Sobre
As the CEO and Co-founder of SilicoLife, Simão Soares leverages his bioinformatics…
Artigos de Simão
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The Future of Natural Product Sustainability - Lessons from Omega-3 Fatty Acids
The Future of Natural Product Sustainability - Lessons from Omega-3 Fatty Acids
De Simão Soares
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A nova realidade das alterações climáticas - in Portuguese
A nova realidade das alterações climáticas - in Portuguese
De Simão Soares
Atividades
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Jumpseller is about to launch Falabella Marketplace integration!
Jumpseller is about to launch Falabella Marketplace integration!
Simão Soares gostou
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DARPA is looking to fund some big new ideas at the intersection of AI and Bio. The San Francisco event to meet the program managers is next Friday…
DARPA is looking to fund some big new ideas at the intersection of AI and Bio. The San Francisco event to meet the program managers is next Friday…
Simão Soares gostou
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Five years ago today I started working at William Reed Ltd. Not only was it my first day at work, it was my son's first day at daycare. He was an…
Five years ago today I started working at William Reed Ltd. Not only was it my first day at work, it was my son's first day at daycare. He was an…
Simão Soares gostou
Experiência
Formação acadêmica
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INSEAD
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INSEAD Blue Ocean Strategy is an executive program offering a new perspective on strategy formulation and execution based on the the theory created by INSEAD professors W. Chan Kim and Renée Mauborgne. Blue Ocean Strategy enables the creation of ‘blue oceans’ of uncontested market space and the discovery of how strategic moves – termed ‘Value Innovation’ – can create powerful leaps in value for both the firm and its customers, rendering rivals obsolete and unleashing new…
INSEAD Blue Ocean Strategy is an executive program offering a new perspective on strategy formulation and execution based on the the theory created by INSEAD professors W. Chan Kim and Renée Mauborgne. Blue Ocean Strategy enables the creation of ‘blue oceans’ of uncontested market space and the discovery of how strategic moves – termed ‘Value Innovation’ – can create powerful leaps in value for both the firm and its customers, rendering rivals obsolete and unleashing new demand.
http://www.insead.edu/executive-education/strategy/blue-ocean-strategy -
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General Management Program is a executive postgraduate program providing a multifunctional view of business, leadership, and of the organization. GMP/CGG (Curso Geral de Gestão) is the oldest and most awarded postgraduate in management in Portugal.
http://exed.novasbe.pt/programasabertos/curso-geral-de-gestao -
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Thesis: "Development of computational tools for integrating ‘omics’ data with bio-molecular interaction networkss"
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Atividades e grupos:CeSIUM, AAUM
Thesis: "Development of computational tools for integrating ‘omics’ data with bio-molecular interaction networkss
MSc Project: "Optimization of mutants in silico with integration of regulatory information"
2008 – AAUM's Department of Recreational Activities - Head of Dep. (Braga),
“Associação Académica da Universidade do Minho” is the University of Minho Students' Union [www.aaum.pt]
2007/2008 – Vice-President of the Board of the UMinho's Computer Science and Systems…Thesis: "Development of computational tools for integrating ‘omics’ data with bio-molecular interaction networkss
MSc Project: "Optimization of mutants in silico with integration of regulatory information"
2008 – AAUM's Department of Recreational Activities - Head of Dep. (Braga),
“Associação Académica da Universidade do Minho” is the University of Minho Students' Union [www.aaum.pt]
2007/2008 – Vice-President of the Board of the UMinho's Computer Science and Systems Engineering Students Center (CeSIUM) [cesium.di.uminho.pt]
IBM DB2 Student Ambassador [cesium.di.uminho.pt/db2] -
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Atividades e grupos:CeSIUM, AAUM
2006, 2007 – Colaborator at AAUM (“Associação Académica da Universidade do Minho” ); and in the Erasmus Student Network (UMinho's section)
2006-2007 – President of the General Assembly of the UMinho's Computer Science and Systems Engineering Students Center (CeSIUM)
2007 – Volunteer for the European Joint Conferences on Theory and Practice of Software (ETAPS07)
Experiência de voluntariado
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Shaper (now Alumni)
Global Shapers Community
- 6 anos
Global Shapers - Lisbon Hub (http://www.globalshaperslisbon.com/)
The Global Shapers Community is an Initiative of the World Economic Forum and is a network of city-based Hubs developed and led by young leaders between 20 and 30 years old who want to develop their leadership potential towards serving society. -
Climate Reality Leader
The Climate Reality Project
- o momento 7 anos
Ambiente
The Climate Reality Project is a non-profit organization involved in education and advocacy related to climate change established in 2011 by Al Gore. The Climate Reality Project also addresses climate change through a network of 10,000 Climate Reality Leaders, the Climate Reality Leadership Corps.
