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

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Submissions from 2019

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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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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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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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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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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

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Path-seq identifies an essential mycolate remodeling program for mycobacterial host adaptation., Eliza Jr Peterson, Rebeca Bailo, Alissa C Rothchild, Mario L Arrieta-Ortiz, Amardeep Kaur, Min Pan, Dat Mai, Abrar A Abidi, Charlotte Cooper, Alan Aderem, Apoorva Bhatt, and Nitin S Baliga

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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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A Pan-Cancer Approach to Predict Responsiveness to Immune Checkpoint Inhibitors by Machine Learning., Maurizio Polano, Marco Chierici, Michele Dal Bo, Davide Gentilini, Federica Di Cintio, Lorena Baboci, David L Gibbs, Cesare Furlanello, and Giuseppe Toffoli

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A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research., M Poyet, M Groussin, S M Gibbons, J Avila-Pacheco, X Jiang, S M Kearney, A R Perrotta, B Berdy, S Zhao, T D Lieberman, P K Swanson, M Smith, S Roesemann, J E Alexander, S A Rich, J Livny, H Vlamakis, C Clish, K Bullock, A Deik, J Scott, K A Pierce, R J Xavier, and E J Alm

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Gene annotation errors are common in the mammalian mitochondrial genomes database., Carlos F Prada and Jeffrey L Boore

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Spatial presentation of biological molecules to cells by localized diffusive transfer., Mary C Regier, Emily Olszewski, Christoph C Carter, John D Aitchison, Alexis Kaushansky, Jennifer Davis, Erwin Berthier, David J Beebe, and Kelly R Stevens

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Opportunities and Challenges in Interpreting and Sharing Personal Genomes., Irit R Rubin and Gustavo Glusman

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In vivo proteomics identifies the competence regulon and AliB oligopeptide transporter as pathogenic factors in pneumococcal meningitis., Frank Schmidt, Niamatullah Kakar, Tanja C Meyer, Maren Depke, Ilias Masouris, Gerhard Burchhardt, Alejandro Gómez-Mejia, Vishnu Dhople, Leiv S Håvarstein, Zhi Sun, Robert L Moritz, Uwe Völker, Uwe Koedel, and Sven Hammerschmidt

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Incorporating In-Source Fragments Improves Metabolite Identification Accuracy in Untargeted LCMS and LCMS/MS Datasets., Brian C Searle, Jacob C Lippincott, and Phillip M Seitzer

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An efficient solution for resolving iTRAQ and TMT channel crosstalk., Brian C Searle and Alfred L Yergey

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Downregulation of CENPF Remodels Prostate Cancer Cells and Alters Cellular Metabolism., Muhammad Shahid, Minhyung Kim, Min Young Lee, Austin Yeon, Sungyong You, Hyung L Kim, and Jayoung Kim

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Downregulation of CENPF Remodels Prostate Cancer Cells and Alters Cellular Metabolism., Muhammad Shahid, Minhyung Kim, Min Young Lee, Austin Yeon, Sungyong You, Hyung L Kim, and Jayoung Kim

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Proteomic Analysis of Plasmodium Merosomes: The Link between Liver and Blood Stages in Malaria., Melanie J Shears, Raja Sekhar Nirujogi, Kristian E Swearingen, Santosh Renuse, Satish Mishra, Panga Jaipal Reddy, Robert L Moritz, Akhilesh Pandey, and Photini Sinnis

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OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling., Fangzhou Shen, Renliang Sun, Jie Yao, Jian Li, Qian Liu, Nathan D Price, Chenguang Liu, and Zhuo Wang

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PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline., David Shteynberg, Eric W Deutsch, David S Campbell, Michael R Hoopmann, Ulrike Kusebauch, Dave Lee, Luis Mendoza, Mukul K Midha, Zhi Sun, Anthony D Whetton, and Robert L Moritz

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Mechanistic inferences on metabolic dysfunction in PTSD from an integrated model and multi-omic analysis: Role of glucocorticoid receptor sensitivity., Pramod R Somvanshi, Synthia H Mellon, Janine D Flory, Duna Abu-Amara, Ptsd Systems Biology Consortium, Owen M Wolkowitz, Rachel Yehuda, Marti Jett, Leroy Hood, Charles Marmar, and Francis J Doyle

