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 2018

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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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Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project., Gilbert S Omenn, Lydie Lane, Christopher M Overall, Fernando J Corrales, Jochen M Schwenk, Young-Ki Paik, Jennifer E Van Eyk, Siqi Liu, Michael Snyder, Mark S Baker, and Eric W Deutsch

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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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Toward Completion of the Human Proteome Parts List: Progress Uncovering Proteins That Are Missing or Have Unknown Function and Developing Analytical Methods., Young-Ki Paik, Christopher M Overall, Fernando Corrales, Eric W Deutsch, Lydie Lane, and Gilbert S Omenn

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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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Comparative transcriptomic analysis of human placentae at term and preterm delivery., Alison G Paquette, Heather M Brockway, Nathan D Price, and Louis J Muglia

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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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A Protein Standard That Emulates Homology for the Characterization of Protein Inference Algorithms., Matthew The, Fredrik Edfors, Yasset Perez-Riverol, Samuel H Payne, Michael R Hoopmann, Magnus Palmblad, Björn Forsström, and Lukas Käll

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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

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Ocean acidification conditions increase resilience of marine diatoms., Jacob J Valenzuela, Adrián López García de Lomana, Allison Lee, E V Armbrust, Mónica V Orellana, and Nitin S Baliga

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Decane-1,2-diol derivatives as potential antitumor agents for the treatment of glioblastoma., Anisha Viswanathan, Anastasia Zhurina, Benedicta Assoah, Aleksi Paakkunainen, Aliyu Musa, Dinesh Kute, Konda Mani Saravanan, Olli Yli-Harja, Nuno R Candeias, and Meenakshisundaram Kandhavelu

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High-speed Raman-encoded molecular imaging of freshly excised tissue surfaces with topically applied SERRS nanoparticles., Yu Winston Wang, Qian Yang, Soyoung Kang, Matthew A Wall, and Jonathan T C Liu

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Integrated measurement of intracellular proteins and transcripts in single cells., Alexander M Xu, Qianhe Liu, Kaitlyn L Takata, Sarah Jeoung, Yapeng Su, Igor Antoshechkin, Sisi Chen, Matthew Thomson, and James R Heath

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Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes., Zhuyi Xue, René L Warren, Ewan A Gibb, Daniel MacMillan, Johnathan Wong, Readman Chiu, S Austin Hammond, Chen Yang, Ka Ming Nip, Catherine A Ennis, Abigail Hahn, Sheila Reynolds, and Inanc Birol

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Habitual sleep duration and sleep duration variation are independently associated with body mass index., X Xu, M P Conomos, O Manor, J E Rohwer, A T Magis, and J C Lovejoy

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S2 Alar-Iliac Screw Insertion: Technical Note with Pictorial Guide., Emre Yilmaz, Amir Abdul-Jabbar, Tamir Tawfik, Joe Iwanaga, Cameron K Schmidt, Jens R Chapman, Ronen Blecher, R Shane Tubbs, and Rod J Oskouian

Submissions from 2017

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New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins., Susan Abbatiello, Bradley L Ackermann, Christoph Borchers, Ralph A Bradshaw, Steven A Carr, Robert Chalkley, Meena Choi, Eric Deutsch, Bruno Domon, Andrew N Hoofnagle, Hasmik Keshishian, Eric Kuhn, Daniel C Liebler, Michael MacCoss, Brendan MacLean, D R Mani, Hendrik Neubert, Derek Smith, Olga Vitek, and Lisa Zimmerman

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IFPA meeting 2016 workshop report I: Genomic communication, bioinformatics, trophoblast biology and transport systems., Christiane Albrecht, Julie C Baker, Cassidy Blundell, Shawn L Chavez, Lucia Carbone, Larry Chamley, Roberta L Hannibal, Nick Illsley, Peter Kurre, Louise C Laurent, Charles McKenzie, Diana Morales-Prieto, Priyadarshini Pantham, Alison Paquette, Katie Powell, Nathan Price, Balaji M Rao, Yoel Sadovsky, Carlos Salomon, Geetu Tuteja, Samantha Wilson, and P F O'Tierney-Ginn

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High resolution time-course mapping of early transcriptomic, molecular and cellular phenotypes in Huntington's disease CAG knock-in mice across multiple genetic backgrounds., Seth A Ament, Jocelynn R Pearl, Andrea Grindeland, Jason St Claire, John C Earls, Marina Kovalenko, Tammy Gillis, Jayalakshmi Mysore, James F Gusella, Jong-Min Lee, Seung Kwak, David Howland, Min Young Lee, David Baxter, Kelsey Scherler, Kai Wang, Donald Geman, Jeffrey B Carroll, Marcy E MacDonald, George Carlson, Vanessa C Wheeler, Nathan D Price, and Leroy Hood

