Andrea Montenegro Benavides, Alejandro Alvarez B, Mario L Arrieta-Ortiz, Luis Miguel Rodriguez-R, David Botero, Javier Felipe Tabima, Luisa Castiblanco, Cesar Trujillo, Silvia Restrepo, and Adriana Bernal

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Molecular modeling and dynamics studies of the synthetic small molecule agonists with GPR17 and P2Y1 receptor., Akshaya Murugesan, Phung Nguyen, Thiyagarajan Ramesh, Olli Yli-Harja, Meenakshisundaram Kandhavelu, and Konda Mani Saravanan

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A systems-level gene regulatory network model for Plasmodium falciparum., Maxwell L Neal, Ling Wei, Eliza Jr Peterson, Mario L Arrieta-Ortiz, Samuel A Danziger, Nitin Baliga, Alexis Kaushansky, and John D Aitchison

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HLA-A, Pavlo A Nesterenko, Jami McLaughlin, Brandon L Tsai, Giselle Burton Sojo, Donghui Cheng, Daniel Zhao, Zhiyuan Mao, Nathanael J Bangayan, Matthew B Obusan, Yapeng Su, Rachel H Ng, William Chour, Jingyi Xie, Yan-Ruide Li, Derek Lee, Miyako Noguchi, Camille Carmona, John W Phillips, Jocelyn T Kim, Lili Yang, James R Heath, Paul C Boutros, and Owen N Witte

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Synthesis and Preclinical Validation of Novel Indole Derivatives as a GPR17 Agonist for Glioblastoma Treatment., Phung Nguyen, Phuong Doan, Tatu Rimpilainen, Saravanan Konda Mani, Akshaya Murugesan, Olli Yli-Harja, Nuno R Candeias, and Meenakshisundaram Kandhavelu

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Autophagy as a Mechanism for Adaptive Prediction-Mediated Emergence of Drug Resistance., Nivedita Nivedita, John D Aitchison, and Nitin Baliga

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PRoBE the cloud toolkit: finding the best biomarkers of drug response within a breast cancer clinical trial., Nicholas O'Grady, David L Gibbs, Kawther Abdilleh, Adam Asare, Smita Asare, Sara Venters, Lamorna Brown-Swigart, Gillian L Hirst, Denise Wolf, Christina Yau, Laura J van 't Veer, Laura Esserman, and Amrita Basu

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Towards early risk biomarkers: serum metabolic signature in childhood predicts cardio-metabolic risk in adulthood., Xiaowei Ojanen, Runtan Cheng, Timo Törmäkangas, Noa Rappaport, Tomasz Wilmanski, Na Wu, Erik Fung, Rozenn Nedelec, Sylvain Sebert, Dimitris Vlachopoulos, Wei Yan, Nathan D Price, Sulin Cheng, and Petri Wiklund

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Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project., Gilbert S Omenn, Lydie Lane, Christopher M Overall, Young-Ki Paik, Ileana M Cristea, Fernando J Corrales, Cecilia Lindskog, Susan Weintraub, Michael H A Roehrl, Siqi Liu, Nuno Bandeira, Sudhir Srivastava, Yu-Ju Chen, Ruedi Aebersold, Robert L Moritz, and Eric W Deutsch

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Marine Polymer-Gels' Relevance in the Atmosphere as Aerosols and CCN., Monica V Orellana, Dennis A Hansell, Patricia A Matrai, and Caroline Leck

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Single Cell Scale Neuronal and Glial Gene Expression and Putative Cell Phenotypes and Networks in the Nucleus Tractus Solitarius in an Alcohol Withdrawal Time Series., Sean J O'Sullivan, Damani McIntosh-Clarke, James H Park, Rajanikanth Vadigepalli, and James S Schwaber

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Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification., Anne E Otwell, Alex V Carr, Erica L W Majumder, Maryann K Ruiz, Regina L Wilpiszeski, Linh T Hoang, Bill Webb, Serdar Turkarslan, Sean M Gibbons, Dwayne A Elias, David A Stahl, Gary Siuzdak, and Nitin S Baliga

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Molecular interaction study of novel indoline derivatives with EGFR-kinase domain using multiple computational analysis., Suresh Palanivel, Olli Yli-Harja, and Meenakshisundaram Kandhavelu

