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
  • R
  • Python, Perl, Java and other programming languages

  • CLC Genomics Workbench
  • Ingenuity Pathways
  • MATLAB
  • 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.J., Frielle, C.; Salzberg, A.C., Rainbow, D.B., Wicker, L.S., Waldner, H. Genome-wide gene expression analysis of islet-specific CD4+ T cells identifies genes controlling type 1 diabetes development.  (submitted to J Immunology).
 
3.      Archibeque, L.D., Battaglioli, E., Barnholtz-Sloan, J., Salzberg A.C., Wilson, R.T. Possible influence of CYP3A43 and vitamin D binding protein polymorphisms on vitamin D metabolite balance among healthy African and European Americans (submitted)
 
4.      Wilson, R.T., Bortner, J.D., Roff, A., Das, A., Richie, J.P., Barnholtz-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 Concentrations.  (in press, Translational Research)
 
5.      Grigoryev, S., Salzberg, A., 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)
 
6.      Waldner, H., Berry, G., Frielle, C., Salzberg, A. 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.      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 (2014).
 
9.      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)
 
10.  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)
 
11.  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).
 
12.  Qi, J., Rice, S.J., Salzberg, A.C., Liao, J., Zander, D.S., Mu, D. MIR-365 Regulates Lung Cancer and Developmental Gene Thyroid Transcription Factor 1. Cell Cycle 11(1):177-86 (2012).
 
13.  Freeman, W.M., Salzberg, A.C., Gonzales, S.W., Grant, K.A., Vrana, K.E. Classification of alcohol abuse by plasma protein biomarkers.  Biological Psychiatry 68(3):219-22 (2010).

Arthur Berg, Ph.D.

aberg1@hmc.psu.edu

 

Anna Salzberg

asalzberg@hmc.psu.edu

Senior Bioinfomaticist in Penn State College of Medicine's Bioinformatics Core. Anna Salzberg has had 15 years experience working in industry as a software-engineer. At Pfizer, she co-developed protein structure computational geometry algorithms to predict target "druggability", which are now used globally, 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.