Skip to content

Instantly share code, notes, and snippets.

@paulo-maia
Created April 18, 2022 15:06
Show Gist options
  • Save paulo-maia/2fe9d5d85d96a4d024af7dc46c38077c to your computer and use it in GitHub Desktop.
Save paulo-maia/2fe9d5d85d96a4d024af7dc46c38077c to your computer and use it in GitHub Desktop.
reactive resume
{
"basics": {
"name": "Paulo Maia",
"email": "pmaia@silicolife.com",
"phone": "(+351) 962 922 605",
"photo": {
"url": "https://media-exp1.licdn.com/dms/image/D4D03AQGFNXqjgpZjBw/profile-displayphoto-shrink_800_800/0/1646641896449?e=1655337600&v=beta&t=raFwa638WRcFxiCVCTbLldfLNE19KSpQXNkSiZWnFFc",
"filters": {
"size": 128,
"shape": "square",
"border": false,
"grayscale": false
},
"visible": true
},
"summary": "**I am a Software Engineer turned Computational Biologist.**",
"website": "",
"headline": "Ph.D. Computational Biology",
"location": {
"city": "Braga",
"region": "",
"address": "",
"country": "PT",
"postalCode": ""
},
"profiles": [
{
"id": "57c18c06-9ea1-4612-982c-481a9e24fbdf",
"url": "https://scholar.google.com/citations?user=41rabEcAAAAJ&hl=en",
"network": "scholar",
"username": "pmaia"
},
{
"id": "3cfe23cf-21ad-4f24-9de9-9bd29f697667",
"url": "https://twitter.com/antisens3",
"network": "twitter",
"username": "antisens3"
},
{
"id": "84fd14f4-2246-4220-aeab-fb6260adf718",
"url": "https://www.linkedin.com/in/paulomaia/",
"network": "linkedin",
"username": "paulomaia"
},
{
"network": "web-CV",
"username": "CV",
"url": "https://rxresu.me/r/0sYx-OW9",
"id": "39e91cee-9bda-4765-87d8-18eeb8b58c2e"
}
]
},
"sections": {
"work": {
"id": "work",
"name": "Work Experience",
"type": "basic",
"items": [
{
"id": "dca1064f-bfd5-4b95-8311-9e7d6ca361b2",
"date": {
"end": "",
"start": "2015-01-01T00:00:00.000Z"
},
"name": "SilicoLife",
"summary": "Since 2015 I have lead the phenotype prediction/strain optimization team at SilicoLife. During this time, I have been responsible for the introduction of new technologies to the company, for the development of some of the platforms within the company, supervision of students and team members, proposal design, preparation and submission, co-coordination of R&D projects, etc.",
"position": "Head of Development"
},
{
"id": "9c9b9c9e-8ed7-421a-b882-b53d406c4480",
"date": {
"end": "2015-01-01T00:00:00.000Z",
"start": "2013-01-01T00:00:00.000Z"
},
"name": "SilicoLife",
"summary": "Near the end of 2013 I joined the SilicoLife team full-time, while finishing writing my PhD thesis. I was responsible for bringing the strain optimization methods developed during my Ph.D. to the company and integrating them within SilicoLife's pipelines.",
"position": "Research Associate"
},
{
"id": "60879cd5-7c93-4017-af82-55ec16fd1ed2",
"date": {
"end": "",
"start": "2010-04-15T00:00:00.000Z"
},
"name": "SilicoLife",
"position": "Co-Founder/partner collaborator",
"url": "www.silicolife.com",
"summary": "Co-founded SilicoLife with colleagues and advisors from the University of Minho as a spin-off of the MIT Portugal Ph.D. Program in Bioengineering, of which I was a Ph.D candidate."
