The Institute for Systems Biology is a not-for-profit biomedical research organization that is part of the Providence St. Joseph Health family. The scientists and engineers at ISB are working to unlock the mystery of the genome to learn how we can keep people healthy well into their 90s.

This is a proactive approach to medicine that will help us shift from a disease focus to a wellness focus. With ISB, we are pursuing research in the areas of breast cancer survivorship, Alzheimer’s, glioblastoma and markers to help us identify and reverse disease at the earliest possible stages. Our partnership gives us the opportunity to bring these advances to people in the communities we serve.

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Submissions from 2020

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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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MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota., Christian Diener, Sean M Gibbons, and Osbaldo Resendis-Antonio

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Glioblastoma Multiforme Stem Cell Cycle Arrest by Alkylaminophenol Through the Modulation of EGFR and CSC Signaling Pathways., Phuong Doan, Aliyu Musa, Akshaya Murugesan, Vili Sipilä, Nuno R Candeias, Frank Emmert-Streib, Pekka Ruusuvuori, Kirsi Granberg, Olli Yli-Harja, and Meenakshisundaram Kandhavelu

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Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis using the PSI Extended FASTA Format (PEFF)., Jimmy K Eng and Eric W Deutsch

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RepeatModeler2 for automated genomic discovery of transposable element families., Jullien M Flynn, Robert Hubley, Clément Goubert, Jeb Rosen, Andrew G Clark, Cédric Feschotte, and Arian F Smit

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Alterations in plasma microRNA and protein levels in war veterans with chronic mild traumatic brain injury., Vikas Ghai, Shannon Fallen, David Baxter, Kelsey Scherler, Taek-Kyun Kim, Yong Zhou, James Meabon, Aric Logsdon, William Allen Banks, Abigail Schindler, David Cook, Elaine Peskind, Inyoul Lee, and Kai Wang

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Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis., Mark A Gillespie, Carmen G Palii, Daniel Sanchez-Taltavull, Paul Shannon, William J R Longabaugh, Damien J Downes, Karthi Sivaraman, Herbert M Espinoza, Jim R Hughes, Nathan D Price, Theodore J Perkins, Jeffrey A Ranish, and Marjorie Brand

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Lumenal calcification and microvasculopathy in fetuin-A-deficient mice lead to multiple organ morbidity., Marietta Herrmann, Anne Babler, Irina Moshkova, Felix Gremse, Fabian Kiessling, Ulrike Kusebauch, Valentin Nelea, Rafael Kramann, Robert L Moritz, Marc D McKee, and Willi Jahnen-Dechent

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Facebook Live: Dr. Rod Hochman, Providence CEO and Prof. Jim Health Ph.D. discuss the science around Coronavirus., Rod Hochman and Jim Heath

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Comparative lipidomics of 5-Fluorouracil-sensitive and -resistant colorectal cancer cells reveals altered sphingomyelin and ceramide controlled by acid sphingomyelinase (SMPD1)., Jae Hun Jung, Kohei Taniguchi, Hyeong Min Lee, Min Young Lee, Raju Bandu, Kazumasa Komura, Kil Yeon Lee, Yukihiro Akao, and Kwang Pyo Kim

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Theory of chemical evolution of molecule compositions in the universe, in the Miller-Urey experiment and the mass distribution of interstellar and intergalactic molecules., Stuart A Kauffman, Dávid Péter Jelenfi, and Gábor Vattay

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Assembly of SNAPc, Bdp1, and TBP on the U6 snRNA gene promoter in Drosophila melanogaster., Mun Kyoung Kim, An Tranvo, Ann Marie Hurlburt, Neha Verma, Phuc Phan, Jie Luo, Jeff Ranish, and William E Stumph

Core transcriptional regulatory circuits in prion diseases., Taek-Kyun Kim, Inyoul Lee, Ji-Hoon Cho, Brenda Canine, Andrew Keller, Nathan D Price, Daehee Hwang, George Carlson, and Leroy Hood

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MEMOTE for standardized genome-scale metabolic model testing., Christian Lieven, Moritz E Beber, Brett G Olivier, Frank T Bergmann, Meric Ataman, Parizad Babaei, Jennifer A Bartell, Lars M Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E Ebert, Janaka N Edirisinghe, José P Faria, Adam M Feist, Georgios Fengos, Ronan M T Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout van Helvoirt, Christopher S Henry, Henning Hermjakob, Markus J Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary King, Steffen Klamt, Edda Klipp, Jasper J Koehorst, Matthias König, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L Medlock, Jonathan M Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Mark Poolman, Nathan D Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J Sánchez, Peter J Schaap, Rahuman S Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A H Wodke, Joana C Xavier, Qianqian Yuan, Maksim Zakhartsev, and Cheng Zhang

