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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/

Dacon, Cherrelle, Re’em Moskovitz, Kristian Swearingen, Lais Da Silva Pereira, Yevel Flores-Garcia, Maya Aleshnick, Sachie Kanatani, et al. 2025. “Protective Antibodies Target Cryptic Epitope Unmasked by Cleavage of Malaria Sporozoite Protein.” Science (New York, N.Y.) 387 (6729): eadr0510. https://doi.org/10.1126/science.adr0510. Cite

Ellrott, Kyle, Christopher K. Wong, Christina Yau, Mauro A. A. Castro, Jordan A. Lee, Brian J. Karlberg, Jasleen K. Grewal, et al. 2025. “Classification of Non-TCGA Cancer Samples to TCGA Molecular Subtypes Using Compact Feature Sets.” Cancer Cell. https://doi.org/10.1016/j.ccell.2024.12.002. Cite

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2024

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

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Armstrong, Sujit Silas, Daniel G. Chen, Sunil Kumar, James R. Heath, Matthew Feinstein, John R. Greenland, Daniel R. Calabrese, Lewis L. Lanier, Klaus Ley, and Avishai Shemesh. 2024. “CITE-Seq Analysis Reveals Human Cytomegalovirus and Diabetes-Associated Adaptive NK Cell Alterations in Cardiovascular Disease.” BioRxiv, 2024–03. https://www.biorxiv.org/content/10.1101/2024.03.22.581997.abstract. Cite Download

Bartolomucci, Alessandro, Alice E. Kane, Lauren Gaydosh, Maria Razzoli, Brianah M. McCoy, Dan Ehninger, Brian H. Chen, Susan E. Howlett, and Noah Snyder-Mackler. 2024. “Animal Models Relevant for Geroscience: Current Trends and Future Perspectives in Biomarkers, and Measures of Biological Aging.” The Journals of Gerontology. Series A, Biological Sciences and Medical Sciences 79 (9): glae135. https://doi.org/10.1093/gerona/glae135. Cite

Baumgartner, Andrew, Sui Huang, Jennifer Hadlock, and Cory Funk. 2024. “Dimensional Reduction of Gradient-like Stochastic Systems with Multiplicative Noise via Fokker-Planck Diffusion Maps.” arXiv. https://doi.org/10.48550/arXiv.2401.03095. Cite Download

Baumgartner, Andrew, Max Robinson, Todd Golde, Suman Jaydev, Sui Huang, Jennifer Hadlock, and Cory Funk. 2024. “Fokker-Planck Diffusion Maps of Multiple Single Cell Microglial Transcriptomes Reveals Radial Differentiation into Substates Associated with Alzheimer’s Pathology.” BioRxiv: The Preprint Server for Biology, 2024.06.21.599924. https://doi.org/10.1101/2024.06.21.599924. Cite

Bronstein, Becky, Molly Griffiths, Claudia McLaughlin Ludwig, Deb L. Morrison, Heidi Smith, and Barbara Steffens. 2024. “Action and Engagement in Climate Science Learning Pedagogy.” Connected Science Learning, 1–3. https://doi.org/10.1080/24758779.2024.2376483. Cite

Byrne, Audrey, Christian Diener, Bryan P. Brown, Brandon S. Maust, Colin Feng, Berenice L. Alinde, Sean M. Gibbons, et al. 2024. “Neonates Exposed to HIV but Uninfected Exhibit an Altered Gut Microbiota and Inflammation Associated with Impaired Breast Milk Antibody Function.” Microbiome 12 (1): 261. https://doi.org/10.1186/s40168-024-01973-z. Cite Download

Camacho, Oscar J. M., Kerry A. Ramsbottom, Ananth Prakash, Zhi Sun, Yasset Perez Riverol, Emily Bowler-Barnett, Maria Martin, et al. 2024. “Phosphorylation in the Plasmodium Falciparum Proteome: A Meta-Analysis of Publicly Available Data Sets.” Journal of Proteome Research 23 (12): 5326–41. https://doi.org/10.1021/acs.jproteome.4c00418. Cite

Chang, Shu-Ching, Gary L. Grunkemeier, Jason D. Goldman, Mansen Wang, Paul A. McKelvey, Jennifer Hadlock, Qi Wei, and George A. Diaz. 2024. “A Simplified Pneumonia Severity Index (PSI) for Clinical Outcome Prediction in COVID-19.” PloS One 19 (5): e0303899. https://doi.org/10.1371/journal.pone.0303899. Cite Download

