Rasmus Kristoffer Pedersen

Mathematical modelling, data visualization and data analysis - +45 23220212 - rasmuspedersen1992@gmail.com

Welcome to my personal website. Here you will find my Curriculum Vitae as well as links to some of my other stuff.

I am currently employed as a PostDoc at Roskilde University, where I am part of the PandemiX research group, investigating historical pandemics and the COVID-19 pandemic. Read more about PandemiX here.
In my Ph.D. I worked with mathematical modelling of MPNs, as part of the Cancitis Research Group. Read more about Cancitis here.

Link to PDF-version of CV


Quick links for various interactive visualizations:


Portfolio

COVID-19 hospitalization-rate for vaccinated individuals

COVID-19 hospitalizations
2022

Heatmap comparing the number of new hospitalizations due to COVID-19 in different age-groups, depending on vaccination-status. Shows the number of hospitalizations per 100,000 citizens in each age-group, including the raw numbers. When I made the figure, the public focus was about the number of new hospitalizations, without regard for the size of the corresponding population-group in general (As an example, week 46 had 80 hospitalizations among vaccinated 80+-year old, with "only" 13 among the unvaccinated in same age-group. Relative to the population-groups however, the unvaccinated where three times as likely to be hospitalized).

COVID-19 hospitalization-rate, additional figures

COVID-19 Nyindlæggelser COVID-19 nyindlagte 20-29

2022

Supplementary figure to the heatmap, illustrating the number of new hospitalizations and hospitalizations per 100,000 for a specific week. To illustrate the main point, I also illustrated the proportion of hospitalization of 20-29 year olds as dots representing 5% of the population-group.

COVID-19 case-fatality ratio

COVID-19 CFR
2022

Illustration of the progression of a naive calculation of the COVID-19 case-fatality rate (CFR) for Denmark from the start of the pandemic until April 2022. The figure shows how CFR declines as the vulnerable are vaccinated, increases as the Delta-variant dominates, and then again declines as booster-vaccinations are carried out and the Omicron variant dominates. Inspired by a similar figure for the UK created by John Burn-Murdoch.

Educational material for Danish high schools (Gymnasium)

Undervisningspakke Youtube screenshot

2022

Development of educational material with the purpose of student-recruitment for the educations at Roskilde University, consisting of a short article, a worksheet and a video.

Material available online: https://ruc.dk/undervisningspakke-epidemier-og-matematiske-modeller

Interative figure for "Kapløb med COVID" article

Oversigtsfigur til artikel Screenshot af interaktiv figur af hospitaliseringer
2021

Interactive figures showing model-calculations of the COVID-19 wave in Denmark during the summer of 2021. Increased vaccine-uptake and reduced sociatal infection meant that COVID-19 was dying out. The arrival of the Delta- and Omicron-variants meant that later COVID-19 waves occured at the end of 2021. Developed for (Danish) article on Videnskab.dk: https://videnskab.dk/krop-sundhed/kaploebet-med-covid-19-kan-det-naa-at-gaa-helt-galt-eller-er-vi-allerede-i-maal/

Visualizations available online: Interaktivt/CovidSommer/cases Interaktivt/CovidSommer/hospData

Interactive “Viral load” figure

Screenshot af viral load figur
2021

Illustration of the viral load of an individual following a COVID-19 infection, and different testing strategies. The figure illustrates how frequent tests with a less sensitive test (e.g. lateral flow tests) can be better at detecting infections when compared to less frequent tests with a higher sensitivity (e.g. PCR-tests). Developed as part of PandemiX's modelling support of governmental investigation before the roll-out of the massive Danish COVID-19 lateral-flow testing strategy at the beginning of 2021.

Visualization available online: InteractiveViralLoad

Interactive prediction of the arrival of the Alpha-variant

Screenshot af interaktiv figur
2021

Decreasing COVID-19 infections following Christmas 2020/2021 and the arrival of the B.1.1.7 variant (later named Alpha), meant that, despite decreasing infections, an increase could be expected within a couple of weeks. Prediction made around week 5, and ended up being accurate for the following weeks. Developted for (Danish) article for Videnskab.dk: https://videnskab.dk/naturvidenskab/britisk-variant-lurer-stadig-denne-interaktive-beregner-viser-hvorfor-vi-er-noedt-til-at-holde-fast/