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The transposable element-rich genome of the cereal pest Sitophilus oryzae., Nicolas Parisot, Carlos Vargas-Chávez, Clément Goubert, Patrice Baa-Puyoulet, Séverine Balmand, Louis Beranger, Caroline Blanc, Aymeric Bonnamour, Matthieu Boulesteix, Nelly Burlet, Federica Calevro, Patrick Callaerts, Théo Chancy, Hubert Charles, Stefano Colella, André Da Silva Barbosa, Elisa Dell'Aglio, Alex Di Genova, Gérard Febvay, Toni Gabaldón, Mariana Galvão Ferrarini, Alexandra Gerber, Benjamin Gillet, Robert Hubley, Sandrine Hughes, Emmanuelle Jacquin-Joly, Justin Maire, Marina Marcet-Houben, Florent Masson, Camille Meslin, Nicolas Montagné, Andrés Moya, Ana Tereza Ribeiro de Vasconcelos, Gautier Richard, Jeb Rosen, Marie-France Sagot, Arian F A Smit, Jessica Storer, Carole Vincent-Monegat, Agnès Vallier, Aurélien Vigneron, Anna Zaidman-Rémy, Waël Zamoum, Cristina Vieira, Rita Rebollo, Amparo Latorre, and Abdelaziz Heddi

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Discovery of Small Molecule Bak Activator for Lung Cancer Therapy., Dongkyoo Park, Abu Syed Md Anisuzzaman, Andrew T Magis, Guo Chen, Maohua Xie, Guojing Zhang, Madhusmita Behera, Gabriel L Sica, Suresh S Ramalingam, Taofeek K Owonikoko, and Xingming Deng

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A Systems Approach to Brain Tumor Treatment., James H Park, Adrian Lopez Garcia de Lomana, Diego M Marzese, Tiffany Juarez, Abdullah Feroze, Parvinder Hothi, Charles Cobbs, Anoop P Patel, Santosh Kesari, Sui Huang, and Nitin S Baliga

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A wide-ranging Pseudomonas aeruginosa PeptideAtlas build: A useful proteomic resource for a versatile pathogen., J A Reales-Calderón, Z Sun, V Mascaraque, E Pérez-Navarro, V Vialás, E W Deutsch, R L Moritz, C Gil, J L Martínez, and G Molero

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Integrative modeling identifies genetic ancestry-associated molecular correlates in human cancer., A Gordon Robertson, Christina Yau, Jian Carrot-Zhang, Jeffrey S Damrauer, Theo A Knijnenburg, Nyasha Chambwe, Katherine A Hoadley, Anab Kemal, Jean C Zenklusen, Andrew D Cherniack, Rameen Beroukhim, and Wanding Zhou

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Lentivirus-mediated Conditional Gene Expression., Leah Rommereim, Ajay Suresh Akhade, Ronald N Germain, Iain D C Fraser, and Naeha Subramanian

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Germline genetic contribution to the immune landscape of cancer., Rosalyn W Sayaman, Mohamad Saad, Vésteinn Thorsson, Donglei Hu, Wouter Hendrickx, Jessica Roelands, Eduard Porta-Pardo, Younes Mokrab, Farshad Farshidfar, Tomas Kirchhoff, Randy F Sweis, Oliver F Bathe, Carolina Heimann, Michael J Campbell, Cynthia Stretch, Scott Huntsman, Rebecca E Graff, Najeeb Syed, Laszlo Radvanyi, Simon Shelley, Denise Wolf, Francesco M Marincola, Michele Ceccarelli, Jérôme Galon, Elad Ziv, and Davide Bedognetti

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TAF8 regions important for TFIID lobe B assembly or for TAF2 interactions are required for embryonic stem cell survival., Elisabeth Scheer, Jie Luo, Andrea Bernardini, Frank Ruffenach, Jean-Marie Garnier, Isabelle Kolb-Cheynel, Kapil Gupta, Imre Berger, Jeff Ranish, and László Tora

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Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison., Tobias Schmidt, Patroklos Samaras, Viktoria Dorfer, Christian Panse, Tobias Kockmann, Leon Bichmann, Bart van Puyvelde, Yasset Perez-Riverol, Eric W Deutsch, Bernhard Kuster, and Mathias Wilhelm

