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.
| 2010 |
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| Gil Atzmon, Miook Cho, Richard M. Cawthon, et al, Genetic Variation in human telomerase is associated with telomere length in Ashkenazi centenarians, PNAS, January 26, 2010 vol. 107 no. suppl 1 1710-1717; doi: 10.1073/pnas.0906191106. |
| Gerald J Wilmink, Caleb L Roth, Bennett L Ibey, et al, Indentification of microRNAs associated with hyperthermia-induced cellular stress response, Cell Stress and Chaperones, 2010; doi:10.1007/s12192-010-0189-7. |
| O.L. Solomon, D.K. Berger, A.A. Myburg, Diurnal and circadian patterns of gene expression in the developing xylem of Eucalyptus trees, South African Journal of Botany, 2010; doi: doi:10.1016/j.sajb.2010.02.087. |
| Tamar Krugman, Veronique Chague, Zvi Peleg, et al, Multilevel regulation and signaling processes associated with adaptation to terminal drought in wild emmer wheat, Functional & Integrative Genomics, 2010; doi: 10.1007/s10142-010-0166-3. |
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Christopher J. Martyniuk, April Feswick, Daniel J. Spade, et al, Effects of acute dieldrin exposure on neurotransmitters and global gene transcription in largemouth bass (Micropterus salmoides) hypothalamus, NeuroToxicology, 2010; doi:10.1016/j.neuro.2010.04.008. Larissa M Williams, Xin Ma, Adam R Boyko, et al, SNP identification, verification, and utility for population genetics in a non-model genus, BMC Genetics, 2010; doi:10.1186/1471-2156-11-32. |
| Nan Mei, James C. Fuscoe, Edward K. Lobenhofer, et al, Application of Microarray-Based Analysis of Gene Expression in the Field of Toxicogenomics, Methods in Molecular Biology, 2010; doi:10.1007/978-1-60327-389-3_16. |
| JinShui Fan, Karen Zeller, Yu-Chi Chen, et al, Time-Dependent c-Myc Transactomes Mapped by Array-Based Nuclear Run-On Reveal Transcriptional Modules in Human B Cells, PLoS ONE, 2010; doi:10.1371/journal.pone.0009691. |
| Teresa R. O’Meara, Diana Norton, Michael S. Price, et al, Interaction of Cryptococcus newoformans Rim101 and Protein Kinase A Regulates Capsule, PLoS Pathogens, 2010; doi:10.1371/journal.ppat.1000776. |
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Peng Xu, Lauren M. McIntyre, Julie Scardina, et al, Transcriptome Profiling of Embryonic Development Rate in Rainbow Trout Advanced Backcross Introgression Lines, Marine Biotechnology, 2010; doi:10.1007/s10126-010-9283-1. Claudia Klein, Kirsten E. Scoggin, Alan D. Ealy, et al, Transcriptional Profiling of Equine Endomentrium During the Time of Maternal Recognition of Pregnancy, Biology of Reproduction, 2010; doi: 10.1095/biolreprod.109.081612. |
| Thomas E Juenger, Saunak Sen, Elizabeth Bray, et al, Exploring genetic and expression differences between physiologically extreme ecotypes: comparative genomic hybridization and gene expression studies of Kas-1 and Tsu-1 accessions of Arabidopsis thaliana, Plant, Cell, & Environment, 2010; doi:10.1111/j.1365-3040.2010.02146. |
| Daniel R Ruzicka, Felipe H Barrios-Masias, Natasha T Hausmann, et al, Tomato root transcriptome response to a nitrogen-enriched soil patch, BMC Plant Biology, 2010; doi:10.1186/1471-2229-10-75. |
| G Benedek, T Paperna, N Avidan, et al, Opposing effects of HLA-DRB1*0301-DQB1*0201 haplotype on the risk for multiple sclerosis in diverse Arab populations in Israel, Genes and Immunity, 2010; doi:10.1038/gene.2010.20. |
| Gil Atzmon, Li Hao, Itsik Pe’er, et al, Abraham’s Children in the Genome Era: Major Jewish Diaspora Populations Comprise Distinct Genetic Clusters with Share Middle Eastern Ancestry, The American Journal of Human Genetics, 2010; doi:10.1016/j.ajhg.2010.04.015. |
