Publications

2014

Bai, Jane P. F., Robert J. Fontana, Nathan D. Price, and Vineet Sangar. 2014. “Systems Pharmacology Modeling: An Approach to Improving Drug Safety.” Biopharmaceutics & Drug Disposition 35 (1). https://doi.org/10.1002/bdd.1871. Cite
Beer, K. D., E. J. Wurtmann, N. Pinel, and N. S. Baliga. 2014. “Model Organisms Have Memory of Complex Ecologically-Relevant Environmental Variation.” Applied and Environmental Microbiology, January. Cite
Benedict, Matthew N., Michael B. Mundy, Christopher S. Henry, Nicholas Chia, and Nathan D. Price. 2014. “Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models.” PLoS Computational Biology 10 (10). https://doi.org/10.1371/journal.pcbi.1003882. Cite
Benedict, Matthew N., James R. Henriksen, William W. Metcalf, Rachel J. Whitaker, and Nathan D. Price. 2014. “ITEP: An Integrated Toolkit for Exploration of Microbial Pan-Genomes.” BMC Genomics 15. https://doi.org/10.1186/1471-2164-15-8. Cite
Brownstein, Catherine A., Alan H. Beggs, Nils Homer, Barry Merriman, Timothy W. Yu, Katherine C. Flannery, Elizabeth T. DeChene, et al. 2014. “An International Effort towards Developing Standards for Best Practices in Analysis, Interpretation and Reporting of Clinical Genome Sequencing Results in the CLARITY Challenge.” Genome Biology 15 (3): R53. https://doi.org/10.1186/gb-2014-15-3-r53. Cite
Bundgaard, Louise, Stine Jacobsen, Mette Aamand Sørensen, Zhi Sun, Eric W. Deutsch, R. L. Moritz, and Emøke Bendixen. 2014. “The Equine PeptideAtlas–a Resource for Developing Proteomics-Based Veterinary Research.” Proteomics. Cite
Caballero, Juan, Arian F. A. Smit, Leroy Hood, and Gustavo Glusman. 2014. “Realistic Artificial DNA Sequences as Negative Controls for Computational Genomics.” Nucleic Acids Research 42 (12): e99. https://doi.org/10.1093/nar/gku356. Cite
Cancer Genome Atlas Research Network. 2014. “Integrated Genomic Characterization of Papillary Thyroid Carcinoma.” Cell 159 (3): 676–90. https://doi.org/10.1016/j.cell.2014.09.050. Cite
Cancer Genome Atlas Research Network. 2014. “Comprehensive Molecular Characterization of Gastric Adenocarcinoma.” Nature 513 (7517): 202–9. https://doi.org/10.1038/nature13480. Cite
Cancer Genome Atlas Research Network. 2014. “Comprehensive Molecular Characterization of Gastric Adenocarcinoma.” Nature 513 (7517): 202–9. https://doi.org/10.1038/nature13480. Cite Download
Carpp, L. N., R. S. Rogers, R. L. Moritz, and J. D. Aitchison. 2014. “Quantitative Proteomic Analysis of Host-Virus Interactions Reveals a Role for GBF1 in Dengue Infection.” Molecular & Cellular Proteomics : MCP, May. Cite
Carr, Steven A., Susan E. Abbatiello, Bradley L. Ackermann, Christoph Borchers, Bruno Domon, Eric W. Deutsch, Russell P. Grant, Andrew N. Hoofnagle, Ruth uumlttenhain, and John M. Koomen. 2014. “Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-Based Assay Development Using a Fit-for-Purpose Approach.” Molecular & Cellular Proteomics, mcp. M113. 036095. Cite
