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2025

2323737 2RQKSFR5 2025 1 chicago-author-date-16th-edition 50 creator asc 1 1 319 https://isbscience.org/wp-content/plugins/zotpress/

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Dirvin, Brooke, Heeju Noh, Lorenzo Tomassoni, Danting Cao, Yizhuo Zhou, Xiangyi Ke, Jun Qian, et al. 2025. “Identification and Targeting of Regulators of SARS-CoV-2-Host Interactions in the Airway Epithelium.” Science Advances 11 (20): eadu2079. http://doi.org/10.1126/sciadv.adu2079. Cite

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Gao, Huanyao, Kate Jensen, Jarred Nesbitt, Mark Ostroot, Gregory A. Cary, Jesse Wiley, Sergey Trushin, et al. 2025. “Mitochondrial Complex I Deficiency Induces Alzheimer’s Disease-like Signatures That Are Reversible by Targeted Therapy.” Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association 21 (8): e70519. http://doi.org/10.1002/alz.70519. Cite

Geng, Linda N., Kristine M. Erlandson, Mady Hornig, Rebecca Letts, Caitlin Selvaggi, Hassan Ashktorab, Ornina Atieh, et al. 2025. “2024 Update of the RECOVER-Adult Long COVID Research Index.” JAMA. http://doi.org/10.1001/jama.2024.24184. Cite

Gilbert, Jack A., Meghan B. Azad, Fredrik Bäckhed, Martin J. Blaser, Mariana Byndloss, Charles Y. Chiu, Hiutung Chu, et al. 2025. “Clinical Translation of Microbiome Research.” Nature Medicine, 1–15. http://doi.org/10.1038/s41591-025-03615-9. Cite

Glen, Amy K., Eric W. Deutsch, and Stephen A. Ramsey. 2025. “PloverDB: A High-Performance Platform for Serving Biomedical Knowledge Graphs as Standards-Compliant Web APIs.” bioRxiv: The Preprint Server for Biology, 2025.03.09.642156. http://doi.org/10.1101/2025.03.09.642156. Cite

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Godsil, Marshall, Nathaniel L. Ritz, Siddarth Venkatesh, and Alexander J. Meeske. 2025. “Gut Phages and Their Interactions with Bacterial and Mammalian Hosts.” Journal of Bacteriology, e0042824. http://doi.org/10.1128/jb.00428-24. Cite

Gomez-Artiguez, Leticia, Samuel de la Cámara-Fuentes, Zhi Sun, María Luisa Hernáez, Ana Borrajo, Aída Pitarch, Gloria Molero, et al. 2025. “Candida Albicans: A Comprehensive View of the Proteome.” Journal of Proteome Research 24 (4): 1636–48. http://doi.org/10.1021/acs.jproteome.4c01020. Cite Download

Grewal, Jasleen K., A. Gordon Robertson, Kyle Ellrott, Christopher K. Wong, Jordan A. Lee, Christina Yau, Bahar Tercan, et al. 2025. “Protocol for Obtaining Cancer Type and Subtype Predictions Using subSCOPE.” STAR Protocols 6 (2): 103705. http://doi.org/10.1016/j.xpro.2025.103705. Cite

Gupta, Anika, Norma Morella, Dmitry Sutormin, Naisi Li, Karl Gaisser, Alexander Robertson, Yaroslav Ispolatov, Georg Seelig, Neelendu Dey, and Anna Kuchina. 2025. “Combinatorial Phenotypic Landscape Enables Bacterial Resistance to Phage Infection.” bioRxiv. http://doi.org/10.1101/2025.01.13.632860. Cite Download

Gupta, Vishal K., Vijaya V. Vaishnavi, Mario L. Arrieta-Ortiz, Abhirami P.s., Jyothsna K.m., Sharumathi Jeyasankar, Varun Raghunathan, Nitin S. Baliga, and Rachit Agarwal. 2025. “3D Hydrogel Culture System Recapitulates Key Tuberculosis Phenotypes and Demonstrates Pyrazinamide Efficacy.” Advanced Healthcare Materials n/a (n/a): 2304299. http://doi.org/10.1002/adhm.202304299. Cite

Gupta, Priya, Nastaran Rezakhani, Lucia Pazzagli, Hardik Patel, Gigliola Zanghi, Mohd Kamil, Alexander Watson, et al. 2025. “Glycosylation of Plasmodium Falciparum TRAP Is Essential for Infection of Mosquito Salivary Glands.” bioRxiv: The Preprint Server for Biology, 2025.06.26.658380. http://doi.org/10.1101/2025.06.26.658380. Cite

Hatzakis, Kiara, Zachary MacMillen, Payton Kirtley, Maya Aleshnick, Thomas Martinson, Priya Gupta, Kristian E. Swearingen, Brandon K. Wilder, James W. Davie, and Marion Avril. 2025. “A 3D Culture Model Facilitates Mass Production of in Vitro Plasmodium Falciparum Haemolymph-like Sporozoites.” Malaria Journal 24 (1): 224. http://doi.org/10.1186/s12936-025-05471-x. Cite

Heath, James R., and RECOVERY Collaborative Group. 2025. “Higher Dose Corticosteroids in Patients Admitted to Hospital with COVID-19 Who Are Hypoxic but Not Requiring Ventilatory Support (RECOVERY): A Randomised, Controlled, Open-Label, Platform Trial.” Lancet (London, England) 401 (10387): 1499–1507. http://doi.org/10.1016/S0140-6736(23)00510-X. Cite Download

Hodges, Frank M., Sundareswar Pullela, Guy Cohen, Akshay Mulgund, Jared C. Roach, and Stephen A. Ramsey. 2025. “Using AI to Improve Diagnosis and Treatment of Rare Diseases: A Chat Agent for Equitable and Accessible Healthcare.” In Artificial Intelligence in Medicine, edited by Riccardo Bellazzi, José Manuel Juarez Herrero, Lucia Sacchi, and Blaž Zupan, 186–91. Cham: Springer Nature Switzerland. http://doi.org/10.1007/978-3-031-95841-0_35. Cite

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Hwang, Yeon-Mi, Jennifer M. Hah, Jennifer E. Bramen, Jennifer J. Hadlock, and Tina Hernandez-Boussard. 2025. “Short-Term Mortality after Opioid Initiation among Opioid-Naïve and Non-Naïve Patients with Dementia: A Retrospective Cohort Study.” BMC Medicine 23 (1): 340. http://doi.org/10.1186/s12916-025-04172-1. Cite Download

Jatt, Lauren P, Kevin M Gillespie, Phuong Van, Stephen L Hoffman, Lisa A Jackson, Sean C Murphy, James R Heath, and James G Kublin. 2025. “Manuscript Title: Cytokines Associated With Moderate and Severe Adverse Events During a Sporozoite Malaria Vaccine Trial with Controlled Human Malaria Infection.” The Journal of Infectious Diseases, jiaf435. http://doi.org/10.1093/infdis/jiaf435. Cite

Jiang, Boyu, Nick Quinn-Bohmann, Christian Diener, Vignesh Bose Nathan, Yu Han-Hallett, Lavanya Reddivari, Sean M. Gibbons, and Priyanka Baloni. 2025. “Understanding Disease-Associated Metabolic Changes in Human Colonic Epithelial Cells Using the iColonEpithelium Metabolic Reconstruction.” PLoS Computational Biology 21 (7): e1013253. http://doi.org/10.1371/journal.pcbi.1013253. Cite

Kalyuzhnyy, Anton, Patrick A. Eyers, Claire E. Eyers, Eric W. Deutsch, and Andrew R. Jones. 2025. “Applying a Conservation-Based Approach for Predicting Novel Phosphorylation Sites in Eukaryotes and Evaluating Their Functional Relevance.” bioRxiv. http://doi.org/10.1101/2025.01.09.632054. Cite Download

Kalyuzhnyy, Anton, Patrick A. Eyers, Claire E. Eyers, Eric W. Deutsch, and Andrew R. Jones. 2025. “Applying a Conservation-Based Approach for Predicting Novel Phosphorylation Sites in Eukaryotes and Evaluating Their Functional Relevance.” Journal of Proteome Research. http://doi.org/10.1021/acs.jproteome.5c00278. Cite

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Lin, Meng-Lay, John W. Hickey, Adam Passman, Emanuela Carlotti, Shruthi Devkumar, Yannick H. Derwa, Joanne ChinAleong, et al. 2025. “Alterations of the Composition and Spatial Organization of the Microenvironment Following Non-Dysplastic Barrett’s Esophagus through Progression to Cancer.” bioRxiv: The Preprint Server for Biology, 2025.06.09.657642. http://doi.org/10.1101/2025.06.09.657642. Cite

Lucas Beckett, Isabelle A., Kate R. Emery, Josiah T. Wagner, Kathleen Jade, Benjamin A. Cosgrove, John Welle, J. B. Rinaldi, et al. 2025. “Geno4ME Study: Implementation of Whole Genome Sequencing for Population Screening in a Large Healthcare System.” Npj Genomic Medicine 10 (1): 50. http://doi.org/10.1038/s41525-025-00508-1. Cite Download

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2323737 2RQKSFR5 2024 1 chicago-author-date-16th-edition 50 creator asc 1 1 319 https://isbscience.org/wp-content/plugins/zotpress/

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Gomez-Artiguez, Leticia, Samuel de la Cámara-Fuentes, Zhi Sun, María Luisa Hernáez, Ana Borrajo, Aída Pitarch, Gloria Molero, et al. 2024. “Candida Albicans a Comprehensive View of the Proteome.” bioRxiv. http://doi.org/10.1101/2024.12.20.629377. Cite Download

Gordon, Ora, Isabelle Lucas Beckett, Kate Emery, Josiah Wagner, Kathleen Jade, Benjamin Cosgrove, John Welle, et al. 2024. “The Genomic Medicine for Everyone (Geno4ME) Study: Implementation of Whole Genome Sequencing for Population Screening in a Large Healthcare System.” Research Square. http://doi.org/10.21203/rs.3.rs-4888286/v1. Cite Download

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2323737 2RQKSFR5 2020 1 chicago-author-date-16th-edition 50 creator asc 1 1 319 https://isbscience.org/wp-content/plugins/zotpress/

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Doan, Phuong, Aliyu Musa, Akshaya Murugesan, Vili Sipilä, Nuno R. Candeias, Frank Emmert-Streib, Pekka Ruusuvuori, Kirsi Granberg, Olli Yli-Harja, and Meenakshisundaram Kandhavelu. 2020. “Glioblastoma Multiforme Stem Cell Cycle Arrest by Alkylaminophenol Through the Modulation of EGFR and CSC Signaling Pathways.” Cells 9 (3). http://doi.org/10.3390/cells9030681. Cite Download

Du, Jiajun, Yapeng Su, Chenxi Qian, Dan Yuan, Kun Miao, Dongkwan Lee, Alphonsus H. C. Ng, et al. 2020. “Raman-Guided Subcellular Pharmaco-Metabolomics for Metastatic Melanoma Cells.” Nature Communications 11 (1): 4830. http://doi.org/10.1038/s41467-020-18376-x. Cite Download

Eddy, James A., Vésteinn Thorsson, Andrew E. Lamb, David L. Gibbs, Carolina Heimann, Jia Xin Yu, Verena Chung, et al. 2020. “CRI iAtlas: An Interactive Portal for Immuno-Oncology Research.” F1000Research 9: 1028. http://doi.org/10.12688/f1000research.25141.1. Cite Download

Emmert-Streib, Frank, Olli Yli-Harja, and Matthias Dehmer. 2020. “Artificial Intelligence: A Clarification of Misconceptions, Myths and Desired Status.” Frontiers in Artificial Intelligence 3: 524339. http://doi.org/10.3389/frai.2020.524339. Cite Download

Eng, Jimmy K., and Eric W. Deutsch. 2020. “Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis Using the PSI Extended FASTA Format.” Proteomics, e1900362. http://doi.org/10.1002/pmic.201900362. Cite

Fishbein, Anna, Weicang Wang, Haixia Yang, Jun Yang, Victoria M. Hallisey, Jianjun Deng, Sanne M. L. Verheul, et al. 2020. “Resolution of Eicosanoid/Cytokine Storm Prevents Carcinogen and Inflammation-Initiated Hepatocellular Cancer Progression.” Proceedings of the National Academy of Sciences of the United States of America 117 (35): 21576–87. http://doi.org/10.1073/pnas.2007412117. Cite

Flores-Valdez, Mario Alberto, Michel de Jesús Aceves-Sánchez, Eliza J. R. Peterson, Nitin Baliga, Jorge Bravo-Madrigal, Miguel Ángel De la Cruz-Villegas, Miguel A. Ares, et al. 2020. “Transcriptional Portrait of M. Bovis BCG during Biofilm Production Shows Genes Differentially Expressed during Intercellular Aggregation and Substrate Attachment.” Scientific Reports 10 (1): 12578. http://doi.org/10.1038/s41598-020-69152-2. Cite Download

Flynn, Jullien M., Robert Hubley, Clément Goubert, Jeb Rosen, Andrew G. Clark, Cédric Feschotte, and Arian F. Smit. 2020. “RepeatModeler2 for Automated Genomic Discovery of Transposable Element Families.” Proceedings of the National Academy of Sciences of the United States of America. http://doi.org/10.1073/pnas.1921046117. Cite Download

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Ghai, Vikas, Shannon Fallen, David Baxter, Kelsey Scherler, Taek-Kyun Kim, Yong Zhou, James S. Meabon, et al. 2020. “Alterations in Plasma microRNA and Protein Levels in War Veterans with Chronic Mild Traumatic Brain Injury.” Journal of Neurotrauma. http://doi.org/10.1089/neu.2019.6826. Cite

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2323737 2RQKSFR5 2019 1 chicago-author-date-16th-edition 50 creator asc 1 1 319 https://isbscience.org/wp-content/plugins/zotpress/

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2323737 2RQKSFR5 2017 1 chicago-author-date-16th-edition 50 creator asc 1 1 319 https://isbscience.org/wp-content/plugins/zotpress/

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2323737 2RQKSFR5 2015 1 chicago-author-date-16th-edition 50 creator asc 1 1 319 https://isbscience.org/wp-content/plugins/zotpress/

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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. http://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. http://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

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Glusman, Gustavo, Hannah C. Cox, and Jared C. Roach. 2014. “Whole-Genome Haplotyping Approaches and Genomic Medicine.” Genome Medicine 6 (9): 73. http://doi.org/10.1186/s13073-014-0073-7. Cite

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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. http://doi.org/10.15252/embj.201488638. Cite

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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

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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. http://doi.org/10.7150/thno.7868. 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. http://doi.org/10.1038/nbt.2895. Cite

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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. http://doi.org/10.1021/jp406428z. Cite

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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. http://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. http://doi.org/10.1038/nsmb.2873. Cite

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2013

2323737 2RQKSFR5 2013 1 chicago-author-date-16th-edition 50 creator asc 1 1 319 https://isbscience.org/wp-content/plugins/zotpress/

Akiyoshi, B., C. R. Nelson, N. Duggan, S. Ceto, J. Ranish, and S. Biggins. 2013. “The Mub1/Ubr2 Ubiquitin Ligase Complex Regulates the Conserved Dsn1 Kinetochore Protein.” PLoS Genet 9 (2): e1003216. Cite

Argyropoulos, C., K. Wang, S. McClarty, D. Huang, J. Bernardo, D. Ellis, T. Orchard, D. Galas, and J. Johnson. 2013. “Urinary MicroRNA Profiling in the Nephropathy of Type 1 Diabetes.” PloS One 8 (1): e54662. Cite

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Boyle, J. 2013. “There and Back Again.” Nat Biotechnol 31 (1): 13–15. Cite

