Paula Ramos Silva, Phd Email & Phone Number

Netherlands

Leiden, South Holland, Netherlands

Consulting services. Evaluator and rapporteur of project proposals for the Horizon Europe funding program.

Amsterdam Area

As a TAS I handle and resolve complex customer issues in spatial biology post-sales. I work with several teams in a cross-functional manner to improve experimental assays, instrumentation, software and data analysis. I find paths to issue resolution and contribute to process improvement, technical notes and customer relationship management.

Leiden, South Holland, Netherlands

I was awarded with European funding to develop genetic tools and study environmental impacts on marine zooplankton. For this project, I have identified novel proteins involved in biomineral formation by creating a new protocol for protein extraction from mm-sized shells. I have written scripts in Python and R, and used bioinformatics tools (e.g Trinity, TransDecoder, AlphaFold, Chimera, Metapredict, OrthoFinder, Nextflow) to characterize medium to large-scale transcriptomics and proteomics datasets. I also supervised two MSc research projects in bioinformatics addressing the transcriptomic responses of marine zooplankton to CO2. These projects included the development of new R scripts for differential gene expression.I communicated research at 10 international conferences, to visitors at Naturalis, and through the creation of a sci-comm video.

Leiden, South Holland, Netherlands

In this position I did RNA extractions and library preparations for Illumina sequencing. I also created a workflow for reproducible analysis of RNAseq data in a dedicated server and supervised MSc research projects in bioinformatics.

Computational Genomics Laboratory, Oeiras, Portugal

In this role I integrated bioinformatics tools and wrote scripts in Python and R for large scale bacterial comparative genomics. I also extracted DNA, benchmarked genome assemblers and annotation tools to characterize new bacterial isolates from soil, and acted as the manager of the in-house server for the research group. As a postdoc, I was awarded with an FCT postdoctoral fellowship (EvoSpore: SFRH/BPD/103171/2014). I lectured in the course 'Research in Bioinformatics' at the University of Lisbon, wrote three scientific publications, and participated and created activities for science communication events.

Informatics Institute, Amsterdam Area, Netherlands

As an Early Stage Researcher of the Marie Curie Initial Training Network Biomineralization: understanding of basic mechanisms for the design of novel strategies in nanobiotechnology (BIOMINTEC) I:• Used bioinformatics tools and wrote scripts in Perl and Java for sequence analysis and interrogation of public databases• Communicated research at five international conferences• Wrote several scientific publications both as main and co-author

Woods Hole, Ma, Usa

In this course I acquired deep knowledge and laboratory practice in stem cells and tissue regeneration with a scholarship from the National Institutes of Health & Howard Hughes Institute

Dijon, Bourgogne-Franche-Comté, France

As an Early Stage Researcher of the Marie Curie Initial Training Network Biomineralization: understanding of basic mechanisms for the design of novel strategies in nanobiotechnology (BIOMINTEC) I:• Integrated tools and wrote scripts in Perl and Java for sequence analysis and interrogation of public databases• Did RNA and DNA extraction, PCR, qPCR, rapid amplification of cDNA ends PCR, 1D and 2D SDS-PAGE, plasmid cloning, scanning electron microscopy• Did protein extractions from skeletal tissues for proteomics• Communicated research at three international conferences

Lyon, Auvergne-Rhône-Alpes, France

Here I programmed and tested bioinformatics tools using JAVA and PostgreSQL to build a relational database of proteins from mineralized tissues

Instituto Superior Técnico, Lisbon

As a junior researcher I developed microbial bioreactors for toluene biodegradation using Rhodococcus erythropolis. I collected and analyzed data from gas chromatography and wrote summary reports and presentations

Doctor Of Philosophy (Ph.D.), Biology, Bioinformatics, Phd

Master, Biological Engineering

Erasmus at BIOREM group – Biotechnology Department, Faculty of Engineering (LTH) - Lund University, Sweden

Bachelors, Biological Engineering