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Identifying novel transcription factors involved in the inflammatory response by using binding site motif scanning in genomic regions defined by histone acetylation., Peter S Askovich, Stephen A Ramsey, Alan H Diercks, Kathleen A Kennedy, Theo A Knijnenburg, and Alan Aderem

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A computational study of VEGF production by patterned retinal epithelial cell colonies as a model for neovascular macular degeneration., Qanita Bani Baker, Gregory J Podgorski, Elizabeth Vargis, and Nicholas S Flann

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The State of Systems Genetics in 2017., Nitin S Baliga, Johan L M Björkegren, Jef D Boeke, Michael Boutros, Nigel P S Crawford, Aimée M Dudley, Charles R Farber, Allan Jones, Allan I Levey, Aldons J Lusis, H Craig Mak, Joseph H Nadeau, Marcus B Noyes, Enrico Petretto, Nicholas T Seyfried, Lars M Steinmetz, and Sibylle C Vonesch

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Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells., Rhishikesh Bargaje, Kalliopi Trachana, Martin N Shelton, Christopher S McGinnis, Joseph X Zhou, Cora Chadick, Savannah Cook, Christopher Cavanaugh, Sui Huang, and Leroy Hood

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Motivational, proteostatic and transcriptional deficits precede synapse loss, gliosis and neurodegeneration in the B6.Htt, Robert M Bragg, Sydney R Coffey, Rory M Weston, Seth A Ament, Jeffrey P Cantle, Shawn Minnig, Cory C Funk, Dominic D Shuttleworth, Emily L Woods, Bonnie R Sullivan, Lindsey Jones, Anne Glickenhaus, John S Anderson, Michael D Anderson, Stephen B Dunnett, Vanessa C Wheeler, Marcy E MacDonald, Simon P Brooks, Nathan D Price, and Jeffrey B Carroll

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Precision Oncology: Between Vaguely Right and Precisely Wrong., Amy Brock and Sui Huang

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Release of Cell-free MicroRNA Tumor Biomarkers into the Blood Circulation with Pulsed Focused Ultrasound: A Noninvasive, Anatomically Localized, Molecular Liquid Biopsy., John R Chevillet, Tatiana D Khokhlova, Maria D Giraldez, George R Schade, Frank Starr, Yak-Nam Wang, Emily N Gallichotte, Kai Wang, Joo Ha Hwang, and Muneesh Tewari

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ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS Experiments., Meena Choi, Zeynep F Eren-Dogu, Christopher Colangelo, John Cottrell, Michael R Hoopmann, Eugene A Kapp, Sangtae Kim, Henry Lam, Thomas A Neubert, Magnus Palmblad, Brett S Phinney, Susan T Weintraub, Brendan MacLean, and Olga Vitek

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Peripheral huntingtin silencing does not ameliorate central signs of disease in the B6.HttQ111/+ mouse model of Huntington's disease., Sydney R Coffey, Robert M Bragg, Shawn Minnig, Seth A Ament, Jeffrey P Cantle, Anne Glickenhaus, Daniel Shelnut, José M Carrillo, Dominic D Shuttleworth, Julie-Anne Rodier, Kimihiro Noguchi, C Frank Bennett, Nathan D Price, Holly B Kordasiewicz, and Jeffrey B Carroll

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Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry., Ben C Collins, Christie L Hunter, Yansheng Liu, Birgit Schilling, George Rosenberger, Samuel L Bader, Daniel W Chan, Bradford W Gibson, Anne-Claude Gingras, Jason M Held, Mio Hirayama-Kurogi, Guixue Hou, Christoph Krisp, Brett Larsen, Liang Lin, Siqi Liu, Mark P Molloy, Robert L Moritz, Sumio Ohtsuki, Ralph Schlapbach, Nathalie Selevsek, Stefani N Thomas, Shin-Cheng Tzeng, Hui Zhang, and Ruedi Aebersold

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Exosomal MicroRNA for Detection of Cardiac Sarcoidosis., Elliott D Crouser, Nabeel Y Hamzeh, Lisa A Maier, Mark W Julian, May Gillespie, Mohammad Rahman, David Baxter, Xiaogang Wu, S Patrick Nana-Sinkam, and Kai Wang

