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

Submissions from 2019

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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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 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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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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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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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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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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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 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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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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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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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