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Overview

Omicsoft is the leading provider of Next Generation Sequencing, Cancer Genomics, Immunology, and Bioinformatics solutions for Next Generation Sequencing Data and Gene Expression Analysis.

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Publications Citing Omicsoft's Bioinformatics Software

Omicsoft regularly lists publications using our software and data services. This includes Array Studio, Oshell, FusionMap, OSA, ImmunoLand, and OncoLand (Cancer Genomics for TCGA analysis and more). 

 

OmicSoft products (software and land service) are widely used in the industry. They are cited in hundreds of publications worldwide.

Below is a partial list. To cite Omicsoft products in your study, please follow our citation instructions.


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Click to expand the publication list citing OmicSoft products in each year or category:

         [2016]

Goldsworthy, Michelle, et al. Haploinsufficiency of the insulin receptor in the presence of a splice-site mutation in Ppp2r2a results in a novel digenic mouse model of type 2 diabetes. Diabetes 65.5 (2016): 1434-1446.

Buschdorf, J. P., et al. Low birth weight associates with hippocampal gene expression. Neuroscience 318 (2016): 190-205.

Gassman, Natalie R., et al. Combined Effects of High-Dose Bisphenol A and Oxidizing Agent (KBrO3) on Cellular Microenvironment, Gene Expression, and Chromatin Structure of Ku70-deficient Mouse Embryonic Fibroblasts. Environmental health perspectives (2016).

Tron, Adriana E., et al. Next-generation sequencing identifies a novel ELAVL1–TYK2 fusion gene in MOLM-16, an AML cell line highly sensitive to the PIM kinase inhibitor AZD1208. Leukemia & lymphoma (2016): 1-3.

He, Bo, et al. Human Glucocorticoid Receptor ß Regulates Gluconeogenesis and Inflammation in Mouse Liver. Molecular and cellular biology 36.5 (2016): 714-730.

Bose, Bipasha, and Sudheer Shenoy. Pluripotent Conversion of Muscle Stem Cells Without Reprogramming Factors or Small Molecules. Stem Cell Reviews and Reports 12.1 (2016): 73-89.

Kang, Hong Soon, et al. Transcription Factor GLIS3: A New and Critical Regulator of Postnatal Stages of Mouse Spermatogenesis. STEM CELLS (2016).

Singh, Ajeet P., et al. Brg1 enables rapid growth of the early embryo by suppressing genes that regulate apoptosis and cell growth arrest. Molecular and cellular biology (2016): MCB-01101.

Koenig, Erik M., et al. The beagle dog MicroRNA tissue atlas: identifying translatable biomarkers of organ toxicity. BMC genomics 17.1 (2016): 649.

Eicher, John D., et al. Platelet-related variants identified by exomechip meta-analysis in 157,293 individuals. The American Journal of Human Genetics 99.1 (2016): 40-55.

Chami, Nathalie, et al. Exome genotyping identifies pleiotropic variants associated with red blood cell traits. The American Journal of Human Genetics 99.1 (2016): 8-21.

Hong, David, et al. Phase I Study of LY2606368, a Checkpoint Kinase 1 Inhibitor, in Patients With Advanced Cancer. Journal of Clinical Oncology 34.15 (2016): 1764-1771.

Zhou, Binbin, et al. Control of brown patch (Rhizoctonia solani) in tall fescue (Festuca arundinacea Schreb.) by host induced gene silencing. Plant cell reports 35.4 (2016): 791-802.

Tajuddin, Salman M., et al. Large-scale exome-wide association analysis identifies loci for white blood cell traits and pleiotropy with immune-mediated diseases. The American Journal of Human Genetics 99.1 (2016): 22-39.

Preidis, Geoffrey A., et al. Microbial-Derived Metabolites Reflect an Altered Intestinal Microbiota during Catch-Up Growth in Undernourished Neonatal Mice. The Journal of nutrition 146.5 (2016): 940-948.

Finalet Ferreiro, Julio, et al. EBV‐Positive and EBV‐Negative Posttransplant Diffuse Large B Cell Lymphomas Have Distinct Genomic and Transcriptomic Features. American Journal of Transplantation 16.2 (2016): 414-425.

Min, Jun S., et al. Systems Analysis of the Complement-Induced Priming Phase of Liver Regeneration. The Journal of Immunology 197.6 (2016): 2500-2508.

Wang, Jinghong, et al. GPR21 KO mice demonstrate no resistance to high fat diet induced obesity or improved glucose tolerance. F1000Research 5 (2016).

Zand, Behrouz, et al. Role of increased n-acetylaspartate levels in cancer. Journal of the National Cancer Institute 108.6 (2016): djv426.

Engels, Alexander C., et al. Pulmonary transcriptome analysis in the rabbit model of surgically-induced. hernia 205 (2016): 112-8.

Engels, Alexander C., et al. Pulmonary transcriptome analysis in the surgically induced rabbit model of diaphragmatic hernia treated with fetal tracheal occlusion. Disease Models and Mechanisms 9.2 (2016): 221-228.

Micci, Francesca, et al. Cytogenetic and Molecular Profile of Endometrial Stromal Sarcoma. Genes, Chromosomes and Cancer (2016).

Muise, Eric S., et al. Effects of Long‐Term Odanacatib Treatment on Bone Gene Expression in Ovariectomized Adult Rhesus Monkeys: Differentiation From Alendronate. Journal of Bone and Mineral Research (2016).

Westergren, Helena U., et al. Insulin resistance, endothelial function, angiogenic factors and clinical outcome in non-diabetic patients with chest pain without myocardial perfusion defects. Cardiovascular diabetology 15.1 (2016): 1.

Blok, J. L., et al. Ustekinumab in hidradenitis suppurativa: clinical results and a search for potential biomarkers in serum. British Journal of Dermatology (2016).

Saito, Kosuke, et al. Gender-and Age-Associated Differences in Serum Metabolite Profiles among Japanese Populations. Biological and Pharmaceutical Bulletin 39.7 (2016): 1179-1186.

Song, Jiao, et al. Polypharmacology of Small-Molecule Modulators of the 5-Lipoxygenase Activating Protein (FLAP) Observed via a High-throughput Lipidomics Platform. Journal of biomolecular screening 21.2 (2016): 127-135.

Hughes, Paul E., et al. In Vitro and In Vivo Activity of AMG 337, a Potent and Selective MET Kinase Inhibitor, in MET-Dependent Cancer Models. Molecular cancer therapeutics (2016): molcanther-0871.

Abeysekara, Nilwala S., et al. The plant immunity inducer pipecolic acid accumulates in the xylem sap and leaves of soybean seedlings following Fusarium virguliforme infection. Plant Science 243 (2016): 105-114.

Van Roosbroeck, Katrien, et al. Genomic alterations of the JAK2 and PDL loci occur in a broad spectrum of lymphoid malignancies. Genes, Chromosomes and Cancer (2016).

Luo, Ting, et al. Consumption of Walnuts in Combination with Other Whole Foods Produces Physiologic, Metabolic, and Gene Expression Changes in Obese C57BL/6J High-Fat–Fed Male Mice. The Journal of Nutrition 146.9 (2016): 1641-1650.

De Ron, P., et al. Correlating behaviour and gene expression endpoints in the dopaminergic system after modafinil administration in mouse. European Neuropsychopharmacology 26.4 (2016): 729-740.

Brown, Dustin G., et al. Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer & metabolism 4.1 (2016): 1.

Itsko, Mark, and Roel M. Schaaper. Transcriptome analysis of Escherichia coli during dGTP Starvation. Journal of bacteriology 198.11 (2016): 1631-1644.

