Submissions from 2018
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
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
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
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
Niche emergence as an autocatalytic process in the evolution of ecosystems., Roberto Cazzolla Gatti, Brian Fath, Wim Hordijk, Stuart Kauffman, and Robert Ulanowicz
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
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
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
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
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
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
Expanding the Use of Spectral Libraries in Proteomics., Eric W Deutsch, Yasset Perez-Riverol, Robert J Chalkley, Mathias Wilhelm, Stephen Tate, Timo Sachsenberg, Mathias Walzer, Lukas Käll, Bernard Delanghe, Sebastian Böcker, Emma L Schymanski, Paul Wilmes, Viktoria Dorfer, Bernhard Kuster, Pieter-Jan Volders, Nico Jehmlich, Johannes P C Vissers, Dennis W Wolan, Ana Y Wang, Luis Mendoza, Jim Shofstahl, Andrew W Dowsey, Johannes Griss, Reza M Salek, Steffen Neumann, Pierre-Alain Binz, Henry Lam, Juan Antonio Vizcaíno, Nuno Bandeira, and Hannes Röst
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
In vitro characterization of alkylaminophenols-induced cell death., Phuong Doan, Olga Anufrieva, Olli Yli-Harja, and Meenakshisundaram Kandhavelu
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
Preparation of Small RNA NGS Libraries from Biofluids., Alton Etheridge, Kai Wang, David Baxter, and David Galas
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
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
Constraint-based modelling captures the metabolic versatility of Desulfovibrio vulgaris., Jason J Flowers, Matthew A Richards, Nitin Baliga, Birte Meyer, and David A Stahl
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
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
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
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
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
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
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
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
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
Lessons Learned as President of the Institute for Systems Biology (2000-2018)., Leroy E Hood
StPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline., Michael R Hoopmann, Jason M Winget, Luis Mendoza, and Robert L Moritz
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
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
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
Novel metrics for quantifying bacterial genome composition skews., Lena M Joesch-Cohen, Max Robinson, Neda Jabbari, Christopher G Lausted, and Gustavo Glusman
Determining Relative Dynamic Stability of Cell States Using Boolean Network Model., Jae Il Joo, Joseph X Zhou, Sui Huang, and Kwang-Hyun Cho
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
Emergence of diversity in homogeneous coupled Boolean networks., Chris Kang, Boris Aguilar, and Ilya Shmulevich
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
The building blocks of successful translation of proteomics to the clinic., Paul Kearney, J Jay Boniface, Nathan D Price, and Leroy Hood
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
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
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
Molecular structure of promoter-bound yeast TFIID., Olga Kolesnikova, Adam Ben-Shem, Jie Luo, Jeff Ranish, Patrick Schultz, and Gabor Papai
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
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
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
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
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
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
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
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
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
Characterization of Peroxisomal Regulation Networks., Fred D Mast and John D Aitchison
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
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
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
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
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
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
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
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
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
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
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
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
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
Comparative transcriptomic analysis of human placentae at term and preterm delivery., Alison G Paquette, Heather M Brockway, Nathan D Price, and Louis J Muglia
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
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
Reply., Alison Paquette, Nathan D Price, and Stephen J Lye
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
Editorial overview: Systems biology: Data, discovery, delivery., Nathan D Price and Eran Segal
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
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
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
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
Genotype Fingerprints Enable Fast and Private Comparison of Genetic Testing Results for Research and Direct-to-Consumer Applications., Max Robinson and Gustavo Glusman
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
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
Identification of novel GPR17-agonists by structural bioinformatics and signaling activation., Konda Mani Saravanan, Suresh Palanivel, Olli Yli-Harja, and Meenakshisundaram Kandhavelu
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
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
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
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
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
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
Radical amino acid mutations persist longer in the absence of sex., Joel Sharbrough, Meagan Luse, Jeffrey L Boore, John M Logsdon, and Maurine Neiman
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
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
Robust determination of differential abundance in shotgun proteomics using nonparametric statistics., Patrick Slama, Michael R Hoopmann, Robert L Moritz, and Donald Geman
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
Plasmodium Parasites Viewed through Proteomics., Kristian E Swearingen and Scott E Lindner
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
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
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
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
Taking Systems Medicine to Heart., Kalliopi Trachana, Rhishikesh Bargaje, Gustavo Glusman, Nathan D Price, Sui Huang, and Leroy E Hood
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
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
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
