We provide bioinformatics and biostatistics services.
- DNA Next Generation Sequencing (NGS) analysis
- Exome-Sequencing analysis
- ChIP-Seq analysis (narrow peaks or wider domains)
- RNA-Seq analysis
- DNA Methylation Sequencing analysis
- Ribo-Seq analysis
- Differential Expression (RNA-Seq & DNA methylation)
- Variant Discovery (DNA & RNA-Seq)
- Junction-based analysis of splicing events
- ENCODE correlations with NGS datasets
- The Cancer Genome Atlas (TCGA) NGS datasets
- Epigenetic Signature discovery
- Transcription Factor Motif discovery
- Phosphorylation prediction
- microRNA Target prediction
- Virus de novo Assembly
- Microarray analysis
- Time-series Microarray analysis
- Biomarker panel design
- Pathway analysis
- Gene Ontology analysis
- Proteomics analysis
- qPCR analysis
- Machine Learning
- Custom scripts/software
- Ingenuity Pathways
- Bioinformatics public software (bowtie, bwa, MACS, RSEG, tophat, cufflinks, samtools, picard, IGV, GATK, GSEA, DAVID, hmmer, etc.)
- R, Python, Perl, Java and other programming languages
- Imamura Kawasawa, Y., Salzberg, A.C., Li, M., Sestan, N., Greer, C.A., Imamura, F. Genome-wide transcriptome analysis of developing olfactory bulb projection neurons (submitted)
- Popova, E.Y., Pinzon-Guzman, C., Salzberg, A.C., Zhang, S.S., Barnstable, C.J. LSD1-mediated demethylation of H3K4me2 is required for the transition from late progenitor to differentiated mouse rod photoreceptor Molecular Neurobiology (2015) (in press)
- Lynch, C., Kimball, S., Xu, Y., Salzberg, A., Kawasawa, Y. Global deletion of BCATm increases expression of skeletal muscle genes associated with protein turnover Physiol Genomics 47(11):569-80 (2015)
- Berry, G.J., Frielle, C.M., Brucklacher, R.M., Salzberg, A.C., Waldner, H. Identifying type 1 diabetes candidate genes by DNA microarray analysis of islet-specific CD4+ T cells Genomics Data 5:184-188 (2015)
- Robey, R.B., ... Salzberg, A.C., ... et al. Metabolic Reprogramming and Dysregulated Metabolism in Cancer: Pleiomorphic Mechanistic Targets, Antagonists, and Enablers of Complex Low Dose Environmental Exposures? Carcinogenesis 36(S1):S203-S231 (2015)
- Goodson III, W.H., ... Salzberg, A.C., ... et al. Assessing the Carcinogenic Potential of Low Dose Exposures to Chemical Mixtures in the Environment: The Challenge Ahead Carcinogenesis 36(S1):S254-S296 (2015)
- Lynch, C.J., Xu, Y, Hajnal, A., Salzberg, A.C., Imamura Kawasawa, Y. RNA Sequencing Reveals a Slow to Fast Muscle Fiber Type Transition after Olanzapine Infusion in Rats. PLoS ONE 10(4):e0123966 (2015)
- Berry, G.J., Frielle, C., Luu, T., Salzberg, A.C., Rainbow, D.B., Wicker, L.S., Waldner, H. Genome-wide transcriptional analyses of islet-specific CD4+ T cells identify Idd9 genes controlling diabetogenic T cell function. J. Immunology 194(6):2654-63 (2015)
- Wilson, R.T., Borner, J.D., Roff, A., Das, A., Richie, J.P., Bamholtz-Sloan, J., Chinchilli, V.M., Berg, A., Liu, G., Salzberg, A.C., El-Bayoumy, K. Genetic and Environmental Influences on Plasma Vitamin D Binding Protein Concetrations. Translational Research 165(6):667-676 (2015)
- Dluzen, D., Sun, D., Salzberg, A.C., Jones, N., Bushey, R., Robertson, G., Lazarus, P. Regulation of UGT1A1 expression and activity by miR-491-3p. JPET, 113.210658 (2014)
- Popova, E.Y., Xu, X., DeWan, A.T.,.Salzberg, A.C., Berg, A., Hoh, J., Zhang, S.S., Barnstable, C.J. Stage and Gene Specific Signatures Defined by Histones H3K4me2 and H3K27me3 Accompany Mammalian Retina Maturation in Vivo. PLoS ONE 7(10):e46867 (2012)
- Qi, J., Rice, S.J., Salzberg, A.C., Liao, J., Zander, D.S., and Mu, D. MiR-365 Regulates Lung Cancer and Developmental Gene Thyroid Transcription Factor 1. Cell Cycle , 11(1), 177-186 (2012)
- Freeman, W.M., Salzberg, A.C., Gonzales, S.W., Grant, K.A., Vrana, K.E. Classification of alcohol abuse by plasma protein biomarkers. Biol Psychiatry, 68(3), 219-222 (2010)
- Sun, Y., El-Bayoumy, K., Imamura, Y., Salzberg, A., Aliaga, C., Gowdahalli, K., Amin, S., Chen, K. Genome-wide analysis of DNA methylation induced by environmental carcinogen dibenzo[def,p]chrysene in ovarian tissues of mice. AACR, 2016.
