Research Publications
Researchers worldwide use JMP Genomics to explore all sorts of research questions and solve problems in a variety of life science disciplines.
Below is a partial listing of reviews, research articles, and thesis publications which cite JMP Genomics.
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- 2009
- 2008
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- 2006
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Research Highlights
New Variations in Genes That Could Affect Recurrent Miscarriages
What the research focused on
The association between genetic variation in placenta-expressed chorionic gonadotropin B-subunit genes (CGBs -- particularly CGB5 and CGB8) and the risk of recurrent miscarriages.
What researchers discovered
Different genetic variants in HCG genes are significantly associated with increased or decreased risk of recurrent miscarriage, especially those located within the CGB8 gene, which encodes a subunit suspected to be under strong functional constraint. Variation within these genes appears to be more important in explaining pregnancy traits than other traditionally tested pregnancy biomarkers, such as immunotolerance at the fetomaternal interface or alterations in fibrinolytic and coagulation pathways.
Why the research matters
Discovery of genetic variations associated with recurrent miscarriage sheds light on the underlying causes of this common pregnancy risk. This research underscores the influence of genetic contributions on pregnancy outcomes, and the future potential of developing relevant diagnostic tests. Understanding the cellular assemblies and pathways influenced by genetic variation may eventually assist in the development of early preventive treatments for recurrent miscarriages.
How JMP Genomics was used
To test the significance of associations between SNPs in the CGB5 and CGB8 genes and the occurrence of recurrent miscarriage using the Cochran-Armitage trend test.
Where to find this research
Kristiina Rull, Liina Nagirnaja, Veli-Matti Ulander, et al. Chorionic Gonadotropin B-Gene Variants Are Associated with Recurrent Miscarriage in Two European Populations, Journal of Clinical Endocrinology and Metabolism Vol. 93, No. 12 (2008):1101
Effect of Variants in FSH Levels on the Male Hormone System
What the research focused on
Genetic variation within the human FSHB gene, which encodes a glycoprotein hormone that regulates gonadal function in both sexes. While the functions of FSH in females have been well characterized, its role in males is less clear. This research sought to examine whether a SNP within the evolutionarily conserved region upstream of the human FSH gene contributed significantly to variation in male serum FSH levels.
What researchers discovered
The first polymorphism in the human FSHB gene to show a significant association with serum FSH hormone levels in human males.
Why the research matters
Findings should encourage future studies of the effects of reduced FSH levels on male health and fertility. Improved understanding of the influences of FSH on reproductive system development may eventually contribute to improving fertility in both sexes.
How JMP Genomics was used
Association tests between a putative regulatory SNP located upstream of FSHB and a variety of quantitative traits in a group of healthy young men.
Where to find this research
Marina Grigorova, Margus Punab, Kristo Ausmees, and Maris Laan. FSHB Promoter Polymorphism within Evolutionary Conserved Element is Associated with Serum FSH level in Men. Human Reproduction Vol. 23, No. 9 (2008):2160-2166.
Inflammatory Response Key to Severity of Ureaplasma-Induced UTI
What the research focused on
The impact of Ureaplasma pathogens on development of urogenital tract disease in a rat model of urinary tract infection (UTI). Specifically, this study examined whether the concentration of Ureaplamsa  inoculum impacted the development and severity of the disease.
What researchers discovered
Subjects inoculated with U. parvum were highly vulnerable to the development of a complicated UTI, and experimental inoculation contributed to the frequency of infections. However, the severity of the complication varied little between doses, suggesting that once infected, a subject’s inflammatory response is the key determinant of UTI severity.
Why the research matters
Findings further our understanding of Ureaplasma involvement in cases of UTI and provide clues about how  to diagnose and cure more severe variants of the disease.
How JMP Genomics was used
Cytokine pattern recognition analysis.
Where to find this research
Leticia Reyes, Mary Reinhard, and Mary B. Brown, Different inflammatory responses are associated with Ureaplasma parvum-induced UTI and urolith formation, BMC Genomics Vol. 9, iss. 1 (2009): 9.
Metallic Nanoparticles, Dangerous for Zebrafish?
What the research focused on
The biological effects of toxic nanoparticulates ( Ag/Cu ), soluble nanometals (Ag/Cu), and non-toxic nanoparticulates on female zebrafish. The main focus was on identifying and comparing particulate-specific expression changes within zebrafish gills .
What researchers discovered
Nanocopper, nanosilver, and nanotitania each evoke distinct transcriptional effects in the zebrafish gill after acute exposure. Also, the release of soluble metals into the water column is not the sole cause of the observed responses to nanocopper and nanosilver, suggesting that more research will be needed in the future to determine other relevant factors.