Kovach, Melissa A., et al. IL-36γ is secreted in microparticles and exosomes by lung macrophages in response to bacteria and bacterial components. Journal of leukocyte biology (2016): jlb-4A0315.

Terpolilli, Jason J., et al. Lipogenesis and redox balance in nitrogen-fixing pea bacteroids. Journal of Bacteriology (2016): JB-00451.

Binder, April K., et al. Expression of Human NSAID Activated Gene 1 in Mice Leads to Altered Mammary Gland Differentiation and Impaired Lactation. PloS one 11.1 (2016): e0146518.

Wolenski, Francis S., et al. Identification of microRNA biomarker candidates in urine and plasma from rats with kidney or liver damage. Journal of Applied Toxicology (2016).

Rulifson, Ingrid C., et al. Identification of Human Islet Amyloid Polypeptide as a BACE2 Substrate. PloS one 11.2 (2016): e0147254.

Dhanik, Ankur, et al. In-silico discovery of cancer-specific peptide-HLA complexes for targeted therapy. BMC bioinformatics 17.1 (2016): 286.

Domingos, Sara, et al. Molecular candidates for early-stage flower-to-fruit transition in stenospermocarpic table grape (Vitis vinifera L.) inflorescences ascribed by differential transcriptome and metabolome profiles. Plant Science 244 (2016): 40-56.

Shirai, Makoto, et al. Decreased hepatic phosphorylated p38 mitogen-activated protein kinase contributes to attenuation of thioacetamide-induced hepatic necrosis in diet-induced obese mice. The Journal of toxicological sciences 41.2 (2016): 245-253.

Shaked, Abraham, et al. An ectopically expressed serum miRNA signature is prognostic, diagnostic, and biologically related to liver allograft rejection. Hepatology (2016).

Rafikova, Olga, et al. Metabolic Changes Precede the Development of Pulmonary Hypertension in the Monocrotaline Exposed Rat Lung. PloS one 11.3 (2016): e0150480.

Domingos, Sara, et al. Shared and divergent pathways for flower abscission are triggered by gibberellic acid and carbon starvation in seedless Vitis vinifera L. BMC plant biology 16.1 (2016): 1.

Colletti, Nicholas J. TLR3 Signaling in Human BDCA-3 Dendritic Cells Results in the Formation of Several ILT3 and ILT4 Populations. (2016).

Richter, Jute, et al. Proton-pump inhibitor omeprazole attenuates hyperoxia induced lung injury. Journal of Translational Medicine 14.1 (2016): 247.

Colletti, Nicholas J., et al. Tlr3 signaling Promotes the induction of Unique human BDca-3 Dendritic cell Populations. Frontiers in immunology 7 (2016).

Jiang, Liyan, et al. Genomic Landscape Survey Identifies SRSF1 as a Key Oncodriver in Small Cell Lung Cancer. PLoS Genet 12.4 (2016): e1005895.

Loiodice, Simon, et al. Pramipexole induced place preference after L-dopa therapy and nigral dopaminergic loss: linking behavior to transcriptional modifications. Psychopharmacology (2016): 1-13.

Fursov, Natalie, et al. Monoclonal antibodies targeting ST2L Domain 1 or Domain 3 differentially modulate IL-33-induced cytokine release by human mast cell and basophilic cell lines. Molecular immunology 75 (2016): 178-187.

Nelson, Matthew R., et al. The genetics of drug efficacy: opportunities and challenges. Nature Reviews Genetics 17.4 (2016): 197-206.

Johnson, Amy R., et al. Metabolic reprogramming through fatty acid transport protein 1 (FATP1) regulates macrophage inflammatory potential and adipose inflammation. Molecular Metabolism (2016).

Nagaraja, Archana S., et al. Sustained adrenergic signaling leads to increased metastasis in ovarian cancer via increased PGE2 synthesis. Oncogene 35.18 (2016): 2390-2397.

Olivry, Thierry, et al. Early Activation of Th2/Th22 Inflammatory and Pruritogenic Pathways in Acute Canine Atopic Dermatitis Skin Lesions. Journal of Investigative Dermatology (2016).

Georgiadis, Panagiotis, et al. Omics for prediction of environmental health effects: Blood leukocyte-based cross-omic profiling reliably predicts diseases associated with tobacco smoking. Scientific reports 6 (2016).

Foy, Jean-Philippe, et al. The dynamics of gene expression changes in a mouse model of oral tumorigenesis may help refine prevention and treatment strategies in patients with oral cancer. Oncotarget (2016).

Forloni, Matteo, et al. Oncogenic EGFR Represses the TET1 DNA Demethylase to Induce Silencing of Tumor Suppressors in Cancer Cells. Cell reports 16.2 (2016): 457-471.

Leow, Shi Chi, et al. The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis. Development 143.6 (2016): 950-961.

Broom, Ashley J., et al. Effects of mid-respiratory chain inhibition on mitochondrial function in vitro and in vivo. Toxicology Research 5.1 (2016): 136-150.

Walsh, Alice M., et al. Integrative genomic deconvolution of rheumatoid arthritis GWAS loci into gene and cell type associations. Genome biology 17.1 (2016): 1.

Tripathi, Rashmi, et al. Next-generation sequencing revolution through big data analytics. Frontiers in Life Science (2016): 1-31.

Westergren Utkovic, Helena. Insulin resistance and cardiovascular function-Observational, translational and interventional studies. (2016).


         [2015]

Cheung, Leo WK, et al. Mutation Impact of Targeted Genes in Diffuse Large B-Cell Lymphoma Patients Treated with Ibrutinib. Blood 126.23 (2015): 2642-2642.

Mesa, Ruben A., et al. Effects of ruxolitinib treatment on metabolic and nutritional parameters in patients with myelofibrosis from COMFORT-I. Clinical Lymphoma Myeloma and Leukemia 15.4 (2015): 214-221.

Ilie, Marius, et al. Setting up a wide panel of patient‐derived tumor xenografts of non–small cell lung cancer by improving the preanalytical steps. Cancer medicine 4.2 (2015): 201-211.

Lieblein-Boff, Jacqueline C., et al. Exploratory metabolomic analyses reveal compounds correlated with lutein concentration in frontal cortex, hippocampus, and occipital cortex of human infant brain. PloS one 10.8 (2015): e0136904.

Le, Huong, Chun Chen, and Chetan T. Goudar. An evaluation of public genomic references for mapping RNA‐Seq data from Chinese hamster ovary cells. Biotechnology and bioengineering 112.11 (2015): 2412-2416.

Silkoff, P. E., et al. Asthma characteristics and biomarkers from the Airways Disease Endotyping for Personalized Therapeutics (ADEPT) longitudinal profiling study. Respiratory research 16.1 (2015): 1.

Mandelbaum, Jonathan, et al. Identification of a lung cancer cell line deficient in atg7-dependent autophagy. Autophagy just-accepted (2015): 00-00.

Dong, Hua, et al. Genomic and transcriptome profiling identified both human and HBV genetic variations and their interactions in Chinese hepatocellular carcinoma. Genomics data 6 (2015): 1-3.

Jaeger, Savina, et al. Evaluation of PD-L1 mRNA and protein expression in non-small cell lung and hepatocellular carcinoma. Cancer Research 75.15 Supplement (2015): 1314-1314.

Blok, J. L., et al. Gene expression profiling of skin and blood in hidradenitis suppurativa. British Journal of Dermatology (2015).

