Completed Research Projects

• Prospective study of the predictive power of mass spectrometric profiles of plasma proteins and peptides in detecting early stage breast cancer

• Contribution of ATM mutations to breast cancer susceptibility

• Thorstenson, Yvonne R et al. “Contributions of ATM mutations to familial breast and ovarian cancer.” Cancer research vol. 63,12 (2003): 3325-33. 

• Stanford Human OligoExome Resource

• Natsoulis, Georges et al. “A flexible approach for highly multiplexed candidate gene targeted resequencing.” PloS one vol. 6,6 (2011): e21088. doi:10.1371/journal.pone.0021088

• The Dynamics of the Vaginal Microbiome During Infertility Therapy with In Vitro Fertilization-Embryo Transfer 

• Hyman, Richard W et al. “The dynamics of the vaginal microbiome during infertility therapy with in vitro fertilization-embryo transfer.” Journal of assisted reproduction and genetics vol. 29,2 (2012): 105-15. doi:10.1007/s10815-011-9694-6 

• A New Human Transcriptome Array for Clinical Research

• W. Xu, J. Seok, M.N. Mindrinos, A.C. Schweitzer, H. Jiang, J. Wilhelmy, T.A. Clark, K. Kapur, Y. Xing, M. Faham, J.D. Storey, L.L. Moldawer, R.V. Maier, R.G. Tompkins, W.H. Wong, R.W. Davis, W. Xiao, & the Inflammation and Host Response to Injury Large-Scale Collaborative Research Program, Human transcriptome array for high-throughput clinical studies, Proc. Natl. Acad. Sci. U.S.A. 108.9 (2011): 3707-3712 https://doi.org/10.1073/pnas.1019753108  

• Use of Molecular Probes with Barcodes to Identify Microbes

• Hyman, Richard W et al. “Multiplex identification of microbes.” Applied and environmental microbiology vol. 76,12 (2010): 3904-10. doi:10.1128/AEM.02785-09

• A New Statistical Method for Time Course Microarray Experiments

• Storey, John D et al. “Significance analysis of time course microarray experiments.” Proceedings of the National Academy of Sciences of the United States of America vol. 102,36 (2005): 12837-42. doi:10.1073/pnas.0504609102 

• Viral Metagenomics Discovering New Viruses

• Wide Spectrum Viral And Target Gene Enrichment

• High-throughput Proteomics for Biomarker Discovery

• Network Knowledge Base Analysis of High-Throughput Genomic Data

• Proximity Ligation for Protein Analyses - Multiplexing protein detection on DNA microarrays

• Cell Specific Gene Expression Pattern in Severe Trauma

• K. Laudanski, C. Miller-Graziano, W. Xiao, M.N. Mindrinos, D.R. Richards, A. De, L.L. Moldawer, R.V. Maier, P. Bankey, H.V. Baker, B.H. Brownstein, J.P. Cobb, S.E. Calvano, R.W. Davis, & R.G. Tompkins, Cell-specific expression and pathway analyses reveal alterations in trauma-related human T cell and monocyte pathways, Proc. Natl. Acad. Sci. U.S.A. 103.42 (2006): 15564-15569, https://doi.org/10.1073/pnas.0607028103.

• Inflammation and the host response to injury (Glue Grant) 

• A New Statistical Method for Analyzing Time Course Multifactor Expression Data

• Computational Biology Group at SGTC and Data Interpretation Core of the Glue Grant

• MIPs in cancer

• A Knowledge-based Approach for Genome-wide Genotyping Analysis of Parkinson's Disease

• Biomarker Detection in Colorectal Cancer

• Extended Big Data Study

• Computation for Genome Technology & Medicine

• Computational Design of Oligonucleotide Bar Code Tag Sequences

• Novel Affymetrix GeneChip Arrays: Large-Scale Data Visualization and Analysis

• Functional Genomics of the Origin of Stem Cells

• Identifying and studying small molecules that inhibit meiotic development and fertility in eukaryotic organisms

