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Maria Teresa Lopez Cascales

@mariateresalopezcasc

Computational biologist at Erasmus MC developing biomarker pipelines and co-inventing an HNSCC metastasis stratification patent.

Netherlands

Message

At Erasmus MC, I analyze single-cell and other sequencing data to study cancer progression across HNSCC, gastric, and skin malignancies. I developed and validated an ML-based biomarker selection pipeline on clinical FFPE cohorts with a pharmaceutical partner, and contributed analysis and patient stratification to a patent for HNSCC metastasis biomarkers.

At Instituto de Neurociencias CSIC, I integrated RNA-seq, ChIP-seq, ATAC-seq, and RiboTRAP-seq data in neuronal systems. My analyses contributed to publications in Science Advances and Advanced Science, including work identifying axon guidance regulators.

I’m developing POKEMON-hub, my own algorithm and tool for pathway organization, enrichment, and multi-omics networks. Across oncology and neuroscience, I translate biological questions into analyses and figures that help interpret the underlying biology.

Experience

Work history, roles, and key accomplishments

Current

Postdoctoral Bioinformatician

Current

Erasmus MC

Feb 2023 - Present (3 years 8 months)

Led end-to-end computational analysis as sole bioinformatician for scRNA-seq, scTCR-seq, ChIP-seq, ATAC-seq, EM-seq, RiboTRAP-seq, and single-cell VASA-seq datasets to dissect molecular mechanisms of cancer progression across HNSCC, gastric, and skin malignancies. Developed and validated an ML-based biomarker selection pipeline on clinical FFPE cohorts in collaboration with a pharmaceutical partne

ScRNA Seq TCR Seq ChIP Seq ATAC Seq DNA Methylation EM Seq RiboTRAP Seq VASA Seq InferCNV Numbat Machine Learning Bootstrapping Cross Validation R Python BASH Git HPC

PhD Researcher

Instituto de Neurociencias CSIC

Jul 2019 - Feb 2026 (6 years 7 months)

Sole bioinformatician across peer-reviewed publications, with full pipeline ownership from raw sequencing data to publication figures and methods sections. Integrated multi-omics data including RNA-seq, ChIP-seq, ATAC-seq, and RiboTRAP-seq in neuronal systems, identifying novel axon guidance regulators.

RNAseq ChIP Seq ATAC Seq RiboTRAP Seq Multi omics Data Integration R Git NCBI Gene Expression Omnibus (GEO)

Bioinformatics Scientist

Instituto de Neurociencias CSIC

Jan 2016 - Jun 2019 (3 years 5 months)

Performed NGS data analysis for neuronal epigenomics, including RNA-seq, ChIP-seq, and ATAC-seq, and developed custom R scripts for preprocessing, differential analysis, and visualization. Contributed as co-second author to a Nature Neuroscience publication on epigenomic signatures of neuronal activation.

RNAseq ChIP Seq ATAC Seq R Differential Expression Visualization

Education

Degrees, certifications, and relevant coursework

CDISC

Course, Clinical Data Standards

Course in progress on CDISC standards, including SDTM data transformation using the sdtm.oak R package.

Instituto de Neurociencias CSIC / Universidad Miguel Hernández

PhD, Neuroscience & Bioinformatics

2017 - 2026

Grade: Excellent

PhD in Neuroscience & Bioinformatics with grade Excellent. Research focused on bioinformatics and neuroscience, including multi-omics integration and publication-grade analyses.