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     What do we do?


The Bioinformatics & Systems Biology Core both develops new bioinformatics and systems biology methods and tools and supports Center staff in providing bioinformatic and statistical services. Working with the Center's research collaborators, the Core stores, retrieves and analyses the vast amount of data from the Center’s experiments. The availability of a responsive and dedicated bioinformatics and statistical support team enables the Core to provide rapid data management and processing support facilitating the timely and accurate analysis and interpretation of the results. In addition, the Bioinformatics & Systems Biology Core develops user-friendly and open access tools available to the entire research community including NeuroPred (a prohormone processing and peptide predictor), PepShop (one stop integration of peptide sequence and mass spectra information) and neuroProsight (a top down proteomics toolset). These resources are complemented with an array of transcriptomic and proteomics analyses workflows for a range of experimental designs developed and tested by the Bioinformatics & Systems Biology Core. Combining these efforts with the world-class computational and informatics capabilities available at the University of Illinois, the Bioinformatics & Systems Biology Core provides a vast range of technical support services to the neuroscience research community.

Representative publications

Accurate Assignment of Significance to Neuropeptide Identifications Using Monte Carlo K-Permuted Decoy Databases, M.N. Akhtar, B.R. Southey, P.E. Andrén, J.V. Sweedler, S.L. Rodriguez-Zas, PLoS ONE 9, 2014, e111112. DOI:10.1371/journal.pone.0111112

The C-Score: A Bayesian Framework to Sharply Improve Proteoform Scoring in High-Throughput Top Down Proteomics, R.D. LeDuc, R.T. Fellers, B.P. Early, J.B. Greer, P.M. Thomas, N.L. Kelleher, J. Proteome Res. 13, 2014, 3231-3240. DOI: 10.1021/pr401277r

Comparing Label-free Quantitative Peptidomics Approaches to Characterize Diurnal Variation of Peptides in the Rat Suprachiasmatic Nucleus, B.R. Southey, J.E. Lee, L. Zamdborg, N. Atkins, Jr., J.W. Mitchell, M. Li, M.U. Gillette, N.L. Kelleher, J.V. Sweedler, Anal. Chem., 86, 2014, 443–452. DOI:10.1021/ac4023378

Evaluation of Database Search Programs for Accurate Detection of Neuropeptides in Tandem Mass Spectrometry Experiment, M.N. Akhtar, B.R.Southey, P.E.Andrén, J.V. Sweedler, S.L. Rodriguez-Zas, J. Proteome Res. 11, 2012, 6044–6055. DOI:10.1021/pr3007123