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Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing., Christian Lieven, Moritz E Beber, Brett G Olivier, Frank T Bergmann, Meric Ataman, Parizad Babaei, Jennifer A Bartell, Lars M Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E Ebert, Janaka N Edirisinghe, José P Faria, Adam M Feist, Georgios Fengos, Ronan M T Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout van Helvoirt, Christopher S Henry, Henning Hermjakob, Markus J Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary King, Steffen Klamt, Edda Klipp, Jasper J Koehorst, Matthias König, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L Medlock, Jonathan M Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Mark Poolman, Nathan D Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J Sánchez, Peter J Schaap, Rahuman S Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A H Wodke, Joana C Xavier, Qianqian Yuan, Maksim Zakhartsev, and Cheng Zhang

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iREAD: a tool for intron retention detection from RNA-seq data., Hong-Dong Li, Cory C Funk, and Nathan D Price

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Author Correction: New paradigms for understanding and step changes in treating active and chronic, persistent apicomplexan infections., Martin McPhillie, Ying Zhou, Kamal El Bissati, Jitender Dubey, Hernan Lorenzi, Michael Capper, Amanda K Lukens, Mark Hickman, Stephen Muench, Shiv Kumar Verma, Christopher R Weber, Kelsey Wheeler, James Gordon, Justin Sanders, Hong Moulton, Kai Wang, Taek-Kyun Kim, Yuqing He, Tatiana Santos, Stuart Woods, Patty Lee, David Donkin, Eric Kim, Laura Fraczek, Joseph Lykins, Farida Esaa, Fatima Alibana-Clouser, Sarah Dovgin, Louis Weiss, Gael Brasseur, Dyann Wirth, Michael Kent, Leroy Hood, Brigitte Meunieur, Craig W Roberts, S Samar Hasnain, Svetlana V Antonyuk, Colin Fishwick, and Rima McLeod

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A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups., Sheenah M Mische, Nancy C Fisher, Susan M Meyn, Katia Sol Church, Rebecca L Hegstad-Davies, Frances Weis-Garcia, Marie Adams, John M Ashton, Kym M Delventhal, Julie A Dragon, Laura Holmes, Pratik Jagtap, Christopher E Mason, Magnus Palmblad, Brian C Searle, Christoph W Turck, and Kevin L Knudtson

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Deep phenotyping during pregnancy for predictive and preventive medicine., Alison G Paquette, Leroy Hood, Nathan D Price, and Yoel Sadovsky

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Ageotypes: Distinct Biomolecular Trajectories in Human Aging., Brian D. Piening, Jennifer Lovejoy, and John C Earls

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Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries., Lindsay K Pino, Seth C Just, Michael J MacCoss, and Brian C Searle

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Generating high quality libraries for DIA MS with empirically corrected peptide predictions., Brian C Searle, Kristian E Swearingen, Christopher A Barnes, Tobias Schmidt, Siegfried Gessulat, Bernhard Küster, and Mathias Wilhelm

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Current Status and Future Prospects of Genome-Scale Metabolic Modeling to Optimize the Use of Mesenchymal Stem Cells in Regenerative Medicine., Þóra Sigmarsdóttir, Sarah McGarrity, Óttar Rolfsson, James T Yurkovich, and Ólafur E Sigurjónsson

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Dynamics of a birth-death process based on combinatorial innovation., Mike Steel, Wim Hordijk, and Stuart A Kauffman

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Active learning narrows achievement gaps for underrepresented students in undergraduate science, technology, engineering, and math., Elli J Theobald, Mariah J Hill, Elisa Tran, Sweta Agrawal, E Nicole Arroyo, Shawn Behling, Nyasha Chambwe, Dianne Laboy Cintrón, Jacob D Cooper, Gideon Dunster, Jared A Grummer, Kelly Hennessey, Jennifer Hsiao, Nicole Iranon, Leonard Jones, Hannah Jordt, Marlowe Keller, Melissa E Lacey, Caitlin E Littlefield, Alexander Lowe, Shannon Newman, Vera Okolo, Savannah Olroyd, Brandon R Peecook, Sarah B Pickett, David L Slager, Itzue W Caviedes-Solis, Kathryn E Stanchak, Vasudha Sundaravardan, Camila Valdebenito, Claire R Williams, Kaitlin Zinsli, and Scott Freeman

