Raúl Méndez-Giráldez
Houston,TX
Summary
Accomplished Computational Biologist with expertise in computer programming, data analysis, and computational algorithms. Deep understanding of biological principles, biochemistry, and molecular biology. Consistently utilize advanced bioinformatics tools to analyze and interpret large-scale datasets. Contributions have led to advancements in genomics, proteomics, and epigenetics. Diverse research experience across prestigious institutions, developing innovative computational methods and providing valuable insights into complex biological systems.
Overview
26
26
years of professional experience
Work History
Field Application Scientist
Beckman Coulter Life Sciences
11.2022 - Current
- Customer support for the Cytobank platform, a computer platform running on the AWS cloud for the analysis of flow cytometry, CyTOF, and/or spectral data
- Troubleshooting analysis and/or data analysis using Cytobank, providing information to customers through a ticket system based on Zendesk (cytobank_support@beckman.com)
- Training customers: o Premium users online on the most important functionalities of Cytobank: data QC, data management, manual gating, automatic gating (deep learning approach), dimensionality reduction methods (tSNE, UMAP), clustering (FlowSOM), and illustrator editor
- (2 sessions, 3 h each) o Enterprise users online, tailored to the needs of a given company organization (1.5 h) or on- site ( ≥ 3h)
- Data (flow cytometry/CyTOF/spectral) analysis projects, from beginning to end, upon signature of an agreement between the customer and Beckman Coulter Life Sciences
- These involve the use of external computational tools based on R/Bioconductor packages through a script tailored to the needs of the customer and shared with them upon completion of the project
- A final report and presentation are also provided
- Demo the Cytobank platform to potential new customers (mostly online)
- Attendance to Flow Cytometry conferences/exhibitions/road shows.
Bioinformatics Scientist (contractor)
Kelly
11.2020 - 11.2022
- Development of computational methods for single-cell dynamic trajectory analysis using machine learning methods (random forests – eXtreme Gradient Boosting) for feature selection, and minimum spanning trees for data visualization
- Application of those methods to the study of cell differentiation process using data from single-cell RNA-seq or CyTOF experiments
- Research of the early different cell populations driving drug resistance in the early stages of chemotherapy treatments in Acute Myeloid Leukemia patients, leveraging time course CyTOF data and the novel computational framework Dynamic Spanning Forest Mixtures (DSFMix), which extends the capabilities of the SPADE program
- Elucidation of the role of Glis3 transcription factor in the maturation process from progenitor to - cells from mice pancreas, using single-cell RNA-seq time course data from WT and Glis3 KO mice, and the DSFMix computational approach to visualize the changes in different cell lineages.
Research Associate (Computational Biologist)
Lineberger Comprehensive Cancer Center, the University of North
02.2018 - 11.2020
- Development of computational pipelines for the analysis of Next Generation Sequencing Data (Chip- seq, RNA-seq, GRO-seq, single-cell RNA- and ATAC-seq) in several projects
- Study of the effect of FOXA1 acetyl-mimic mutants on DNA binding and gene expression, employing ChIP-seq and RNA-seq respectively
- Study of the role of enhancer RNA, utilizing CRISPR-dCas9 KRAB knockout screens followed by RNA-seq
- Single-cell RNA-seq and ATAC-seq on 20 samples from real patient tumors (Breast, Ovarian, and
- Endometrial) to highlight the similarities and differences between cancer types at the cellular level in terms of gene expression and chromatin accessibility.
Postdoctoral Research Associate
The University of North Carolina at Chapel Hill
02.2015 - 01.2018
- Research on Genetic Epidemiology and Pharmacogenomics to link Electrocardiographic (ECG) phenotype with genetic background and with drug-gene interaction, both using DNA microarray data and statistical computation
- Research on Epigenetics versus weather exposures
- In both, cases functional annotation of the relevant variants using Epigenetic and Chromatin 3D structure data
- Genome-Wide Association Study of QT interval (an ECG measure) in Hispanic/Latino populations, a project in collaboration with the ECG Working Group
- Genome-Wide Association Study of the interaction between the University of Arizona Certified Drugs and QT interval, a project within the CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) Pharmacogenetics Working Group.
- Set up a pipeline in R to deal with longitudinal data.
Postdoctoral Research Associate
The University of North Carolina at Chapel Hill
02.2013 - 01.2015
- Several projects involving computational techniques to design, study dynamics, and predict the structure of proteins and protein-protein complexes
- Computational design of proteins to stimulate the immune response against HIV infection
- Use a Monte Carlo-based side-chain optimization and all-atoms discrete molecular dynamics
- Designed proteins are then experimentally obtained by other members of the group
- Study of RyR (Ryanodine receptor), through molecular dynamics simulations and comparison with experiments on channel conductance upon different mutants at the pore helix region
- Virtual screening on molecules to prevent binding of integrins to CIB1 (calcium, integrin-binding protein), utilizing MedusaDock that allows both protein side chain and ligand rotamer optimization through MC simulations.
