Bioinformatics

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We provide bioinformatics and biostatistics services.

  • ChIP-Sequencing Analysis
  • Next Generation Sequencing Analysis
  • RNA-seq Analysis
  • DNA Methylation Analysis
  • Microarray Analysis
  • miRNA Target Prediction
  • Proteomics Analysis
  • Virus de novo Assembly
  • Pathway Analysis
  • Gene Ontology Analysis
  • Machine Learning
  • Miscellaneous custom scripts/software in collaboration with PI
  • Biostatistics

 

A fee schedule is currently being developed for the Bioinformatics Core.  

  • CLC Genomics Workbench
  • Ingenuity Pathways
  • MATLAB
  • 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

Recent Publications

  1. Popova, E.Y., Pinzon-Guzman, C., Salzberg, A.C., Berg, A., Barnstable, C.J., Zhang, S. LSD1-mediated demethylation of H3K4me2 is required for the transition from late progenitor to differentiated rod photoreceptor during mouse retina development (submitted to Developmental Biology)
  2. Berry, G., Salzberg, A.C., Frielle, C., Waldner, H. Genome-wide gene expression analysis of islet-specific CD4+ T cells identified genes controlling type I diabetes development (submitted to The Journal of Immunology)
  3. Goodson III, W.H. et al. Assessing the Carcinogenic Potential of Low Dose Exposures to Chemical Mixtures in the Environment: The Challenge Ahead (submitted to Carcinogenesis)
  4. R. Brooks Robey, R.B. et al. Metabolic Reprogramming and Dysregulated Metabolism in Cancer: Pleiomorphic Mechanistic Targets, Antagonists, and Enablers of Complex Low Dose Environmental Exposures? (submitted to Carcinogenesis)
  5. 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 (2014) (in press)
  6. 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)
  7. 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)
  8. 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)
  9. 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)
  10. 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)
  11. 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)
  12. 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)
  13. 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)
  14. 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)

Arthur Berg, Ph.D.

aberg1@hmc.psu.edu

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.

Anna Salzberg

asalzberg@hmc.psu.edu

Senior Bioinfomaticist in the Penn State College of Medicine's Bioinformatics Core. Anna Salzberg has had over 10 years experience working in industry as a software engineer. More recently she became very enthusiastic about Bioinformatics and Biology and during the last 10 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 is involved in developing algorithms for bioinformatics and computational biology, including genomics and epigenomics.