Cary, G. A., S. H. Yoon, C. Garmendia Torres, K. Wang, M. Hays, C. Ludlow, D. R. Goodlett, and A. M. Dudley. 2014. “Identification and Characterization of a Drug-Sensitive Strain Enables Puromycin-Based Translational Assays in Saccharomyces Cerevisiae.” Yeast 31 (5): 167–78. Cite
Cermelli, Silvia, In Sock Jang, Brady Bernard, and Carla Grandori. 2014. “Synthetic Lethal Screens as a Means to Understand and Treat MYC-Driven Cancers.” Cold Spring Harbor Perspectives in Medicine 4 (3). https://doi.org/10.1101/cshperspect.a014209. Cite
Chalkley, Robert J., Nuno Bandeira, Matthew C. Chambers, Karl R. Clauser, John S. Cottrell, Eric W. Deutsch, Eugene A. Kapp, et al. 2014. “Proteome Informatics Research Group (IPRG)_2012: A Study on Detecting Modified Peptides in a Complex Mixture.” Molecular & Cellular Proteomics: MCP 13 (1): 360–71. https://doi.org/10.1074/mcp.M113.032813. Cite
Chevillet, J. R., I. Lee, H. A. Briggs, Y. He, and K. Wang. 2014. “Issues and Prospects of MicroRNA-Based Biomarkers in Blood and Other Body Fluids.” Molecules 19 (5): 6080–6105. Cite
Chiang, Jung-Hsien, Wan-Shu Cheng, Leroy Hood, and Qiang Tian. 2014. “An Epigenetic Biomarker Panel for Glioblastoma Multiforme Personalized Medicine through DNA Methylation Analysis of Human Embryonic Stem Cell-like Signature.” Omics: A Journal of Integrative Biology. Cite
Cho, J. H., I. Lee, R. Hammamieh, K. Wang, D. Baxter, K. Scherler, A. Etheridge, et al. 2014. “Molecular Evidence of Stress-Induced Acute Heart Injury in a Mouse Model Simulating Posttraumatic Stress Disorder.” Proceedings of the National Academy of Sciences of the United States of America 111 (8): 3188–93. Cite
Christian, N., A. Skupin, S. Morante, K. Jansen, G. Rossi, and O. Ebenhoh. 2014. “Mesoscopic Behavior from Microscopic Markov Dynamics and Its Application to Calcium Release Channels.” Journal of Theoretical Biology 343 (February): 102–12. https://doi.org/10.1016/j.jtbi.2013.11.010. Cite
Craig, Theodore A., Yuji Zhang, Andrew T. Magis, Cory C. Funk, Nathan D. Price, Stephen C. Ekker, and Rajiv Kumar. 2014. “Detection of 1α,25-Dihydroxyvitamin D-Regulated MiRNAs in Zebrafish by Whole Transcriptome Sequencing.” Zebrafish 11 (3): 207–18. https://doi.org/10.1089/zeb.2013.0899. Cite
Danziger, S. A., A. V. Ratushny, J. J. Smith, R. A. Saleem, Y. Wan, C. E. Arens, A. M. Armstrong, et al. 2014. “Molecular Mechanisms of System Responses to Novel Stimuli Are Predictable from Public Data.” Nucleic Acids Research 42 (3): 1442–60. https://doi.org/10.1093/nar/gkt938. Cite
Daugherty, M. D., J. M. Young, J. A. Kerns, and H. S. Malik. 2014. “Rapid Evolution of PARP Genes Suggests a Broad Role for ADP-Ribosylation in Host-Virus Conflicts.” PLoS Genetics 10 (5): e1004403. Cite
Deng, Yuliang, Yu Zhang, Shuai Sun, Zhihua Wang, Minjiao Wang, Beiqin Yu, Daniel M. Czajkowsky, et al. 2014. “An Integrated Microfluidic Chip System for Single-Cell Secretion Profiling of Rare Circulating Tumor Cells.” Scientific Reports 4: 7499. https://doi.org/10.1038/srep07499. Cite Download
Ekici, Seda, Serdar Turkarslan, Grzegorz Pawlik, Andrew Dancis, Nitin S. Baliga, Hans-Georg Koch, and Fevzi Daldal. 2014. “Intracytoplasmic Copper Homeostasis Controls Cytochrome c Oxidase Production.” MBio 5 (1): e01055-13. Cite
