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2025

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

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Cyriaque, Valentine, Rodrigo Ibarra-Chávez, Anna Kuchina, Georg Seelig, Joseph Nesme, and Jonas Stenløkke Madsen. 2024. “Single-Cell RNA Sequencing Reveals Plasmid Constrains Bacterial Population Heterogeneity and Identifies a Non-Conjugating Subpopulation.” Nature Communications 15 (1): 5853. https://doi.org/10.1038/s41467-024-49793-x. Cite

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Ellrott, Kyle, Chris K. Wong, Christina Yau, Mauro A. Castro, Jordan Lee, Brian Karlberg, Jasleen K. Grewal, et al. 2024. “Abstract 6548: Leveraging Compact Feature Sets for TCGA-Based Molecular Subtype Classification on New Samples.” Cancer Research 84 (6_Supplement): 6548. https://doi.org/10.1158/1538-7445.AM2024-6548. Cite

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Flores-Valdez, Mario Alberto, Eliza J. R. Peterson, Michel de Jesús Aceves-Sánchez, Nitin S. Baliga, Yasu S. Morita, Ian L. Sparks, Deepak Kumar Saini, et al. 2024. “Comparison of the Transcriptome, Lipidome, and c-Di-GMP Production between BCGΔBCG1419c and BCG, with Mincle- and Myd88-Dependent Induction of Proinflammatory Cytokines in Murine Macrophages.” Scientific Reports 14 (1): 11898. https://doi.org/10.1038/s41598-024-61815-8. Cite Download

Flower, Cameron T., Chunmei Liu, Hui-Yu Chuang, Xiaoyang Ye, Hanjun Cheng, James R. Heath, Wei Wei, and Forest M. White. 2024. “Signaling and Transcriptional Dynamics Underlying Early Adaptation to Oncogenic BRAF Inhibition.” BioRxiv, 2024–02. https://www.biorxiv.org/content/10.1101/2024.02.19.581004.abstract. Cite Download

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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. https://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. https://doi.org/10.21203/rs.3.rs-4888286/v1. Cite Download

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Huang, Qiongrong, Zhiyuan Hu, Qiwen Zheng, Xuemei Mao, Wenxi Lv, Fei Wu, Dapeng Fu, et al. 2024. “A Proactive Intervention Study in Metabolic Syndrome High-Risk Populations Using Phenome-Based Actionable P4 Medicine Strategy.” Phenomics (Cham, Switzerland) 4 (2): 91–108. https://doi.org/10.1007/s43657-023-00115-z. Cite

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Hwang, Yeon Mi, Ryan T. Roper, Samantha N. Piekos, Daniel A. Enquobahrie, Mary F. Hebert, Alison G. Paquette, Priyanka Baloni, Nathan D. Price, Leroy Hood, and Jennifer J. Hadlock. 2024. “Timing of Selective Serotonin Reuptake Inhibitor Use and Risk for Preterm Birth and Related Adverse Events: With a Consideration of the COVID-19 Pandemic Period.” The Journal of Maternal-Fetal & Neonatal Medicine 37 (1): 2313364. https://doi.org/10.1080/14767058.2024.2313364. Cite Download

Hwang, Yeon Mi, Samantha N. Piekos, Alison G. Paquette, Qi Wei, Nathan D. Price, Leroy Hood, and Jennifer J. Hadlock. 2024. “Accelerating Adverse Pregnancy Outcomes Research amidst Rising Medication Use: Parallel Retrospective Cohort Analyses for Signal Prioritization.” BMC Medicine 22 (1): 495. https://doi.org/10.1186/s12916-024-03717-0. Cite Download

Hwang, Yeon Mi, Samantha N. Piekos, Qi Wei, Nathan D. Price, Leroy Hood, and Jennifer J. Hadlock. 2024. “Detection of Drug Effect Signals Associated with Adverse Pregnancy Outcomes Using Propensity Score Matching at Scale.” medRxiv. https://doi.org/10.1101/2024.03.21.24304579. Cite Download