Visualization available online: InteractiveExponential

Interactive SIR-model

Screenshot af interaktiv figur
2020, 2021, 2022

The SIR-model is a classic model within epidemiology, and one of the mathematical arguments behind the COVID-19 lockdown in March 2020. During the COVID-19 pandemic, I made a number of interactive visualizations of the SIR-model for make it easier for laypersons to get an intuitive understnaindg of how the model works, and the model parameters.
Developed for (Danish) articles for Videnskab.dk:
https://videnskab.dk/krop-sundhed/tilbage-til-begyndelsen-lav-dine-egne-corona-kurver/
https://videnskab.dk/krop-sundhed/vender-covid-19-for-alvor-tilbage/

Visualizations available online:
Interactive/SIR/ and Interactive/SIRS/ and Interactive/SIR_simple/

Interactive SIR-model, agent-based

Screenshot af interaktiv simulering
2016 and 2017

Long before COVID-19 made disease-spread and epidemiology common terms, I worked with mathematical epidemiology as a student. During my education, I was part of the Science Show at Roskilde University, in which we made public dissemination of various student-projets in an effort to attract new student to Roskilde University. For the Science Show presentations, I developed an agent-based visualization of the SIR-model, to illustrate different epidemiological aspects.

Visualizations available online:
SIR

Scientific publications

"COVID-19 mortality attenuated during widespread Omicron transmission, Denmark, 2020 to 2022"

Nikolaj U. Friis, Tomas Martin-Bertelsen, Rasmus K. Pedersen, Jens Nielsen, Tyra G. Krause, Viggo Andreasen, Lasse S. Vestergaard

Published in Eurosurveillance, Volume 28, Issue 3, 2023

"Understanding Hematopoietic Stem Cell Dynamics - Insights from Mathematical Modelling"

Rasmus K. Pedersen, Morten Andersen, Thomas Stiehl, Johnny T. Ottesen

Published in Current Stem Cell Reports, 2023

"HSC niche dynamics in regeneration, pre-malignancy and cancer: Insights from mathematical modeling"

Rasmus K. Pedersen, Morten Andersen, Vibe Skov, Lasse Kjær, Hans C. Hasselbalch, Johnny T. Ottesen, Thomas Stiehl

Published in Stem Cells, 2022

"Temperate climate malaria in nineteenth century Denmark"

Mathias Mølbak Ingholt, Tzu Tung Chen, Franziska Hildebrandt, Rasmus K. Pedersen, Lone Simonsen

Published in BMC Infectious Diseases, Volume 22, Article number 432, 2022

"A novel integrated biomarker index for the assessment of hematological responses in MPNs during treatment with hydroxyurea and interferon-alpha2"

Marc J.B. Dam, Rasmus K. Pedersen, Trine A. Knudsen, Morten Andersen, Christina Ellervik, Morten K. Larsen, Lasse Kjær, Vibe Skov, Hans C. Hasselbalch, Johnny T. Ottesen

Published in Cancer Medicine, (Early view), 2022

"Dose-dependent mathematical modeling of interferon-α-treatment for personalized treatment of myeloproliferative neoplasms"

Rasmus K. Pedersen, Morten Andersen, Trine A. Knudsen, Vibe Skov, Lasse Kjær, Hans C. Hasselbalch, Johnny T. Ottesen

Published in Computational and Systems Oncology, Volume 1, Issue 4, 2021
Published in Journal of Theoretical Biology, Volume 518, 2021
Published in European Journal of Haematology, Volume 107, 2021

"Mathematical Modeling of MPNs Offers Understanding and Decision Support for Personalized Treatment."

Johnny T. Ottesen, Rasmus K. Pedersen, Marc J. B. Dam, Trine A. Knudsen, Vibe Skov, Lasse Kjær, Morten Andersen

Published in Cancers, 2020, 12(8)

"Data-driven analysis of JAK2V617F kinetics during interferon-alpha2 treatment of patients with polycythemia vera and related neoplasms"

Rasmus K. Pedersen, Morten Andersen, Trine A. Knudsen, Zamra Sajid, Johanne Gudmand-Hoeyer, Marc J. B. Dam, Vibe Skov, Lasse Kjær, Christina Ellervik, Thomas S. Larsen, Dennis Hansen, Niels Pallisgaard, Hans C. Hasselbalch, Johnny T. Ottesen

