Maria Beatriz

Postdoc Maria Beatriz Walter Costa from Brazil starts in the VEO Group

Building models to understand the association between bacterial genomes and their environments
Maria Beatriz
Image: Maria Beatriz Walter Costa
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Published: | By: Sybille Huck

Introduction

Bia Walter Costa is a Bioinformatician and focuses on data analysis using Bioinformatics tools such as linux, python and bash. Her major interest is in extracting valuable information from biological data. For that she collaborates with specialists from different areas of biology.

In our group, she will apply machine learning to connect bacterial genomes to their environments. She is using labelled data to build models. With this, she wants to better understand how certain genomic features of bacteria allow them to survive in different environments. 

Career path

Career Path

Image: Maria Beatriz Walter Costa

Representative research

The SSS-test, Selection on the Secondary Structure test, is one representative research of Bia Walter Costa. This test was the first in the scientific community that could detect positive selection in ncRNA structures. She developed it to address an important demand in the field of RNA evolution. Previous research focused on structural conservation, which is used to find functional molecules. However, no tool existed to find positive selection within a conserved group. Bia's tool calculates selection scores based on nucleotide mutations and indels that impact the structure. By applying this tool in ~15 000 long ncRNA orthologs of primates, she found a small set of ~110 human long ncRNAs that have signs of positive selection. This analysis helped colleagues of experimental fields to explore molecules that are important for species-specific traits.

Local structure orthologs of long ncRNA LINC02217. The structure of a) humans has a positive selection signal and is clearly different than the conserved structures of b) chimpanzee/bonobo and c) gorilla. The selection signal was detected by the SSS-test.

Image: Maria Beatriz Walter Costa

Publications

  1. M. B. Walter Costa*, C. Gärtner*, M. Schmidt, T. Berg, D. Seehofer and  T. Kaiser (2023): “Revising the MELD Score to Address Sex-Bias in Liver Transplant Prioritization for a German Cohort”External link, Journal of Personalized Medicine 13(6), doi: https://doi.org/10.3390/jpm13060963External link.
  2. M. B. Walter Costa*, M. Wernsdorfer M*, A. Kehrer A, et al (2021): "The Clinical Decision Support System AMPEL for Laboratory Diagnostics: Implementation and Technical Evaluation"External link, JMIR Medical Informatics 9(6),doi: https://doi.org/10.2196/20407External link.
  3. M. B. Walter Costa, C. Höner zu Siederdissen, M. Dunjić, P. Stadler, K. Nowick (2019): "SSS-Test: A novel test for detecting selection on the secondary structures of non-coding RNAsExternal link", BMC Bioinformatics 20(151), doi: https://doi.org/10.1186/s12859-019-2711-yExternal link.
  4. M. B. Walter Costa, C. Höner zu Siederdissen, D Tulpan, P. Stadler, K. Nowick (2018): "Temporal ordering of substitutions in RNA evolution: Uncovering the structural evolution of the Human Accelerated Region 1"External link, Journal of Theoretical Biology 438: 143-150, doi: https://doi.org/10.1016/j.jtbi.2017.11.015External link.
  5. A. Q. Maranhão, M. B. Costa, L. Guedes, P. M. Moraes-Vieira, T. Raiol, M. M. Brigido (2013): "A Mouse variable gene fragment binds to DNA independently of the BCR context: A Possible role for immature B-Cell repertoire establishmentExternal link", Plos One. doi: https://doi.org/10.1371/journal.pone.0072625External link.

*equal contribution