Chen, Daniel G., Jingyi Xie, Jongchan Choi, Rachel H. Ng, Rongyu Zhang, Sarah Li, Rick Edmark, et al. 2024. “Integrative Systems Biology Reveals NKG2A-Biased Immune Responses Correlate with Protection in Infectious Disease, Autoimmune Disease, and Cancer.” Cell Reports 43 (3). https://doi.org/10.1016/j.celrep.2024.113872. Cite Download

Chen, Xinyi, Yapeng Su, Chloe Dai, Jason D. Goldman, James R. Heath, Si Liu, and Wei Sun. 2024. “Association between COVID-19 Disease Severity and T Cell Receptor Repertoire.” bioRxiv. https://doi.org/10.1101/2024.11.26.625333. Cite Download

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

Deutsch, Eric W., Leron W. Kok, Jonathan M. Mudge, Jorge Ruiz-Orera, Ivo Fierro-Monti, Zhi Sun, Jennifer G. Abelin, et al. 2024. “High-Quality Peptide Evidence for Annotating Non-Canonical Open Reading Frames as Human Proteins.” BioRxiv: The Preprint Server for Biology, 2024.09.09.612016. https://doi.org/10.1101/2024.09.09.612016. Cite

Diener, Christian, and Sean M. Gibbons. 2024. “Metagenomic Estimation of Dietary Intake from Human Stool.” BioRxiv: The Preprint Server for Biology, 2024.02.02.578701. https://doi.org/10.1101/2024.02.02.578701. Cite Download

Dirvin, Brooke, Heeju Noh, Lorenzo Tomassoni, Danting Cao, Yizhuo Zhou, Xiangyi Ke, Jun Qian, et al. 2024. “Identification and Targeting of Regulators of SARS-CoV-2-Host Interactions in the Airway Epithelium.” BioRxiv: The Preprint Server for Biology, 2024.10.11.617898. https://doi.org/10.1101/2024.10.11.617898. Cite Download

Don, Janith, Andrew J. Schork, Gwênlyn Glusman, Noa Rappaport, Steve R. Cummings, David Duggan, Anish Raju, et al. 2024. “The Relationship between 11 Different Polygenic Longevity Scores, Parental Lifespan, and Disease Diagnosis in the UK Biobank.” GeroScience. https://doi.org/10.1007/s11357-024-01107-1. Cite Download

Eklund, Jen, Kelsie Fowler, Caroline Kiehle, Lori Henrickson, and Deb L. Morrison. 2024. “Make Climate Learning Happen Exactly Where You Are.” Connected Science Learning 0 (0): 1–7. https://doi.org/10.1080/24758779.2024.2371759. Cite

Faust, Saul N., Richard Haynes, Christine E. Jones, Natalie Staplin, Elizabeth Whittaker, Thomas Jaki, Ed Juszczak, Enti Spata, Mandy Wan, and James R. Heath. 2024. “Immunomodulatory Therapy in Children with Paediatric Inflammatory Multisystem Syndrome Temporally Associated with SARS-CoV-2 (PIMS-TS, MIS-C; RECOVERY): A Randomised, Controlled, Open-Label, Platform Trial.” The Lancet Child & Adolescent Health 8 (3): 190–200. https://www.thelancet.com/journals/lanchi/article/PIIS2352-4642(23)00316-4/fulltext. Cite

Firsanov, Denis, Max Zacher, Xiao Tian, Todd L. Sformo, Yang Zhao, Greg Tombline, J. Yuyang Lu, et al. 2024. “DNA Repair and Anti-Cancer Mechanisms in the Long-Lived Bowhead Whale.” BioRxiv: The Preprint Server for Biology, 2023.05.07.539748. https://doi.org/10.1101/2023.05.07.539748. 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

Funk, Cory C., Martin Darvas, Christine Johnston, Max Robinson, Caitlyn Schaffer, Christian Battaglia, Martine Aubert, and Jesse C. Wiley. 2024. “Basic Science and Pathogenesis.” Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association 20 Suppl 1:e093497. https://doi.org/10.1002/alz.093497. Cite

Funk, Cory C., Tom Paterson, Jennifer Rohrs, and Timothy J. Hohman. 2024. “Basic Science and Pathogenesis.” Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association 20 Suppl 1:e092897. https://doi.org/10.1002/alz.092897. Cite

