Bionformatics Tools for Genome-Wide Dataset Analyses

TETRAMER provides an interative approach to interrogate the capacity of each TF - retrieved on reconstructed GRN to drive cell fate transitions. For it, the temporal transcriptional regulation cascade derived from each TF is scrutinized as a way to verify its influence on the reconstitution of the differential gene expression patterns associated to the cell fate transition.


-Gene regulatory networks
-Transcription regulation


M. A. Mendoza-Parra et al.
Genome Res. 2016;
doi: 10.1101/gr.208926.116


MeDiChI-seq is a regression-based method for peak detection in the context of profiling of protein-chromatin interaction patterns. As the first step MeDiChI computes a model of multiple binding events present in a particular ChIP-seq profile. Likely binding events are then identified by comparison of particular peak with the model. Predicted binding events are further characterized in the context of their significance by the non-parametric bootstrapping statistical approach.

-massive parallel sequencing
-Peak caller

M. A. Mendoza-Parra et al.
BMC Genomics. 2013;
doi: 10.1186/1471-2164-14-834


Comparative analysis between ChIP-seq and other NGS datasets requires prior characterization of their degree of technical similarity. NGS Q/C Generator infer Quality indicators from the distribution of sequenced reads associated to a particular NGS profile. Such information is then used for comparative purposes and for defining strategies aiming to improve the quality of the sample-derived datasets.

-Next Generation Sequencing
-Quality indicators

M. A. Mendoza-Parra et al.
Nucl. Acids Res. 2013;
doi: 10.1093/nar/gkt829


LinDA is a high-fidelity, single-tube Linear DNA amplification method for ChIP-seq and other genome-wide studies based on massive parallel sequencing.

  -DNA amplification
-massive parallel sequencing
-polyA adapter trimming script

S. Pattabhiraman et al. Nature Methods. 2011 Jun 5;8(7):565-7

S. Pattabhiraman et al. Nature Protoc. 2012 Jan 26;7(2):328-38. doi: 10.1038/nprot.2011.447

M. A. Mendoza-Parra et al. Protocol exchange, DOI 10.1038/protex.2011.256

  POLYPHEMUS: R package for comparative analysis of genome-wide RNA Polymerase II Chip-seq data using non-linear normalisation approaches
  -RNA Polymerase II
  M. A. Mendoza-Parra et al.
Nucl. Acids Res. 2011;
doi: 10.1093/nar/gkr1205
  A miscellaneous of our favorite scripts used for massive parallel sequencing data processing... but not only.   miscellaneous   DG. Ceschin et al. Genes & Dev. Jun 1;25(11):1132-46 (2011)

Marco Mendoza
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