Gómez-Úriz, Ana M., et al. Obesity and ischemic stroke modulate the methylation levels of KCNQ1 in white blood cells. Human molecular genetics 24.5 (2015): 1432-1440.

Song, Jiao, et al. Phenotyping drug polypharmacology via eicosanoid profiling of blood. Journal of lipid research 56.8 (2015): 1492-1500.

Wagenaar, Timothy R., et al. Anti–miR-21 Suppresses Hepatocellular Carcinoma Growth via Broad Transcriptional Network Deregulation. Molecular Cancer Research 13.6 (2015): 1009-1021.

Zhao, Shanrong, and Baohong Zhang. Impact of Gene Annotation on RNA-seq Data Analysis. (2015).

Panagopoulos, Ioannis, et al. Novel TNS3-MAP3K3 and ZFPM2-ELF5 fusion genes identified by RNA sequencing in multicystic mesothelioma with t (7; 17)(p12; q23) and t (8; 11)(q23; p13). Cancer letters 357.2 (2015): 502-509.

Kouidhi, Magali, et al. Characterization of Human Knee and Chin Adipose-Derived Stromal Cells. Stem cells international 2015 (2015).

Yu, De-Hua, et al. Oncogenic HER2 fusions in gastric cancer. Journal of translational medicine 13.1 (2015): 1.

Dong, Hua, et al. Identification of HBV-MLL4 integration and its molecular basis in Chinese hepatocellular carcinoma. PloS one 10.4 (2015): e0123175.

Panagopoulos, Ioannis, et al. Novel KAT6B-KANSL1 fusion gene identified by RNA sequencing in retroperitoneal leiomyoma with t (10; 17)(q22; q21). PloS one 10.1 (2015): e0117010.

Schlessinger, Karni, et al. Gene expression in WAT from healthy humans and monkeys correlates with FGF21‐induced browning of WAT in mice. Obesity 23.9 (2015): 1818-1829.

Lu, Lei, et al. Transcriptional modulation of intestinal innate defense/inflammation genes by preterm infant microbiota in a humanized gnotobiotic mouse model. PloS one 10.4 (2015): e0124504.

Le, Huong, Matthew Jerums, and Chetan T. Goudar. Characterization of intrinsic variability in time‐series metabolomic data of cultured mammalian cells. Biotechnology and bioengineering 112.11 (2015): 2276-2283.

Kovach, Melissa A., et al. Microarray analysis identifies IL-1 receptor type 2 as a novel candidate biomarker in patients with acute respiratory distress syndrome. Respiratory research 16.1 (2015): 1.

Betts, Joanna C., et al. Gene expression changes caused by the p38 MAPK inhibitor dilmapimod in COPD patients: analysis of blood and sputum samples from a randomized, placebo‐controlled clinical trial. Pharmacology research & perspectives 3.1 (2015).

Chen, Chun, Huong Le, and Chetan T. Goudar. An automated RNA‐Seq analysis pipeline to identify and visualize differentially expressed genes and pathways in CHO cells. Biotechnology progress 31.5 (2015): 1150-1162.

Fomina-Yadlin, Dina, et al. Transcriptome analysis of a CHO cell line expressing a recombinant therapeutic protein treated with inducers of protein expression. Journal of biotechnology 212 (2015): 106-115.

Zhao, Shanrong, and Baohong Zhang. A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification. BMC genomics 16.1 (2015): 1.

Joseph, Roy, et al. ACSL1 is associated with fetal programming of insulin sensitivity and cellular lipid content. Molecular Endocrinology 29.6 (2015): 909-920.

Kang, Sohye, et al. Metabolic markers associated with high mannose glycan levels of therapeutic recombinant monoclonal antibodies.B> Journal of biotechnology 203 (2015): 22-31.

Winkel, Angelika F., et al. Characterization of RA839, a noncovalent small molecule binder to Keap1 and selective activator of Nrf2 signaling. Journal of Biological Chemistry 290.47 (2015): 28446-28455.

Domingos, Sara, et al. Flower abscission in Vitis vinifera L. triggered by gibberellic acid and shade discloses differences in the underlying metabolic pathways. Frontiers in plant science 6 (2015).

Bossen, Claudia, et al. The chromatin remodeler Brg1 activates enhancer repertoires to establish B cell identity and modulate cell growth. Nature immunology 16.7 (2015): 775-784.

Shirai, Makoto, et al. Hepatic glutathione contributes to attenuation of thioacetamide-induced hepatic necrosis due to suppression of oxidative stress in diet-induced obese mice. The Journal of toxicological sciences 40.4 (2015): 509-521.

Gorden, D. Lee, et al. Biomarkers of NAFLD progression: a lipidomics approach to an epidemic. Journal of lipid research 56.3 (2015): 722-736.

Goyal, Ravi, and Lawrence D. Longo. Metabolic Profiles in Ovine Carotid Arteries with Developmental Maturation and Long-Term Hypoxia. PloS one 10.6 (2015): e0130739.

Richardson, Jason, et al. Metabolomics analysis of soy hydrolysates for the identification of productivity markers of mammalian cells for manufacturing therapeutic proteins. Biotechnology progress 31.2 (2015): 522-531.

Tuna, Musaffe. Next‐Generation Sequencing in Cancer: Tools for Fusion Gene Detection. eLS (2015).

Zhao, Xiaobei, et al. Combined targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) using UNCseq and NGScopy, and RNA sequencing using UNCqeR for the detection of genetic aberrations in NSCLC. PloS one 10.6 (2015): e0129280.

Liu, Changlu, et al. GPR139, an orphan receptor highly enriched in the habenula and septum, is activated by the essential amino acids L-tryptophan and L-phenylalanine. Molecular pharmacology 88.5 (2015): 911-925.

Regazzetti, Claire, et al. Transcriptional analysis of vitiligo skin reveals the alteration of WNT pathway: a promising target for repigmenting vitiligo patients. Journal of Investigative Dermatology 135.12 (2015): 3105-3114.

Veeranagouda, Yaligara, et al. Identification of microRNAs in Macaca fascicularis (Cynomolgus Monkey) by Homology Search and Experimental Validation by Small RNA-Seq and RT-qPCR Using Kidney Cortex Tissues. PloS one 10.11 (2015): e0142708.

Clements, Meghan, et al. Differential Ly6C expression after renal ischemia-reperfusion identifies unique macrophage populations. Journal of the American Society of Nephrology (2015): ASN-2014111138.

Li, Fang, et al. FGFR-mediated reactivation of MAPK signaling attenuates antitumor effects of imatinib in gastrointestinal stromal tumors. Cancer discovery 5.4 (2015): 438-451.

Maxwell, Joseph R., et al. Differential roles for interleukin-23 and interleukin-17 in intestinal immunoregulation. Immunity 43.4 (2015): 739-750.

Joardar, Archi, et al. PPAR gamma activation is neuroprotective in a Drosophila model of ALS based on TDP-43. Human molecular genetics 24.6 (2015): 1741-1754.

Haw, T. J., et al. A pathogenic role for tumor necrosis factor-related apoptosis-inducing ligand in chronic obstructive pulmonary disease. Mucosal immunology (2015).

Broadbent, Kate M., et al. Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA. BMC genomics 16.1 (2015): 1.


