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 2021

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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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Proteomic/transcriptomic analysis of erythropoiesis., Marjorie Brand and Jeffrey A Ranish

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A redox-active crosslinker reveals an essential and inhibitable oxidative folding network in the endoplasmic reticulum of malaria parasites., David W Cobb, Heather M Kudyba, Alejandra Villegas, Michael R Hoopmann, Rodrigo P Baptista, Baylee Bruton, Michelle Krakowiak, Robert L Moritz, and Vasant Muralidharan

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Circulating exosomal microRNA expression patterns distinguish cardiac sarcoidosis from myocardial ischemia., Elliott D Crouser, Mark W Julian, Sabahattin Bicer, Vikas Ghai, Taek-Kyun Kim, Lisa A Maier, May Gillespie, Nabeel Y Hamzeh, and Kai Wang

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Lettuce (Lactuca sativa) productivity influenced by microbial inocula under nitrogen-limited conditions in aquaponics., Jessica A Day, Christian Diener, Anne E Otwell, Kourtney E Tams, Brad Bebout, Angela M Detweiler, Michael D Lee, Madeline T Scott, Wilson Ta, Monica Ha, Shienna A Carreon, Kenny Tong, Abdirizak A Ali, Sean M Gibbons, and Nitin S Baliga

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Non-responder phenotype reveals apparent microbiome-wide antibiotic tolerance in the murine gut., Christian Diener, Anna C H Hoge, Sean M Kearney, Ulrike Kusebauch, Sushmita Patwardhan, Robert L Moritz, Susan E Erdman, and Sean M Gibbons

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Single-cell analysis of erythropoiesis in Rpl11 haploinsufficient mice reveals insight into the pathogenesis of Diamond Blackfan anemia., Raymond T Doty, Xiaowei Yan, Changting Meng, Christopher Lausted, Qiang Tian, and Janis L Abkowitz

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Application of MCAT Questions as a Testing Tool and Evaluation Metric for Knowledge Graph-based Reasoning Systems., Karamarie Fecho, James Balhoff, Chris Bizon, William E Byrd, Sui Huang, David Koslicki, Stefano E Rensi, Patrick L Schmitt, Mathias J Wawer, Mark Williams, and Stanley C Ahalt

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Identifying the miRNA Signature Association with Aging-Related Senescence in Glioblastoma., Mutharasu Gnanavel, Akshaya Murugesan, Saravanan Konda Mani, Olli Yli-Harja, and Meenakshisundaram Kandhavelu

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

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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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

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 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

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Selective carbon sources influence the end products of microbial nitrate respiration., Hans K Carlson, Lauren M Lui, Morgan N Price, Alexey E Kazakov, Alex V Carr, Jennifer V Kuehl, Trenton K Owens, Torben Nielsen, Adam P Arkin, and Adam M Deutschbauer

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Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer., Jian Carrot-Zhang, Nyasha Chambwe, Jeffrey S Damrauer, Theo A Knijnenburg, A Gordon Robertson, Christina Yau, Wanding Zhou, Ashton C Berger, Kuan-Lin Huang, Justin Y Newberg, R Jay Mashl, Alessandro Romanel, Rosalyn W Sayaman, Francesca Demichelis, Ina Felau, Garrett M Frampton, Seunghun Han, Katherine A Hoadley, Anab Kemal, Peter W Laird, Alexander J Lazar, Xiuning Le, Ninad Oak, Hui Shen, Christopher K Wong, Jean C Zenklusen, Elad Ziv, Cancer Genome Atlas Analysis Network, Andrew D Cherniack, and Rameen Beroukhim

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Systematic comparison of sea urchin and sea star developmental gene regulatory networks explains how novelty is incorporated in early development., Gregory A Cary, Brenna S McCauley, Olga Zueva, Joseph Pattinato, William J R Longabaugh, and Veronica F Hinman