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Phenotypic heterogeneity and evolution of melanoma cells associated with targeted therapy resistance., Yapeng Su, Marcus Bintz, Yezi Yang, Lidia Robert, Alphonsus H C Ng, Victoria Liu, Antoni Ribas, James R Heath, and Wei Wei

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A Tandem Mass Spectrometry Sequence Database Search Method for Identification of O-Fucosylated Proteins by Mass Spectrometry., Kristian E Swearingen, Jimmy K Eng, David Shteynberg, Vladimir Vigdorovich, Timothy A Springer, Luis Mendoza, D Noah Sather, Eric W Deutsch, Stefan H I Kappe, and Robert L Moritz

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Circulatory metastin/kisspeptin-1 in polycystic ovary syndrome: a systematic review and meta-analysis with diagnostic test accuracy., Seshadri Reddy Varikasuvu, V Satya Prasad, V C Vamshika, M V Satyanarayana, and Panga Jaipal Reddy

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Circulating Angiopoietin-like 8 protein (ANGPTL8/Betatrophin) in patients with polycystic ovary syndrome: a systematic review and multi effect size meta-analysis., Seshadri Reddy Varikasuvu, Panga Jaipal Reddy, and M V Satyanarayana

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Plasmodium Secretion Induces Hepatocyte Lysosome Exocytosis and Promotes Parasite Entry., Kamalakannan Vijayan, Igor Cestari, Fred D Mast, Elizabeth K K Glennon, Suzanne M McDermott, Heather S Kain, Alyssa M Brokaw, John D Aitchison, Kenneth Stuart, and Alexis Kaushansky

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2-(2-(2,4-dioxopentan-3-ylidene)hydrazineyl)benzonitrile as novel inhibitor of receptor tyrosine kinase and PI3K/AKT/mTOR signaling pathway in glioblastoma., Anisha Viswanathan, Dinesh Kute, Aliyu Musa, Saravanan Konda Mani, Vili Sipilä, Frank Emmert-Streib, Fedor I Zubkov, Atash V Gurbanov, Olli Yli-Harja, and Meenakshisundaram Kandhavelu

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Battling Glioblastoma: A Novel Tyrosine Kinase Inhibitor with Multi-Dimensional Anti-Tumor Effect (Running Title: Cancer Cells Death Signalling Activation)., Anisha Viswanathan, Aliyu Musa, Akshaya Murugesan, João R Vale, Carlos A M Afonso, Saravanan Konda Mani, Olli Yli-Harja, Nuno R Candeias, and Meenakshisundaram Kandhavelu

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The Human Immunopeptidome Project: a roadmap to predict and treat immune diseases., Juan Antonio Vizcaíno, Peter Kubiniok, Kevin Kovalchik, Qing Ma, Jérôme Despault Duquette, Ian Mongrain, Eric W Deutsch, Bjoern Peters, Alessandro Sette, Isabelle Sirois, and Etienne Caron

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Differential Effects of Influenza Virus NA, HA Head, and HA Stalk Antibodies on Peripheral Blood Leukocyte Gene Expression during Human Infection., Kathie-Anne Walters, Ruoqing Zhu, Michael Welge, Kelsey Scherler, Jae-Keun Park, Zainab Rahil, Hao Wang, Loretta Auvil, Colleen Bushell, Min Young Lee, David Baxter, Tyler Bristol, Luz Angela Rosas, Adriana Cervantes-Medina, Lindsay Czajkowski, Alison Han, Matthew J Memoli, Jeffery K Taubenberger, and John C Kash

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Special Issue on Software Tools and Resources: Acknowledging the Toolmakers of Science., Susan T Weintraub, Michael R Hoopmann, and Magnus Palmblad

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Special Issue on Single-Cell Multiomics for Immuno-Oncology and Cancer Systems Biology., Wei Wei and Rong Fan

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Buparlisib in Patients With Recurrent Glioblastoma Harboring Phosphatidylinositol 3-Kinase Pathway Activation: An Open-Label, Multicenter, Multi-Arm, Phase II Trial., Patrick Y Wen, Mehdi Touat, Brian M Alexander, Ingo K Mellinghoff, Shakti Ramkissoon, Christine S McCluskey, Kristine Pelton, Sam Haidar, Sankha S Basu, Sarah C Gaffey, Loreal E Brown, Juan Emmanuel Martinez-Ledesma, Shaofang Wu, Jungwoo Kim, Wei Wei, Mi-Ae Park, Jason T Huse, John G Kuhn, Mikael L Rinne, Howard Colman, Nathalie Y R Agar, Antonio M Omuro, Lisa M DeAngelis, Mark R Gilbert, John F de Groot, Timothy F Cloughesy, Andrew S Chi, Thomas M Roberts, Jean J Zhao, Eudocia Q Lee, Lakshmi Nayak, James R Heath, Laura L Horky, Tracy T Batchelor, Rameen Beroukhim, Susan M Chang, Azra H Ligon, Ian F Dunn, Dimpy Koul, Geoffrey S Young, Michael D Prados, David A Reardon, W K Alfred Yung, and Keith L Ligon