         [2014]

Chang, K., Zhao, Y., Kang, J., Pant, S., Qiu, P. and others, Validation of Next Generation Sequencing Cancer Panels for Clinical Somatic Mutation Profiling-Identification of Source of Variations and Artifacts using FFPE Tissues, Next Generat Sequenc and Applic (2014)

Cheng, J., Yang, L., Kumar, V. and Agarwal, P., Systematic evaluation of connectivity map for disease indications, Genome medicine (2014)

Chow, J., Panasevich, M.R., Alexander, D., Vester Boler, B.M., Rossoni Serao, M.C., Faber, T.A., Bauer, L.L. and Fahey, G.C., Fecal metabolomics of healthy breast-fed versus formula-fed infants before and during in vitro batch culture fermentation, Journal of proteome research (2014)

Erve, T.J., Wagner, B.A., Martin, S.M., Knudson, C.M., Blendowski, R., Keaton, M., Holt, T., Hess, J.R., Buettner, G.R., Ryckman, K.K. and others, The heritability of metabolite concentrations in stored human red blood cells, Transfusion (2014)

Ferreiro, J.F., Rouhigharabaei, L., Urbankova, H., van der Krogt, J.-A., Michaux, L., Shetty, S., Krenacs, L., Tousseyn, T., De Paepe, P., Uyttebroeck, A. and others, Integrative genomic and transcriptomic analysis identified candidate genes implicated in the pathogenesis of hepatosplenic T-cell lymphoma, PloS one (2014)

Fomina-Yadlin, D., Du, Z. and McGrew, J.T., Gene expression measurements normalized to cell number reveal large scale differences due to cell size changes, transcriptional amplification and transcriptional repression in CHO cells, Journal of biotechnology (2014)

Gomez-Uriz, A.M., Milagro, F.I., Mansego, M.L., Cordero, P., Abete, I., De Arce, A., Goyenechea, E., Blazquez, V., Martinez-Zabaleta, M., Martinez, J.A. and others, Obesity and ischemic stroke modulate the methylation levels of KCNQ1 in white blood cells, Human molecular genetics (2014)

Guo, Y., Zhao, S., Bjoring, M. and Han, L., Advanced Datamining Using RNAseq Data, Big Data Analytics in Bioinformatics and Healthcare (2014)

Hu, J. and Tzeng, J.-Y., Integrative gene set analysis of multi-platform data with sample heterogeneity, Bioinformatics (2014)

Ilie, M., Nunes, M., Blot, L., Hofman, V., Long-Mira, E., Butori, C., Selva, E., Merino-Trigo, A., Venissac, N., Mouroux, J. and others, Setting up a wide panel of patient-derived tumor xenografts of non--small cell lung cancer by improving the preanalytical steps, Cancer medicine (2014)

Ippolito, D.L., Lewis, J.A., Yu, C., Leon, L.R. and Stallings, J.D., Alteration in circulating metabolites during and after heat stress in the conscious rat: potential biomarkers of exposure and organ-specific injury., BMC physiology (2014)

Joardar, A., Menzl, J., Podolsky, T.C., Manzo, E., Estes, P.S., Ashford, S. and Zarnescu, D.C., PPAR gamma activation is neuroprotective in a Drosophila model of ALS based on TDP-43, Human molecular genetics (2014)

Kang, S., Ren, D., Xiao, G., Daris, K., Buck, L., Enyenihi, A.A., Zubarev, R., Bondarenko, P.V. and Deshpande, R., Cell line profiling to improve monoclonal antibody production, Biotechnology and bioengineering (2014)

Kang, S., Xiao, G., Ren, D., Zhang, Z., Le, N., Trentalange, M., Gupta, S., Lin, H. and Bondarenko, P.V., Proteomics analysis of altered cellular metabolism induced by insufficient copper level, Journal of biotechnology (2014)

Kelhala, H.-L., Palatsi, R., Fyhrquist, N., Lehtimaki, S., Vayrynen, J.P., Kallioinen, M., Kubin, M.E., Greco, D., Tasanen, K., Alenius, H. and others, IL-17/Th17 Pathway Is Activated in Acne Lesions, PloS one (2014)

Kerr, K.M., Wehmeyer, K.R., Wang, F., Fieno, A.M. and Mills, K.J., Noninvasive method for measuring metabolites for skin health, US Patent (2014)

Kuzaj, P., Kuhn, J., Michalek, R.D., Karoly, E.D., Faust, I., Dabisch-Ruthe, M., Knabbe, C. and Hendig, D., Large-Scaled Metabolic Profiling of Human Dermal Fibroblasts Derived from Pseudoxanthoma Elasticum Patients and Healthy Controls, PloS one (2014)

Lee, Y.K., Alexander, D., Wulff, J. and Olsen, J.E., Changes in metabolite profiles in Norway spruce shoot tips during short-day induced winter bud development and long-day induced bud flush, Metabolomics (2014)

Li, J., Hu, J., Newman, M., Liu, K. and Ge, H., RNA-Seq Analysis Pipeline Based on Oshell Environment, IEEE/ACM Transactions on Computational Biology and Bioinformatics (2014)

Lim, L., Balakrishnan, A., Huskey, N., Jones, K.D., Jodari, M., Ng, R., Song, G., Riordan, J., Anderton, B., Cheung, S.-T. and others, MicroRNA-494 within an oncogenic microRNA megacluster regulates G1/S transition in liver tumorigenesis through suppression of mutated in colorectal cancer, Hepatology (2014)

Liu, H., Park, J., Manning, C., Goehlmann, H.W. and Marshall, D.J., Metastatic signature in lung cancer is associated with sensitivity to anti-integrin alphaV monoclonal antibody intetumumab, Genes, Chromosomes and Cancer (2014)

Liu, S., Song, W., Boulanger, J.H., Tang, W., Sabbagh, Y., Kelley, B., Gotschall, R., Ryan, S., Phillips, L., Malley, K. and others, Role of TGF-beta in a Mouse Model of High Turnover Renal Osteodystrophy, Journal of Bone and Mineral Research (2014)

Mesa, R.A., Verstovsek, S., Gupta, V., Mascarenhas, J., Atallah, E., Burn, T., Sun, W., Sandor, V. and Gotlib, J., Effects of Ruxolitinib Treatment on Metabolic and Nutritional Parameters in Patients With Myelofibrosis From COMFORT-I, Clinical Lymphoma Myeloma and Leukemia (2014)

Micci, F., Gorunova, L., Gatius, S., Matias-Guiu, X., Davidson, B., Heim, S. and Panagopoulos, I., MEAF6/PHF1 is a recurrent gene fusion in endometrial stromal sarcoma, Cancer letters (2014)

Mielcarek, M., Inuabasi, L., Bondulich, M.K., Muller, T., Osborne, G.F., Franklin, S.A., Smith, D.L., Neueder, A., Rosinski, J., Rattray, I. and others, Dysfunction of the CNS-heart axis in mouse models of Huntington's disease, PLoS genetics (2014)

Morscio, J., Dierickx, D., Nijs, J., Verhoef, G., Bittoun, E., Vanoeteren, X., Wlodarska, I., Sagaert, X. and Tousseyn, T., Clinicopathologic comparison of plasmablastic lymphoma in HIV-positive, immunocompetent, and posttransplant patients: single-center series of 25 cases and meta-analysis of 277 reported cases, The American journal of surgical pathology (2014)

Panagopoulos, I., Torkildsen, S., Gorunova, L., Tierens, A., Tjonnfjord, G.E. and Heim, S., Comparison between Karyotyping-FISH-Reverse Transcription PCR and RNA-Sequencing-Fusion Gene Identification Programs in the Detection of KAT6A-CREBBP in Acute Myeloid Leukemia, PloS one (2014)

Panagopoulos, I., Gorunova, L., Bjerkehagen, B. and Heim, S., The “Grep� Command But Not FusionMap, FusionFinder or ChimeraScan Captures the CIC-DUX4 Fusion Gene from Whole Transcriptome Sequencing Data on a Small Round Cell Tumor with t (4; 19)(q35; q13), PloS one (2014)

