Guilherme Bauer Negrini

Biomedical Data Scientist | Postdoctoral Associate

University of Pittsburgh

I am a biomedical data scientist passionate about data analysis, data visualization, and biomedical software development. I have interdisciplinary experience in biomedical science and informatics applied to problem solving in biological sciences, health and medicine.

Currently, I am focused on developing machine learning models and utilizing data-driven approaches for imaging biomarkers analysis in neurodegenerative conditions.

Read more about me

Interests

Neuroimaging
Data Science
Deep Learning
Bioinformatics
Biomedical Informatics

Education

PhD in Biochemistry, 2018 - 2022
Universidade Federal do Rio Grande do Sul (UFRGS)
BSc in Biomedical Informatics, 2018 - 2021
Universidade Federal do Ciências da Saúde de Porto Alegre (UFCSPA)
Continued Education Course in Higher Education Teaching, 2018 - 2019
Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
MSc in Neuroscience, 2016 - 2018
Universidade Federal do Rio Grande do Sul (UFRGS)
BSc in Biomedical Sciences, 2012 - 2016
Universidade Federal do Rio Grande do Sul (UFRGS)

Recent Posts

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 little. One alternative is to use Windows Subsystem for Linux. Here, I’ll show you how to do it!

Guilherme Bauer Negrini

Last updated on Jun 23, 2021 2 min read

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 science discovery. Here is a listing of some resources that I have found while researching and studying this field.

Guilherme Bauer Negrini

Last updated on Apr 22, 2021 9 min read

Best biomedical and health data science books and resources

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 going to combine NER and rule-based matching to extract the drug names and dosages reported in each transcription.

Guilherme Bauer Negrini

Last updated on Apr 15, 2021 10 min read

Biomedical text natural language processing (BioNLP) using scispaCy

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. Could we solve this problem using artificial neural networks?

Guilherme Bauer Negrini

Last updated on Apr 15, 2021 9 min read

Tolkien character or prescription drug name?

GitHub Projects

Last updated on Oct 24, 2023

Usability evaluation of circRNA tools

This repository contains files to reproduce the heuristic evaluation environment described in the paper “Usability evaluation of circRNA identification tools - Development of a heuristic-based framework and analysis”.

Last updated on Feb 28, 2022

Interaction Design Patterns for Bioinformatics

Interaction design patterns to help bioinformatics software developers to improve the productivity and efficiency of their design process.

Last updated on Feb 28, 2022

Tolkien character or prescription drug name?

Classification using character-level Long Short-Term Memory (LSTM) neural networks

Last updated on Feb 28, 2022

HL7® FHIR® server using Cloud Healthcare API

Creation of an HL7® FHIR® server using cloud computing resources from the Google Cloud Platform (Portuguese-BR)

Last updated on Feb 28, 2022

Automated miRDB custom target search

Command-line tool to automate the search for microRNA targets in the miRDB base and extract the number of binding sites

Last updated on Mar 27, 2021

Hebbie Ann

Chatbot for interaction on topics in Artificial Neural Networks (Portuguese-BR)

Last updated on Feb 28, 2022

PMdataX - PubMed data eXtraction

A command-line tool to fetch data from articles available on PubMed

Last updated on Feb 28, 2022

Speech-to-Text pipeline

A personal use pipeline integrating Google Cloud services to transcribe audio files

Last updated on Feb 28, 2022

Word2Vec on ASD papers

Word2Vec word embedding analysis on Autism Spectrum Disorder (ASD) articles abstracts available on PubMed

Scientific Publications

A comprehensive bioinformatics analysis of circRNA expression in the brain of distinct mouse models of Autism Spectrum Disorder

Guilherme Bauer Negrini, Guilherme Cordenonsi da Fonseca, Carmem Gottfried

Brain morphometric and metabolic changes in Subjective Cognitive Decline individuals

Andrei Bieger, Laura Willers Souza, Wyllians Vendramini Borelli, Guilherme Bauer Negrini, Guilherme Povala, Marco Antônio De Bastiani, Cécile Tissot, João Pedro Ferrari‐Souza, Raphael Machado Castilhos, Diogo O Souza, Pedro Rosa‐Neto, Tharick A Pascoal, Artur Francisco Schumacher‐Schuh, Jonathan M DuBois, Eduardo R Zimmer

Usability evaluation of circRNA identification tools: Development of a heuristic-based framework and analysis

Guilherme Bauer Negrini, Guilherme Cordenonsi da Fonseca, Carmem Gottfried, Juliana Herbert

Resveratrol Prevents Cytoarchitectural and Interneuronal Alterations in the Valproic Acid Rat Model of Autism

Júlio Santos-Terra, Iohanna Deckmann, Giovanna Carello-Collar, Gustavo Della-Flora Nunes, Guilherme Bauer Negrini, Gustavo Brum Schwingel, Mellanie Fontes-Dutra, Rudimar Riesgo, Carmem Gottfried

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