| Shihui Yang, Miriam L. Land, Dawn M. Klingeman, et al, Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae, PNAS, 2010; doi:10.1073/pnas.0914506107. |
| Soonok Kim, Jinnan Hu, Yeonyee Oh, et al, Combining ChIP-chip and Expression Profiling to model MoCRZ1 Mediated Circuit for Ca2+/Calcineurin Signaling in the Rice Blast Fungus, PLoS Pathogens, 2010; doi:10.1371/journal.ppat.1000909. |
| Joseph P. McElroy, Bruce A. C. Cree, Stacy J. Caillier, et al, Refining the association of MHC with multiple sclerosis in African Americans, Human Molecular Genetics, 2010; doi:10.1093/hmg/ddq197. |
| Doug Hinchliffe, William Meredith, Kathleen Yeater, Near-isogenic cotton germplasm lines that differ in fiber-bundle strength have temporal differences in fiber gene expression patterns as revealed by comparative high-throughput profiling, Theoretical and Applied Genetics, 2010; doi:10.1007/s00122-010-1260-6. |
| Trakooljul N, Hicks JA, Liu HC, Identification of target genes and pathways associated with chicken microRNA miR-143, Animal Genetics, 2010; |
| James Todd Auman, Howard L. McLeod, Colorectal Cancer Cell Lines Lack the Molecular Heterogeneity of Clinical Colorectal Tumors, Clinical Colorectal Cancer, 2009; doi:10.3816/CCC.2010.n.005. |
| 2009 |
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Ashley A. McAnally, Lev Y. Yampolsky, Widespread Transcriptional Autosomal Dosage Compensation in Drosophila Correlates with Gene Expression Level, Genome Biology and Evolution, 2009; doi:10.1093/gbe/evp054. |
| B. Loureiro, L. Oliveira, P. J. Hansen, 244 Changes in the Transcriptome of the Bovine Pre-Implantation Embryo Induced by Colony-Stimulating Factor-2, Csiro Publishing, 2009; doi: 10.1071/RDv22n1Ab244. |
| Rungnapa Pankla, Surachat Buddhisa, Matthew Berry, et al, Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis, Genome Biology, 2009; doi:10.1186/gb-2009-10-11-r127. |
| Tetsuo Fujimaki, Kimihiko Kato, Kiyoshi Yokoi, et al, Association of genetic variants in SEMA3F, CLE16A, LAMA3, and PCSK2 with myocardial infarction in Japanese individuals, Atheroschlerosis, 2009; doi:10.1016/j.atherosclerosis.2009.11.050. |
| Tilahun Abebe, Roger P. Wise, Ronald W. Skadsen, Comparative Transcriptional Profiling Established the Awn as the Major Photosynthetic Organ of the Barley Spike While the Lemma and the Palea Primarily Protect the Seed, The Plant Genome, 2009; doi: 10.3835/plantgenome.2009.07.0019. |
| Tilahun Abebe, Kalpalatha Melmaiee, Virginia Berg, Drought Response in the spikes of barley: gene expression in the lemma, palea, awn, and seed, Functional & Integrative Genomics, 2009; doi: 10.1007/s10142-009-0149-4. |
| Caird E Rexroad, Roger L Vallejo, Estimates of linkage disequilibrium and effective population size in rainbow trout, BMC Genetics, 2009; doi: 10.1186/1471-2156-10-83. |
| J.E. de Oliveira, S. Druyan, Z. Uni, et al, Prehatch intestinal maturation of turkey embryos demonstrated through gene expression patterns, Poultry Science, 2009; doi: 10.3382/ps.2008-00548. |
| Elizabeth P. Briczinski, Joseph R. Loquasto, Rodolphe Barrangou, et al, Strain-specific genotyping of Bifidobacterium animalis subsp. Lactis using SNPs and INDELs, Applied Environmental Microbiology, 2009; doi: 10.1128/AEM.01430-09. |
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Steven Randall Gray, Functional genomics analysis of carbohydrate conversion to biohydrogen by pure and mixed cultures of hyperthermophilic Thermotoga species, Dissertation, 2009. |
| Wei Huang, Denong Wang, Masao Yamada, et al, Chemoenzymatic Synthesis and Lectin Array Characterization of a Class of N-Glycan Clusters, Journal of the American Chemical Society, 2009; doi: 10.1021/ja9078539. |
| James T. Auman, Howard L. McLeod, Colorectal Cancer Cell Lines Lack the Molecular Heterogeneity of Clinical Colorectal Tumors, Clinical Colorectal Cancer, 2010; doi: 10.3816/CCC.2010.n.005. |
