About

Biography

Hola! My name is Erick Armingol, and I am currently a Postdoctoral Fellow at the Wellcome Sanger Institute. I recently joined the Vento Lab, wherein my research focus is on placental development and the effect of menopause on homeostasis and the dynamic resilience of women. I also have a part-time participation in the Lotfollahi Lab, wherein I am developing AI-based methods to identify complex biology from multiomics data. By combining machine learning and state-of-the-art tools, I aim to find gene expression changes and elucidate how they impact the cellular metabolism and cell-cell interactions.

I did my PhD research in the Lewis Lab at the University of California, San Diego. There, I focused on developing methods for inferring cell-cell interactions from single-cell data.

My research interests are in using single-cell technologies for inferring cell-cell interactions, modeling metabolic fluxes, and analyzing signaling pathways.

Education
PhD in Bioinformatics and Systems Biology

University of California, San Diego (2018 - 2023)

Engineer in Molecular Biotechnology

Universidad de Chile (2009 - 2015)

BS in Molecular Biotechnology

Universidad de Chile (2009 - 2013)

Interests
  • Bioinformatics
  • Systems Biology
  • Biological Modeling
  • Machine Learning
  • Tool Development
You can find me in

Research

Cell-cell interactions and communication

Cell-cell interactions define high-order organizations in multicellular organisms, influencing their phenotypes. In this regard, I am interested in helping to understand how CCIs and phenotype are connected, in both a cellular and molecular level.

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Cellular metabolism

Cellular metabolism orchestrates the supply of resources and energy needed for the diversity of cellular functions. I aim to quantify metabolic activities within individual cells by using metabolic modeling and machine learning to understand physiological functions and dysregulation during aging and diseases.

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Publications

Featured publications, presentations and talks that are available online. A full list of publications is available in Google Scholar.

Review - The diversification of methods for studying cell–cell interactions and communication
This review describes the recent evolution in computational tools that underpin cell-cell interaction studies and discusses improvements in experimental methods enabling more high-throughput analyses. Featured on the cover of the June 2024 issue.

January 2024

Research Article - Inferring a spatial code of cell-cell interactions across a whole animal body
Here we present a computational framework to infer the spatial code underlying cell-cell interactions in a whole animal.

November 2022

Research Article - Context-aware deconvolution of cell-cell communication with Tensor-cell2cell
Here we present a novel computational tool based on tensor factorization to study how cell-cell communication changes across multiple contexts. In contrast to previous approaches, Tensor-cell2cell does not perform pairwise comparisons, and instead it considers all contexts simultaneously.

June 2022

Talk - Tensor-cell2cell: Desde la transcriptómica a entender cómo el contexto biológico afecta la comunicación intercelular
Talk for the seminars about single-cell transcriptomics applied to understand chronic diseases, organized by the Advanced Center for Chronic Diseases (ACCDiS) - Talk in Spanish.

August 2021

Talk - Computational resources for studying cell-cell communication
Talk for the 1st Human Cell Atlas Latin America Single Cell RNA-seq Data Analysis Workshop.

April 2021

Review - Deciphering cell-cell interactions and communication from gene expression
This review describes the state-of-the-art of the analyses used for inferring cell-cell interactions and communication from gene expression.

November 2020

Research Article - Understanding the impact of the cofactor swapping of isocitrate dehydrogenase over the growth phenotype of Escherichia coli on acetate by using constraint-based modeling
In this work, we used constraint-based modeling to investigate the effect of the cofactor swapping of ICDH in terms of energy production, response of alternative sources of NADPH, and partitioning of fluxes between ICDH and isocitrate lyase (ICL) -a crucial bifurcation when the bacterium grows on acetate-.

April 2018

Software/Tools

Computational suite for studying cell-cell interactions and communication

Computational suite implementing different methods to study cell-cell interactions from expression levels of genes/proteins

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Docker container for single-cell analyses

Docker container with a set of tools for single-cell transcriptomic analyses

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Utility for facilitating the use of COBRApy

Tool to facilitate the use of COBRApy and the manipulation of metabolic networks

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Research Training

Postdoctoral Fellow
Wellcome Sanger Institute

Postdoctoral fellow at the Vento Lab and part-time participation at the Lotfollahi Lab. Studying the placental development and the effect of menopause on homeostasis and the dynamic resilience of women.