Publicações
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An Algorithm to Assemble Gene-Protein-Reaction Associations for Genome-Scale Metabolic Model Reconstruction
Pattern Recognition in Bioinformatics/Springer
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Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes
PLoS Computational Biology
Type 2 diabetes mellitus (T2DM) is a disorder characterized by both insulin resistance and impaired insulin secretion. Recent transcriptomics studies related to T2DM have revealed changes in expression of a large number of metabolic genes in a variety of tissues. Identification of the molecular mechanisms underlying these transcriptional changes and their impact on the cellular metabolic phenotype is a challenging task due to the complexity of transcriptional regulation and the highly…
Type 2 diabetes mellitus (T2DM) is a disorder characterized by both insulin resistance and impaired insulin secretion. Recent transcriptomics studies related to T2DM have revealed changes in expression of a large number of metabolic genes in a variety of tissues. Identification of the molecular mechanisms underlying these transcriptional changes and their impact on the cellular metabolic phenotype is a challenging task due to the complexity of transcriptional regulation and the highly interconnected nature of the metabolic network. In this study we integrate skeletal muscle gene expression datasets with human metabolic network reconstructions to identify key metabolic regulatory features of T2DM. These features include reporter metabolitesâmetabolites with significant collective transcriptional response in the associated enzyme-coding genes, and transcription factors with significant enrichment of binding sites in the promoter regions of these genes. In addition to metabolites from TCA cycle, oxidative phosphorylation, and lipid metabolism (known to be associated with T2DM), we identified several reporter metabolites representing novel biomarker candidates. For example, the highly connected metabolites NAD+/NADH and ATP/ADP were also identified as reporter metabolites that are potentially contributing to the widespread gene expression changes observed in T2DM. An algorithm based on the analysis of the promoter regions of the genes associated with reporter metabolites revealed a transcription factor regulatory network connecting several parts of metabolism. The identified transcription factors include members of the CREB, NRF1 and PPAR family, among others, and represent regulatory targets for further experimental analysis. Overall, our results provide a holistic picture of key metabolic and regulatory nodes potentially involved in the pathogenesis of T2DM.
Outros autoresVer publicação -
OptFlux: an open-source software platform for in silico metabolic engineering
BMC Bioinformatics
OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using the methods of…
OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes.
OptFlux also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization algorithms.
The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph.
The OptFlux software is freely available, together with documentation and other resources, thus bridging the gap from research in strain optimization algorithms and the final users. It is a valuable platform for researchers in the field that have available a number of useful tools. Its open-source nature invites contributions by all those interested in making their methods available for the community.
Given its plug-in based architecture it can be extended with new functionalities. Currently, several plug-ins are being developed, including network topology analysis tools and the integration with Boolean network based regulatory models.Outros autoresVer publicação
Projetos
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DeYeastLibrary
- o momento
Development of optimized cell factories for the production of novel compounds is a time-consuming process and represents a significant cost/time burden. DeYeastLibrary project will help overcoming this hurdle by using cutting-edge computational and experimental tools. The project will exploit the biochemical design principles of nature and will accelerate the development of yeast-based bioprocesses.
Project coordinator: European Molecular Biology Laboratory
Partners: European…Development of optimized cell factories for the production of novel compounds is a time-consuming process and represents a significant cost/time burden. DeYeastLibrary project will help overcoming this hurdle by using cutting-edge computational and experimental tools. The project will exploit the biochemical design principles of nature and will accelerate the development of yeast-based bioprocesses.
Project coordinator: European Molecular Biology Laboratory
Partners: European Molecular Biology Laboratory, Germany, University of Minho, Portugal, SilicoLife, Portugal, Johann Wolfgang Goethe-Universitat, Germany, Technical University of Denmark, DenmarkOutros criadoresVer projeto -
IPCRES
- o momento
The project aims is to convert low-value glycerol, a by-product of biodiesel production, to chiral amino alcohol (CAA) and 1,2-propanediol (PDO). CAA is an intermediate in the manufacturing of some medicines, while PDO is used for the de-icing of aircrafts. The project aims to produce bacterial and yeast strains that can convert glycerol into CAA and PDO.
Project coordinator: University College London
Partners: University College London, UK, Jacobs University Bremen, Germany…The project aims is to convert low-value glycerol, a by-product of biodiesel production, to chiral amino alcohol (CAA) and 1,2-propanediol (PDO). CAA is an intermediate in the manufacturing of some medicines, while PDO is used for the de-icing of aircrafts. The project aims to produce bacterial and yeast strains that can convert glycerol into CAA and PDO.
