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Daniel Ruiz-Perez

Computer Scientist

Who am I?

I recently graduated with a Ph.D. in computer science from Florida International University with the best GPA (4.0) and the Overall Outstanding Graduate Student Award. There I worked at the Bioinformatics Research Group (BioRG). My research was on modeling multi-omic heterogeneous causal interactions from temporally misaligned longitudinal data under a Dynamic Bayesian Network framework.

About me

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I'm also a judo black belt!

Life is about balance. Because I spend most of my day working, I do as many outdoor activities as possible in my free time. I like boating, doing different sports, going out on adventures and visiting as many new places as I can. I am a certified judo instructor with years of teaching and coaching experience.

I am a member of Golden Key International Honour Society, Upsilon Pi Epsilon Honor Society, IEEE, ACM and the Microbiology Society and an alumnus of Lambda Chi Alpha fraternity.

Want to know about my professional life instead?

You can see my activity on my live GitHub chart below:

Daniel's updated Github contributions chart

Or check out my résumé! (Last updated 01/01/2021)

Download Résumé
Size: 273 kB

Experience

SF (USA)

2021-

Facebook

Incoming ML Research Scientist

Team to be decided.

2020-2020

ML SWE Intern (Ph.D.)

Summer internship at the Facebook App Monetization Ranking team. Designed, built, and evaluated a ML experimental ranking framework to allow user-specific ads personalization, increasing revenue.

Miami (USA)

2019-2019

Assurant

Data Analyst Intern

Summer internship at the Advanced Data Analytics team. Spearheaded the architecture design and implementation of the end-to-end migration of all on-premise systems to Azure Cloud Ecosystem.

Miami (USA)

2020-2020



2016-2020

Florida International University

Dissertation Year Fellow

Interaction inference and causal discovery on multi-omics time-series microbiome data.

Graduate Assistant

TA of Graduate Theory of Computation, Operating Systems Principles, Intro to Data Mining, Intro to Microcomputers, and Academic Success Initiative Ambassador for 4 courses.

A Coruña (ESP)

2015-2016

ALDABA IT and Services

Software Engineer

Analysis, design, implementation and maintenance of an expert system in Java IBM ODM, a radioactive alarm system, and web application in a SCRUM team.

A Coruña (ESP)

2014-2015

University of A Coruña

Undergraduate Research Assistant

Use of machine learning to analyze genomic data and development of a bioinformatic platform accessible at chromevol.fiu.edu.

Education

Miami (USA)

Dec 2020

Florida International University

Ph.D. Computer science. 4.0 GPA (Top 1%)

Miami (USA)

Dec 2019

Florida International University

M.S. Computer Science. 4.0 GPA (Top 1%)

Coruña (ESP)

Jun 2016

University of A Coruña

M.E. Software Engineering. 3.5 GPA (Top 5%)

Coruña (ESP)

Jun 2015

University of A Coruña

B.S. Computer Science. 3.4 GPA (Top 5%)

Research Work

Journal publications:

  1. Ruiz-Perez, Lugo-Martinez, Bourguignon, Mathee, Lerner, Bar-Joseph, Narasimhan (2020). Dynamic Bayesian networks for integrating multi-omics time-series microbiome data. BiorXiv preprint DOI: 10.1101/835124
  2. Lugo-Martinez†, Ruiz-Perez†, Narasimhan, Bar-Joseph (2019). Dynamic interaction network inference from longitudinal microbiome data. BMC Microbiome, 7:54. †Equal contribution.
  3. Ruiz-Perez, Guan, Madhivanan, Mathee, Narasimhan (2020). So you think you can PLS-DA? BMC Bioinformatics 21, 2.
  4. Sazal, Ruiz-Perez, Cickovski, Narasimhan (2020). Inferring Relationships in Microbiomes from Signed Bayesian Networks. BMC Genomics 21, 663.
  5. Coudray, Ruiz-Perez, Colbert, Krupp, Kumari, Narasimhan, Mathee, Madhivanan (2019) Effect of metronidazole on microbiomes associated with asymptomatic bacterial vaginosis (abstract). Access Microbiology, 1(1A)

Conference proceedings:

  1. Lugo-Martinez, Ruiz-Perez, Narasimhan, Bar-Joseph (2019). Dynamic interaction network inference from longitudinal microbiome data. SMBE at Manchester, UK.
  2. Ruiz-Perez, Lugo-Martinez, Bourguignon, Lerner, Bhansali, Bar-Joseph, Narasimhan, Mathee (2019). Temporal interactions of genes, taxa, and metabolites of the microbiota in patients with inflammatory bowel disease. Asian Conference on Transcription at Dunedin, Otago, New Zealand.
  3. Ruiz-Perez, Guan, Madhivanan, Mathee, Narasimhan (2018). So you think you can PLS-DA?. International Conference on Computational Advances in Bio and medical Sciences (ICCABS) at Las Vegas, NV, USA.
  4. Sazal, Ruiz-Perez, Cickovski, Narasimhan (2018). Inferring Relationships in Microbiomes from Signed Bayesian Networks. ICCABS, Las Vegas, NV, USA.
  5. Ruiz-Perez, Colbert, Coudray, Mathee, Madhivanan, Narasimhan. (2018). Vaginal microbial profile of women with asymptomatic bacterial vaginosis in US. Microbiology Society Annual Conference at Birmingham, UK.