| Manessha Chhikara, Shuibang Wang, Steven J. Kern, et al, Carbon Monoxide Blocks Lipopolysaccharide-Induced Gene Expression by Interfering with Proximal TLR4 to NF-kB Signal Transduction in Human Monocytes, PLoS ONE, 2009; doi: 10.1371/journal.pone.0008139. |
| Tilahun Abebe, Roger P. Wise, Ronal W. Skadsen, Comparative Transcriptional Profiling Established the Awn as the Major Photosynthetic Organ of the Barley Spike While the Lemma and the Palea Primarily Protect the Seed, The Plant Genome, 2009; doi: 10.3835/plantgenome.2009.07.0019. |
| Tamar Krugman, Zvi Peleg, Veronique Chague, Differential Gene Expression in Roots of Wild Emmer Wheat Genotypes Contrasting in Drought Resistance, 2009. |
| Dana Marie Stanley Sisk, Reproductive Gene Expression in Male Sus scrofa: An examination of the Differential Gene Expression of Divergent Testosterone selection and development of a Ribonucleic Acid extraction protocol from whole Porcine Spermatozoa, Master’s Thesis, 2009. |
| Youssef Idaghdour, Wendy Czika, Kevin V Shianna et al. Geographical genomics of human leukocyte gene expression variation in southern Morocco. Nature Genetics; Published online: 6 December 2009; doi:10.1038/ng.495. |
| Marc Libault, Andrew Farmer, Laurent Brechenmacher, et al, Complete transcriptome of the soybean root hair cell, a single cell model, and its alteration in response to Bradyrhizobium japonicum infection, Plant Physiology, 2009; doi: 10.1104/pp.109.148379. |
| Christopher J. Martyniuk, Brian C. Sanchez, Nancy J. Szabo, et al, Aquatic contaminants alter genes involved in neurotransmitter synthesis and gonadotropin release in largemouth bass, Aquatic Toxicology, 2009; doi:10.1016/j.aquatox.2009.06.009. |
| Joanna Trzcinska-Danielewicz, Anna Bilska, Jan Fronk, et al, Global analysis of gene expression in maize leaves treated with low temperature: I. Moderate chilling (14 °C), Plant Science, 2009; doi:10.1016/j.plantsci.2009.09.001. |
| Erin M. Kennerly, Youssef Idaghdour, Natasha J. Olby, et al, Pharmacogenetic association study of 30 genes with Phenobarbital drug response in epileptic dogs, Pharmacogenetics and Genomics, 2009; doi:10.1097/FPC.0b013e3283307cba. |
| Russell S. Thomas, Wenjun Bao, Tzu-Ming Chu, et al, Use of Short-term Transcriptional Profiles to Assess the Long-term Cancer-Related Safety of Environmental and Industrial Chemicals, Toxicological Sciences, 2009; doi: 10.1093/toxsci/kfp233. |
| Amy L. VanFossen, Marcel R. A. Verhaart, Serve M.W. Kengen, et al, Carbohydrate utilization patterns for the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus reveal broad growth substrate preferences, Applied Environmental Microbiology, 2009; doi: 10.1128/AEM.01959-09. |
| Cinda P. Scott, Dean A. Williams, Douglas L. Crawford, The effect of genetic and environmental variation on metabolic gene expression, Molecular Ecology, 2009; doi: 10.1111/j.1365-294X.2009.04235.x. |
| Amber K. Goetz, David J. Dix, Mode of Action for Reproductive and Hepatic Toxicity Inferred from a Genomic Study of Triazole Antifungals, Toxicological Sciences, 2009; doi: 10.1093/toxsci/kfp098. |
| Yoshiji Yamada, Noriyuki Fuku, Masashi Tanaka, et al, Identification of CELSR1 as a susceptibility gene for ischemic stroke in Japanese individuals by a genome-wide association study, Atheroschlerosis, 2009; doi:10.1016/j.atheroschlerosis.2009.03.038. |
| Hong Fang, Stephen C. Harris, Zhenjiang Su, et al, Protein Networks and Pathway Analysis, Humana Press, 2009; doi: 10.1007/978-1-60761-175-2. |
| Susan G. Dorsey, Carmen C. Leitch, Cynthia L. Renn, et al, Genome-Wide Screen Identifies Drug-Induced Regulation of Gene Giant Axonal Neuropathy (Gan) in a Mouse Model of Antiretroviral-Induced Painful Peripheral Neuropathy, Biological Research for Nursing, 2009; doi: 10.1177/1099800409332726. |
