Publications

2016

Allen, Mariet, Jeremy D. Burgess, Travis Ballard, Daniel Serie, Xue Wang, Curtis S. Younkin, Zhifu Sun, et al. 2016. “Gene Expression, Methylation and Neuropathology Correlations at Progressive Supranuclear Palsy Risk Loci.” Acta Neuropathologica, April. https://doi.org/10.1007/s00401-016-1576-7. Cite
Allen, Mariet, Minerva M. Carrasquillo, Cory Funk, Benjamin D. Heavner, Fanggeng Zou, Curtis S. Younkin, Jeremy D. Burgess, et al. 2016. “Human Whole Genome Genotype and Transcriptome Data for Alzheimer’s and Other Neurodegenerative Diseases.” Scientific Data 3: 160089. https://doi.org/10.1038/sdata.2016.89. Cite
Atapattu, Lakmali, Nayanendu Saha, Chanly Chheang, Moritz F. Eissman, Kai Xu, Mary E. Vail, Linda Hii, et al. 2016. “An Activated Form of ADAM10 Is Tumor Selective and Regulates Cancer Stem-like Cells and Tumor Growth.” The Journal of Experimental Medicine 213 (9): 1741–57. https://doi.org/10.1084/jem.20151095. Cite
Borges, G. T., E. F. Vencio, S. I. Quek, A. Chen, D. M. Salvanha, R. Z. Vencio, H. M. Nguyen, et al. 2016. “Conversion of Prostate Adenocarcinoma to Small Cell Carcinoma-Like by Reprogramming.” Journal of Cellular Physiology, January. https://doi.org/10.1002/jcp.25313. Cite
Camargo, M. Constanza, Reanne Bowlby, Andy Chu, Chandra Sekhar Pedamallu, Vesteinn Thorsson, Sandra Elmore, Andrew J. Mungall, Adam J. Bass, Margaret L. Gulley, and Charles S. Rabkin. 2016. “Validation and Calibration of Next-Generation Sequencing to Identify Epstein-Barr Virus-Positive Gastric Cancer in The Cancer Genome Atlas.” Gastric Cancer: Official Journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association 19 (2): 676–81. https://doi.org/10.1007/s10120-015-0508-x. Cite Download
Carrasquillo, Minerva M., Mariet Allen, Jeremy D. Burgess, Xue Wang, Samantha L. Strickland, Shivani Aryal, Joanna Siuda, et al. 2016. “A Candidate Regulatory Variant at the TREM Gene Cluster Associates with Decreased Alzheimer’s Disease Risk and Increased TREML1 and TREM2 Brain Gene Expression.” Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association. https://doi.org/10.1016/j.jalz.2016.10.005. Cite
Chevillet, John R., 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. 2016. “Release of Cell-Free MicroRNA Tumor Biomarkers into the Blood Circulation with Pulsed Focused Ultrasound: A Noninvasive, Anatomically Localized, Molecular Liquid Biopsy.” Radiology, 160024. https://doi.org/10.1148/radiol.2016160024. Cite
Chio, Iok In Christine, Seyed Mehdi Jafarnejad, Mariano Ponz-Sarvise, Youngkyu Park, Keith Rivera, Wilhelm Palm, John Wilson, et al. 2016. “NRF2 Promotes Tumor Maintenance by Modulating MRNA Translation in Pancreatic Cancer.” Cell 166 (4): 963–76. https://doi.org/10.1016/j.cell.2016.06.056. Cite
Craciun, Florin L., Vanesa Bijol, Amrendra K. Ajay, Poornima Rao, Ramya K. Kumar, John Hutchinson, Oliver Hofmann, et al. 2016. “RNA Sequencing Identifies Novel Translational Biomarkers of Kidney Fibrosis.” Journal of the American Society of Nephrology: JASN 27 (6): 1702–13. https://doi.org/10.1681/ASN.2015020225. Cite
Daude, Nathalie, Inyoul Lee, Taek-Kyun Kim, Christopher Janus, John Paul Glaves, Hristina Gapeshina, Jing Yang, et al. 2016. “A Common Phenotype Polymorphism in Mammalian Brains Defined by Concomitant Production of Prolactin and Growth Hormone.” PloS One 11 (2): e0149410. https://doi.org/10.1371/journal.pone.0149410. Cite
