Epithelial Systems Biology Laboratory

 Home Page Research Water Balance
Vasopressin and its
Aquaporins Systems Biology Protein Mass
Phosphoproteomics Deep Sequencing
in Epithelia
Computational Tools
Proteomics &
Transcriptomics Databases
Integrated Antibody Design Kidney Systems Biology Project Isolated Perfused

Bioinformatic and Computational Tools Developed in the ESBL

Often, the rate-limiting element in projects that use proteomics and/or deep sequencing techniques is the bioinformatic analysis of the data. The Epithelial Systems Biology Laboratory, headed by Mark Knepper, has developed a number of computational tools for analysis of proteomic data and have made them available to the community (1-7). The following links allow users to access online versions of the tools or download executables:


  1. Pisitkun T, Dummer P, Somparn P, Hirankarn N, Kopp JB, Knepper MA. Integrated design of antibodies for systems biology using AbDesigner. J Proteomics Bioinform. 2014; 7:088-94. PMID: 25328345.

  2. Saethang T, Hodge K, Kimkong I, Payne DM, Knepper MA, Pisitkun T. AbDesigner3D: a structure-guided tool for peptide-based antibody production. Bioinformatics. 2018; 34:2158-2160. PMID: 29408997.

  3. Saeed F, Pisitkun T, Hoffert JD, Rashidian S, Wang G, Gucek M, Knepper MA. PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data. Proteome Sci. 2013; 1 1:S14. PMID: 24565028.

  4. Saeed F, Pisitkun T, Hoffert JD, Wang G, Gucek M, Knepper MA. An efficient dynamic programming algorithm for phosphorylation site assignment of large-scale mass spectrometry data. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2012; 618-625. PMID: 23471519.

  5. Zhao B, Pisitkun T, Hoffert JD, Knepper MA, Saeed F. CPhos: a program to calculate and visualize evolutionarily conserved functional phosphorylation sites. Proteomics. 2012; 12: 3299-303. PMID: 23001821.

  6. Douglass J, Gunaratne R, Bradford D, Saeed F, Hoffert JD, Steinbach PJ, Knepper MA, Pisitkun T. Identifying protein kinase target preferences using mass spectrometry. Am J Physiol Cell Physiol. 2012; 303:C715-27 PMID: 22723110.

  7. Saethang T, Hodge K, Yang CR, Zhao Y, Kimkong I, Knepper MA, Pisitkun T. PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities. Bioinformatics 2019. pii: btz568. PMID: 31318409.