Publications and Preprints

@misc{harrington2026fibermultiparameterpersistenthomology,  
      title={The fiber of multiparameter persistent homology for simplicial complexes},  
      author={Heather A. Harrington and Ulrike Tillmann and Maria Torras-Pérez},  
      year={2026},  
      eprint={2608.04640},  
      archivePrefix={arXiv},  
      primaryClass={math.AT},  
      url={https://arxiv.org/abs/2608.04640},  
}

@article{jiang2026diversity,
  title={Diversity in transcriptomics without cell types},
  author={Jiang, Leyi and Benjamin, Katherine and Veenvliet, Jesse and Roff, Emily and Harrington, Heather},
  journal={bioRxiv},
  pages={2026--07},
  year={2026},
  publisher={Cold Spring Harbor Laboratory}
}

@misc{pellegrinelli2026tensoranalysislipidtransport,
      title={Tensor analysis for lipid transport}, 
      author={Ilaria Pellegrinelli and Vincenzo Galgano and Mathilda Lennartz and André Nadler and Heather A. Harrington},
      year={2026},
      eprint={2607.20215},
      archivePrefix={arXiv},
      primaryClass={q-bio.QM},
      url={https://arxiv.org/abs/2607.20215}, 
}

@misc{sadovek2026colorfulgeneralizationsgoodmanpollacktransversal,
      title={On colorful generalizations of the Goodman--Pollack transversal problem}, 
      author={Nikola Sadovek},
      year={2026},
      eprint={2604.19644},
      archivePrefix={arXiv},
      primaryClass={math.CO},
      url={https://arxiv.org/abs/2604.19644}, 
}

@misc{natarajan2026topologymultispecieslocalization,
      title={Topology of Multi-species Localization}, 
      author={Abhinav Natarajan and Thomas Chaplin and Joshua A. Bull and Eoghan J. Mulholland-Illingworth and Simon J. Leedham and Helen M. Byrne and Maria-Jose Jimenez and Heather A. Harrington},
      year={2026},
      eprint={2603.03237},
      archivePrefix={arXiv},
      primaryClass={math.AT},
      url={https://arxiv.org/abs/2603.03237}, 
}

@misc{yang2026topologicalshapetransformthymus,
      title={Topological shape transform for thymus structures}, 
      author={Haochen Yang and Vadim Lebovici and Andreas Tarcevski and Liliana Tchernev and Saulius Zuklys and Georg A. Holländer and Helen M. Byrne and Heather A. Harrington},
      year={2026},
      eprint={2602.18889},
      archivePrefix={arXiv},
      primaryClass={math.AT},
      url={https://arxiv.org/abs/2602.18889}, 
}

@misc{recke2026identifiabilitygraphicaldiscretelyapunov,
      title={Identifiability in Graphical Discrete Lyapunov Models}, 
      author={Cecilie Olesen Recke and Sarah Lumpp and Nataliia Kushnerchuk and Janike Oldekop and Jiayi Li and Jane Ivy Coons and Elina Robeva},
      year={2026},
      eprint={2601.21818},
      archivePrefix={arXiv},
      primaryClass={math.ST},
      url={https://arxiv.org/abs/2601.21818}, 
}

@misc{tanburn2025nondimensionalizationscienceart,
      title={Nondimensionalization is more science than art}, 
      author={Richard Tanburn and Danny Hendron and Philip Maini and Silviana Amethyst and Emilie Dufresne and Heather A. Harrington},
      year={2025},
      eprint={2512.13455},
      archivePrefix={arXiv},
      primaryClass={q-bio.QM},
      url={https://arxiv.org/abs/2512.13455}, 
}

@misc{lenzen2025persistentcyclerepresentativesgeneralized,
      title={Persistent Cycle Representatives and Generalized Landscapes for Codimension 1 Persistent Homology}, 
      author={Fabian Lenzen and Leon Renkin},
      year={2025},
      eprint={2512.09668},
      archivePrefix={arXiv},
      primaryClass={math.AT},
      url={https://arxiv.org/abs/2512.09668}, 
}

@article{zhou2025development,
  title={Development of a universal imaging “phenome” using Shape, Appearance and Motion (SAM) features and the SAM Observation Tool (SPOT)},
  author={Zhou, Felix Y and Norton-Steele, Adam and Marsh, Lewis and Byrne, Helen M and Harrington, Heather A and Lu, Xin},
  journal={bioRxiv},
  pages={2025--11},
  year={2025},
  publisher={Cold Spring Harbor Laboratory}
}

