Guilherme Bauer Negrini

Biomedical Data Scientist | Scientific Software Developer

I am a biomedical scientist, a PhD candidate in biochemistry and an undergraduate student in biomedical informatics. My interests are mostly related to biological and health sciences, including data analysis, data visualization, bioinformatics, and biomedical software.

My research projects involve RNA sequencing data analysis and usability evaluation of bioinformatics tools. I am deeply interested in software engineering and human-computer interaction applied to bioinformatics and scientific software development.

You can know a little more about me here.

Interests

Neuroscience
Data Science
Bioinformatics
Human-Computer Interaction

Education

PhD in Biochemistry, 2018 - 2022
Universidade Federal do Rio Grande do Sul (UFRGS)
BSc in Biomedical Informatics, 2018 - 2022
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

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

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

Effects of single-dose antipurinergic therapy on behavioral and molecular alterations in the valproic acid-induced animal model of autism

Mauro Mozael Hirsch, Iohanna Deckmann, Júlio Santos-Terra, Gabriela Zanotto Staevie, Mellanie Fontes-Dutra, Giovanna Carello-Collar, Marília Körbes-Rockenbach, Gustavo Brum Schwingel, Guilherme Bauer Negrini, Bruna Rabelo, Maria C.B. Gonçalves, Juliana Corrêa-Velloso, Yahaira Naaldijk, Ana R. Castillo, Tomasz Schneider, Victorio Bambini-Junior, Henning Ulrich, Carmem Gottfried

Abnormal empathy-like pro-social behaviour in the valproic acid model of autism spectrum disorder

Mellanie Fontes-Dutra, Gustavo Della-Flora Nunes, Júlio Santos-Terra, Walquíria Souza-Nunes, Guilherme Bauer Negrini, Mauro Mozael Hirsch, Lily Green, Rudimar Riesgo, Carmem Gottfried, Victorio Bambini-Junior

See all publications

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