Bioinformatics

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We provide bioinformatics and biostatistics services.

  • DNA Next Generation Sequencing (NGS) 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
  • Microarray Analysis
  • Pathway Analysis
  • Gene Ontology Analysis
  • miRNA Target Prediction
  • Proteomics Analysis
  • Virus de novo Assembly
  • TCGA
  • Machine Learning
  • Miscellaneous custom scripts/software in collaboration with PI
  • Biostatistics

 

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

  • 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)
  2. Lynch, C.J., Xu, Y, Hajnal, A., Salzberg, A., Imamura Kawasawa, Y. RNA Sequencing Reveals a Slow to Fast Muscle Fiber Type Transition after Olanzapine Infusion in Rats. PLoS ONE (2015) (in press)
  3. 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? Carcinogenesis (2015) (in press)
  4. Goodson III, W.H. et al. Assessing the Carcinogenic Potential of Low Dose Exposures to Chemical Mixtures in the Environment: The Challenge Ahead Carcinogenesis (2015) (in press)
  5. 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)
  6. 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)
  7. 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)
  8. 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)
  9. 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)
  10. 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)

Abstracts

  1. 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. American Association for Cancer Research. April, 2015.
  2. 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.  American Association for Cancer Research. April, 2015.
  3. 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)
  4. 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)
  5. 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)
  6. 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)
  7. 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)
  8. 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)
  9. 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)
  10. 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.
  11. Ritty, T.M.; Frauenhoffer, E.; Fox, E.J.; Salzberg, A.C.; Stanley, B.  Proteomics Identification of Grade-Specific Tumor Biomarkers from Archival FFPE Tissues.  Orthopaedic Research Society.  March,  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 Bioinformatician 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.