Deutsch, Eric W., Zhi Sun, David S. Campbell, Pierre-Alain Binz, Terry Farrah, David Shteynberg, Luis Mendoza, Gilbert S. Omenn, and Robert L. Moritz. 2016. “Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.6b00445. Cite
Deutsch, Eric W., Christopher M. Overall, Jennifer E. Van Eyk, Mark S. Baker, Young-Ki Paik, Susan T. Weintraub, Lydie Lane, et al. 2016. “Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.6b00392. Cite
Dhankani, Varsha, David L. Gibbs, Theo Knijnenburg, Roger Kramer, Joseph Vockley, John Niederhuber, Ilya Shmulevich, and Brady Bernard. 2016. “Using Incomplete Trios to Boost Confidence in Family Based Association Studies.” Frontiers in Genetics 7: 34. https://doi.org/10.3389/fgene.2016.00034. Cite
Dinov, Ivo D., Ben Heavner, Ming Tang, Gustavo Glusman, Kyle Chard, Mike Darcy, Ravi Madduri, et al. 2016. “Predictive Big Data Analytics: A Study of Parkinson’s Disease Using Large, Complex, Heterogeneous, Incongruent, Multi-Source and Incomplete Observations.” PloS One 11 (8): e0157077. https://doi.org/10.1371/journal.pone.0157077. Cite
Dumontier, Michel, Alasdair J. G. Gray, M. Scott Marshall, Vladimir Alexiev, Peter Ansell, Gary Bader, Joachim Baran, et al. 2016. “The Health Care and Life Sciences Community Profile for Dataset Descriptions.” PeerJ 4: e2331. https://doi.org/10.7717/peerj.2331. Cite
Ghai, Vikas, and Kai Wang. 2016. “Recent Progress toward the Use of Circulating MicroRNAs as Clinical Biomarkers.” Archives of Toxicology. https://doi.org/10.1007/s00204-016-1828-2. Cite
Ghosh, Dhiman, Ilya V. Ulasov, LiPing Chen, Lualhati E. Harkins, Karolina Wallenborg, Parvinder Hothi, Steven Rostad, Leroy Hood, and Charles S. Cobbs. 2016. “TGFβ-Responsive HMOX1 Expression Is Associated with Stemness and Invasion in Glioblastoma Multiforme.” Stem Cells (Dayton, Ohio) 34 (9): 2276–89. https://doi.org/10.1002/stem.2411. Cite
Goldmann, Jakob M., Wendy S. W. Wong, Michele Pinelli, Terry Farrah, Dale Bodian, Anna B. Stittrich, Gustavo Glusman, et al. 2016. “Parent-of-Origin-Specific Signatures of de Novo Mutations.” Nature Genetics. https://doi.org/10.1038/ng.3597. Cite
Gonzalez, A., Y. Vázquez-Baeza, J. B. Pettengill, A. Ottesen, D. McDonald, and R. Knight. 2016. “Avoiding Pandemic Fears in the Subway and Conquering the Platypus.” MSystems 1 (3). https://doi.org/10.1128/mSystems.00050-16. Cite
Hampton, Henry, Carolyn Hutcheon, and Naeha Subramanian. 2016. “NAGging Hexokinase PEPs up NLRP3.” Cell Host & Microbe 20 (2): 130–32. https://doi.org/10.1016/j.chom.2016.07.017. Cite Download
Hoofnagle, A. N., J. R. Whiteaker, S. A. Carr, E. Kuhn, T. Liu, S. A. Massoni, S. N. Thomas, et al. 2016. “Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays.” Clinical Chemistry 62 (January): 48–69. https://doi.org/10.1373/clinchem.2015.250563. Cite
Hoopmann, Michael R., Luis Mendoza, Eric W. Deutsch, David Shteynberg, and Robert L. Moritz. 2016. “An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results.” Journal of the American Society for Mass Spectrometry. https://doi.org/10.1007/s13361-016-1435-8. Cite
Huang, S. 2016. “Where to Go: Breaking the Symmetry in Cell Motility.” PLoS Biology 14 (5): e1002463. https://doi.org/10.1371/journal.pbio.1002463. Cite
Hubley, R., R. D. Finn, J. Clements, S. R. Eddy, T. A. Jones, W. Bao, A. F. Smit, and T. J. Wheeler. 2016. “The Dfam Database of Repetitive DNA Families.” Nucleic Acids Research 44 (January): D81-9. https://doi.org/10.1093/nar/gkv1272. Cite