Gaisser, Karl D., Sophie N. Skloss, Leandra M. Brettner, Luana Paleologu, Charles M. Roco, Alexander B. Rosenberg, Matthew Hirano, R. William DePaolo, Georg Seelig, and Anna Kuchina. 2024. “High-Throughput Single-Cell Transcriptomics of Bacteria Using Combinatorial Barcoding.” Nature Protocols. https://doi.org/10.1038/s41596-024-01007-w. Cite

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

Geyer, Philipp E., Daniel Hornburg, Maria Pernemalm, Stefanie M. Hauck, Krishnan K. Palaniappan, Vincent Albrecht, Laura F. Dagley, et al. 2024. “The Circulating Proteome─Technological Developments, Current Challenges, and Future Trends.” Journal of Proteome Research 23 (12): 5279–95. https://doi.org/10.1021/acs.jproteome.4c00586. Cite

Goetz, Skye L., Amy K. Glen, and Gwênlyn Glusman. 2024. “MicrobiomeKG: Bridging Microbiome Research and Host Health Through Knowledge Graphs.” BioRxiv: The Preprint Server for Biology, 2024.10.10.617697. https://doi.org/10.1101/2024.10.10.617697. Cite Download

Griffin, Patrick T., Alice Kane, Alexandre Trapp, Jien Li, Matthew Arnold, Jesse R. Poganik, Ryan J. Conway, et al. 2024. “TIME-Seq Reduces Time and Cost of DNA Methylation Measurement for Epigenetic Clock Construction.” Nature Aging. https://doi.org/10.1038/s43587-023-00555-2. Cite

Hariharan, Ramkumar, Leroy Hood, and Nathan D. Price. 2024. “A Data-Driven Approach to Improve Wellness and Reduce Recurrence in Cancer Survivors.” Frontiers in Oncology 14:1397008. https://doi.org/10.3389/fonc.2024.1397008. Cite Download

He, Fuchu, Ruedi Aebersold, Mark S. Baker, Xiuwu Bian, Xiaochen Bo, Daniel W. Chan, Cheng Chang, et al. 2024. “π-HuB: The Proteomic Navigator of the Human Body.” Nature 636 (8042): 322–31. https://doi.org/10.1038/s41586-024-08280-5. Cite

He, Fuchu, Ruedi Aebersold, Mark S. Baker, Xiuwu Bian, Xiaochen Bo, Daniel W. Chan, Cheng Chang, et al. 2024. “Author Correction: π-HuB: The Proteomic Navigator of the Human Body.” Nature. https://doi.org/10.1038/s41586-024-08555-x. Cite

Heath, James R. 2024. “Abstract SY41-02: Experimental Methods for High Throughput Discovery and Validation of Tumor Antigens.” Cancer Research 84 (7_Supplement): SY41-02. https://aacrjournals.org/cancerres/article/84/7_Supplement/SY41-02/742137. Cite

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

Hunt, Kristopher A., Alex V. Carr, Anne E. Otwell, Jacob J. Valenzuela, Kathleen S. Walker, Emma R. Dixon, Lauren M. Lui, et al. 2024. “Contribution of Microorganisms with the Clade II Nitrous Oxide Reductase to Suppression of Surface Emissions of Nitrous Oxide.” Environmental Science & Technology. https://doi.org/10.1021/acs.est.3c07972. Cite

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, 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

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

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

Kader, Tanjina, Jia-Ren Lin, Clemens B. Hug, Shannon Coy, Yu-An Chen, Ino de Bruijn, Natalie Shih, et al. 2024. “Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma.” Cancer Discovery. https://doi.org/10.1158/2159-8290.CD-24-1366. Cite

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

Kane, Alice E., Karthikeyani Chellappa, Michael B. Schultz, Matthew Arnold, Jien Li, Joao Amorim, Christian Diener, et al. 2024. “Long-Term NMN Treatment Increases Lifespan and Healthspan in Mice in a Sex Dependent Manner.” bioRxiv. https://doi.org/10.1101/2024.06.21.599604. Cite Download

Kim, Jungwoo, Rachel H. Ng, JingXin Liang, Dazy Johnson, Young Shik Shin, Arion F. Chatziioannou, Michael E. Phelps, Wei Wei, Raphael D. Levine, and James R. Heath. 2024. “Kinetic Trajectories of Glucose Uptake in Single Cancer Cells Reveal a Drug-Induced Cell-State Change Within Hours of Drug Treatment.” The Journal of Physical Chemistry. B. https://doi.org/10.1021/acs.jpcb.4c03663. Cite

