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- title: General Information
type: map
contents:
- name: Full Name
value: Francisco Pinto Berkemeier
- name: Date of Birth
value: 22 July 1993
- name: Affiliation
value: Departments of Pathology and Genetics, University of Cambridge
- name: Position
value: Postdoctoral Researcher
- title: Education
type: time_table
contents:
- title: Doctor of Philosophy
institution: University College London, London, United Kingdom
year: 2018 - 2022
description:
- 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."
- title: Master of Science
institution: King Abdullah University of Science and Technology, Saudi Arabia
year: 2016 - 2018
description:
- Master's degree in Applied Mathematics and Computer Science.
- Thesis title. A priori regularity of parabolic partialdifferential equations.
- "Supervisor: Diogo A. Gomes."
- title: Bachelor of Science
institution: Instituto Superior Técnico, University of Lisbon, Portugal
year: 2012 - 2016
description:
- Bachelor's degree in Applied Mathematics and Computer Science.
- title: Experience
type: time_table
contents:
- title: Postdoctoral Researcher
institution: Departments of Pathology and Genetics, University of Cambridge
year: 2022 - Now
description:
- Research Associateship at the University of Cambridge, in the Boemo Group.
- "Supervisor: Michael A. Boemo."
- title: "Main areas of research:"
contents:
- DNA replication.
- Computational genetics.
- Physics-informed machine learning
- title: Postdoctoral Research Associate
institution: Queens' College, University of Cambridge
year: 2023 - Now
description:
- Rokos PDRA at Queens' College, University of Cambridge.
- title: College Supervisor
institution: Queens' College, University of Cambridge
year: 2023 - Now
description:
- Supervision of multiple undergraduate modules in Mathematics and Natural Sciences.
- title: Master's Project Supervisor
institution: Department of Pathology, University of Cambridge
year: 2023 - 2024
description:
- 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).
- title: Lecturer
institution: Applied Mathematics, University College London
year: 2020 - 2021
description:
- 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."
- title: Teaching Assistant
institution: Applied Mathematics, University College London & KAUST
year: 2017 - 2022
description:
- 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."
- title: University-level Tutor
institution: Pure and Applied Mathematics, Lisbon, Portugal
year: 2015 - 2016
description:
- Tutored students in several university tutoring centers and collaborated with the student math association at IST.
- title: High School Tutor
institution: Mathematics, Physics, and Natural Sciences, Lisbon, Portugal
year: 2015 - 2016
description:
- Provided tutoring services in high school-level tutoring academies.
- title: Visiting Student
institution: KAUST, Saudi Arabia
year: 2014
description:
- 4-month undergraduate Visiting Student Research Program (VSRP).
- "Research topics: Mean-Field Games, PDEs, and Functional Analysis."
- "Supervisor: Prof. Diogo A. Gomes."
- title: Talks
type: time_table
contents:
- title: Research Pitch at LUSO 2024
institution: PARSUK
year: Oct 2024
description:
- Presentation on current research at the Portuguese Association of Students and Researchers in the UK (PARSUK).
- title: UK DNA Replication Meeting 2024, Poster Session
institution: Churchill College, University of Cambridge
year: Sep 2024
description:
- Presentation of the poster 'A Whole-Genome Mathematical Model of DNA Replication'.
- title: Invited Talk, Mathematics and Applications Colloquium - AMCS (CEMSE)
institution: King Abdullah University of Science and Technology
year: May 2024
description:
- Invited talk on mathematical modelling of DNA replication.
- title: Plenary Talk, Pathology Annual Symposium
institution: Li Ka Shing Centre, Cancer Research UK Cambridge Institute
year: Mar 2024
- title: SCR Talk, MCR-SCR Research Talks
institution: Queens' College, University of Cambridge
year: Mar 2024
- title: Research Seminar, Genetics Internal Seminars
institution: Department of Genetics, University of Cambridge
year: Mar 2024
- title: UCL Talk, Mathematical Biology Seminar
institution: Department of Mathematics, University College London
year: Jan 2024
description:
- Talk on current research, specifically on the development of a whole-genome mathematical model of DNA replication in human cells.
- title: Research in Genetics Day 2023, Poster Session
institution: Department of Genetics, University of Cambridge
year: Nov 2023
description:
- Presentation of the poster 'A Whole-Genome Mathematical Model of DNA Replication'.
- title: OxML 2023, Machine Learning Summer School
institution: Mathematical Institute, Oxford
year: Jul 2023
description:
- 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.