| Anthony T. Athippozhy, Liping Huang, Tianyong Zhao, et al, Utilizing a mixed model approach to compare to lactating rat transcriptome against age-matched control virgins, BMC Bioinformatics, 2009; doi: 10.1186/1471-2105-10-S7-A16. |
| Youssef Idaghdour, Genetic and Environmental Components of Human Leukocyte Gene Expression Variation in Morocco, Dissertation, 2009. |
| Charlotte R. Cooper, Amanda J. Daugherty, Sabrina Tachdjian, et al, Role of vapBC toxin-antitoxin loci in the thermal stress response of sulfolobus solfataricus, Molecular Biology of Archaea, 2009; doi: 10.1042/BST0370123. |
| Jong-II Kim, Young Seok Ju, Hansoo Park, et al, A highly annotated whole-genome sequence of a Korean individual, Nature, 2009; doi: 10.1038/nature08211. |
| Lisa M. Goering, Priscilla K. Hunt, Cassandra Heighington, et al, Association of orthodenticle with Natural Variation for Early Embryonic Patterning in Drosophila melanogaster, Journal of Experimental Zoology, 2009; doi: 10.1002/jez.b.21299. |
| G. Pakalapati, L. Li, N. Gretz, et al, Influence of red clover (Trifolium pretense) isoflavones on gene and protein expression profiles in liver of ovariectomized rats, Phytomedicine, 2009; |
| Jiang, L.C. Krous, N. Knowlton, et al, Ablation of Stat3 by siRNA Alters Gene Expression Profiles in JEG-3 Cells: A Systems Biology Approach, Placenta, 2009; doi: 10.1016/j.placenta.2009.06.006. |
| Robert A. Philibert, Alexandre Todorov, Allan Anderson, et al, Examination of the Nicotine Depedence (NICSNP) Consortium findings in the Iowa adoption studies population, Nicotine and Tobacco Research, 2009; doi: 10.1093/ntr/ntn034. |
| Steve R. Bischoff, Shengdar Tsai, Nicholas Hardison, et al, Characterization of Conserved and Nonconserved Imprinted Genes in Swine, Biology of Reproduction, 2009; doi: 10.1095/biolreprod.109.078139. |
| James N. Jarvis, Kaiyu Jiang, Mark Barton Frank, et al, Gene Expression Profiling in Neutrophils From Children With Polyarticular Juvenile Idiopathic Arthritis, Arthritis and Rheumatism, 2009; doi: 10.1002/art.24450; |
| Amber K. Goetz, David J. Dix,Toxicogenomic effects common to triazole antifungals and conserved between rats and humans, Toxicology and Applied Pharmacology, 2009; doi: 10.1016/j.taap.2009.04.016. |
| Yamada Y, et al. Identification of CELSR1 as a susceptibility gene for ischemic stroke in Japanese individuals by a genome-wide association study. Atherosclerosis (2009), doi:10.1016/j.atherosclerosis.2009.03.038 |
| Karl V. Voelkerding, Next-Generation Sequencing: From Basic Research to Diagnostics, Clinical Chemistry, 2009; doi:10.1373/clinchem.2008.112789 |
| Mitsutoshi Oguri, Kimihiko Kato, Kiyoshi Yokoi, Tatsuo Itoh, Tetsuro Yoshida, Sachiro Watanabe, Norifumi Metoki, Hidemi Yoshida, Kei Satoh, Yukitoshi Aoyagi, Yutaka Nishigaki, Masashi Tanaka, Yoshinori Nozawa and Yoshiji Yamada, Association of genetic variants with myocardial infarction in Japanese individuals with metabolic syndrome, Atherosclerosis, 2009; doi:10.1016/j.atherosclerosis.2009.02.037. |
| Leticia Reyes, Mary Reinhard, and Mary B. Brown, Different inflammatory responses are associated with Ureaplasma parvum-induced UTI and urolith formation, BMC Genomics, 2009; doi:10.1186/1471-2334-9-9. |
| Tetsuro Yoshidaa, Kimihiko Katob, Tetsuo Fujimakib, Kiyoshi Yokoib, Mitsutoshi Oguric, Sachiro Watanabed, Norifumi Metokie, Hidemi Yoshidaf, Kei Satohf, Yukitoshi Aoyagig, Yutaka Nishigakig, Masashi Tanakag, Yoshinori Nozawah and Yoshiji Yamada, Association of a polymorphism of apolipoprotein E gene with chronic kidney disease in Japanese individuals with metabolic syndrome, Genomics, 2009; doi:10.1016/j.ygeno.2008.11.001. |
