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 2019

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

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

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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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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

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

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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

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The building blocks of successful translation of proteomics to the clinic., Paul Kearney, J Jay Boniface, Nathan D Price, and Leroy Hood

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Serum lipidomic analysis for the discovery of biomarkers for major depressive disorder in drug-free patients., Eun Young Kim, Jae Won Lee, Min Young Lee, Se Hyun Kim, Hyuck Jun Mok, Kyooseob Ha, Yong Min Ahn, and Kwang Pyo Kim

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Integrative structure and functional anatomy of a nuclear pore complex., Seung Joong Kim, Javier Fernandez-Martinez, Ilona Nudelman, Yi Shi, Wenzhu Zhang, Barak Raveh, Thurston Herricks, Brian D Slaughter, Joanna A Hogan, Paula Upla, Ilan E Chemmama, Riccardo Pellarin, Ignacia Echeverria, Manjunatha Shivaraju, Azraa S Chaudhury, Junjie Wang, Rosemary Williams, Jay R Unruh, Charles H Greenberg, Erica Y Jacobs, Zhiheng Yu, M Jason de la Cruz, Roxana Mironska, David L Stokes, John D Aitchison, Martin F Jarrold, Jennifer L Gerton, Steven J Ludtke, Christopher W Akey, Brian T Chait, Andrej Sali, and Michael P Rout

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Molecular structure of promoter-bound yeast TFIID., Olga Kolesnikova, Adam Ben-Shem, Jie Luo, Jeff Ranish, Patrick Schultz, and Gabor Papai

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Selected reaction monitoring mass spectrometry of mastitis milk reveals pathogen-specific regulation of bovine host response proteins., Ulrike Kusebauch, Lorenzo E Hernández-Castellano, Stine L Bislev, Robert L Moritz, Christine M Røntved, and Emøke Bendixen

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ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data., Joon-Yong Lee, Hyungwon Choi, Christopher M Colangelo, Darryl Davis, Michael R Hoopmann, Lukas Käll, Henry Lam, Samuel H Payne, Yasset Perez-Riverol, Matthew The, Ryan Wilson, Susan T Weintraub, and Magnus Palmblad

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Reply to "Precision medicine in the clouds"., Andrew T Magis, John C Earls, Gustavo Glusman, Gilbert S Omenn, Jennifer C Lovejoy, Nathan D Price, and Leroy Hood

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The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals., Frank Maixner, Dmitrij Turaev, Amaury Cazenave-Gassiot, Marek Janko, Ben Krause-Kyora, Michael R Hoopmann, Ulrike Kusebauch, Mark Sartain, Gea Guerriero, Niall O'Sullivan, Matthew Teasdale, Giovanna Cipollini, Alice Paladin, Valeria Mattiangeli, Marco Samadelli, Umberto Tecchiati, Andreas Putzer, Mine Palazoglu, John Meissen, Sandra Lösch, Philipp Rausch, John F Baines, Bum Jin Kim, Hyun-Joo An, Paul Gostner, Eduard Egarter-Vigl, Peter Malfertheiner, Andreas Keller, Robert W Stark, Markus Wenk, David Bishop, Daniel G Bradley, Oliver Fiehn, Lars Engstrand, Robert L Moritz, Philip Doble, Andre Franke, Almut Nebel, Klaus Oeggl, Thomas Rattei, Rudolf Grimm, and Albert Zink

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mRNA transcript distribution bias between Borrelia burgdorferi bacteria and their outer membrane vesicles., Anjali Malge, Vikas Ghai, Panga Jaipal Reddy, David Baxter, Taek-Kyun Kim, Robert L Moritz, and Kai Wang

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A Multi-omic Association Study of Trimethylamine N-Oxide., Ohad Manor, Niha Zubair, Matthew P Conomos, Xiaojing Xu, Jesse E Rohwer, Cynthia E Krafft, Jennifer C Lovejoy, and Andrew T Magis