Postdoctoral Researcher (JAE investigator)
Center for Molecular Biology "Severo Ochoa"
11.2007 - 01.2013
- Research on computational methods to model protein flexibility and evolution
- Study of the DNA replication in A. Thaliana
- Development of an elastic network model in dihedral angle space to predict protein conformational flexibility, implemented in a program written in C language
- Population dynamics simulations to study how effective population size can affect nucleotide usage in bacteria implemented on a program written in C language.
- Collaborative project on the analysis of epigenetic marks to study DNA replication in plants, using ChIP-seq data.
- Collaborative project within Centrosome 3D Consortium (http://ub.cbm.uam.es/centrosome/index.php), to study intrinsically disordered proteins in the human centrosome.
Graduate Student
Université Libre de Bruxelles
10.2002 - 09.2007
- Evaluation of computational methods to predict the structure of protein-protein complexes within the CAPRI international experiment.
- Development of a fully automated protocol based on Perl scripting (See results for rounds 1 – 7 at http://capri.ebi.ac.uk/)
- Analysis of conformational changes in protein-protein complexes.
Marie Curie Fellow
Marie Curie, Université Libre de Bruxelles
10.2001 - 09.2002
- Setting up the CAPRI experiment and its first two evaluation rounds
- Classification of Homeodomain proteins, final DEA work
Intern
Laboratoris Dr. Esteve
03.1999 - 09.1999
- Study of the expression of some glutamate neuroreceptors upon chronic antipsychotic treatment in animal models within the Molecular Laboratory.
Education
Ph.D. - Bioinformatics
Université Libre De Bruxelles
Brussels, Belgium09.2007
Master of Science - Bioinformatics
Université Libre De Bruxelles
Brussels, Belgium09.2003
Master of Science - Biotechnology
Universitat De Barcelona
Barcelona, Spain09.1999
Bachelor of Science - Chemistry
Universitat De Barcelona
Barcelona, Spain09.1997
Skills
- R programming
- Python Programming
- Perl & Bash scripting
- C Programming
- Jupyter Notebooks and RStudio (IDE for R and Python)
- NGS data analysis
- Flow and/or Mass Cytometry data analysis
- UCSC Genome Browser
- Statistical Genetics analysis
- GROMACS molecular Dynamics package
- Linux, and command line languages (Awk, Sed)
Accomplishments
- Automatized CAPRI model evaluation through Perl programming.
- I currently help customer optimize their Flow/Mass Cytometry analysis pipelines using R coding.
Awards
- Marie Curie Fellowship, Université Libre de Bruxelles, 2002
- Best Poster presenter, CHARGE meeting NYC, 2017
Publications
- Gene expression biomarkers differentiate overall survival of colorectal cancer upon targeted therapies., Yazdani A, Yazdani A, Mendez-Giraldez R, et al., Research Square, 2024, 10.21203/rs.3.rs-4047331/v1
- Gene signatures derived from transcriptomic-causal networks stratified colorectal cancer patients for effective targeted therapy., Yazdani A, Lenz HJ, Pillonetto G, et al., Research Square, 2024, 10.21203/rs.3.rs3673588/v1
- Broadcaster receivers, functional groups of metabolites and the link to heart failure progression using polygenic factors., Yazdani A, Mendez-Giraldez R, et al., Metabolomics, 2024, 10.21203/rs.3.rs-3246406/v1
- Immune profiling of age and adjuvant-specific activation of human blood mononuclear cells in vitro., Dowling D, Schüller S, Barman S, et al., Communications Biology, 2024, 10.1038/s42003-024-06390-4
- Differential gene regulatory pattern in the human brain from schizophrenia using transcriptomic-causal network., Yazdani A, Mendez-Giraldez R, et al., BMC Bioinformatics, 2020, 10.1186/s12859-020-03753-6
Company
Beckman Coulter Life Sciences
Languages
English
Full Professional
Spanish
Native or Bilingual
French
Professional Working
Catalan
Native or Bilingual
Timeline
Field Application Scientist
Beckman Coulter Life Sciences
11.2022 - Current
Bioinformatics Scientist (contractor)
Kelly
11.2020 - 11.2022
Research Associate (Computational Biologist)
Lineberger Comprehensive Cancer Center, the University of North
02.2018 - 11.2020
Postdoctoral Research Associate
The University of North Carolina at Chapel Hill
02.2015 - 01.2018
Postdoctoral Research Associate
The University of North Carolina at Chapel Hill
02.2013 - 01.2015
Postdoctoral Researcher (JAE investigator)
Center for Molecular Biology "Severo Ochoa"
11.2007 - 01.2013
Graduate Student
Université Libre de Bruxelles
10.2002 - 09.2007
Marie Curie Fellow
Marie Curie, Université Libre de Bruxelles
10.2001 - 09.2002
Intern
Laboratoris Dr. Esteve
03.1999 - 09.1999
Ph.D. - Bioinformatics
Université Libre De Bruxelles
Master of Science - Bioinformatics
Université Libre De Bruxelles
Master of Science - Biotechnology
Universitat De Barcelona
Bachelor of Science - Chemistry
Universitat De Barcelona
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