November 2023 - Present
Graduate Researcher
University of California, San Diego

PhD Student in Bioinformatics & Systems Biology. Worked on inferring cell-cell interactions from gene expression at the Lewis Lab. First-year lab rotations were about:

  • Cell-cell interactions in the whole body of C. elegans (Dr. Nathan E. Lewis)
  • Machine learning for simulating protein expression from ME-models (Dr. Bernhard Palsson)
  • Relationship between microbiome composition and chronic diseases (Dr. Rob Knight)

September 2018 - July 2023
Undergraduate Researcher
Universidad de Chile

Worked on my thesis project for obtaining the degree of Engineer in Molecular Biotechnology. Research conducted at the Laboratory of Biochemistry and Molecular Biology at College of Sciences. Advisor: Dr. Ricardo Cabrera Paucar. Main points of the research include:

  • Used Datsenko & Wanner method to construct E. coli strains. Verification by sequencing the modified region.
  • Determined physiological parameters (growth rate, carbon source uptake rate and biomass yield) of different strains. Analyzed the concentration of carbon source by HPLC.
  • Simulated the metabolic behavior of strains. Used Flux Balance Analysis to explore the impact of mutations.

September 2013 – February 2015
Volunteer Undergraduate Researcher
Universidad de Chile

Flux Balance Analysis of the Escherichia coli icd-NAD strain. College of Sciences. Advisor: Dr. Ricardo Cabrera Paucar. Main points include:

  • Modeled the metabolic phenotype of an E. coli strain in different scenarios by using COBRA and Flux Balance Analysis.
  • Analyzed data after simulations on MATLAB and created “Flux-Array” on Python to visualize differences between two flux distributions.

March 2013 – July 2013
Volunteer Undergraduate Researcher
Universidad de Chile

Analysis of Humoral and Cell-Mediated immune response in blood of patients with malignant melanoma. College of Medicine. Advisor: Dr. Flavio Salazar Onfray. Main points include:

  • Performed ELISA to quantify antigens, western blot to analyze humoral response of patients and flow cytometry to study cell populations in blood.
  • Maintained and cultured melanoma cell lines.

August 2011 – March 2012
Volunteer Undergraduate Researcher
Universidad de Chile

Nicotinic profile of motor activity in adult Zebrafish. College of Sciences. Advisor: Dr. Patricio Iturriaga Vasquez. Main points include:

  • Maintenance and care of Zebrafish (Danio rerio).
  • Analyzed the behavior of Zebrafish in a trapezoid model of tank after immersing them in a beaker with different concentrations of nicotine and other drugs.
  • Tracked the movement of Zebrafish in the tank by using DanioTrack.

May 2010 – December 2010

Honors & Awards

2023-24 Jean Fort Dissertation Prize
University of California, San Diego

The prize is awarded annually to a Ph.D. recipient of unusual intellectual breadth whose doctoral research has met the highest standards of academic excellence and may make a significant contribution on an issue of humanitarian or public concern.

2024
Siebel Scholar, Class of 2023
Siebel Scholars Foundation

Awarded annually for academic excellence and demonstrated leadership to over 90 top students from the world’s leading graduate schools.

2022 - 2023
Academic Hardware Grant
NVIDIA

Awarded a NVIDIA RTX A6000 for developing Tensor-cell2cell

2022
Fellowship by the Government of Chile
ANID - Becas Chile

Pre-doctoral fellowship

2018 - 2022
Fulbright fellowship
Fullbright Commission

Pre-doctoral fellowship

2018 - 2022
Winning Talk
ANEIB Chile

Best oral presentation at the II National Congress of Biotechnology Students.

2013

Skills

Languages, Operating Systems & Tools
  • Python
  • R
  • git
  • linux
  • bash
Containers & Cloud
Data Management
  • MySQL
  • SQLite
Controller Boards
  • Arduino
  • Raspberry Pi
Hobbies
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