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Buparlisib in Patients With Recurrent Glioblastoma Harboring Phosphatidylinositol 3-Kinase Pathway Activation: An Open-Label, Multicenter, Multi-Arm, Phase II Trial., Patrick Y Wen, Mehdi Touat, Brian M Alexander, Ingo K Mellinghoff, Shakti Ramkissoon, Christine S McCluskey, Kristine Pelton, Sam Haidar, Sankha S Basu, Sarah C Gaffey, Loreal E Brown, Juan Emmanuel Martinez-Ledesma, Shaofang Wu, Jungwoo Kim, Wei Wei, Mi-Ae Park, Jason T Huse, John G Kuhn, Mikael L Rinne, Howard Colman, Nathalie Y R Agar, Antonio M Omuro, Lisa M DeAngelis, Mark R Gilbert, John F de Groot, Timothy F Cloughesy, Andrew S Chi, Thomas M Roberts, Jean J Zhao, Eudocia Q Lee, Lakshmi Nayak, James R Heath, Laura L Horky, Tracy T Batchelor, Rameen Beroukhim, Susan M Chang, Azra H Ligon, Ian F Dunn, Dimpy Koul, Geoffrey S Young, Michael D Prados, David A Reardon, W K Alfred Yung, and Keith L Ligon

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Blood metabolome predicts gut microbiome α-diversity in humans., Tomasz Wilmanski, Noa Rappaport, John C Earls, Andrew T Magis, Ohad Manor, Jennifer Lovejoy, Gilbert S Omenn, Leroy Hood, Sean M Gibbons, and Nathan D Price

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Proximate grassland and shrub-encroached sites show dramatic restructuring of soil bacterial communities., Xingjia Xiang, Sean M Gibbons, He Li, Haihua Shen, and Haiyan Chu

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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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Blood Is a Window into Health and Disease., James T Yurkovich and Leroy Hood

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A systems approach to clinical oncology uses deep phenotyping to deliver personalized care., James T Yurkovich, Qiang Tian, Nathan D Price, and Leroy Hood

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EcoFABs: advancing microbiome science through standardized fabricated ecosystems., Karsten Zengler, Kirsten Hofmockel, Nitin Baliga, Scott W Behie, Hans C Bernstein, James B Brown, José R Dinneny, Sheri A Floge, Samuel P Forry, Matthias Hess, Scott A Jackson, Christer Jansson, Stephen R Lindemann, Jennifer Pett-Ridge, Costas Maranas, Ophelia S Venturelli, Matthew D Wallenstein, Elizabeth A Shank, and Trent R Northen

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Survivin is a prognostic marker and therapeutic target for extranodal, nasal-type natural killer/T cell lymphoma., Li Zhang, Yi Wei, Xiaowei Yan, Na Li, Haolan Song, Li Yang, Yang Wu, Yu-Feng Xi, Hua-Wei Weng, Jian-Hua Li, Edward H Lin, and Li-Qun Zou

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Adaptive Evolution within Gut Microbiomes of Healthy People., Shijie Zhao, Tami D Lieberman, Mathilde Poyet, Kathryn M Kauffman, Sean M Gibbons, Mathieu Groussin, Ramnik J Xavier, and Eric J Alm

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Evaluation of Stein-O'Brien et al.: To See a World in a Grain of Sand-How to Reveal a Common Latent Space through Multiple Platform Omics Data., Joseph X Zhou