Panagopoulos, I., Brandal, P., Gorunova, L., Bjerkehagen, B. and Heim, S., Novel CSF1-S100A10 fusion gene and CSF1 transcript identified by RNA sequencing in tenosynovial giant cell tumors, International journal of oncology (2014)

Panagopoulos, I., Bjerkehagen, B., Gorunova, L., Berner, J.-M., Boye, K. and Heim, S., Several fusion genes identified by whole transcriptome sequencing in a spindle cell sarcoma with rearrangements of chromosome arm 12q and MDM2 amplification, International journal of oncology (2014)

Petrini, I., Meltzer, P.S., Kim, I.-K., Lucchi, M., Park, K.-S., Fontanini, G., Gao, J., Zucali, P.A., Calabrese, F., Favaretto, A. and others, A specific missense mutation in GTF2I occurs at high frequency in thymic epithelial tumors, Nature genetics (2014)

Plotkin, J.L., Day, M., Peterson, J.D., Xie, Z., Kress, G.J., Rafalovich, I., Kondapalli, J., Gertler, T.S., Flajolet, M., Greengard, P. and others, Impaired TrkB Receptor Signaling Underlies Corticostriatal Dysfunction in Huntington’s Disease, Neuron (2014)

Preidis, G.A., Keaton, M.A., Campeau, P.M., Bessard, B.C., Conner, M.E. and Hotez, P.J., The undernourished neonatal mouse metabolome reveals evidence of liver and biliary dysfunction, inflammation, and oxidative stress, The Journal of nutrition (2014)

Rosenberg, A., Fan, H., Chiu, Y.G., Bolce, R., Tabechian, D., Barrett, R., Moorehead, S., Baribaud, F., Liu, H., Peffer, N. and others, Divergent Gene Activation in Peripheral Blood and Tissues of Patients with Rheumatoid Arthritis, Psoriatic Arthritis and Psoriasis following Infliximab Therapy, PloS one (2014)

Saiki, A.Y., Caenepeel, S., Yu, D., Lofgren, J.A., Osgood, T., Robertson, R., Canon, J., Su, C., Jones, A., Zhao, X. and others, MDM2 antagonists synergize broadly and robustly with compounds targeting fundamental oncogenic signaling pathways, Oncotarget (2014)

Salphati, L., Chu, X., Chen, L., Prasad, B., Dallas, S., Evers, R., Mamaril-Fishman, D., Geier, E.G., Kehler, J., Kunta, J. and others, Evaluation of Organic Anion Transporting Polypeptide 1B1 and 1B3 Humanized Mice as a Translational Model to Study the Pharmacokinetics of Statins, Drug Metabolism and Disposition (2014)

Scharfmann, R., Pechberty, S., Hazhouz, Y., von Bulow, M., Bricout-Neveu, E., Grenier-Godard, M., Guez, F., Rachdi, L., Lohmann, M., Czernichow, P. and others, Development of a conditionally immortalized human pancreatic beta cell line, The Journal of clinical investigation (2014)

Stone, V.M., Dhayal, S., Brocklehurst, K.J., Lenaghan, C., Winzell, M.S., Hammar, M., Xu, X., Smith, D.M. and Morgan, N.G., GPR120 (FFAR4) is preferentially expressed in pancreatic delta cells and regulates somatostatin secretion from murine islets of Langerhans, Diabetologia (2014)

Sukarieh, R., Joseph, R., Leow, S.C., Li, Y., Loffler, M., Aris, I.M., Tan, J.H., Teh, A.L., Chen, L., Holbrook, J.D. and others, Molecular pathways reflecting poor intrauterine growth are found in Wharton's jelly-derived mesenchymal stem cells, Human Reproduction (2014)

Wittmann, B.M., Stirdivant, S.M., Mitchell, M.W., Wulff, J.E., McDunn, J.E., Li, Z., Dennis-Barrie, A., Neri, B.P., Milburn, M.V., Lotan, Y. and others, Bladder Cancer Biomarker Discovery Using Global Metabolomic Profiling of Urine, PloS one (2014)

Xu, H., Sobue, T., Thompson, A., Xie, Z., Poon, K., Ricker, A., Cervantes, J., Diaz, P. and Dongari-Bagtzoglou, A., Streptococcal co-infection augments Candida pathogenicity by amplifying the mucosal inflammatory response, Cellular microbiology (2014)

Yu, D., Zhang, X., Wang, H., Zhang, L., Chen, H., Hu, M., Dong, Z., Zhu, G., Qian, Z., Fan, J. and others, The essential role of TNIK gene amplification in gastric cancer growth, Oncogenesis (2014)

Zhao, S., Assessment of the impact of using a reference transcriptome in mapping short RNA-Seq reads, PloS one (2014)

Zhao, S., Fung-Leung, W.-P., Bittner, A., Ngo, K. and Liu, X., Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells, PLoS One (2014)


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Assaf, C.A., Lierman, E., Devos, T., Graux, C., Billiet, J. and Vandenberghe, P., JAK2 V617F-Negative and MPL W515K/L-Negative Essential Thrombocythemia: A High Resolution SNP Array Study, Blood (2013)

Barlow, J.L., Peel, S., Fox, J., Panova, V., Hardman, C.S., Camelo, A., Bucks, C., Wu, X., Kane, C.M., Neill, D.R. and others, IL-33 is more potent than IL-25 in provoking IL-13--producing nuocytes (type 2 innate lymphoid cells) and airway contraction, Journal of Allergy and Clinical Immunology (2013)

Brown, M.V., Compton, S.A., Milburn, M.V., Lawton, K.A. and Cheatham, B., Metabolomic signatures in lipid-loaded HepaRGs reveal pathways involved in steatotic progression, Obesity (2013)

Carrara, M., Beccuti, M., Cavallo, F., Donatelli, S., Lazzarato, F., Cordero, F. and Calogero, R.A., State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues?, BMC bioinformatics (2013)

Chen, Y. and Wei, J., Single Nucleotide Variant Calling Tools for RNA-Seq, Journal of Medical and Bioengineering Vol (2013)

Cheng, J. and Yang, L., Comparing gene expression similarity metrics for connectivity map, IEEE International Conference on Bioinformatics and Biomedicine 2013 (2013)

Cheng, J., Xie, Q., Kumar, V., Hurle, M., Freudenberg, J.M., Yang, L. and Agarwal, P., Evaluation of analytical methods for connectivity map data, Pacific Symposium on Biocomputing (2013)

Cheng, J. and Yang, L., Quantitative Sciences, GlaxoSmithKline R&D, Collegeville, PA 19426, USA, Bioinformatics and Biomedicine (BIBM), 2013 IEEE International Conference (2013)

Cordero, P., Campion, J., Milagro, F.I. and Martinez, J.A., Transcriptomic and epigenetic changes in early liver steatosis associated to obesity: effect of dietary methyl donor supplementation, Molecular genetics and metabolism (2013)

Dorai, H., Liu, S., Yao, X., Wang, Y., Tekindemir, U., Lewis, M.J., Wu, S.-L. and Hancock, W., Proteomic analysis of bioreactor cultures of an antibody expressing CHO-GS cell line that promotes high productivity, J Proteomics Bioinform (2013)

Feng, H., Qin, Z. and Zhang, X., Opportunities and methods for studying alternative splicing in cancer with RNA-Seq, Cancer letters (2013)