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Utilization of machine learning for identifying symptom severity military-related PTSD subtypes and their biological correlates., Carole E Siegel, Eugene M Laska, Ziqiang Lin, Mu Xu, Duna Abu-Amara, Michelle K Jeffers, Meng Qian, Nicholas Milton, Janine D Flory, Rasha Hammamieh, Bernie J Daigle, Aarti Gautam, Kelsey R Dean, Victor I Reus, Owen M Wolkowitz, Synthia H Mellon, Kerry J Ressler, Rachel Yehuda, Kai Wang, Leroy Hood, Francis J Doyle, Marti Jett, and Charles R Marmar

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Transcriptome signature of cell viability predicts drug response and drug interaction in, Vivek Srinivas, Rene A Ruiz, Min Pan, Selva Rupa Christinal Immanuel, Eliza Jr Peterson, and Nitin S Baliga

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Platelet derived growth factor receptor β (PDGFRβ) is a host receptor for the human malaria parasite adhesin TRAP., Ryan W J Steel, Vladimir Vigdorovich, Nicholas Dambrauskas, Brandon K Wilder, Silvia A Arredondo, Debashree Goswami, Sudhir Kumar, Sara Carbonetti, Kristian E Swearingen, Thao Nguyen, Will Betz, Nelly Camargo, Bridget S Fisher, Jo Soden, Helen Thomas, Jim Freeth, Robert L Moritz, D Noah Sather, and Stefan H I Kappe

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Partial inhibition of mitochondrial complex I ameliorates Alzheimer's disease pathology and cognition in APP/PS1 female mice., Andrea Stojakovic, Sergey Trushin, Anthony Sheu, Layla Khalili, Su-Youne Chang, Xing Li, Trace Christensen, Jeffrey L Salisbury, Rachel E Geroux, Benjamin Gateno, Padraig J Flannery, Mrunal Dehankar, Cory C Funk, Jordan Wilkins, Anna Stepanova, Tara O'Hagan, Alexander Galkin, Jarred Nesbitt, Xiujuan Zhu, Utkarsh Tripathi, Slobodan Macura, Tamar Tchkonia, Tamar Pirtskhalava, James L Kirkland, Rachel A Kudgus, Renee A Schoon, Joel M Reid, Yu Yamazaki, Takahisa Kanekiyo, Song Zhang, Emirhan Nemutlu, Petras Dzeja, Adam Jaspersen, Ye In Christopher Kwon, Michael K Lee, and Eugenia Trushina

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Curation Guidelines for de novo Generated Transposable Element Families., Jessica Storer, Robert Hubley, Jeb Rosen, and Arian F A Smit

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The Dfam community resource of transposable element families, sequence models, and genome annotations., Jessica Storer, Robert Hubley, Jeb Rosen, Travis J Wheeler, and Arian F Smit

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Mouse Organ-Specific Proteins and Functions., Bingyun Sun, Cynthia Lorang, Shizhen Qin, Yijuan Zhang, Ken Liu, Gray Li, Zhi Sun, Ashley Francke, Angelita G Utleg, Zhiyuan Hu, Kai Wang, Robert L Moritz, and Leroy Hood

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Race differences in predictors of weight gain among a community sample of smokers enrolled in a randomized controlled trial of a multiple behavior change intervention., Marcia M Tan, Terry Bush, Jennifer C Lovejoy, Harold Javitz, Alula Jimenez Torres, Ken Wassum, and Bonnie Spring

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Functional characterization of HIC, a P2Y1 agonist, as a p53 stabilizer for prostate cancer cell death induction., Hien Thi Thu Le, Akshaya Murugesan, Nuno R Candeias, Olli Yli-Harja, and Meenakshisundaram Kandhavelu

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Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions., Serdar Turkarslan, Nejc Stopnisek, Anne W Thompson, Christina E Arens, Jacob J Valenzuela, James Wilson, Kristopher A Hunt, Jessica Hardwicke, Adrián López García de Lomana, Sujung Lim, Yee Mey Seah, Ying Fu, Liyou Wu, Jizhong Zhou, Kristina L Hillesland, David A Stahl, and Nitin Baliga

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Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities"., Pajau Vangay, Josephine Burgin, Anjanette Johnston, Kristen L Beck, Daniel C Berrios, Kai Blumberg, Shane Canon, Patrick Chain, John-Marc Chandonia, Danielle Christianson, Sylvain V Costes, Joan Damerow, William D Duncan, Jose Pablo Dundore-Arias, Kjiersten Fagnan, Jonathan M Galazka, Sean M Gibbons, David Hays, Judson Hervey, Bin Hu, Bonnie L Hurwitz, Pankaj Jaiswal, Marcin P Joachimiak, Linda Kinkel, Joshua Ladau, Stanton L Martin, Lee Ann McCue, Kayd Miller, Nigel Mouncey, Chris Mungall, Evangelos Pafilis, T B K Reddy, Lorna Richardson, Simon Roux, Lynn M Schriml, Justin P Shaffer, Jagadish Chandrabose Sundaramurthi, Luke R Thompson, Ruth E Timme, Jie Zheng, Elisha M Wood-Charlson, and Emiley A Eloe-Fadrosh

