Experience

Flomics

• Spain
• Biotechnology Research
• 1 - 100 Employee

• Bioinformatics Senior Scientist

  • Dec 2022 - Present

  Barcelona, Catalonia, Spain



Centre for Genomic Regulation (CRG)

• Spain
• Biotechnology Research
• 200 - 300 Employee

• Postdoctoral Researcher

  • May 2015 - Jul 2022

  Barcelona, Catalonia, Spain RESEARCH - Developed a quantitative model of protein synthesis using data integration of multiple omics data (ribosome profiling, RNA-seq, RNA half-lives, tRNA-seq, proteomics, protein half-lives) and random forest regressor, in collaboration with 4 experimental scientists. - Investigated the impact of amino acid composition on protein expression using large-scale statistical analysis of 1500+ bacterial genome sequences and high-throughput experimental assay, in collaboration with 3… Show more RESEARCH - Developed a quantitative model of protein synthesis using data integration of multiple omics data (ribosome profiling, RNA-seq, RNA half-lives, tRNA-seq, proteomics, protein half-lives) and random forest regressor, in collaboration with 4 experimental scientists. - Investigated the impact of amino acid composition on protein expression using large-scale statistical analysis of 1500+ bacterial genome sequences and high-throughput experimental assay, in collaboration with 3 experimental scientists. - Analyzed data, performed statistical analyses, and participated in experimental designs for 7 collaborative projects in Systems Biology within teams of 3-6 scientists. - Built data visualizations of complex datasets in Python. - Developed end-to-end RNA-seq pipeline, from raw data extraction to statistical analysis and scientific hypothesis testing. MANAGEMENT / LEADERSHIP - Supervised and co-supervised the research projects of 3 master students, including: . - a project on modeling cell-type specific responses of the STAT signaling pathway, in the context of supporting the rational engineering of cytokines for therapeutic applications. . - a project using supervised learning (Support Vector Machine) to classify tumors of origin of metastatic and circulating tumor cells using single cell and bulk RNA-seq data. COMMUNICATION - Wrote 2 first-author research articles, co-authored 5 research articles, and reviewed 3 master thesis manuscripts. - Presented results at 2 international conferences, 5 departmental seminars, and 20 group meetings to audiences ranging from 20 to 80+ researchers with diverse scientific backgrounds.

• Instructor for workshop on whole-cell modelling

  • Apr 2016 - Apr 2016

  Barcelona Area, Spain Instructor for the workshop training on flux-balance analysis (FBA) using COBRA Python module. Created and taught 4 hours session tutorial for students to learn COBRA usage and applications in modeling metabolic networks in E. coli. http://www.wholecell.org/school-2016/ https://github.com/webermarcolivier/metabolic_modelling_jupyter_tutorial



Universitat de Barcelona

• Spain
• Research Services
• 700 & Above Employee

• Ph.D. student

  • Sep 2008 - Jun 2014

  Barcelona, Catalonia, Spain - Investigated stochasticity in bacterial gene regulatory networks leading to 4 first-author publications. - Developed from scratch agent-based simulation software in C++ using Gillespie and Langevin stochastic algorithms. - Developed mathematical models of gene regulatory networks using ODEs. - Gave research talks at 2 local and 1 international conferences. - Wrote a Ph.D. thesis to unify and put into a larger context 4 research projects.



UC San Diego

• United States
• Higher Education
• 700 & Above Employee

• Visiting grad student

  • Dec 2010 - Mar 2011

  - Visiting grad student, short research stay at Hasty & Tsimring's Biodynamics lab at UCSD. - Learned and applied fluorescence microscopy and microfluidics technology to study gene regulatory network dynamics in bacteria and implemented this technology in our lab in Barcelona.



Universitat de Barcelona

• Spain
• Research Services
• 700 & Above Employee

• Stochastic Description of Kinetic Proofreading

  • Sep 2007 - Oct 2007

  FuncDyn exchange grant of the European Science Fundation. University of Barcelona, Barcelona, Spain.



Universitat de Barcelona

• Spain
• Research Services
• 700 & Above Employee

• Monte-Carlo simulation of polymer on 2D lattice

  • Feb 2007 - Mar 2007

  HPC-Europa exchange grant at the Barcelona Supercomputing Center, in collaboration with the goup of Statistical Biophysics of the EPFL in Switzerland and the Department of Fundamental Physics of the University of Barcelona. University of Barcelona, Barcelona, Spain. Code development of a Monte-Carlo simulation of polymers on 2D lattice, using the supercomputer of the BSC. Experience gained in parallel coding, parallel system environment, Monte-Carlo simulation, scientific… Show more HPC-Europa exchange grant at the Barcelona Supercomputing Center, in collaboration with the goup of Statistical Biophysics of the EPFL in Switzerland and the Department of Fundamental Physics of the University of Barcelona. University of Barcelona, Barcelona, Spain. Code development of a Monte-Carlo simulation of polymers on 2D lattice, using the supercomputer of the BSC. Experience gained in parallel coding, parallel system environment, Monte-Carlo simulation, scientific collaboration. Show less



IR Microsystems

• Automation Machinery Manufacturing
• 1 - 100 Employee

• Intern

  • Sep 2004 - Oct 2004

  Development of an experimental setup for mid-infrared spectroscopy of liquid samples.