Klein, Joshua, Henry Lam, Tytus D. Mak, Wout Bittremieux, Yasset Perez-Riverol, Ralf Gabriels, Jim Shofstahl, et al. 2024. “The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: MzSpecLib and MzPAF.” Analytical Chemistry 96 (46): 18491–501. https://doi.org/10.1021/acs.analchem.4c04091. Cite

Kopp, Audrey, Mehar Un Nissa, Roberta Dollinger, Jeff Ranish, and Marjorie Brand. 2024. “3106 – PROTEOMICS AND GENOMICS STUDIES REVEALED A NEW ROLE FOR MLL PARTIAL TANDEM DUPLICATION (PTD) IN MYELODYSPLASTIC SYNDROME (MDS) AND ACUTE MYELOID LEUKEMIA (AML).” Experimental Hematology, SUPP:EXPHEM Abstracts 2024, 137:104428. https://doi.org/10.1016/j.exphem.2024.104428. Cite

Kornilov, Sergey A., Nathan D. Price, Richard Gelinas, Juan Acosta, Mary E. Brunkow, Tiffany Gervasi-Follmar, Ryan C. Winger, et al. 2024. “Multi-Omic Characterization of the Effects of Ocrelizumab in Patients with Relapsing-Remitting Multiple Sclerosis.” Journal of the Neurological Sciences 467:123303. https://doi.org/10.1016/j.jns.2024.123303. Cite

Kumari, Suman, Christopher Lausted, Kelsey Scherler, Alphonsus H. C. Ng, Yue Lu, Inyoul Lee, Leroy Hood, and Kai Wang. 2024. “Approaches and Challenges in Characterizing the Molecular Content of Extracellular Vesicles for Biomarker Discovery.” Biomolecules 14 (12): 1599. https://doi.org/10.3390/biom14121599. Cite Download

L Rocha, Heber, Boris Aguilar, Michael Getz, Ilya Shmulevich, and Paul Macklin. 2024. “A Multiscale Model of Immune Surveillance in Micrometastases Gives Insights on Cancer Patient Digital Twins.” NPJ Systems Biology and Applications 10 (1): 144. https://doi.org/10.1038/s41540-024-00472-z. Cite

Laubenbacher, Reinhard, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L. Fonseca, James Glazier, et al. 2024. “Toward Mechanistic Medical Digital Twins: Some Use Cases in Immunology.” Frontiers in Digital Health 6:1349595. https://doi.org/10.3389/fdgth.2024.1349595. Cite Download

Laubenbacher, Reinhard, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L. Fonseca, James Glazier, et al. 2024. “Forum on Immune Digital Twins: A Meeting Report.” NPJ Systems Biology and Applications 10 (1): 19. https://doi.org/10.1038/s41540-024-00345-5. Cite Download

Laubenbacher, R., B. Mehrad, I. Shmulevich, and N. Trayanova. 2024. “Digital Twins in Medicine.” Nature Computational Science 4 (3): 184–91. https://doi.org/10.1038/s43588-024-00607-6. Cite Download

Leblebici, Asim, Ceren Sancar, Bahar Tercan, Zerrin Isik, Mehmet Emin Arayici, Ender Berat Ellidokuz, Yasemin Basbinar, and Nuri Yildirim. 2024. “In Silico Approach to Molecular Profiling of the Transition from Ovarian Epithelial Cells to Low-Grade Serous Ovarian Tumors for Targeted Therapeutic Insights.” Current Issues in Molecular Biology 46 (3): 1777–98. https://doi.org/10.3390/cimb46030117. 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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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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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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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

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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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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

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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

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2006

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

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2005

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2323737 2RQKSFR5 2003 1 chicago-author-date 50 creator asc 1 1 319 https://isbscience.org/wp-content/plugins/zotpress/

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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

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2323737 2RQKSFR5 2002 1 chicago-author-date 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. https://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). https://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. https://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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Shiio, Y., S. Donohoe, E. C. Yi, D. R. Goodlett, R. Aebersold, and R. N. Eisenman. 2002. “Quantitative Proteomic Analysis of Myc Oncoprotein Function.” EMBO J 21 (19): 5088–96. Cite

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Smith, J. J., M. Marelli, R. H. Christmas, F. J. Vizeacoumar, D. J. Dilworth, T. Ideker, T. Galitski, K. Dimitrov, R. A. Rachubinski, and J. D. Aitchison. 2002. “Transcriptome Profiling to Identify Genes Involved in Peroxisome Assembly and Function.” J Cell Biol 158 (2): 259–71. Cite

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2001

2323737 2RQKSFR5 2001 1 chicago-author-date 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