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Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities., Pajau Vangay, Josephine Burgin, Anjanette Johnston, Kristen L Beck, Daniel C Berrios, Kai Blumberg, Shane Canon, Patrick Chain, John-Marc Chandonia, Danielle Christianson, Sylvain V Costes, Joan Damerow, William D Duncan, Jose Pablo Dundore-Arias, Kjiersten Fagnan, Jonathan M Galazka, Sean M Gibbons, David Hays, Judson Hervey, Bin Hu, Bonnie L Hurwitz, Pankaj Jaiswal, Marcin P Joachimiak, Linda Kinkel, Joshua Ladau, Stanton L Martin, Lee Ann McCue, Kayd Miller, Nigel Mouncey, Chris Mungall, Evangelos Pafilis, T B K Reddy, Lorna Richardson, Simon Roux, Justin P Shaffer, Jagadish Chandrabose Sundaramurthi, Luke R Thompson, Ruth E Timme, Jie Zheng, Elisha M Wood-Charlson, and Emiley A Eloe-Fadrosh

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Bile acid synthesis, modulation, and dementia: A metabolomic, transcriptomic, and pharmacoepidemiologic study., Vijay R Varma, Youjin Wang, Yang An, Sudhir Varma, Murat Bilgel, Jimit Doshi, Cristina Legido-Quigley, João C Delgado, Anup M Oommen, Jackson A Roberts, Dean F Wong, Christos Davatzikos, Susan M Resnick, Juan C Troncoso, Olga Pletnikova, Richard O'Brien, Eelko Hak, Brenda N Baak, Ruth Pfeiffer, Priyanka Baloni, Siamak Mohmoudiandehkordi, Kwangsik Nho, Rima Kaddurah-Daouk, David A Bennett, Shahinaz M Gadalla, and Madhav Thambisetty

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Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance., Christian R Voolstra, Jacob J Valenzuela, Serdar Turkarslan, Anny Cárdenas, Benjamin C C Hume, Gabriela Perna, Carol Buitrago-López, Katherine Rowe, Monica V Orellana, Nitin S Baliga, Suman Paranjape, Guilhem Banc-Prandi, Jessica Bellworthy, Maoz Fine, Sarah Frias-Torres, and Daniel J Barshis

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The viral hypothesis: how herpesviruses may contribute to Alzheimer's disease., Michael Wainberg, Tain Luquez, David M Koelle, Ben Readhead, Christine Johnston, Martin Darvas, and Cory C Funk

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Genetic program activity delineates risk, relapse, and therapy responsiveness in multiple myeloma., Matthew A Wall, Serdar Turkarslan, Wei-Ju Wu, Samuel A Danziger, David J Reiss, Mike J Mason, Andrew P Dervan, Matthew W B Trotter, Douglas Bassett, Robert M Hershberg, Adrián López García de Lomana, Alexander V Ratushny, and Nitin S Baliga

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Alzheimer's disease and progressive supranuclear palsy share similar transcriptomic changes in distinct brain regions., Xue Wang, Mariet Allen, Özkan İş, Joseph S Reddy, Frederick Q Tutor-New, Monica Castanedes Casey, Minerva M Carrasquillo, Stephanie R Oatman, Yuhao Min, Yan W Asmann, Cory C Funk, Thuy Nguyen, Charlotte Cg Ho, Kimberly G Malphrus, Nicholas T Seyfried, Allan I Levey, Steven G Younkin, Melissa E Murray, Dennis W Dickson, Nathan D Price, Todd E Golde, and Nilufer Ertekin-Taner

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Circulating activated immune cells as a potential blood biomarkers of non-small cell lung cancer occurrence and progression., Yingyi Wang, Na Zhou, Rui Zhu, Xiaoyuan Li, Zhao Sun, Yang Gao, Wei Liu, Changting Meng, Yuping Ge, Chunmei Bai, Taisheng Li, and Hongsheng Liu

