Guilherme Bauer-Negrini

Guilherme Bauer-Negrini

Biomedical Data Scientist

Bio

Computational neuroscientist working at the intersection of machine learning, biomedical imaging, and human genetics in neurodegenerative disease. My work applies deep learning to high-dimensional medical images, harmonizes imaging measurements across sites and acquisition protocols, and integrates imaging with genomic, proteomic, and longitudinal clinical data to characterise Alzheimer’s disease and related dementias, with particular focus on fluid and imaging biomarkers of neurodegeneration.

Experience

Postdoctoral Research Associate

Pascoal Lab, University of Pittsburgh

Deep learning on 3D medical images: Developed 3D convolutional networks with transfer learning to classify and stage Alzheimer’s disease from volumetric tau-PET, training separate models per radiotracer and transferring representations between them to compensate for limited labelled data. Used leakage-safe subject-level cross-validation throughout. Secured funding as Principal Investigator through an Alzheimer’s Association Research Fellowship (USD $200,000) for “A deep learning tool to generalize tau-PET to predict Alzheimer’s disease progression.”

Image registration, harmonization & quality control: Co-developed Uniτ (uni-tau.com), a voxel-wise transformation placing images from four different tau PET radiotracers onto a single quantitative scale, including reference-region definition, spatial normalisation to common templates, and systematic QC of registration and segmentation across a multi-centre head-to-head cohort. Performed imaging processing and interpretation work for the HEAD Study, the largest Alzheimer’s disease methodological imaging study to date (co-author in The Lancet).

Population-scale genetics and longitudinal clinical records: Computed polygenic risk scores for 200,000+ participants and built cohort-definition and phenotyping pipelines over longitudinal electronic health records (NIH All of Us), testing genetic liability for ADHD as a predictor of incident mild cognitive impairment and dementia. First and co-first author in JAMA Psychiatry and JAMA Network Open.

Genetic risk linked to imaging and fluid biomarkers: In Alzheimer’s disease cohorts, related genetic liability to molecular and imaging outcomes and modelled joint structure across tau-PET, amyloid-PET, MRI, fluid biomarkers, and longitudinal cognition (co-author in Alzheimer’s & Dementia; Molecular Psychiatry).

Collaboration & dissemination: Worked across international institutions in the US, Canada, Brazil, Spain, and the Netherlands; presented as first author or speaker at major Alzheimer’s disease conferences (Human Amyloid Imaging, Alzheimer’s Imaging Consortium, Alzheimer’s Association International Conference); mentored junior researchers and contributed to grant applications.

Data Scientist

Portal Telemedicine · Full-time

São Paulo, Brazil · Remote

Data scientist in an R&D project funded by UNICEF to map overdue vaccinations and issue alerts to health workers; built healthcare data interfaces using HL7 FHIR; developed the containerized developer environment with Docker, poetry, and Bitbucket Pipelines; contributed to AI-enabled public-health alerting. The pilot project in Brazil involved 3,876 children and resulted in a promising initial increase in vaccine coverage, from 53% to 56%, a 3% improvement in just two months.

Education

PhD in Biochemistry

Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil

Bioinformatics of circRNAs: analysis in animal models of Autism Spectrum Disorder and development of a method for evaluating the usability of the identification software used.

BSc in Biomedical Informatics

Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Brazil

A proposal of an interaction design pattern language oriented to microRNAs databases.

MSc in Neuroscience

Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil

Analysis of behavioral, synaptic, and immunological parameters in BALB/c nude mouse strain.

Continued Education Course in Higher Education Teaching

Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil

Virtual Laboratory to Support Teaching of Central Nervous System Electrophysiology.

BSc in Biomedical Sciences

Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil

Quantitative and qualitative evaluation of T cells in lymphoid organs of mice in the animal model of autism induced by prenatal exposure to valproic acid.
Recent Publications
Blog
How to run FreeSurfer on Windows with WSL2 featured image

How to run FreeSurfer on Windows with WSL2

Freesurfer is available only for the Linux and Mac OS X operating systems. You can run FreeSurfer in Windows using a virtual machine, but that can slow down the processing a …

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Guilherme Bauer-Negrini
Best biomedical and health data science books and resources featured image

Best biomedical and health data science books and resources

Biomedical data science spans a range of biological and medical research challenges that are data-intensive and focused on the creation of novel methodologies to advance biomedical …

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Guilherme Bauer-Negrini
Biomedical text natural language processing (BioNLP) using scispaCy featured image

Biomedical text natural language processing (BioNLP) using scispaCy

Here we are going to see how to use scispaCy named entity recognition (NER) models to identify drug and disease names mentioned in a medical transcription dataset. Moreover, we are …

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Guilherme Bauer-Negrini
Tolkien character or prescription drug name? featured image

Tolkien character or prescription drug name?

Bilbo, Silenor, Avandaryl, Nardil, Cymbalta. Only one of these is actually the name of a character created by J.R.R.Tolkien, author of the classic *The Lord of the Rings* trilogy. …

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Guilherme Bauer-Negrini