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Multiplatform Integrative Analysis of Immunogenomic Data for Biomarker Discovery., Vésteinn Thorsson

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BioHackathon 2015: Semantics of data for life sciences and reproducible research., Rutger A Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P Aoki, Kazuharu Arakawa, Jerven T Bolleman, Evan Bolton, Raoul J P Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin B Cohen, Eric W Deutsch, Jesualdo T Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy Nguyen-Xuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C Yoshizawa, Michel Dumontier, Kenjiro Kosaki, and Toshihisa Takagi

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Loss of the neural-specific BAF subunit ACTL6B relieves repression of early response genes and causes recessive autism., Wendy Wenderski, Lu Wang, Andrey Krokhotin, Jessica J Walsh, Hongjie Li, Hirotaka Shoji, Shereen Ghosh, Renee D George, Erik L Miller, Laura Elias, Mark A Gillespie, Esther Y Son, Brett T Staahl, Seung Tae Baek, Valentina Stanley, Cynthia Moncada, Zohar Shipony, Sara B Linker, Maria C N Marchetto, Fred H Gage, Dillon Chen, Tipu Sultan, Maha S Zaki, Jeffrey A Ranish, Tsuyoshi Miyakawa, Liqun Luo, Robert C Malenka, Gerald R Crabtree, and Joseph G Gleeson

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Autocatalytic chemical networks at the origin of metabolism., Joana C Xavier, Wim Hordijk, Stuart Kauffman, Mike Steel, and William F Martin

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The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View., Joao B Xavier, Vincent B Young, Joseph Skufca, Fiona Ginty, Traci Testerman, Alexander T Pearson, Paul Macklin, Amir Mitchell, Ilya Shmulevich, Lei Xie, J Gregory Caporaso, Keith A Crandall, Nicole L Simone, Filipa Godoy-Vitorino, Timothy J Griffin, Katrine L Whiteson, Heather H Gustafson, Daniel J Slade, Thomas M Schmidt, Marina R S Walther-Antonio, Tal Korem, Bobbie-Jo M Webb-Robertson, Mark P Styczynski, W Evan Johnson, Christian Jobin, Jason M Ridlon, Andrew Y Koh, Michael Yu, Libusha Kelly, and Jennifer A Wargo

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Combining deep learning with token selection for patient phenotyping from electronic health records., Zhen Yang, Matthias Dehmer, Olli Yli-Harja, and Frank Emmert-Streib

Submissions from 2019

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Protein-Catalyzed Capture Agents., Heather D Agnew, Matthew B Coppock, Matthew N Idso, Bert T Lai, JingXin Liang, Amy M McCarthy-Torrens, Carmen M Warren, and James R Heath

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Clinical Data: Sources and Types, Regulatory Constraints, Applications., Stanley C Ahalt, Christopher G Chute, Karamarie Fecho, Gustavo Glusman, Jennifer Hadlock, Casey Overby Taylor, Emily R Pfaff, Peter N Robinson, Harold Solbrig, Casey Ta, Nicholas Tatonetti, and Chunhua Weng

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Personalized Nutrition: Translating the Science of NutriGenomics Into Practice: Proceedings From the 2018 American College of Nutrition Meeting., Okezie I Aruoma, Sharon Hausman-Cohen, Jessica Pizano, Michael A Schmidt, Deanna M Minich, Yael Joffe, Sebastian Brandhorst, Simon J Evans, and David M Brady

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Genome-scale metabolic model of the rat liver predicts effects of diet restriction., Priyanka Baloni, Vineet Sangar, James T Yurkovich, Max Robinson, Scott Taylor, Christine M Karbowski, Hisham K Hamadeh, Yudong D He, and Nathan D Price

