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Benjamín J. Sánchez

Research Scientist

Chr. Hansen

Hi! I’m Ben

I’m a computational biologist, passionate about understanding biology using math and computers. I’m currently located in Copenhagen, Denmark, working as a research scientist in Chr. Hansen. Nice to meet you!

Interests

  • Comparative Genomics
  • Metabolic Modeling
  • Software Development
  • Running
  • Climbing
  • Improv Theater
  • Table-top RPG’s

Education

  • PhD in Systems Biology, 2019

    Chalmers University of Technology

  • MSc in Chemical and Bioprocess Engineering, 2014

    Pontificia Universidad Católica de Chile

  • BSc in Biotechnology Engineering, 2012

    Pontificia Universidad Católica de Chile

Recent Publications

Quickly discover relevant content by filtering publications.

MEMOTE for standardized genome-scale metabolic model testing

A community tool for evaluating quality of metabolic models
Christian Lieven, Moritz E. Beber, Brett G. Olivier, Frank T. Bergmann, Meric Ataman, Parizad Babaei, Jennifer A. Bartell, Lars M. Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E. Ebert, Janaka N. Edirisinghe, José P. Faria, Adam M. Feist, Georgios Fengos, Ronan M. T. Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout van Helvoirt, Christopher S. Henry, Henning Hermjakob, Markus J. Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary King, Stefen Klamt, Edda Klipp, Jasper J. Koehorst, Matthias König, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E. Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L. Medlock, Jonathan M. Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O. Palsson, Jason A. Papin, Kiran R. Patil, Mark Poolman, Nathan D. Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J. Sánchez, Peter J. Schaap, Rahuman S. Malik Sherif, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A. H. Wodke, Joana C. Xavier, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang
PDF Code DOI

Model-Assisted Fine-Tuning of Central Carbon Metabolism in Yeast through dCas9-Based Regulation

Over-producing acetyl/malonyl-CoA using in silico & experimental methods
PDF Dataset DOI

A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

The consensus metabolic model of yeast as a standard in the community
PDF Code DOI

SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

A genome-scale method for simulating energy costs of lipid metabolism
PDF Code DOI

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

A Matlab toolbox for metabolic network reconstruction
PDF Code DOI
See all publications

Recent Posts

Applying for unemployment money in Sweden

A step-by-step guide tailored to international researchers
Last updated on 2020-04-05 6 min read

Experience

 
 
 
 
 

Research Scientist

Chr. Hansen

Mar 2021 – Present Hørsholm, Denmark
  • Studying microbial diversity and its application in the food, nutritional, pharmaceutical and agricultural industries
  • Working at the bioinformatics and modeling department
 
 
 
 
 

Postdoctoral Researcher

Technical University of Denmark

Oct 2019 – Feb 2021 Lyngby, Denmark
 
 
 
 
 

PhD in Systems Biology

Chalmers University of Technology

Oct 2014 – Mar 2019 Gothenburg, Sweden
 
 
 
 
 

Project Manager

Pontificia Universidad Católica de Chile

Feb 2014 – Sep 2014 Santiago, Chile
  • Role: Leading and coordinating laboratory and field activities
  • Project between the university and winemaking industries: “Management of REDOX potential in the wine elaboration chain and its impact on quality”
  • Main supervisor: Prof. Eduardo Agosin
 
 
 
 
 

Modeler and R&D Supervisor

Biofiltro S.P.A.

Jan 2013 – Dec 2013 Santiago, Chile
  • Role: Optimizing an earthworm filter for wastewater treatment
  • Duties: Prototype development, mathematical modeling, experimental measurements, field supervision
  • Part-time job
  • Main supervisor: Matías Sjögren (CEO)
 
 
 
 
 

MSc in Chemical and Bioprocess Engineering

Pontificia Universidad Católica de Chile

Mar 2012 – Jan 2014 Santiago, Chile
 
 
 
 
 

BSc in Engineering

Pontificia Universidad Católica de Chile

Mar 2007 – Jul 2012 Santiago, Chile
  • Teacher assistant in Calculus I, Calculus II, Thermodynamics, Transport Phenomena, Microbial Biotechnology and Chemical Process Design.
  • Co-designer of the biological engineering major (2011)
  • University delegate in the Chilean association of biotechnology engineering students (2011-2012)
  • Research coordinator in the university chapter of AIChE (2012)