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Anticancer activity study of A, Gabriella Marucci, Claudia Santinelli, Michela Buccioni, Aleix Martí Navia, Catia Lambertucci, Anastasia Zhurina, Olli Yli-Harja, Rosaria Volpini, and Meenakshisundaram Kandhavelu

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Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes., Nazar Mashtalir, Andrew R D'Avino, Brittany C Michel, Jie Luo, Joshua Pan, Jordan E Otto, Hayley J Zullow, Zachary M McKenzie, Rachel L Kubiak, Roodolph St Pierre, Alfredo M Valencia, Steven J Poynter, Seth H Cassel, Jeffrey A Ranish, and Cigall Kadoch

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Characterization of Peroxisomal Regulation Networks., Fred D Mast and John D Aitchison

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ESCRT-III is required for scissioning new peroxisomes from the endoplasmic reticulum., Fred D Mast, Thurston Herricks, Kathleen M Strehler, Leslie R Miller, Ramsey A Saleem, Richard A Rachubinski, and John D Aitchison

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Analysis and visualization of linked molecular and clinical cancer data by using Oncoscape., Lisa G McFerrin, Michael Zager, Jianan Zhang, Gretchen Krenn, Robert McDermott, Desert Horse-Grant, Emily Silgard, Kara Colevas, Paul Shannon, Hamid Bolouri, and Eric C Holland

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The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data., Gerben Menschaert, Xiaojing Wang, Andrew R Jones, Fawaz Ghali, David Fenyö, Volodimir Olexiouk, Bing Zhang, Eric W Deutsch, Tobias Ternent, and Juan Antonio Vizcaíno

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Targeting TWIST1 through loss of function inhibits tumorigenicity of human glioblastoma., Andrei M Mikheev, Svetlana A Mikheeva, Liza J Severs, Cory C Funk, Lei Huang, José L McFaline-Figueroa, Jeanette Schwensen, Cole Trapnell, Nathan D Price, Stephen Wong, and Robert C Rostomily

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Simulation Study of cDNA Dataset to Investigate Possible Association of Differentially Expressed Genes of Human THP1-Monocytic Cells in Cancer Progression Affected by Bacterial Shiga Toxins., Syed A Muhammad, Jinlei Guo, Thanh M Nguyen, Xiaogang Wu, Baogang Bai, X Frank Yang, and Jake Y Chen

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Increased levels of RECQ5 shift DNA repair from canonical to alternative pathways., Henry C Olson, Luther Davis, Kostantin Kiianitsa, Kevin J Khoo, Yilun Liu, Theo A Knijnenburg, and Nancy Maizels

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Systems biology approaches towards predictive microbial ecology., Anne E Otwell, Adrián López García de Lomana, Sean M Gibbons, Mónica V Orellana, and Nitin S Baliga

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Transcription Activation Domains of the Yeast Factors Met4 and Ino2: Tandem Activation Domains with Properties Similar to the Yeast Gcn4 Activator., Derek Pacheco, Linda Warfield, Michelle Brajcich, Hannah Robbins, Jie Luo, Jeff Ranish, and Steven Hahn

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Temporal Transcriptomic Analysis of Metabolic Genes in Maternal Organs and Placenta During Murine Pregnancy., Alison Paquette, Priyanka Baloni, Anisa Holloman, Sanjay Nigam, Theo Bammler, Qingcheng Mao, and Nathan D Price

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Distinct communication patterns of trophoblastic miRNA among the maternal-placental-fetal compartments., Alison G Paquette, Tianjiao Chu, Xiaogang Wu, Kai Wang, Nathan D Price, and Yoel Sadovsky

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Comparative analysis of gene expression in maternal peripheral blood and monocytes during spontaneous preterm labor., Alison G Paquette, Oksana Shynlova, Mark Kibschull, Nathan D Price, and Stephen J Lye

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Reply., Alison Paquette, Nathan D Price, and Stephen J Lye