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Toward a comprehensive view of cancer immune responsiveness: a synopsis from the SITC workshop., Davide Bedognetti, Michele Ceccarelli, Lorenzo Galluzzi, Rongze Lu, Karolina Palucka, Josue Samayoa, Stefani Spranger, Sarah Warren, Kwok-Kin Wong, Elad Ziv, Diego Chowell, Lisa M Coussens, Daniel D De Carvalho, David G DeNardo, Jérôme Galon, Howard L Kaufman, Tomas Kirchhoff, Michael T Lotze, Jason J Luke, Andy J Minn, Katerina Politi, Leonard D Shultz, Richard Simon, Vésteinn Thórsson, Joanne B Weidhaas, Maria Libera Ascierto, Paolo Antonio Ascierto, James M Barnes, Valentin Barsan, Praveen K Bommareddy, Adrian Bot, Sarah E Church, Gennaro Ciliberto, Andrea De Maria, Dobrin Draganov, Winson S Ho, Heather M McGee, Anne Monette, Joseph F Murphy, Paola Nisticò, Wungki Park, Maulik Patel, Michael Quigley, Laszlo Radvanyi, Harry Raftopoulos, Nils-Petter Rudqvist, Alexandra Snyder, Randy F Sweis, Sara Valpione, Lisa H Butterfield, Mary L Disis, Bernard A Fox, Alessandra Cesano, and Francesco M Marincola

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Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2., Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian C Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily K Cope, Ricardo Da Silva, Christian Diener, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Sean M Gibbons, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin A Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin D Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan G I Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie T Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin J J van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Charles H D Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight, and J Gregory Caporaso

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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2., Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian C Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily K Cope, Ricardo Da Silva, Christian Diener, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Sean M Gibbons, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin A Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin D Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan G I Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie T Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin J J van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Charles H D Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight, and J Gregory Caporaso

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Ensembles, dynamics, and cell types: Revisiting the statistical mechanics perspective on cellular regulation., Stefan Bornholdt and Stuart Kauffman

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Use and abuse of correlation analyses in microbial ecology., Alex Carr, Christian Diener, Nitin Baliga, and Sean M Gibbons

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Mcl-1 Interacts with Akt to Promote Lung Cancer Progression., Guo Chen, Dongkyoo Park, Andrew T Magis, Madhusmita Behera, Suresh S Ramalingam, Taofeek K Owonikoko, Gabriel L Sica, Keqiang Ye, Chao Zhang, Zhengjia Chen, Walter J Curran, and Xingming Deng

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Predicting drug synergy for precision medicine using network biology and machine learning., Ali Cuvitoglu, Joseph X Zhou, Sui Huang, and Zerrin Isik

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ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells., Samuel A Danziger, David L Gibbs, Ilya Shmulevich, Mark McConnell, Matthew W B Trotter, Frank Schmitz, David J Reiss, and Alexander V Ratushny

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Multi-omic biomarker identification and validation for diagnosing warzone-related post-traumatic stress disorder., Kelsey R Dean, Rasha Hammamieh, Synthia H Mellon, Duna Abu-Amara, Janine D Flory, Guia Guffanti, Kai Wang, Bernie J Daigle, Aarti Gautam, Inyoul Lee, Ruoting Yang, Lynn M Almli, F Saverio Bersani, Nabarun Chakraborty, Duncan Donohue, Kimberly Kerley, Taek-Kyun Kim, Eugene Laska, Min Young Lee, Daniel Lindqvist, Adriana Lori, Liangqun Lu, Burook Misganaw, Seid Muhie, Jennifer Newman, Nathan D Price, Shizhen Qin, Victor I Reus, Carole Siegel, Pramod R Somvanshi, Gunjan S Thakur, Yong Zhou, Leroy Hood, Kerry J Ressler, Owen M Wolkowitz, Rachel Yehuda, Marti Jett, Francis J Doyle, and Charles Marmar

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The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics., Eric W Deutsch, Nuno Bandeira, Vagisha Sharma, Yasset Perez-Riverol, Jeremy J Carver, Deepti J Kundu, David García-Seisdedos, Andrew F Jarnuczak, Suresh Hewapathirana, Benjamin S Pullman, Julie Wertz, Zhi Sun, Shin Kawano, Shujiro Okuda, Yu Watanabe, Henning Hermjakob, Brendan MacLean, Michael J MacCoss, Yunping Zhu, Yasushi Ishihama, and Juan A Vizcaíno

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Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0., Eric W Deutsch, Lydie Lane, Christopher M Overall, Nuno Bandeira, Mark S Baker, Charles Pineau, Robert L Moritz, Fernando Corrales, Sandra Orchard, Jennifer E Van Eyk, Young-Ki Paik, Susan T Weintraub, Yves Vandenbrouck, and Gilbert S Omenn

