Michel Mourra

I have been working with several bioinformatic tools focussed on the measurement of RNA expression during certain conditions. One of these are TEcount and TElocal which has as purpose the quantification of transposable elements transcripts for subfamilies and individual insertions respectively across the given samples in the dataset. Then we take the resulting files to process it we deseq2 and perform a statistical analysis by comparing the samples that belong to different condition with the purpose of finding TEs that has been significant up and downregulared

• Tools: Trimmomatic , STAR , TEcount , TElocal , Deseq2

I possess extensive experience in the field of phylogenetic analysis, specifically focusing on transposable elements (TEs) and regulatory research pertaining to transcription factors binding sites (TFBSs). Throughout my career, I have actively engaged in studying the evolutionary relationships of TEs and their impact on genome structure and function. My expertise in conducting phylogenetic analysis has allowed me to trace the origins and movements of TEs across mouse during embryonic development, while identifying conserved regions crucial for their activity and regulation. Additionally, I have conducted research on TFBSs, investigating their evolutionary conservation and divergence to gain insights into gene regulatory network evolution. My contributions in this field have not only enhanced our understanding of genome evolution but also provided valuable insights into the genetic basis of disease and the mechanisms driving biological diversity.

• Phylogenetic analysis: IQTREE , ITOL
• Regulatory Analysis: RSAT , TOMTOM , APE

I have gained valuable experience in the generation of genomic tracks specifically for RNA-seq data. Throughout my career, I have actively engaged in the analysis and processing of RNA-seq datasets to generate informative genomic tracks. This includes utilizing specialized bioinformatics tools and pipelines to align RNA-seq reads to the reference genome, quantify gene expression levels, and identify differential expression patterns. Additionally, I am proficient in visualizing and interpreting these genomic tracks, providing valuable insights into gene expression dynamics and regulatory elements. My experience in generating genomic tracks for RNA-seq data has enhanced my understanding of transcriptional regulation and has equipped me with valuable skills in data analysis and interpretation in the field of genomics.

• Tools: IGV Browser , Deep Tools

I have extensive experience in modeling protein structures using 3D visualization software such as PyMOL. Throughout my career, I have actively utilized PyMOL and other similar tools to create accurate and detailed representations of protein structures. I am proficient in generating molecular graphics, manipulating protein models, and performing complex structural analyses. This includes tasks such as protein alignment, structural superimposition, and the identification of key structural features. My experience in modeling protein structures using 3D visualization software has not only honed my technical skills but has also enhanced my understanding of protein function and structure-function relationships.

• Tools: Pymol , Coot

I have been actively engaged in utilizing specialized software to identify clusters of rare codons within mRNA sequences that encode for specific proteins in various organisms. Throughout my work, I have demonstrated proficiency in leveraging this software to analyze and identify regions within mRNA that contain rare codons, which are known to impact translation efficiency and protein expression. By identifying these clusters, I have contributed to a deeper understanding of the regulatory mechanisms governing protein synthesis and the potential implications for protein function. My experience in working with such software has equipped me with the skills to conduct thorough analyses of codon usage patterns and has strengthened my ability to interpret and analyze genomic data in the context of protein synthesis.

• Tools: Minmax

I have gained extensive experience working with specialized software that enables me to measure the free energy release resulting from amino acid contacts. Throughout my work, I have effectively utilized this software to assess the energetic interactions between amino acids and evaluate the stability and folding of proteins. By quantifying the free energy release, I have contributed to a deeper understanding of protein structure-function relationships and the thermodynamics of protein folding. My proficiency in using this software has allowed me to perform accurate and comprehensive analyses, providing valuable insights into the energetics of protein-protein interactions and the impact on protein stability. This experience has enhanced my ability to assess and interpret the thermodynamic properties of proteins, making me a valuable asset in the field of protein research.

• Tools: Shaknovich

I have successfully developed multiple bioinformatic tools aimed at assisting the Abasy Atlas database in associating synonymous genes across different IDs to a unique and specific tag. Through my work, I have demonstrated strong programming and bioinformatics skills, enabling me to design and implement robust algorithms for data processing and integration. These tools have effectively addressed the challenge of mapping synonymous genes, streamlining the data analysis process and enhancing the accuracy and efficiency of gene annotation. My contributions to the development of these bioinformatic tools have significantly contributed to the functionality and reliability of the Abasy Atlas database, ultimately facilitating comprehensive and reliable gene identification and analysis.

• Tools: Abasy Atlas

During my tenure as a student in a laboratory focused on systems biology, I have gained a comprehensive understanding of the concepts underlying biological networks. With a strong grasp of network theory and its application to biological systems, I have actively utilized various bioinformatic packages to explore and analyze the properties within these networks. By leveraging these tools, I have successfully identified key properties such as connectivity, centrality, and modularity within biological networks, allowing for a deeper understanding of their structural and functional characteristics. My experience in working with bioinformatic packages has enabled me to effectively analyze complex network data and extract meaningful insights that contribute to our understanding of biological systems from a systems biology perspective.

• Tools: Networkx

Throughout my professional journey, I have gained extensive experience in accessing and retrieving information from various biological databases. By proficiently establishing remote access using different coding languages, I have successfully connected to diverse biological databases, enabling me to retrieve valuable data for a range of purposes. Furthermore, my expertise extends to efficiently parsing and organizing the acquired information, ensuring its suitability for different research objectives. With a strong command of coding languages, I have automated these processes, streamlining the data retrieval and analysis workflow. This expertise in obtaining and parsing information from biological databases underscores my ability to leverage these resources effectively, supporting data-driven research and scientific investigations.

• Tools: Uniprot , NCBI , ENA , PDB ,
• Tools: urllib