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2021 Special Issue on Software Tools and Resources: Finding the Right Tools for the Job., Susan T Weintraub, Michael R Hoopmann, and Magnus Palmblad

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CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation., Damien B Wilburn, Alicia L Richards, Danielle L Swaney, and Brian C Searle

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Author Correction: Gut microbiome pattern reflects healthy ageing and predicts survival in humans., Tomasz Wilmanski, Christian Diener, Noa Rappaport, Sushmita Patwardhan, Jack Wiedrick, Jodi Lapidus, John C Earls, Anat Zimmer, Gustavo Glusman, Max Robinson, James T Yurkovich, Deborah M Kado, Jane A Cauley, Joseph Zmuda, Nancy E Lane, Andrew T Magis, Jennifer C Lovejoy, Leroy Hood, Sean M Gibbons, Eric S Orwoll, and Nathan D Price

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Gut microbiome pattern reflects healthy ageing and predicts survival in humans., Tomasz Wilmanski, Christian Diener, Noa Rappaport, Sushmita Patwardhan, Jack Wiedrick, Jodi Lapidus, John C Earls, Anat Zimmer, Gustavo Glusman, Max Robinson, James T Yurkovich, Deborah M Kado, Jane A Cauley, Joseph Zmuda, Nancy E Lane, Andrew T Magis, Jennifer C Lovejoy, Leroy Hood, Sean M Gibbons, Eric S Orwoll, and Nathan D Price

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From taxonomy to metabolic output: what factors define gut microbiome health?, Tomasz Wilmanski, Noa Rappaport, Christian Diener, Sean M Gibbons, and Nathan D Price

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Serum brain-derived neurotrophic factor remains elevated after long term follow-up of combat veterans with chronic post-traumatic stress disorder., Gwyneth W Y Wu, Owen M Wolkowitz, Victor I Reus, Jee In Kang, Mathea Elnar, Reuben Sarwal, Janine D Flory, Duna Abu-Amara, Rasha Hammamieh, Aarti Gautam, Francis J Doyle, Rachel Yehuda, Charles R Marmar, Marti Jett, Synthia H Mellon, SBPBC Collaborators, Leroy Hood, Kai Wang, and Inyoul Lee

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Hexokinase 2 discerns a novel circulating tumor cell population associated with poor prognosis in lung cancer patients., Liu Yang, Xiaowei Yan, Jie Chen, Qiong Zhan, Yingqi Hua, Shili Xu, Ziming Li, Zhuo Wang, Yu Dong, Dongqing Zuo, Min Xue, Yin Tang, Harvey R Herschman, Shun Lu, Qihui Shi, and Wei Wei

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A DNA methylation clock associated with age-related illnesses and mortality is accelerated in men with combat PTSD., Ruoting Yang, Gwyneth W Y Wu, Josine E Verhoeven, Aarti Gautam, Victor I Reus, Jee In Kang, Janine D Flory, Duna Abu-Amara, PTSD Systems Biology Consortium, Leroy Hood, Francis J Doyle, Rachel Yehuda, Charles R Marmar, Marti Jett, Rasha Hammamieh, Synthia H Mellon, and Owen M Wolkowitz

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Lung proteomic biomarkers associated with chronic obstructive pulmonary disease., Yu-Hang Zhang, Michael R Hoopmann, Peter J Castaldi, Kirsten Simonsen, Mukul K Midha, Michael H Cho, Gerard J Criner, Raphael Bueno, Jiangyuan Liu, Robert L Moritz, and Edwin K Silverman

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Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity across viruses., Hong Zheng, Aditya M Rao, Denis Dermadi, Jiaying Toh, Lara Murphy Jones, Michele Donato, Yiran Liu, Yapeng Su, Cheng L Dai, Sergey A Kornilov, Minas Karagiannis, Theodoros Marantos, Yehudit Hasin-Brumshtein, Yudong D He, Evangelos J Giamarellos-Bourboulis, James R Heath, and Purvesh Khatri

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The geometry of clinical labs and wellness states from deeply phenotyped humans., Anat Zimmer, Yael Korem, Noa Rappaport, Tomasz Wilmanski, Priyanka Baloni, Kathleen Jade, Max Robinson, Andrew T Magis, Jennifer Lovejoy, Sean M Gibbons, Leroy Hood, and Nathan D Price