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An indicator cell assay for blood-based diagnostics., Samuel A Danziger, Leslie R Miller, Karanbir Singh, G Adam Whitney, Elaine R Peskind, Ge Li, Robert J Lipshutz, John D Aitchison, and Jennifer J Smith

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The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition., Eric W Deutsch, Attila Csordas, Zhi Sun, Andrew Jarnuczak, Yasset Perez-Riverol, Tobias Ternent, David S Campbell, Manuel Bernal-Llinares, Shujiro Okuda, Shin Kawano, Robert L Moritz, Jeremy J Carver, Mingxun Wang, Yasushi Ishihama, Nuno Bandeira, Henning Hermjakob, and Juan Antonio Vizcaíno

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Proteomics Standards Initiative: Fifteen Years of Progress and Future Work., Eric W Deutsch, Sandra Orchard, Pierre-Alain Binz, Wout Bittremieux, Martin Eisenacher, Henning Hermjakob, Shin Kawano, Henry Lam, Gerhard Mayer, Gerben Menschaert, Yasset Perez-Riverol, Reza M Salek, David L Tabb, Stefan Tenzer, Juan Antonio Vizcaíno, Mathias Walzer, and Andrew R Jones

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Effect of alkylaminophenols on growth inhibition and apoptosis of bone cancer cells., Phuong Doan, Tien Nguyen, Olli Yli-Harja, Nuno R Candeias, and Meenakshisundaram Kandhavelu

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Cancer immunotherapy: Opportunities and challenges in the rapidly evolving clinical landscape., Leisha A Emens, Paolo A Ascierto, Phillip K Darcy, Sandra Demaria, Alexander M M Eggermont, William L. Redmond, Barbara Seliger, and Francesco M Marincola

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Applying attractor dynamics to infer gene regulatory interactions involved in cellular differentiation., Ahmadreza Ghaffarizadeh, Gregory J Podgorski, and Nicholas S Flann

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A Cell-Surface Membrane Protein Signature for Glioblastoma., Dhimankrishna Ghosh, Cory C Funk, Juan Caballero, Nameeta Shah, Katherine Rouleau, John C Earls, Liliana Soroceanu, Greg Foltz, Charles Cobbs, Nathan D Price, and Leroy Hood

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Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle., David L Gibbs and Ilya Shmulevich

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Ultrafast Comparison of Personal Genomes via Precomputed Genome Fingerprints., Gustavo Glusman, Denise E Mauldin, Leroy E Hood, and Max Robinson

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Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework., Gustavo Glusman, Peter W Rose, Andreas Prlić, Jennifer Dougherty, José M Duarte, Andrew S Hoffman, Geoffrey J Barton, Emøke Bendixen, Timothy Bergquist, Christian Bock, Elizabeth Brunk, Marija Buljan, Stephen K Burley, Binghuang Cai, Hannah Carter, JianJiong Gao, Adam Godzik, Michael Heuer, Michael Hicks, Thomas Hrabe, Rachel Karchin, Julia Koehler Leman, Lydie Lane, David L Masica, Sean D Mooney, John Moult, Gilbert S Omenn, Frances Pearl, Vikas Pejaver, Sheila M Reynolds, Ariel Rokem, Torsten Schwede, Sicheng Song, Hagen Tilgner, Yana Valasatava, Yang Zhang, and Eric W Deutsch

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Whole-genome DNA methylation status associated with clinical PTSD measures of OIF/OEF veterans., R Hammamieh, N Chakraborty, A Gautam, S Muhie, R Yang, D Donohue, R Kumar, B J Daigle, Y Zhang, D A Amara, S-A Miller, S Srinivasan, J Flory, R Yehuda, L Petzold, O M Wolkowitz, S H Mellon, L Hood, F J Doyle, C Marmar, and M Jett

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One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY!, Thurston Herricks, David J Dilworth, Fred D Mast, Song Li, Jennifer J Smith, Alexander V Ratushny, and John D Aitchison

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ODELAY: A Large-scale Method for Multi-parameter Quantification of Yeast Growth., Thurston Herricks, Fred D Mast, Song Li, and John D Aitchison

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A Systematic Study of Dysregulated MicroRNA in Type 2 Diabetes Mellitus., Yuqing He, Yuanlin Ding, Biyu Liang, Juanjuan Lin, Taek-Kyun Kim, Haibing Yu, Hanwei Hang, and Kai Wang