Iorio, Francesco, Theo A. Knijnenburg, Daniel J. Vis, Graham R. Bignell, Michael P. Menden, Michael Schubert, Nanne Aben, et al. 2016. “A Landscape of Pharmacogenomic Interactions in Cancer.” Cell 166 (3): 740–54. https://doi.org/10.1016/j.cell.2016.06.017. Cite
Katkova, E. V., A. V. Onufriev, B. Aguilar, and V. B. Sulimov. 2016. “Accuracy Comparison of Several Common Implicit Solvent Models and Their Implementations in the Context of Protein-Ligand Binding.” Journal of Molecular Graphics & Modelling 72: 70–80. https://doi.org/10.1016/j.jmgm.2016.12.011. Cite
Keller, Mark P., Pradyut K. Paul, Mary E. Rabaglia, Donnie S. Stapleton, Kathryn L. Schueler, Aimee Teo Broman, Shuyun Isabella Ye, et al. 2016. “The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets.” PLoS Genetics 12 (12): e1006466. https://doi.org/10.1371/journal.pgen.1006466. Cite
Knijnenburg, Theo A., Gunnar W. Klau, Francesco Iorio, Mathew J. Garnett, Ultan McDermott, Ilya Shmulevich, and Lodewyk F. A. Wessels. 2016. “Logic Models to Predict Continuous Outputs Based on Binary Inputs with an Application to Personalized Cancer Therapy.” Scientific Reports 6: 36812. https://doi.org/10.1038/srep36812. Cite
Kusebauch, Ulrike, David S. Campbell, Eric W. Deutsch, Caroline S. Chu, Douglas A. Spicer, Mi-Youn Brusniak, Joseph Slagel, et al. 2016. “Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome.” Cell 166 (3): 766–78. https://doi.org/10.1016/j.cell.2016.06.041. Cite
Lee, Min Young, Eun Young Kim, Se Hyun Kim, Kyung-Cho Cho, Kyooseob Ha, Kwang Pyo Kim, and Yong Min Ahn. 2016. “Discovery of Serum Protein Biomarkers in Drug-Free Patients with Major Depressive Disorder.” Progress in Neuro-Psychopharmacology & Biological Psychiatry 69 (April): 60–68. https://doi.org/10.1016/j.pnpbp.2016.04.009. Cite
Lee, L. James, Zhaogang Yang, Mohammad Rahman, Junyu Ma, Kwang Joo Kwak, Joseph McElroy, Konstantin Shilo, et al. 2016. “Extracellular MRNA Detected by Tethered Lipoplex Nanoparticle Biochip for Lung Adenocarcinoma Detection.” American Journal of Respiratory and Critical Care Medicine 193 (12): 1431–33. https://doi.org/10.1164/rccm.201511-2129LE. Cite
Lee, Inyoul, David Baxter, Min Young Lee, Kelsey Scherler, and Kai Wang. 2016. “The Importance of Standardization on Analyzing Circulating RNA.” Molecular Diagnosis & Therapy. https://doi.org/10.1007/s40291-016-0251-y. Cite
Li, Hong-Dong, Rajasree Menon, Ridvan Eksi, Aysam Guerler, Yang Zhang, Gilbert S. Omenn, and Yuanfang Guan. 2016. “A Network of Splice Isoforms for the Mouse.” Scientific Reports 6: 24507. https://doi.org/10.1038/srep24507. Cite
Li, Qin, Anders Wennborg, Erik Aurell, Erez Dekel, Jie-Zhi Zou, Yuting Xu, S. Huang, and Ingemar Ernberg. 2016. “Dynamics inside the Cancer Cell Attractor Reveal Cell Heterogeneity, Limits of Stability, and Escape.” Proceedings of the National Academy of Sciences of the United States of America 113 (10): 2672–77. https://doi.org/10.1073/pnas.1519210113. Cite
Liu, Xindong, Huiping Lu, Tingting Chen, Kalyan C. Nallaparaju, Xiaowei Yan, Shinya Tanaka, Kenji Ichiyama, et al. 2016. “Genome-Wide Analysis Identifies Bcl6-Controlled Regulatory Networks during T Follicular Helper Cell Differentiation.” Cell Reports 14 (7): 1735–47. https://doi.org/10.1016/j.celrep.2016.01.038. Cite
Maishman, Luke, Samson O. Obado, Sam Alsford, Jean-Mathieu Bart, Wei-Ming Chen, Alexander V. Ratushny, Miguel Navarro, et al. 2016. “Co-Dependence between Trypanosome Nuclear Lamina Components in Nuclear Stability and Control of Gene Expression.” Nucleic Acids Research. https://doi.org/10.1093/nar/gkw751. Cite
