About

Renne Lab

Principal Investigator: Rolf Renne
Henry E. Innes Professor of Cancer Research
University of Florida
UF Health Cancer Center
UF Department of Molecular Genetics and Microbiology
UF Genetics Institute

Lead Developer

Changelog

  • 0.3.0a (ongoing) Major Codebase And API Overhaul. Changes include:

    • Simplifying HybRecord API

    • Simplifying FoldRecord API

    • Unifying settings information for argparse and module

    • Removing Support for ViennaD format

    • Addition of “NON” value to “target_reg” flag in specification

    • Moving identifier-parsing code to module type_finder

    • Moving target region analysis code to module region_finder

    • Moving code for settings into a “settings” module

    • Renamed HybRecord type_analysis and mirna_analysis to eval_types and eval_mirna, respectively to differentiate from analysis module functions

    • Reimplemented analyses methods as classes

    • Added error checking / catching to HybFoldIter

    • Removed Target-Region Analysis and associated files due to lack of archival database information, pending furure development

    • Added DynamicFoldRecord class for non-identical fold/hybrid sequence handling

    • Implemented hyb_analysis, hyb_exclude_fold, and hyb_fold_analysis executables

    • Added shell implementation to all example pipelines

    • Remove support for Python3.6

  • 0.2.0 (2020-03) Added Command-line Toolkit. Code Refinements.

  • 0.1.9 (2020-03) Fix for Module Path Finding for Python > 3.6

  • 0.1.8 (2020-03) Streamlining, PyPI / PIP Initial Release

  • 0.1.0 (2020-01) Initial Implementation

References

ViennaFormat
CTFormat
Zuker2003

Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003 Jul 1;31(13):3406-15. doi: 10.1093/nar/gkg595. PMID: 12824337; PMCID: PMC169194.

Hunter2007

J. Hunter, “Matplotlib: A 2D Graphics Environment” in Computing in Science & Engineering, vol. 9, no. 03, pp. 90-95, 2007. doi: 10.1109/MCSE.2007.55

Cock2009

Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009 Jun 1;25(11):1422-3. doi: 10.1093/bioinformatics/btp163. Epub 2009 Mar 20. PMID: 19304878; PMCID: PMC2682512.

Lorenz2011

Lorenz, R., Bernhart, S.H., Höner zu Siederdissen, C. et al. ViennaRNA Package 2.0. Algorithms Mol Biol 6, 26 (2011). doi: 10.1186/1748-7188-6-26

Helwak2013

Helwak A, Kudla G, Dudnakova T, Tollervey D. Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell. 2013 Apr 25;153(3):654-65. doi: 10.1016/j.cell.2013.03.043. PMID: 23622248; PMCID: PMC3650559.

Travis2014

Travis AJ, et al. Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data. Methods. 2014 Feb;65(3):263-73. doi: 10.1016/j.ymeth.2013.10.015.

Gay2018

Gay LA, Sethuraman S, Thomas M, Turner PC, Renne R. Modified Cross-Linking, Ligation, and Sequencing of Hybrids (qCLASH) Identifies Kaposi’s Sarcoma-Associated Herpesvirus MicroRNA Targets in Endothelial Cells. J Virol. 2018 Mar 28;92(8):e02138-17. doi: 10.1128/JVI.02138-17. PMID: 29386283; PMCID: PMC5874430.