Project coordinator: University College London
Partners: University College London, UK, Jacobs University Bremen, Germany, SilicoLife, Portugal, Technical University of Denmark, Denmark, Autonomous University of Barcelona, Spain, Bio-Prodict, Austria, Ingenza, UK, University of Strathclyde, UK.Outros criadoresVer projeto -
BRIGIT
- o momento
New tailor-made biopolymers produced from lignocellulosic sugars waste for highly demanding fire-resistant applications
Outros criadoresVer projeto -
OptFlux
- o momento
OptFlux is an open-source and modular software to support in silico metabolic engineering tasks aimed at being the reference computational application in the field.
Outros criadoresVer projeto -
PEM - Platform for Metabolic Engineering
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PEM is a joint effort by SilicoLife and University of Minho for the development of new bio-based solutions. The project combines the in silico design of microbial cell factories with wet lab validation and is co-financed by the Portuguese National Strategic Reference Framework.
Outros criadoresVer projeto
Idiomas
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Englisch
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Recomendações recebidas
4 pessoas recomendaram Simão
Cadastre-se agora para visualizarMais atividade de Simão
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Looking forward to meeting you in Milan!
Looking forward to meeting you in Milan!
Simão Soares gostou
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I’m grateful to Forbes Portugal for recognising me among a group of exceptionally successful women. It's incredibly rewarding to have my…
I’m grateful to Forbes Portugal for recognising me among a group of exceptionally successful women. It's incredibly rewarding to have my…
Simão Soares gostou
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Dear network, As you may have heard, Ginkgo Bioworks, Inc. announced a large reduction in force in May and laid off 35% of their US-based employees…
Dear network, As you may have heard, Ginkgo Bioworks, Inc. announced a large reduction in force in May and laid off 35% of their US-based employees…
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🌏 We're back from summer vacations and fully prepared for Vitafoods Asia in Bangkok, Thailand! From 18-20 September 2024, SilicoLife will be at…
🌏 We're back from summer vacations and fully prepared for Vitafoods Asia in Bangkok, Thailand! From 18-20 September 2024, SilicoLife will be at…
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Meet the semi-finalists for the #iCapitalAwards! 🏆 These cities are promoting cutting-edge #innovation and technologies for the betterment of their…
Meet the semi-finalists for the #iCapitalAwards! 🏆 These cities are promoting cutting-edge #innovation and technologies for the betterment of their…
Simão Soares gostou
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O mercado dos suplementos de longevidade está em franca expansão, prevendo-se que atinja o valor de cerca de 2,3 mil milhões de dólares até…
O mercado dos suplementos de longevidade está em franca expansão, prevendo-se que atinja o valor de cerca de 2,3 mil milhões de dólares até…
Simão Soares gostou
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📣 A PluggableAI está ativamente à procura de pessoas incríveis, apaixonadas por tecnologia e com espírito empreendedor! Se é perante o desafio que…
📣 A PluggableAI está ativamente à procura de pessoas incríveis, apaixonadas por tecnologia e com espírito empreendedor! Se é perante o desafio que…
Simão Soares gostou
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Back in 2016, I went to @Stanford to learn from the best about business. My studies there were particularly marked by a small improvised talk John…
Back in 2016, I went to @Stanford to learn from the best about business. My studies there were particularly marked by a small improvised talk John…
Simão Soares gostou
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Our latest work showcasing how generative machine learning can enhance metabolic research has been published. You can find it here:…
Our latest work showcasing how generative machine learning can enhance metabolic research has been published. You can find it here:…
Simão Soares gostou
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Everyone has a different definition for Seed, Series A, B, C… So here’s my complete guide to Venture Milestones 🙌 All jammed into one image 😃 I…
Everyone has a different definition for Seed, Series A, B, C… So here’s my complete guide to Venture Milestones 🙌 All jammed into one image 😃 I…
Simão Soares gostou
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I had the chance to interview with BioVox (great work by Christopher Playfoot, Ph.D.) recently to discuss NIUM‘s innovative food testing platform…
I had the chance to interview with BioVox (great work by Christopher Playfoot, Ph.D.) recently to discuss NIUM‘s innovative food testing platform…
Simão Soares gostou
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I’m starting a new position as Investment Senior Associate at Hevolution Foundation! Will be starting in September and back to Boston, please find me…
I’m starting a new position as Investment Senior Associate at Hevolution Foundation! Will be starting in September and back to Boston, please find me…
Simão Soares gostou
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I'm speaking at this year's edition of SupplySide West & Food ingredients North America, and I couldn't be more excited! Register here 👉…
I'm speaking at this year's edition of SupplySide West & Food ingredients North America, and I couldn't be more excited! Register here 👉…
Simão Soares gostou
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