Natalia Faraj Murad

San Francisco · CA · nataliafmurad@gmail.com

I am a highly skilled bioinformatician and data scientist with a strong background in genetics and molecular biology. My professional journey includes working as a Postdoctoral Researcher at the Buck Institute for Research on Aging, where I focused on bioinformatics analysis of various types of omics data to identify aging signatures and biomarkers.

My expertise also extends to statistical analysis, experimental design, and the development of machine learning models and automated pipelines for large-scale data analysis. Throughout my academic journey, I received prestigious research grants and has published numerous articles in esteemed scientific journals.

In addition to my research expertise, I have continuously pursued professional development, completing various courses in data science, genomic data analysis, Python, big data, and more. I possess advanced programming skills in R, Python, SQL, and Bash, and I'm proficient in tools such as Docker, Snakemake, Bioconductor, and machine learning libraries. With a strong foundation in bioinformatics, data analysis, and research methodologies, I am well-equipped to contribute to cutting-edge scientific projects and make significant advancements in the field of biological research.

Experience

Data Scientist & Bioinformatician

Buck Institute for Research on Aging

Bioinformatics analysis of different types of data like metabolomics, scRNA-seq, bulk RNA-seq, spatial transcriptomics, metabolomics data, multiomics. Analyzing data to identify senescent biomarkers, brain disease association factors, aging signatures.

January 2022 - Present

Data Scientist

University of Campinas

Data management, statistical analysis, and bioinformatics. My work involved identifying genes related to biomass yield and bioethanol production, as well as exploring the influence of microorganisms on ethanol production through metagenomics analysis. I also colaborated writing grants and administrative support.

September 2018 - October 2021

Education

University of Campinas

PhD in Genetics & Molecular Biology - Bioinformatics
Thesis: Gene regulatory networks to identify adaptations of two Spodoptera frugiperda strains to different diets

Activities: I focused on gene regulatory networks and multiomics analysis. I developed innovative methods to improve the identification of responses to different diets and conditions in S. frugiperda (a moth). My research involved integrating biological data at various levels, utilizing SQL databases, and applying clustering methods and enrichment analyses.

March 2013 - March 2018

University of Campinas

MSc in Genetics & Molecular Biology - Bioinformatics
Dissertation: Gene regulatory networks of the sucrose metabolism in sugarcane using bayesian networks

Activities: I identified the genes closely interacting with the sucrose phosphate synthase which helps to develop strategies to improve sugarcane for sugar and alcohol production. I mapped how the genes related to sugar production were changing their expression in response to cold as well as which pathways were being affected.

March 2011 - March 2013

Federal University of Lavras

Bachelor of Biological Sciences
Dissertation: Mixed models applied to microarray data in humans

Activities: I applied different approaches of Mixed Linear Models to microarray data and evaluated which strategy was working better. It allowed to develop my own pipeline for microarray data analysis as well as model fitting evaluation.

August 2002 - May 2006

Skills

Programming Languages & Tools
Workflow
  • Data analysis: RNA-seq, Single-cell, ATAC-seq, Spatial transcriptomics, Proteomics, Metabolomics, Metagenomics (shotgun & 16S)
  • Multi-omics, Data integration, Systems Biology
  • Machine Learning & Predictive Models: Supervised, Unsupervised and Reinforcement methods. Linear models, k-neighbors, k-means, SVM, Decision trees, Random forest, Boosting (XgBoost, LightGBM) etc.
  • Data Management & Data Manipulation: pandas, numpy, scipy, dplyr, reshape, data.table, tidyR, SQL tools and more.
  • Automated Pipelines: Snakemake, Singularity, Docker, Shell/Bash/AWK scripts, R/Python scripts.

Interests

Besides being a scientist, I like to be active most of the time. I practice exercises every day. I like going to the gym to do weight training and also practice body combat or boxing. I love outdoor sports like running or cycling. I like being in contact with nature, going for hikes and discovering different places, watching the sunset or the stars.

I spend a lot of my free time reading or watching videos about philosophy, psychology and self-improvement. I'm very curious about time, the universe, how everything follows patterns and whether it's possible to predict the future. So I also like to read physics and probability.

