Head of Computational Biology
NextRNA Therapeutics
Biography
Experienced computational biologist focused on developing strategy in Biotechs with need of genomic regulation and data integration analyses. 13 years of experience in biological data analysis using the most well-established tools and contributing to novel algorithms to improve the quantification and visualization of genomic data. I approach scientific challenges with passion and believe that a collaboration and not an individual alone can successfully conquer them.
Community
JOSS editor. Join our women in bioinformatics in Boston area.
My tools
| Tool | Downloads |
|---|---|
| mirtop |  |
| seqbuster |  |
| seqcluster |  |
| seqclusterViz |  |
| isomiRs |  |
| DEGreport |  |
contributed to: nf-core, bcbio-nextgen, cloudbiolinux, bcbioRNASeq, bioconda, multiqc
Hobbies
Interests
- Transcriptomic
- Methods optimization
- Genomic Visualization
Education
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PhD in Biomedicine, 2011
Pompeu Fabra University
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Ms in Bioinformatics, 2008
Pompeu Fabra University
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BSc in Biochemistry, 2005
University of Granada
Skills
OMICS-data
Strategy
Visualization
AWS Infrastructure
Machine-learning
Experience
Director, Head of Computational Biology
NextRNA Therapeutics
Responsibilities include:
- Preparing slides and data packages for partners and BoD
- Leading the in-silico Target discovery pipelines integrating genomic data
- Leading RNA-Protein interaction prediction from high-throughput sequencing data
- Leading visualization plarforms in the discovery program
- Mantaining and evolving bioinformatic infrastructure to ensure reproducibility and scalability under budget restrictions
- Multi-omics analysis of (genomics and clinical) data available through TCGA, PCAWG, and other type of controlled data
- Senior Manager and Mentor
Principal Scientist in Computational Biology
Axcella Health
Responsibilities include:
- Leading R&D pipelines with computational strategies
- Analysing metabolimic/transcriptomic data
- Leading visualization plarform to boost biological interpretation
- Developing bioinformatic infrastructure to ensure reproducibility and scalability
- Senior Manager and Mentor
Senior Computational Biologist
eGenesis Bio
Responsibilities include:
- Leading genome editing QC pipeline
- Analysing genomic/transcriptomic data
- Developing bioinformatic tools
- Data structure architect
- Managing knowledge-base platform
- Mentoring
Research Scientist
Harvard Chan School
Responsibilities include:
- Leading computational analysis under a multi-group collaboration with Boehringer-ingelheim for 3 years
- Leading miRNA transcriptomic open project
- Analysing genomic data
- Developing bioinformatic tools
- Managing knowledge-base platform
- Mentoring
Research Associate
Harvard Chan School
Analyzed sequencing data in pathogenic conditions. Developed bioinformatics tools for sequencing data (RNA-seq, smallRNA-seq, ChIP-seq, ATAC-seq).
Post-doctoral fellow
Institute of Biotechnology and Biomedicine
Detected de-novo transcripts as effect of inversion in the HapMap population.Expression quantitive trait loci analysis of inversion in the HapMap population.
Post-doctoral fellow
Institute of Predictive and Personalized Medicine of Cancer
Determined small RNA characterization in human sperm samples.
Recent Posts
My story with cancer - Jimmy fund walk Oct 1st
My personal experience with cancer and how much work still to do
How to set up cellranger to make your hpc admin happy
I found myself to force to use cellranger. Meanwhile it helps a lot to run from bcl files to single cell counts matrixes, I discovered that is quite difficult to control many options related to optimization.
How to set up public dataset analysis with bcbio-nextgen
We use bcbio-nextgen for the analysis of sequencing data, mainly, (sc)RNAseq, smallRNAseq, DNASeq and ChIPSeq. It is not rare that we get collaborators who wants to re-analyze public data-set.
Inside bcbio, we have bcbio_prepare_samples.
Recent & Upcoming Talks
Women in Life Sciences: How do we Close the Gender Gap in Leadership?
With a global push in recent years to encourage young women toward careers in STEM, the life sciences have benefited enormously from …
Inside a Bioinformatics Startup – with NextRNA Therapeutics
In this podcast, Rob Lalonde of Seqera Labs speaks with Lorena Pantano, head of Computational Biology at NextRNA, a firm leading the …
miRNA variants (isomiRs): real molecules or sequencing artifacts?
Advances in high-throughput sequencing technologies led to the discovery of isomiRs, which are miRNA sequence variants. In the last …
MiRNA Wars: The isomiRs menance
MicroRNAs (miRNAs) are small RNA molecules (~22 nucleotide long) involved in post-transcriptional gene regulation. Advances in …
Featured Publications
Multi omics analysis of fibrotic kidneys in two mouse models.
Kidney fibrosis represents an urgent unmet clinical need due to the lack of effective therapies and an inadequate understanding of the …
Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API
Background: MicroRNAs (miRNAs) are small RNA molecules (̃22 nucleotide long) involved in post-transcriptional gene regulation. Advances …
The circulating metabolome of human starvation
The human adaptive starvation response allows for survival during long-term caloric deprivation. Whether the physiology of starvation …
Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans
We empirically examined the strengths and weaknesses of two human genome-wide DNA methylation platforms: rapid multiplexed reduced …
Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis.
MOTIVATION: Most computational tools for small non-coding RNAs (sRNA) sequencing data analysis focus in microRNAs (miRNAs), overlooking …
The small RNA content of human sperm reveals pseudogene-derived piRNAs complementary to protein-coding genes.
At the end of mammalian sperm development, sperm cells expel most of their cytoplasm and dispose of the majority of their RNA. Yet, …
A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.
MOTIVATION: Recent progress in high-throughput sequencing technologies has largely contributed to reveal a highly complex landscape of …
Recent Publications
Quickly discover relevant content by filtering publications.
Single-cell cloning of human T-cell lines reveals clonal variation in cell death responses to chemotherapeutics.
Genetic modification of human leukemic cell lines using CRISPR-Cas9 has become a staple of gene-function studies. Single-cell cloning …
Sex Differences in Adrenal Bmal1 Deletion-Induced Augmentation of Glucocorticoid Responses to Stress and ACTH in Mice.
The circadian glucocorticoid (GC) rhythm is dependent on a molecular clock in the suprachiasmatic nucleus (SCN) and an adrenal clock …