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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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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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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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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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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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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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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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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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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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 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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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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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

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A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms., Nazar Mashtalir, Hiroshi Suzuki, Daniel P Farrell, Akshay Sankar, Jie Luo, Martin Filipovski, Andrew R D'Avino, Roodolph St Pierre, Alfredo M Valencia, Takashi Onikubo, Robert G Roeder, Yan Han, Yuan He, Jeffrey A Ranish, Frank DiMaio, Thomas Walz, and Cigall Kadoch

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Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality., Fred D Mast, Arti T Navare, Almer M van der Sloot, Jasmin Coulombe-Huntington, Michael P Rout, Nitin Baliga, Alexis Kaushansky, Brian T Chait, Alan Aderem, Charles M Rice, Andrej Sali, Mike Tyers, and John D Aitchison

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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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Chronic elevation of plasma vascular endothelial growth factor-A (VEGF-A) is associated with a history of blast exposure., James S Meabon, David G Cook, Mayumi Yagi, Garth E Terry, Donna J Cross, Mark Muzi, Kathleen F Pagulayan, Aric F Logsdon, Abigail G Schindler, Vikas Ghai, Kai Wang, Shannon Fallen, Yong Zhou, Taek-Kyun Kim, Inyoul Lee, William A Banks, Erik S Carlson, Cynthia Mayer, Rebecca C Hendrickson, Murray A Raskind, Desiree A Marshall, Daniel P Perl, C Dirk Keene, and Elaine R Peskind

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DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics., Mukul K Midha, David S Campbell, Charu Kapil, Ulrike Kusebauch, Michael R Hoopmann, Samuel L Bader, and Robert L Moritz

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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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Design and synthesis of novel quinic acid derivatives:, Akshaya Murugesan, Suvi Holmstedt, Kenna C Brown, Alisa Koivuporras, Ana S Macedo, Nga Nguyen, Pedro Fonte, Patrícia Rijo, Olli Yli-Harja, Nuno R Candeias, and Meenakshisundaram Kandhavelu

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Antiproliferative and apoptotic effects of indole derivative, N-(2-hydroxy-5-nitrophenyl (4'-methylphenyl) methyl) indoline in breast cancer cells., Suresh Palanivel, Akshaya Murugesan, Kumar Subramanian, Olli Yli-Harja, and Meenakshisundaram Kandhavelu

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Inflammation resolution: a dual-pronged approach to averting cytokine storms in COVID-19?, Dipak Panigrahy, Molly M Gilligan, Sui Huang, Allison Gartung, Irene Cortés-Puch, Patricia J Sime, Richard P Phipps, Charles N Serhan, and Bruce D Hammock

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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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Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model., Jae-Keun Park, Yongli Xiao, Mitchell D Ramuta, Luz Angela Rosas, Sharon Fong, Alexis M Matthews, Ashley D Freeman, Monica A Gouzoulis, Natalia A Batchenkova, Xingdong Yang, Kelsey Scherler, Li Qi, Susan Reed, Rani Athota, Lindsay Czajkowski, Alison Han, David M Morens, Kathie-Anne Walters, Matthew J Memoli, John C Kash, and Jeffery K Taubenberger

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Investigating the Effects of Brainstem Neuronal Adaptation on Cardiovascular Homeostasis., James H Park, Jonathan Gorky, Babatunde Ogunnaike, Rajanikanth Vadigepalli, and James S Schwaber

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Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis., Eliza Jr Peterson, Abrar A Abidi, Mario L Arrieta-Ortiz, Boris Aguilar, James T Yurkovich, Amardeep Kaur, Min Pan, Vivek Srinivas, Ilya Shmulevich, and Nitin Baliga

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Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity., Patrick V Phaneuf, James T Yurkovich, David Heckmann, Muyao Wu, Troy E Sandberg, Zachary A King, Justin Tan, Bernhard O Palsson, and Adam M Feist

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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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Absence of full-length dystrophin impairs normal maturation and contraction of cardiomyocytes derived from human-induced pluripotent stem cells., J Manuel Pioner, Xuan Guan, Jordan M Klaiman, Alice W Racca, Lil Pabon, Veronica Muskheli, Jesse Macadangdang, Cecilia Ferrantini, Michael R Hoopmann, Robert L Moritz, Deok-Ho Kim, Chiara Tesi, Corrado Poggesi, Charles E Murry, Martin K Childers, David L Mack, and Michael Regnier

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Composition of Caenorhabditis elegans extracellular vesicles suggests roles in metabolism, immunity, and aging., Joshua C Russell, Taek-Kyun Kim, Ayush Noori, Gennifer E Merrihew, Julia E Robbins, Alexandra Golubeva, Kai Wang, Michael J MacCoss, and Matt Kaeberlein

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Advancing human health in the decade ahead: pregnancy as a key window for discovery: A Burroughs Wellcome Fund Pregnancy Think Tank., Yoel Sadovsky, Sam Mesiano, Graham J Burton, Michelle Lampl, Jeffrey C Murray, Rachel M Freathy, Anita Mahadevan-Jansen, Ashley Moffett, Nathan D Price, Paul H Wise, Derek E Wildman, Ralph Snyderman, Nigel Paneth, John Anthony Capra, Marcelo A Nobrega, Yaacov Barak, and Louis J Muglia