Publications

  • Murad, N. F.; Silva-Brandão, K. L.; Brandão, M. M. Mechanisms behind polyphagia in a pest insect: Responses of Spodoptera frugiperda (J.E. Smith) strains to preferential and alternative larval host plants assessed with gene regulatory networks. BBA Gene Regulatory Mechanisms. 2021. [DOI: 10.1016/j.bbagrm.2021.194687] [PMID: 33561559]
  • Murad, N.F.; Brandão,M.M. Probabilistic Graphical Models Applied to Biological Networks.In: Vischi Winck, F. (eds) Advances in Plant Omics and Systems Biology Approaches. Advances in Experimental Medicine and Biology, vol 1346. Springer, Cham. 2022. [DOI: 10.1007/978-3-030-80352-0_7]
  • SenNet Consortium. NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health. Nature Aging. 2022. [DOI: 10.1038/s43587-022-00326-5] [PMID: 36936385]
  • Markov, N. T.; Lindbergh, C. A.; Staffaroni, A. M.; Perez, K.; Stevens, M.; Nguyen, K.; Murad, N. F.; Fonseca, C.; Campisi, J.; Kramer, J.; Furman, D. Age-related brain atrophy is not a homogenous process: Different functional brain networks associate differentially with aging and blood factors. PNAS. 2022. [DOI: 10.1073/pnas.2207181119] [PMID: 36459652]
  • Ciamponi, F. E.; Procopio, D. P.; Murad, N. F.; Franco, T. T.; Basso, T. O.; Brandão, M. M. Multi-omics network model reveals key genes associated with p-coumaric acid stress response in an industrial yeast strain. Scientific Reports. 2022 [DOI: 10.1038/s41598-022-26843-2] [PMID: 36577778]
  • Almeida, D. A.; Horta, M. A. C.; Ferreira-Filho, J. A.; Murad, N. F.; De Souza, A. P. The synergistic actions of hydrolytic genes reveal the mechanism of Trichoderma harzianum for cellulose degradation. Journal of Biotechnology. [DOI: /10.1016/j.jbiotec.2021.05.001] [PMID: 33992696]
  • Ferreira Filho, J. A., Horta, M. A. C., dos Santos, C. A.; Almeida, D. A.; Murad, N. F.; Mendes, J. S.; Sforça, D. A.; Silva, C. B. C.; Crucello, A.; Souza, A. P. Integrative genomic analysis of the bioprospection of identifying biomarkers regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum). BMC Genomics 21, 757, 2020. [DOI: 10.1186/s12864-020-07158-w] [PMID: 33138770] [PMCID: PMC7607812]
  • Silva-Brandão, K. L; Murad, N. F.; Peruchi, A.; Martins, C. H. Z.; Omoto, C.; Figueira, A.; Brandão, M. M.; Trigo, J. R. Transcriptome differential co-expression reveals distinct molecular response of fall-armyworm strains. Pest Management Science. v.76, p.ps.6051, 2020. [DOI:10.1002/ps.6051] [PMID: 32815313]
  • Horta, M. A. C.; Filho, J. A. F.; Murad, N. F.; De Oliveira Santos, E.; Dos Santos, C. A.; Mendes, J. S.; Brandão, M. M.; Azonni, S. F.; De Souza, A. P. Network of proteins, enzymes and genes linked to biomass degradation shared by Trichoderma species. Scientific Reports. v.8, p.1341, 2018. [DOI: 10.1038/s41598-018-19671- w] [PMID: 29358662] [PMCID: PMC5778038]
  • Silva-Brandão, K. L.; Peruchi, A.; Seraphim, N.; Murad, N. F.; Carvalho, R. A.; Farias, J. R.; Omoto, C.; Cônsoli, F. L.; Figueira, A.; Brandão, M. M. Loci under selection and markers associated with host plant and host-related strains shape the genetic structure of Brazilian populations of Spodoptera frugiperda (Lepidoptera, Noctuidae). PLoS One. v. 13, p.e0197378, 2018. [DOI: 10.1371/journal.pone.0197378] [PMID: 29787608] [PMCID: PMC5963752]
  • Bajay, S. K.; Cruz, M. V.; Silva, C. C.; Murad, N. F.; Brandão, M. M.; Souza, A. P. Extremophytes under climate change scenarios: Transcriptional coordination of genes reveals distinct selective responses to equatorial and subtropical environments. Frontiers in Plant Science. v.9, p.1376, 2018. [DOI: 10.3389/fpls.2018.01376] [PMID: 30283484] [PMCID: PMC6156123]