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Structure of human TFIID and mechanism of TBP loading onto promoter DNA., Avinash B Patel, Robert K Louder, Basil J Greber, Sebastian Grünberg, Jie Luo, Jie Fang, Yutong Liu, Jeff Ranish, Steve Hahn, and Eva Nogales

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Editorial overview: Systems biology: Data, discovery, delivery., Nathan D Price and Eran Segal

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Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations., Wei Qin, Shady A Amin, Rachel A Lundeen, Katherine R Heal, Willm Martens-Habbena, Serdar Turkarslan, Hidetoshi Urakawa, Kyle C Costa, Erik L Hendrickson, Tony Wang, David Ac Beck, Sonia M Tiquia-Arashiro, Fred Taub, Andrew D Holmes, Neeraja Vajrala, Paul M Berube, Todd M Lowe, James W Moffett, Allan H Devol, Nitin S Baliga, Daniel J Arp, Luis A Sayavedra-Soto, Murray Hackett, E Virginia Armbrust, Anitra E Ingalls, and David A Stahl

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The Integrated Genomic Landscape of Thymic Epithelial Tumors., Milan Radovich, Curtis R Pickering, Ina Felau, Gavin Ha, Hailei Zhang, Heejoon Jo, Katherine A Hoadley, Pavana Anur, Jiexin Zhang, Mike McLellan, Reanne Bowlby, Thomas Matthew, Ludmila Danilova, Apurva M Hegde, Jaegil Kim, Mark D M Leiserson, Geetika Sethi, Charles Lu, Michael Ryan, Xiaoping Su, Andrew D Cherniack, Gordon Robertson, Rehan Akbani, Paul Spellman, John N Weinstein, D Neil Hayes, Ben Raphael, Tara Lichtenberg, Kristen Leraas, Jean Claude Zenklusen, Junya Fujimoto, Cristovam Scapulatempo-Neto, Andre L Moreira, David Hwang, James Huang, Mirella Marino, Robert Korst, Giuseppe Giaccone, Yesim Gokmen-Polar, Sunil Badve, Arun Rajan, Philipp Ströbel, Nicolas Girard, Ming S Tsao, Alexander Marx, Anne S Tsao, and Patrick J Loehrer

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Multiscale Analysis of Independent Alzheimer's Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus., Ben Readhead, Jean-Vianney Haure-Mirande, Cory C Funk, Matthew A Richards, Paul Shannon, Vahram Haroutunian, Mary Sano, Winnie S Liang, Noam D Beckmann, Nathan D Price, Eric M Reiman, Eric E Schadt, Michelle E Ehrlich, Sam Gandy, and Joel T Dudley

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Correction to: Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer's disease resilience., Perry G Ridge, Celeste M Karch, Simon Hsu, Ivan Arano, Craig C Teerlink, Mark T W Ebbert, Josue D Gonzalez Murcia, James M Farnham, Anna R Damato, Mariet Allen, Xue Wang, Oscar Harari, Victoria M Fernandez, Rita Guerreiro, Jose Bras, John Hardy, Ronald Munger, Maria Norton, Celeste Sassi, Andrew Singleton, Steven G Younkin, Dennis W Dickson, Todd E Golde, Nathan D Price, Nilüfer Ertekin-Taner, Carlos Cruchaga, Alison M Goate, Christopher Corcoran, JoAnn Tschanz, Lisa A Cannon-Albright, and John S K Kauwe

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Genotype Fingerprints Enable Fast and Private Comparison of Genetic Testing Results for Research and Direct-to-Consumer Applications., Max Robinson and Gustavo Glusman

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The Microbiome Stress Project: Toward a Global Meta-Analysis of Environmental Stressors and Their Effects on Microbial Communities., Jennifer D Rocca, Marie Simonin, Joanna R Blaszczak, Jessica G Ernakovich, Sean M Gibbons, Firas S Midani, and Alex D Washburne