Farrah, Terry, Eric W. Deutsch, Gilbert S. Omenn, Zhi Sun, Julian D. Watts, Tadashi Yamamoto, David Shteynberg, Micheleen M. Harris, and Robert L. Moritz. 2014. “State of the Human Proteome in 2013 as Viewed through PeptideAtlas: Comparing the Kidney, Urine, and Plasma Proteomes for the Biology- and Disease-Driven Human Proteome Project.” Journal of Proteome Research 13 (1): 60–75. https://doi.org/10.1021/pr4010037. Cite
Galhardo, Mafalda, Lasse Sinkkonen, Philipp Berninger, Jake Lin, Thomas Sauter, and Merja Heinäniemi. 2014. “Integrated Analysis of Transcript-Level Regulation of Metabolism Reveals Disease-Relevant Nodes of the Human Metabolic Network.” Nucleic Acids Res 42 (February): 1474–96. https://doi.org/10.1093/nar/gkt989. Cite
Garmendia-Torres, C., A. Skupin, S. A. Michael, P. Ruusuvuori, N. J. Kuwada, D. Falconnet, G. A. Cary, C. Hansen, P. A. Wiggins, and A. M. Dudley. 2014. “Unidirectional P-Body Transport during the Yeast Cell Cycle.” PLoS ONE 9 (6): e99428. Cite
Ghaffarizadeh, A., G. J. Podgorski, and N. S. Flann. 2014. “Modeling and Visualizing Cell Type Switching.” Computational and Mathematical Methods in Medicine 2014: 293980. Cite
Gierman, Hinco J., Kristen Fortney, Jared C. Roach, Natalie S. Coles, Hong Li, Gustavo Glusman, Glenn J. Markov, et al. 2014. “Whole-Genome Sequencing of the World’s Oldest People.” PloS One 9 (11): e112430. https://doi.org/10.1371/journal.pone.0112430. Cite
Glusman, Gustavo, Hannah C. Cox, and Jared C. Roach. 2014. “Whole-Genome Haplotyping Approaches and Genomic Medicine.” Genome Medicine 6 (9): 73. https://doi.org/10.1186/s13073-014-0073-7. Cite
Goldberg, R., S. Kauffman, and E. J. Topol. 2014. “Study Design and the Drug Development Process.” JAMA : The Journal of the American Medical Association 311 (19): 2023. Cite
Guo, Fei, Brittany C. Parker Kerrigan, Da Yang, Limei Hu, Ilya Shmulevich, Anil K. Sood, Fengxia Xue, and Wei Zhang. 2014. “Post-Transcriptional Regulatory Network of Epithelial-to-Mesenchymal and Mesenchymal-to-Epithelial Transitions.” J Hematol Oncol 7: 19. https://doi.org/10.1186/1756-8722-7-19. Cite
Han, Yan, Jie Luo, Jeffrey Ranish, and Steven Hahn. 2014. “Architecture of the Saccharomyces Cerevisiae SAGA Transcription Coactivator Complex.” The EMBO Journal 33 (21): 2534–46. https://doi.org/10.15252/embj.201488638. Cite
Hao, D., G. Wang, Z. Yin, C. Li, Y. Cui, and M. Zhou. 2014. “Systematic Large-Scale Study of the Inheritance Mode of Mendelian Disorders Provides New Insight into Human Diseasome.” European Journal of Human Genetics : EJHG, January. Cite
Hillesland, K. L., S. Lim, J. J. Flowers, S. Turkarslan, N. Pinel, G. M. Zane, N. Elliott, et al. 2014. “Erosion of Functional Independence Early in the Evolution of a Microbial Mutualism.” Proceedings of the National Academy of Sciences of the United States of America, September. Cite