Published in Cancer Medicine, 2020, 9(6)

"Bridging blood cancers and inflammation: The reduced Cancitis model"

Johnny T. Ottesen, Rasmus K. Pedersen, Zamra Sajid, Johanne Gudmand-Hoeyer, Katrine O. Bangsgaard, Vibe Skov, Lasse Kjær, Trine A. Knudsen, Niels Pallisgaard, Hans Carl Hasselbalch, Morten Andersen

Published in Journal of Theoretical Biology, 2019, Volume 465

"Mathematical Modelling as a Proof of Concept for MPNs as a Human Inflammation Model for Cancer Development"

Morten Andersen, Zamra Sajid, Rasmus K. Pedersen, Johanne Gudmand-Hoeyer, Christina Ellervik, Vibe Skov, Lasse Kjær, Niels Pallisgaard, Torben A. Kruse, Mads Thomassen, Jesper Troelsen, Hans Carl Hasselbalch, Johnny T. Ottesen

Published in PLoS One, 2017, 12(8)

Presentations, posters and more

"Epidemics 9”, Bologna, Italy - November 30th, 2023
"Data-driven mechanistic mathematical modelling for life-science applications” 2023, Gothenburg, Sweden - October 23rd, 2023

"How to visualize your science"

Invited presentation

"PhD-day 2023”, Department of Science and Environment, Roskilde University - October 6th, 2023
ECMTB 2022, Heidelberg, Germany - September 22nd, 2022

"Mathematical Modelling of Myeloproliferative Neoplasms and Hematopoietic Stem Cells"

Contributed Talk

The Second Nordic Biomathematics Days, Roskilde, Denmark - May 10th, 2022

"Modelling Hematopoietic Stem Cells and their Interaction with the Bone Marrow Micro-Environment."

Contributed Talk (Cancelled due to Corona-Virus)

ECMTB 2020, Heidelberg, Germany - September 2020 (Cancelled due to Corona-Virus)
Chalmers, Gothenburg, Sweden - April 21st, 2020
The First Nordic Biomathematics Days, Helsinki, Finland - October 22nd, 2019
Roskilde University, Denmark - September 18th, 2019

"Modelling the Dynamics of Hematopoietic Stem Cells"

Poster at "SIAM Conference on Applications of Dynamical Systems"

Snowbird, Utah, USA - May, 2019

"Modelling of Quiescent Stem Cells in Relation to Myeloproliferative Neoplasms"

Poster at "European Conference on Mathematical and Theoretical Biology"

Lisbon, Portugal - July, 2018

Additional science-communication

In 2021 and 2022, I wrote and co-wrote a number of science-communication-articles, for the broad public, published at danish science-news website videnskab.dk. For a complete list, see here.

"Communicating Mathematics with Interactive Visualizations"

Talk at Studiensfonds Community Conference, Bielefeld, Germany

August 9th, 2022

"Communicating Science and Mathematics with Interactive Visualizations"

Talk at DataViz CPH meetup

September 23rd, 2021
Copenhagen, Denmark - January 31st, 2020

Education

September 2017 - November 2020

Master of science in mathematics and physics

MSc, Roskilde University
August 2015 - August 2017

Bachelor-degree in mathematics and physics

Bach. Scient., Roskilde University
August 2011 - June 2014

HTX

Slotshaven, Holbæk

Physics A-level / Mathematics A-level

August 2008 - July 2011

Experience

Research assistant at Department of Science and Environment

Roskilde University
Fall 2021

PostDoc at PandemiX research center

Roskilde University
Spring 2021

Course teacher - "Modelling Populations and Epidemics"

Roskilde University
Fall 2020

Course teacher - "Mathematical modelling and dynamic systems"

Roskilde University
Fall 2018 and Fall 2019

Teaching assistant - BK2: "Experimental Methods"

Roskilde University
Spring 2017

Teaching assistant - Calculus

Roskilde University
Fall 2016

Teaching assistant - BK1: "Empirical Data"

Roskilde University
Fall 2015

Developer and active part of Science Show

Roskilde University
September 2016 - June 2017

Full-time substitute mathematics teacher

Roskilde Gymnasium
I had the sole responsibility for the math-education of two first year high-school classes
September 2014 - June 2015

Competencies

IT-Competencies

Language

Volunteer work