},
{
"id": "aa665cca-b43f-444c-bb1c-79c8ddc11086",
"date": {
"end": "2018-01-01T00:00:00.000Z",
"start": "2016-01-01T00:00:00.000Z"
},
"name": "University of Minho",
"summary": "I was the responsible teacher during two semesters, this included theorethical and pratical classes, exam preparation and grading. The courses were 1) Bioinformatics and Systems Biology course to the Integrated Masters in Biological Engineering and the Masters in Biotechnology and 2) Systems Biology course to the Masters in Bioinformatics.",
"position": "Invited lecturer - Systems Biology / Bioinformatics"
},
{
"id": "184dec38-c1d2-4bcd-bacc-760e86c917d0",
"date": {
"end": "2010-06-01T00:00:00.000Z",
"start": "2010-01-01T00:00:00.000Z"
},
"name": "E.I. DuPont De Nemours & Co. Inc.",
"summary": "Software Engineering and Computational Biology consultant for DuPont during a semester. This included a two week stay at DuPont Experimental Station in Delaware/USA.",
"position": "External consultant"
},
{
"id": "ca4ce616-b311-43f7-a833-4ef45c23ed9c",
"date": {
"end": "2009-01-01T00:00:00.000Z",
"start": "2007-01-01T00:00:00.000Z"
},
"name": "University of Minho",
"summary": "Research in Systems Biology and software engineering. From 2008 onward this was a Science & Engineering Grant funded by the multinational company E.I. DuPont De Nemours & Co, Inc. I was the lead developer of OptFlux, an application built to perform complex metabolic engineering tasks.",
"position": "Grantee researcher"
},
{
"id": "408b8961-d90e-4fe7-9006-890b4953da65",
"date": {
"end": "2007-01-01T00:00:00.000Z",
"start": "2006-01-01T00:00:00.000Z"
},
"name": "University of Minho",
"summary": "Research in Bioinformatics / Data-mining / Artificial Intelligence.",
"position": "Junior grantee researcher"
}
],
"columns": 2,
"visible": true
},
"awards": {
"id": "awards",
"name": "Awards",
"type": "basic",
"items": [
{
"id": "37a910c3-a5a6-4944-bb06-d43782f76e9c",
"date": "",
"title": "Full 4 year PhD Scholarship",
"awarder": "FCT, Portuguese Technology & Science Foundation"
},
{
"id": "cb271aa7-69a8-467a-907e-cb763e493581",
"date": "",
"title": "MSc research grant",
"awarder": "E.I. DuPont de Nemours university awards"
}
],
"columns": 2,
"visible": true
},
"skills": {
"id": "skills",
"name": "Skills",
"type": "basic",
"items": [
{
"id": "d2319fe4-fc4a-44e4-b753-bab1cbbda90b",
"name": "Computational Biology",
"level": "Expert",
"keywords": [
"GSM Reconstruction",
"Flux Balance Analysis methods",
"Metabolic Engineering",
"Strain Optimization",
"ChemInformatics",
"Bioretrosynthesis"
],
"levelNum": 9
},
{
"id": "723cca21-4044-4387-9c7d-7893b62d2a4e",
"name": "Bioinformatics",
"level": "Senior",
"keywords": [
"Sequence alignment",
"Philogeny Analysis",
"Gene finding"
],
"levelNum": 7
},
{
"id": "1e108ed9-0156-48c6-8c38-48030e17ec06",
"name": "Programming",
"level": "Expert",
"keywords": [
"Java",
"R",
"RDBMs / NoSQL DBs"
],
"levelNum": 9
},
{
"id": "32b32835-3480-491d-b643-efbda23f3d9e",
"name": "Programming",
"level": "Senior",
"keywords": [
"Python",
"Haskell",
"Others"
],
"levelNum": 7
},
{
"id": "1ae94848-c855-438a-898b-eadc8b4e1561",
"name": "Frameworks",
"level": "Expert",
"keywords": [
"Spring/SpringBoot",
"Hibernate",
"Spring Security",
"Spring Data",
"Spring JPA",
"Swagger/OpenAPI"
],
"levelNum": 9
},
{
"id": "f5d3f945-cb97-4fb5-831a-1e26c194cb34",
"name": "AI/Data Science/Machine Learning",
"level": "Senior",
"keywords": [
"Data ETL",
"Visualization",
"Supervised/Unsupervised learning",
"Feature selection",
"Optimization and AI"
],
"levelNum": 7
},
{
"id": "35efb026-c841-49d9-920b-dc3389691348",