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Society for Immunotherapy of Cancer clinical and biomarkers data sharing resource document: Volume II-practical challenges., Alessandra Cesano, Michael A Cannarile, Sacha Gnjatic, Bruno Gomes, Justin Guinney, Vaios Karanikas, Mohan Karkada, John M Kirkwood, Beatrix Kotlan, Giuseppe V Masucci, Els Meeusen, Anne Monette, Aung Naing, Vésteinn Thorsson, Nicholas Tschernia, Ena Wang, Daniel K Wells, Timothy L Wyant, and Sergio Rutella

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Cancer Systems Biology in the Era of Single-Cell Multi-Omics., Hanjun Cheng, Rong Fan, and Wei Wei

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A novel landscape of nuclear human CDK2 substrates revealed by in situ phosphorylation., Yong Chi, John H Carter, Jherek Swanger, Alexander V Mazin, Robert L Moritz, and Bruce E Clurman

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Unique challenges for glioblastoma immunotherapy - Discussions across neuro-oncology and non-neuro-oncology experts in cancer immunology., Pavlina Chuntova, Frances Chow, Payal Watchmaker, Mildred Galvez, Amy B Heimberger, Evan W Newell, Aaron Diaz, Ronald A DePinho, Ming O Li, E John Wherry, Duane Mitchell, Masaki Terabe, Derek A Wainwright, Jay A Berzofsky, Christel Herold-Mende, James R Heath, Michael Lim, Kim A Margolin, E Antonio Chiocca, Noriyuki Kasahara, Benjamin M Ellingson, Christine Brown, Yvonne Chen, Peter Fecci, David A Reardon, Gavin P Dunn, Linda M Liau, Joseph F Costello, Wolfgang Wick, Timothy Cloughesy, William C Timmer, Patrick Y Wen, Robert M Prins, Michael Platten, and Hideho Okada

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Inferring evolutionary pathways and directed genotype networks of foodborne pathogens., Oliver M Cliff, Natalia McLean, Vitali Sintchenko, Kristopher M Fair, Tania C Sorrell, Stuart Kauffman, and Mikhail Prokopenko

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Synthesizing Systems Biology Knowledge from Omics Using Genome-Scale Models., Sanjeev Dahal, James T Yurkovich, Hao Xu, Bernhard O Palsson, and Laurence Yang

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Characterizing diversity in the tumor-immune microenvironment of distinct subclasses of gastroesophageal adenocarcinomas., S Derks, L K de Klerk, X Xu, T Fleitas, K X Liu, Y Liu, F Dietlein, C Margolis, A M Chiaravalli, A C Da Silva, S Ogino, F G Akarca, G J Freeman, S J Rodig, J L Hornick, E van Allen, B Li, S X Liu, V Thorsson, and A J Bass

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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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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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Progressive Shifts in the Gut Microbiome Reflect Prediabetes and Diabetes Development in a Treatment-Naive Mexican Cohort., Christian Diener, María de Lourdes Reyes-Escogido, Lilia M Jimenez-Ceja, Mariana Matus, Claudia M Gomez-Navarro, Nathaniel D Chu, Vivian Zhong, M Elizabeth Tejero, Eric Alm, Osbaldo Resendis-Antonio, and Rodolfo Guardado-Mendoza

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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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Raman-guided subcellular pharmaco-metabolomics for metastatic melanoma cells., Jiajun Du, Yapeng Su, Chenxi Qian, Dan Yuan, Kun Miao, Dongkwan Lee, Alphonsus H C Ng, Reto S Wijker, Antoni Ribas, Raphael D Levine, James R Heath, and Lu Wei

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CRI iAtlas: an interactive portal for immuno-oncology research., James A Eddy, Vésteinn Thorsson, Andrew E Lamb, David L Gibbs, Carolina Heimann, Jia Xin Yu, Verena Chung, Yooree Chae, Kristen Dang, Benjamin G Vincent, Ilya Shmulevich, and Justin Guinney

