Skip to content
View imarranz's full-sized avatar
💭
Working on my Doctoral Thesis
💭
Working on my Doctoral Thesis

Highlights

  • Pro
Block or Report

Block or report imarranz

Block user

Prevent this user from interacting with your repositories and sending you notifications. Learn more about blocking users.

You must be logged in to block users.

Please don't include any personal information such as legal names or email addresses. Maximum 100 characters, markdown supported. This note will be visible to only you.
Report abuse

Contact GitHub support about this user’s behavior. Learn more about reporting abuse.

Report abuse
imarranz/README.md

👨‍💻 About Me

Hi 👋, I'm Ibon

I am Ibon Martínez-Arranz and I got my BSc. in Mathematics from the University of the Basque Country (EHU/UPV) and performed a MSc. in Current Applied Statistics Techniques and a MSc. in Mathematical Modeling Research, Statistical Analysis and Computing Sciences. In 2004, I joined the Basque Country Health Service (The Department of Health of the Basque Country Government and Osakidetza) as a data analyst and my work was mainly focused on the epidemiological report of renal patients. When I joined OWL Metabolomics in 2010, first I worked as a researcher in the Metabolomics Department and in 2017, I became the head of the Data Science Department, being responsible for prediction and statistical computation management since then. This high experience provide support to metabolomics services, laboratory processes, data handling, R&D projects and technology transfer processes.

Education
INSTITUTION
AND LOCATION
DEGREE COMPLETION
DATE
FIELD OF
STUDY
University of Basque Country (UPV/EHU) (Biscay, Spain) BSc. 06/2003 Mathematics
National University of Distance Education (Spain) Expert degree 07/2007 Statistics Applied to Health Sciences
National University of Distance Education (Spain) Expert degree 07/2008 Advanced Methods of Applied Statistics
National University of Distance Education (Spain) MSc. 07/2012 Current Applied Statistics Techniques
National University of Distance Education (Spain) Expert degree 07/2013 Multivariate Statistical Techniques
University of Basque Country (UPV/EHU) (Biscay, Spain) MSc. 05/2016 Mathematical Modeling, Statistical Analysis and Computation
University of basque Country (UPV/EHU) (Biscay, Spain) Ongoing PhD. Expected 2024 Applied Mathematics

Currently, I am doing a doctoral thesis entitled Genetic Algorithms Applied to Translational Strategy in NASH. Learning from Mouse Models in which I apply 🧬 genetic algorithms 🧬 for the selection of NAFLD subtypes. This procedure could be applied to any disease that is based on metabolic changes. This work also has implications in the field of precision medicine.

Contributions to Science
Author of 24 publications. Scopus H-index = 16. Researcher unique identifier

Data Science of 'omics' data

'Omics' research generates a large amount of data for every sample. OWL has established a well-defined workflow and a set of guidelines for analyzing omics data. It includes statistical design of experiments, data structuration and predictive modelling.

Peer-reviewed papers:

  1. Martínez-Arranz, I, et al. Enhancing metabolomics research through data mining, J. Proteomics, 2015;127(B)275-288.
  2. Barr J, et al. Obesity-dependent metabolic signatures associated with nonalcoholic fatty liver disease progression. J. Proteome Res 2012;11(4),2521-32
  3. Arbelaiz A, et al. Serum extracellular vesicles contain protein biomarkers for primary sclerosing cholangitis and cholangiocarcinoma. Hepatology. 2017; 10.1002/hep.29291.
  4. Cano A, et al. A Metabolomics Signature Linked To Liver Fibrosis In The Serum Of Transplanted Hepatitis C Patients. Scientific Reports. 2017;7(1):10497.

Predictive algorithms for disease diagnosis

We have developed predictive algorithms for several diseases. We have been really involved in the development and validation of the OWLiver, OWLiver F2+ and OWLiver DM2 tests.