"name": "DevOps",
"level": "Senior",
"keywords": [
"Pipeline automation",
"Docker",
"GCP",
"GitLab CI/CD",
"Portainer",
"Artifactory",
"OAuth/OpenIDConnect",
"KeyCloak"
],
"levelNum": 8
},
{
"id": "872aa4cb-7493-4aa0-838a-ddca69de4038",
"name": "SysAdmin",
"level": "Senior",
"keywords": [
"Cluster administration (ROCKs)",
"Linux sysadmin",
"shell/bash scripting",
"Backup automation",
"NAS administration",
"Network and security administrationa"
],
"levelNum": 8
}
],
"columns": 2,
"visible": true
},
"projects": {
"id": "projects",
"name": "Projects",
"type": "basic",
"items": [],
"columns": 2,
"visible": true
},
"education": {
"id": "education",
"name": "Education",
"type": "basic",
"items": [
{
"id": "d157df7d-3c92-4952-b394-f2dc5b329c41",
"area": "Bioengineering",
"date": {
"end": "2015-01-01T00:00:00.000Z",
"start": "2009-01-01T00:00:00.000Z"
},
"degree": "Ph.D.",
"courses": [],
"institution": "University of Minho | MIT Portugal"
},
{
"id": "90851f70-8536-42a4-b018-46402513d221",
"area": "Bioinformatics",
"date": {
"end": "2009-01-01T00:00:00.000Z",
"start": "2007-01-01T00:00:00.000Z"
},
"degree": "M.Sc.",
"courses": [],
"institution": "University of Minho"
},
{
"id": "0954defc-f06d-41b9-a04c-4e7e11400dfe",
"area": "Systems and Informatics Engineering",
"date": {
"end": "2007-01-01T00:00:00.000Z",
"start": "2000-01-01T00:00:00.000Z"
},
"degree": "Bachelors",
"courses": [],
"institution": "University of Minho"
}
],
"columns": 2,
"visible": true
},
"interests": {
"id": "interests",
"name": "Interests",
"type": "basic",
"items": [
{
"id": "bca1d98b-2c3d-4d87-afc5-ebbd045e467b",
"name": "Music",
"keywords": []
},
{
"id": "b534dcb7-5a4d-4153-9a98-9c4e68a13676",
"name": "Cinema",
"keywords": []
},
{
"id": "793e4b71-086e-440d-8417-e767e9bc7799",
"name": "Ethical Hacking",
"keywords": []
},
{
"id": "38b6c64c-0eeb-419f-8e07-45e1bd54cb5e",
"name": "Open Source",
"keywords": []
},
{
"id": "865d23ed-5472-47e8-9c4f-11162f24cc1f",
"name": "Entrepreneurship",
"keywords": []
}
],
"columns": 2,
"visible": false
},
"languages": {
"id": "languages",
"name": "Languages",
"type": "basic",
"items": [
{
"id": "0c52c8a6-be19-47ad-80eb-258454837a35",
"name": "Porguese",
"level": "Native",
"levelNum": 10
},
{
"id": "b0f62662-c50b-4d95-8a4a-7f53c0847f4f",
"name": "English",
"level": "Expert",
"levelNum": 9
},
{
"id": "bf2a5e4b-631a-469d-864e-17985824dfda",
"name": "Spanish",
"level": "Independent",
"levelNum": 6
},
{
"id": "42a8c9cb-0f4b-486f-b49b-03446cd9c77f",
"name": "French",
"level": "Reading proficiency",
"levelNum": 5
}
],
"columns": 2,
"visible": true
},
"volunteer": {
"id": "volunteer",
"name": "Volunteer Experience",
"type": "basic",
"items": [],
"columns": 2,
"visible": true
},
"references": {
"id": "references",
"name": "References",
"type": "basic",
"items": [],
"columns": 2,
"visible": true
},
"publications": {
"id": "publications",
"name": "Publications",
"type": "basic",
"items": [
{
"id": "560ecda0-bd56-4beb-b55e-917be1e0cbe5",
"url": "https://doi.org/10.15252/msb.202110253",
"date": "2021-06-30T23:00:00.000Z",
"name": "Model‐guided development of an evolutionarily stable yeast chassis",
"summary": "",
"publisher": "Molecular systems biology"
},
{
"id": "5d077a07-6202-414f-a5c5-5608064f10b0",
"url": "https://doi.org/10.1038/s41587-020-0446-y",
"date": "2020-03-01T00:00:00.000Z",
"name": "MEMOTE for standardized genome-scale metabolic model testing",
"summary": "",
"publisher": "Nature biotechnology"
},
{
"id": "56e2df6d-4b91-4af9-b603-73c5a0d2d328",
"url": "https://doi.org/10.1186/s12859-019-2934-y",
