CV
My Curriculum Vitae
General Information
Full Name | Francisco Pinto Berkemeier |
Date of Birth | 22 July 1993 |
Affiliation | Departments of Pathology and Genetics, University of Cambridge |
Position | Postdoctoral Researcher |
Education
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2018 - 2022 Doctor of Philosophy
University College London, London, United Kingdom - PhD in Applied Mathematics.
- Thesis title: Cell-cell interactions in epithelial patterning: Notch-Delta signalling and evolutionary dynamics.
- Supervisors: Karen M. Page and Nadia Sidorova.
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2016 - 2018 Master of Science
King Abdullah University of Science and Technology, Saudi Arabia - Master's degree in Applied Mathematics and Computer Science.
- Thesis title. A priori regularity of parabolic partialdifferential equations.
- Supervisor: Diogo A. Gomes.
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2012 - 2016 Bachelor of Science
Instituto Superior Técnico, University of Lisbon, Portugal - Bachelor's degree in Applied Mathematics and Computer Science.
Experience
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2022 - Now Postdoctoral Researcher
Departments of Pathology and Genetics, University of Cambridge - Research Associateship at the University of Cambridge, in the Boemo Group.
- Supervisor: Michael A. Boemo.
- Main areas of research:
- DNA replication.
- Computational genetics.
- Physics-informed machine learning
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2023 - Now Postdoctoral Research Associate
Queens' College, University of Cambridge - Rokos PDRA at Queens' College, University of Cambridge.
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2023 - Now College Supervisor
Queens' College, University of Cambridge - Supervision of multiple undergraduate modules in Mathematics and Natural Sciences.
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2023 - 2024 Master's Project Supervisor
Department of Pathology, University of Cambridge - Supervision and mentorship of a master's student during a year-long placement research project on modelling DNA replication as part of an integrated master’s in Biochemistry (University of St. Andrews).
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2020 - 2021 Lecturer
Applied Mathematics, University College London - Lecturer of an undergraduate mathematics course (Mathematics for Engineers 1)
- Topics: differentiation, integration, differential equations, vectors, probability, statistics, and numerical methods.
- Other duties: homework/exam structuring, marking, and office hours.
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2017 - 2022 Teaching Assistant
Applied Mathematics, University College London & KAUST - Provided teaching assistance at undergraduate and master's levels
- Main duties: tutorial classes, exam/homework marking, and office hours.
- Topics: calculus, linear algebra, complex analysis, mechanics, and numerical analysis.
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2015 - 2016 University-level Tutor
Pure and Applied Mathematics, Lisbon, Portugal - Tutored students in several university tutoring centers and collaborated with the student math association at IST.
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2015 - 2016 High School Tutor
Mathematics, Physics, and Natural Sciences, Lisbon, Portugal - Provided tutoring services in high school-level tutoring academies.
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2014 Visiting Student
KAUST, Saudi Arabia - 4-month undergraduate Visiting Student Research Program (VSRP).
- Research topics: Mean-Field Games, PDEs, and Functional Analysis.
- Supervisor: Prof. Diogo A. Gomes.
Talks
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Oct 2024 Research Pitch at LUSO 2024
PARSUK - Presentation on current research at the Portuguese Association of Students and Researchers in the UK (PARSUK).
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Sep 2024 UK DNA Replication Meeting 2024, Poster Session
Churchill College, University of Cambridge - Presentation of the poster 'A Whole-Genome Mathematical Model of DNA Replication'.
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May 2024 Invited Talk, Mathematics and Applications Colloquium - AMCS (CEMSE)
King Abdullah University of Science and Technology - Invited talk on mathematical modelling of DNA replication.
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Mar 2024 Plenary Talk, Pathology Annual Symposium
Li Ka Shing Centre, Cancer Research UK Cambridge Institute -
Mar 2024 SCR Talk, MCR-SCR Research Talks
Queens' College, University of Cambridge -
Mar 2024 Research Seminar, Genetics Internal Seminars
Department of Genetics, University of Cambridge -
Jan 2024 UCL Talk, Mathematical Biology Seminar
Department of Mathematics, University College London - Talk on current research, specifically on the development of a whole-genome mathematical model of DNA replication in human cells.
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Nov 2023 Research in Genetics Day 2023, Poster Session
Department of Genetics, University of Cambridge - Presentation of the poster 'A Whole-Genome Mathematical Model of DNA Replication'.
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Jul 2023 OxML 2023, Machine Learning Summer School
Mathematical Institute, Oxford - Participation in the Oxford Machine Learning Summer School, focused on statistical/probabilistic ML, representation learning, reinforcement learning, causal inference, vision & NLP, geometrical DL, among other topics.
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Oct 2022 CMP Seminar, Cellular and Molecular Pathology Seminar Series
University of Cambridge - Talk on Notch-Delta long-range signalling dynamics via cell protrusions.