Brennan, Cameron W., Roel G. W. Verhaak, Aaron McKenna, Benito Campos, Houtan Noushmehr, Sofie R. Salama, Siyuan Zheng, et al. 2013. “The Somatic Genomic Landscape of Glioblastoma.” Cell 155 (October): 462–77. http://doi.org/10.1016/j.cell.2013.09.034. Cite

Cancer Genome Atlas Research Network. 2013. “Comprehensive Molecular Characterization of Clear Cell Renal Cell Carcinoma.” Nature 499 (July): 43–49. http://doi.org/10.1038/nature12222. Cite

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Chen, W. M., S. A. Danziger, J. H. Chiang, and J. D. Aitchison. 2013. “PhosphoChain: A Novel Algorithm to Predict Kinase and Phosphatase Networks from High-Throughput Expression Data.” Bioinformatics 29 (19): 2435–44. Cite

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Cromie, G. A., K. E. Hyma, C. L. Ludlow, C. Garmendia-Torres, T. L. Gilbert, P. May, A. A. Huang, A. M. Dudley, and J. C. Fay. 2013. “Genomic Sequence Diversity and Population Structure of Saccharomyces Cerevisiae Assessed by RAD-Seq.” G3 (Bethesda) 3 (12): 2163–71. Cite

Dong, Yiran, Charu Gupta Kumar, Nicholas Chia, Pan-Jun Kim, Philip A. Miller, Nathan D. Price, Isaac K. O. Cann, et al. 2013. “Halomonas Sulfidaeris-Dominated Microbial Community Inhabits a 1.8 Km-Deep Subsurface Cambrian Sandstone Reservoir.” Environ Microbiol, November. http://doi.org/10.1111/1462-2920.12325. Cite

Earls, John C., James A. Eddy, Cory C. Funk, Younhee Ko, Andrew T. Magis, and Nathan D. Price. 2013. “AUREA: An Open-Source Software System for Accurate and User-Friendly Identification of Relative Expression Molecular Signatures.” BMC Bioinformatics 14. http://doi.org/10.1186/1471-2105-14-78. Cite

Flores, Mauricio, Gustavo Glusman, Kristin Brogaard, Nathan D. Price, and Leroy Hood. 2013. “P4 Medicine: How Systems Medicine Will Transform the Healthcare Sector and Society.” Personalized Medicine 10 (6). http://doi.org/10.2217/PME.13.57. Cite

Glusman, G. 2013. “Clinical Applications of Sequencing Take Center Stage.” Genome Biol 14 (3): 303. Cite

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Goverman, J., A. Woods, L. Larson, L. P. Weiner, L. Hood, and D. M. Zaller. 2013. “Pillars Article: Transgenic Mice That Express a Myelin Basic Protein-Specific T Cell Receptor Develop Spontaneous Autoimmunity. Cell. 1993. 72: 551-560.” J Immunol 190 (7): 3018–27. Cite

H, Skubatz, M. V. Orellana, and W. N. Howald. 2013. “A NAD(P) Reductase like Protein Is the Salicylic Acid Receptor in the Appendix of the Sauromatum Guttatum Inflorescence.” Landes Bioscience 1 (Intrinsic Disordered Proteins). Cite

Haitjema, Anneke, Bernd W. Brandt, Najim Ameziane, Patrick May, Jaap Heringa, Johan P. de Winter, Hans Joenje, and Josephine C. Dorsman. 2013. “A Protein Prioritization Approach Tailored for the FA/BRCA Pathway.” PLoS One 8: e62017. http://doi.org/10.1371/journal.pone.0062017. Cite

Heavner, Benjamin D., Kieran Smallbone, Nathan D. Price, and Larry P. Walker. 2013. “Version 6 of the Consensus Yeast Metabolic Network Refines Biochemical Coverage and Improves Model Performance.” Database : The Journal of Biological Databases and Curation 2013. http://doi.org/10.1093/database/bat059. Cite

Heinäniemi, Merja, Matti Nykter, Roger Kramer, Anke Wienecke-Baldacchino, Lasse Sinkkonen, Joseph Xu Zhou, Richard Kreisberg, Stuart A. Kauffman, Sui Huang, and Ilya Shmulevich. 2013. “Gene-Pair Expression Signatures Reveal Lineage Control.” Nat Methods 10: 577–83. http://doi.org/10.1038/nmeth.2445. Cite

Hood, Leroy. 2013. “Systems Biology and P4 Medicine: Past, Present, and Future.” Rambam Maimonides Med J 4 (April): e0012. http://doi.org/10.5041/RMMJ.10112. Cite

Hood, L. 2013. “Interview with Leroy Hood.” Bioanalysis 5 (12): 1475–78. Cite

Hood, L., and C. Auffray. 2013. “Participatory Medicine: A Driving Force for Revolutionizing Healthcare.” Genome Medicine 5 (12): 110. Cite

Hood, L. E., and E. D. Lazowska. 2013. “Every Life Has Equal Value.” Cell 154 (6): 1178–79. Cite

Hood, L., and L. Rowen. 2013. “The Human Genome Project: Big Science Transforms Biology and Medicine.” Genome Med 5 (9): 79. Cite

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Huang, S. 2013. “Genetic and Non-Genetic Instability in Tumor Progression: Link between the Fitness Landscape and the Epigenetic Landscape of Cancer Cells.” Cancer Metastasis Rev 32 (3–4): 423–48. Cite

Huang, S. 2013. “Hybrid T-Helper Cells: Stabilizing the Moderate Center in a Polarized System.” PLoS Biol 11 (8): e1001632. Cite

Huang, Sui. 2013. “When Peers Are Not Peers and Don’t Know It: The Dunning-Kruger Effect and Self-Fulfilling Prophecy in Peer-Review.” BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology. Cite

Huang, S., and S. Kauffman. 2013. “How to Escape the Cancer Attractor: Rationale and Limitations of Multi-Target Drugs.” Semin Cancer Biol 23 (4): 270–78. Cite

Huttenhain, R., S. Surinova, R. Ossola, Z. Sun, D. Campbell, F. Cerciello, R. Schiess, et al. 2013. “N-Glycoprotein SRMAtlas: A Resource of Mass-Spectrometric Assays for N-Glycosites Enabling Consistent and Multiplexed Protein Quantification for Clinical Applications.” Molecular & Cellular Proteomics : MCP, February. Cite

Jensen, H. A., L. E. Styskal, R. Tasseff, R. P. Bunaciu, J. Congleton, J. D. Varner, and A. Yen. 2013. “The Src-Family Kinase Inhibitor PP2 Rescues Inducible Differentiation Events in Emergent Retinoic Acid-Resistant Myeloblastic Leukemia Cells.” PLoS One 8 (3): e58621. Cite

Jung, S., J. J. Smith, P. D. von Haller, D. J. Dilworth, K. A. Sitko, L. R. Miller, R. A. Saleem, D. R. Goodlett, and J. D. Aitchison. 2013. “Global Analysis of Condition-Specific Subcellular Protein Distribution and Abundance.” Mol Cell Proteomics 12 (5): 1421–35. Cite

Kadoch, C., D. C. Hargreaves, C. Hodges, L. Elias, L. Ho, J. Ranish, and G. R. Crabtree. 2013. “Proteomic and Bioinformatic Analysis of Mammalian SWI/SNF Complexes Identifies Extensive Roles in Human Malignancy.” Nat Genet, May. Cite

Kay, P., R. Choudhury, M. Nel, M. V. Orellana, and P. M.Durand. 2013. “Multicolour Flow Cytometry Analyses and Autofluorescence in Chlorophytes: Lessons from Programmed Cell Death Studies in Chlamydomonas Reinhardtii.” Journal of Applied Phycology 25 (5): 1473–82. Cite

Ko, Younhee, Seth A. Ament, James A. Eddy, Juan Caballero, John C. Earls, Leroy Hood, and Nathan D. Price. 2013. “Cell Type-Specific Genes Show Striking and Distinct Patterns of Spatial Expression in the Mouse Brain.” Proceedings of the National Academy of Sciences of the United States of America 110 (8): 3095–3100. http://doi.org/10.1073/pnas.1222897110. Cite

Kolodkin, Alexey, Evangelos Simeonidis, and Hans V. Westerhoff. 2013. “Computing Life: Add Logos to Biology and Bios to Physics.” Progress in Biophysics and Molecular Biology 111 (2–3). http://doi.org/10.1016/j.pbiomolbio.2012.10.003. Cite

Labhsetwar, Piyush, John Andrew Cole, Elijah Roberts, Nathan D. Price, and Zaida A. Luthey-Schulten. 2013. “Heterogeneity in Protein Expression Induces Metabolic Variability in a Modeled Escherichia Coli Population.” Proceedings of the National Academy of Sciences of the United States of America 110 (34): 14006–11. http://doi.org/10.1073/pnas.1222569110. Cite

Larjo, A., I. Shmulevich, and H. Lahdesmaki. 2013. “Structure Learning for Bayesian Networks as Models of Biological Networks.” Methods in Molecular Biology 939: 35–45. Cite

Li, Xiao-jun, Clive Hayward, Pui-Yee Fong, Michel Dominguez, Stephen W. Hunsucker, Lik Wee Lee, Matthew McLean, et al. 2013. “A Blood-Based Proteomic Classifier for the Molecular Characterization of Pulmonary Nodules.” Science Translational Medicine 5 (207). http://doi.org/10.1126/scitranslmed.3007013. Cite

Lin, Jake, Richard Kreisberg, Aleksi Kallio, Aimée M. Dudley, Matti Nykter, Ilya Shmulevich, Patrick May, and Reija Autio. 2013. “POMO–Plotting Omics Analysis Results for Multiple Organisms.” BMC Genomics 14: 918. http://doi.org/10.1186/1471-2164-14-918. Cite

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Liu, S., H. Im, A. Bairoch, M. Cristofanilli, R. Chen, E. W. Deutsch, S. Dalton, et al. 2013. “A Chromosome-Centric Human Proteome Project (C-HPP) to Characterize the Sets of Proteins Encoded in Chromosome 17.” Journal of Proteome Research 12 (1): 45–57. Cite

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2012

2323737 2RQKSFR5 2012 1 chicago-author-date-16th-edition 50 creator asc 1 1 319 https://isbscience.org/wp-content/plugins/zotpress/

Aitchison, J. D., and M. P. Rout. 2012. “The Yeast Nuclear Pore Complex and Transport through It.” Genetics 190 (3): 855–83. Cite

Auffray, Charles, and Leroy Hood. 2012. “Editorial: Systems Biology and Personalized Medicine – the Future Is Now.” Biotechnol J 7 (August): 938–39. http://doi.org/10.1002/biot.201200242. Cite

Austin, R. J., H. M. Smidansky, C. A. Holstein, D. K. Chang, A. Epp, N. C. Josephson, and D. B. Martin. 2012. “Proteomic Analysis of the Androgen Receptor via MS-Compatible Purification of Biotinylated Protein on Streptavidin Resin.” Proteomics 12 (1): 43–53. Cite

Austin, R. J., D. K. Chang, C. A. Holstein, L. W. Lee, J. Risler, J. H. Wang, L. Adams, N. B. Krusberski, and D. B. Martin. 2012. “IQcat: Multiplexed Protein Quantification by Isoelectric QconCAT.” Proteomics 12 (13): 2078–83. Cite

Bare, J. C., and N. S. Baliga. 2012. “Architecture for Interoperable Software in Biology.” Briefings in Bioinformatics, December. Cite

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Benedict, Matthew N., Matthew C. Gonnerman, William W. Metcalf, and Nathan D. Price. 2012. “Genome-Scale Metabolic Reconstruction and Hypothesis Testing in the Methanogenic Archaeon Methanosarcina Acetivorans C2A.” Journal of Bacteriology 194 (4): 855–65. http://doi.org/10.1128/JB.06040-11. Cite

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Brusniak, M. Y., C. S. Chu, U. Kusebauch, M. J. Sartain, J. D. Watts, and R. L. Moritz. 2012. “An Assessment of Current Bioinformatic Solutions for Analyzing LC-MS Data Acquired by Selected Reaction Monitoring Technology.” Proteomics 12 (8): 1176–84. Cite

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2009

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Aebersold, R. 2009. “A Stress Test for Mass Spectrometry-Based Proteomics.” Nat Methods 6 (6): 411–12. Cite

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Anderson, N. L., N. G. Anderson, T. W. Pearson, C. H. Borchers, A. G. Paulovich, S. D. Patterson, M. Gillette, R. Aebersold, and S. A. Carr. 2009. “A Human Proteome Detection and Quantitation Project.” Mol Cell Proteomics 8 (5): 883–86. Cite

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Beck, M., J. A. Malmstrom, V. Lange, A. Schmidt, E. W. Deutsch, and R. Aebersold. 2009. “Visual Proteomics of the Human Pathogen Leptospira Interrogans.” Nat Methods 6 (11): 817–23. Cite

Bell, A. W., E. W. Deutsch, C. E. Au, R. E. Kearney, R. Beavis, S. Sechi, T. Nilsson, and J. J. Bergeron. 2009. “A HUPO Test Sample Study Reveals Common Problems in Mass Spectrometry-Based Proteomics.” Nat Methods 6 (6): 423–30. Cite

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Carapito, C., C. Klemm, R. Aebersold, and B. Domon. 2009. “Systematic LC-MS Analysis of Labile Post-Translational Modifications in Complex Mixtures.” J Proteome Res 8 (5): 2608–14. Cite

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Di Paolo, N. C., E. A. Miao, Y. Iwakura, K. Murali-Krishna, A. Aderem, R. A. Flavell, T. Papayannopoulou, and D. M. Shayakhmetov. 2009. “Virus Binding to a Plasma Membrane Receptor Triggers Interleukin-1 Alpha-Mediated Proinflammatory Macrophage Response in Vivo.” Immunity 31 (1): 110–21. Cite

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Domon, B., B. Bodenmiller, C. Carapito, Z. Hao, A. Huehmer, and R. Aebersold. 2009. “Electron Transfer Dissociation in Conjunction with Collision Activation to Investigate the Drosophila Melanogaster Phosphoproteome.” J Proteome Res 8 (6): 2633–39. Cite

Eddy, James A., Donald Geman, and Nathan D. Price. 2009. “Relative Expression Analysis for Identifying Perturbed Pathways.” Conference Proceedings : … Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference 2009: 5456–59. http://doi.org/10.1109/IEMBS.2009.5334063. Cite

Edelman, Lucas B., Giuseppe Toia, Donald Geman, Wei Zhang, and Nathan D. Price. 2009. “Two-Transcript Gene Expression Classifiers in the Diagnosis and Prognosis of Human Diseases.” BMC Genomics 10. http://doi.org/10.1186/1471-2164-10-583. Cite

Eisenacher, M., L. Martens, T. Hardt, M. Kohl, H. Barsnes, K. Helsens, J. Hakkinen, et al. 2009. “Getting a Grip on Proteomics Data – Proteomics Data Collection (ProDaC).” Proteomics 9 (15): 3928–33. Cite

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Foltz, G., J. G. Yoon, H. Lee, T. C. Ryken, Z. Sibenaller, M. Ehrich, L. Hood, and A. Madan. 2009. “DNA Methyltransferase-Mediated Transcriptional Silencing in Malignant Glioma: A Combined Whole-Genome Microarray and Promoter Array Analysis.” Oncogene 28 (29): 2667–77. Cite

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Galas, D. J., and L. Hood. 2009. “Systems Biology and Emerging Technologies Will Catalyze the Transition from Reactive Medicine to Predictive, Personalized, Preventive and Participatory (P4) Medicine.” Interdisciplinary Bio Central 1 (2): 0006. Cite