Holden, J. M., L. Koreny, S. Obado, A. V. Ratushny, W. M. Chen, J. H. Chiang, S. Kelly, et al. 2014. “Nuclear Pore Complex Evolution: A Trypanosome Mlp Analogue Functions in Chromosomal Segregation but Lacks Transcriptional Barrier Activity.” Molecular Biology of the Cell 25 (9): 1421–36. Cite
Hood, Leroy, and Nathan D. Price. 2014. “Demystifying Disease, Democratizing Health Care.” Science Translational Medicine 6 (225). https://doi.org/10.1126/scitranslmed.3008665. Cite
Hu, Hao, Jared C. Roach, Hilary Coon, Stephen L. Guthery, Karl V. Voelkerding, Rebecca L. Margraf, Jacob D. Durtschi, et al. 2014. “A Unified Test of Linkage Analysis and Rare-Variant Association for Analysis of Pedigree Sequence Data.” Nature Biotechnology 32 (7): 663–69. https://doi.org/10.1038/nbt.2895. Cite
Hu, Zhiyuan, Christopher Lausted, Hyuntae Yoo, Xiaowei Yan, Amy Brightman, Jiankui Chen, Weizhi Wang, Xiangli Bu, and Leroy Hood. 2014. “Quantitative Liver-Specific Protein Fingerprint in Blood: A Signature for Hepatotoxicity.” Theranostics 4 (2): 215–28. https://doi.org/10.7150/thno.7868. Cite
Huang, S. 2014. “When Correlation and Causation Coincide.” Bioessays 36 (January): 1–2. https://doi.org/10.1002/bies.201370003. Cite
Huang, S. 2014. “The War on Cancer: Lessons from the War on Terror.” Frontiers in Oncology 4 (October). https://doi.org/10.3389/fonc.2014.00293. Cite Download
Jing, Yi, Xinyu Bao, Wei Wei, Chun Li, Ke Sun, David P. R. Aplin, Yong Ding, Zhong-Lin Wang, Yoshio Bando, and Deli Wang. 2014. “Catalyst-Free Heteroepitaxial MOCVD Growth of InAs Nanowires on Si Substrates.” The Journal of Physical Chemistry C 118 (3): 1696–1705. https://doi.org/10.1021/jp406428z. Cite
Kang, Seunghwa, Simon Kahan, Jason McDermott, Nicholas Flann, and Ilya Shmulevich. 2014. “Biocellion: Accelerating Computer Simulation of Multicellular Biological System Models.” Bioinformatics (Oxford, England) 30 (21): 3101–8. https://doi.org/10.1093/bioinformatics/btu498. Cite
Kash, J. C., Y. Xiao, A. S. Davis, K.A. Walters, D. S. Chertow, J. D. Easterbrook, R. L. Dunfee, et al. 2014. “Treatment with the Reactive Oxygen Species Scavenger EUK-207 Reduces Lung Damage and Increases Survival during 1918 Influenza Virus Infection in Mice.” Free Radical Biology & Medicine 67 (February): 235–47. Cite
Kauffman, S. A. 2014. “Prolegomenon to Patterns in Evolution.” Bio Systems, April. Cite
Kemp, Christopher J., James M. Moore, Russell Moser, Brady Bernard, Matt Teater, Leslie E. Smith, Natalia A. Rabaia, et al. 2014. “CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer.” Cell Reports 7 (4): 1020–29. https://doi.org/10.1016/j.celrep.2014.04.004. Cite
Knijnenburg, Theo A., Stephen A. Ramsey, Benjamin P. Berman, Kathleen A. Kennedy, Arian F. A. Smit, Lodewyk F. A. Wessels, Peter W. Laird, Alan Aderem, and Ilya Shmulevich. 2014. “Multiscale Representation of Genomic Signals.” Nature Methods 11 (6): 689–94. https://doi.org/10.1038/nmeth.2924. Cite
Knutson, Bruce A., Jie Luo, Jeffrey Ranish, and Steven Hahn. 2014. “Architecture of the Saccharomyces Cerevisiae RNA Polymerase I Core Factor Complex.” Nature Structural & Molecular Biology 21 (9): 810–16. https://doi.org/10.1038/nsmb.2873. Cite