Ji, Y., Qian, Z. and Wei, J., Evaluation of RNA-Seq software in gene expression quantification, Scientific Research Publishing (2013)

Jorgensen, S.B., O’Neill, H.M., Sylow, L., Honeyman, J., Hewitt, K.A., Palanivel, R., Fullerton, M.D., Oberg, L., Balendran, A., Galic, S. and others, Deletion of skeletal muscle SOCS3 prevents insulin resistance in obesity, Diabetes (2013)

Keaton, M.A., Rosato, R.R., Plata, K.B., Singh, C.R. and Rosato, A.E., Exposure of Clinical MRSA Heterogeneous Strains to beta-Lactams Redirects Metabolism to Optimize Energy Production through the TCA Cycle, PloS one (2013)

Lee, D.P., Alexander, D. and Jonnalgadda, S.S., Diversity of Nutrient Content in Grains-A Pilot Metabolomics Analysis, J Nutr Food Sci (2013)

Lu, J. and Bushel, P.R., Dynamic expression of 3 prime UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: implications in gene expression profiling, Gene (2013)

Massarelli, E., CXCR2 EXPRESSION IN TUMOR CELLS IS A POOR PROGNOSTIC FACTOR AND PROMOTES INVASION AND METASTASIS IN LUNG ADENOCARCINOMA, Thesis, The Texas Medical Center (2013)

McDunn, J.E., Li, Z., Adam, K.-P., Neri, B.P., Wolfert, R.L., Milburn, M.V., Lotan, Y. and Wheeler, T.M., Metabolomic signatures of aggressive prostate cancer, The Prostate (2013)

Mehta, N.N., Li, K., Szapary, P., Krueger, J. and Brodmerkel, C., Modulation of cardiometabolic pathways in skin and serum from patients with psoriasis, J Transl Med (2013)

Micci, F., Thorsen, J., Panagopoulos, I., Nyquist, K., Zeller, B., Tierens, A. and Heim, S., High-throughput sequencing identifies an NFIA/CBFA2T3 fusion gene in acute erythroid leukemia with t (1; 16)(p31; q24), Leukemia (2013)

Moleres, A., Campion, J., Milagro, F.I., Marcos, A., Campoy, C., Garagorri, J.M., Gomez-Martinez, S., Martinez, J.A., Azcona-Sanjulian, M.C. and Marti, A., Differential DNA methylation patterns between high and low responders to a weight loss intervention in overweight or obese adolescents: the EVASYON study, The FASEB Journal (2013)

Morscio, J., Dierickx, D., Ferreiro, J., Herreman, A., Van Loo, P., Bittoun, E., Verhoef, G., Matthys, P., Cools, J., Wlodarska, I. and others, Gene Expression Profiling Reveals Clear Differences Between EBV-Positive and EBV-Negative Posttransplant Lymphoproliferative Disorders, American Journal of Transplantation (2013)

Muller, G.A., Tarasov, K.V., Gundry, R.L. and Boheler, K.R., Human ESC/iPSC-based ‘omics’ and bioinformatics for translational research, Drug Discovery Today: Disease Models (2013)

Nyquist, K.B., Gene-level consequences of new cancer-specific chromosomal rearrangements, PhD Thesis, University of Oslo (2013)

Panagopoulos, I., Thorsen, J., Gorunova, L., Haugom, L., Bjerkehagen, B., Davidson, B., Heim, S. and Micci, F., Fusion of the ZC3H7B and BCOR genes in endometrial stromal sarcomas carrying an X; 22-translocation, Genes, Chromosomes and Cancer (2013)

Panagopoulos, I., Gorunova, L., Zeller, B., Tierens, A. and Heim, S., Cryptic FUS-ERG fusion identified by RNA-sequencing in childhood acute myeloid leukemia, Oncology reports (2013)

Panagopoulos, I., Micci, F., Thorsen, J., Haugom, L., Buechner, J., Kerndrup, G., Tierens, A., Zeller, B. and Heim, S., Fusion of ZMYND8 and RELA genes in acute erythroid leukemia, PloS one (2013)

Panagopoulos, I., Thorsen, J., Gorunova, L., Micci, F., Haugom, L., Davidson, B. and Heim, S., RNA sequencing identifies fusion of the EWSR1 and YY1 genes in mesothelioma with t (14; 22)(q32; q12), Genes, Chromosomes and Cancer (2013)

Rouhigharabaei, L., Ferreiro, J.F., Put, N., Michaux, L., Tousseyn, T., Lefebvre, C., Gardiner, A., Kelver, W., Demuynck, H., Verschuere, J. and others, BMI1, The polycomb-group gene, is recurrently targeted by genomic rearrangements in progressive B-cell leukemia/lymphoma, Genes, Chromosomes and Cancer (2013)

Saintigny, P., Massarelli, E., Lin, S., Ahn, Y.-H., Chen, Y., Goswami, S., Erez, B., O'Reilly, M.S., Liu, D., Lee, J.J. and others, CXCR2 expression in tumor cells is a poor prognostic factor and promotes invasion and metastasis in lung adenocarcinoma, Cancer research (2013)

Smith, S.B., Magid-Slav, M. and Brown, J.R., Host Response to Respiratory Bacterial Pathogens as Identified by Integrated Analysis of Human Gene Expression Data, PloS one (2013)

Song, J., Liu, X., Wu, J., Meehan, M.J., Blevitt, J.M., Dorrestein, P.C. and Milla, M.E., A highly efficient, high-throughput lipidomics platform for the quantitative detection of eicosanoids in human whole blood, Analytical biochemistry (2013)

Tandle, A., Shankavaram, U., Brown, M., Ho, J., Graves, C. and others, Urinary metabolomic profiling of patients with glioblastoma multiforme, J Proteomics Bioinform S (2013)

Veerappa, A.M., Saldanha, M., Padakannaya, P. and Ramachandra, N.B., Family-based genome-wide copy number scan identifies five new genes of dyslexia involved in dendritic spinal plasticity, Journal of human genetics (2013)

Veerappa, A.M., Saldanha, M., Padakannaya, P. and Ramachandra, N.B., Genome-wide copy number scan identifies disruption of PCDH11X in developmental dyslexia, American Journal of Medical Genetics Part B: Neuropsychiatric Genetics (2013)

Vignier, N., Amor, F., Fogel, P., Duvallet, A., Poupiot, J., Charrier, S., Arock, M., Montus, M., Nelson, I., Richard, I. and others, Distinctive serum miRNA profile in mouse models of striated muscular pathologies, PLoS One (2013)

Webb, D., Leahy, M.M., Milner, J.A., Allison, D.B., Dodd, K.W., Gaine, P.C., Matthews, R.A., Schneeman, B.O., Tucker, K.L. and Young, S.S., Strategies to optimize the impact of nutritional surveys and epidemiological studies, Advances in Nutrition: An International Review Journal (2013)

Wohlfart, P., Linz, W., Hubschle, T., Linz, D., Huber, J., Hess, S., Crowther, D., Werner, U. and Ruetten, H., Cardioprotective effects of lixisenatide in rat myocardial ischemia-reperfusion injury studies, J Transl Med (2013)

Wu, P.-Y., Phan, J.H. and Wang, M.D., Assessing the impact of human genome annotation choice on RNA-seq expression estimates, BMC bioinformatics (2013)

Zhao, S., Prenger, K. and Smith, L., Stormbow: a cloud-based tool for reads mapping and expression quantification in large-scale RNA-Seq studies, International Scholarly Research Notices (2013)