| Robert J. Griffitt, Kelly Hyndman, Nancy D. Denslow and Davis S. Barber, Comparison of Molecular and Histological Changes in Zebrafish Gills Exposed to Metallic Nanoparticles, Toxicological Sciences, 2009; doi:10.1093/toxsci/kfn256. |
| 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. |
| Kelci Miclaus, Russ Wolfinger, and Wendy Czika, SNP selection and multidimensional scaling to quantify population structure, Genetic Epidemiology, 2009; doi:10.1002/gepi.20401. |
| Scott CP, VanWye J, McDonald MD, Crawford DL, Technical Analysis of cDNA Microarrays, PLoS ONE, 2009; doi:10.1371/journal.pone.0004486. |
| Erin Michelle Kennerly, Genomic Exploration of Infectious and Genetic Disease in Canids, Dissertation, 2009; |
| Deric R. Learman, Haakrho Yi, Steven D. Brown, Stanton L. Martin, Gill G. Geesey, Ann M. Stevens, and Michael F. Hochella Jr., Involvement of Shewanella Oneidensis MR-1 LuxS in Biofilm Development and Sulfur Metabolism, Applied and Environmental Microbiology, 2009; doi:10.1128/AEM.01393-08. |
| M. A. Azcarate-Peril, R. Tallon and T. R. Klaenhammer, Temporal Gene Expression and Probiotic Attributes of Lactobacillus Acidophilus During Growth in Milk, Journal of Dairy Science, 2009; doi:10.3168/jds.2008-1457. |
| 2008 |
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| Stephanie Hirner, Christian Krohne, Alexander Schuster, et al, MuRF1-dependant Regulation of Systemic Carbohydrate Metabolism as Revealed from Transgenic Mouse Studies, Journal of Molecular Biology, 2008; doi: 10.1016/j.jmb.2008.03.049. |
| Minjung Kwak, Jungnam Joo, and Gang Zheng, A Robust Test for Two-Stage Design in Genome-Wide Association Studies, Biometrics, 2008; doi: 10.1111/j.1541-0420.2008.01187.x. |
| C. Herskind, L. Li, F. Wenz, Differential Gene Expression and Phenotypic Changes in Human Fibroblasts after Irradiation In Vitro, International Journal of Radiation Oncology*Biology*Physics, 2008; doi:10.1016/j.ijrobp.2008.06.578 |
| Gustavo A. Ramírez-Carvajal, Alison M. Morse and John M. Davis, Transcript profiles of the cytokinin response regulator gene family in Populus imply diverse roles in plant development, New Phytologist, 2008; doi:10.1111/j.1469-8137.2007.02240.x. |
| Andrew D. B. Leakey, Fanxiu Xu, Kelly M. Gillespie, Justin M. McGrath, Elizabeth A. Ainsworth, and Donald R. Ort, Genomic basis for stimulated respiration by plants growing under elevated carbon dioxide, Plant Biology, 2008; doi: 10.1073/pnas.0810955106. |
| Marjorie F. Oleksiak, Changes in Gene Expression due to Chronic Exposure to Environmental Pollutants, Aquatic Toxicology, 2008; doi:10.1016/j.aquatox.2008.08.010. |
| Ozden, Ozkan, Expression of Claudin Tight Junction Proteins in Response to Varying Environmental and Physiological Conditions, Dissertation, 2008; |
| Deric Ronald Learman, Shewanella oneidensis MR-1 cell-to-cell signaling and its influences on biogeochemical processes, Master's Thesis, 2008; |
| Kathryne S. Auernik and Robert M. Kelly, Identification of Components of Electron Transport Chains in the Extremely Thermoacidophilic Crenarchaeon Metallosphaera sedula through Iron and Sulfur Compound Oxidation Transcriptomes, Applied and Environmental Microbiology, 2008; doi:10.1128/AEM.01545-08. |
| Kristiina Rull, Liina Nagirnaja, Veli-Matti Ulander, Piret Kelgo, Tõnu Margus, Milja Kaare, Kristiina Aittomäki and Maris Laan, Chorionic Gonadotropin ß-Gene Variants Are Associated with Recurrent Miscarriage in Two European Populations, Journal of Clinical Endocrinology & Metabolism, 2008; doi:10.1210/jc.2008-1101. |
| 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, 2008; doi:10.1093/humrep/den216. |
| Jason G. Powers, Tim L. Sit, Curtis Heinsohn, et al, The Red clover necrotic mosaic virus RNA-2 encoded movement protein is a second suppressor of RNA silencing, Virology, 2008; doi:10.1016/j.virol.2008.09.004. |