Posters:

  1. Ruiz-Perez, Sazal, Park, Cickovski, Lee, Cho, Hwang, Narasimhan (2019). Role of gut microbiota and their temporal interactions in kidney transplant recipients. LXAI at NeurIPS, Vancouver, Canada.
  2. Sazal, Ruiz-Perez, Valdes, Cickovski, Stebliankin, Mehta, Mathee, Narasimhan (2019). Signed Causal Bayesian Networks for Microbiomes. LXAI at NeurIPS, Vancouver, Canada.
  3. Lugo-Martinez, Ruiz-Perez, Narasimhan, Bar-Joseph (2019). Dynamic interaction network inference from longitudinal microbiome data. RECOMB at Washington, DC, USA.
  4. Coudray, Ruiz-Perez, Colbert, Krupp, Kumari, Mathee, Narasimhan (2019). P371 Effect of metronidazole treatment on recurrent and persistent bacterial vaginosis: a pilot study. The BMJ Sexually Transmitted Infections;95:A187
  5. Madhivanan, Coudray, Ruiz-Perez, Colbert, Krupp, Kumari, Mathee, Narasimhan (2019). P372 Bacterial vaginosis and high-risk human papillomavirus coinfection among African American women in the United States. The BMJ Sexually Transmitted Infections;95:A188.
  6. Madhivanan, Coudray, Ruiz-Perez, Colbert, Krupp, Kumar, Narasimhan, Mathee (2019). P373 Co-occurrence of bacterial vaginosis and Trichomonas vaginalis among young African American women. The BMJ Sexually Transmitted Infections;95:A188.
  7. Lugo-Martinez, Ruiz-Perez, Narasimhan, Bar-Joseph (2019). Dynamic interaction network inference from longitudinal microbiome data. ACM-BCB at Niagara Falls, NY, USA.
  8. Colbert, Coudray, Ruiz-Perez, Kumari, Madhivanan, Narasimhan, Mathee. (2018). To Treat or Not to Treat: Bacterial Vaginosis and its Relationship to Human Papillomavirus. Microbiology Society Annual Conference at Birmingham, UK.
  9. Suarez-Ulloa, Aguiar-Pulido, Ruiz-Perez, Narasimhan, Eirin-Lopez (2016). Network-based analysis of chromatin-associated gene expression dynamics in response to environmental stress. ISMB at Orlando, USA.

Academic Ancestors: [Courtesy of the Mathematical Genealogy Project] Giri Narasimhan (1989), Rachel Manber (1982), Victor Klee (1949), Edward McShane (1930), Lawrence Graves (1924), Gilbert Bliss (1900), Oskar Bolza (1886), C. Felix Klein (1868), Rudlof Lipschitz (1853), Gustav Dirichlet (1827), Julius Plucker (1823), Jean-Baptiste Fourier (?), Christian Gerling (1812), Martin Ohm (1811), Simeon Poisson (?), Carl Gauss (1799), Jospeh Lagranage (no degree), Johann Pfaff (1786), Karl von Langsdorf (1781), Abraham Kaestner (1739), Leonhard Euler (1726), Christian Hausen (1713), Johann Bernoulli (1694), Jacob Bernoulli (?), Johann Wichmannshausen (1685), Gottfried Leibniz (1666), Otto Mencke (1665), Erhard Weigel (1650).

Programming Languages & My Skills

Awards


  1. Overall Outstanding Graduate Student Award, SCIS, Florida International University, USA, 2020.
  2. Dissertation Year Fellowship, Florida International University, USA, 2019.
  3. Best Graduate Student in Teaching Award, Florida International University, USA, 2019.
  4. Charles Perry Graduate Scholarship, Florida International University, USA, 2019.
  5. Research Grant, Golden Key International Honor Society, 2019.
  6. Conference Travel Fellowships from:
    1. Conference on Neural Information Processing Systems (NeurIPS), 2019.
    2. NeurIPS LatinX in Artificial Intelligence (LXAI) Research Workshop, 2019.
    3. ACM-IMS Interdisciplinary Summit on the Foundations of Data Science, 2019.
    4. Michigan Institute for Data Science Consortium and Annual Symposium, 2019.
    5. International Conference on Computational Advances in Bio and medical Sciences (ICCABS), 2018
    6. FIU Graduate and Professional Student Committee: 2017 and 2018.
    7. FIU School of Computing and Information Sciences: 2017 and 2018.
  7. Golden Key full scholarship and best project award, International Scholar Laureate Program, 2018.
  8. Biomedical Research Initiative Award, Florida International University, USA, 2017.
  9. Graduate Assistantship, Florida International University, USA, 2016-Present.
  10. Undergraduate research scholarship, Ministry of Science and Education, Spain, 2015.
  11. Research learning fellowship, University of A Coruña, Spain, 2015.
  12. Graduated from high school with the highest honors. GPA: 3.98, 2011.
  13. Exceptional athlete recognition, Cambre City Council, 2007-2010.


Languages

languages