@article {Zhou2025.11.28.691111,
 author = {Zhou, Felix Y. and Jacobs, Brittany-Amber and Norton-Steele, Adam and Han, Xiaoyue and Zhou, Linna and Carroll, Thomas M. and Ruiz Puig, Carlos and Chadwick, Joseph and Qin, Xiao and Lisle, Richard and Marsh, Lewis and Byrne, Helen M. and Harrington, Heather A. and Lu, Xin},
 title = {Identifying phenotype-genotype-function coupling in 3D organoid imaging using Shape, Appearance and Motion Phenotype Observation Tool (SPOT)},
 elocation-id = {2025.11.28.691111},
 year = {2025},
 doi = {10.1101/2025.11.28.691111},
 publisher = {Cold Spring Harbor Laboratory},
 abstract = {Live cells in tissue are plastic, phenotypically dynamic, and modify their function in response to genetic and environmental perturbations. To unleash the power of live-cell imaging to identify phenotype-genotype-function coupling over time, we report the development of a standardized Shape-Appearance-Motion (SAM) {\textquotedblleft}phenome{\textquotedblright} and SAM-Phenotype-Observation-Tool (SPOT), that act as an image-{\textquotedblleft}transcriptome{\textquotedblright} and image-{\textquotedblleft}transcriptome analyzer{\textquotedblright} respectively, and provide unbiased and comprehensive description of morpho-dynamic phenotypes without prior knowledge. We developed and applied SAM-SPOT to our simulated organoids database with known ground-truth and \>1.6 million mouse and human organoid instances with defined genetic and chemical perturbations. SAM-SPOT can effectively and robustly characterize 3D morpho-dynamics from 2D projection videos. Combined with single-cell RNA sequencing, SAM-SPOT revealed that altered WNT signaling, but not mutant RAS or p53, predisposes intestinal organoids to irregular morphogenesis. SAM-SPOT advances biomedical discovery by empowering live-cell imaging to identify phenotype-genotype-function relationships through large-scale and cost-effective label-free live-cell imaging.Competing Interest StatementTMC is a founder, employee, and shareholder of a diagnostics company (Cleancard Ltd). A provisional patent is pending for SPOT.},
 URL = {https://www.biorxiv.org/content/early/2025/11/29/2025.11.28.691111},
 eprint = {https://www.biorxiv.org/content/early/2025/11/29/2025.11.28.691111.full.pdf},
 journal = {bioRxiv}
}

@misc{adams2025quantifyingdiscontinuity,
      title={Quantifying discontinuity}, 
      author={Henry Adams and Florian Frick and Michael Harrison and Sunhyuk Lim and Nikola Sadovek and Matt Superdock},
      year={2025},
      eprint={2511.07636},
      archivePrefix={arXiv},
      primaryClass={math.MG},
      url={https://arxiv.org/abs/2511.07636}, 
}

@misc{iváñez2025toproitopologyinformednetworkapproach,
      title={TopROI: A topology-informed network approach for tissue partitioning}, 
      author={Sergio Serrano de Haro Iváñez and Joshua W. Moore and Lucile Grzesiak and Eoghan J. Mullholand and Heather Harrington and Simon J. Leedham and Helen M. Byrne},
      year={2025},
      eprint={2510.12772},
      archivePrefix={arXiv},
      primaryClass={q-bio.QM},
      url={https://arxiv.org/abs/2510.12772}, 
}

@article{milor2025topological,
  title={A topological approach to the Cahn-Hilliard equation and hyperuniform fields},
  author={Milor, Abel HG and Sumray, Otto and Harrington, Heather A and Voigt, Axel and Salvalaglio, Marco},
  journal={arXiv preprint arXiv:2509.05339},
  year={2025}
}

@article{beers2025intrinsic,
  title={Intrinsic Bottleneck Distance for Merge Trees},
  author={Beers, David and Grindstaff, Gillian},
  journal={arXiv preprint arXiv:2509.02755},
  year={2025}
}

@misc{çelik2025strataecologicalcoexistencegrassmannians,
      title={Strata of Ecological Coexistence via Grassmannians}, 
      author={Türkü Özlüm Çelik and Pierre A. Haas and Georgy Scholten and Kexin Wang and Giulio Zucal},
      year={2025},
      eprint={2509.00165},
      archivePrefix={arXiv},
      primaryClass={math.AG},
      url={https://arxiv.org/abs/2509.00165}, 
}

@misc{hess2025intervalspheremodelstructures,
      title={Interval-sphere model structures}, 
      author={Kathryn Hess and Samuel Lavenir and Kelly Maggs},
      year={2025},
      eprint={2507.02382},
      archivePrefix={arXiv},
      primaryClass={math.AT},
      url={https://arxiv.org/abs/2507.02382}, 
}

@misc{connelly2025gametheorypackagemacaulay2,
      title={The GameTheory package for Macaulay2}, 
      author={Erin Connelly and Vincenzo Galgano and Zhuang He and Giacomo Maletto and Elke Neuhaus and Irem Portakal and Hannah Tillmann-Morris and Chenyang Zhao},
      year={2025},
      eprint={2507.16755},
      archivePrefix={arXiv},
      primaryClass={math.AG},
      url={https://arxiv.org/abs/2507.16755}, 
}