Peer-reviewed papers:

  1. Barr J, et al. Obesity-dependent metabolic signatures associated with nonalcoholic fatty liver disease progression. J. Proteome Res. 2012;11(4):2521-32.
  2. Cano A, et al. A Metabolomics Signature Linked To Liver Fibrosis In The Serum Of Transplanted Hepatitis C Patients. Scientific Reports. 2017;7(1):10497.
  3. Herreros-Villanueva M, et al. Plasma MicroRNA Signature Validation for Early Detection of Colorectal Cancer. Clin Transl Gastroenterol. 2019 Jan;10(1).
  4. Matorras R, et al. The lipidome of endometrial fluid differs between implantative and non-implantative IVF cycles. J Assist Reprod Genet. 2020;37(2):385-94.
  5. Martínez-Arranz I, et al. Metabolomic-based noninvasive serum test to diagnose nonalcoholic steatohepatitis: Results from discovery and validation cohorts. Hepatol Commun. 2018 May 4;2(7):807-820.

Selected publications focused in Machine Learning and Modelling (within last 5 years)

Peer-reviewed papers:

  1. Alonso C, et al. Metabolomic Identification of Subtypes of Nonalcoholic Steatohepatitis. Gastroenterology 2017;152(6):1449-61.
  2. Iruarrizaga-Lejarreta M, et al. Role of Aramchol in steatohepatitis and fibrosis in mice. Hepatology Communications 2017;1(9):911-27.
  3. Banales JM, et al. Serum metabolites as diagnostic biomarkers for cholangiocarcinoma, hepatocellular carcinoma and primary sclerosing cholangitis. Hepatology 2019;70(2):547-65.
  4. Herreros-Villanueva M, et al. Plasma MicroRNA Signature Validation for Early Detection of Colorectal Cancer. Clin Transl Gastroenterol. 2019 Jan;10(1).
  5. Matorras R, et al. The lipidome of endometrial fluid differs between implantative and non-implantative IVF cycles. J Assist Reprod Genet. 2020;37(2):385-94.
Skills
TOPIC SOFTWARE SKILLS
Programming Languages for Data Science Python
R
SQL
🟥🟥🟥🟥🟥
🟥🟥🟥🟥⬜
🟥🟥🟥🟥⬜
Data Analysis Pandas
Pingouin
🟥🟥🟥🟥🟥
🟥🟥🟥🟥🟥
Data Computation Numpy
Scipy
🟥🟥🟥🟥🟥
🟥🟥🟥🟥⬜
Data Bases MySQL
SQLite
MongoDB
🟥🟥🟥⬜⬜
🟥🟥🟥🟥⬜
🟥🟥⬜⬜⬜
Machine Learning Scikit-Learn 🟥🟥🟥🟥⬜
Big Data H2O 🟥🟥🟥🟥⬜
Visualization Tools Matplotlib
Seaborn
Altair
🟥🟥🟥🟥⬜
🟥🟥🟥🟥🟥
🟥🟥🟥🟥⬜
Web Shiny
Streamlit
🟥🟥🟥🟥⬜
🟥🟥🟥⬜⬜
Patents and Pendings
PUBLICATION
NUMBER
TITLE INTERNATIONAL
FILING DATE
WO2021028562 Lipid signatures for determining the outcome of embryo implantation during in vitro fertilization 14.08.2020
WO2018007511 Diagnostic methods based on lipid profiles 06.07.2017
WO2018007422 Identification of human Non-Alcoholic Fatty Liver Disease (NAFLD) subtypes 05.07.2017
WO2017055397 Metabolomic signature of diagnosis and disease progression in Non-Alcoholic Fatty Liver Disease (NAFLD) 29.09.2016

🔬 Scientific Production

Pubmed ORCID Scopus Kaggle

Publications

🟨 NAFLD Disease 🟩 Subtypes 🟧 Machine Learning and Modelling 🟪 In Vitro Diagnostic test

