プロフィール詳細

プロジェクトを作成

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Dr. Amira B.に依頼

France

Bioinformatics PhD | Computational Biology | Genomics, NGS, Structural Bioinformatics | Reproducible Pipelines

プロフィール概要

I help research teams and companies turn raw biological data into results they can publish or act on. My work covers the full path from sequencing reads to figures, reports, and reproducible pipelines. I hold a PhD in bioinformatics and molecular evolution (Paris-Saclay, CNRS) and currently work as a postdoctoral researcher at the Technical University of Munich, in population genetics. Over the past seven years I have delivered more than 65 freelance bioinformatics projects with consistently high client satisfaction, alongside my academic research. My main areas: Genomics and population genetics. GWAS and co-GWAS (PLINK2, Firth regression), population structure (PCA, ADMIXTURE, FST), ancient DNA analysis (qpAdm, qpWave, ADMIXTOOLS2), variant calling and annotation. Genome assembly and annotation. De novo assembly from Nanopore and Illumina reads, gene prediction, functional annotation, comparative genomics. Transcriptomics. RNA-seq differential expression, co-expression networks, pathway enrichment. Structural bioinformatics. AlphaFold2 structure prediction, FoldSeek structural comparison, molecular docking (ClusPro, AutoDock Vina, HADDOCK), visualization in PyMOL and ChimeraX. Phylogenetics and molecular evolution. Tree inference (IQ-TREE2, RAxML), selection analysis, gene family and protein evolution. Pipeline development. Reproducible workflows, documented and tested, that a team can run without me. Scientific writing and review. Methods sections, technical reports, manuscript figures, and code or pipeline review. I program in Python, R, and Bash, and work on Linux. Deliverables come as documented code with publication-ready figures and clear reports. I respond quickly and I am precise about what is feasible and by when.

専門分野

• ★ Bioinformatics
• ☆ Computational Biology
• ☆ Evolutionary Biology
• ☆ Molecular Biology
• ☆ Genetics
• ☆ Omics
• ☆ Genomics
• ☆ Molecular Evolution
• ☆ Next Generation Sequencing (NGS)
• ☆ DNA Sequencing
• ☆ RNA Sequencing
• ☆ Computer Science
• ☆ Structural Bioinformatics
• ☆ Phylogenetics
• ☆ Population Genetics
• ☆ Python
• ☆ R

サービス

• Writing
• Research
• Consulting
• Data & AI

Writing Technical Writing

Research Scientific and Technical Research, Systematic Literature Review, Secondary Data Collection

Consulting Scientific and Technical Consulting

Data & AI Predictive Modeling, Statistical Analysis, Data Visualization, Big Data Analytics, Text Mining & Analytics, Data Mining, Data Cleaning, Data Processing, Data Insights

職務経験

Postdoc in Evolutionary Biology Research

Technical University of Munich, Freising, Germany

3月 2025 - 現在

PhD

Institute of Integrative Biology of the Cell

10月 2021 - 現在

学歴

PhD molecular evolution (Biology)

University of Paris-Saclay

10月 2021 - 9月 2024

MSc Bioinformatics and modeling (Bioinformatics )

Sorbonne Université

9月 2019 - 6月 2021

Bachlor in Computer science (Computer sciences)

Paris Descartes University

9月 2016 - 6月 2019

認定資格

• Claude 101

  Claude

  3月 2026 - 現在

• Bioinformatics Methods I

  coursera

  https://www.coursera.org/account/accomplishments/verify/27FZM5WXXFWR?utm_source=link&utm_medium=certificate&utm_content=cert_image&utm_campaign=sharing_cta&utm_product=course

  12月 2021 - 現在

出版物

PREPRINT

Amira Boukherissa, Siva Sankari, Tatiana Timchenko, Mickaël Bourge, Peter Mergaert, George C. diCenzo, Jacqui A. Shykoff, Benoît Alunni, Ricardo C. Rodríguez de la Vega (2025). Structure-based phylogenetic analysis reveals multiple events of convergent evolution of cysteine-rich antimicrobial peptides in legume-rhizobium symbiosis .

Amira Boukherissa, Nicholas T. Smith, Kiera Antaya, Graeme W. Howe, Ricardo C Rodríguez de la Vega, Jacqui A. Shykoff, Benoît Alunni, George C. diCenzo (2024). Taxonomic distribution of SbmA/BacA and BacA-like antimicrobial peptide transporters suggests independent recruitment and convergent evolution in host-microbe interactions .

Amira Boukherissa, Joy Lachat, Gaëlle Lextrait, Romain Jouan, Aya Yokota, Seonghan Jang, Kota Ishigami, Ryo Futahashi, Raynald Cossard, Delphine Naquin, et al. (2023). Hundreds of antimicrobial peptides create a selective barrier for insect gut symbionts .

JOURNAL ARTICLE

Amira Boukherissa, Pascal Büttiker, Simon Weissenberger, Martin Anders, Jiri Raboch, George B. Stefano (2025). AlphaFold 2: Insights and Future Directions in Psychiatry . THE MIND Bulletin on Mind-Body Medicine Research.

Amira Boukherissa, Pascal Büttiker, Simon Weissenberger, Martin Anders, Jiri Raboch, George B. Stefano (2025). AlphaFold 2: Insights and Future Directions in Psychiatry . THE MIND Bulletin on Mind-Body Medicine Research.

Amira Boukherissa, Nicholas T. Smith, Kiera Antaya, Graeme W. Howe, Peter Mergaert, Ricardo C. Rodríguez de la Vega, Jacqui A. Shykoff, Benoît Alunni, George C. diCenzo (2025). Taxonomic distribution of SbmA/BacA and BacA-like antimicrobial peptide transporters suggests independent recruitment and convergent evolution in host–microbe interactions . Microbial Genomics.

Amira Boukherissa, Besma Bouznif, Yan Jaszczyszyn, Mohamed Mars, Tatiana Timchenko, Jacqui A. Shykoff, Beno&#238;t Alunni (2024). Complete and circularized genome sequences of five nitrogen-fixing <i>Bradyrhizobium</i> sp. strains isolated from root nodules of peanut, <i>Arachis hypogaea</i> , cultivated in Tunisia . Microbiology Resource Announcements.

DISSERTATION THESIS

(2024). Study ot the coevolution between antimicrobial peptides and peptide transporters in legume-rhizobium symbiosis .