Jeanette E Eckel-Passow
Affiliation: Mayo Clinic
- ANKS1B is a smoking-related molecular alteration in clear cell renal cell carcinomaJeanette E Eckel-Passow
Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
BMC Urol 14:14. 2014..We used a multi-stage design to identify and validate genes that are associated with smoking-related ccRCC...
- Tissue microarrays: one size does not fit allJeanette E Eckel-Passow
Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
Diagn Pathol 5:48. 2010..Furthermore, TMA performance across multiple biomarkers has not been systematically explored...
- An insight into high-resolution mass-spectrometry dataJ E Eckel-Passow
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
Biostatistics 10:481-500. 2009..Areas in need of statistical research for proteomic data include alignment, experimental design, abundance normalization, and statistical analysis...
- Quality assessment metrics for whole genome gene expression profiling of paraffin embedded samplesDouglas W Mahoney
Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
BMC Res Notes 6:33. 2013....
- A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysisSarah E Reese
Department of Biostatistics, Biostatistics Shared Resource Core, VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23284, USA, Division of Biomedical Statistics and Informatics and Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
Bioinformatics 29:2877-83. 2013..However, PCA yields linear combinations of the variables that contribute maximum variance and thus will not necessarily detect batch effects if they are not the largest source of variability in the data...
- A method for automatically interpreting mass spectra of 18O-labeled isotopic clustersChristopher J Mason
Mayo Proteomics Research Center, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
Mol Cell Proteomics 6:305-18. 2007..We describe in detail the operation of the algorithm and demonstrate its use on datasets with known and unknown ratios...
- Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencingZhifu Sun
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
PLoS ONE 6:e17490. 2011..The role of gene amplification/deletion appears to more modest, although several potentially significant genes appear to be regulated by copy number aberrations...
- Incidence of Pseudomonas aeruginosa bacteremia: a population-based studyMajdi N Al-Hasan
Department of Medicine, Division of Infectious Diseases, College of Medicine, Mayo Clinic, Rochester, MN 55905, USA
Am J Med 121:702-8. 2008..The incidence of Pseudomonas aeruginosa bacteremia has not been defined in a population-based investigation...
- Regression analysis for comparing protein samples with 16O/18O stable-isotope labeled mass spectrometryJ E Eckel-Passow
Division of Biostatistics, Department of Health Sciences Research 200 First Street SW, Rochester, MN 55905, USA
Bioinformatics 22:2739-45. 2006..Although discussed in the context of (16)O/(18)O stable-isotope labeled data, the multivariable regression models are generalizable to other stable-isotope labeled technologies...
- An integrated model of the transcriptome of HER2-positive breast cancerKrishna R Kalari
Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States of America Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
PLoS ONE 8:e79298. 2013....
- Expression of endothelin 2 and localized clear cell renal cell carcinomaBrian M Bot
Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
Hum Pathol 43:843-9. 2012..If supportive mechanistic data can be produced, endothelin 2 could represent a potential target for chemopreventive or neoadjuvant therapeutics for clear cell renal cell carcinoma...
- Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platformJeanette E Eckel-Passow
Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
BMC Bioinformatics 12:220. 2011..0. We compared bias and variance in the locus-level copy number data, the concordance amongst regions of copy number gains/deletions and the false-positive rate amongst deleted segments...
- Identification of a novel percent mammographic density locus at 12q24Kristen N Stevens
Department of Health Sciences Research, Mayo Clinic, Charlton 6 239, 200 First St SW, Rochester, MN 55905, USA
Hum Mol Genet 21:3299-305. 2012..Understanding the mechanism underlying this association will provide insight into the genetics of breast tissue composition...
- Comparison of fluorescence in situ hybridization (FISH) and dual-ISH (DISH) in the determination of HER2 status in breast cancerAaron S Mansfield
Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
Am J Clin Pathol 139:144-50. 2013..Using a cohort of difficult specimens, we observed less than 95% concordance between FISH and DISH. DISH may underestimate the HER2/chromosome 17 ratio, or FISH may overestimate this ratio...
- A prospective longitudinal analysis of cytomegalovirus (CMV)-specific CD4+ and CD8+ T cells in kidney allograft recipients at risk of CMV infectionAlbert J Eid
Divisions of Infectious Diseases, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
Transpl Int 23:506-13. 2010..On the other hand, the clinical utility of CMV-specific T cell assays will need to be assessed in a larger cohort of CMV D+/R- kidney recipients who remain at high-risk of delayed-onset CMV disease...
- Statistical analysis of relative labeled mass spectrometry data from complex samples using ANOVAAnn L Oberg
Division of Biostatistics, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, USA
J Proteome Res 7:225-33. 2008..The modeling approach, implementation, and useful visualization tools are demonstrated via a case study of complex biological samples assessed using the iTRAQ relative labeling protocol...
- Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL® platformMonica M Reinholz
Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, Minnesota 55905, USA
BMC Med Genomics 3:60. 2010..5K) and 24,526-gene panel (24K) platforms at differentiating nine human epidermal growth factor receptor 2- positive (HER2+) and 11 HER2-negative (HER2-) paraffin-embedded breast tumors...
- Progressive but previously untreated CLL patients with greater array CGH complexity exhibit a less durable response to chemoimmunotherapyNeil E Kay
Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
Cancer Genet Cytogenet 203:161-8. 2010..1 deletion and in the more favorable genetic subtype characterized by the presence of 13q14.1 deletion. This aCGH study adds information on the association between poor trial response and increasing genetic complexity as CLL progresses...
- Experimental design and analysis of antibody microarrays: applying methods from cDNA arraysJeanette E Eckel-Passow
Department of Health Sciences Research, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
Cancer Res 65:2985-9. 2005..The objective of this article is to discuss statistical methods that have been developed for cDNA arrays and describe how the methods can be directly applied to antibody arrays...
- Kinetics of interferon-gamma producing cytomegalovirus (CMV)-specific CD4+ and CD8+ T lymphocytes and the risk of subsequent CMV viremia after allogeneic hematopoietic stem cell transplantationA J Eid
Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
Transpl Infect Dis 11:519-28. 2009..Deficiencies in cytomegalovirus (CMV)-specific T lymphocytes impair the immunologic response against CMV reactivation after allogeneic hematopoietic stem cell transplantation (HSCT)...