| Kathryne S. Auernik, Yukari Maezato, Paul H. Blum, and Robert M. Kelly, The Genome Sequence of the Metal-Mobilizing, Extremely Thermoacidophilic Archaeon Metallosphaera sedula Provides Insights into Bioleaching-Associated Metabolism, Applied and Environmental Microbiology, 2008; doi:10.1128/AEM.02019-07. |
| Carrie A. Smith, Dominique Robertson, Bethan Yates, et al, The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus Flavus, Current Genetics, 2008; doi:10.1007/s00294-008-0215-9. |
| Michael J. Boedigheimer, Russel D. Wolfinger, Michael B. Bass, et al, Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories, BMC Genomics, 2008; doi:10.1186/1471-2164-9-285. |
| Steven David Buckingham, Scientific software: seeing the SNPs between us, Nature Methods, 2008; doi: 10.1038/nmeth1008-903. |
| Kyriacos N. Felekkis, Panayiota Koupepidou, Evdokia Kastanos, et al, Mutant polycystin-2 induces proliferation in primary rat tubular epithelial cells in a STAT-1/p21-independent fashion accompanied instead by alterations in expression of p57KIP2 and Cdk2, BMC Nephrology, 2008; doi:10.1186/1471-2369-9-10. |
| Steve R. Bischoff, Shengdar Tsai, Nicholas E. Hardison, et al, Identification of SNPs and INDELS in swine transcribed sequences using short oligonucleotide microarrays, BMC Genomics, 2008; doi:10.1186/1471-2164-9-252. |
| Stephen F. Kingsmore, Neil Kennedy, Henry L. Halliday, et al, Identification of diagnostic biomarkers for infection in premature neonates, Molecular and Cellular Proteomics, 2008; Manuscript M800175-MCP200. |
| Harmen J. G. van de Werken, Marcel R. A. Verhaart, Amy L. VanFossen, et al, Hydrogenomics of the extremely thermophillic bacterium Caldicellulosiruptor saccharolyticus, AEM, 2008; doi:10.1128/AEM.00968-08. |
| Jose Trinidad Ascencio-Ibanex, Rosangela Sozzani, Tae-Jin Lee, et al, Global Analysis of Arabidopsis Gene Expression Uncovers a Complex Array of Changes Impacting Pathogen Response and Cell Cylce during Geminivirus Infection, Plant Physiology, 2008; doi:10.1104/pp.108.121038. |
| Joann Mudge, Neil A. Miller, Irina Khrebtukova, et al, Genomic Convergence Analysis of Schizophrenia: mRNA Sequencing Reveals Altered Synaptic Vesicular Transport in Post-Mortem Cerebellum, Plos One, 2008; doi:10.1371/journal.pone.0003625. |
| S. Druyan, J. E. deOliveira, and C. M. Ashwell, Focused Microarrays as a Method to Evaluate Subtle Changes in Gene Expression, Poultry Science, 2008; doi:10.3382/ps. 2007-00513. |
| N. Garcia-Reyero, R. J. Griffitt, L. Liu, K. J. Kroll, et al, Construction of a robust microarray from a non-model species largemouth bass, Micropterus salmoides, using pyrosequencing technology, Journal of Fish Biology, 2008; doi:10.1111/j.1095-8649.2008.01904. |
| Wang L, Zhang B, Wolfinger RD, Chen X, An Integrated Approach for the Analysis of Biological Pathways using Mixed Models, PLoS Genetics, 2008; doi:10.1371/journal.pgen.1000115. |
| Jean-Christophe Corvol, Daniel Pelletier, Roland G. Henry, et al, Abrogation of T cell quiescence characterizes patients at high risk for multiple sclerosis after the initial neurological event, PNAS, 2008; doi:10.1073/0805065105. |
| Youssef Idaghdour, John D. Storey, Sami J. Jadallah, Greg Gibson, A Genome-Wide Gene Expression Signature of Environmental Geography in Leukocytes of Moroccan Amazighs, PLoS Genetics, 2008; doi:10.1371/journal.pgen.1000052. |
| Erin Kennerly, Anne Ballman, Stanton Martin, et al, A gene expression signature of confinement in peripheral blood of red wolves (Canis rufus), Molecular Ecology, 2008; doi:10.1111/j.1365-294X.2008.03775.x. |
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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