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Development of Hematopoietic Stem Cell-Engineered Invariant Natural Killer T Cell Therapy for Cancer., Yanni Zhu, Drake J Smith, Yang Zhou, Yan-Ruide Li, Jiaji Yu, Derek Lee, Yu-Chen Wang, Stefano Di Biase, Xi Wang, Christian Hardoy, Josh Ku, Tasha Tsao, Levina J Lin, Alexander T Pham, Heesung Moon, Jami McLaughlin, Donghui Cheng, Roger P Hollis, Beatriz Campo-Fernandez, Fabrizia Urbinati, Liu Wei, Larry Pang, Valerie Rezek, Beata Berent-Maoz, Mignonette H Macabali, David Gjertson, Xiaoyan Wang, Zoran Galic, Scott G Kitchen, Dong Sung An, Siwen Hu-Lieskovan, Paula J Kaplan-Lefko, Satiro N De Oliveira, Christopher S Seet, Sarah M Larson, Stephen J Forman, James R Heath, Jerome A Zack, Gay M Crooks, Caius G Radu, Antoni Ribas, Donald B Kohn, Owen N Witte, and Lili Yang

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Genetic Predisposition Impacts Clinical Changes in a Lifestyle Coaching Program., Niha Zubair, Matthew P Conomos, Leroy Hood, Gilbert S Omenn, Nathan D Price, Bonnie J Spring, Andrew T Magis, and Jennifer C Lovejoy

Submissions from 2018

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Cell death as a trigger for morphogenesis., Boris Aguilar, Ahmadreza Ghaffarizadeh, Christopher D Johnson, Gregory J Podgorski, Ilya Shmulevich, and Nicholas S Flann

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Divergent brain gene expression patterns associate with distinct cell-specific tau neuropathology traits in progressive supranuclear palsy., Mariet Allen, Xue Wang, Daniel J Serie, Samantha L Strickland, Jeremy D Burgess, Shunsuke Koga, Curtis S Younkin, Thuy T Nguyen, Kimberly G Malphrus, Sarah J Lincoln, Melissa Alamprese, Kuixi Zhu, Rui Chang, Minerva M Carrasquillo, Naomi Kouri, Melissa E Murray, Joseph S Reddy, Cory Funk, Nathan D Price, Todd E Golde, Steven G Younkin, Yan W Asmann, Julia E Crook, Dennis W Dickson, and Nilüfer Ertekin-Taner

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Transcriptional regulatory networks underlying gene expression changes in Huntington's disease., Seth A Ament, Jocelynn R Pearl, Jeffrey P Cantle, Robert M Bragg, Peter J Skene, Sydney R Coffey, Dani E Bergey, Vanessa C Wheeler, Marcy E MacDonald, Nitin S Baliga, Jim Rosinski, Leroy E Hood, Jeffrey B Carroll, and Nathan D Price

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The Micronemal, Silvia A Arredondo, Kristian E Swearingen, Thomas Martinson, Ryan Steel, Dorender A Dankwa, Anke Harupa, Nelly Camargo, William Betz, Vladimir Vigdorovich, Brian G Oliver, Niwat Kangwanrangsan, Tomoko Ishino, Noah Sather, Sebastian Mikolajczak, Ashley M Vaughan, Motomi Torii, Robert L Moritz, and Stefan H I Kappe

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Efficient region-based test strategy uncovers genetic risk factors for functional outcome in bipolar disorder., Monika Budde, Stefanie Friedrichs, Ney Alliey-Rodriguez, Seth Ament, Judith A Badner, Wade H Berrettini, Cinnamon S Bloss, William Byerley, Sven Cichon, Ashley L Comes, William Coryell, David W Craig, Franziska Degenhardt, Howard J Edenberg, Tatiana Foroud, Andreas J Forstner, Josef Frank, Elliot S Gershon, Fernando S Goes, Tiffany A Greenwood, Yiran Guo, Maria Hipolito, Leroy Hood, Brendan J Keating, Daniel L Koller, William B Lawson, Chunyu Liu, Pamela B Mahon, Melvin G McInnis, Francis J McMahon, Sandra M Meier, Thomas W Mühleisen, Sarah S Murray, Caroline M Nievergelt, John I Nurnberger, Evaristus A Nwulia, James B Potash, Danjuma Quarless, John Rice, Jared C Roach, William A Scheftner, Nicholas J Schork, Tatyana Shekhtman, Paul D Shilling, Erin N Smith, Fabian Streit, Jana Strohmaier, Szabolcs Szelinger, Jens Treutlein, Stephanie H Witt, Peter P Zandi, Peng Zhang, Sebastian Zöllner, Heike Bickeböller, Peter G Falkai, John R Kelsoe, Markus M Nöthen, Marcella Rietschel, Thomas G Schulze, and Dörthe Malzahn