"date": "2019-12-01T00:00:00.000Z",
"name": "Comparison of pathway analysis and constraint-based methods for cell factory design",
"summary": "",
"publisher": "BMC bioinformatics"
},
{
"id": "38a60770-ad67-49a8-b2c0-2034454d7f99",
"url": "https://doi.org/10.1021/acssynbio.8b00248",
"date": "2019-03-01T00:00:00.000Z",
"name": "Turnover dependent phenotypic simulation: a quantitative constraint-based simulation method that accommodates all main strain design strategies",
"summary": "",
"publisher": "ACS Synthetic Biology"
},
{
"id": "2ce34de8-10b7-4ee6-a37b-8ceafe4ecf90",
"url": "https://doi.org/10.1016/j.nbt.2018.05.181",
"date": "2018-10-09T23:00:00.000Z",
"name": "Yeast chassis design for production of dicarboxylic acids",
"summary": "",
"publisher": "New Biotechnology"
},
{
"id": "d93520ea-5ba5-4e32-9585-ca47e5488b32",
"url": "https://doi.org/10.3389/fmicb.2018.01690",
"date": "2018-01-01T00:00:00.000Z",
"name": "A review of dynamic modeling approaches and their application in computational strain optimization for metabolic engineering",
"summary": "",
"publisher": "Frontiers in Microbiology"
},
{
"id": "972f7b9d-d387-4078-b644-06b6ec7ba94a",
"url": "https://doi.org/10.1007/978-1-4939-7528-0_2",
"date": "2018-01-01T00:00:00.000Z",
"name": "Analyzing and designing cell factories with OptFlux",
"summary": "",
"publisher": "Metabolic Network Reconstruction and Modeling"
},
{
"id": "b206e28b-c4bc-4fe4-8227-2c3525643f02",
"url": "https://doi.org/10.1145/3067695.3082542",
"date": "2017-07-14T23:00:00.000Z",
"name": "Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction",
"summary": "",
"publisher": "Proceedings of the Genetic and Evolutionary Computation Conference Companion"
},
{
"id": "baca52b7-dbb7-4f7e-8659-f0d3548d8631",
"url": "https://doi.org/10.1007/s12539-017-0218-7",
"date": "2017-03-01T00:00:00.000Z",
"name": "Development of a framework for metabolic pathway analysis-driven strain optimization methods",
"summary": "",
"publisher": "Interdisciplinary Sciences: Computational Life Sciences"
},
{
"id": "12a4da6a-b07d-4d50-a5ed-e250865f5ac7",
"url": "https://doi.org/10.1007/978-3-319-40126-3_20",
"date": "2016-05-31T23:00:00.000Z",
"name": "Development of an integrated framework for minimal cut set enumeration in constraint-based models",
"summary": "",
"publisher": "International Conference on Practical Applications of Computational Biology & Bioinformatics"
},
{
"id": "6891f185-6a02-436e-b2a5-729744932e6e",
"url": "https://doi.org/10.1128/MMBR.00014-15",
"date": "2016-03-01T00:00:00.000Z",
"name": "In silico constraint-based strain optimization methods: the quest for optimal cell factories",
"summary": "",
"publisher": "Microbiology and Molecular Biology Reviews"
},
{
"id": "6704c461-8c6e-43fc-aff9-6384196b482e",
"url": "https://doi.org/10.1186/s12918-014-0123-1",
"date": "2014-12-01T00:00:00.000Z",
"name": "CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data",
"summary": "",
"publisher": "BMC systems biology"
},
{
"id": "9bccb798-4573-4742-8838-07963d2935d9",
"url": "https://doi.org/10.1109/CEC.2013.6557571",
"date": "2013-06-19T23:00:00.000Z",
"name": "An integrated framework for strain optimization",
"summary": "",
"publisher": "IEEE Congress on Evolutionary Computation"
},
{
"id": "fc54dab7-4850-4b98-a382-3ae8e4c2a5e2",
"url": "https://doi.org/10.1504/IJDMB.2012.049292",
"date": "2012-01-01T00:00:00.000Z",
"name": "An integrated computational environment for elementary modes analysis of biochemical networks",
"summary": "",
"publisher": "International journal of data mining and bioinformatics"