Gehlenborg, N., W. Yan, I. Lee, H. Yoo, K. Nieselt, D. Hwang, R. Aebersold, and L. Hood. 2009. “Prequips–an Extensible Software Platform for Integration, Visualization and Analysis of LC-MS/MS Proteomics Data.” Bioinformatics 25 (5): 682–83. Cite

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2008

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Aderem, A. 2008. “Alan Aderem: From Molecules to Megabytes. Interviewed by Nicole LeBrasseur.” J Cell Biol 180 (2): 252–53. Cite

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Ao, P., D. J. Galas, L. Hood, and X. Zhu. 2008. “Cancer as Robust Intrinsic State of Endogenous Molecular-Cellular Network Shaped by Evolution.” Med Hypotheses 70 (3): 678–84. Cite

Baliga, N. S. 2008. “Systems Biology. The Scale of Prediction.” Science 320 (5881): 1297–98. Cite

Balleza, E., E. R. Alvarez-Buylla, A. Chaos, S. Kauffman, I. Shmulevich, and M. Aldana. 2008. “Critical Dynamics in Genetic Regulatory Networks: Examples from Four Kingdoms.” PLoS OnePLoS ONE 3 (6): e2456. Cite

Bao, Xin-Yu, Cesare Soci, Darija Susac, Jon Bratvold, David P. R. Aplin, Wei Wei, Ching-Yang Chen, Shadi A. Dayeh, Karen L. Kavanagh, and Deli Wang. 2008. “Heteroepitaxial Growth of Vertical GaAs Nanowires on Si (111) Substrates by Metal−Organic Chemical Vapor Deposition.” Nano Letters 8 (11): 3755–60. http://doi.org/10.1021/nl802062y. Cite

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Deutsch, E. W., H. Lam, and R. Aebersold. 2008. “Data Analysis and Bioinformatics Tools for Tandem Mass Spectrometry in Proteomics.” Physiol Genomics 33 (1): 18–25. Cite

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Lam, H., E. W. Deutsch, J. S. Eddes, J. K. Eng, S. E. Stein, and R. Aebersold. 2008. “Building Consensus Spectral Libraries for Peptide Identification in Proteomics.” Nat Methods 5 (10): 873–75. Cite

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Lange, V., J. A. Malmstrom, J. Didion, N. L. King, B. P. Johansson, J. Schafer, J. Rameseder, et al. 2008. “Targeted Quantitative Analysis of Streptococcus Pyogenes Virulence Factors by Multiple Reaction Monitoring.” Mol Cell Proteomics 7 (8): 1489–1500. Cite

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Lee, W. W., D. Cui, M. Czesnikiewicz-Guzik, R. Z. Vencio, I. Shmulevich, A. Aderem, C. M. Weyand, and J. J. Goronzy. 2008. “Age-Dependent Signature of Metallothionein Expression in Primary CD4 T Cell Responses Is Due to Sustained Zinc Signaling.” Rejuvenation Res 11 (6): 1001–11. Cite

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2007

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Aderem, A. 2007. “Systems Biology.” Current Opinion in Biotechnology 18 (4): 331–32. Cite

Ahdesmaki, M., H. Lahdesmaki, A. Gracey, I. Shmulevich, and O. Yli-Harja. 2007. “Robust Regression for Periodicity Detection in Non-Uniformly Sampled Time-Course Gene Expression Data.” BMC Bioinformatics 8: 233. Cite

Ahrens, C. H., E. Brunner, E. Hafen, R. Aebersold, and K. Basler. 2007. “A Proteome Catalog of Drosophila Melanogaster: An Essential Resource for Targeted Quantitative Proteomics.” Fly (Austin) 1 (3): 182–86. Cite

Aitchison, J. D., and R. W. Wozniak. 2007. “Cell Biology: Pore Puzzle.” Nature 450 (7170): 621–22. Cite

Andersen-Nissen, E., T. R. Hawn, K. D. Smith, A. Nachman, A. E. Lampano, S. Uematsu, S. Akira, and A. Aderem. 2007. “Cutting Edge: Tlr5-/- Mice Are More Susceptible to Escherichia Coli Urinary Tract Infection.” J Immunol 178 (8): 4717–20. Cite

Andersen-Nissen, E., K. D. Smith, R. Bonneau, R. K. Strong, and A. Aderem. 2007. “A Conserved Surface on Toll-like Receptor 5 Recognizes Bacterial Flagellin.” J Exp Med 204 (2): 393–403. Cite

Au, Edmund, Miranda W. Richter, Adele J. Vincent, Wolfram Tetzlaff, Ruedi Aebersold, E. Helene Sage, and A. Jane Roskams. 2007. “SPARC from Olfactory Ensheathing Cells Stimulates Schwann Cells to Promote Neurite Outgrowth and Enhances Spinal Cord Repair.” The Journal of Neuroscience 27 (27): 7208–21. http://doi.org/10.1523/JNEUROSCI.0509-07.2007. Cite Download

Avila-Campillo, I., K. Drew, J. Lin, D. J. Reiss, and R. Bonneau. 2007. “BioNetBuilder: Automatic Integration of Biological Networks.” Bioinformatics 23 (3): 392–93. Cite

Bare, J. C., P. Shannon, A. K. Schmid, and N. S. Baliga. 2007. “The Firegoose: Two-Way Integration of Diverse Data from Different Bioinformatics Web Resources with Desktop Applications.” BMC Bioinformatics 8 (1): 456. Cite

Bekris, L. M., C. Shephard, M. Janer, J. Graham, B. McNeney, J. Shin, M. Zarghami, et al. 2007. “Glutamate Cysteine Ligase Catalytic Subunit Promoter Polymorphisms and Associations with Type 1 Diabetes Age-at-Onset and GAD65 Autoantibody Levels.” Exp Clin Endocrinol Diabetes 115 (4): 221–28. Cite

Bochud, P. Y., M. Hersberger, P. Taffe, M. Bochud, C. M. Stein, S. D. Rodrigues, T. Calandra, et al. 2007. “Polymorphisms in Toll-like Receptor 9 Influence the Clinical Course of HIV-1 Infection.” AIDS 21 (4): 441–46. Cite

Bochud, P. Y., A. S. Magaret, D. M. Koelle, A. Aderem, and A. Wald. 2007. “Polymorphisms in TLR2 Are Associated with Increased Viral Shedding and Lesional Rate in Patients with Genital Herpes Simplex Virus Type 2 Infection.” J Infect Dis 196 (4): 505–9. Cite

Bodenmiller, B., J. Malmstrom, B. Gerrits, D. Campbell, H. Lam, A. Schmidt, O. Rinner, et al. 2007. “PhosphoPep–a Phosphoproteome Resource for Systems Biology Research in Drosophila Kc167 Cells.” Mol Syst Biol 3: 139. Cite

Bodenmiller, B., L. N. Mueller, M. Mueller, B. Domon, and R. Aebersold. 2007. “Reproducible Isolation of Distinct, Overlapping Segments of the Phosphoproteome.” Nat Methods 4 (3): 231–37. Cite

Bodenmiller, B., L. N. Mueller, P. G. Pedrioli, D. Pflieger, M. A. Junger, J. K. Eng, R. Aebersold, and W. A. Tao. 2007. “An Integrated Chemical, Mass Spectrometric and Computational Strategy for (Quantitative) Phosphoproteomics: Application to Drosophila Melanogaster Kc167 Cells.” Mol Biosyst 3 (4): 275–86. Cite

Bonneau, R., M. T. Facciotti, D. J. Reiss, A. K. Schmid, M. Pan, A. Kaur, V. Thorsson, et al. 2007. “A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell.” Cell 131 (7): 1354–65. Cite

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Camp, N. J., L. A. Cannon-Albright, J. M. Farnham, A. B. Baffoe-Bonnie, A. George, I. Powell, J. E. Bailey-Wilson, et al. 2007. “Compelling Evidence for a Prostate Cancer Gene at 22q12.3 by the International Consortium for Prostate Cancer Genetics.” Hum Mol Genet 16 (11): 1271–78. Cite

Carter, G. W., S. Prinz, C. Neou, J. P. Shelby, B. Marzolf, V. Thorsson, and T. Galitski. 2007. “Prediction of Phenotype and Gene Expression for Combinations of Mutations.” Mol Syst Biol 3: 96. Cite

Chen, R., T. A. Brentnall, S. Pan, K. Cooke, K. W. Moyes, Z. Lane, D. A. Crispin, D. R. Goodlett, R. Aebersold, and M. P. Bronner. 2007. “Quantitative Proteomics Analysis Reveals That Proteins Differentially Expressed in Chronic Pancreatitis Are Also Frequently Involved in Pancreatic Cancer.” Mol Cell Proteomics 6 (8): 1331–42. Cite

Chen, R., S. Pan, R. Aebersold, and T. A. Brentnall. 2007. “Proteomics Studies of Pancreatic Cancer.” Proteomics Clin Appl 1 (12): 1582–91. Cite

Chen, R., S. Pan, K. Cooke, K. W. Moyes, M. P. Bronner, D. R. Goodlett, R. Aebersold, and T. A. Brentnall. 2007. “Comparison of Pancreas Juice Proteins from Cancer versus Pancreatitis Using Quantitative Proteomic Analysis.” Pancreas 34 (1): 70–79. Cite

Choi, J., B. Kim, K. Heo, K. Kim, H. Kim, Y. Zhan, J. Ranish, and W. An. 2007. “Purification and Characterization of Cellular Proteins Associated with Histone H4 Tails.” J Biol Chem 282 (29): 21024–31. Cite

Cline, M. S., M. Smoot, E. Cerami, A. Kuchinsky, N. Landys, C. Workman, R. Christmas, et al. 2007. “Integration of Biological Networks and Gene Expression Data Using Cytoscape.” Nat Protoc 2 (10): 2366–82. Cite

Dall’Era, M. A., A. Oudes, D. B. Martin, and A. Y. Liu. 2007. “HSP27 and HSP70 Interact with CD10 in C4-2 Prostate Cancer Cells.” Prostate 67 (7): 714–21. Cite

Bivort, Benjamin de, Sui Huang, and Yaneer Bar-Yam. 2007. “Empirical Multiscale Networks of Cellular Regulation.” PLoS Computational Biology 3 (10): 1968–78. http://doi.org/10.1371/journal.pcbi.0030207. Cite

Jong, B. C. de, P. C. Hill, A. Aiken, D. J. Jeffries, A. Onipede, P. M. Small, R. A. Adegbola, and T. P. Corrah. 2007. “Clinical Presentation and Outcome of Tuberculosis Patients Infected by M. Africanum versus M. Tuberculosis.” Int J Tuberc Lung Dis 11 (4): 450–56. Cite

Demers, C., C. P. Chaturvedi, J. Ranish, G. Juban, P. Lai, F. Morle, R. Aebersold, F. J. Dilworth, M. Groudine, and M. Brand. 2007. “Activator-Mediated Recruitment of the MLL2 Methyltransferase Complex to the Beta-Globin Locus.” Mol Cell 27 (4): 573–84. Cite

Djouder, N., S. C. Metzler, A. Schmidt, C. Wirbelauer, M. Gstaiger, R. Aebersold, D. Hess, and W. Krek. 2007. “S6K1-Mediated Disassembly of Mitochondrial URI/PP1gamma Complexes Activates a Negative Feedback Program That Counters S6K1 Survival Signaling.” Mol Cell 28 (1): 28–40. Cite

Facciotti, M. T., D. J. Reiss, M. Pan, A. Kaur, M. Vuthoori, R. Bonneau, P. Shannon, et al. 2007. “General Transcription Factor Specified Global Gene Regulation in Archaea.” Proc Natl Acad Sci U S A 104 (11): 4630–35. Cite

Fu, E., S. A. Ramsey, J. Chen, T. M. Chinowsky, B. Wiley, Y. Xia, and P. Yager. 2007. “Resonance Wavelength-Dependent Signal of Absorptive Particles in Surface Plasmon Resonance-Based Detection.” Sens Actuators B Chem 123 (1): 606–13. Cite

Fu, E., S. A. Ramsey, and P. Yager. 2007. “Dependence of the Signal Amplification Potential of Colloidal Gold Nanoparticles on Resonance Wavelength in Surface Plasmon Resonance-Based Detection.” Anal Chim Acta 599 (1): 118–23. Cite

Gagneux, S., and P. M. Small. 2007. “Global Phylogeography of Mycobacterium Tuberculosis and Implications for Tuberculosis Product Development.” Lancet Infect Dis 7 (5): 328–37. Cite

Gingras, A. C., M. Gstaiger, B. Raught, and R. Aebersold. 2007. “Analysis of Protein Complexes Using Mass Spectrometry.” Nat Rev Mol Cell Biol 8 (8): 645–54. Cite

Hawn, T. R., E. A. Misch, S. J. Dunstan, G. E. Thwaites, N. T. Lan, H. T. Quy, T. T. Chau, et al. 2007. “A Common Human TLR1 Polymorphism Regulates the Innate Immune Response to Lipopeptides.” Eur J Immunol 37 (8): 2280–89. Cite

Hawn, T. R., W. R. Berrington, I. A. Smith, S. Uematsu, S. Akira, A. Aderem, K. D. Smith, and S. J. Skerrett. 2007. “Altered Inflammatory Responses in TLR5-Deficient Mice Infected with Legionella Pneumophila.” J Immunol 179 (10): 6981–87. Cite

He, X. C., T. Yin, J. C. Grindley, Q. Tian, T. Sato, W. A. Tao, R. Dirisina, et al. 2007. “PTEN-Deficient Intestinal Stem Cells Initiate Intestinal Polyposis.” Nat Genet 39 (2): 189–98. Cite

Heo, K., B. Kim, K. Kim, J. Choi, H. Kim, Y. Zhan, J. Ranish, and W. An. 2007. “Isolation and Characterization of Proteins Associated with Histone H3 Tails in Vivo.” J Biol Chem 282 (21): 15476–83. Cite

Hu, Z., L. Hood, and Q. Tian. 2007. “Quantitative Proteomic Approaches for Biomarker Discovery.” Proteomics Clin Appl 1 (9): 1036–41. Cite

Huang, Sui, Yan-Ping Guo, Gillian May, and Tariq Enver. 2007. “Bifurcation Dynamics in Lineage-Commitment in Bipotent Progenitor Cells.” Developmental Biology 305 (2): 695–713. http://doi.org/10.1016/j.ydbio.2007.02.036. Cite

Hulbert, E. M., L. J. Smink, E. C. Adlem, J. E. Allen, D. B. Burdick, O. S. Burren, V. M. Cassen, et al. 2007. “T1DBase: Integration and Presentation of Complex Data for Type 1 Diabetes Research.” Nucleic Acids Res 35 (Database issue): D742-6. Cite

Ibrahim, S. F., A. H. Diercks, T. W. Petersen, and G. van den Engh. 2007. “Kinetic Analyses as a Critical Parameter in Defining the Side Population (SP) Phenotype.” Exp Cell Res 313 (9): 1921–26. Cite

Iyer, S., K. Deutsch, X. Yan, and B. Lin. 2007. “Batch RNAi Selector: A Standalone Program to Predict Specific siRNA Candidates in Batches with Enhanced Sensitivity.” Comput Methods Programs Biomed 85 (3): 203–9. Cite

Jasavala, R., H. Martinez, J. Thumar, A. Andaya, A. C. Gingras, J. K. Eng, R. Aebersold, D. K. Han, and M. E. Wright. 2007. “Identification of Putative Androgen Receptor Interaction Protein Modules: Cytoskeleton and Endosomes Modulate Androgen Receptor Signaling in Prostate Cancer Cells.” Mol Cell Proteomics 6 (2): 252–71. Cite