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Simultaneous vs. sequential treatment for smoking and weight management in tobacco quitlines: 6 and 12 month outcomes from a randomized trial., Terry Bush, Jennifer Lovejoy, Harold Javitz, Alula Jimenez Torres, Ken Wassum, Marcia M Tan, and Bonnie Spring

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Niche emergence as an autocatalytic process in the evolution of ecosystems., Roberto Cazzolla Gatti, Brian Fath, Wim Hordijk, Stuart Kauffman, and Robert Ulanowicz

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TLR5 decoy receptor as a novel anti-amyloid therapeutic for Alzheimer's disease., Paramita Chakrabarty, Andrew Li, Thomas B Ladd, Michael R Strickland, Emily J Koller, Jeremy D Burgess, Cory C Funk, Pedro E Cruz, Mariet Allen, Mariya Yaroshenko, Xue Wang, Curtis Younkin, Joseph Reddy, Benjamin Lohrer, Leonie Mehrke, Brenda D Moore, Xuefei Liu, Carolina Ceballos-Diaz, Awilda M Rosario, Christopher Medway, Christopher Janus, Hong-Dong Li, Dennis W Dickson, Benoit I Giasson, Nathan D Price, Steven G Younkin, Nilüfer Ertekin-Taner, and Todd E Golde

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Chemotherapy-generated cell debris stimulates colon carcinoma tumor growth via osteopontin., Jaimie Chang, Swati S Bhasin, Diane R Bielenberg, Vikas P Sukhatme, Manoj Bhasin, Sui Huang, Mark W Kieran, and Dipak Panigrahy

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Targeting Mcl-1 enhances DNA replication stress sensitivity to cancer therapy., Guo Chen, Andrew T Magis, Ke Xu, Dongkyoo Park, David S Yu, Taofeek K Owonikoko, Gabriel L Sica, Sarah W Satola, Suresh S Ramalingam, Walter J Curran, Paul W Doetsch, and Xingming Deng

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Genome-wide pleiotropy analysis of neuropathological traits related to Alzheimer's disease., Jaeyoon Chung, Xiaoling Zhang, Mariet Allen, Xue Wang, Yiyi Ma, Gary Beecham, Thomas J Montine, Steven G Younkin, Dennis W Dickson, Todd E Golde, Nathan D Price, Nilüfer Ertekin-Taner, Kathryn L Lunetta, Jesse Mez, Richard Mayeux, Jonathan L Haines, Margaret A Pericak-Vance, Gerard Schellenberg, Gyungah R Jun, and Lindsay A Farrer

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Criticality Distinguishes the Ensemble of Biological Regulatory Networks., Bryan C Daniels, Hyunju Kim, Douglas Moore, Siyu Zhou, Harrison B Smith, Bradley Karas, Stuart A Kauffman, and Sara I Walker

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The Cytoscape Automation app article collection., Barry Demchak, David Otasek, Alexander R Pico, Gary D Bader, Keiichiro Ono, Brett Settle, Eric Sage, John H Morris, William Longabaugh, Christian Lopes, Michael Kucera, Adam Treister, Benno Schwikowski, Piet Molenaar, and Trey Ideker

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Expanding the Use of Spectral Libraries in Proteomics., Eric W Deutsch, Yasset Perez-Riverol, Robert J Chalkley, Mathias Wilhelm, Stephen Tate, Timo Sachsenberg, Mathias Walzer, Lukas Käll, Bernard Delanghe, Sebastian Böcker, Emma L Schymanski, Paul Wilmes, Viktoria Dorfer, Bernhard Kuster, Pieter-Jan Volders, Nico Jehmlich, Johannes P C Vissers, Dennis W Wolan, Ana Y Wang, Luis Mendoza, Jim Shofstahl, Andrew W Dowsey, Johannes Griss, Reza M Salek, Steffen Neumann, Pierre-Alain Binz, Henry Lam, Juan Antonio Vizcaíno, Nuno Bandeira, and Hannes Röst

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Digitizing omics profiles by divergence from a baseline., Wikum Dinalankara, Qian Ke, Yiran Xu, Lanlan Ji, Nicole Pagane, Anching Lien, Tejasvi Matam, Elana J Fertig, Nathan D Price, Laurent Younes, Luigi Marchionni, and Donald Geman

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In vitro characterization of alkylaminophenols-induced cell death., Phuong Doan, Olga Anufrieva, Olli Yli-Harja, and Meenakshisundaram Kandhavelu