ARTICLE DOI PURPOSE
Serum identification of At-Risk MASH: The Metabolomics-Advanced steatohepatitis fibrosis score (MASEF) 🟨🟧🟪
Role of Intracellular Drug Disposition in the Response of Acute Myeloid Leukemia to Cytarabine and Idarubicin Induction Chemotherapy. (2023) 🟧
Metabolic subtypes of nonalcoholic fatty liver disease patients exhibit distinctive cardiovascular risk profiles. (2022) 🟨🟩🟧
A Novel Serum Metabolomic Profile for the Differential Diagnosis of Distal Cholangiocarcinoma and Pancreatic Ductal Adenocarcinoma. (2020) 🟧
Agonist of RORA Attenuates Nonalcoholic Fatty Liver Progression in Mice via Up-regulation of MicroRNA 122. (2020) 🟨
CA19-9 capability as predictor of pancreatic cancer resectability in a Spanish cohort. (2020) 🟧
The lipidome of endometrial fluid differs between implantative and non-implantative IVF cycles. (2020) 🟧
Metabolomics Discloses a New Non-invasive Method for the Diagnosis and Prognosis of Patients with Alcoholic Hepatitis. (2019) 🟨🟧🟪
Plasma MicroRNA Signature Validation for Early Detection of Colorectal Cancer. (2019) 🟧
Metabolomics discloses potential biomarkers to predict the acute HVPG response to propranolol in patients with cirrhosis. (2019) 🟧
Serum Metabolites as Diagnostic Biomarkers for Cholangiocarcinoma, Hepatocellular Carcinoma, and Primary Sclerosing Cholangitis. (2019) 🟧
Obeticholic Acid Modulates Serum Metabolites and Gene Signatures Characteristic of Human NASH and Attenuates Inflammation and Fibrosis Progression in Ldlr-/-.Leiden Mice. (2018) 🟩
Targeted UPLC-MS Metabolic Analysis of Human Faeces Reveals Novel Low-Invasive Candidate Markers for Colorectal Cancer. (2018) 🟧
Metabolomic-based noninvasive serum test to diagnose nonalcoholic steatohepatitis: Results from discovery and validation cohorts. (2018) 🟨🟧🟪
Use of a metabolomic approach to non-invasively diagnose non-alcoholic fatty liver disease in patients with type 2 diabetes mellitus. (2018) 🟨🟧🟪
Role of Aramchol in steatohepatitis and fibrosis in mice. (2017) 🟨🟩🟧
A Metabolomics Signature Linked To Liver Fibrosis In The Serum Of Transplanted Hepatitis C Patients. (2017) 🟧
Metabolomic Identification of Subtypes of Nonalcoholic Steatohepatitis. (2017) 🟨🟩🟧
Data in support of enhancing metabolomics research through data mining. (2015) 🟧
Enhancing metabolomics research through data mining. (2015) 🟧
Excess S-adenosylmethionine reroutes phosphatidylethanolamine towards phosphatidylcholine and triglyceride synthesis. (2013) 🟧
Solute carrier family 2 member 1 is involved in the development of nonalcoholic fatty liver disease. (2013) 🟧
Obesity-Dependent Metabolic Signatures Associated with Nonalcoholic Fatty Liver Disease Progression. (2012) 🟨🟧

🔍 More Details

  • 📌 I’m currently working as 📊 Senior Data Scientist 📊 @ OWL Metabolomics.
  • 📌 I’m currently learning Streamlit, Panel and MongoDB, ...
  • 📌 I'm interested in: 👨‍🔬 Data Science 🐍 Python 🐼 Pandas 🤖 Machine Learning 🗂️ SQL and DataBases 📊 Data Analysis 🚀 SKlearn
  • 📌 I want to learn about: ⚙️ awk
  • 📌 I use daily: .ipynb, .py, .sql, .sqlite, .yaml, .R, .tex, ...
  • 📌 Ask me about 🧬 Genetic Algorithms 🧬
  • 📌 I Love Data Visualization 📊📈📉.
  • 📌 Fun fact: I'm a huge fan of The Lord of the Rings and LEGO®

🚀 Personal Projects


🔥 GitHub Stats


📫 How to Reach Me

Github Twiter Gmail LinkedIn

Pinned

  1. pygenmet pygenmet Public

    Genetic Algorithms Applied to Translational Strategy in NASH. Learning from Mouse Models

    Python

  2. pygenmet-manual pygenmet-manual Public

    Manual of PYGENMET a Genetic Algorithms Applied to Translational Strategy in NASH.

  3. personal-cv personal-cv Public

    My Personal Resume

    Shell

  4. mcm mcm Public

    Tool to analyze a confusion matrix from performance of a classification model.

    Jupyter Notebook 1

  5. eda-course eda-course Public

    Exploratory Data Analysis Course

    HTML

  6. data-science-workflow-management data-science-workflow-management Public

    This repository is a collection of code, documentation, and other resources that support the management and automation of a Data Science project.

    Makefile 1