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Alkylaminophenol Induces G1/S Phase Cell Cycle Arrest in Glioblastoma Cells Through p53 and Cyclin-Dependent Kinase Signaling Pathway., Phuong Doan, Aliyu Musa, Nuno R Candeias, Frank Emmert-Streib, Olli Yli-Harja, and Meenakshisundaram Kandhavelu

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Multi-Omic Biological Age Estimation and Its Correlation With Wellness and Disease Phenotypes: A Longitudinal Study of 3,558 Individuals., John C Earls, Noa Rappaport, Laura M Heath, Tomasz Wilmanski, Andrew T Magis, Nicholas J Schork, Gilbert S Omenn, Jennifer Lovejoy, Leroy Hood, and Nathan D Price

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Ensuring Quality Standards and Reproducible Research for Data Analysis Services in Oncology: A Cooperative Service Model., Frank Emmert-Streib, Matthias Dehmer, and Olli Yli-Harja

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Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data., Galen F Gao, Joel S Parker, Sheila M Reynolds, Tiago C Silva, Liang-Bo Wang, Wanding Zhou, Rehan Akbani, Matthew Bailey, Saianand Balu, Benjamin P Berman, Denise Brooks, Hu Chen, Andrew D Cherniack, John A Demchok, Li Ding, Ina Felau, Sharon Gaheen, Daniela S Gerhard, David I Heiman, Kyle M Hernandez, Katherine A Hoadley, Reyka Jayasinghe, Anab Kemal, Theo A Knijnenburg, Peter W Laird, Michael K A Mensah, Andrew J Mungall, A Gordon Robertson, Hui Shen, Roy Tarnuzzer, Zhining Wang, Matthew Wyczalkowski, Liming Yang, Jean C Zenklusen, Zhenyu Zhang, Han Liang, and Michael S Noble

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Suppression of chemotherapy-induced cytokine/lipid mediator surge and ovarian cancer by a dual COX-2/sEH inhibitor., Allison Gartung, Jun Yang, Vikas P Sukhatme, Diane R Bielenberg, Djanira Fernandes, Jaimie Chang, Birgitta A Schmidt, Sung Hee Hwang, David Zurakowski, Sui Huang, Mark W Kieran, Bruce D Hammock, and Dipak Panigrahy

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Extracellular Vesicle Encapsulated MicroRNAs in Patients with Type 2 Diabetes Are Affected by Metformin Treatment., Vikas Ghai, Taek-Kyun Kim, Alton Etheridge, Trine Nielsen, Torben Hansen, Oluf Pedersen, David Galas, and Kai Wang

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Defining Microbiome Health through a Host Lens., Sean M Gibbons

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Aspirin-triggered proresolving mediators stimulate resolution in cancer., Molly M Gilligan, Allison Gartung, Megan L Sulciner, Paul C Norris, Vikas P Sukhatme, Diane R Bielenberg, Sui Huang, Mark W Kieran, Charles N Serhan, and Dipak Panigrahy

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Fe limitation decreases transcriptional regulation over the diel cycle in the model diatom Thalassiosira pseudonana., Johanna A L Goldman, Megan J Schatz, Chris T Berthiaume, Sacha N Coesel, Mónica V Orellana, and E Virginia Armbrust

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Measuring Aging and Identifying Aging Phenotypes in Cancer Survivors., Jennifer L Guida, Tim A Ahles, Daniel Belsky, Judith Campisi, Harvey Jay Cohen, James DeGregori, Rebecca Fuldner, Luigi Ferrucci, Lisa Gallicchio, Leonid Gavrilov, Natalia Gavrilova, Paige A Green, Chamelli Jhappan, Ronald Kohanski, Kevin Krull, Jeanne Mandelblatt, Kirsten K Ness, Ann O'Mara, Nathan D Price, Jennifer Schrack, Stephanie Studenski, Olga Theou, Russell P Tracy, and Arti Hurria

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Histone Octamer Structure Is Altered Early in ISW2 ATP-Dependent Nucleosome Remodeling., Arjan Hada, Swetansu K Hota, Jie Luo, Yuan-Chi Lin, Seyit Kale, Alexey K Shaytan, Saurabh K Bhardwaj, Jim Persinger, Jeff Ranish, Anna R Panchenko, and Blaine Bartholomew

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Lymphatic Migration of Immune Cells., Henry R Hampton and Tatyana Chtanova

