Emma Ricart Altimiras, PhD

Data Engineering | Scientific Software | AI for Life Sciences

Resume

About Me

Bioinformatics data engineer and scientific software engineer with more than 10 years of experience developing scalable data pipelines, machine learning models, and research software for genomics and mass spectrometry. My work combines data engineering, statistical modeling, and software development to transform complex biological datasets into reproducible computational solutions. I enjoy designing maintainable software and promoting reproducible research through modern engineering practices!

Experience

Harvard Medical School logo

Harvard Medical School | Massachusetts General Hospital - Gulhan Lab

Research Scientist - -

I worked at the intersection of data engineering, data science, and bioinformatics, developing scalable computational solutions for genomic and liquid biopsy research:

  • Designed scalable and reproducible bioinformatics workflows for preprocessing, integration, and analysis of large-scale genomic sequencing data.
  • Developed machine learning models and statistical analyses to infer gene expression patterns and classify tumor subtypes using circulating cell-free DNA (cfDNA).
  • Applied data engineering and computational methods to support liquid biopsy applications for cancer diagnosis, disease monitoring, and patient stratification.
  • Mentored junior researchers in workflow development, software engineering best practices, and reproducible computational research.
Python Machine Learning Data Science Data Engineering Bioinformatics Genomics cfDNA Nextflow HPC SLURM Docker Git
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AGORA Cancer Research Center - Bassani Lab

Bioinformatician | Database administrator - -

My responsabilities in Prof. Michal Bassani lab were multiple and diverse. From pipeline and software development to data storage and visualization:

  • Developed a workflow for large-scale identification and quantification of HLAI/HLAII peptides from mass spectrometry experiments
  • Implemented an ETL process for the creation of an immunopeptidomics data warehouse which included +1.000.000 peptides identified with the workflow
  • Used the collected data to create a scoring system for the prioritization of neoantigens, directly impacting the clinical trials
  • Build a web interface for querying and visualizing the database
Python R Bash Nextflow HPC Immunopeptidomics Mass spectrometry Data Visualization Biological Data Analysis Docker Software development Git
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Swiss Institute of Bioinformatics - Proteome Informatics Group

Ph. D. Student - -

I was granted with a SIB PhD Fellowship in the group of Frederique Lisacek, a group highly focused on the computational side of bioinformatics, where I adquired experience in software development and good programming practices:

  • Developed rBAN, a java package and web application tool for the retro biosynthesis of non-ribosomal peptides
  • Developed NRPro, a web application tool for the identification and annotation of tandem mass spectra from peptidic natural products
  • Worked with SMILES format and graph structures for the substructures search and the fragmentation algorithms used by the tools
  • Build a NoSQL database for the backend of NRPro integrating data from Norine, ChEBI and Natural Products Atlas
Java R Maven MongoDB AngularJS Mass spectrometry Peptidomics Data Visualization Biological Data Analysis Software development Git
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JAX Cancer Center - The Chuang Lab

Bioinformatics researcher - -

Short experience in the field of transcriptomics. During this period I worked remotely for the team of Prof. Jeffrey H. Chuang.

  • Analyzed iCLIP data from ENCODE project to study RNA-protein binding sides
Python R Perl Bash HPC Biological Data Analysis Statistics Data Visualization Transcriptomics
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Barcelona Biomedical Research Park - Computational Genomics Group

Bioinformatics researcher - -

I contributed in the group of Prof. Eduardo Eyras by bringing my expertise in proteomics (adquired during my master thesis) in one of their studies:

  • Analyzed and quantified iTRAQ mass spectrometry data from the TCGA project to validate findings identified at RNA level
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Lund University - Computational Proteomics group

Master's Student - -

My first practical experience in bioinformatics was in this group leaded by Fredrik Levander. I learned the principles of proteomics, MS/MS interpretation and I performed some data analysis:

  • Identified and quantified of protein variants using a combination of shotgun proteomics and DIA LC-MS
  • Applied statistical analysis to the proteins identified for biomarkers discovery

Bioinformatic tools

NRPro

ipMSDB

KFP

rBAN

Education / Training

University of Geneva

Ph.D. in Bioinformatics - -

I performed my PhD in a computational research group mainly focused on the development of software tools for biological applications, in particular for mass spectrometry analysis. I worked with IT engineers, physicist, chemists and biologist. During this period I acquired my development skills. In the "Experience" section there are more details about my PhD work.

University of Barcelona & Polytechnic University of Catalonia

Master's degree in Biomedical Engineering - -

The master's degree introduced the electrical, mechanical and chemical principals necessary to modify/monitor biological systems in order to design tools for diagnosis or treatment of diseases. Some of the subjects were:
  • Statistical analysis and computation of biomedical data, Modeling and systems physiology, Biomaterials, Biomedical Devices, Biomedical Images, Biomedical Signals, Tissue engineering and Nanotechnology

University of Vic - Central University of Catalonia

Bachelor's degree in Biotechnology - -

The degree included practical work in the laboratory as well as computational disciplines such as programming and statistics. Some of the subjects were:
  • Bioinformatics, Biostatistics, Genetic engineering, Microbiology, Proteomics, Bioreactors, Immunology and Biochemical engineering

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