Submissions from 2020

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A high-stringency blueprint of the human proteome., Subash Adhikari, Edouard C Nice, Eric W Deutsch, Lydie Lane, Gilbert S Omenn, Stephen R Pennington, Young-Ki Paik, Christopher M Overall, Fernando J Corrales, Ileana M Cristea, Jennifer E Van Eyk, Mathias Uhlén, Cecilia Lindskog, Daniel W Chan, Amos Bairoch, James C Waddington, Joshua L Justice, Joshua LaBaer, Henry Rodriguez, Fuchu He, Markus Kostrzewa, Peipei Ping, Rebekah L Gundry, Peter Stewart, Sanjeeva Srivastava, Sudhir Srivastava, Fabio C S Nogueira, Gilberto B Domont, Yves Vandenbrouck, Maggie P Y Lam, Sara Wennersten, Juan Antonio Vizcaino, Marc Wilkins, Jochen M Schwenk, Emma Lundberg, Nuno Bandeira, Gyorgy Marko-Varga, Susan T Weintraub, Charles Pineau, Ulrike Kusebauch, Robert L Moritz, Seong Beom Ahn, Magnus Palmblad, Michael P Snyder, Ruedi Aebersold, and Mark S Baker

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A Near-Optimal Control Method for Stochastic Boolean Networks., Boris Aguilar, Pan Fang, Reinhard Laubenbacher, and David Murrugarra

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A generalizable data-driven multicellular model of pancreatic ductal adenocarcinoma., Boris Aguilar, David L Gibbs, David J Reiss, Mark McConnell, Samuel A Danziger, Andrew Dervan, Matthew Trotter, Douglas Bassett, Robert Hershberg, Alexander V Ratushny, and Ilya Shmulevich

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Type 1 interferon-dependent repression of NLRC4 and iPLA2 licenses down-regulation of, Ajay Suresh Akhade, Shaikh M Atif, Bhavana S Lakshmi, Neha Dikshit, Kelly T Hughes, Ayub Qadri, and Naeha Subramanian

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The Proteasome Activators Blm10/PA200 Enhance the Proteasomal Degradation of N-Terminal Huntingtin., Azzam Aladdin, Yanhua Yao, Ciyu Yang, Günther Kahlert, Marvi Ghani, Nikolett Király, Anita Boratkó, Karen Uray, Gunnar Dittmar, and Krisztina Tar

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Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks., Mario L Arrieta-Ortiz, Christoph Hafemeister, Bentley Shuster, Nitin Baliga, Richard Bonneau, and Patrick Eichenberger

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Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer's Disease., Priyanka Baloni, Cory C Funk, Jingwen Yan, James T Yurkovich, Alexandra Kueider-Paisley, Kwangsik Nho, Almut Heinken, Wei Jia, Siamak Mahmoudiandehkordi, Gregory Louie, Andrew J Saykin, Matthias Arnold, Gabi Kastenmüller, William J Griffiths, Ines Thiele, Alzheimer’s Disease Metabolomics Consortium, Rima Kaddurah-Daouk, and Nathan D Price

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Integrative network modeling reveals mechanisms underlying T cell exhaustion., Hamid Bolouri, Mary Young, Joshua Beilke, Rebecca Johnson, Brian Fox, Lu Huang, Cristina Costa Santini, Christopher Mark Hill, Anne-Renee van der Vuurst de Vries, Paul Shannon, Andrew Dervan, Pallavur Sivakumar, Matthew Trotter, Douglas Bassett, and Alexander Ratushny

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Visualizing metabolic network dynamics through time-series metabolomic data., Lea F Buchweitz, James T Yurkovich, Christoph Blessing, Veronika Kohler, Fabian Schwarzkopf, Zachary A King, Laurence Yang, Freyr Jóhannsson, Ólafur E Sigurjónsson, Óttar Rolfsson, Julian Heinrich, and Andreas Dräger

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Discovery of driver non-coding splice-site-creating mutations in cancer., Song Cao, Daniel Cui Zhou, Clara Oh, Reyka G Jayasinghe, Yanyan Zhao, Christopher J Yoon, Matthew A Wyczalkowski, Matthew H Bailey, Terrence Tsou, Qingsong Gao, Andrew Malone, Sheila Reynolds, Ilya Shmulevich, Michael C Wendl, Feng Chen, and Li Ding

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Community standards to facilitate development and address challenges in metabolic modeling., Maureen A Carey, Andreas Dräger, Moritz E Beber, Jason A Papin, and James T Yurkovich