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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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Processes on the emergent landscapes of biochemical reaction networks and heterogeneous cell population dynamics: differentiation in living matters., Sui Huang, Fangting Li, Joseph X Zhou, and Hong Qian

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Evolutionary history of Tibetans inferred from whole-genome sequencing., Hao Hu, Nayia Petousi, Gustavo Glusman, Yao Yu, Ryan Bohlender, Tsewang Tashi, Jonathan M Downie, Jared C Roach, Amy M Cole, Felipe R Lorenzo, Alan R Rogers, Mary E Brunkow, Gianpiero Cavalleri, Leroy Hood, Sama M Alpatty, Josef T Prchal, Lynn B Jorde, Peter A Robbins, Tatum S Simonson, and Chad D Huff

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Differences between the genomes of lymphoblastoid cell lines and blood-derived samples., Lena M Joesch-Cohen and Gustavo Glusman

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Longitudinal peripheral blood transcriptional analysis of a patient with severe Ebola virus disease., John C Kash, Kathie-Anne Walters, Jason Kindrachuk, David Baxter, Kelsey Scherler, Krisztina B Janosko, Rick D Adams, Andrew S Herbert, Rebekah M James, Spencer W Stonier, Matthew J Memoli, John M Dye, Richard T Davey, Daniel S Chertow, and Jeffery K Taubenberger

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Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding., E V Katkova, A V Onufriev, B Aguilar, and V B Sulimov

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Diagnosis of major depressive disorder by combining multimodal information from heart rate dynamics and serum proteomics using machine-learning algorithm., Eun Young Kim, Min Young Lee, Se Hyun Kim, Kyooseob Ha, Kwang Pyo Kim, and Yong Min Ahn

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Mutational Landscapes of Smoking-Related Cancers in Caucasians and African Americans: Precision Oncology Perspectives at Wake Forest Baptist Comprehensive Cancer Center., Ville Kytola, Umit Topaloglu, Lance D Miller, Rhonda L Bitting, Michael M Goodman, Ralph B D Agostino, Rodwige J Desnoyers, Carol Albright, George Yacoub, Shadi A Qasem, Barry DeYoung, Vesteinn Thorsson, Ilya Shmulevich, Meng Yang, Anastasia Shcherban, Matthew Pagni, Liang Liu, Matti Nykter, Kexin Chen, Gregory A Hawkins, Stefan C Grant, W Jeffrey Petty, Angela Tatiana Alistar, Edward A Levine, Edgar D Staren, Carl D Langefeld, Vincent Miller, Gaurav Singal, Robin M Petro, Mac Robinson, William Blackstock, Bayard L Powell, Lynne I Wagner, Kristie L Foley, Edward Abraham, Boris Pasche, and Wei Zhang

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The Importance of Standardization on Analyzing Circulating RNA., Inyoul Lee, David Baxter, Min Young Lee, Kelsey Scherler, and Kai Wang

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Remodeling of heterochromatin structure slows neuropathological progression and prolongs survival in an animal model of Huntington's disease., Junghee Lee, Yu Jin Hwang, Yunha Kim, Min Young Lee, Seung Jae Hyeon, Soojin Lee, Dong Hyun Kim, Sung Jae Jang, Hyoenjoo Im, Sun-Joon Min, Hyunah Choo, Ae Nim Pae, Dong Jin Kim, Kyung Sang Cho, Neil W Kowall, and Hoon Ryu

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Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks., Hongdong Li, Yang Zhang, Yuanfang Guan, Rajasree Menon, and Gilbert S Omenn

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Modulation of Bax and mTOR for Cancer Therapeutics., Rui Li, Chunyong Ding, Jun Zhang, Maohua Xie, Dongkyoo Park, Ye Ding, Guo Chen, Guojing Zhang, Melissa Gilbert-Ross, Wei Zhou, Adam I Marcus, Shi-Yong Sun, Zhuo G Chen, Gabriel L Sica, Suresh S Ramalingam, Andrew T Magis, Haian Fu, Fadlo R Khuri, Walter J Curran, Taofeek K Owonikoko, Dong M Shin, Jia Zhou, and Xingming Deng

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Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network., William J R Longabaugh, Weihua Zeng, Jingli A Zhang, Hiroyuki Hosokawa, Camden S Jansen, Long Li, Maile Romero-Wolf, Pentao Liu, Hao Yuan Kueh, Ali Mortazavi, and Ellen V Rothenberg

