Algebraic Systems Biology Group

Contact details

Mathematical Institute
Radcliffe Observatory Quarter
Woodstock Road
Oxford OX2 6GG
United Kingdom

Email: lastname@maths.ox.ac.uk
Phone: +44 (0)1865273510

Current members

Principal Investigator

Heather A Harrington
CV
Biography

Postdoctoral Researchers

Hamid Rahkooy

Postdoctoral Researcher funded by Royal Society
(from October 2022)

Adam Brown

Postdoctoral Researcher in Centre for TDA
(from October 2022)

Pedro Soto

Postdoctoral Researcher in Wellcome Centre of Human Genetics
(from September 2022)

Oliver Gäfvert

Postdoctoral Researcher in Centre for Topological Data Analysis
(from October 2021)

Gillian Grindstaff

Postdoctoral Researcher in Centre for Topological Data Analysis and Royal Society Grant
(from September 2021, returning September 2023 as NSF Postdoctoral Fellow)

Hee Rhang (Iris) Yoon

Postdoctoral Researcher in Centre for Topological Data Analysis and Mathematical Biology
(from April 2022)

Graduate Students

Piotr Sliwa (jointly supervised with Gesine Reinert and Julian Knight)

Mathematics DPhil student (from October 2021)

Katherine Benjamin (jointly supervised with Ulrike Tillmann)

Mathematics DPhil student (from October 2021)

Robert McDonald (jointly supervised with Helen Byrne)

Mathematics DPhil student (from October 2021)

Thomas Chaplin (jointly supervised with Ulrike Tillmann)

Mathematics DPhil student (from October 2020)

Otto Sumray (jointly supervised with Vidit Nanda and Xin Lu)

Ludwig Institute DPhil student (from October 2020)

David Beers (jointly supervised with Alain Goriely)

Mathematics DPhil student (from October 2019)

Lewis Marsh (jointly supervised with Helen Byrne and Xin Lu)

Mathematics DPhil student (from October 2019)

Previous Members

M Adamer, B Stolz-Pretzer, HA Harrington, A Barbensi, and P Edwards at SIAM AG19

Topological Data Analysis Post-lockdown Reunion and Pizza (October 2021). Photo credit: V Nanda

Postdoctoral Researchers

Renee Hoekzema

Postdoctoral Researcher in Centre for Topological Data Analysis and Ludwig Institute

Placement: TT Assistant Professor and Veni Fellow, Free University of Amsterdam

Kelly Spendlove

Postdoctoral Researcher in Centre for Topological Data Analysis

Placement: Google

Gregory Henselman-Petrusek

Postdoctoral Researcher in Centre for Topological Data Analysis

Placement: Pacific Northwest National Laboratory (PNNL)

Emilie Dufresne

John Fell Fund postdoc developing algebraic methods for model identification with application to biology

Placement: Research fellow in Mathematical Sciences at University of Nottingham

Placement: Lecturer in Algebra, Department of Mathematics at University of York

Adam MacLean (joint mentor with Helen Byrne)

Methods for model identification in signaling pathways.

Placement: Postdoc in Nie Lab at UC Irvine

Placement: Assistant Professor, University of Southern California

Graduate Students

Jacob Leygonie (jointly supervised with Ulrike Tillmann)

Mathematics DPhil student (from October 2018)

Robert MacDonald (jointly supervised with Maria Bruna)

Mathematical Modelling and Scientific Computing MSc research student (May - Sept 2020)

Placement: DPhil student in Mathematical Biology and Applied Topology (Oxford)

Lewis Marsh

Mathematical Foundations of Computer Science MSc research student (April - Sept 2019)

Placement: DPhil in Mathematics Institute (Topological Data Analysis)

Agnese Barbensi (jointly supervised with Marc Lackenby and Dorothy Buck)

Mathematics DPhil student funded by EPSRC/Royal Society Award

• Placement: Hooke Research Fellow (Oxford)
• Placement: University of Melbourne (from 2021)

