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

  • 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.
  • 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.
  • 2012 - 2016
    Bachelor of Science
    Instituto Superior Técnico, University of Lisbon, Portugal
    • Bachelor's degree in Applied Mathematics and Computer Science.

Experience

  • 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
  • 2023 - Now
    Postdoctoral Research Associate
    Queens' College, University of Cambridge
    • Rokos PDRA at Queens' College, University of Cambridge.
  • 2023 - Now
    College Supervisor
    Queens' College, University of Cambridge
    • Supervision of multiple undergraduate modules in Mathematics and Natural Sciences.
  • 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).
  • 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.
  • 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.
  • 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.
  • 2015 - 2016
    High School Tutor
    Mathematics, Physics, and Natural Sciences, Lisbon, Portugal
    • Provided tutoring services in high school-level tutoring academies.
  • 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

  • Oct 2024
    Research Pitch at LUSO 2024
    PARSUK
    • Presentation on current research at the Portuguese Association of Students and Researchers in the UK (PARSUK).
  • 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'.
  • 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.
  • 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.
  • 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'.
  • 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.
  • Oct 2022
    CMP Seminar, Cellular and Molecular Pathology Seminar Series
    University of Cambridge
    • Talk on Notch-Delta long-range signalling dynamics via cell protrusions.
  • 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'.
  • 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'.
  • 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'.
  • 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.
  • 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.
  • 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

  • 2024 - Now
    RepliFit
    • Toolkit for analyzing DNA replication timing, origin firing rates, and genomic stability.
  • 2018 - Now
    Interactive Epithelium
    • A beautiful, practical tool for epithelial cell signalling simulations.
  • 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.
  • 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

  • 2018 - 2019
    London Mathematical Society Courses
    London Taught Course Centre (LTCC), London Mathematical Society
    • Topics: Dynamical Systems, Stochastic Processes, Models, and Measure Theory.
  • 2018
    Teaching Training
    Institute of Education (IoE), UCL
    • Completion of the 'Teaching Undergraduates Mathematics or Statistics' (TUMIPS) program.
  • 2017
    TOEFL
    • Score: 108/120.

Skills & Abilities

  • Programming
    • Python, PyTorch, MatLab, R, Wolfram Mathematica, C, C#, C++, Beacon Calculus.
  • Software
    • Writing: LaTeX, MS Office.
    • Teaching: Crowdmark, Blackboard Learn, STACK, WISEflow.
  • Languages
    • Portuguese (Native speaker), English (fluent), comfortable with Spanish and French.

Academic Interests

  • Biology
    • DNA replication dynamics
    • Replication stress and chemotherapy
    • Genome stability and cancer
    • Cell-cell signalling
    • Pattern formation
    • Evolutionary dynamics
  • Mathematics
    • Partial differential equations
    • Stochastic processes
    • Game theory
    • Functional analysis
  • Machine Learning
    • Physics-informed machine learning
    • Neural operators

Extracurricular Activities

  • 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.
  • 2018 - 2022
    Student Union
    University College London
    • Member of the Classical Guitar, Chamber Music, and Hiking Societies at UCL.
  • 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.
  • 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.
  • 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.
  • 2005 - Now
    Sports
    • Engaged in amateur-level sports, including football, tennis, swimming, and skiing. Two years of federated-level football experience.