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Single cell analyses demonstrate that a heme - GATA1 feedback loop regulates red cell differentiation., Raymond T Doty, Xiaowei Yan, Christopher Lausted, Adam D Munday, Zhantao Yang, Danielle Yi, Neda Jabbari, Li Liu, Siobán B Keel, Qiang Tian, and Janis L Abkowitz

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Preparation of Small RNA NGS Libraries from Biofluids., Alton Etheridge, Kai Wang, David Baxter, and David Galas

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Extracellular vesicle RNAs reflect placenta dysfunction and are a biomarker source for preterm labour., Shannon Fallen, David Baxter, Xiaogang Wu, Taek-Kyun Kim, Oksana Shynlova, Min Young Lee, Kelsey Scherler, Stephen Lye, Leroy Hood, and Kai Wang

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The BCGΔBCG1419c Vaccine Candidate Reduces Lung Pathology, IL-6, TNF-α, and IL-10 During Chronic TB Infection., Mario A Flores-Valdez, César Pedroza-Roldán, Michel de Jesús Aceves-Sánchez, Eliza J R Peterson, Nitin S Baliga, Rogelio Hernández-Pando, JoLynn Troudt, Elizabeth Creissen, Linda Izzo, Helle Bielefeldt-Ohmann, Thomas Bickett, and Angelo A Izzo

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Constraint-based modelling captures the metabolic versatility of Desulfovibrio vulgaris., Jason J Flowers, Matthew A Richards, Nitin Baliga, Birte Meyer, and David A Stahl

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Genome-wide Profiling of Urinary Extracellular Vesicle microRNAs Associated With Diabetic Nephropathy in Type 1 Diabetes., Vikas Ghai, Xiaogang Wu, Anjalei Bheda-Malge, Christos P Argyropoulos, José F Bernardo, Trevor Orchard, David Galas, and Kai Wang

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Droplet Digital PCR for Absolute Quantification of Extracellular MicroRNAs in Plasma and Serum: Quantification of the Cancer Biomarker hsa-miR-141., Maria D Giraldez, John R Chevillet, and Muneesh Tewari

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Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling., Maria D Giraldez, Ryan M Spengler, Alton Etheridge, Paula M Godoy, Andrea J Barczak, Srimeenakshi Srinivasan, Peter L De Hoff, Kahraman Tanriverdi, Amanda Courtright, Shulin Lu, Joseph Khoory, Renee Rubio, David Baxter, Tom A P Driedonks, Henk P J Buermans, Esther N M Nolte-'t Hoen, Hui Jiang, Kai Wang, Ionita Ghiran, Yaoyu E Wang, Kendall Van Keuren-Jensen, Jane E Freedman, Prescott G Woodruff, Louise C Laurent, David J Erle, David J Galas, and Muneesh Tewari

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Author Correction: Parent-of-origin-specific signatures of de novo mutations., Jakob M Goldmann, Wendy S W Wong, Michele Pinelli, Terry Farrah, Dale Bodian, Anna B Stittrich, Gustavo Glusman, Lisenka E L M Vissers, Alexander Hoischen, Jared C Roach, Joseph G Vockley, Joris A Veltman, Benjamin D Solomon, Christian Gilissen, and John E Niederhuber

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RAD54 N-terminal domain is a DNA sensor that couples ATP hydrolysis with branch migration of Holliday junctions., Nadish Goyal, Matthew J Rossi, Olga M Mazina, Yong Chi, Robert L Moritz, Bruce E Clurman, and Alexander V Mazin

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Loss of inter-cellular cooperation by complete epithelial-mesenchymal transition supports favorable outcomes in basal breast cancer patients., Anne Grosse-Wilde, Rolf E Kuestner, Stephanie M Skelton, Ellie MacIntosh, Aymeric Fouquier d'Hérouël, Gökhan Ertaylan, Antonio Del Sol, Alexander Skupin, and Sui Huang

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A rare loss-of-function variant of ADAM17 is associated with late-onset familial Alzheimer disease., Daniela Hartl, Patrick May, Wei Gu, Manuel Mayhaus, Sabrina Pichler, Christian Spaniol, Enrico Glaab, Dheeraj Reddy Bobbili, Paul Antony, Sandra Koegelsberger, Alexander Kurz, Timo Grimmer, Kevin Morgan, Badri N Vardarajan, Christiane Reitz, John Hardy, Jose Bras, Rita Guerreiro, Rudi Balling, Jochen G Schneider, and Matthias Riemenschneider

