Guilherme Bauer Negrini

Biomedical Data Scientist

I am deeply fascinated by biological and health sciences, especially data analysis, data visualization, bioinformatics, and biomedical software.

My research projects and interests are currently focused on non-coding RNAs in neurodevelopmental disorders and Human-Computer Interaction applied to bioinformatics software development.

Read more about me

Interests

Neuroscience
Data Science
Bioinformatics
Human-Computer Interaction

Education

PhD in Biochemistry, 2018 - current

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

How to run FreeSurfer on Windows with WSL2

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

freesurfer_wrapper

freesurfer_wrapper aims to facilitate the creation of a multiprocessing pipeline using FreeSurfer. It is a Python wrapper to execute parallel runs of recon-all and some pial edits algorithms.

Interaction Design Patterns for Bioinformatics

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

Tolkien character or prescription drug name?

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

HL7® FHIR® server using Cloud Healthcare API

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

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

Hebbie Ann

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

PMdataX - PubMed data eXtraction

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

Speech-to-Text pipeline

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

Word2Vec on ASD papers

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

Scientific Publications

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

The role of T-cells in neurobehavioural development: Insights from the immunodeficient nude mice

Guilherme Bauer Negrini, Iohanna Deckmann, Gustavo Brum Schwingel, Mauro Mozael Hirsch, Mellanie Fontes-Dutra, Giovanna Carello-Collar, Diane E Halliwell, Maria Paraskevaidi, Camilo L M Morais, Francis L Martin, Rudimar Riesgo, Carmem Gottfried, Victorio Bambini-Junior

Resveratrol prevents brain edema, blood–brain barrier permeability, and altered aquaporin profile in autism animal model

Iohanna Deckmann, Mellanie Fontes-Dutra, Júlio Santos-Terra, Marília Körbes-Rockenbach, Guilherme Bauer Negrini, Gustavo Brum Schwingel, Rudimar Riesgo, Victorio Bambini-Junior, Carmem Gottfried

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