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Artificial Intelligence: A Clarification of Misconceptions, Myths and Desired Status., Frank Emmert-Streib, Olli Yli-Harja, and Matthias Dehmer

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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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Resolution of eicosanoid/cytokine storm prevents carcinogen and inflammation-initiated hepatocellular cancer progression., Anna Fishbein, Weicang Wang, Haixia Yang, Jun Yang, Victoria M Hallisey, Jianjun Deng, Sanne M L Verheul, Sung Hee Hwang, Allison Gartung, Yuxin Wang, Diane R Bielenberg, Sui Huang, Mark W Kieran, Bruce D Hammock, and Dipak Panigrahy

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Transcriptional portrait of M. bovis BCG during biofilm production shows genes differentially expressed during intercellular aggregation and substrate attachment., Mario Alberto Flores-Valdez, Michel de Jesús Aceves-Sánchez, Eliza Jr Peterson, Nitin Baliga, Jorge Bravo-Madrigal, Miguel Ángel De la Cruz-Villegas, Miguel A Ares, Sarah Born, Martin Voskuil, Nayeli Areli Pérez-Padilla, Mirna Burciaga-Flores, Tanya Amanda Camacho-Villegas, and María Guadalupe Espinoza-Jorge

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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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Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types., Cory C Funk, Alex M Casella, Segun Jung, Matthew A Richards, Alex Rodriguez, Paul Shannon, Rory Donovan-Maiye, Ben Heavner, Kyle Chard, Yukai Xiao, Gustavo Glusman, Nilufer Ertekin-Taner, Todd E Golde, Arthur Toga, Leroy Hood, John D Van Horn, Carl Kesselman, Ian Foster, Ravi Madduri, Nathan D Price, and Seth A Ament

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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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Keystone taxa indispensable for microbiome recovery., Sean M Gibbons

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Publisher Correction: Keystone taxa indispensable for microbiome recovery., Sean M Gibbons

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Absolute quantification of transcription factors in human erythropoiesis using selected reaction monitoring mass spectrometry., Mark A Gillespie, Carmen G Palii, Daniel Sanchez-Taltavull, Theodore J Perkins, Marjorie Brand, and Jeffrey A Ranish

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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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Interdisciplinary Profile: An Established Chemist Journeys into Different Disciplines., James R Heath

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Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance., Malte Herold, Susana Martínez Arbas, Shaman Narayanasamy, Abdul R Sheik, Luise A K Kleine-Borgmann, Laura A Lebrun, Benoît J Kunath, Hugo Roume, Irina Bessarab, Rohan B H Williams, John D Gillece, James M Schupp, Paul S Keim, Christian Jäger, Michael R Hoopmann, Robert L Moritz, Yuzhen Ye, Sujun Li, Haixu Tang, Anna Heintz-Buschart, Patrick May, Emilie E L Muller, Cedric C Laczny, and Paul Wilmes

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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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Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project., Michael R Hoopmann, Ulrike Kusebauch, Magnus Palmblad, Nuno Bandeira, David Shteynberg, Lingjie He, Bin Xia, Stoyan H Stoychev, Gilbert S Omenn, Susan T Weintraub, and Robert L Moritz

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

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Building a circular RNA centered gene regulation network associated with cervical squamous cell carcinoma., Wei Hu, Qingqing Li, Xiaoyi He, Ming Gao, Zhanfu Zheng, Yuanlin Ding, Kai Wang, and Yuqing He

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Modulation of Immune Checkpoints by Chemotherapy in Human Colorectal Liver Metastases., Neda Jabbari, Heidi L Kenerson, Christopher Lausted, Xiaowei Yan, Changting Meng, Kevin M Sullivan, Priyanka Baloni, Dani E Bergey, Venu G Pillarisetty, Leroy Hood, Raymond S Yeung, and Qiang Tian

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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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Answering Schrödinger's "What Is Life?", Stuart Kauffman