• The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes

• Hillenmeyer, Maureen E et al. “The chemical genomic portrait of yeast: uncovering a phenotype for all genes.” Science (New York, N.Y.) vol. 320,5874 (2008): 362-5. doi:10.1126/science.1150021  

• Expression Profiling at the Microscale

• Wang, Q. T., Xiao, W., Mindrinos, M., & Davis, R. W. Yeast tRNA as Carrier in the Isolation of Microscale RNA for Global Amplification and Expression Profiling. BioTechniques, 33.4 (2002): 788–796. https://doi.org/10.2144/02334st02

• Complex Trait Analysis in Yeast

• Sinha, Himanshu et al. “Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast.” Genetics vol. 180,3 (2008): 1661-70. doi:10.1534/genetics.108.092932

• Mitochondria in genetics and disease: proteomics of yeast mitochondria

• Yeast Genome Deletion Project

• Haplotype and linkage block structure in human genome

• Building technology to monitor alternative splicing on a genomic scale

• Lin, Shengrong et al. “A molecular inversion probe assay for detecting alternative splicing.” BMC genomics 712.11 (2010) doi:10.1186/1471-2164-11-712

Yeast Chemical Genomics

•  

• Gardnerella vaginalis genome project

• Gardnerella vaginalis ATCC 14018 = JCM 11026 strain ATCC 14018, whole genome shotgun sequencing project

• Atopobium vaginae genome project

• Fannyhessea vaginae DSM 15829, whole genome shotgun sequencing project

• Biofuel yeast sequencing

• Babrzadeh, Farbod et al. “Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1.” Molecular genetics and genomics : MGG vol. 287.6 (2012): 485-94. doi:10.1007/s00438-012-0695-7

  Gene Expression Analysis of Human Endotoxin Response

• YJM789 genome sequence

• W. Wei, J.H. McCusker, R.W. Hyman, T. Jones, Y. Ning, Z. Cao, Z. Gu, D. Bruno, M. Miranda, M. Nguyen, J. Wilhelmy, C. Komp, R. Tamse, X. Wang, P. Jia, P. Luedi, P.J. Oefner, L. David, F.S. Dietrich, Y. Li, R.W. Davis, & L.M. Steinmetz, Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789, Proc. Natl. Acad. Sci. U.S.A. 104.31 (2007): 12825-12830. https://doi.org/10.1073/pnas.0701291104

• Comparative genetic history of Samaritan patri- and matrilineages based on Y-chromosome and mitochondrial DNA sequence variation

• Shen, Peidong et al. “Reconstruction of patrilineages and matrilineages of Samaritans and other Israeli populations from Y-chromosome and mitochondrial DNA sequence variation.” Human mutation vol. 24.3 (2004): 248-60. doi:10.1002/humu.20077

• Maize gene discovery project: RescueMu and EST sequencing

• Lunde, China F et al. “Progress in maize gene discovery: a project update.” Functional & integrative genomics vol. 3.1-2 (2003): 25-32. doi:10.1007/s10142-002-0078-y

• Human sequencing project

• Cryptococcus neoformans genome project

• Malaria genome project: plasmodium falciparum chromosome 12

• Gardner, M., Hall, N., Fung, E. et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419 (2002): 498–511. https://doi.org/10.1038/nature01097

• Candida albicans

• Arabidopsis sequencing

• The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408 (2000): 796–815. https://doi.org/10.1038/35048692

• Global expression studies of the Arabidopsis genome

• Chlamydia

• Kalman, Sue, et al. “Comparative Genomes of Chlamydia Pneumoniae and C. Trachomatis.” Nature Genetics, EBSCOhost, 21.4 (1999): 385. https://doi.org/10.1038/7716.

Saccharomyces

• Molecular Diagnostic Probes

• Analysis Tools for Clinical Genomics

• Rapid Detection of Text Snippets

• Integrated Knowledge Bases for Complex Biological Systems