Skills

Programming Languages

Python, R, Bash, Matlab

Mathematical Modeling

Stoichiometric Models, Kinetic Models, Network Analysis

Software Development

Version Control, Continuous Integration, Containers

Analysis of Big Data

Comparative Genomics, Proteomics, Transcriptomics, Kinetomics

Lab Experience

Fermentation Science, HPLC, Cellular Biology

Spoken Languages

English (full proficiency), Swedish (basic), Spanish (native speaker)

Presentations

Reconstruction Workshop for Genome-Scale Modeling of Fish

Finse, Norway Apr 2019
Invited speaker: Version-controlled GEMs

V Conference on Constraint-Based Reconstruction and Analysis (COBRA)

Seattle, U.S.A. Oct 2018
Oral presentation: yeast-GEM: reviving the consensus genome-scale model of S. cerevisiae as a standard in the community

XII Metabolic Engineering Conference (ME-12)

Munich, Germany Jun 2018
Poster presentation: The Consensus Genome-Scale Model of Yeast & Constraints on Lipid Metabolism

VI Winter Quantitative Biology Conference (Q-Bio)

Wailea, U.S.A. Feb 2018
Poster presentation: Enzyme usage in yeast during stress

Center for Biosustainability (CfB) Annual Meeting

Lyngby, Denmark Sep 2016
Oral presentation: GECKO: Enhancing a genome-scale model with enzymatic constraints

XVII International Conference on Systems Biology (ICSB)

Barcelona, Spain Sep 2016
Poster presentation: Yeast genome scale modeling with enzyme constraints

XI Metabolic Engineering Conference (ME-11)

Kobe, Japan Jun 2016
Poster presentation: How much is it? Predicting enzyme costs with a genome scale model of yeast: applications to metabolic engineering

IV Conference on Constraint-Based Reconstruction and Analysis (COBRA)

Heidelberg, Germany Sep 2015
Poster presentation: Expanding a yeast genome scale model to account for enzymatic limitations (awarded 3rd prize in the poster competition)

XI International Conference on Pathways, Networks and Systems Medicine

Chania, Greece Jun 2015
Poster presentation: Reconciling proteomic data into genome scale models

LXXXII Meeting of the Chilean Mathematical Society

Olmué, Chile Nov 2013
Oral presentation: Reparametrización de un modelo dinámico del metabolismo celular de S. cerevisiae

I Cell Factories and Biosustainability Conference

Hillerød, Denmark May 2013
Poster presentation: Reparameterization analysis of a S. cerevisiae dynamic genome-scaled metabolic model

VI Chilean Conference of Chemical Engineering Students

Santiago, Chile Oct 2012
Oral presentation: Procedimiento iterativo heurístico de reparametrización de modelos dinámicos en procesos químicos y biológicos

VII Chilean Meeting of Biotechnology Engineering Students

Antofagasta, Chile Oct 2012
Poster presentation: Modelación metabólica dinámica a escala genómica para la producción de terpenos en S. cerevisiae

XXV Interamerican Conference of Chemical Engineering

Santiago, Chile Nov 2011
Poster presentation: Técnicas para el estudio de la diferenciación celular en progenitores musculares adultos: aplicaciones a la ingeniería de tejidos y proyecciones

VI Chilean Meeting of Biotechnology Engineering Students

Viña del Mar, Chile Aug 2011
Oral presentation: Estudio de la Diferenciación de Células Progenitoras Musculares y proyecciones para la Ingeniería de Tejidos

Accomplish­ments

PhD Scholarship CONICYT #6222 / 2014

CONICYT Oct 2014
Scholarship awarded by the government of Chile

MSc Scholarship CONICYT #221320015

CONICYT Apr 2013
Scholarship awarded by the government of Chile

“Dow Chemical” MSc award

Dow Chemical Chile S.A. Apr 2013
Awarded yearly to one student of the Msc program

Engineering Teacher Assistant Award

Pontificia Universidad Católica de Chile Nov 2011
Awarded yearly to a selection of TAs recognized by both students and teachers

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