Johanneson, B., K. Deutsch, L. McIntosh, D. M. Friedrichsen-Karyadi, M. Janer, E. M. Kwon, L. Iwasaki, L. Hood, E. A. Ostrander, and J. L. Stanford. 2007. “Suggestive Genetic Linkage to Chromosome 11p11.2-Q12.2 in Hereditary Prostate Cancer Families with Primary Kidney Cancer.” Prostate 67 (7): 732–42. Cite

Jones, A. R., M. Miller, R. Aebersold, R. Apweiler, C. A. Ball, A. Brazma, J. Degreef, et al. 2007. “The Functional Genomics Experiment Model (FuGE): An Extensible Framework for Standards in Functional Genomics.” Nat Biotechnol 25 (10): 1127–33. Cite

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Kim, B., A. I. Nesvizhskii, P. G. Rani, S. Hahn, R. Aebersold, and J. Ranish. 2007. “The Transcription Elongation Factor TFIIS Is a Component of RNA Polymerase II Preinitiation Complexes.” Proc Natl Acad Sci U S A 104 (41): 16068–73. Cite

Krawitz, P., and I. Shmulevich. 2007. “Entropy of Complex Relevant Components of Boolean Networks.” Phys Rev E Stat Nonlin Soft Matter Phys 76 (3 Pt 2): 036115. Cite

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2006

2323737 2RQKSFR5 2006 1 chicago-author-date-16th-edition 50 creator asc 1 1 319 https://isbscience.org/wp-content/plugins/zotpress/

Aga, R. S., E. Fair, N. F. Abernethy, K. Deriemer, E. A. Paz, L. M. Kawamura, P. M. Small, and M. Kato-Maeda. 2006. “Microevolution of the Direct Repeat Locus of Mycobacterium Tuberculosis in a Strain Prevalent in San Francisco.” J Clin Microbiol 44 (4): 1558–60. Cite

Allen, Timothy E., Nathan D. Price, Andrew R. Joyce, and Bernhard O. Palsson. 2006. “Long-Range Periodic Patterns in Microbial Genomes Indicate Significant Multi-Scale Chromosomal Organization.” PLoS Computational Biology 2 (1). http://doi.org/10.1371/journal.pcbi.0020002. Cite

Barrett, Christian L., Nathan D. Price, and Bernhard O. Palsson. 2006. “Network-Level Analysis of Metabolic Regulation in the Human Red Blood Cell Using Random Sampling and Singular Value Decomposition.” BMC Bioinformatics 7. http://doi.org/10.1186/1471-2105-7-132. Cite

Becker, Scott A., Nathan D. Price, and Bernhard O. Palsson. 2006. “Metabolite Coupling in Genome-Scale Metabolic Networks.” BMC Bioinformatics 7. http://doi.org/10.1186/1471-2105-7-111. Cite

Bonneau, R., D. J. Reiss, P. Shannon, M. Facciotti, L. Hood, N. S. Baliga, and V. Thorsson. 2006. “The Inferelator: An Algorithm for Learning Parsimonious Regulatory Networks from Systems-Biology Data Sets de Novo.” Genome Biol 7 (5): R36. Cite

Bradshaw, R. A., A. L. Burlingame, S. Carr, and R. Aebersold. 2006. “Reporting Protein Identification Data: The next Generation of Guidelines.” Mol Cell Proteomics 5 (5): 787–88. Cite

Brown, V., R. A. Brown, A. Ozinsky, J. R. Hesselberth, and S. Fields. 2006. “Binding Specificity of Toll-like Receptor Cytoplasmic Domains.” Eur J Immunol 36 (3): 742–53. Cite

Burrage, K., L. Hood, and M. A. Ragan. 2006. “Advanced Computing for Systems Biology.” Brief Bioinform 7 (4): 390–98. Cite

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Carter, G. W., S. Rupp, G. R. Fink, and T. Galitski. 2006. “Disentangling Information Flow in the Ras-cAMP Signaling Network.” Genome Res 16 (4): 520–26. Cite

Chen, R., S. Pan, E. C. Yi, S. Donohoe, M. P. Bronner, J. D. Potter, D. R. Goodlett, R. Aebersold, and T. A. Brentnall. 2006. “Quantitative Proteomic Profiling of Pancreatic Cancer Juice.” Proteomics 6 (13): 3871–79. Cite

Chung, Y., X. Yang, S. H. Chang, L. Ma, Q. Tian, and C. Dong. 2006. “Expression and Regulation of IL-22 in the IL-17-Producing CD4+ T Lymphocytes.” Cell Res 16 (11): 902–7. Cite

Jong, B. C. de, P. C. Hill, R. H. Brookes, S. Gagneux, D. J. Jeffries, J. K. Otu, S. A. Donkor, et al. 2006. “Mycobacterium Africanum Elicits an Attenuated T Cell Response to Early Secreted Antigenic Target, 6 kDa, in Patients with Tuberculosis and Their Household Contacts.” J Infect Dis 193 (9): 1279–86. Cite

Desiere, F., E. W. Deutsch, N. L. King, A. I. Nesvizhskii, P. Mallick, J. Eng, S. Chen, J. Eddes, S. N. Loevenich, and R. Aebersold. 2006. “The PeptideAtlas Project.” Nucleic Acids Res 34 (Database issue): D655-8. Cite

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Domon, B., and R. Aebersold. 2006. “Mass Spectrometry and Protein Analysis.” Science 312 (5771): 212–17. Cite

Domon, B., and R. Aebersold. 2006. “Challenges and Opportunities in Proteomics Data Analysis.” Mol Cell Proteomics 5 (10): 1921–26. Cite

Ehlers, M., H. Fukuyama, T. L. McGaha, A. Aderem, and J. V. Ravetch. 2006. “TLR9/MyD88 Signaling Is Required for Class Switching to Pathogenic IgG2a and 2b Autoantibodies in SLE.” J Exp Med 203 (3): 553–61. Cite

Fagarasanu, A., M. Fagarasanu, G. A. Eitzen, J. D. Aitchison, and R. A. Rachubinski. 2006. “The Peroxisomal Membrane Protein Inp2p Is the Peroxisome-Specific Receptor for the Myosin V Motor Myo2p of Saccharomyces Cerevisiae.” Dev Cell 10 (5): 587–600. Cite

Fischbach, M. A., H. Lin, L. Zhou, Y. Yu, R. J. Abergel, D. R. Liu, K. N. Raymond, et al. 2006. “The Pathogen-Associated iroA Gene Cluster Mediates Bacterial Evasion of Lipocalin 2.” Proc Natl Acad Sci U S A 103 (44): 16502–7. Cite

Flory, M. R., H. Lee, R. Bonneau, P. Mallick, K. Serikawa, D. R. Morris, and R. Aebersold. 2006. “Quantitative Proteomic Analysis of the Budding Yeast Cell Cycle Using Acid-Cleavable Isotope-Coded Affinity Tag Reagents.” Proteomics 6 (23): 6146–57. Cite

Foltz, G., G. Y. Ryu, J. G. Yoon, T. Nelson, J. Fahey, A. Frakes, H. Lee, et al. 2006. “Genome-Wide Analysis of Epigenetic Silencing Identifies BEX1 and BEX2 as Candidate Tumor Suppressor Genes in Malignant Glioma.” Cancer Res 66 (13): 6665–74. Cite

Fu, E., S. Ramsey, R. Thariani, and P. Yager. 2006. “One-Dimensional Surface Plasmon Resonance Imaging System Using Wavelength Interrogation.” Review of Scientific Instruments 77: 076106. Cite

Gagneux, S., M. V. Burgos, K. Deriemer, A. Encisco, S. Munoz, P. C. Hopewell, P. M. Small, and A. S. Pym. 2006. “Impact of Bacterial Genetics on the Transmission of Isoniazid-Resistant Mycobacterium Tuberculosis.” PLoS Pathog 2 (6): e61. Cite

Gagneux, S., K. Deriemer, T. Van, M. Kato-Maeda, B. C. de Jong, S. Narayanan, M. Nicol, et al. 2006. “Variable Host-Pathogen Compatibility in Mycobacterium Tuberculosis.” Proc Natl Acad Sci U S A 103 (8): 2869–73. Cite

Gagneux, S., C. D. Long, P. M. Small, T. Van, G. K. Schoolnik, and B. J. Bohannan. 2006. “The Competitive Cost of Antibiotic Resistance in Mycobacterium Tuberculosis.” Science 312 (5782): 1944–46. Cite

Gan, R. R., E. C. Yi, Y. Chiu, H. Lee, Y. C. Kao, T. H. Wu, R. Aebersold, D. R. Goodlett, and W. V. Ng. 2006. “Proteome Analysis of Halobacterium Sp. NRC-1 Facilitated by the Biomodule Analysis Tool BMSorter.” Mol Cell Proteomics 5 (6): 987–97. Cite

Gessler, D., C. Dye, P. Farmer, M. Murray, T. Navin, R. Reves, T. Shinnick, P. M. Small, T. Yates, and G. Simpson. 2006. “Public Health. A National Tuberculosis Archive.” Science 311 (5765): 1245–46. Cite

Gianchandani, Erwin P., Jason A. Papin, Nathan D. Price, Andrew R. Joyce, and Bernhard O. Palsson. 2006. “Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems.” PLoS Computational Biology 2 (8). http://doi.org/10.1371/journal.pcbi.0020101. Cite

Gilchrist, M., V. Thorsson, B. Li, A. G. Rust, M. Korb, J. Roach, K. Kennedy, T. Hai, H. Bolouri, and A. Aderem. 2006. “Systems Biology Approaches Identify ATF3 as a Negative Regulator of Toll-like Receptor 4.” Nature 441 (7090): 173–78. Cite

Glusman, G., S. Qin, M. R. El-Gewely, A. F. Siegel, J. Roach, L. Hood, and A. Smit. 2006. “A Third Approach to Gene Prediction Suggests Thousands of Additional Human Transcribed Regions.” PLoS Comput Biol 2 (3): e18. Cite

Guo, Z., L. Hood, M. Malkki, and E. W. Petersdorf. 2006. “Long-Range Multilocus Haplotype Phasing of the MHC.” Proc Natl Acad Sci U S A 103 (18): 6964–69. Cite

Gupta, N., B. Wollscheid, J. Watts, B. Scheer, R. Aebersold, and A. L. DeFranco. 2006. “Quantitative Proteomic Analysis of B Cell Lipid Rafts Reveals That Ezrin Regulates Antigen Receptor-Mediated Lipid Raft Dynamics.” Nat Immunol 7 (6): 625–33. Cite

Hardwidge, P. R., S. Donohoe, R. Aebersold, and B. B. Finlay. 2006. “Proteomic Analysis of the Binding Partners to Enteropathogenic Escherichia Coli Virulence Proteins Expressed in Saccharomyces Cerevisiae.” Proteomics 6 (7): 2174–79. Cite

Hawn, T. R., K. D. Smith, A. Aderem, and S. J. Skerrett. 2006. “Myeloid Differentiation Primary Response Gene (88)- and Toll-like Receptor 2-Deficient Mice Are Susceptible to Infection with Aerosolized Legionella Pneumophila.” J Infect Dis 193 (12): 1693–1702. Cite

Hawn, T. R., S. J. Dunstan, G. E. Thwaites, C. P. Simmons, N. T. Thuong, N. T. Lan, H. T. Quy, et al. 2006. “A Polymorphism in Toll-Interleukin 1 Receptor Domain Containing Adaptor Protein Is Associated with Susceptibility to Meningeal Tuberculosis.” J Infect Dis 194 (8): 1127–34. Cite

Hongay, C. F., P. L. Grisafi, T. Galitski, and G. R. Fink. 2006. “Antisense Transcription Controls Cell Fate in Saccharomyces Cerevisiae.” Cell 127 (4): 735–45. Cite

Huang, Sui, and Donald E. Ingber. 2006. “A Non-Genetic Basis for Cancer Progression and Metastasis: Self-Organizing Attractors in Cell Regulatory Networks.” Breast Disease 26: 27–54. Cite

Huang, Sui, and J. Wikswo. 2006. “Dimensions of Systems Biology.” Reviews of Physiology, Biochemistry and Pharmacology 157: 81–104. Cite

Jiang, R., C. Mircean, I. Shmulevich, D. Cogdell, Y. Jia, I. Tabus, K. Aldape, et al. 2006. “Pathway Alterations during Glioma Progression Revealed by Reverse Phase Protein Lysate Arrays.” Proteomics 6 (10): 2964–71. Cite

Jimenez-Corona, M. E., L. Garcia-Garcia, K. Deriemer, L. Ferreyra-Reyes, M. Bobadilla-del-Valle, B. Cano-Arellano, S. Canizales-Quintero, et al. 2006. “Gender Differentials of Pulmonary Tuberculosis Transmission and Reactivation in an Endemic Area.” Thorax 61 (4): 348–53. Cite

Kaur, A., M. Pan, M. Meislin, M. T. Facciotti, R. El-Geweley, and N. S. Baliga. 2006. “A Systems View of Haloarchaeal Strategies to Withstand Stress from Transition Metals.” Genome Res 16 (June): 841–54. Cite

King, N. L., E. W. Deutsch, J. Ranish, A. I. Nesvizhskii, J. S. Eddes, P. Mallick, J. Eng, et al. 2006. “Analysis of the Saccharomyces Cerevisiae Proteome with PeptideAtlas.” Genome Biol 7 (11): R106. Cite

Kowalewska, J., K. D. Smith, K. L. Hudkins, A. Chang, A. B. Fogo, D. Houghton, D. Leslie, J. D. Aitchison, R. F. Nicosia, and C. E. Alpers. 2006. “Membranous Glomerulopathy with Spherules: An Uncommon Variant with Obscure Pathogenesis.” Am J Kidney Dis 47 (6): 983–92. Cite

Lahdesmaki, H., S. Hautaniemi, I. Shmulevich, and O. Yli-Harja. 2006. “Relationships between Probabilistic Boolean Networks and Dynamic Bayesian Networks as Models of Gene Regulatory Networks.” Signal Processing 86 (4): 814–34. Cite

Lausted, C., C. B. Warren, L. E. Hood, and S. R. Lasky. 2006. “Printing Your Own Inkjet Microarrays.” Methods Enzymol 410: 168–89. Cite

Lee, S. I., D. Pe’er, A. M. Dudley, G. M. Church, and D. Koller. 2006. “Identifying Regulatory Mechanisms Using Individual Variation Reveals Key Role for Chromatin Modification.” Proc Natl Acad Sci U S A 103 (38): 14062–67. Cite

Leslie, D. M., B. Timney, M. P. Rout, and J. D. Aitchison. 2006. “Studying Nuclear Protein Import in Yeast.” Methods 39 (4): 291–308. Cite

Longabaugh, W., and H. Bolouri. 2006. “Understanding the Dynamic Behavior of Genetic Regulatory Networks by Functional Decomposition.” Curr Genomics 7 (6): 333–41. Cite

Lu, W., D. Zhou, G. Glusman, A. G. Utleg, J. T. White, P. S. Nelson, T. J. Vasicek, L. Hood, and B. Lin. 2006. “KLK31P Is a Novel Androgen Regulated and Transcribed Pseudogene of Kallikreins That Is Expressed at Lower Levels in Prostate Cancer Cells than in Normal Prostate Cells.” Prostate 66 (9): 936–44. Cite

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2005

2323737 2RQKSFR5 2005 1 chicago-author-date-16th-edition 50 creator asc 1 1 319 https://isbscience.org/wp-content/plugins/zotpress/

Aderem, A. 2005. “Systems Biology: Its Practice and Challenges.” Cell 121 (4): 511–13. Cite

Aebersold, R. 2005. “Molecular Systems Biology: A New Journal for a New Biology?” Mol Syst Biol 1: 2005 0005. Cite

Aebersold, R., L. Anderson, R. Caprioli, B. Druker, L. Hartwell, and R. Smith. 2005. “Perspective: A Program to Improve Protein Biomarker Discovery for Cancer.” J Proteome Res 4 (4): 1104–9. Cite