Maixner, F., B. Krause-Kyora, D. Turaev, A. Herbig, M. R. Hoopmann, J. L. Hallows, U. Kusebauch, et al. 2016. “The 5300-Year-Old Helicobacter Pylori Genome of the Iceman.” Science 351: 162–65. https://doi.org/10.1126/science.aad2545. Cite
Marr, Carsten, Joseph X. Zhou, and Sui Huang. 2016. “Single-Cell Gene Expression Profiling and Cell State Dynamics: Collecting Data, Correlating Data Points and Connecting the Dots.” Current Opinion in Biotechnology 39: 207–14. https://doi.org/10.1016/j.copbio.2016.04.015. Cite
Mast, Fred D., Arvind Jamakhandi, Ramsey A. Saleem, David J. Dilworth, Richard S. Rogers, Richard A. Rachubinski, and John D. Aitchison. 2016. “Peroxins Pex30 and Pex29 Dynamically Associate with Reticulons to Regulate Peroxisome Biogenesis from the Endoplasmic Reticulum.” The Journal of Biological Chemistry, April. https://doi.org/10.1074/jbc.M116.728154. Cite
McDermott, Suzanne M., Jie Luo, Jason Carnes, Jeff A. Ranish, and Kenneth Stuart. 2016. “The Architecture of Trypanosoma Brucei Editosomes.” Proceedings of the National Academy of Sciences of the United States of America 113 (42): E6476–85. https://doi.org/10.1073/pnas.1610177113. Cite
McDonald, D., G. Glusman, and N.D. Price. 2016. “Personalized Nutrition through Big Data.” Nature Biotechnology 34 (2): 152–54. https://doi.org/10.1038/nbt.3476. Cite
McPhillie, Martin, Ying Zhou, Kamal El Bissati, Jitender Dubey, Hernan Lorenzi, Michael Capper, Amanda K. Lukens, et al. 2016. “New Paradigms for Understanding and Step Changes in Treating Active and Chronic, Persistent Apicomplexan Infections.” Scientific Reports 6: 29179. https://doi.org/10.1038/srep29179. Cite
Mohamadlou, Hamid, Gregory J. Podgorski, and Nicholas S. Flann. 2016. “Modular Genetic Regulatory Networks Increase Organization during Pattern Formation.” Bio Systems. https://doi.org/10.1016/j.biosystems.2016.04.004. Cite
Mojtahedi, Mitra, Alexander Skupin, Joseph Zhou, Ivan G. Castaño, Rebecca Y. Y. Leong-Quong, Hannah Chang, Kalliopi Trachana, Alessandro Giuliani, and Sui Huang. 2016. “Cell Fate Decision as High-Dimensional Critical State Transition.” PLoS Biology 14 (12): e2000640. https://doi.org/10.1371/journal.pbio.2000640. Cite
Murrugarra, David, Alan Veliz-Cuba, Boris Aguilar, and Reinhard Laubenbacher. 2016. “Identification of Control Targets in Boolean Molecular Network Models via Computational Algebra.” BMC Systems Biology 10 (1): 94. https://doi.org/10.1186/s12918-016-0332-x. Cite
Omenn, Gilbert S., Lydie Lane, Emma K. Lundberg, Ronald C. Beavis, Christopher M. Overall, and Eric W. Deutsch. 2016. “Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications.” Journal of Proteome Research 15 (11): 3951–60. https://doi.org/10.1021/acs.jproteome.6b00511. Cite
Paik, Young-Ki, Christopher M. Overall, Eric W. Deutsch, William S. Hancock, and Gilbert S. Omenn. 2016. “Progress in the Chromosome-Centric Human Proteome Project as Highlighted in the Annual Special Issue IV.” Journal of Proteome Research 15 (11): 3945–50. https://doi.org/10.1021/acs.jproteome.6b00803. Cite
Paquette, Suzanne M., Kalle Leinonen, and William J. R. Longabaugh. 2016. “BioTapestry Now Provides a Web Application and Improved Drawing and Layout Tools.” F1000Research 5: 39. https://doi.org/10.12688/f1000research.7620.1. Cite