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Extracellular vesicles in DLBCL provide abundant clues to aberrant transcriptional programming and genomic alterations., Sarah C Rutherford, Angela A Fachel, Sheng Li, Seema Sawh, Ashlesha Muley, Jennifer Ishii, Ashish Saxena, Pilar M Dominguez, Eloisi Caldas Lopes, Xabier Agirre, Nyasha Chambwe, Fabian Correa, Yanwen Jiang, Kristy L Richards, Doron Betel, and Rita Shaknovich

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Identification of novel GPR17-agonists by structural bioinformatics and signaling activation., Konda Mani Saravanan, Suresh Palanivel, Olli Yli-Harja, and Meenakshisundaram Kandhavelu

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Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas., Franz X Schaub, Varsha Dhankani, Ashton C Berger, Mihir Trivedi, Anne B Richardson, Reid Shaw, Wei Zhao, Xiaoyang Zhang, Andrea Ventura, Yuexin Liu, Donald E Ayer, Peter J Hurlin, Andrew D Cherniack, Robert N Eisenman, Brady Bernard, Carla Grandori, and Bernard Brady

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A tissue-based draft map of the murine MHC class I immunopeptidome., Heiko Schuster, Wenguang Shao, Tobias Weiss, Patrick G A Pedrioli, Patrick Roth, Michael Weller, David S Campbell, Eric W Deutsch, Robert L Moritz, Oliver Planz, Hans-Georg Rammensee, Ruedi Aebersold, and Etienne Caron

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Centromere protein F (CENPF), a microtubule binding protein, modulates cancer metabolism by regulating pyruvate kinase M2 phosphorylation signaling., Muhammad Shahid, Minyoung Lee, Honit Piplani, Allen M Andres, Bo Zhou, Austin Yeon, Minjung Kim, Hyung L Kim, and Jayoung Kim

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Menthol, a unique urinary volatile compound, is associated with chronic inflammation in interstitial cystitis., Muhammad Shahid, Min Young Lee, Austin Yeon, Eunho Cho, Vikram Sairam, Luis Valdiviez, Sungyong You, and Jayoung Kim

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A Chemical Approach for Profiling Intracellular AKT Signaling Dynamics from Single Cells., Shiqun Shao, Zhonghan Li, Hanjun Cheng, Siwen Wang, Nicole G Perkins, Priyanka Sarkar, Wei Wei, and Min Xue

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The SysteMHC Atlas project., Wenguang Shao, Patrick G A Pedrioli, Witold Wolski, Cristian Scurtescu, Emanuel Schmid, Juan A Vizcaíno, Mathieu Courcelles, Heiko Schuster, Daniel Kowalewski, Fabio Marino, Cecilia S L Arlehamn, Kerrie Vaughan, Bjoern Peters, Alessandro Sette, Tom H M Ottenhoff, Krista E Meijgaarden, Natalie Nieuwenhuizen, Stefan H E Kaufmann, Ralph Schlapbach, John C Castle, Alexey I Nesvizhskii, Morten Nielsen, Eric W Deutsch, David S Campbell, Robert L Moritz, Roman A Zubarev, Anders Jimmy Ytterberg, Anthony W Purcell, Miguel Marcilla, Alberto Paradela, Qi Wang, Catherine E Costello, Nicola Ternette, Peter A van Veelen, Cécile A C M van Els, Albert J R Heck, Gustavo A de Souza, Ludvig M Sollid, Arie Admon, Stefan Stevanovic, Hans-Georg Rammensee, Pierre Thibault, Claude Perreault, Michal Bassani-Sternberg, Ruedi Aebersold, and Etienne Caron

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Radical amino acid mutations persist longer in the absence of sex., Joel Sharbrough, Meagan Luse, Jeffrey L Boore, John M Logsdon, and Maurine Neiman