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Investigation of lipid metabolism dysregulation and the effects on immune microenvironments in pan-cancer using multiple omics data., Yang Hao, Daixi Li, Yong Xu, Jian Ouyang, Yongkun Wang, Yuqi Zhang, Baoguo Li, Lu Xie, and Guangrong Qin

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Framing technology challenges associated with improving cancer immunotherapies., James R Heath

Average Fitness Differences on NK Landscapes., Wim Hordijk, Stuart A Kauffman, and Peter F Stadler

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Molecular Diversity Required for the Formation of Autocatalytic Sets., Wim Hordijk, Mike Steel, and Stuart A Kauffman

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A Blueprint for Systems Biology., Trey Ideker and Leroy Hood

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Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data., Vera Ignjatovic, Philipp E Geyer, Krishnan K Palaniappan, Jessica E Chaaban, Gilbert S Omenn, Mark S Baker, Eric W Deutsch, and Jochen M Schwenk

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Data-driven multiscale modeling reveals the role of metabolic coupling for the spatio-temporal growth dynamics of yeast colonies., Jukka Intosalmi, Adrian C Scott, Michelle Hays, Nicholas Flann, Olli Yli-Harja, Harri Lähdesmäki, Aimée M Dudley, and Alexander Skupin

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Six Month Abstinence Heterogeneity in the Best Quit Study., Harold S Javitz, Terry M Bush, Jennifer C Lovejoy, Alula J Torres, Tallie Wetzel, Ken P Wassum, Marcia M Tan, Nabil Alshurafa, and Bonnie Spring

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Cancer cell population growth kinetics at low densities deviate from the exponential growth model and suggest an Allee effect., Kaitlyn E Johnson, Grant Howard, William Mo, Michael K Strasser, Ernesto A B F Lima, Sui Huang, and Amy Brock

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Cancer cell population growth kinetics at low densities deviate from the exponential growth model and suggest an Allee effect., Kaitlyn E Johnson, Grant Howard, William Mo, Michael K Strasser, Ernesto A B F Lima, Sui Huang, and Amy Brock

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Assessing protein sequence database suitability using de novo sequencing., Richard Johnson, Brian C Searle, Brook L Nunn, Jason M Gilmore, Molly Phillips, Chris T Amemiya, Michelle Heck, and Michael J MacCoss

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An Inflammatory Landscape for Preoperative Neurologic Deficits in Glioblastoma., Amal Katrib, Hyun-Hwan Jeong, Nina L Fransen, Kristin S Henzel, and Jeremy A Miller

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Genomic and molecular characterization of preterm birth., Theo A Knijnenburg, Joseph G Vockley, Nyasha Chambwe, David L Gibbs, Crystal Humphries, Kathi C Huddleston, Elisabeth Klein, Prachi Kothiyal, Ryan Tasseff, Varsha Dhankani, Dale L Bodian, Wendy S W Wong, Gustavo Glusman, Denise E Mauldin, Michael Miller, Joseph Slagel, Summer Elasady, Jared C Roach, Roger Kramer, Kalle Leinonen, Jasper Linthorst, Rajiv Baveja, Robin Baker, Benjamin D Solomon, Greg Eley, Ramaswamy K Iyer, George L Maxwell, Brady Bernard, Ilya Shmulevich, Leroy Hood, and John E Niederhuber

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The Impact of Moyamoya Disease and, Ming-Jen Lee, Shannon Fallen, Yong Zhou, David Baxter, Kelsey Scherler, Meng-Fai Kuo, and Kai Wang

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Distinct Profiles of Cell-Free MicroRNAs in Plasma of Veterans with Post-Traumatic Stress Disorder., Min Young Lee, David Baxter, Kelsey Scherler, Taek-Kyun Kim, Xiaogang Wu, Duna Abu-Amara, Janine Flory, Rachel Yehuda, Charles Marmar, Marti Jett, Inyoul Lee, Kai Wang, and Leroy Hood

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A biological function based biomarker panel optimization process., Min Young Lee, Taek-Kyun Kim, Kathie-Anne Walters, and Kai Wang

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Characterizing the cancer-associated microbiome with small RNA sequencing data., Wei-Hao Lee, Kai-Pu Chen, Kai Wang, Hsuan-Cheng Huang, and Hsueh-Fen Juan