},
{
"id": "fb6b4ad7-98a7-4a25-8052-b48111f6cb5b",
"url": "https://doi.org/10.1007/978-3-642-23960-1_6",
"date": "2012-03-09T00:00:00.000Z",
"name": "A software platform for evolutionary computation with pluggable parallelism and quality assurance",
"summary": "",
"publisher": "Artificial Intelligence Applications and Innovations"
},
{
"id": "0c7fb409-a828-4424-8948-03d491f0b344",
"url": "https://doi.org/10.1007/978-3-642-19914-1_43",
"date": "2011-01-01T00:00:00.000Z",
"name": "A study on the robustness of strain optimization algorithms",
"summary": "",
"publisher": "5th International Conference on Practical Applications of Computational Biology & Bioinformatics"
},
{
"id": "dcc2952d-36e3-488c-bcc4-e8f5df3dd67e",
"url": "https://doi.org/10.1186/1752-0509-4-45",
"date": "2010-12-01T00:00:00.000Z",
"name": "OptFlux: an open-source software platform for in silico metabolic engineering",
"summary": "",
"publisher": "BMC systems biology"
},
{
"id": "2ba9868c-19c4-4dd9-a82b-9e6e06e45b04",
"url": "https://doi.org/10.1016/j.cmpb.2009.12.003",
"date": "2010-04-30T23:00:00.000Z",
"name": "AIBench: a rapid application development framework for translational research in biomedicine",
"summary": "",
"publisher": "Computer methods and programs in biomedicine"
},
{
"id": "64f14599-5e55-45ec-aed0-49b0b53d1352",
"url": "https://doi.org/10.1007/978-3-642-13214-8_28",
"date": "2010-01-01T00:00:00.000Z",
"name": "Enhancing Elementary Flux Modes Analysis Using Filtering Techniques in an Integrated Environment",
"summary": "",
"publisher": "Advances in Bioinformatics"
},
{
"id": "ef4cfac5-c30c-42e6-ade5-f315a36921d4",
"url": "https://doi.org/10.1109/ISDA.2009.161",
"date": "2009-11-30T00:00:00.000Z",
"name": "Implementing metaheuristic optimization algorithms with jecoli",
"summary": "",
"publisher": "IEEE"
},
{
"id": "f0f2319f-6961-4aff-9bca-08f48d6a13e8",
"url": "https://doi.org/10.1016/j.jbi.2009.04.002",
"date": "2009-07-31T23:00:00.000Z",
"name": "@ Note: a workbench for biomedical text mining",
"summary": "",
"publisher": "Journal of biomedical informatics"
},
{
"id": "f2f879bf-f8d9-4d53-b26c-6967603fc5f2",
"url": "https://doi.org/10.1186/1471-2105-9-499",
"date": "2008-12-01T00:00:00.000Z",
"name": "Natural computation meta-heuristics for the in silico optimization of microbial strains",
"summary": "",
"publisher": "BMC Bioinformatics"
}
],
"columns": 2,
"visible": true
},
"certifications": {
"id": "certifications",
"name": "Certifications",
"type": "basic",
"items": [],
"columns": 2,
"visible": true
},
"a5930813-1d8a-4ad5-8708-7d4217eb81a6": {
"name": "Communications",
"type": "custom",
"items": [
{
"id": "e7f074fc-da85-4248-bea1-ecd1e79fc5bb",
"url": "http://xpto.com",
"date": {
"end": "",
"start": "2010-01-01T00:00:00.000Z"
},
"level": "",
"title": "talk",
"summary": "",
"keywords": [],
"levelNum": 0,
"subtitle": "sub talk"
}
],
"columns": 2,
"visible": true
}
},
"metadata": {
"css": {
"value": "/* Enter custom CSS here */\n\n* {\n outline: 1px solid #000;\n}",
"visible": false
},
"date": {
"format": "YYYY"
},
"theme": {
"text": "#000000",
"primary": "#4896d5",
"background": "#ffffff"
},
"layout": [
[
[
"work",
"education",
"projects"
],
[
"references",
"certifications",
"volunteer"
]
],
[
[
"languages",
"skills",
"awards",
"publications",
"a5930813-1d8a-4ad5-8708-7d4217eb81a6",
"interests"
],
[]
]
],
"locale": "en",
"template": "onyx",
"typography": {
"size": {
"body": 12,
"heading": 36
},
"family": {
"body": "Open Sans",
"heading": "Open Sans"
}
}
},
"public": false
}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment