DEVELOPED SOFTWARE

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  • Micrographite Pathway analysis procedure for matched gene and miRNA expression profiles
  • Reference: Wiring miRNAs to pathways: a topological approach to integrate miRNA and mRNA expression profiles. Nucleic Acids Res.. 014;42(11):e96. doi: 10.1093/nar/gku354. Epub 2014 May 6.
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  • MAGIA2 web tool for the integrative analysis of miRNA and genes expression data
  • Reference: MAGIA2: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update).. NUCLEIC ACIDS RES. 2012 Jul;40(Web Server issue):W13-21. Epub 2012 May 21..
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  • CliPPER A tool for topological pathway analysis.
  • Reference: Along signal paths: an empirical gene set approach exploiting pathway topology NAR. 2013.
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  • Graphite Web A tool for the analysis and visualization of biological networks
  • Reference: Graphite Web: Web tool for gene set analysis exploiting pathway topology NAR. 2013
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  • Extension of the pipeline miR&more, for the discovery, characterization and quantification of small RNAs to the case of multiple samples.
  • Reference: For 1.0 version of miR&more see: Characterization and discovery of novel miRNAs and moRNAs in JAK2V617F-mutated SET2 cells. Blood. 2012
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  • Reverse engineering pipeline, Refining the structure of a pathway with a view to prediction of gene silencing effects
  • Reference: Djordjilovic, Vera et al. (2014) Proceedings of the 29 th workshop on statistical modelling. 2012
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  • Cancer exome analysis pipeline, A pipeline for the analysis of exome data for the identification of relevant somatic variants, mutated genes and pathways in cancer/normal matched samples. The pipeline uses gold standard tools, databases and custom made scripts for calling, filtering and prioritizing genomic variants from exome sequencing data (both Illunima and Ion Proton). Variants are prioritized according to their recurrence in the samples, predicted effect on transcripts and annotation in disease databases. The mutation recurrence of higher order biological entities, genes and gene network in particular, is also evaluated┬áto circumvent the classical scenario in which is very uncommon to identify variants recurrently mutated in cohorts of patients harboring the same disease. prediction of gene silencing effects
  • Reference: Coppe et al. Blood e-letter 2016; Coppe et al. Under evaluation . 2012
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  • RNA-Seq pipeline, Qualitative and quantitative characterization of transcriptome from RNA-seq data and expression comparison between conditions. Automatized and modular pipeline for multisample RNA-seq data analysis. Parallelized execution of analysis steps. Provides transcript sequences and gene and transcript expression level estimation, also for non-annotated transcripts; gene and transcript differential expression assessment.
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  • Circular pipeline, Circular RNA (circRNA) detection and quantification grounding on different methods used in parallel for back-splice junctions detection from mapping data and for circRNA prioritization. The pipeline allows comparing circular and linear transcripts and the estimation of circRNA expression, specifically in relation with the linear isoforms counterparts.