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Synthesis and preclinical validation of novel P2Y1 receptor ligands as a potent anti-prostate cancer agent., Hien Thi Thu Le, Tatu Rimpilainen, Saravanan Konda Mani, Akshaya Murugesan, Olli Yli-Harja, Nuno R Candeias, and Meenakshisundaram Kandhavelu

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Inhibition of heme sequestration of histidine-rich protein 2 using multiple epitope-targeted peptides., JingXin Liang, David N Bunck, Anvita Mishra, Sunga Hong, Matthew N Idso, and James R Heath

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Inhibition of heme sequestration of histidine-rich protein 2 using multiple epitope-targeted peptides., JingXin Liang, David N Bunck, Anvita Mishra, Sunga Hong, Matthew N Idso, and James R Heath

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Time-dependent saddle-node bifurcation: Breaking time and the point of no return in a non-autonomous model of critical transitions., Jeremiah H Li, Felix X-F Ye, Hong Qian, and Sui Huang

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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, Michael P Walker, Erin N Vrana, Kevin J Hart, Allen M Minns, Photini Sinnis, Robert L Moritz, and Stefan H I Kappe

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Genome-wide analysis identifies NR4A1 as a key mediator of T cell dysfunction., Xindong Liu, Yun Wang, Huiping Lu, Jing Li, Xiaowei Yan, Minglu Xiao, Jing Hao, Andrei Alekseev, Hiep Khong, Tenghui Chen, Rui Huang, Jin Wu, Qiwen Zhao, Qi Wu, Senlin Xu, Xiaohu Wang, Wei Jin, Shicang Yu, Yan Wang, Lai Wei, Aibo Wang, Bo Zhong, Ling Ni, Xiaolong Liu, Roza Nurieva, Lilin Ye, Qiang Tian, Xiu-Wu Bian, and Chen Dong

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Liquid biopsy-based single-cell metabolic phenotyping of lung cancer patients for informative diagnostics., Ziming Li, Zhuo Wang, Yin Tang, Xiang Lu, Jie Chen, Yu Dong, Baojun Wu, Chunying Wang, Liu Yang, Zhili Guo, Min Xue, Shun Lu, Wei Wei, and Qihui Shi

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Precision Medicine in Pancreatic Disease-Knowledge Gaps and Research Opportunities: Summary of a National Institute of Diabetes and Digestive and Kidney Diseases Workshop., Mark E Lowe, Dana K Andersen, Richard M Caprioli, Jyoti Choudhary, Zobeida Cruz-Monserrate, Anil K Dasyam, Christopher E Forsmark, Fred S Gorelick, Joe W Gray, Mark Haupt, Kimberly A Kelly, Kenneth P Olive, Sylvia K Plevritis, Noa Rappaport, Holger R Roth, Hanno Steen, S Joshua Swamidass, Temel Tirkes, Aliye Uc, Kirill Veselkov, David C Whitcomb, and Aida Habtezion

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Identification of Cross-linked Peptides Using Isotopomeric Cross-linkers., Jie Luo, Jacob Bassett, and Jeff Ranish

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4D electron microscopy of T cell activation., Yue Lu, Byung-Kuk Yoo, Alphonsus H C Ng, Jungwoo Kim, Sinchul Yeom, Jau Tang, Milo M Lin, Ahmed H Zewail, and James R Heath

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Reproducible big data science: A case study in continuous FAIRness., Ravi Madduri, Kyle Chard, Mike D'Arcy, Segun C Jung, Alexis Rodriguez, Dinanath Sulakhe, Eric W Deutsch, Cory C Funk, Ben Heavner, Matthew A Richards, Paul Shannon, Gustavo Glusman, Nathan D Price, Carl Kesselman, and Ian Foster

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Influenza A Reinfection in Sequential Human Challenge: Implications for Protective Immunity and "Universal" Vaccine Development., Matthew J Memoli, Alison Han, Kathie-Anne Walters, Lindsay Czajkowski, Susan Reed, Rani Athota, Luz Angela Rosas, Adriana Cervantes-Medina, Jae-Keun Park, David M Morens, John C Kash, and Jeffery K Taubenberger

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MITF has a central role in regulating starvation-induced autophagy in melanoma., Katrin Möller, Sara Sigurbjornsdottir, Asgeir O Arnthorsson, Vivian Pogenberg, Ramile Dilshat, Valerie Fock, Solveig H Brynjolfsdottir, Christian Bindesboll, Margret Bessadottir, Helga M Ogmundsdottir, Anne Simonsen, Lionel Larue, Matthias Wilmanns, Vesteinn Thorsson, Eirikur Steingrimsson, and Margret H Ogmundsdottir