- title: CMP Seminar, Cellular and Molecular Pathology Seminar Series
institution: University of Cambridge
year: Oct 2022
description:
- Talk on Notch-Delta long-range signalling dynamics via cell protrusions.
- title: ECMTB 2022 Talk, European Conference on Mathematical and Theoretical Biology
institution: Heidelberg University
year: Sep 2022
description:
- "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'."
- title: SLCU Talk
institution: Sainsbury Laboratory, University of Cambridge
year: Apr 2022
description:
- Invited talk at Dr Henrik Jönsson's research group meeting on PhD research, titled 'Long-range signalling and patterns in the fly wing'.
- title: IPLS Talk, Institute for the Physics of Living Systems
institution: University College London
year: Nov 2021
description:
- 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'.
- title: Math Bio Talk, Departmental Computational Biology Group
institution: University College London
year: Nov 2021
description:
- 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.
- title: Poster Competition Panel Member
institution: Pure and Applied Mathematics Undergraduate Projects, UCL
year: 2020 - 2021
description:
- 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.
- title: Cambridge Conference, 'Evolution Evolving' Conference
institution: University of Cambridge
year: 2019
description:
- 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.
- title: Projects
type: time_table
contents:
- title: <a href="https://github.com/fberkemeier/DNA_replication_model">RepliFit</a>
year: 2024 - Now
description: Toolkit for analyzing DNA replication timing, origin firing rates, and genomic stability.
- title: <a href="https://github.com/fberkemeier/Notch-Delta-Coupling">Interactive Epithelium</a>
year: 2018 - Now
description: A beautiful, practical tool for epithelial cell signalling simulations.
- title: Live StackOverflow
institution: Postgraduate Research Group, UCL/LMCB
year: 2021
description:
- 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.
- title: M\(\LaTeX\)
institution: KAUST
year: 2016
description:
- Windows implementation of the saving directories of 'MLaTeX', a set of tools simplifying the interface between LaTeX and Mathematica.
- title: Tests & Certifications
type: time_table
contents:
- title: London Mathematical Society Courses
institution: London Taught Course Centre (LTCC), London Mathematical Society
year: 2018 - 2019
description:
- "Topics: Dynamical Systems, Stochastic Processes, Models, and Measure Theory."
- title: Teaching Training
institution: Institute of Education (IoE), UCL
year: 2018
description:
- Completion of the 'Teaching Undergraduates Mathematics or Statistics' (TUMIPS) program.
- title: TOEFL
year: 2017
description:
- "Score: 108/120."
#- title: General GRE
#year: 2017
#description:
#- "Scores: Analytical Writing: 3.5/6.0, Verbal Reasoning: 152/170, Quantitative Reasoning: 164/170."
- title: Skills & Abilities
type: nested_list
contents:
- title: Programming
items:
- Python, PyTorch, MatLab, R, Wolfram Mathematica, C, C#, C++, Beacon Calculus.
- title: Software
items:
- "Writing: LaTeX, MS Office."
- "Teaching: Crowdmark, Blackboard Learn, STACK, WISEflow."
- title: Languages
items:
- Portuguese (Native speaker), English (fluent), comfortable with Spanish and French.
- title: Academic Interests
type: nested_list
contents:
- title: Biology
items:
- DNA replication dynamics
- Replication stress and chemotherapy
- Genome stability and cancer
- Cell-cell signalling
- Pattern formation
- Evolutionary dynamics
- title: Mathematics
items:
- Partial differential equations
- Stochastic processes
- Game theory
- Functional analysis
- title: Machine Learning
items:
- Physics-informed machine learning
- Neural operators
- title: Extracurricular Activities
type: time_table
contents:
- title: Presidency
institution: Cambridge University Portuguese Society
year: 2023 - 2024
description:
- 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.
- title: Student Union
institution: University College London
year: 2018 - 2022
description:
- Member of the Classical Guitar, Chamber Music, and Hiking Societies at UCL.
- title: Classical Guitar
year: 2005 - Now
description:
- 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.
- title: Almada's Music Academy
institution: Portugal
year: 2005 - 2012
description:
- 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.
- title: Volunteering
year: 2012 - 2016
description:
- title: "Participation in various volunteering activities, including:"
contents:
- Elderly home visits
- Beach cleaning
- Organization of homeless dinners.
- Leadership role in a non-governmental volunteering organization in workshops in Portugal and Germany.
- title: Sports
year: 2005 - Now
description:
- Engaged in amateur-level sports, including football, tennis, swimming, and skiing. Two years of federated-level football experience.