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Scopus Author ID: 56367355900

Keywords

Mathematical Modeling, Systems Biology, Omics Data

Biography

I am a computational biologist, specialized in Systems Biology. I have interests in data science, mathematical modeling and challenging biological problems. Always learning from the scientific community!

Activities

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Employment (5)

Novonesis: Hørsholm, Region Hovestaden, DK

2024-02-01 to present | Senior Scientist (Computational Microbiology)
Employment
Source: Self-asserted source
Benjamín J. Sánchez

Chr. Hansen (Denmark): Hørsholm, Hovedstaden, DK

2021-03-01 to 2024-01-31 | Research Scientist (Systems Biology)
Employment
Source: Self-asserted source
Benjamín J. Sánchez

Technical University of Denmark: Kongens Lyngby, Hovedstaden, DK

2019-10-01 to 2021-02-28 | Postdoc (Bioengineering)
Employment
Source: Self-asserted source
Benjamín J. Sánchez

Pontificia Universidad Catolica de Chile: Santiago, CL

2014-01-01 to 2014-09-12 | Research Engineer (Chemical & Bioprocess Engineering Department)
Employment
Source: Self-asserted source
Benjamín J. Sánchez

Biofiltro SPA: Santiago, CL

2013-01-01 to 2013-12-31 | Modeler and Supervisor in R+D Project
Employment
Source: Self-asserted source
Benjamín J. Sánchez

Education and qualifications (3)

Chalmers University of Technology: Gothenburg, SE

2014-10-01 to 2019-03-31 | PhD (Biology and Biological Engineering)
Education
Source: Self-asserted source
Benjamín J. Sánchez

Pontificia Universidad Catolica de Chile: Santiago, CL

2012-03-01 to 2014-01-13 | M.Sc. (Eng) (Chemical and Bioprocess Engineering Department)
Education
Source: Self-asserted source
Benjamín J. Sánchez

Pontificia Universidad Catolica de Chile: Santiago, CL

2007-03-01 to 2012-07-31 | B.Sc. - Biotechnology Major - Process Engineering Minor (Faculty of Engineering)
Education
Source: Self-asserted source
Benjamín J. Sánchez

Funding (3)

PhD Scholarship

2014-10 to 2018-09 | Grant
Ministerio de Educación, Gobierno de Chile (Santiago, CL)
GRANT_NUMBER:

6222/2014
Source: Self-asserted source
Benjamín J. Sánchez

Msc Scholarship

2013-04 to 2014-01 | Grant
Ministerio de Educación, Gobierno de Chile (Santiago, CL)
GRANT_NUMBER:

221320015
Source: Self-asserted source
Benjamín J. Sánchez

"Dow Chemical" Award 2012

Award
Dow Chemical Company (MI, MI, US)
Source: Self-asserted source
Benjamín J. Sánchez

Works (19)

Mechanistic modeling of the dynamics of phage attack during milk acidification in the cheese-making process

Journal of Food Engineering
2025-02 | Journal article
DOI: 10.1016/j.jfoodeng.2024.112329
Contributors: Michèle Bou Habib; Emmanuel Bernuau; Benjamín José Sánchez; Dominique Swennen; Ahmad A. Zeidan; Ioan-Cristian Trelea; Jannik Vindeloev
Source: check_circle
Crossref

Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community

Molecular Systems Biology
2024-08-12 | Journal article
DOI: 10.1038/s44320-024-00060-7
Contributors: Chengyu Zhang; Benjamín J Sánchez; Feiran Li; Cheng Wei Quan Eiden; William T Scott; Ulf W Liebal; Lars M Blank; Hendrik G Mengers; Mihail Anton; Albert Tafur Rangel et al.
Source: check_circle
Crossref

Genome-scale modeling drives 70-fold improvement of intracellular heme production in Saccharomyces cerevisiae

Proceedings of the National Academy of Sciences
2022-07-26 | Journal article
DOI: 10.1073/pnas.2108245119
Contributors: Olena P. Ishchuk; Iván Domenzain; Benjamín J. Sánchez; Facundo Muñiz-Paredes; José L. Martínez; Jens Nielsen; Dina Petranovic
Source: check_circle
Crossref

Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

Nature Communications
2022-06-30 | Journal article
DOI: 10.1038/s41467-022-31421-1
Contributors: Iván Domenzain; Benjamín Sánchez; Mihail Anton; Eduard J. Kerkhoven; Aarón Millán-Oropeza; Céline Henry; Verena Siewers; John P. Morrissey; Nikolaus Sonnenschein; Jens Nielsen
Source: check_circle
Crossref

Benchmarking accuracy and precision of intensity‐based absolute quantification of protein abundances in Saccharomyces cerevisiae

PROTEOMICS
2021-03 | Journal article
DOI: 10.1002/pmic.202000093
Contributors: Benjamín J. Sánchez; Petri‐Jaan Lahtvee; Kate Campbell; Sergo Kasvandik; Rosemary Yu; Iván Domenzain; Aleksej Zelezniak; Jens Nielsen
Source: check_circle
Crossref

Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

2021-03-05 | Preprint
DOI: 10.1101/2021.03.05.433259
Contributors: Iván Domenzain; Benjamín Sánchez; Mihail Anton; Eduard J. Kerkhoven; Aarón Millán-Oropeza; Céline Henry; Verena Siewers; John P. Morrissey; Nikolaus Sonnenschein; Jens Nielsen
Source: check_circle
Crossref

Genome-scale metabolic modelling ofP. thermoglucosidasiusNCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism

2021-02-01 | Preprint
DOI: 10.1101/2021.02.01.429138
Contributors: Viviënne Mol; Martyn Bennett; Benjamín J. Sánchez; Beata K. Lisowska; Markus J. Herrgård; Alex Toftgaard Nielsen; David J. Leak; Nikolaus Sonnenschein
Source: check_circle
Crossref

Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances inSaccharomyces cerevisiae

2020-03-24 | Preprint
DOI: 10.1101/2020.03.23.998237
Contributors: Benjamín J. Sánchez; Petri-Jaan Lahtvee; Kate Campbell; Sergo Kasvandik; Rosemary Yu; Iván Domenzain; Aleksej Zelezniak; Jens Nielsen
Source: check_circle
Crossref

Predictive engineering and optimization of tryptophan metabolism in yeast through a combination of mechanistic and machine learning models

bioRxiv
2019-11 | Preprint
DOI: 10.1101/858464
Source: Self-asserted source
Benjamín J. Sánchez

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

ACS synthetic biology
2019-10 | Journal article
DOI: 10.1021/acssynbio.9b00258
PMID: 31577419
Contributors: Ferreira R; Skrekas C; Hedin A; Sánchez BJ; Siewers V; Nielsen J; David F
Source: Self-asserted source
Benjamín J. Sánchez via Europe PubMed Central

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

Nature communications
2019-08 | Journal article
DOI: 10.1038/s41467-019-11581-3
PMID: 31395883
PMC: PMC6687777
Contributors: Lu H; Li F; Sánchez BJ; Zhu Z; Li G; Domenzain I; Marcišauskas S; Anton PM; Lappa D; Lieven C et al.
Source: Self-asserted source
Benjamín J. Sánchez via Europe PubMed Central

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

BMC systems biology
2019-01 | Journal article
DOI: 10.1186/s12918-018-0673-8
PMID: 30634957
PMC: PMC6330394
Contributors: Sánchez BJ; Li F; Kerkhoven EJ; Nielsen J
Source: Self-asserted source
Benjamín J. Sánchez via Europe PubMed Central

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

PLoS computational biology
2018-10 | Journal article
DOI: 10.1371/journal.pcbi.1006541
PMID: 30335785
PMC: PMC6207324
Contributors: Wang H; Marcišauskas S; Sánchez BJ; Domenzain I; Hermansson D; Agren R; Nielsen J; Kerkhoven EJ
Source: Self-asserted source
Benjamín J. Sánchez via Europe PubMed Central

Memote: A community driven effort towards a standardized genome-scale metabolic model test suite

bioRxiv
2018-06 | Preprint
DOI: 10.1101/350991
Source: Self-asserted source
Benjamín J. Sánchez

Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints.

Molecular systems biology
2017-08 | Journal article
DOI: 10.15252/msb.20167411
PMID: 28779005
PMC: PMC5572397
Contributors: Sánchez BJ; Zhang C; Nilsson A; Lahtvee PJ; Kerkhoven EJ; Nielsen J
Source: Self-asserted source
Benjamín J. Sánchez via Europe PubMed Central
grade
Preferred source (of 2)‎

Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast.

Cell systems
2017-03 | Journal article
DOI: 10.1016/j.cels.2017.03.003
PMID: 28365149
Contributors: Lahtvee PJ; Sánchez BJ; Smialowska A; Kasvandik S; Elsemman IE; Gatto F; Nielsen J
Source: Self-asserted source
Benjamín J. Sánchez via Europe PubMed Central

Genome scale models of yeast: towards standardized evaluation and consistent omic integration.

Integrative biology
2015-08 | Journal article
DOI: 10.1039/c5ib00083a
PMID: 26079294
Source: Self-asserted source
Benjamín J. Sánchez
grade
Preferred source (of 2)‎

HIPPO: An Iterative Reparametrization Method for Identification and Calibration of Dynamic Bioreactor Models of Complex Processes

Industrial & Engineering Chemistry Research
2014-12 | Journal article
DOI: 10.1021/ie501298b
Part of ISSN: 0888-5885
Part of ISSN: 1520-5045
Source: Self-asserted source
Benjamín J. Sánchez

Construction of robust dynamic genome-scale metabolic model structures of Saccharomyces cerevisiae through iterative re-parameterization.

Metabolic engineering
2014-07 | Journal article
DOI: 10.1016/j.ymben.2014.07.004
PMID: 25046158
Contributors: Sánchez BJ; Pérez-Correa JR; Agosin E
Source: Self-asserted source
Benjamín J. Sánchez via Europe PubMed Central

Peer review (1 review for 1 publication/grant)

Review activity for PLoS computational biology. (1)
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