Alsam, S., J. Sissons, R. Dudley, and N. A. Khan. 2005. “Mechanisms Associated with Acanthamoeba Castellanii (T4) Phagocytosis.” Parasitol Res 96 (6): 402–9. Cite

Andersen-Nissen, E., K. D. Smith, K. L. Strobe, S. L. Barrett, B. T. Cookson, S. M. Logan, and A. Aderem. 2005. “Evasion of Toll-like Receptor 5 by Flagellated Bacteria.” Proc Natl Acad Sci U S A 102 (26): 9247–52. Cite

Avila, G. E., X. Zheng, X. X. Cui, A. D. Ryan, A. Hansson, J. Suh, A. B. Rabson, et al. 2005. “Inhibitory Effects of 12-O-Tetradecanoylphorbol-13-Acetate Alone or in Combination with All-Trans Retinoic Acid on the Growth of Cultured Human Pancreas Cancer Cells and Pancreas Tumor Xenografts in Immunodeficient Mice.” J Pharmacol Exp Ther 315 (1): 170–87. Cite

Bergman, M. A., L. A. Cummings, S. L. Barrett, K. D. Smith, J. C. Lara, A. Aderem, and B. T. Cookson. 2005. “CD4+ T Cells and Toll-like Receptors Recognize Salmonella Antigens Expressed in Bacterial Surface Organelles.” Infect Immun 73 (3): 1350–56. Cite

Bradshaw, R. A., A. L. Burlingame, S. Carr, and R. Aebersold. 2005. “Protein Identification: The Good, the Bad, and the Ugly.” Mol Cell Proteomics 4 (9): 1221–22. Cite

Brun, M., E. R. Dougherty, and I. Shmulevich. 2005. “Steady-State Probabilities for Attractors in Probabilistic Boolean Networks.” Signal Processing 85 (10): 1993–2013. Cite

Carter, G. W. 2005. “Inferring Network Interactions within a Cell.” Brief Bioinform 6 (4): 380–89. Cite

Chen, S. S., and R. Aebersold. 2005. “LC-MS Solvent Composition Monitoring and Chromatography Alignment Using Mobile Phase Tracer Molecules.” J Chromatogr B Analyt Technol Biomed Life Sci 829 (1–2): 107–14. Cite

Chen, R., S. Pan, T. A. Brentnall, and R. Aebersold. 2005. “Proteomic Profiling of Pancreatic Cancer for Biomarker Discovery.” Mol Cell Proteomics 4 (4): 523–33. Cite

Chen, R., E. C. Yi, S. Donohoe, S. Pan, J. Eng, K. Cooke, D. A. Crispin, et al. 2005. “Pancreatic Cancer Proteome: The Proteins That Underlie Invasion, Metastasis, and Immunologic Escape.” Gastroenterology 129 (4): 1187–97. Cite

Chen, S. S., E. W. Deutsch, E. C. Yi, X. J. Li, D. R. Goodlett, and R. Aebersold. 2005. “Improving Mass and Liquid Chromatography Based Identification of Proteins Using Bayesian Scoring.” J Proteome Res 4 (6): 2174–84. Cite

Cieslewicz, M. J., D. Chaffin, G. Glusman, D. Kasper, A. Madan, S. Rodrigues, J. Fahey, M. R. Wessels, and C. E. Rubens. 2005. “Structural and Genetic Diversity of Group B Streptococcus Capsular Polysaccharides.” Infect Immun 73 (5): 3096–3103. Cite

Corthals, G. L., R. Aebersold, and D. R. Goodlett. 2005. “Identification of Phosphorylation Sites Using Microimmobilized Metal Affinity Chromatography.” Methods Enzymol 405: 66–81. Cite

Atauri, P. de, D. Orrell, S. Ramsey, and H. Bolouri. 2005. “Is the Regulation of Galactose 1-Phosphate Tuned against Gene Expression Noise?” Biochem J 387 (Pt 1): 77–84. Cite

Jong, B. C. de, A. Onipede, A. S. Pym, S. Gagneux, R. S. Aga, K. Deriemer, and P. M. Small. 2005. “Does Resistance to Pyrazinamide Accurately Indicate the Presence of Mycobacterium Bovis?” J Clin Microbiol 43 (7): 3530–32. Cite

Jong, B. C. de, P. C. Hill, R. H. Brookes, J. K. Otu, K. L. Peterson, P. M. Small, and R. A. Adegbola. 2005. “Mycobacterium Africanum: A New Opportunistic Pathogen in HIV Infection?” AIDS 19 (15): 1714–15. Cite

Deriemer, K., L. Garcia-Garcia, M. Bobadilla-del-Valle, M. Palacios-Martinez, A. Martinez-Gamboa, P. M. Small, J. Sifuentes-Osornio, and A. Ponce-de-Leon. 2005. “Does DOTS Work in Populations with Drug-Resistant Tuberculosis?” Lancet 365 (9466): 1239–45. Cite

Desiere, F., E. W. Deutsch, A. I. Nesvizhskii, P. Mallick, N. L. King, J. K. Eng, A. Aderem, et al. 2005. “Integration with the Human Genome of Peptide Sequences Obtained by High-Throughput Mass Spectrometry.” Genome Biol 6 (1): R9. Cite

Deutsch, E. W., J. K. Eng, H. Zhang, N. L. King, A. I. Nesvizhskii, B. Lin, H. Lee, E. C. Yi, R. Ossola, and R. Aebersold. 2005. “Human Plasma PeptideAtlas.” Proteomics 5 (13): 3497–3500. Cite

Dilworth, D. J., A. J. Tackett, R. S. Rogers, E. C. Yi, R. H. Christmas, J. J. Smith, A. F. Siegel, B. T. Chait, R. W. Wozniak, and J. D. Aitchison. 2005. “The Mobile Nucleoporin Nup2p and Chromatin-Bound Prp20p Function in Endogenous NPC-Mediated Transcriptional Control.” J Cell Biol 171 (6): 955–65. Cite

Drees, B. L., V. Thorsson, G. W. Carter, A. W. Rives, M. Z. Raymond, I. Avila-Campillo, P. Shannon, and T. Galitski. 2005. “Derivation of Genetic Interaction Networks from Quantitative Phenotype Data.” Genome Biol 6 (4): R38. Cite

Dunstan, S. J., T. R. Hawn, N. T. Hue, C. P. Parry, V. A. Ho, H. Vinh, T. S. Diep, et al. 2005. “Host Susceptibility and Clinical Outcomes in Toll-like Receptor 5-Deficient Patients with Typhoid Fever in Vietnam.” J Infect Dis 191 (7): 1068–71. Cite

Fagarasanu, M., A. Fagarasanu, Y. Y. Tam, J. D. Aitchison, and R. A. Rachubinski. 2005. “Inp1p Is a Peroxisomal Membrane Protein Required for Peroxisome Inheritance in Saccharomyces Cerevisiae.” J Cell Biol 169 (5): 765–75. Cite

Freeman, R., M. Kato-Maeda, K. A. Hauge, K. L. Horan, E. Oren, M. Narita, C. K. Wallis, et al. 2005. “Use of Rapid Genomic Deletion Typing to Monitor a Tuberculosis Outbreak within an Urban Homeless Population.” J Clin Microbiol 43 (11): 5550–54. Cite

Gao, Q., K. E. Kripke, A. J. Saldanha, W. Yan, S. Holmes, and P. M. Small. 2005. “Gene Expression Diversity among Mycobacterium Tuberculosis Clinical Isolates.” Microbiology 151 (Pt 1): 5–14. Cite

Gershenson, C., S. A. Kauffman, and I. Shmulevich. 2005. “The Role of Redundancy in the Robustness of Random Boolean Networks.” Arxiv Preprint Nlin/0511018. Cite

Gilad, Y., O. Man, and G. Glusman. 2005. “A Comparison of the Human and Chimpanzee Olfactory Receptor Gene Repertoires.” Genome Res 15 (2): 224–30. Cite

Gingras, A. C., M. Caballero, M. Zarske, A. Sanchez, T. R. Hazbun, S. Fields, N. Sonenberg, E. Hafen, B. Raught, and R. Aebersold. 2005. “A Novel, Evolutionarily Conserved Protein Phosphatase Complex Involved in Cisplatin Sensitivity.” Mol Cell Proteomics 4 (11): 1725–40. Cite

Gingras, A. C., R. Aebersold, and B. Raught. 2005. “Advances in Protein Complex Analysis Using Mass Spectrometry.” J Physiol 563 (Pt 1): 11–21. Cite

Hawn, T. R., A. Ozinsky, L. M. Williams, S. Rodrigues, A. Clark, U. Pham, H. R. Hill, H. Ochs, A. Aderem, and W. C. Liles. 2005. “Hyper-IgE Syndrome Is Not Associated with Defects in Several Candidate Toll-like Receptor Pathway Genes.” Hum Immunol 66 (7): 842–47. Cite

Hawn, T. R., A. Verbon, M. Janer, L. P. Zhao, B. Beutler, and A. Aderem. 2005. “Toll-like Receptor 4 Polymorphisms Are Associated with Resistance to Legionnaires’ Disease.” Proc Natl Acad Sci U S A 102 (7): 2487–89. Cite

Hawn, T. R., H. Wu, J. M. Grossman, B. H. Hahn, B. P. Tsao, and A. Aderem. 2005. “A Stop Codon Polymorphism of Toll-like Receptor 5 Is Associated with Resistance to Systemic Lupus Erythematosus.” Proc Natl Acad Sci U S A 102 (30): 10593–97. Cite

Heller, M., M. Ye, P. E. Michel, P. Morier, D. Stalder, M. A. Junger, R. Aebersold, F. Reymond, and J. S. Rossier. 2005. “Added Value for Tandem Mass Spectrometry Shotgun Proteomics Data Validation through Isoelectric Focusing of Peptides.” J Proteome Res 4 (6): 2273–82. Cite

Hwang, D., J. J. Smith, D. M. Leslie, A. D. Weston, A. G. Rust, S. Ramsey, P. de Atauri, et al. 2005. “A Data Integration Methodology for Systems Biology: Experimental Verification.” Proc Natl Acad Sci U S A 102 (48): 17302–7. Cite

Iliev, D. B., J. Roach, S. Mackenzie, J. V. Planas, and F. W. Goetz. 2005. “Endotoxin Recognition: In Fish or Not in Fish?” FEBS Lett 579 (29): 6519–28. Cite

Iyer, R., N. S. Baliga, and A. Camilli. 2005. “Catabolite Control Protein A (CcpA) Contributes to Virulence and Regulation of Sugar Metabolism in Streptococcus Pneumoniae.” J Bacteriol 187 (24): 8340–49. Cite

Jacobson, L. M., M. de Lourdes Garcia-Garcia, J. E. Hernandez-Avila, B. Cano-Arellano, P. M. Small, J. Sifuentes-Osornio, and A. Ponce-de-Leon. 2005. “Changes in the Geographical Distribution of Tuberculosis Patients in Veracruz, Mexico, after Reinforcement of a Tuberculosis Control Programme.” Trop Med Int Health 10 (4): 305–11. Cite

Keller, A., J. Eng, N. Zhang, X. J. Li, and R. Aebersold. 2005. “A Uniform Proteomics MS/MS Analysis Platform Utilizing Open XML File Formats.” Mol Syst Biol 1: 2005 0017. Cite

Knudsen, B. S., J. M. Lucas, L. Fazli, S. Hawley, S. Falcon, I. M. Coleman, D. B. Martin, et al. 2005. “Regulation of Hepatocyte Activator Inhibitor-1 Expression by Androgen and Oncogenic Transformation in the Prostate.” Am J Pathol 167 (1): 255–66. Cite

Kuster, B., M. Schirle, P. Mallick, and R. Aebersold. 2005. “Scoring Proteomes with Proteotypic Peptide Probes.” Nat Rev Mol Cell Biol 6 (7): 577–83. Cite

Li, X. J., E. C. Yi, C. J. Kemp, H. Zhang, and R. Aebersold. 2005. “A Software Suite for the Generation and Comparison of Peptide Arrays from Sets of Data Collected by Liquid Chromatography-Mass Spectrometry.” Mol Cell Proteomics 4 (9): 1328–40. Cite

Lin, B., J. T. White, W. Lu, T. Xie, A. G. Utleg, X. Yan, E. C. Yi, et al. 2005. “Evidence for the Presence of Disease-Perturbed Networks in Prostate Cancer Cells by Genomic and Proteomic Analyses: A Systems Approach to Disease.” Cancer Res 65 (8): 3081–91. Cite

Longabaugh, W., E. H. Davidson, and H. Bolouri. 2005. “Computational Representation of Developmental Genetic Regulatory Networks.” Dev Biol 283 (1): 1–16. Cite

Martin, D. B., J. K. Eng, A. I. Nesvizhskii, A. Gemmill, and R. Aebersold. 2005. “Investigation of Neutral Loss during Collision-Induced Dissociation of Peptide Ions.” Anal Chem 77 (15): 4870–82. Cite

Nesvizhskii, A. I., and R. Aebersold. 2005. “Interpretation of Shotgun Proteomic Data: The Protein Inference Problem.” Mol Cell Proteomics 4 (10): 1419–40. Cite

Niemisto, A., V. Dunmire, O. Yli-Harja, W. Zhang, and I. Shmulevich. 2005. “Analysis of Angiogenesis Using in Vitro Experiments and Stochastic Growth Models.” Phys Rev E Stat Nonlin Soft Matter Phys 72 (6 Pt 1): 062902. Cite

Niemisto, A., I. Shmulevich, O. Yli-Harja, L. R. Chirieac, and S. R. Hamilton. 2005. “Automated Quantification of Lymph Node Size and Number in Surgical Specimens of Stage II Colorectal Cancer.” Conf Proc IEEE Eng Med Biol Soc 6: 6313–16. Cite

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2004

2323737 2RQKSFR5 2004 1 chicago-author-date-16th-edition 50 creator asc 1 1 319 https://isbscience.org/wp-content/plugins/zotpress/

Aderem, A., and K. D. Smith. 2004. “A Systems Approach to Dissecting Immunity and Inflammation.” Semin Immunol 16 (1): 55–67. Cite

Andalis, A. A., Z. Storchova, C. Styles, T. Galitski, D. Pellman, and G. R. Fink. 2004. “Defects Arising from Whole-Genome Duplications in Saccharomyces Cerevisiae.” Genetics 167 (3): 1109–21. Cite

Baliga, N. S., S. J. Bjork, R. Bonneau, M. Pan, C. Iloanusi, M. C. Kottemann, L. Hood, and J. DiRuggiero. 2004. “Systems Level Insights into the Stress Response to UV Radiation in the Halophilic Archaeon Halobacterium NRC-1.” Genome Res 14 (6): 1025–35. Cite

Baliga, N. S., R. Bonneau, M. T. Facciotti, M. Pan, G. Glusman, E. W. Deutsch, P. Shannon, et al. 2004. “Genome Sequence of Haloarcula Marismortui: A Halophilic Archaeon from the Dead Sea.” Genome Res 14 (11): 2221–34. Cite

Bonneau, R., N. S. Baliga, E. W. Deutsch, P. Shannon, and L. Hood. 2004. “Comprehensive de Novo Structure Prediction in a Systems-Biology Context for the Archaea Halobacterium Sp. NRC-1.” Genome Biol 5 (8): R52. Cite

Bottari, P., R. Aebersold, F. Turecek, and M. H. Gelb. 2004. “Design and Synthesis of Visible Isotope-Coded Affinity Tags for the Absolute Quantification of Specific Proteins in Complex Mixtures.” Bioconjug Chem 15 (2): 380–88. Cite