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Integrative Molecular Characterization of Malignant Pleural Mesothelioma., Julija Hmeljak, Francisco Sanchez-Vega, Katherine A Hoadley, Juliann Shih, Chip Stewart, David Heiman, Patrick Tarpey, Ludmila Danilova, Esther Drill, Ewan A Gibb, Reanne Bowlby, Rupa Kanchi, Hatice U Osmanbeyoglu, Yoshitaka Sekido, Jumpei Takeshita, Yulia Newton, Kiley Graim, Manaswi Gupta, Carl M Gay, Lixia Diao, David L Gibbs, Vesteinn Thorsson, Lisa Iype, Havish Kantheti, David T Severson, Gloria Ravegnini, Patrice Desmeules, Achim A Jungbluth, William D Travis, Sanja Dacic, Lucian R Chirieac, Françoise Galateau-Sallé, Junya Fujimoto, Aliya N Husain, Henrique C Silveira, Valerie W Rusch, Robert C Rintoul, Harvey Pass, Hedy Kindler, Marjorie G Zauderer, David J Kwiatkowski, Raphael Bueno, Anne S Tsao, Jenette Creaney, Tara Lichtenberg, Kristen Leraas, Jay Bowen, Ina Felau, Jean Claude Zenklusen, Rehan Akbani, Andrew D Cherniack, Lauren A Byers, Michael S Noble, Jonathan A Fletcher, A Gordon Robertson, Ronglai Shen, Hiroyuki Aburatani, Bruce W Robinson, Peter Campbell, and Marc Ladanyi

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Involvement in surface antigen expression by a moonlighting FG-repeat nucleoporin in trypanosomes., Jennifer M Holden, Ludek Koreny, Samson Obado, Alexander V Ratushny, Wei-Ming Chen, Jean-Mathieu Bart, Miguel Navarro, Brian T Chait, John D Aitchison, Michael P Rout, and Mark C Field

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Lessons Learned as President of the Institute for Systems Biology (2000-2018)., Leroy E Hood

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StPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline., Michael R Hoopmann, Jason M Winget, Luis Mendoza, and Robert L Moritz

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Author Correction: A population-specific reference panel empowers genetic studies of Anabaptist populations., Liping Hou, Rachel L Kember, Jared C Roach, Jeffrey R O'Connell, David W Craig, Maja Bucan, William K Scott, Margaret Pericak-Vance, Jonathan L Haines, Michael H Crawford, Alan R Shuldiner, and Francis J McMahon

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Whole genome sequence and comparative analysis of Borrelia burgdorferi MM1., Neda Jabbari, Gustavo Glusman, Lena M Joesch-Cohen, Panga Jaipal Reddy, Robert L Moritz, Leroy Hood, and Christopher G Lausted

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Systematic Analysis of Splice-Site-Creating Mutations in Cancer., Reyka G Jayasinghe, Song Cao, Qingsong Gao, Michael C Wendl, Nam Sy Vo, Sheila M Reynolds, Yanyan Zhao, Héctor Climente-González, Shengjie Chai, Fang Wang, Rajees Varghese, Mo Huang, Wen-Wei Liang, Matthew A Wyczalkowski, Sohini Sengupta, Zhi Li, Samuel H Payne, David Fenyö, Jeffrey H Miner, Matthew J Walter, Benjamin Vincent, Eduardo Eyras, Ken Chen, Ilya Shmulevich, Feng Chen, and Li Ding

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Novel metrics for quantifying bacterial genome composition skews., Lena M Joesch-Cohen, Max Robinson, Neda Jabbari, Christopher G Lausted, and Gustavo Glusman

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Determining Relative Dynamic Stability of Cell States Using Boolean Network Model., Jae Il Joo, Joseph X Zhou, Sui Huang, and Kwang-Hyun Cho

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An RNAi screen in human cell lines reveals conserved DNA damage repair pathways that mitigate formaldehyde sensitivity., Eleonora Juarez, Nyasha Chambwe, Weiliang Tang, Asia D Mitchell, Nichole Owen, Anuradha Kumari, Raymond J Monnat, and Amanda K McCullough

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Emergence of diversity in homogeneous coupled Boolean networks., Chris Kang, Boris Aguilar, and Ilya Shmulevich