Smith, Richard D.

Genomic responses in mouse models poorly mimic human inflammatory diseases

Seok, J., Warren, H. S., Cuenca, A. G., Mindrinos, M. N., Baker, H. V., Xu, W., Richards, D. R., McDonald-Smith, G. P., Gao, H., Hennessy, L., et al. (2013) · Proceedings of the National Academy of Sciences

Animal testing and alternativesImmune Response and Inflammation

Cited by 3,005

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma

Gillette, M. A., Satpathy, S., Cao, S., Dhanasekaran, S. M., Vasaikar, S. V., Krug, K., Petralia, F., Li, Y., Liang, W.-W., Reva, B., et al. (2020) · Cell

Lung Cancer Treatments and MutationsLung Cancer Research Studies

Cited by 820

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

Vasaikar, S., Huang, C., Wang, X., Petyuk, V. A., Savage, S. R., Wen, B., Dou, Y., Zhang, Y., Shi, Z., Arshad, O. A., et al. (2019) · Cell

Advanced Proteomics Techniques and ApplicationsCancer Genomics and Diagnostics

Cited by 799

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

Clark, D. J., Dhanasekaran, S. M., Petralia, F., Pan, J., Song, X., Hu, Y., da Veiga Leprevost, F., Reva, B., Lih, T.-S. M., Chang, H.-Y., et al. (2019) · Cell

Renal cell carcinoma treatmentCancer Genomics and Diagnostics

Cited by 730

Proteogenomic and metabolomic characterization of human glioblastoma

Wang, L.-B., Karpova, A., Gritsenko, M. A., Kyle, J. E., Cao, S., Li, Y., Rykunov, D., Colaprico, A., Rothstein, J. H., Hong, R., et al. (2021) · Cancer Cell

Glioma Diagnosis and TreatmentCancer Genomics and Diagnostics

Cited by 661

Comparative analysis of proteome and transcriptome variation in mouse

Ghazalpour, A., Bennett, B., Petyuk, V. A., Orozco, L., Hagopian, R., Mungrue, I. N., Farber, C. R., Sinsheimer, J., Kang, H. M., Furlotte, N., et al. (2011) · PLoS Genetics

Advanced Proteomics Techniques and ApplicationsBioinformatics and Genomic Networks

Cited by 624

Identification of Proteins in Human Cytomegalovirus (HCMV) Particles: the HCMV Proteome

Varnum, S. M., Streblow, D. N., Monroe, M. E., Smith, P., Auberry, K. J., Paša-Tolić, L., Wang, D., Camp, D. G., Rodland, K., Wiley, S., et al. (2004) · Journal of Virology

Cytomegalovirus and herpesvirus researchAdvanced Proteomics Techniques and Applications

Cited by 598

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

Zhu, Y., Piehowski, P. D., Zhao, R., Chen, J., Shen, Y., Moore, R. J., Shukla, A. K., Petyuk, V. A., Campbell-Thompson, M., Mathews, C. E., et al. (2018) · Nature Communications

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 587

Proteogenomic characterization of pancreatic ductal adenocarcinoma

Cao, L., Huang, C., Cui Zhou, D., Hu, Y., Lih, T. M., Savage, S. R., Krug, K., Clark, D. J., Schnaubelt, M., Chen, L., et al. (2021) · Cell

Pancreatic and Hepatic Oncology ResearchCancer Genomics and Diagnostics

Cited by 578

Proteogenomic Characterization of Endometrial Carcinoma

Dou, Y., Kawaler, E. A., Cui Zhou, D., Gritsenko, M. A., Huang, C., Blumenberg, L., Karpova, A., Petyuk, V. A., Savage, S. R., Satpathy, S., et al. (2020) · Cell

Endometrial and Cervical Cancer TreatmentsAdvanced Proteomics Techniques and Applications

Cited by 485

A Perspective on the Maillard Reaction and the Analysis of Protein Glycation by Mass Spectrometry: Probing the Pathogenesis of Chronic Disease

Zhang, Q., Ames, J. M., Smith, R. D., Baynes, J. W., & Metz, T. O. (2009) · Journal of Proteome Research

Advanced Glycation End Products researchPotato Plant Research

Cited by 421

Normalization and missing value imputation for label-free LC-MS analysis

Karpievitch, Y. V., Dabney, A. R., & Smith, R. D. (2012) · BMC Bioinformatics

Advanced Proteomics Techniques and ApplicationsGene expression and cancer classification