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Integrated Molecular Characterization of Testicular Germ Cell Tumors., Hui Shen, Juliann Shih, Daniel P Hollern, Linghua Wang, Reanne Bowlby, Satish K Tickoo, Vésteinn Thorsson, Andrew J Mungall, Yulia Newton, Apurva M Hegde, Joshua Armenia, Francisco Sánchez-Vega, John Pluta, Louise C Pyle, Rohit Mehra, Victor E Reuter, Guilherme Godoy, Jeffrey Jones, Carl S Shelley, Darren R Feldman, Daniel O Vidal, Davor Lessel, Tomislav Kulis, Flavio M Cárcano, Kristen M Leraas, Tara M Lichtenberg, Denise Brooks, Andrew D Cherniack, Juok Cho, David I Heiman, Katayoon Kasaian, Minwei Liu, Michael S Noble, Liu Xi, Hailei Zhang, Wanding Zhou, Jean C ZenKlusen, Carolyn M Hutter, Ina Felau, Jiashan Zhang, Nikolaus Schultz, Gad Getz, Matthew Meyerson, Joshua M Stuart, Rehan Akbani, David A Wheeler, Peter W Laird, Katherine L Nathanson, Victoria K Cortessis, and Katherine A Hoadley

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Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding., Leah V Sibener, Ricardo A Fernandes, Elizabeth M Kolawole, Catherine B Carbone, Fan Liu, Darren McAffee, Michael E Birnbaum, Xinbo Yang, Laura F Su, Wong Yu, Shen Dong, Marvin H Gee, Kevin M Jude, Mark M Davis, Jay T Groves, William A Goddard, James R Heath, Brian D Evavold, Ronald D Vale, and K Christopher Garcia

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Robust determination of differential abundance in shotgun proteomics using nonparametric statistics., Patrick Slama, Michael R Hoopmann, Robert L Moritz, and Donald Geman

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Lineage marker synchrony in hematopoietic genealogies refutes the PU.1/GATA1 toggle switch paradigm., Michael K Strasser, Philipp S Hoppe, Dirk Loeffler, Konstantinos D Kokkaliaris, Timm Schroeder, Fabian J Theis, and Carsten Marr

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Plasmodium Parasites Viewed through Proteomics., Kristian E Swearingen and Scott E Lindner

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Regulation of Pathogenic T Helper 17 Cell Differentiation by Steroid Receptor Coactivator-3., Kentaro Tanaka, Gustavo J Martinez, Xiaowei Yan, Weiwen Long, Kenji Ichiyama, Xinxin Chi, Byung-Seok Kim, Joseph M Reynolds, Yeonseok Chung, Shinya Tanaka, Lan Liao, Yoichi Nakanishi, Akihiko Yoshimura, Pan Zheng, Xiaohu Wang, Qiang Tian, Jianming Xu, Bert W O'Malley, and Chen Dong

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Regulation of Pathogenic T Helper 17 Cell Differentiation by Steroid Receptor Coactivator-3., Kentaro Tanaka, Gustavo J Martinez, Xiaowei Yan, Weiwen Long, Kenji Ichiyama, Xinxin Chi, Byung-Seok Kim, Joseph M Reynolds, Yeonseok Chung, Shinya Tanaka, Lan Liao, Yoichi Nakanishi, Akihiko Yoshimura, Pan Zheng, Xiaohu Wang, Qiang Tian, Jianming Xu, Bert W O'Malley, and Chen Dong

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Anatomic Study of Nutrient Foramina of Posterior Axis with Application to C2 Pedicle Screw Placement., Tamir Tawfik, Joe Iwanaga, Emre Yilmaz, Paul Choi, Charlotte Wilson, Emily Simonds, Jared J Marks, Haynes L Harkey, Rod J Oskouian, and R Shane Tubbs

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Taking Systems Medicine to Heart., Kalliopi Trachana, Rhishikesh Bargaje, Gustavo Glusman, Nathan D Price, Sui Huang, and Leroy E Hood

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Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex., Lisa M Tuttle, Derek Pacheco, Linda Warfield, Jie Luo, Jeff Ranish, Steven Hahn, and Rachel E Klevit