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Defining the proteolytic landscape during enterovirus infection., Mohsan Saeed, Sebastian Kapell, Nicholas T Hertz, Xianfang Wu, Kierstin Bell, Alison W Ashbrook, Milica Tesic Mark, Henry A Zebroski, Maxwell L Neal, Malin Flodström-Tullberg, Margaret R MacDonald, John D Aitchison, Henrik Molina, and Charles M Rice

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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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Serum-borne lipids amplify TLR-activated inflammatory responses., Naveen Sharma, Ajay Suresh Akhade, Sana Ismaeel, and Ayub Qadri

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Circulating MicroRNAs and Extracellular Vesicle-Containing MicroRNAs as Response Biomarkers of Anti-programmed Cell Death Protein 1 or Programmed Death-Ligand 1 Therapy in NSCLC., Takehito Shukuya, Vikas Ghai, Joseph M Amann, Tamio Okimoto, Konstantin Shilo, Taek-Kyun Kim, Kai Wang, and David P Carbone

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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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Behavior-related gene regulatory networks: A new level of organization in the brain., Saurabh Sinha, Beryl M Jones, Ian M Traniello, Syed A Bukhari, Marc S Halfon, Hans A Hofmann, Sui Huang, Paul S Katz, Jason Keagy, Vincent J Lynch, Marla B Sokolowski, Lisa J Stubbs, Shayan Tabe-Bordbar, Mariana F Wolfner, and Gene E Robinson

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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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Multiomic Immunophenotyping of COVID-19 Patients Reveals Early Infection Trajectories., Yapeng Su, Daniel Chen, Christopher Lausted, Dan Yuan, Jongchan Choi, Cheng Dai, Valentin Voillet, Kelsey Scherler, Pamela Troisch, Venkata R Duvvuri, Priyanka Baloni, Guangrong Qin, Brett Smith, Sergey Kornilov, Clifford Rostomily, Alex Xu, Jing Li, Shen Dong, Alissa Rothchild, Jing Zhou, Kim Murray, Rick Edmark, Sunga Hong, Lesley Jones, Yong Zhou, Ryan Roper, Sean Mackay, D Shane O'Mahony, Christopher Dale, Julie A Wallick, Heather A Algren, Zager A Michael, Andrew T Magis, Wei Wei, Nathan D Price, Sui Huang, Naeha Subramanian, Kai Wang, Jennifer Hadlock, Leroy Hood, Alan Aderem, Jeffrey A Bluestone, Lewis L Lanier, Phil Greenberg, Raphael Gottardo, Mark M Davis, Jason D Goldman, James R Heath, and ISB-Swedish COVID19 Biobanking Unit

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Multi-omics resolves a sharp disease-state shift between mild and moderate COVID-19, Yapeng Su, Daniel Chen, Dan Yuan, Christopher Lausted, Jongchan Choi, Chengzhen L Dai, Valentin Voillet, Venkata R Duvvuri, Kelsey Scherler, Pamela Troisch, Priyanka Baloni, Guangrong Qin, Brett Smith, Sergey A Kornilov, Clifford Rostomily, Alex Xu, Jing Li, Shen Dong, Alissa Rothchild, Jing Zhou, Kim Murray, Rick Edmark, Sunga Hong, John Heath, John Earls, Rongyu Zhang, Jingyi Xie, Sarah Li, Ryan Roper, Lesley Jones, Yong Zhou, Lee Rowen, Rachel Liu, Sean Mackay, D Shane O'Mahony, chris dale, Julie A Wallick, Heather A Algren, Zager A. Michael, ISB-Swedish COVID19 Biobanking Unit, Wei Wei, Nathan D Price, Sui Huang, Naeha Subramanian, Kai Wang, Andrew T Magis, Jennifer Hadlock, Leroy Hood, Alan Aderem, Jeffrey A. Bluestone, Lewis L. Lanier, Philip D. Greenberg, Raphael Gottardo, Mark M. Davis, Jason D Goldman, and James R. Heath

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Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line., Yapeng Su, Melissa E Ko, Hanjun Cheng, Ronghui Zhu, Min Xue, Jessica Wang, Jihoon W Lee, Luke Frankiw, Alexander Xu, Stephanie Wong, Lidia Robert, Kaitlyn Takata, Dan Yuan, Yue Lu, Sui Huang, Antoni Ribas, Raphael Levine, Garry P Nolan, Wei Wei, Sylvia K Plevritis, Guideng Li, David Baltimore, and James R Heath

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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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Sequential Wnt Agonist Then Antagonist Treatment Accelerates Tissue Repair and Minimizes Fibrosis., Xiao-Jun Tian, Dong Zhou, Haiyan Fu, Rong Zhang, Xiaojie Wang, Sui Huang, Youhua Liu, and Jianhua Xing