Why the research matters
Furthers knowledge about the potential dangers of unintended release of nanomaterials into the environment and the toxicity of these substances to aquatic life.
How JMP Genomics was used
Calculating missing values using the Missing Value Imputation function. Identification of differentially expressed genes from microarray data using ANOVA with the Benjamini and Hochberg FDR multiple testing correction.
Where to find this research
Robert J. Griffitt, Kelly Hyndman, Nancy D. Denslow, David S. Barber, Comparison of Molecular and Histological Changes in Zebrafish Gills Exposed to Metallic Nanoparticles, Toxicological Sciences Vol. 107 (2009):404-415
Effect of Oxygen in Zymomonas Mobilis Fermentation
What the research focused on
Effects of anaerobic versus aerobic fermentation conditions on production of alternative industrial fuels by Zymomonas Mobilis (ZM4).
What researchers discovered
High oxygen concentrations in ZM4 cultures during fermentation negatively influence the fermentation process. Anaerobically grown ZM4 cultures utilized glucose more rapidly, grew more quickly and produced more ethanol. Also, transcriptional profiles of aerobic and anaerobic cultures differed more greatly at 26 hours than at three hours.
Why the research matters
An improved understanding of the effects of oxygen on ethanol production by ZM4 could potentially aid future efforts to use this microbe for alternative fuel production.
How JMP Genomics was used
Statistical analysis of microarray data from quality assessment using distribution analysis and correlation and principal components analysis, normalization and various graphics to display significant genes.
Where to find this research
Shihui Yang, Timother J Tschaplinski, Nancy L. Engle, Sue L. Carroll, Staton L. Martin, Brian H. Davison, Anthony V. Palumbo, Miguel Rodriguez Jr., and Steven D. Brown, Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations, BMC Genomics, 2009; doi:10.1186/1471-2164-10-34.
Significance of Genetic Variants in Patients with Metabolic Disease at Risk for Myocardial Infarction
What the research focused on
Identifying genetic variants contributing to susceptibility to myocardial infarction (MI) in individuals diagnosed with metabolic syndrome (MetS).
What researchers discovered
A number of polymorphisms (UTS2, FABP2, ADIP0Q, EDNRA, and PDX1) were significantly associated with MI. Specific genotypes at these loci were associated with increased risk of MI in Japanese individuals with MetS.
Why the research matters
Accurate prediction of risk and interventions to alter disease course may help reduce future cardiovascular events. A better understanding of MetS and the relative contributions of genetic variants may help predict individuals who are at most risk for MI in the future.
How JMP Genomics was used
Forward step-wise regression to determine statistical significance of associations between specific genetic variants and MI.
Where to find this research
Tetsuro Yoshida, Kimihiko Kato, Tetsuo Fujimaki, Kiyoshi Yokoi, Mitsutoshi Oguri, Sachiro Watanabe, Norifumi Metoki, Hidemi Yoshida, Kei Satoh, Yukitoshi Aoyagi, Yutaka Nishigaki, Masashi Tanaka, Yoshinori Nozawa and Yoshiji Yamada, Association of a polymorphism of apolipoprotein E gene with chronic kidney disease in Japanese individuals with metabolic syndrome, Atheroschlerosis, 2009;doi:10.1016/j.atherosclerosis.2009.02.037.
Significance of Bone Marrow Gene Expression in SLE
What the research focused on
Gene expression patterns in bone marrow and peripheral blood mononuclear cells of patients diagnosed with systemic lupus erythematosus (SLE) as compared to healthy individuals and patients with osteoarthritis.
What researchers discovered
Expression differences from bone marrow could be used to differentiate active from inactive SLE, and suggested an important role for apoptosis and granulocytes in the pathogenesis of this disease. Of the 102 genes found to be differentially expressed between SLE patients and controls, 53 are known to be involved in major networks of cell death, differentiation, and growth.
Why the research matters
Results underscore the importance of bone marrow and neutrophils in SLE, and may suggest new treatment avenues for patients with SLE.
How JMP Genomics was used
JMP Genomics was used for analysis of the correlation between gene expression and SLE Disease Activity Index using linear models, and for hierarchical clustering.
Find this research
Magdalene Nakou, Nicholas Knowlton, Mark B. Frank, et al. Gene Expression in Systemic Lupus Erythematosus, Arthritis & Rheumatism Vol. 58, No. 11 (2008):3541-3549
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