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Andrulis, M., Penzel, R., Weichert, W., von Deimling, A. and Capper, D., Application of a BRAF V600E Mutation-specific Antibody for the Diagnosis of Hairy Cell Leukemia, American Journal of Surgical Pathology (2012)

Chau, B.N., Xin, C., Hartner, J., Ren, S., Castano, A.P., Linn, G., Li, J., Tran, P.T., Kaimal, V., Huang, X. and others, MicroRNA-21 promotes fibrosis of the kidney by silencing metabolic pathways, Science translational medicine (2012)

Costell, M.H., Ancellin, N., Bernard, R.E., Zhao, S., Upson, J.J., Morgan, L.A., Maniscalco, K., Olzinski, A.R., Ballard, V.L., Herry, K. and others, Comparison of soluble guanylate cyclase stimulators and activators in models of cardiovascular disease associated with oxidative stress, Frontiers in pharmacology (2012)

Grimley, R., Polyakova, O., Vamathevan, J., McKenary, J., Hayes, B., Patel, C., Smith, J., Bridges, A., Fosberry, A., Bhardwaja, A. and others, Over expression of wild type or a catalytically dead mutant of Sirtuin 6 does not influence NFkappaB responses, PloS one (2012)

Gunst, P.R., Brown, M.V., McDunn, J.E., Smith, E.M., Milburn, M.V., Troyer, D.A. and Lawton, K.A., Cancer detection and biopsy classification using concurrent histopathological and metabolomic analysis of core biopsies, Genome Medicine (2012)

Hu, J., Ge, H., Newman, M. and Liu, K., OSA: a fast and accurate alignment tool for RNA-Seq, Bioinformatics (2012)

Lawton, K.A., Cudkowicz, M.E., Brown, M.V., Alexander, D., Caffrey, R., Wulff, J.E., Bowser, R., Lawson, R., Jaffa, M., Milburn, M.V. and others, Biochemical alterations associated with ALS, Amyotrophic Lateral Sclerosis (2012)

Li, Y., Venkatiahgari, J., Jin, L., Cheng, D.T. and Cai, J., In Silico Target Portal: An integrated Oncology target discovery web portal, Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference on (2012)

Loebel, A.D. and Silva, R.M., Treatment and management of cns disorders, US Patent (2012)

Loza, M.J., Watt, R., Baribaud, F., Barnathan, E.S. and Rennard, S.I., Systemic inflammatory profile and response to anti-tumor necrosis factor therapy in chronic obstructive pulmonary disease, Respir Res (2012)

McDunn, J., Perichon, R., Goodison, S. and Rosser, C.J., Abstract LB-86: Metabolic presentation of bladder cancer in urine, Cancer Research (2012)

Monsivais, D., Bray, J.D., Su, E., Pavone, M.E., Dyson, M.T., Navarro, A., Kakinuma, T. and Bulun, S.E., Activated glucocorticoid and eicosanoid pathways in endometriosis, Fertility and sterility (2012)

Pichichero, M. and Liu, K., Composition and methods related to s100 a2, US Patent (2012)

Pluess-Li, Y., Bongiovanni, S., Oakeley, E.J., Johnson, K.J. and Staedtler, F., The virtuous technology cycle concept and its application in next-generation sequencing, Drug discovery today (2012)

Qie, S., Liang, D., Yin, C., Gu, W., Meng, M., Wang, C. and Sang, N., Glutamine depletion and glucose depletion trigger growth inhibition via distinctive gene expression reprogramming, Cell Cycle (2012)

Quijano, C., Cao, L., Fergusson, M.M., Romero, H., Liu, J., Gutkind, S., Rovira, I.I., Mohney, R.P., Karoly, E.D. and Finkel, T., Oncogene-induced senescence results in marked metabolic and bioenergetic alterations, Cell Cycle (2012)

Rathore, K. and Wang, H.-C.R., Green tea catechin extract in intervention of chronic breast cell carcinogenesis induced by environmental carcinogens, Molecular carcinogenesis (2012)

Sainger, R., Grau, J.B., Branchetti, E., Poggio, P., Seefried, W.F., Field, B.C., Acker, M.A., Gorman, R.C., Gorman, J.H., Hargrove, C.W. and others, Human myxomatous mitral valve prolapse: role of bone morphogenetic protein 4 in valvular interstitial cell activation, Journal of cellular physiology (2012)

Smith, S.B., Dampier, W., Tozeren, A., Brown, J.R. and Magid-Slav, M., Identification of common biological pathways and drug targets across multiple respiratory viruses based on human host gene expression analysis, PloS one (2012)

Spitale, R.C., Cheng, M.Y., Chun, K.A., Gorell, E.S., Munoz, C.A., Kern, D.G., Wood, S.M., Knaggs, H.E., Wulff, J., Beebe, K.D. and others, Differential effects of dietary supplements on metabolomic profile of smokers versus non-smokers, Genome Med (2012)

Stunkel, W., Pan, H., Chew, S.B., Tng, E., Tan, J.H., Chen, L., Joseph, R., Cheong, C.Y., Ong, M.-L., Lee, Y.S. and others, Transcriptome changes affecting Hedgehog and cytokine signalling in the umbilical cord: implications for disease risk, PloS one (2012)

Toedter, G., Li, K., Sague, S., Ma, K., Marano, C., Macoritto, M., Park, J., Deehan, R., Matthews, A., Wu, G.D. and others, Genes associated with intestinal permeability in ulcerative colitis: changes in expression following infliximab therapy, Inflammatory bowel diseases (2012)

Tran, H.T., Liu, Y., Zurita, A.J., Lin, Y., Baker-Neblett, K.L., Martin, A.-M., Figlin, R.A., Hutson, T.E., Sternberg, C.N., Amado, R.G. and others, Prognostic or predictive plasma cytokines and angiogenic factors for patients treated with pazopanib for metastatic renal-cell cancer: a retrospective analysis of phase 2 and phase 3 trials, The lancet oncology (2012)

Urbankova, H., Baens, M., Michaux, L., Tousseyn, T., Rack, K., Katrincsakova, B., Ferreiro, J.F., Van Loo, P., De Kelver, W., Dierickx, D. and others, Recurrent breakpoints in 14q32. 13/TCL1A region in mature B-cell neoplasms with villous lymphocytes, Leukemia & lymphoma (2012)

Wu, P.-Y., Phan, J.H. and Wang, M.D., The effect of human genome annotation complexity on RNA-Seq gene expression quantification, Bioinformatics and Biomedicine Workshops (BIBMW), 2012 IEEE International Conference (2012)

Wu, Y., McDade, T.W., Kuzawa, C.W., Borja, J., Li, Y., Adair, L.S., Mohlke, K.L. and Lange, L.A., Genome-wide association with C-reactive protein levels in CLHNS: evidence for the CRP and HNF1A loci and their interaction with exposure to a pathogenic environment, Inflammation (2012)

Wu, T., Xie, C., Han, J., Ye, Y., Weiel, J., Li, Q., Blanco, I., Ahn, C., Olsen, N., Putterman, C. and others, Metabolic disturbances associated with systemic lupus erythematosus, PLoS One (2012)

Zhao, H., Deneau, J., Che, G.O., Li, S., Vagnini, F., Azadi, P., Sonon, R., Ramjit, R., Lee, S.M. and Bojanowski, K., Angelica sinensis isolate SBD. 4: composition, gene expression profiling, mechanism of action and effect on wounds, in rats and humans, European Journal of Dermatology (2012)

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Bleam, M., Gilmer, T.M., Greger, J.G., Laquerre, S.G. and Liu, L., Method of treatment with braf inhibitor, US Patent (2011)