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Biofilms of the non-tuberculous Mycobacterium chelonae form an extracellular matrix and display distinct expression patterns, Perla Vega-Dominguez, Eliza Jr Peterson, Min Pan, Alessandro Di Maio, Saumya Singh, Siva Umapathy, Deepak K Saini, Nitin Baliga, and Apoorva Bhatt

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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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Multiomic blood correlates of genetic risk identify presymptomatic disease alterations., Michael Wainberg, Andrew T Magis, John C Earls, Jennifer C Lovejoy, Nasa Sinnott-Armstrong, Gilbert S Omenn, Leroy Hood, and Nathan D Price

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Circulating activated lymphocyte subsets as potential blood biomarkers of cancer progression., Ying-Yi Wang, Na Zhou, Hong-Sheng Liu, Xiao-Lei Gong, Rui Zhu, Xiao-Yuan Li, Zhao Sun, Xu-Hong Zong, Ning-Ning Li, Chang-Ting Meng, Chun-Mei Bai, and Tai-Sheng Li

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Meta-Analysis of the Alzheimer's Disease Human Brain Transcriptome and Functional Dissection in Mouse Models., Ying-Wooi Wan, Rami Al-Ouran, Carl G Mangleburg, Thanneer M Perumal, Tom V Lee, Katherine Allison, Vivek Swarup, Cory C Funk, Chris Gaiteri, Mariet Allen, Minghui Wang, Sarah M Neuner, Catherine C Kaczorowski, Vivek M Philip, Gareth R Howell, Heidi Martini-Stoica, Hui Zheng, Hongkang Mei, Xiaoyan Zhong, Jungwoo Wren Kim, Valina L Dawson, Ted M Dawson, Ping-Chieh Pao, Li-Huei Tsai, Jean-Vianney Haure-Mirande, Michelle E Ehrlich, Paramita Chakrabarty, Yona Levites, Xue Wang, Eric B Dammer, Gyan Srivastava, Sumit Mukherjee, Solveig K Sieberts, Larsson Omberg, Kristen D Dang, James A Eddy, Phil Snyder, Yooree Chae, Sandeep Amberkar, Wenbin Wei, Winston Hide, Christoph Preuss, Ayla Ergun, Phillip J Ebert, David C Airey, Sara Mostafavi, Lei Yu, Hans-Ulrich Klein, Accelerating Medicines Partnership, Alzheimer’s Disease Consortium, Gregory W Carter, David A Collier, Todd E Golde, Allan I Levey, David A Bennett, Karol Estrada, T Matthew Townsend, Bin Zhang, Eric Schadt, Philip L De Jager, Nathan D Price, Nilüfer Ertekin-Taner, Zhandong Liu, Joshua M Shulman, Lara M Mangravite, and Benjamin A Logsdon

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Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction., Daniel K Wells, Marit M van Buuren, Kristen K Dang, Vanessa M Hubbard-Lucey, Kathleen C F Sheehan, Katie M Campbell, Andrew Lamb, Jeffrey P Ward, John Sidney, Ana B Blazquez, Andrew J Rech, Jesse M Zaretsky, Begonya Comin-Anduix, Alphonsus H C Ng, William Chour, Thomas V Yu, Hira Rizvi, Jia M Chen, Patrice Manning, Gabriela M Steiner, Xengie C Doan, Taha Merghoub, Justin Guinney, Adam Kolom, Cheryl Selinsky, Antoni Ribas, Matthew D Hellmann, Nir Hacohen, Alessandro Sette, James R Heath, Nina Bhardwaj, Fred Ramsdell, Robert D Schreiber, Ton N Schumacher, Pia Kvistborg, and Nadine A Defranoux

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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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SOSTDC1-producing follicular helper T cells promote regulatory follicular T cell differentiation., Xin Wu, Yun Wang, Rui Huang, Qujing Gai, Haofei Liu, Meimei Shi, Xiang Zhang, Yonglin Zuo, Longjuan Chen, Qiwen Zhao, Yu Shi, Fengchao Wang, Xiaowei Yan, Huiping Lu, Senlin Xu, Xiaohong Yao, Lin Chen, Xia Zhang, Qiang Tian, Ziyan Yang, Bo Zhong, Chen Dong, Yan Wang, Xiu-Wu Bian, and Xindong Liu

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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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Correction to: Small Molecule KRAS Agonist for Mutant KRAS Cancer Therapy., Ke Xu, Dongkyoo Park, Andrew T Magis, Jun Zhang, Wei Zhou, Gabriel L Sica, Suresh S Ramalingam, Walter J Curran, and Xingming Deng

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Correction: 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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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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Proteomics Standards Initiative Extended FASTA Format., Pierre-Alain Binz, Jim Shofstahl, Juan Antonio Vizcaíno, Harald Barsnes, Robert J Chalkley, Gerben Menschaert, Emanuele Alpi, Karl Clauser, Jimmy K Eng, Lydie Lane, Sean L Seymour, Luis Francisco Hernández Sánchez, Gerhard Mayer, Martin Eisenacher, Yasset Perez-Riverol, Eugene A Kapp, Luis Mendoza, Peter R Baker, Andrew Collins, Tim Van Den Bossche, and Eric W Deutsch

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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