Cited by 345

Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer

Petralia, F., Tignor, N., Reva, B., Koptyra, M., Chowdhury, S., Rykunov, D., Krek, A., Ma, W., Zhu, Y., Ji, J., et al. (2020) · Cell

Glioma Diagnosis and TreatmentCancer Genomics and Diagnostics

Cited by 317

Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics

Webb-Robertson, B.-J. M., Wiberg, H. K., Matzke, M. M., Brown, J. N., Wang, J., McDermott, J. E., Smith, R. D., Rodland, K. D., Metz, T. O., Pounds, J. G., et al. (2015) · Journal of Proteome Research

Advanced Proteomics Techniques and ApplicationsGene expression and cancer classification

Cited by 294

In silico method for modelling metabolism and gene product expression at genome scale

Lerman, J. A., Hyduke, D. R., Latif, H., Portnoy, V. A., Lewis, N. E., Orth, J. D., Schrimpe-Rutledge, A. C., Smith, R. D., Adkins, J. N., Zengler, K., et al. (2012) · Nature Communications

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 266

Pyroptosis by caspase11/4‐gasdermin‐D pathway in alcoholic hepatitis in mice and patients

Khanova, E., Wu, R., Wang, W., Yan, R., Chen, Y., French, S. W., Llorente, C., Pan, S. Q., Yang, Q., Li, Y., et al. (2018) · Hepatology

Inflammasome and immune disordersAlcohol Consumption and Health Effects

Cited by 228

Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data

Jaitly, N., Mayampurath, A., Littlefield, K., Adkins, J. N., Anderson, G. A., & Smith, R. D. (2009) · BMC Bioinformatics

Metabolomics and Mass Spectrometry StudiesAdvanced Proteomics Techniques and Applications

Cited by 217

Enhanced Detection of Low Abundance Human Plasma Proteins Using a Tandem IgY12-SuperMix Immunoaffinity Separation Strategy

Qian, W.-J., Kaleta, D. T., Petritis, B. O., Jiang, H., Liu, T., Zhang, X., Mottaz, H. M., Varnum, S. M., Camp, D. G., Huang, L., et al. (2008) · Molecular & Cellular Proteomics

Advanced Proteomics Techniques and ApplicationsAdvanced Biosensing Techniques and Applications

Cited by 208

A statistical framework for protein quantitation in bottom-up MS-based proteomics

Karpievitch, Y., Stanley, J., Taverner, T., Huang, J., Adkins, J. N., Ansong, C., Heffron, F., Metz, T. O., Qian, W.-J., Yoon, H., et al. (2009) · Bioinformatics

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 176

Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data

Ting, Y. S., Egertson, J. D., Payne, S. H., Kim, S., MacLean, B., Käll, L., Aebersold, R., Smith, R. D., Noble, W. S., & MacCoss, M. J. (2015) · Molecular & Cellular Proteomics

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 175

Free 25-Hydroxyvitamin D: Impact of Vitamin D Binding Protein Assays on Racial-Genotypic Associations

Nielson, C. M., Jones, K. S., Chun, R. F., Jacobs, J. M., Wang, Y., Hewison, M., Adams, J. S., Swanson, C. M., Lee, C. G., Vanderschueren, D., et al. (2016) · The Journal of Clinical Endocrinology & Metabolism

Vitamin D Research StudiesBone health and osteoporosis research

Cited by 163

Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions

Ansong, C., Wu, S., Meng, D., Liu, X., Brewer, H. M., Deatherage Kaiser, B. L., Nakayasu, E. S., Cort, J. R., Pevzner, P., Smith, R. D., et al. (2013) · Proceedings of the National Academy of Sciences

Advanced Proteomics Techniques and ApplicationsRedox biology and oxidative stress

Cited by 157

Protein Identification Using Top-Down Spectra

Liu, X., Sirotkin, Y., Shen, Y., Anderson, G., Tsai, Y. S., Ting, Y. S., Goodlett, D. R., Smith, R. D., Bafna, V., & Pevzner, P. A. (2012) · Molecular & Cellular Proteomics

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 153

Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets

Zhu, Y., Dou, M., Piehowski, P. D., Liang, Y., Wang, F., Chu, R. K., Chrisler, W. B., Smith, J. N., Schwarz, K. C., Shen, Y., et al. (2018) · Molecular & Cellular Proteomics

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 147