Bernadette Stolz-Pretzer (jointly supervised with Jared Tanner)

Mathematics DPhil student, Systems Approaches to Biomedical Science DTC

• Previous project: Analysis of persistent homology in neuronal networks.
  July - September 2015, DTC short project jointly supervised with Mason A Porter
• Previous project: Classification of pathological tumour tissue data and biomarker discovery using topological data analysis.
  May - July 2015, DTC short project jointly supervised with Jared Tanner
• Previous project: Computational Topology in Neuroscience
  Mathematical Modelling and Scientific Computing MSc
  Summer 2014, jointly supervised with Mason A Porter
• Placement: Oxford Centre fro TDA, now postdoc at EPFL

Michael Adamer (jointly supervised with Thomas Woolley and Eamonn Gaffney)

Mathematics DPhil student, Systems Biology CDT

• Placement: ETH Zurich (present), MPI Leipzig (July - January 2020)

Wojciech Reise (jointly supervised with Mariano Beguerisse, Spotify)

Masters research student in Computational Science and Engineering, EPFL (Feb -June 2019)

• Placement: Spotify internship (July - September 2019)

Gregory Greif (jointly supervised with Andreas Muench)

Mathematical Foundations of Computer Science MSc research student (April - Sept 2019)

Nina Otter (jointly supervised with Ulrike Tillmann)

Mathematics DPhil.

• Placement: MPI Leipzig (July - December 2018)
• Placement: ULCA Department of Mathematics (From 2019)

Dimitri Lozeve

Statistics MSc, dissertation project (July - September)

Rohan Arambepola (jointly supervised with Frances Kirwan and Emilie Dufresne)

Systems Biology Centre for Doctoral Trainings, short project (July - September 2017)

Parker Edwards (jointly supervised with Emilie Dufresne)

Mathematical Foundations of Computer Science MSc research student (April - Sept 2016)

Placement: Mathematics PhD program at University of Florida

Matishalin Patel (jointly supervised with Michael Bonsall)

Interdisciplinary Bioscience Doctoral Training Partnership research student (April - July 2016)

Leo Speidel (jointly supervised with Mason A Porter and Jon Chapman)

Systems Biology Centre for Doctoral Training research student (April - July 2016)

Placement: Department of Statistics, DPhil with Simon Myers

Erin Price-Wright (jointly supervised with Mason A Porter)

Mathematical Foundations of Computer Science MSc research student (Summer 2015)

Placement: Business Development at Palantir Technologies

Dorian Levy (jointly supervised with Robert Van Gorder)

Mathematical Modelling and Scientific Computing MSc research student (Summer 2015)

Placement: Development and Operations Engineer at StarLeaf

Alice Schwarze (jointly supervised with Antonis Papachristodoulou and James Anderson)

Complete controllability analysis of the Wnt signalling pathway.
Systems Approaches to Biomedical Science DTC short project (May - July 2015)

Placement: Oxford Mathematical Institute, DPhil with Mason A Porter

Jake Taylor-King (jointly supervised with Mason A Porter and David Basanta)

A simple model for osteocyte network formation.
Systems Approaches to Biomedical Science(SABS) DTC short project (July - September 2014)

Placement: Oxford Mathematical Institute, DPhil with Mason A Porter and Jon Chapman

Andrew Parker (jointly supervised with Helen Byrne and Blanca Rodriguez)

Model choice for heart models.
Systems Biology DTC short project (July - September 2014)

Placement: Oxford Mathematical Institute, DPhil with Ruth Baker

Barbara Mahler (jointly supervised with Mason A Porter)

Systems Biology DTC project (May - July 2014)

• Placement: Mathematics DPhil student (Ulrike Tillmann and Mason A Porter)
  

Florian Klimm (jointly supervised with Mason Porter )

Persistent homology and random-walker threshold models for social influence
Visiting masters student from Humboldt-Universitaet Berlin (Summer 2013)

Placement: Systems Approaches to Biomedical Science DTC at Oxford

Photo credit: M. Beguerisse