Brand, M., J. Ranish, N. T. Kummer, J. Hamilton, K. Igarashi, C. Francastel, T. H. Chi, G. R. Crabtree, R. Aebersold, and M. Groudine. 2004. “Dynamic Changes in Transcription Factor Complexes during Erythroid Differentiation Revealed by Quantitative Proteomics.” Nat Struct Mol Biol 11 (1): 73–80. Cite

Bunimovich, Y. L., G. Ge, K. C. Beverly, R. S. Ries, L. Hood, and J. R. Heath. 2004. “Electrochemically Programmed, Spatially Selective Biofunctionalization of Silicon Wires.” Langmuir 20 (24): 10630–38. Cite

Camacho-Carvajal, M. M., B. Wollscheid, R. Aebersold, V. Steimle, and W. W. Schamel. 2004. “Two-Dimensional Blue Native/SDS Gel Electrophoresis of Multi-Protein Complexes from Whole Cellular Lysates: A Proteomics Approach.” Mol Cell Proteomics 3 (2): 176–82. Cite

Carr, S., R. Aebersold, M. Baldwin, A. Burlingame, K. Clauser, A. Nesvizhskii, Peptide Working Group on Publication Guidelines for, and Data Protein Identification. 2004. “The Need for Guidelines in Publication of Peptide and Protein Identification Data: Working Group on Publication Guidelines for Peptide and Protein Identification Data.” Mol Cell Proteomics 3 (6): 531–33. Cite

Chen, X., Y. Chi, A. Bloecher, R. Aebersold, B. E. Clurman, and J. M. Roberts. 2004. “N-Acetylation and Ubiquitin-Independent Proteasomal Degradation of P21(Cip1).” Mol Cell 16 (5): 839–47. Cite

Chin, W. C., M. V. Orellana, I. Quesada, and P. Verdugo. 2004. “Secretion in Unicellular Marine Phytoplankton: Demonstration of Regulated Exocytosis in Phaeocystis Globosa.” Plant Cell Physiol 45 (5): 535–42. Cite

Croteau, G. A., D. B. Martin, J. Camp, M. Yost, C. Conrad, P. L. Zeitlin, and A. E. Heald. 2004. “Evaluation of Exposure and Health Care Worker Response to Nebulized Administration of tgAAVCF to Patients with Cystic Fibrosis.” Ann Occup Hyg 48 (8): 673–81. Cite

Daza-Vamenta, R., G. Glusman, L. Rowen, B. Guthrie, and D. E. Geraghty. 2004. “Genetic Divergence of the Rhesus Macaque Major Histocompatibility Complex.” Genome Res 14 (8): 1501–15. Cite

Atauri, P. de, D. Orrell, S. Ramsey, and H. Bolouri. 2004. “Evolution of ’design’ Principles in Biochemical Networks.” Syst Biol (Stevenage) 1 (1): 28–40. Cite

Eng, Jimmy, Daniel Martin, and R. Aebersold. 2004. “Tandem Mass Spectrometry Database Searching.” In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, edited by S. Subramaniam. John Wiley & Sons, Ltd. Cite

Facciotti, M. T., R. Bonneau, L. Hood, and N. S. Baliga. 2004. “Systems Biology Experimental Design – Considerations for Building Predictive Gene Regulatory Network Models for Prokaryotic Systems.” Current Genomics 5 (7): 527-544(18). Cite

Facciotti, M. T., V. S. Cheung, C. S. Lunde, S. Rouhani, N. S. Baliga, and R. M. Glaeser. 2004. “Specificity of Anion Binding in the Substrate Pocket of Bacteriorhodopsin.” Biochemistry 43 (17): 4934–43. Cite

Flo, T. H., K. D. Smith, S. Sato, D. J. Rodriguez, M. A. Holmes, R. K. Strong, S. Akira, and A. Aderem. 2004. “Lipocalin 2 Mediates an Innate Immune Response to Bacterial Infection by Sequestrating Iron.” Nature 432 (7019): 917–21. Cite

Flory, M. R., A. R. Carson, E. G. Muller, and R. Aebersold. 2004. “An SMC-Domain Protein in Fission Yeast Links Telomeres to the Meiotic Centrosome.” Mol Cell 16 (4): 619–30. Cite

Friedrichsen, D. M., J. L. Stanford, S. D. Isaacs, M. Janer, B. L. Chang, K. Deutsch, E. Gillanders, et al. 2004. “Identification of a Prostate Cancer Susceptibility Locus on Chromosome 7q11-21 in Jewish Families.” Proc Natl Acad Sci U S A 101 (7): 1939–44. Cite

Galitski, T. 2004. “Molecular Networks in Model Systems.” Annu Rev Genomics Hum Genet 5: 177–87. Cite

Giglia-Mari, G., F. Coin, J. Ranish, D. Hoogstraten, A. Theil, N. Wijgers, N. G. Jaspers, et al. 2004. “A New, Tenth Subunit of TFIIH Is Responsible for the DNA Repair Syndrome Trichothiodystrophy Group A.” Nat Genet 36 (7): 714–19. Cite

Glusman, G., A. Kaur, L. Hood, and L. Rowen. 2004. “An Enigmatic Fourth Runt Domain Gene in the Fugu Genome: Ancestral Gene Loss versus Accelerated Evolution.” BMC Evol Biol 4 (November): 43. Cite

Gold, E. S., R. M. Simmons, T. W. Petersen, L. A. Campbell, C. C. Kuo, and A. Aderem. 2004. “Amphiphysin IIm Is Required for Survival of Chlamydia Pneumoniae in Macrophages.” J Exp Med 200 (5): 581–86. Cite

Goo, Y. A., J. Roach, G. Glusman, N. S. Baliga, K. Deutsch, M. Pan, S. Kennedy, S. DasSarma, W. V. Ng, and L. Hood. 2004. “Low-Pass Sequencing for Microbial Comparative Genomics.” BMC Genomics 5 (1): 3. Cite

Graveley, B. R., A. Kaur, D. Gunning, S. L. Zipursky, L. Rowen, and J. C. Clemens. 2004. “The Organization and Evolution of the Dipteran and Hymenopteran Down Syndrome Cell Adhesion Molecule (Dscam) Genes.” RNA 10 (10): 1499–1506. Cite

Hardwidge, P. R., I. Rodriguez-Escudero, D. Goode, S. Donohoe, J. Eng, D. R. Goodlett, R. Aebersold, and B. B. Finlay. 2004. “Proteomic Analysis of the Intestinal Epithelial Cell Response to Enteropathogenic Escherichia Coli.” J Biol Chem 279 (19): 20127–36. Cite

Hartwell, L., L. Hood, M. L. Goldberg, A. E. Reynolds, L. M. Silver, and R. C. Veres. 2004. Genetics: From Genes to Genomes. 2nd ed. McGraw-Hill New York, NY. Cite

He, X. C., J. Zhang, W. G. Tong, O. Tawfik, J. Ross, D. H. Scoville, Q. Tian, et al. 2004. “BMP Signaling Inhibits Intestinal Stem Cell Self-Renewal through Suppression of Wnt-Beta-Catenin Signaling.” Nat Genet 36 (10): 1117–21. Cite

Himeda, C. L., J. Ranish, J. C. Angello, P. Maire, R. Aebersold, and S. D. Hauschka. 2004. “Quantitative Proteomic Identification of Six4 as the Trex-Binding Factor in the Muscle Creatine Kinase Enhancer.” Mol Cell Biol 24 (5): 2132–43. Cite

Hood, L. 2004. “Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins.” In , edited by B. F. Francis Oullette, 3rd ed., Foreword. Wiley-Liss, Inc. Cite

Hood, L. 2004. “Biotechnology Annual Review.” In , Preface. Amsterdam: Elsevieer. Cite

Hood, L., and R. M. Perlmutter. 2004. “The Impact of Systems Approaches on Biological Problems in Drug Discovery.” Nat Biotechnol 22 (10): 1215–17. Cite

Hood, L., James R. Heath, M. E. Phelps, and B. Lin. 2004. “Systems Biology and New Technologies Enable Predictive and Preventative Medicine.” Science 306 (5696): 640–43. Cite

International Human Genome Sequencing, Consortium. 2004. “Finishing the Euchromatic Sequence of the Human Genome.” Nature 431 (7011): 931–45. Cite

Jeffrey Chen, Z., Jianlin Wang, Lu Tian, Hyeon-Se Lee, Jiyuan J. Wang, Meng Chen, Jinsuk J. Lee, et al. 2004. “The Development of an Arabidopsis Model System for Genome-Wide Analysis of Polyploidy Effects.” Biol J Linn Soc Lond 82 (August): 689–700. http://doi.org/10.1111/j.1095-8312.2004.00351.x. Cite

Kao, W. C., Y. R. Chen, E. C. Yi, H. Lee, Q. Tian, K. M. Wu, S. F. Tsai, et al. 2004. “Quantitative Proteomic Analysis of Metabolic Regulation by Copper Ions in Methylococcus Capsulatus (Bath).” J Biol Chem 279 (49): 51554–60. Cite

Lausted, C., T. Dahl, C. Warren, K. King, K. Smith, M. Johnson, R. Saleem, J. D. Aitchison, L. Hood, and S. R. Lasky. 2004. “POSaM: A Fast, Flexible, Open-Source, Inkjet Oligonucleotide Synthesizer and Microarrayer.” Genome Biol 5 (8): R58. Cite

Lee, H., E. C. Yi, B. Wen, T. P. Reily, L. Pohl, S. Nelson, R. Aebersold, and D. R. Goodlett. 2004. “Optimization of Reversed-Phase Microcapillary Liquid Chromatography for Quantitative Proteomics.” J Chromatogr B Analyt Technol Biomed Life Sci 803 (1): 101–10. Cite

Lefkir, Y., M. Malbouyres, D. Gotthardt, A. Ozinsky, S. Cornillon, F. Bruckert, A. Aderem, T. Soldati, P. Cosson, and F. Letourneur. 2004. “Involvement of the AP-1 Adaptor Complex in Early Steps of Phagocytosis and Macropinocytosis.” Mol Biol Cell 15 (2): 861–69. Cite

Leslie, D. M., W. Zhang, B. L. Timney, B. T. Chait, M. P. Rout, R. W. Wozniak, and J. D. Aitchison. 2004. “Characterization of Karyopherin Cargoes Reveals Unique Mechanisms of Kap121p-Mediated Nuclear Import.” Mol Cell Biol 24 (19): 8487–8503. Cite

Li, X. J., P. G. Pedrioli, J. Eng, D. Martin, E. C. Yi, H. Lee, and R. Aebersold. 2004. “A Tool to Visualize and Evaluate Data Obtained by Liquid Chromatography-Electrospray Ionization-Mass Spectrometry.” Anal Chem 76 (13): 3856–60. Cite

Liu, A. Y., K. D. Brubaker, Y. A. Goo, J. E. Quinn, S. Kral, C. M. Sorensen, R. L. Vessella, A. S. Belldegrun, and L. E. Hood. 2004. “Lineage Relationship between LNCaP and LNCaP-Derived Prostate Cancer Cell Lines.” Prostate 60 (2): 98–108. Cite

MacKay, V. L., X. Li, M. R. Flory, E. Turcott, G. L. Law, K. A. Serikawa, X. L. Xu, et al. 2004. “Gene Expression Analyzed by High-Resolution State Array Analysis and Quantitative Proteomics: Response of Yeast to Mating Pheromone.” Mol Cell Proteomics 3 (5): 478–89. Cite

Marelli, M., J. J. Smith, S. Jung, E. Yi, A. I. Nesvizhskii, R. H. Christmas, R. A. Saleem, et al. 2004. “Quantitative Mass Spectrometry Reveals a Role for the GTPase Rho1p in Actin Organization on the Peroxisome Membrane.” J Cell Biol 167 (6): 1099–1112. Cite

Martin, D. B., D. R. Gifford, M. E. Wright, A. Keller, E. Yi, D. R. Goodlett, R. Aebersold, and P. S. Nelson. 2004. “Quantitative Proteomic Analysis of Proteins Released by Neoplastic Prostate Epithelium.” Cancer Res 64 (1): 347–55. Cite

Marzolf, B., and M. H. Johnson. 2004. “Validation of Microarray Image Analysis Accuracy.” Biotechniques 36 (2): 304–8. Cite

Matsumoto, M., D. Einhaus, E. S. Gold, and A. Aderem. 2004. “Simvastatin Augments Lipopolysaccharide-Induced Proinflammatory Responses in Macrophages by Differential Regulation of the c-Fos and c-Jun Transcription Factors.” J Immunol 172 (12): 7377–84. Cite

Mayer, M. L., I. Pot, M. Chang, H. Xu, V. Aneliunas, T. Kwok, R. Newitt, et al. 2004. “Identification of Protein Complexes Required for Efficient Sister Chromatid Cohesion.” Mol Biol Cell 15 (4): 1736–45. Cite

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Aderem, A. 2003. “Phagocytosis and the Inflammatory Response.” J Infect Dis 187 Suppl 2 (June): S340-5. Cite

Aebersold, R. 2003. “Quantitative Proteome Analysis: Methods and Applications.” J Infect Dis 187 Suppl 2 (June): S315-20. Cite

Aebersold, R. 2003. “Constellations in a Cellular Universe.” Nature 422 (6928): 115–16. Cite

Aebersold, R. 2003. “A Mass Spectrometric Journey into Protein and Proteome Research.” J Am Soc Mass Spectrom 14 (7): 685–95. Cite

Aebersold, R., and M. Mann. 2003. “Mass Spectrometry-Based Proteomics.” Nature 422 (6928): 198–207. Cite

Aitchison, J. D. 2003. “Systems Biology and Elephants.” Nature Cell Biology 5: 285. Cite

Aitchison, J. D., and T. Galitski. 2003. “Inventories to Insights.” J Cell Biol 161 (3): 465–69. Cite

Anderson, J. P., G. H. Learn, A. G. Rodrigo, X. He, Y. Wang, H. Weinstock, M. L. Kalish, K. E. Robbins, L. Hood, and J. I. Mullins. 2003. “Predicting Demographic Group Structures Based on DNA Sequence Data.” Mol Biol Evol 20 (7): 1168–80. Cite

Auffray, C., S. Imbeaud, M. Roux-Rouquie, and L. Hood. 2003. “Self-Organized Living Systems: Conjunction of a Stable Organization with Chaotic Fluctuations in Biological Space-Time.” Philos Transact A Math Phys Eng Sci 361 (1807): 1125–39. Cite

Auffray, C., Z. Chen, L. Hood, B. Soares, and S. Sugano. 2003. “Foreword: From the TRANSCRIPTOME Conferences to the SYSTEMOSCOPE International Consortium.” C R Biol 326 (10–11): 867–75. Cite

Auffray, C., S. Imbeaud, M. Roux-Rouquie, and L. Hood. 2003. “From Functional Genomics to Systems Biology: Concepts and Practices.” C R Biol 326 (10–11): 879–92. Cite

Bochud, P. Y., T. R. Hawn, and A. Aderem. 2003. “Cutting Edge: A Toll-like Receptor 2 Polymorphism That Is Associated with Lepromatous Leprosy Is Unable to Mediate Mycobacterial Signaling.” J Immunol 170 (7): 3451–54. Cite

Britten, R. J., L. Rowen, J. Williams, and R. A. Cameron. 2003. “Majority of Divergence between Closely Related DNA Samples Is Due to Indels.” Proc Natl Acad Sci U S A 100 (8): 4661–65. Cite

Chikamori, K., D. R. Grabowski, M. Kinter, B. B. Willard, S. Yadav, R. Aebersold, R. M. Bukowski, et al. 2003. “Phosphorylation of Serine 1106 in the Catalytic Domain of Topoisomerase II Alpha Regulates Enzymatic Activity and Drug Sensitivity.” J Biol Chem 278 (15): 12696–702. Cite