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Systems Pharmacogenomic Landscape of Drug Similarities from LINCS data: Drug Association Networks., Aliyu Musa, Shailesh Tripathi, Matthias Dehmer, Olli Yli-Harja, Stuart A Kauffman, and Frank Emmert-Streib

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Publisher Correction: Toxoplasma Modulates Signature Pathways of Human Epilepsy, Neurodegeneration & Cancer., Huân M Ngô, Ying Zhou, Hernan Lorenzi, Kai Wang, Taek-Kyun Kim, Yong Zhou, Kamal El Bissati, Ernest Mui, Laura Fraczek, Seesandra V Rajagopala, Craig W Roberts, Fiona L Henriquez, Alexandre Montpetit, Jenefer M Blackwell, Sarra E Jamieson, Kelsey Wheeler, Ian J Begeman, Carlos Naranjo-Galvis, Ney Alliey-Rodriguez, Roderick G Davis, Liliana Soroceanu, Charles Cobbs, Dennis A Steindler, Kenneth Boyer, A Gwendolyn Noble, Charles N Swisher, Peter T Heydemann, Peter Rabiah, Shawn Withers, Patricia Soteropoulos, Leroy Hood, and Rima McLeod

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BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree., Charles J Norsigian, Neha Pusarla, John Luke McConn, James T Yurkovich, Andreas Dräger, Bernhard O Palsson, and Zachary King

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Single-Cell Glia and Neuron Gene Expression in the Central Amygdala in Opioid Withdrawal Suggests Inflammation With Correlated Gut Dysbiosis., Sean J O'Sullivan, Evangelia Malahias, James Park, Ankita Srivastava, Beverly A S Reyes, Jon Gorky, Rajanikanth Vadigepalli, Elisabeth J Van Bockstaele, and James S Schwaber

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Advances in Identifying and Characterizing the Human Proteome., Young-Ki Paik, Christopher M Overall, Fernando Corrales, Eric W Deutsch, Lydie Lane, and Gilbert S Omenn

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Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate., Carmen G Palii, Qian Cheng, Mark A Gillespie, Paul Shannon, Michalina Mazurczyk, Giorgio Napolitani, Nathan D Price, Jeffrey A Ranish, Edward Morrissey, Douglas R Higgs, and Marjorie Brand

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Preoperative stimulation of resolution and inflammation blockade eradicates micrometastases., Dipak Panigrahy, Allison Gartung, Jun Yang, Haixia Yang, Molly M Gilligan, Megan L Sulciner, Swati S Bhasin, Diane R Bielenberg, Jaimie Chang, Birgitta A Schmidt, Julia Piwowarski, Anna Fishbein, Dulce Soler-Ferran, Matthew A Sparks, Steven J Staffa, Vidula Sukhatme, Bruce D Hammock, Mark W Kieran, Sui Huang, Manoj Bhasin, Charles N Serhan, and Vikas P Sukhatme

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MicroRNA-transcriptome networks in whole blood and monocytes of women undergoing preterm labour., Alison G Paquette, Oksana Shynlova, Xiaogang Wu, Mark Kibschull, Kai Wang, Nathan D Price, and Stephen J Lye

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Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement., Avinash B Patel, Camille M Moore, Basil J Greber, Jie Luo, Stefan A Zukin, Jeff Ranish, and Eva Nogales

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Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders., Jocelynn R Pearl, Carlo Colantuoni, Dani E Bergey, Cory C Funk, Paul Shannon, Bijoya Basu, Alex M Casella, Rediet T Oshone, Leroy Hood, Nathan D Price, and Seth A Ament

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Sensitive Detection and Analysis of Neoantigen-Specific T Cell Populations from Tumors and Blood., Songming Peng, Jesse M Zaretsky, Alphonsus H C Ng, William Chour, Michael T Bethune, Jongchan Choi, Alice Hsu, Elizabeth Holman, Xiaozhe Ding, Katherine Guo, Jungwoo Kim, Alexander M Xu, John E Heath, Won Jun Noh, Jing Zhou, Yapeng Su, Yue Lu, Jami McLaughlin, Donghui Cheng, Owen N Witte, David Baltimore, Antoni Ribas, and James R Heath