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

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Submissions from 2018

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MAMMOTh: A new database for curated mathematical models of biomolecular systems., Fedor Kazantsev, Ilya Akberdin, Sergey Lashin, Natalia Ree, Vladimir Timonov, Alexander Ratushny, Tamara Khlebodarova, and Vitaly Likhoshvai

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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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ProbAnnoWeb and ProbAnnoPy: probabilistic annotation and gap-filling of metabolic reconstructions., Brendan King, Terry Farrah, Matthew A Richards, Michael Mundy, Evangelos Simeonidis, and Nathan D Price

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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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Surface Immobilization of Redox-Labile Fluorescent Probes: Enabling Single-Cell Co-Profiling of Aerobic Glycolysis and Oncogenic Protein Signaling Activities., Zhonghan Li, Hanjun Cheng, Shiqun Shao, Xiang Lu, Li Mo, Jonathan Tsang, Pu Zeng, Zhili Guo, Siwen Wang, David A Nathanson, James R Heath, Wei Wei, and Min Xue

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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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Allosteric Inhibitor of KRas Identified Using a Barcoded Assay Microchip Platform., Amy M McCarthy, Jungwoo Kim, A Katrine Museth, Ryan K Henning, John E Heath, Emma Winson, Joseph J Oh, Jingxin Liang, Sunga Hong, and James R Heath

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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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Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper., Luis Mendoza, Eric W Deutsch, Zhi Sun, David S Campbell, David Shteynberg, and Robert L Moritz

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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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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