Conlon, E. M., E. L. Goode, M. Gibbs, J. L. Stanford, M. Badzioch, M. Janer, S. Kolb, et al. 2003. “Oligogenic Segregation Analysis of Hereditary Prostate Cancer Pedigrees: Evidence for Multiple Loci Affecting Age at Onset.” Int J Cancer 105 (5): 630–35. Cite

Davidson, E. H., D. R. McClay, and L. Hood. 2003. “Regulatory Gene Networks and the Properties of the Developmental Process.” Proc Natl Acad Sci U S A 100 (4): 1475–80. Cite

Flory, M. R., and R. Aebersold. 2003. “Proteomic Approaches for the Identification of Cell Cycle-Related Drug Targets.” Prog Cell Cycle Res 5: 167–71. Cite

Goo, Y. A., E. C. Yi, N. S. Baliga, W. A. Tao, M. Pan, R. Aebersold, D. R. Goodlett, L. Hood, and W. V. Ng. 2003. “Proteomic Analysis of an Extreme Halophilic Archaeon, Halobacterium Sp. NRC-1.” Mol Cell Proteomics 2 (8): 506–24. Cite

Griffin, T. J., C. M. Lock, X. J. Li, A. Patel, I. Chervetsova, H. Lee, M. E. Wright, J. Ranish, S. S. Chen, and R. Aebersold. 2003. “Abundance Ratio-Dependent Proteomic Analysis by Mass Spectrometry.” Anal Chem 75 (4): 867–74. Cite

Guina, T., S. O. Purvine, E. C. Yi, J. Eng, D. R. Goodlett, R. Aebersold, and S. I. Miller. 2003. “Quantitative Proteomic Analysis Indicates Increased Synthesis of a Quinolone by Pseudomonas Aeruginosa Isolates from Cystic Fibrosis Airways.” Proc Natl Acad Sci U S A 100 (5): 2771–76. Cite

Guina, T., M. Wu, S. I. Miller, S. O. Purvine, E. C. Yi, J. Eng, D. R. Goodlett, R. Aebersold, R. K. Ernst, and K. A. Lee. 2003. “Proteomic Analysis of Pseudomonas Aeruginosa Grown under Magnesium Limitation.” J Am Soc Mass Spectrom 14 (7): 742–51. Cite

Ha, S. A., J. Torabinejad, D. B. DeWald, M. R. Wenk, L. Lucast, P. De Camilli, R. A. Newitt, R. Aebersold, and S. F. Nothwehr. 2003. “The Synaptojanin-like Protein Inp53/Sjl3 Functions with Clathrin in a Yeast TGN-to-Endosome Pathway Distinct from the GGA Protein-Dependent Pathway.” Mol Biol Cell 14 (4): 1319–33. Cite

Haendeler, J., G. Yin, Y. Hojo, Y. Saito, M. Melaragno, C. Yan, V. K. Sharma, M. Heller, R. Aebersold, and B. C. Berk. 2003. “GIT1 Mediates Src-Dependent Activation of Phospholipase Cgamma by Angiotensin II and Epidermal Growth Factor.” J Biol Chem 278 (50): 49936–44. Cite

Hawn, T. R., A. Verbon, K. D. Lettinga, L. P. Zhao, S. S. Li, R. J. Laws, S. J. Skerrett, et al. 2003. “A Common Dominant TLR5 Stop Codon Polymorphism Abolishes Flagellin Signaling and Is Associated with Susceptibility to Legionnaires’ Disease.” J Exp Med 198 (10): 1563–72. Cite

Heath, James R., M. E. Phelps, and L. Hood. 2003. “NanoSystems Biology.” Mol Imaging Biol 5 (5): 312–25. Cite

Heilig, R., R. Eckenberg, J. L. Petit, N. Fonknechten, C. Da Silva, L. Cattolico, M. Levy, et al. 2003. “The DNA Sequence and Analysis of Human Chromosome 14.” Nature 421 (6923): 601–7. Cite

Hood, L. 2003. “Systems Biology: Integrating Technology, Biology, and Computation.” Mech Ageing Dev 124 (1): 9–16. Cite

Hood, L. 2003. “Leroy Hood Expounds the Principles, Practice and Future of Systems Biology.” Drug Discov Today 8 (10): 436–38. Cite

Hood, L., and D. J. Galas. 2003. “The Digital Code of DNA.” Nature 421 (6921): 444–48. Cite

Hu, S., Z. Le, R. Newitt, R. Aebersold, J. R. Kraly, M. Jones, and N. J. Dovichi. 2003. “Identification of Proteins in Single-Cell Capillary Electrophoresis Fingerprints Based on Comigration with Standard Proteins.” Anal Chem 75 (14): 3502–5. Cite

Hubley, R. M., E. Zitzler, and J. Roach. 2003. “Evolutionary Algorithms for the Selection of Single Nucleotide Polymorphisms.” BMC Bioinformatics 4 (July): 30. Cite

Janer, M., D. M. Friedrichsen, J. L. Stanford, M. D. Badzioch, S. Kolb, K. Deutsch, M. A. Peters, et al. 2003. “Genomic Scan of 254 Hereditary Prostate Cancer Families.” Prostate 57 (4): 309–19. Cite

Kolker, E., S. Purvine, M. Y. Galperin, S. Stolyar, D. R. Goodlett, A. I. Nesvizhskii, A. Keller, et al. 2003. “Initial Proteome Analysis of Model Microorganism Haemophilus Influenzae Strain Rd KW20.” J Bacteriol 185 (15): 4593–4602. Cite

Li, X. J., H. Zhang, J. Ranish, and R. Aebersold. 2003. “Automated Statistical Analysis of Protein Abundance Ratios from Data Generated by Stable-Isotope Dilution and Tandem Mass Spectrometry.” Anal Chem 75 (23): 6648–57. Cite

Lin, F., K. Cordes, L. Li, L. Hood, W. G. Couser, S. J. Shankland, and P. Igarashi. 2003. “Hematopoietic Stem Cells Contribute to the Regeneration of Renal Tubules after Renal Ischemia-Reperfusion Injury in Mice.” J Am Soc Nephrol 14 (5): 1188–99. Cite

Lin, B., J. T. White, A. G. Utleg, S. Wang, C. Ferguson, L. D. True, R. Vessella, L. Hood, and P. S. Nelson. 2003. “Isolation and Characterization of Human and Mouse WDR19,a Novel WD-Repeat Protein Exhibiting Androgen-Regulated Expression in Prostate Epithelium.” Genomics 82 (3): 331–42. Cite

Makhnevych, T., C. P. Lusk, A. M. Anderson, J. D. Aitchison, and R. W. Wozniak. 2003. “Cell Cycle Regulated Transport Controlled by Alterations in the Nuclear Pore Complex.” Cell 115 (7): 813–23. Cite

Marr, K. A., S. A. Balajee, T. R. Hawn, A. Ozinsky, U. Pham, S. Akira, A. Aderem, and W. C. Liles. 2003. “Differential Role of MyD88 in Macrophage-Mediated Responses to Opportunistic Fungal Pathogens.” Infect Immun 71 (9): 5280–86. Cite

McBride, C. M., K. I. Pollak, J. Garst, F. Keefe, P. Lyna, L. Fish, and L. Hood. 2003. “Distress and Motivation for Smoking Cessation among Lung Cancer Patients’ Relatives Who Smoke.” J Cancer Educ 18 (3): 150–56. Cite

Means, T. K., F. Hayashi, K. D. Smith, A. Aderem, and A. D. Luster. 2003. “The Toll-like Receptor 5 Stimulus Bacterial Flagellin Induces Maturation and Chemokine Production in Human Dendritic Cells.” J Immunol 170 (10): 5165–75. Cite

Nesvizhskii, A. I., A. Keller, E. Kolker, and R. Aebersold. 2003. “A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry.” Anal Chem 75 (17): 4646–58. Cite

Orellana, M. V., and P. Verdugo. 2003. “Ultraviolet Radiation Inhibits the Exchange between Dissolved and Particulate Organic Matter.” Luminol. Oceanogr 48 (4): 1618–23. Cite

Orellana, M. V., E. J. Lessard, E. Dycus, W.-C. Chin, M. S. Foy, and P. Verdugo. 2003. “Tracing the Source and Fate of Biopolymers in Seawater: Application of an Immunological Technique.” Marine Chemistry 83: 89–99. Cite

Palsson, B. O., N. D. Price, and J. A. Papin. 2003. “Development of Network-Based Pathway Definitions: The Need to Analyze Real Metabolic Networks.” Trends in Biotechnology 21 (5): 195–98. Cite

Papin, Jason A., Nathan D. Price, Sharon J. Wiback, David A. Fell, and Bernhard O. Palsson. 2003. “Metabolic Pathways in the Post-Genome Era.” Trends in Biochemical Sciences 28 (5): 250–58. http://doi.org/10.1016/S0968-0004(03)00064-1. Cite

Patterson, S. D., and R. Aebersold. 2003. “Proteomics: The First Decade and Beyond.” Nat Genet 33 Suppl (March): 311–23. Cite

Picard, C., A. Puel, M. Bonnet, C. L. Ku, J. Bustamante, K. Yang, C. Soudais, et al. 2003. “Pyogenic Bacterial Infections in Humans with IRAK-4 Deficiency.” Science 299 (5615): 2076–79. Cite

Price, Nathan D., Jason A. Papin, Christophe H. Schilling, and Bernhard O. Palsson. 2003. “Genome-Scale Microbial in Silico Models: The Constraints-Based Approach.” Trends in Biotechnology 21 (4): 162–69. http://doi.org/10.1016/S0167-7799(03)00030-1. Cite

Price, Nathan D., Jennifer L. Reed, Jason A. Papin, Sharon J. Wiback, and Bernhard O. Palsson. 2003. “Network-Based Analysis of Metabolic Regulation in the Human Red Blood Cell.” Journal of Theoretical Biology 225 (2): 185–94. Cite

Price, Nathan D., Jennifer L. Reed, Jason A. Papin, Iman Famili, and Bernhard O. Palsson. 2003. “Analysis of Metabolic Capabilities Using Singular Value Decomposition of Extreme Pathway Matrices.” Biophysical Journal 84 (2 Pt 1). http://doi.org/10.1016/S0006-3495(03)74899-1. Cite

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2002

2323737 2RQKSFR5 2002 1 chicago-author-date-16th-edition 50 creator asc 1 1 319 https://isbscience.org/wp-content/plugins/zotpress/

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Graham, J., W. A. Hagopian, I. Kockum, L. S. Li, C. B. Sanjeevi, R. M. Lowe, J. B. Schaefer, et al. 2002. “Genetic Effects on Age-Dependent Onset and Islet Cell Autoantibody Markers in Type 1 Diabetes.” Diabetes 51 (5): 1346–55. Cite

Griffin, T. J., S. P. Gygi, T. Ideker, B. Rist, J. Eng, L. Hood, and R. Aebersold. 2002. “Complementary Profiling of Gene Expression at the Transcriptome and Proteome Levels in Saccharomyces Cerevisiae.” Mol Cell Proteomics 1 (4): 323–33. Cite

Guo, Z., M. S. Gatterman, L. Hood, J. A. Hansen, and E. W. Petersdorf. 2002. “Oligonucleotide Arrays for High-Throughput SNPs Detection in the MHC Class I Genes: HLA-B as a Model System.” Genome Res 12 (3): 447–57. Cite

Gygi, S. P., B. Rist, T. J. Griffin, J. Eng, and R. Aebersold. 2002. “Proteome Analysis of Low-Abundance Proteins Using Multidimensional Chromatography and Isotope-Coded Affinity Tags.” J Proteome Res 1 (1): 47–54. Cite

Hamerman, J. A., F. Hayashi, L. A. Schroeder, S. P. Gygi, A. L. Haas, L. Hampson, P. Coughlin, R. Aebersold, and A. Aderem. 2002. “Serpin 2a Is Induced in Activated Macrophages and Conjugates to a Ubiquitin Homolog.” J Immunol 168 (5): 2415–23. Cite

Hawn, T. R., A. Ozinsky, D. M. Underhill, F. S. Buckner, S. Akira, and A. Aderem. 2002. “Leishmania Major Activates IL-1 Alpha Expression in Macrophages through a MyD88-Dependent Pathway.” Microbes Infect 4 (8): 763–71. Cite

Hood, L. 2002. “The InTouch Interview with Biotech Man Leroy Hood, MD, PhD. Interview by Peter Tarr.” InTouch 4 (3): 28–32. Cite

Hood, L. 2002. “A Personal View of Molecular Technology and How It Has Changed Biology.” J Proteome Res 1 (5): 399–409. Cite

James, E. A., S. P. Gygi, M. L. Adams, R. H. Pierce, N. Fausto, R. Aebersold, S. D. Nelson, and S. A. Bruschi. 2002. “Mitochondrial Aconitase Modification, Functional Inhibition, and Evidence for a Supramolecular Complex of the TCA Cycle by the Renal Toxicant S-(1,1,2,2-Tetrafluoroethyl)-L-Cysteine.” Biochemistry 41 (21): 6789–97. Cite

Kabak, S., B. J. Skaggs, M. R. Gold, M. Affolter, K. L. West, M. S. Foster, K. Siemasko, A. C. Chan, R. Aebersold, and M. R. Clark. 2002. “The Direct Recruitment of BLNK to Immunoglobulin Alpha Couples the B-Cell Antigen Receptor to Distal Signaling Pathways.” Mol Cell Biol 22 (8): 2524–35. Cite

Keller, A., S. Purvine, A. I. Nesvizhskii, S. Stolyar, D. R. Goodlett, and E. Kolker. 2002. “Experimental Protein Mixture for Validating Tandem Mass Spectral Analysis.” OMICS 6 (2): 207–12. Cite

Keller, A., A. I. Nesvizhskii, E. Kolker, and R. Aebersold. 2002. “Empirical Statistical Model to Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search.” Anal Chem 74 (20): 5383–92. Cite

Kumanovics, A., A. Madan, S. Qin, L. Rowen, L. Hood, and K. Fischer Lindahl. 2002. “QUOD ERAT FACIENDUM: Sequence Analysis of the H2-D and H2-Q Regions of 129/SvJ Mice.” Immunogenetics 54 (7): 479–89. Cite

Lane, R. P., J. C. Roach, I. Lee, C. Boysen, A. Smit, B. J. Trask, and L. Hood. 2002. “Genomic Analysis of the Olfactory Receptor Region of the Mouse and Human T-Cell Receptor Alpha/Delta Loci.” Genome Research 12 (1): 81–87. Cite

Lane, R. P., T. Cutforth, R. Axel, L. Hood, and B. J. Trask. 2002. “Sequence Analysis of Mouse Vomeronasal Receptor Gene Clusters Reveals Common Promoter Motifs and a History of Recent Expansion.” Proc Natl Acad Sci U S A 99 (1): 291–96. Cite

Lee, H., T. J. Griffin, S. P. Gygi, B. Rist, and R. Aebersold. 2002. “Development of a Multiplexed Microcapillary Liquid Chromatography System for High-Throughput Proteome Analysis.” Anal Chem 74 (17): 4353–60. Cite

Leong, K. G., X. Hu, L. Li, M. Noseda, B. Larrivee, C. Hull, L. Hood, F. Wong, and A. Karsan. 2002. “Activated Notch4 Inhibits Angiogenesis: Role of Beta 1-Integrin Activation.” Mol Cell Biol 22 (8): 2830–41. Cite

Leslie, D. M., B. Grill, M. P. Rout, R. W. Wozniak, and J. D. Aitchison. 2002. “Kap121p-Mediated Nuclear Import Is Required for Mating and Cellular Differentiation in Yeast.” Mol Cell Biol 22 (8): 2544–55. Cite