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Adaptive Prediction Emerges Over Short Evolutionary Time Scales., Adrián López García de Lomana, Amardeep Kaur, Serdar Turkarslan, Karlyn D Beer, Fred D Mast, Jennifer J Smith, John D Aitchison, and Nitin S Baliga

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An integrated transcriptomics-guided genome-wide promoter analysis and next-generation proteomics approach to mine factor(s) regulating cellular differentiation., Kamal Mandal, Samuel L Bader, Pankaj Kumar, Dipankar Malakar, David S Campbell, Bhola Shankar Pradhan, Rajesh K Sarkar, Neerja Wadhwa, Souvik Sensharma, Vaibhav Jain, Robert L Moritz, and Subeer S Majumdar

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Recessive mutations in SLC35A3 cause early onset epileptic encephalopathy with skeletal defects., Carla Marini, Katia Hardies, Tiziana Pisano, Patrick May, Sarah Weckhuysen, Elena Cellini, Arvid Suls, Davide Mei, Rudi Balling, Peter D Jonghe, Ingo Helbig, Domenico Garozzo, and Renzo Guerrini

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Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform, Amy Marshall-Colon, Stephen P Long, Douglas K Allen, Gabrielle Allen, Daniel A Beard, Bedrich Benes, Susanne von Caemmerer, A J Christensen, Donna J Cox, John C Hart, Peter M Hirst, Kavya Kannan, Daniel S Katz, Jonathan P Lynch, Andrew J Millar, Balaji Panneerselvam, Nathan D Price, Przemyslaw Prusinkiewicz, David Raila, Rachel G Shekar, Stuti Shrivastava, Diwakar Shukla, Venkatraman Srinivasan, Mark Stitt, Matthew J Turk, Eberhard O Voit, Yu Wang, Xinyou Yin, and Xin-Guang Zhu

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The PeptideAtlas of the Domestic Laying Hen., James McCord, Zhi Sun, Eric W Deutsch, Robert L Moritz, and David C Muddiman

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A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions., Stephan Michalik, Maren Depke, Annette Murr, Manuela Gesell Salazar, Ulrike Kusebauch, Zhi Sun, Tanja C Meyer, Kristin Surmann, Henrike Pförtner, Petra Hildebrandt, Stefan Weiss, Laura Marcela Palma Medina, Melanie Gutjahr, Elke Hammer, Dörte Becher, Thomas Pribyl, Sven Hammerschmidt, Eric W Deutsch, Samuel L Bader, Michael Hecker, Robert L Moritz, Ulrike Mäder, Uwe Völker, and Frank Schmidt

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Cellular Signaling Pathways in Insulin Resistance-Systems Biology Analyses of Microarray Dataset Reveals New Drug Target Gene Signatures of Type 2 Diabetes Mellitus., Syed Aun Muhammad, Waseem Raza, Thanh Nguyen, Baogang Bai, Xiaogang Wu, and Jake Chen

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SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters., Robert T Nakayama, John L Pulice, Alfredo M Valencia, Matthew J McBride, Zachary M McKenzie, Mark A Gillespie, Wai Lim Ku, Mingxiang Teng, Kairong Cui, Robert T Williams, Seth H Cassel, He Qing, Christian J Widmer, George D Demetri, Rafael A Irizarry, Keji Zhao, Jeffrey A Ranish, and Cigall Kadoch

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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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Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project., Gilbert S Omenn, Lydie Lane, Emma K Lundberg, Christopher M Overall, and Eric W Deutsch

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Progress and Future Direction of Chromosome-Centric Human Proteome Project., Young-Ki Paik, Christopher M Overall, Eric W Deutsch, Jennifer E Van Eyk, and Gilbert S Omenn

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A genome wide dosage suppressor network reveals genomic robustness., Biranchi Patra, Yoshiko Kon, Gitanjali Yadav, Anthony W Sevold, Jesse P Frumkin, Ravishankar R Vallabhajosyula, Arend Hintze, Bjørn Østman, Jory Schossau, Ashish Bhan, Bruz Marzolf, Jenna K Tamashiro, Amardeep Kaur, Nitin S Baliga, Elizabeth J Grayhack, Christoph Adami, David J Galas, Alpan Raval, Eric M Phizicky, and Animesh Ray

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Enhanced retinal responses in Huntington's disease patients., Jocelynn R Pearl, Laura M Heath, Dani E Bergey, John P Kelly, Corrie Smith, Mercy Y Laurino, Avery Weiss, Nathan D Price, Albert LaSpada, Thomas D Bird, and Suman Jayadev