Croteau-Chonka, D.C., Marvelle, A.F., Lange, E.M., Lee, N.R., Adair, L.S., Lange, L.A. and Mohlke, K.L., Genome-Wide Association Study of Anthropometric Traits and Evidence of Interactions With Age and Study Year in Filipino Women, Obesity (2011)

Deneau, J., Ahmed, T., Blotsky, R. and Bojanowski, K., Anti-Diabetic Activity of a Mineraloid Isolate, in vitro and in Genetically Diabetic Mice, International Journal for Vitamin and Nutrition Research (2011)

Dias, C.V., Mendes, J.S., dos Santos, A.C., Pirovani, C.P., da Silva Gesteira, A., Micheli, F., Gramacho, K.P., Hammerstone, J., Mazzafera, P. and de Mattos Cascardo, J.C., Hydrogen peroxide formation in cacao tissues infected by the hemibiotrophic fungus Moniliophthora perniciosa, Plant physiology and biochemistry (2011)

Ge, H., Liu, K., Juan, T., Fang, F., Newman, M. and Hoeck, W., FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution, Bioinformatics (2011)

Holbrook, J.D., Parker, J.S., Gallagher, K.T., Halsey, W.S., Hughes, A.M., Weigman, V.J., Lebowitz, P.F. and Kumar, R., Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine, J Transl Med (2011)

Johnson, K.J., McDowell, E.N., Viereck, M.P. and Xia, J.Q., Species-specific dibutyl phthalate fetal testis endocrine disruption correlates with inhibition of SREBP2-dependent gene expression pathways, Toxicological Sciences (2011)

Karkera, J., Steiner, H., Li, W., Skradski, V., Moser, P.L., Riethdorf, S., Reddy, M., Puchalski, T., Safer, K., Prabhakar, U. and others, The anti-interleukin-6 antibody siltuximab down-regulates genes implicated in tumorigenesis in prostate cancer patients from a phase I study, The Prostate (2011)

Klein, M., Small Molecule Directed Differentiation of Pluripotent Stem Cells and the Outcome on Cardiogenesis., PhD Thesis, Drexel University (2011)

Leir, S.-H. and Harris, A., MUC6 mucin expression inhibits tumor cell invasion, Experimental cell research (2011)

Morgillo, F., Cascone, T., D'aiuto, E., Martinelli, E., Troiani, T., Saintigny, P., De Palma, R., Heymach, J., Berrino, L., Tuccillo, C. and others, Antitumour efficacy of MEK inhibitors in human lung cancer cells and their derivatives with acquired resistance to different tyrosine kinase inhibitors, British journal of cancer (2011)

Park, C., Yan, W., Ward, S.M., Hwang, S.J., Wu, Q., Hatton, W.J., Park, J.K., Sanders, K.M. and Ro, S., MicroRNAs dynamically remodel gastrointestinal smooth muscle cells, PLoS One (2011)

Rathore, K., Suppression of Chronically Induced Breast Carcinogenesis and Role of Mesenchymal Stem-like Cells, PhD Thesis, University of Tennessee (2011)

Toedter, G., Li, K., Marano, C., Ma, K., Sague, S., Huang, C.C., Song, X.-Y., Rutgeerts, P. and Baribaud, F., Gene expression profiling and response signatures associated with differential responses to infliximab treatment in ulcerative colitis, The American journal of gastroenterology (2011)

Blackham, S., Baillie, A., Al-Hababi, F., Remlinger, K., You, S., Hamatake, R. and McGarvey, M.J., Gene expression profiling indicates the roles of host oxidative stress, apoptosis, lipid metabolism, and intracellular transport genes in the replication of hepatitis C virus, Journal of virology (2010)

Blaveri, E., Kelly, F., Mallei, A., Harris, K., Taylor, A., Reid, J., Razzoli, M., Carboni, L., Piubelli, C., Musazzi, L. and others, Expression profiling of a genetic animal model of depression reveals novel molecular pathways underlying depressive-like behaviours, PloS one (2010)

Cullen, J.M., Falls, J.G., Brown, H.R., Yoon, L.W., Cariello, N.F., Faiola, B., Kimbrough, C.L., Jordan, H.L. and Miller, R.T., Time course gene expression using laser capture microscopy-extracted bile ducts, but not hepatic parenchyma, reveals acute alpha-naphthylisothiocyanate toxicity, Toxicologic pathology (2010)

Dangaria, S.J., Ito, Y., Luan, X. and Diekwisch, T.G., Differentiation of neural-crest-derived intermediate pluripotent progenitors into committed periodontal populations involves unique molecular signature changes, cohort shifts, and epigenetic modifications, Stem cells and development (2010)

Forer, L., Schonherr, S., Weissensteiner, H., Haider, F., Kluckner, T., Gieger, C., Wichmann, H.-E., Specht, G., Kronenberg, F. and Kloss-Brandstatter, A., CONAN: copy number variation analysis software for genome-wide association studies, BMC bioinformatics (2010)

Hoffman, B.E., Newman-Tarr, T.M., Gibbard, A., Wang, S., Hanning, C., Pratta, M.A., Boyle, R.J., Kumar, S. and Majumdar, M.K., Development and characterization of a human articular cartilage-derived chondrocyte cell line that retains chondrocyte phenotype, Journal of cellular physiology (2010)

Lange, L.A., Croteau-Chonka, D.C., Marvelle, A.F., Qin, L., Gaulton, K.J., Kuzawa, C.W., McDade, T.W., Wang, Y., Li, Y., Levy, S. and others, Genome-wide association study of homocysteine levels in Filipinos provides evidence for CPS1 in women and a stronger MTHFR effect in young adults, Human molecular genetics (2010)

Liu, K., Casey, J. and Pichichero, M., Serum intercellular adhesion molecule 1 variations in young children with acute otitis media, Clinical and vaccine immunology (2010)

Perry, K., Tsui, K., Baldwin, C., de las Morenas, A. and Rosenberg, C., Copy number variants in histologically normal breast epithelium from reduction mammoplasty controls and breast cancer cases, Cancer Research (2010)

Willett, J.D., Podugu, N., Sudama, G., Kopecky, J.J. and Isbister, J., Applications of cold temperature stress to age fractionate Caenorhabditis elegans: A simple inexpensive technique, The Journals of Gerontology Series A: Biological Sciences and Medical Sciences (2010)

Wu, Y., Li, Y., Lange, E.M., Croteau-Chonka, D.C., Kuzawa, C.W., McDade, T.W., Qin, L., Curocichin, G., Borja, J.B., Lange, L.A. and others, Genome-wide association study for adiponectin levels in Filipino women identifies CDH13 and a novel uncommon haplotype at KNG1--ADIPOQ, Human molecular genetics (2010)

Harris, S.M., Microarray Time Course Assays of Cho-Cells Impaled on Vertically Arrayed Nanofibers, PhD Thesis, Oklahoma State University (2009)

Smith, A.M., Rahman, F.Z., Hayee, B., Graham, S.J., Marks, D.J., Sewell, G.W., Palmer, C.D., Wilde, J., Foxwell, B.M., Gloger, I.S. and others, Disordered macrophage cytokine secretion underlies impaired acute inflammation and bacterial clearance in Crohn's disease, The Journal of experimental medicine (2009)

Vickers, T.A., Lima, W.F., Wu, H., Nichols, J.G., Linsley, P.S. and Crooke, S.T., Off-target and a portion of target-specific siRNA mediated mRNA degradation is Ago2 ‘Slicer’independent and can be mediated by Ago1, Nucleic acids research (2009)

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