Liu, A. Y., P. S. Nelson, G. van den Engh, and L. Hood. 2002. “Human Prostate Epithelial Cell-Type cDNA Libraries and Prostate Expression Patterns.” Prostate 50 (2): 92–103. Cite

Lusk, C. P., T. Makhnevych, M. Marelli, J. D. Aitchison, and R. W. Wozniak. 2002. “Karyopherins in Nuclear Pore Biogenesis: A Role for Kap121p in the Assembly of Nup53p into Nuclear Pore Complexes.” J Cell Biol 159 (2): 267–78. Cite

Marotti, Jr, R. Newitt, Y. Wang, R. Aebersold, and H. G. Dohlman. 2002. “Direct Identification of a G Protein Ubiquitination Site by Mass Spectrometry.” Biochemistry 41 (16): 5067–74. Cite

Mouse Genome Sequencing, Consortium, R. H. Waterston, K. Lindblad-Toh, E. Birney, J. Rogers, J. F. Abril, P. Agarwal, et al. 2002. “Initial Sequencing and Comparative Analysis of the Mouse Genome.” Nature 420 (6915): 520–62. Cite

Nelson, P. S., N. Clegg, H. Arnold, C. Ferguson, M. Bonham, J. White, L. Hood, and B. Lin. 2002. “The Program of Androgen-Responsive Genes in Neoplastic Prostate Epithelium.” Proc Natl Acad Sci U S A 99 (18): 11890–95. Cite

Papin, Jason A., Nathan D. Price, and Bernhard O. Palsson. 2002. “Extreme Pathway Lengths and Reaction Participation in Genome-Scale Metabolic Networks.” Genome Research 12 (12): 1889–1900. http://doi.org/10.1101/gr.327702. Cite

Papin, Jason A., Nathan D. Price, Jeremy S. Edwards, and Bernhard O. Palsson B. 2002. “The Genome-Scale Metabolic Extreme Pathway Structure in Haemophilus Influenzae Shows Significant Network Redundancy.” Journal of Theoretical Biology 215 (1). http://doi.org/10.1006/jtbi.2001.2499. Cite

Park, I. K., Y. He, F. Lin, O. D. Laerum, Q. Tian, R. Bumgarner, C. A. Klug, et al. 2002. “Differential Gene Expression Profiling of Adult Murine Hematopoietic Stem Cells.” Blood 99 (2): 488–98. Cite

Price, N. D., J. A. Papin, and B. O. Palsson. 2002. “Determination of Redundancy and Systems Properties of the Metabolic Network of Helicobacter Pylori Using Genome-Scale Extreme Pathway Analysis.” Genome Research 12 (5): 760–69. Cite

Price, Nathan D., Iman Famili, Daniel A. Beard, and Bernhard O. Palsson. 2002. “Extreme Pathways and Kirchhoff’s Second Law.” Biophysical Journal 83 (5): 2879–82. http://doi.org/10.1016/S0006-3495(02)75297-1. Cite

Rabilloud, T., M. Heller, F. Gasnier, S. Luche, C. Rey, R. Aebersold, M. Benahmed, P. Louisot, and J. Lunardi. 2002. “Proteomics Analysis of Cellular Response to Oxidative Stress. Evidence for in Vivo Overoxidation of Peroxiredoxins at Their Active Site.” J Biol Chem 277 (22): 19396–401. Cite

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2323737 2RQKSFR5 2001 1 chicago-author-date-16th-edition 50 creator asc 1 1 319 https://isbscience.org/wp-content/plugins/zotpress/

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Allen, E. E., and L. Hood. 2000. “Biotechnology, Inquiry, and Public Education.” Trends Biotechnol 18 (8): 329–30. Cite

Anderson, J. P., A. G. Rodrigo, G. H. Learn, A. Madan, C. Delahunty, M. Coon, M. Girard, S. Osmanov, L. Hood, and J. I. Mullins. 2000. “Testing the Hypothesis of a Recombinant Origin of Human Immunodeficiency Virus Type 1 Subtype E.” J Virol 74 (22): 10752–65. Cite

Baliga, N. S., Y. A. Goo, W. V. Ng, L. Hood, C. J. Daniels, and S. DasSarma. 2000. “Is Gene Expression in Halobacterium NRC-1 Regulated by Multiple TBP and TFB Transcription Factors?” Mol Microbiol 36 (5): 1184–85. Cite

Brewster, J. L., S. L. Martin, J. Toms, D. Goss, K. Wang, K. Zachrone, A. Davis, G. Carlson, L. Hood, and J. D. Coffin. 2000. “Deletion of Dad1 in Mice Induces an Apoptosis-Associated Embryonic Death.” Genesis 26 (4): 271–78. Cite

Cameron, R. A., G. Mahairas, J. P. Rast, P. Martinez, T. R. Biondi, S. Swartzell, J. C. Wallace, et al. 2000. “A Sea Urchin Genome Project: Sequence Scan, Virtual Map, and Additional Resources.” Proc Natl Acad Sci U S A 97 (17): 9514–18. Cite

Chaudhary, P. M., M. T. Eby, A. Jasmin, A. Kumar, L. Liu, and L. Hood. 2000. “Activation of the NF-kappaB Pathway by Caspase 8 and Its Homologs.” Oncogene 19 (39): 4451–60. Cite

Deng, Y., A. Madan, A. B. Banta, C. Friedman, B. J. Trask, L. Hood, and L. Li. 2000. “Characterization, Chromosomal Localization, and the Complete 30-Kb DNA Sequence of the Human Jagged2 (JAG2) Gene.” Genomics 63 (1): 133–38. Cite

Ebrini, I., D. Agnello, I. Miller, P. Villa, M. Fratelli, P. Ghezzi, M. Gemeiner, J. Chan, R. Aebersold, and E. Gianazza. 2000. “Proteins of Rat Serum V: Adjuvant Arthritis and Its Modulation by Nonsteroidal Anti-Inflammatory Drugs.” Electrophoresis 21 (11): 2170–79. Cite

Gan, L., I. Lee, R. Smith, R. Argonza-Barrett, H. Lei, J. McCuaig, P. Moss, B. Paeper, and K. Wang. 2000. “Sequencing and Expression Analysis of the Serine Protease Gene Cluster Located in Chromosome 19q13 Region.” Gene 257 (1): 119–30. Cite

Gibbs, M., J. L. Stanford, G. P. Jarvik, M. Janer, M. Badzioch, M. A. Peters, E. L. Goode, et al. 2000. “A Genomic Scan of Families with Prostate Cancer Identifies Multiple Regions of Interest.” Am J Hum Genet 67 (1): 100–109. Cite

Gold, E. S., N. S. Morrissette, D. M. Underhill, J. Guo, M. Bassetti, and A. Aderem. 2000. “Amphiphysin IIm, a Novel Amphiphysin II Isoform, Is Required for Macrophage Phagocytosis.” Immunity 12 (3): 285–92. Cite

Goode, E. L., J. L. Stanford, L. Chakrabarti, M. Gibbs, S. Kolb, R. A. McIndoe, V. A. Buckley, et al. 2000. “Linkage Analysis of 150 High-Risk Prostate Cancer Families at 1q24-25.” Genet Epidemiol 18 (3): 251–75. Cite

Goodlett, D. R., J. E. Bruce, G. A. Anderson, B. Rist, L. Pasa-Tolic, O. Fiehn, R. D. Smith, and R. Aebersold. 2000. “Protein Identification with a Single Accurate Mass of a Cysteine-Containing Peptide and Constrained Database Searching.” Anal Chem 72 (6): 1112–18. Cite

Goodlett, D. R., R. Aebersold, and J. Watts. 2000. “Quantitative in Vitro Kinase Reaction as a Guide for Phosphoprotein Analysis by Mass Spectrometry.” Rapid Commun Mass Spectrom 14 (5): 344–48. Cite

Gregory, K. E., J. T. Oxford, Y. Chen, J. E. Gambee, S. P. Gygi, R. Aebersold, P. J. Neame, D. E. Mechling, H. P. Bachinger, and N. P. Morris. 2000. “Structural Organization of Distinct Domains within the Non-Collagenous N-Terminal Region of Collagen Type XI.” J Biol Chem 275 (15): 11498–506. Cite

Gygi, S. P., and R. Aebersold. 2000. “Using Mass Spectrometry for Quantitative Proteomics.” Trends in Biotechnology 18 (Supp. 1) (July): 31–36. Cite

Gygi, S. P., and R. Aebersold. 2000. “Mass Spectrometry and Proteomics.” Curr Opin Chem Biol 4 (5): 489–94. Cite

Gygi, S. P., B. Rist, and R. Aebersold. 2000. “Measuring Gene Expression by Quantitative Proteome Analysis.” Curr Opin Biotechnol 11 (4): 396–401. Cite

Gygi, S. P., G. L. Corthals, Y. Zhang, Y. Rochon, and R. Aebersold. 2000. “Evaluation of Two-Dimensional Gel Electrophoresis-Based Proteome Analysis Technology.” Proc Natl Acad Sci U S A 97 (17): 9390–95. Cite

Haynes, P. A., and R. Aebersold. 2000. “Simultaneous Detection and Identification of O-GlcNAc-Modified Glycoproteins Using Liquid Chromatography-Tandem Mass Spectrometry.” Anal Chem 72 (21): 5402–10. Cite

Heller, M., D. R. Goodlett, J. Watts, and R. Aebersold. 2000. “A Comprehensive Characterization of the T-Cell Antigen Receptor Complex Composition by Microcapillary Liquid Chromatography-Tandem Mass Spectrometry.” Electrophoresis 21 (11): 2180–95. Cite

Hood, L. 2000. “The Human Genome Project–Launch Pad for Human Genetic Engineering.” In Engineering the Human Germline (1st Edition), edited by J. Campbell, 17–24. New York: Oxford University Press. Cite

Ideker, T., V. Thorsson, A. F. Siegel, and L. E. Hood. 2000. “Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of Microarray Data.” J Comput Biol 7 (6): 805–17. Cite

Ideker, T. E., V. Thorsson, and R. M. Karp. 2000. “Discovery of Regulatory Interactions through Perturbation: Inference and Experimental Design.” Pac Symp Biocomput, 305–16. Cite

Katze, M. G., B. Kwieciszewski, D. R. Goodlett, C. M. Blakely, P. Neddermann, S. L. Tan, and R. Aebersold. 2000. “Ser(2194) Is a Highly Conserved Major Phosphorylation Site of the Hepatitis C Virus Nonstructural Protein NS5A.” Virology 278 (2): 501–13. Cite

Liao, D. F., Z. G. Jin, A. S. Baas, G. Daum, S. P. Gygi, R. Aebersold, and B. C. Berk. 2000. “Purification and Identification of Secreted Oxidative Stress-Induced Factors from Vascular Smooth Muscle Cells.” J Biol Chem 275 (1): 189–96. Cite

Lin, B., J. T. White, C. Ferguson, R. Bumgarner, C. Friedman, B. Trask, W. Ellis, P. Lange, L. Hood, and P. S. Nelson. 2000. “PART-1: A Novel Human Prostate-Specific, Androgen-Regulated Gene That Maps to Chromosome 5q12.” Cancer Res 60 (4): 858–63. Cite

Livak, F., D. B. Burtrum, L. Rowen, D. G. Schatz, and H. T. Petrie. 2000. “Genetic Modulation of T Cell Receptor Gene Segment Usage during Somatic Recombination.” J Exp Med 192 (8): 1191–96. Cite

Mikheev, A. M., S. A. Mikheev, Y. Zhang, R. Aebersold, and H. Zarbl. 2000. “CArG Binding Factor A (CBF-A) Is Involved in Transcriptional Regulation of the Rat Ha-Ras Promoter.” Nucleic Acids Res 28 (19): 3762–70. Cite

Morrison, D. L., A. Yee, H. B. Paddon, D. Vilimek, R. Aebersold, and S. L. Pelech. 2000. “Regulation of the Meiosis-Inhibited Protein Kinase, a P38(MAPK) Isoform, during Meiosis and Following Fertilization of Seastar Oocytes.” J Biol Chem 275 (44): 34236–44. Cite

Nelson, P. S., N. Clegg, B. Eroglu, V. Hawkins, R. Bumgarner, T. Smith, and L. Hood. 2000. “The Prostate Expression Database (PEDB): Status and Enhancements in 2000.” Nucleic Acids Res 28 (1): 212–13. Cite

Nelson, P. S., D. Han, Y. Rochon, G. L. Corthals, B. Lin, A. Monson, V. Nguyen, et al. 2000. “Comprehensive Analyses of Prostate Gene Expression: Convergence of Expressed Sequence Tag Databases, Transcript Profiling and Proteomics.” Electrophoresis 21 (9): 1823–31. Cite

Ng, W. V., S. P. Kennedy, G. G. Mahairas, B. Berquist, M. Pan, H. D. Shukla, S. R. Lasky, et al. 2000. “Genome Sequence of Halobacterium Species NRC-1.” Proc Natl Acad Sci U S A 97 (22): 12176–81. Cite

Ostrowski, J., D. S. Schullery, O. N. Denisenko, Y. Higaki, J. Watts, R. Aebersold, L. Stempka, M. Gschwendt, and K. Bomsztyk. 2000. “Role of Tyrosine Phosphorylation in the Regulation of the Interaction of Heterogenous Nuclear Ribonucleoprotein K Protein with Its Protein and RNA Partners.” J Biol Chem 275 (5): 3619–28. Cite

Ozinsky, A., D. M. Underhill, J. D. Fontenot, A. M. Hajjar, K. D. Smith, C. B. Wilson, L. Schroeder, and A. Aderem. 2000. “The Repertoire for Pattern Recognition of Pathogens by the Innate Immune System Is Defined by Cooperation between Toll-like Receptors.” Proc Natl Acad Sci U S A 97 (25): 13766–71. Cite

Rampazzo, A., F. Pivotto, G. Occhi, N. Tiso, S. Bortoluzzi, L. Rowen, L. Hood, A. Nava, and G. A. Danieli. 2000. “Characterization of C14orf4, a Novel Intronless Human Gene Containing a Polyglutamine Repeat, Mapped to the ARVD1 Critical Region.” Biochem Biophys Res Commun 278 (3): 766–74. Cite

Raught, B., A. C. Gingras, S. P. Gygi, H. Imataka, S. Morino, A. Gradi, R. Aebersold, and N. Sonenberg. 2000. “Serum-Stimulated, Rapamycin-Sensitive Phosphorylation Sites in the Eukaryotic Translation Initiation Factor 4GI.” EMBO J 19 (3): 434–44. Cite

Roach, J., V. Thorsson, and A. F. Siegel. 2000. “Parking Strategies for Genome Sequencing.” Genome Res 10 (7): 1020–30. Cite

Rowen, L., G. K. Wong, R. P. Lane, and L. Hood. 2000. “Intellectual Property. Publication Rights in the Era of Open Data Release Policies.” Science 289 (5486): 1881. Cite

Siegel, A. F., G. van den Engh, L. Hood, B. Trask, and J. Roach. 2000. “Modeling the Feasibility of Whole Genome Shotgun Sequencing Using a Pairwise End Strategy.” Genomics 68 (3): 237–46. Cite

Timperman, A. T., and R. Aebersold. 2000. “Peptide Electroextraction for Direct Coupling of In-Gel Digests with Capillary LC-MS/MS for Protein Identification and Sequencing.” Anal Chem 72 (17): 4115–21. Cite

Yu, G., M. Nishimura, S. Arawaka, D. Levitan, L. Zhang, A. Tandon, Y. Q. Song, et al. 2000. “Nicastrin Modulates Presenilin-Mediated Notch/Glp-1 Signal Transduction and betaAPP Processing.” Nature 407 (6800): 48–54. Cite