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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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An Exploratory Pilot Study with Plasma Protein Signatures Associated with Response of Patients with Depression to Antidepressant Treatment for 10 Weeks., Eun Young Kim, Hee-Sung Ahn, Min Young Lee, Jiyoung Yu, Jeonghun Yeom, Hwangkyo Jeong, Hophil Min, Hyun Jeong Lee, Kyunggon Kim, and Yong Min Ahn

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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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Plasma levels of soluble ACE2are associated with sex, Metabolic Syndrome, and its biomarkers in a large cohort, pointing to a possible mechanism for increased severity in COVID-19., Sergey A Kornilov, Isabelle Lucas, Kathleen Jade, Chengzhen L Dai, Jennifer C Lovejoy, and Andrew T Magis

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Epigenome signatures landscaped by histone H3K9me3 are associated with the synaptic dysfunction in Alzheimer's disease., Min Young Lee, Junghee Lee, Seung Jae Hyeon, Hyesun Cho, Yu Jin Hwang, Jong-Yeon Shin, Ann C McKee, Neil W Kowall, Jong-Il Kim, Thor D Stein, Daehee Hwang, and Hoon Ryu

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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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Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry., Alexander Leitner, Alexandre M J J Bonvin, Christoph H Borchers, Robert J Chalkley, Julia Chamot-Rooke, Colin W Combe, Jürgen Cox, Meng-Qiu Dong, Lutz Fischer, Michael Götze, Fabio C Gozzo, Albert J R Heck, Michael R Hoopmann, Lan Huang, Yasushi Ishihama, Andrew R Jones, Nir Kalisman, Oliver Kohlbacher, Karl Mechtler, Robert L Moritz, Eugen Netz, Petr Novak, Evgeniy Petrotchenko, Andrej Sali, Richard A Scheltema, Carla Schmidt, David Schriemer, Andrea Sinz, Frank Sobott, Florian Stengel, Konstantinos Thalassinos, Henning Urlaub, Rosa Viner, Juan A Vizcaíno, Marc R Wilkins, and Juri Rappsilber

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Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome., Roie Levy, Andrew T Magis, John C Earls, Ohad Manor, Tomasz Wilmanski, Jennifer Lovejoy, Sean M Gibbons, Gilbert S Omenn, Leroy Hood, and Nathan D Price

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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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IsoResolve: Predicting Splice Isoform Functions by Integrating Gene and Isoform-level Features with Domain Adaptation., Hong-Dong Li, Changhuo Yang, Zhimin Zhang, Mengyun Yang, Fang-Xiang Wu, Gilbert S Omenn, and Jianxin Wang

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Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum., Adrián López García de Lomana, Ulrike Kusebauch, Arjun V Raman, Min Pan, Serdar Turkarslan, Alan P R Lorenzetti, Robert L Moritz, and Nitin Baliga

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A synthesis of bacterial and archaeal phenotypic trait data., Joshua S Madin, Daniel A Nielsen, Maria Brbic, Ross Corkrey, David Danko, Kyle Edwards, Martin K M Engqvist, Noah Fierer, Jemma L Geoghegan, Michael Gillings, Nikos C Kyrpides, Elena Litchman, Christopher E Mason, Lisa Moore, Søren L Nielsen, Ian T Paulsen, Nathan D Price, T B K Reddy, Matthew A Richards, Eduardo P C Rocha, Thomas M Schmidt, Heba Shaaban, Maulik Shukla, Fran Supek, Sasha G Tetu, Sara Vieira-Silva, Alice R Wattam, David A Westfall, and Mark Westoby

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Untargeted longitudinal analysis of a wellness cohort identifies markers of metastatic cancer years prior to diagnosis., Andrew T Magis, Noa Rappaport, Matthew P Conomos, Gilbert S Omenn, Jennifer C Lovejoy, Leroy Hood, and Nathan D Price

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Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance., Kalifa Manjang, Shailesh Tripathi, Olli Yli-Harja, Matthias Dehmer, and Frank Emmert-Streib