- Lee, S.Y., Zhu, J., Salzberg, A., Liu, D.J., Connor, J.R. Association study between HFE polymorphisms and survival of glioblastoma patients in TCGA database. Neuro Oncol (suppl 5): v82 (2015)
- Weisz, J., Shearer, D., Salzberg, A. Adaptation to chronic oxidative stress (OxS) during latent states of carcinogenesis: an evolutionary complex adaptive system based model of breast carcinogenesis. J. of International Society of Antioxidants in Health & Nutrition 1(1) (2015)
- Popova, E., Pinzon-Guzman, C., Salzberg, A., Hass, D., Zhang, S.S., Barnstable, C.J. The role of Lysine demethylase 1 in mouse rod photoreceptor development and maturation. Investigative Ophthalmology & Visual Science 56(7):438 (2015)
- Sun, Y., Chen, K., Imamura Kawasawa, Y., Salzberg, A., Aliaga, C., Gowdahalli, K., Amin, S., Stoner, G., El-Bayoumy, K. The effects of the environmental carcinogen dibenzo[a,l]pyrene on genome-wide methylation and the impact of dietary black raspberry in mouse oral tissues. Cancer Research 75 (15 Supplement), 2955-2955 (2015).
- Weisz, J., Shearer, D., Salzberg, A.C. Using reduction mammoplasty tissues from healthy young women living in USA's high breast cancer (BC) risk posing environment to open up to study the "black box" of latent stages of breat carcinogenesis: a key to develop strategies for BC prevention. Cancer Research 75 (15 Supplement), 4558-4558 (2015).
- Berg, A., Imamura Kawasawa, Y., Salzberg, A., Bixler, E.O., He, F., Liao, D. Abstract P260: Obesity is associated with DNA Methylation in Population-Based Adolescents. Circulation 131 (Suppl 1), AP260-AP260 (2015)
- Rodriguez-Colon, S.M., Berg, A., Imamura Kawasawa, Y., Salzberg A., Bixler, E.O., Fernandez-Mendoza, J., Vgontzas, A.N, Liao, D. Abstract MP91: Abdominal Obesity, Independent of General Obesity, is Associated With Reduced Circadian Pattern of Cardiac Autonomic Modulation in Adolescents. Circulation 131 (Suppl 1), AMP91-AMP91 (2015)
- Popova, E., Pinzon-Guzman, C., Salzberg, A., Berg, A., Zhang, S.S., Barnstable, C.J. Lysine demethylase 1 is required for mouse rod photoreceptor development. Investigative Ophthalmology & Visual Science 55(13):4998-4998 (2014)
- Waldner, H., Berry, G., Frielle, C., Salzberg, A.C. Identification of candidate genes for type 1 diabetes by microarray expression analysis of islet-specific CD4+ T cells (IRM6P.726). The Journal of Immunology 192 (1 Supplement), 63.18-63.18 (2014)
- Lehman, H., Welsh, P., Mass, J., Salzberg, A., Berg, A., Stairs, D. Investigating the mechanisms of esophageal squamous cell carcinoma invasion (59.9). The FASEB Journal 28 (1 Supplement), 59.9 (2014)
- Grigoryev, S., Salzberg, A.C., Berg, A., Harris-Becker, A., Loughran, T., Claxton, D. Genome-wide mapping of large organized heterochromatin domains reveals hotspots of epigenetic and transcriptional changes associated with myeloid differentiation and acute myeloid leukemia (565.1). The FASEB Journal 28 (1 Supplement), 565.1 (2014)
- Archibeque, L.D., Barnholtz-Sloan, J., Battaglioli, E.J., Salzberg, A.C., Wilson, R.T. Polymorphisms in CYP24A1 and CYP3A43: possible effect modification by the vitamin D binding protein and vitamin D receptor. American Institute for Cancer Research. November, 2013.
- Spratt, T.E., Gowda, A.S., Salzberg, A., Berg, A., Song, C., Dovat, S.S. Binding of benzo[a]pyrene diol epoxide to the genome. Abstracts of Papers of the American Chemical Society 246 (2013)
- Dluzen, D.F., Salzberg, A., Sun, D., Jones, N., Bushey, R., Lazarus, P. miR-491-3p regulation of the UDP-glucuronosyltransferase (UGT) 1A gene family. Cancer Research 73 (8) (2013)
- MacNeill, C; Salzberg, A.C.; Phelps, D.S; Umstead, T.M.; Floros, J.; Weisz, J. Proteomic Studies of Vestibular Swab Extracts Identify Reduced Levels of Serine Protease Inhibitors in Patients with Vulvodynia. ISSVD XXII World Congress. October, 2013.
- Qi, J; Rice, S.J.; Salzberg, A.C.; Runkle, A.; Liao, J.; Zander, D.S.; Mu, D. MiR-365 regulates lung cancer and developmental gene TTF-1. Cancer Research 72 (8 Supplement), 2307-2307 (2012)
Arthur Berg, Ph.D.
Dr. Berg enjoys all aspects of statistics and biostatistics, including methodological research, collaboration, and education. His general research interests include, but are not limited to, Statistical Genetics, Time Series Analysis, Survival Analysis, Functional Smoothing, Bootstrap, Subsampling, Nonparametric Statistics, Density Estimation, Simulation, Bayesian Statistics, and Longitudinal Data Analysis. As a faculty member of Penn State's Center for Statistical Genetics, Dr. Berg is passionate about unlocking the mysteries of DNA and its connection to human health. Located in the newly constructed Cancer Institute on the Penn State Hershey campus, Dr. Berg works in close proximity to clinical researchers allowing for convenient collaborations on grants and publications across all areas of human health.
Senior Bioinformatician in the Penn State College of Medicine's Genomic Sciences Core and Institute of Personalized Medicine. Anna Salzberg has had over 10 years experience working in industry as a principal software engineer. More recently she became very enthusiastic about bioinformatics and biology and during the last 11 years she worked as a bioinformatician first at Pfizer and then at the Penn State College of Medicine. At Pfizer, she co-developed protein structure computational geometry algorithms to predict target "druggability", as well as novel graph theoretic algorithms for binding site fingerprinting to predict function and small molecule selectivity. At Penn State she provides general bioinformatics services as listed here, including genomics and epigenomics analyses.