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Sep 2022 ECMTB 2022 Talk, European Conference on Mathematical and Theoretical Biology
Heidelberg University - Participation on the mini-symposium 'Bistable genetic switches across time, space, and disciplines' at ECMTB 2022. Talk title: 'The dynamics of long-range signalling via the Notch-Delta pathway'.
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Apr 2022 SLCU Talk
Sainsbury Laboratory, University of Cambridge - Invited talk at Dr Henrik Jönsson's research group meeting on PhD research, titled 'Long-range signalling and patterns in the fly wing'.
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Nov 2021 IPLS Talk, Institute for the Physics of Living Systems
University College London - Talk and discussion on mathematical models of signalling pathways vs stretch-induced deformations on the wing disc, titled 'How stretch affects patterning in the fly wing'.
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Nov 2021 Math Bio Talk, Departmental Computational Biology Group
University College London - Presentation at the multi-disciplinary computational biology group meeting on the mathematical analysis of long-range signalling systems, including linear and stochastic stability analysis and applications. Supervised by Philip Pearce.
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2020 - 2021 Poster Competition Panel Member
Pure and Applied Mathematics Undergraduate Projects, UCL - Supervised the annual UCL mathematics undergraduate poster competition, where students presented their second-year projects on topics ranging from theoretical exercises in differential geometry to dynamical systems applied to the study of pandemic evolution.
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2019 Cambridge Conference, 'Evolution Evolving' Conference
University of Cambridge - Participated in the 'Evolution Evolving' conference at Churchill College, University of Cambridge. Topics included evolutionary causes and consequences of developmental bias, plasticity, niche construction, and extra-genetic inheritance, approached from mathematical, biological, and philosophical perspectives.
Projects
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2024 - Now RepliFit
- Toolkit for analyzing DNA replication timing, origin firing rates, and genomic stability.
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2018 - Now Interactive Epithelium
- A beautiful, practical tool for epithelial cell signalling simulations.
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2021 Live StackOverflow
Postgraduate Research Group, UCL/LMCB - Co-founder and organiser of 'Live StackOverflow', a weekly meeting group for PhD and postdoc students working in applied mathematics, physics, and computational biology at UCL. The group provides a friendly, non-formal platform for discussions on improving social, presentation, and research skills among new postgraduate students.
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2016 M\(\LaTeX\)
KAUST - Windows implementation of the saving directories of 'MLaTeX', a set of tools simplifying the interface between LaTeX and Mathematica.
Tests & Certifications
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2018 - 2019 London Mathematical Society Courses
London Taught Course Centre (LTCC), London Mathematical Society - Topics: Dynamical Systems, Stochastic Processes, Models, and Measure Theory.
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2018 Teaching Training
Institute of Education (IoE), UCL - Completion of the 'Teaching Undergraduates Mathematics or Statistics' (TUMIPS) program.
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2017 TOEFL
- Score: 108/120.
Skills & Abilities
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Programming
- Python, PyTorch, MatLab, R, Wolfram Mathematica, C, C#, C++, Beacon Calculus.
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Software
- Writing: LaTeX, MS Office.
- Teaching: Crowdmark, Blackboard Learn, STACK, WISEflow.
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Languages
- Portuguese (Native speaker), English (fluent), comfortable with Spanish and French.
Academic Interests
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Biology
- DNA replication dynamics
- Replication stress and chemotherapy
- Genome stability and cancer
- Cell-cell signalling
- Pattern formation
- Evolutionary dynamics
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Mathematics
- Partial differential equations
- Stochastic processes
- Game theory
- Functional analysis
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Machine Learning
- Physics-informed machine learning
- Neural operators
Extracurricular Activities
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2023 - 2024 Presidency
Cambridge University Portuguese Society - As President of the Cambridge University Portuguese Society (CUPor), I helped leading a dynamic cultural community, coordinating a diverse range of events, managing an executive committee, organizing sociocultural events, and advocating for Portuguese students at the university.
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2018 - 2022 Student Union
University College London - Member of the Classical Guitar, Chamber Music, and Hiking Societies at UCL.
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2005 - Now Classical Guitar
- Experienced in playing various styles including Classical, Jazz, and Bossa Nova in a range of events.
- Contributed to group musical arrangements and participated actively in ensemble performances.
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2005 - 2012 Almada's Music Academy
Portugal - Completed undergraduate studies in classical guitar (8th degree).
- Participated in several guitar contests and talent shows, winning first and second prizes, as well as honorable mentions.
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2012 - 2016 Volunteering
- Participation in various volunteering activities, including:
- Elderly home visits
- Beach cleaning
- Organization of homeless dinners.
- Leadership role in a non-governmental volunteering organization in workshops in Portugal and Germany.
- Participation in various volunteering activities, including:
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2005 - Now Sports
- Engaged in amateur-level sports, including football, tennis, swimming, and skiing. Two years of federated-level football experience.