Hwang, Yeon Mi, Qi Wei, Samantha N. Piekos, Bhargav Vemuri, Sevda Molani, Philip Mease, Leroy Hood, and Jennifer Hadlock. 2024. “Maternal-Fetal Outcomes in Patients with Immune-Mediated Inflammatory Diseases, with Consideration of Comorbidities: A Retrospective Cohort Study in a Large U.S. Healthcare System.” EClinicalMedicine 68:102435. https://doi.org/10.1016/j.eclinm.2024.102435. Cite Download Download

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Johnson-Martínez, Johannes P., Christian Diener, Anne E. Levine, Tomasz Wilmanski, David L. Suskind, Alexandra Ralevski, Jennifer Hadlock, et al. 2024. “Aberrant Bowel Movement Frequencies Coincide with Increased Microbe-Derived Blood Metabolites Associated with Reduced Organ Function.” Cell Reports. Medicine 5 (7): 101646. https://doi.org/10.1016/j.xcrm.2024.101646. Cite

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Kane, Alice. 2024. “TRANSLATIONAL BIOMARKERS FOR AGING AND FRAILTY: IMPORTANT SEX DIFFERENCES.” Innovation in Aging 8 (Suppl 1): 504. https://doi.org/10.1093/geroni/igae098.1645. Cite Download

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

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Aladdin, Azzam, Yanhua Yao, Ciyu Yang, Günther Kahlert, Marvi Ghani, Nikolett Király, Anita Boratkó, Karen Uray, Gunnar Dittmar, and Krisztina Tar. 2020. “The Proteasome Activators Blm10/PA200 Enhance the Proteasomal Degradation of N-Terminal Huntingtin.” Biomolecules 10 (11). https://doi.org/10.3390/biom10111581. Cite Download

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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). https://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. https://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. https://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. https://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. https://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. https://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. https://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. https://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. https://doi.org/10.1089/neu.2019.6826. Cite

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Herold, Malte, Susana Martínez Arbas, Shaman Narayanasamy, Abdul R. Sheik, Luise A. K. Kleine-Borgmann, Laura A. Lebrun, Benoît J. Kunath, et al. 2020. “Integration of Time-Series Meta-Omics Data Reveals How Microbial Ecosystems Respond to Disturbance.” Nature Communications 11 (1): 5281. https://doi.org/10.1038/s41467-020-19006-2. Cite Download

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

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

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2323737 2RQKSFR5 2014 1 chicago-author-date 50 creator asc 1 1 319 https://isbscience.org/wp-content/plugins/zotpress/

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2013

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

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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. https://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. https://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. https://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. https://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

Hoopmann, M. R., and R. L. Moritz. 2013. “Current Algorithmic Solutions for Peptide-Based Proteomics Data Generation and Identification.” Curr Opin Biotechnol 24 (1): 31–38. Cite

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. https://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). https://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. https://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). https://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. https://doi.org/10.1186/1471-2164-14-918. Cite

Lindner, S. E., K. E. Swearingen, A. Harupa, A. M. Vaughan, P. Sinnis, R. L. Moritz, and S. H. Kappe. 2013. “Total and Putative Surface Proteomics of Malaria Parasite Salivary Gland Sporozoites.” Molecular & Cellular Proteomics : MCP, January. Cite

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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Mandin, P., A. Toledo-Arana, A. Fouquier d’Hérouel, and F. Repoila. 2013. “RNA-Mediated Control of Bacterial Gene Expression: Role of Regulatory Non-Coding RNAs.” Encyclopedia of Molecular Cell Biology and Molecular Medicine, 1–36. Cite

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2012

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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. https://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

Bebek, Gurkan, Mehmet Koyuturk, Nathan D. Price, and Mark R. Chance. 2012. “Network Biology Methods Integrating Biological Data for Translational Science.” Briefings in Bioinformatics 13 (4): 446–59. https://doi.org/10.1093/bib/bbr075. Cite

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. https://doi.org/10.1128/JB.06040-11. Cite

Bernard, B., V. Thorsson, H. Rovira, and I. Shmulevich. 2012. “Increasing Coverage of Transcription Factor Position Weight Matrices through Domain-Level Homology.” PloS One 7 (8): e42779. Cite

Bislev, S. L., U. Kusebauch, M. C. Codrea, R. J. Beynon, V. M. Harman, C. M. Rontved, R. Aebersold, R. L. Moritz, and E. Bendixen. 2012. “Quantotypic Properties of QconCAT Peptides Targeting Bovine Host Response to Streptococcus Uberis.” Journal of Proteome Research 11 (3): 1832–43. Cite

Bislev, S. L., E. W. Deutsch, Z. Sun, T. Farrah, R. Aebersold, R. L. Moritz, E. Bendixen, and M. C. Codrea. 2012. “A Bovine PeptideAtlas of Milk and Mammary Gland Proteomes.” Proteomics, July. Cite

Boyle, J., R. Kreisberg, R. Bressler, and S. Killcoyne. 2012. “Methods for Visual Mining of Genomic and Proteomic Data Atlases.” BMC Bioinformatics 13:58. Cite

Bressler, R., J. Lin, A. Eakin, T. Robinson, R. Kreisberg, H. Rovira, T. Knijnenburg, J. Boyle, and I. Shmulevich. 2012. “Fastbreak: A Tool for Analysis and Visualization of Structural Variations in Genomic Data.” EURASIP Journal on Bioinformatics & Systems Biology 2012 (1): 15. Cite

Brogaard, K., L. Xi, J. P. Wang, and J. Widom. 2012. “A Map of Nucleosome Positions in Yeast at Base-Pair Resolution.” Nature 486 (7404): 496–501. Cite

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

Buchner, D. A., J. M. Geisinger, P. A. Glazebrook, M. G. Morgan, S. H. Spiezio, K. J. Kaiyala, M. W. Schwartz, et al. 2012. “The Juxtaparanodal Proteins CNTNAP2 and TAG1 Regulate Diet-Induced Obesity.” Mammalian Genome : Official Journal of the International Mammalian Genome Society 23 (7–8): 431–42. Cite

Cancer Genome Atlas Network. 2012. “Comprehensive Molecular Characterization of Human Colon and Rectal Cancer.” Nature 487 (7407): 330–37. https://doi.org/10.1038/nature11252. Cite Download

Cancer Genome Atlas Research Network. 2012. “Comprehensive Molecular Characterization of Human Colon and Rectal Cancer.” Nature 487 (July):330–37. https://doi.org/10.1038/nature11252. Cite

Chambers, M. C., B. Maclean, R. Burke, D. Amodei, D. L. Ruderman, S. Neumann, L. Gatto, et al. 2012. “A Cross-Platform Toolkit for Mass Spectrometry and Proteomics.” Nature Biotechnology 30 (10): 918–20. Cite

Chen, L. Y., K. C. Wei, A. C. Huang, K. Wang, C. Y. Huang, D. Yi, C. Y. Tang, D. J. Galas, and L. E. Hood. 2012. “RNASEQR–a Streamlined and Accurate RNA-Seq Sequence Analysis Program.” Nucleic Acids Research 40 (6): e42. Cite

Craig, Theodore A., Yuji Zhang, Melissa S. McNulty, Sumit Middha, Hemamalini Ketha, Ravinder J. Singh, Andrew T. Magis, et al. 2012. “Research Resource: Whole Transcriptome RNA Sequencing Detects Multiple 1alpha,25-Dihydroxyvitamin D(3)-Sensitive Metabolic Pathways in Developing Zebrafish.” Molecular Endocrinology (Baltimore, Md.) 26 (9): 1630–42. https://doi.org/10.1210/me.2012-1113. Cite

Cruz-Ramirez, A., S. Diaz-Trivino, I. Blilou, V. A. Grieneisen, R. Sozzani, C. Zamioudis, P. Miskolczi, et al. 2012. “A Bistable Circuit Involving SCARECROW-RETINOBLASTOMA Integrates Cues to Inform Asymmetric Stem Cell Division.” Cell 150 (5): 1002–15. Cite

DeGracia, Donald J., Zhi-Feng Huang, and Sui Huang. 2012. “A Nonlinear Dynamical Theory of Cell Injury.” J Cereb Blood Flow Metab 32 (June):1000–1013. https://doi.org/10.1038/jcbfm.2012.10. Cite

Deus, H. F., E. Prud’hommeaux, M. Miller, J. Zhao, J. Malone, T. Adamusiak, J. McCusker, et al. 2012. “Translating Standards into Practice – One Semantic Web API for Gene Expression.” Journal of Biomedical Informatics 45 (4): 782–94. Cite

Deutsch, E. W. 2012. “File Formats Commonly Used in Mass Spectrometry Proteomics.” Molecular & Cellular Proteomics : MCP, September. Cite

Deutsch, E. W., M. Chambers, S. Neumann, F. Levander, P. A. Binz, J. Shofstahl, D. S. Campbell, et al. 2012. “TraML–A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists.” Molecular & Cellular Proteomics : MCP 11 (4): R111 015040. Cite

Diamond, Deborah L., Alexei L. Krasnoselsky, Kristin E. Burnum, Matthew E. Monroe, Bobbie-Jo Webb-Robertson, Jason E. McDermott, Matthew M. Yeh, et al. 2012. “Proteome and Computational Analyses Reveal New Insights into the Mechanisms of Hepatitis C Virus-Mediated Liver Disease Posttransplantation.” Hepatology 56 (July):28–38. https://doi.org/10.1002/hep.25649. Cite

Dougherty, E. R., and I. Shmulevich. 2012. “On the Limitations of Biological Knowledge.” Current Genomics 13 (7): 574–87. Cite

Dubois, K. N., S. Alsford, J. M. Holden, J. Buisson, M. Swiderski, J. M. Bart, A. V. Ratushny, et al. 2012. “NUP-1 Is a Large Coiled-Coil Nucleoskeletal Protein in Trypanosomes with Lamin-Like Functions.” PLoS Biology 10 (3): e1001287. Cite

Edgar, Rachel S., Edward W. Green, Yuwei Zhao, Gerben van Ooijen, Maria Olmedo, Ximing Qin, Yao Xu, et al. 2012. “Peroxiredoxins Are Conserved Markers of Circadian Rhythms.” Nature 485 (May):459–64. https://doi.org/10.1038/nature11088. Cite

Ezzie, M. E., M. Crawford, J. H. Cho, R. Orellana, S. Zhang, R. Gelinas, K. Batte, et al. 2012. “Gene Expression Networks in COPD: MicroRNA and MRNA Regulation.” Thorax 67 (2): 122–31. Cite

Farrah, T., E. W. Deutsch, R. Kreisberg, Z. Sun, D. S. Campbell, L. Mendoza, U. Kusebauch, et al. 2012. “PASSEL: The PeptideAtlas SRM Experiment Library.” Proteomics, February. Cite

Farrah, T., E. W. Deutsch, M. R. Hoopmann, J. L. Hallows, Z. Sun, C. Y. Huang, and R. L. Moritz. 2012. “The State of the Human Proteome in 2012 as Viewed through PeptideAtlas.” Journal of Proteome Research, December. Cite

Glusman, Gustavo, Mike Cariaso, Rafael Jimenez, Daniel Swan, Bastian Greshake, Jong Bhak, Darren W. Logan, and Manuel Corpas. 2012. “Low Budget Analysis of Direct-To-Consumer Genomic Testing Familial Data.” F1000Research 1:3. https://doi.org/10.12688/f1000research.1-3.v1. Cite

Gold, E. S., S. A. Ramsey, M. J. Sartain, J. Selinummi, I. Podolsky, D. J. Rodriguez, R. L. Moritz, and A. Aderem. 2012. “ATF3 Protects against Atherosclerosis by Suppressing 25-Hydroxycholesterol-Induced Lipid Body Formation.” The Journal of Experimental Medicine 209 (4): 807–17. Cite

Halley, J. D., K. Smith-Miles, D. A. Winkler, T. Kalkan, S. Huang, and A. Smith. 2012. “Self-Organizing Circuitry and Emergent Computation in Mouse Embryonic Stem Cells.” Stem Cell Res 8 (March):324–33. https://doi.org/10.1016/j.scr.2011.11.001. Cite

Han, Xu, Xuefeng Fang, Xiaoyan Lou, Dasong Hua, Wenchao Ding, Gregory Foltz, Leroy Hood, Ying Yuan, and Biaoyang Lin. 2012. “Silencing SOX2 Induced Mesenchymal-Epithelial Transition and Its Expression Predicts Liver and Lymph Node Metastasis of CRC Patients.” PLoS One 7:e41335. https://doi.org/10.1371/journal.pone.0041335. Cite

Ho, Hsiu J., Tsung I. Lin, Hannah H. Chang, Steven B. Haase, S. Huang, and Saumyadipta Pyne. 2012. “Parametric Modeling of Cellular State Transitions as Measured with Flow Cytometry.” BMC Bioinformatics 13 Suppl 5:S5. https://doi.org/10.1186/1471-2105-13-S5-S5. Cite

Holmes, K. M., M. Annala, C. Y. Chua, S. M. Dunlap, Y. Liu, N. Hugen, L. M. Moore, et al. 2012. “Insulin-like Growth Factor-Binding Protein 2-Driven Glioma Progression Is Prevented by Blocking a Clinically Significant Integrin, Integrin-Linked Kinase, and NF-KappaB Network.” Proceedings of the National Academy of Sciences of the United States of America 109 (9): 3475–80. Cite

Hood, L. 2012. “Tackling the Microbiome.” Science 336 (6086): 1209. https://doi.org/10.1126/science.1225475. Cite

Hood, Leroy, and Mauricio Flores. 2012. “A Personal View on Systems Medicine and the Emergence of Proactive P4 Medicine: Predictive, Preventive, Personalized and Participatory.” N Biotechnol 29 (September):613–24. https://doi.org/10.1016/j.nbt.2012.03.004. Cite

Hood, Leroy, and Qiang Tian. 2012. “Systems Approaches to Biology and Disease Enable Translational Systems Medicine.” Genomics Proteomics Bioinformatics 10 (August):181–85. https://doi.org/10.1016/j.gpb.2012.08.004. Cite

Hood, L. E., G. S. Omenn, R. L. Moritz, R. Aebersold, R. Yamamoto K, M. Amos, J. Hunter-Cevera, and L. Locascio. 2012. “New and Improved Proteomics Technologies for Understanding Complex Biological Systems: Addressing a Grand Challenge in the Life Sciences.” Proteomics, July. Cite

Hood, Leroy, Rudi Balling, and Charles Auffray. 2012. “Revolutionizing Medicine in the 21st Century through Systems Approaches.” Biotechnol J 7 (August):992–1001. https://doi.org/10.1002/biot.201100306. Cite

Hoopmann, M. R., M. J. MacCoss, and R. L. Moritz. 2012. “Identification of Peptide Features in Precursor Spectra Using Hardklor and Kronik.” In Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis … [et Al.], 2012/03/06 ed., Chapter 13:Unit13 18. Cite

Huang, S. 2012. “The Molecular and Mathematical Basis of Waddington’s Epigenetic Landscape: A Framework for Post-Darwinian Biology?” BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology 34 (2): 149–57. Cite

Huang, S. 2012. “Tumor Progression: Chance and Necessity in Darwinian and Lamarckian Somatic (Mutationless) Evolution.” Progress in Biophysics and Molecular Biology, May. Cite

Huang, S, M. Holzel, T. Knijnenburg, A. Schlicker, P. Roepman, U. McDermott, M. Garnett, et al. 2012. “MED12 Controls the Response to Multiple Cancer Drugs through Regulation of TGF-Beta Receptor Signaling.” Cell 151 (5): 937–50. Cite

Huttenhain, R., M. Soste, N. Selevsek, H. Rost, A. Sethi, C. Carapito, T. Farrah, et al. 2012. “Reproducible Quantification of Cancer-Associated Proteins in Body Fluids Using Targeted Proteomics.” Science Translational Medicine 4 (142): 142ra94. Cite

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2011

2323737 2RQKSFR5 2011 1 chicago-author-date 50 creator asc 1 1 319 https://isbscience.org/wp-content/plugins/zotpress/

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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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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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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. https://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. https://doi.org/10.1186/1471-2164-10-583. 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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Glatter, T., A. Wepf, R. Aebersold, and M. Gstaiger. 2009. “An Integrated Workflow for Charting the Human Interaction Proteome: Insights into the PP2A System.” Mol Syst Biol 5:237. Cite

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Heath, James R., M. E. Davis, and L. Hood. 2009. “Nanomedicine Targets Cancer.” Sci Am 300 (2): 44–51. Cite

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