@misc{galgano2025discretesignaturetensorspersistence,
      title={Discrete signature tensors for persistence landscapes}, 
      author={Vincenzo Galgano and Heather A. Harrington and Daniel Tolosa},
      year={2025},
      eprint={2505.02800},
      archivePrefix={arXiv},
      primaryClass={math.AT},
      url={https://arxiv.org/abs/2505.02800}, 
}

@article{scoccola2025cover,
  title={Cover Learning for Large-Scale Topology Representation},
  author={Scoccola, Luis and Lim, Uzu and Harrington, Heather A},
  journal={arXiv preprint arXiv:2503.09767},
  year={2025}
}

@misc{grindstaff2025tropicalbisectorscarliniwagnerattacks,
      title={Tropical Bisectors and Carlini-Wagner Attacks}, 
      author={Gillian Grindstaff and Julia Lindberg and Daniela Schkoda and Miruna-Stefana Sorea and Ruriko Yoshida},
      year={2025},
      eprint={2503.22653},
      archivePrefix={arXiv},
      primaryClass={cs.LG},
      url={https://arxiv.org/abs/2503.22653}, 
}

@article{maggs2025topology,
  title={Topology identifies concurrent cyclic processes in single-cell transcriptomics and androgen receptor function},
  author={Maggs, Kelly and Youssef, Markus K and Pulver, Cyril and Isma, Jovan and Nguy{\^e}n, T{\^a}m J and Arzt, Matthias and Karthaus, Wouter and Harrington, Heather A and Hess, Kathryn and Dotto, G Paolo},
  journal={bioRxiv},
  pages={2025--01},
  year={2025},
  publisher={Cold Spring Harbor Laboratory}
}

@misc{natarajan2025morsetheorychromaticdelaunay,
      title={Morse theory for chromatic Delaunay triangulations}, 
      author={Abhinav Natarajan and Thomas Chaplin and Adam Brown and Maria-Jose Jimenez},
      year={2025},
      eprint={2405.19303},
      archivePrefix={arXiv},
      primaryClass={math.AT},
      url={https://arxiv.org/abs/2405.19303}, 
}

@misc{hess2025celldecompositionspersistentminimal,
      title={Cell decompositions of persistent minimal models}, 
      author={Kathryn Hess and Samuel Lavenir and Kelly Maggs},
      year={2025},
      eprint={2312.08326},
      archivePrefix={arXiv},
      primaryClass={math.AT},
      url={https://arxiv.org/abs/2312.08326}, 
}

@misc{chaplin2024notionhomotopydirectedgraphs,
      title={A notion of homotopy for directed graphs and their flag complexes}, 
      author={Thomas Chaplin and Heather A. Harrington and Ulrike Tillmann},
      year={2024},
      eprint={2411.04572},
      archivePrefix={arXiv},
      primaryClass={math.AT},
      url={https://arxiv.org/abs/2411.04572}, 
}

@misc{beers2024fiberspointcloudpersistence,
      title={Fibers of point cloud persistence}, 
      author={David Beers and Heather A Harrington and Jacob Leygonie and Uzu Lim and Louis Theran},
      year={2024},
      eprint={2411.08201},
      archivePrefix={arXiv},
      primaryClass={math.AT},
      url={https://arxiv.org/abs/2411.08201}, 
}

@misc{sumray2024quiverlaplaciansfeatureselection,
      title={Quiver Laplacians and Feature Selection}, 
      author={Otto Sumray and Heather A. Harrington and Vidit Nanda},
      year={2024},
      eprint={2404.06993},
      archivePrefix={arXiv},
      primaryClass={stat.ML},
      url={https://arxiv.org/abs/2404.06993}, 
}

@article{yoon2024deciphering,
  title={Deciphering the diversity and sequence of extracellular matrix and cellular spatial patterns in lung adenocarcinoma using topological data analysis},
  author={Yoon, Iris HR and Jenkins, Robert and Colliver, Emma and Zhang, Hanyun and Novo, David and Moore, David and Ramsden, Zoe and Rullan, Antonio and Fu, Xiao and Yuan, Yinyin and others},
  journal={bioRxiv},
  pages={2024--01},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}

@article{lim2023geometry,
  title={Geometry of navigation identifies genetic-risk and clinical Alzheimer’s disease},
  author={Lim, Uzu and Cervantes, Rodrigo Leal and Coughlan, Gillian and Lambiotte, Renaud and Spiers, Hugo J and Hornberger, Michael and Harrington, Heather A},
  journal={medRxiv},
  pages={2023--10},
  year={2023},
  publisher={Cold Spring Harbor Laboratory Press}
}

@misc{offord2022topologicaldataanalysisdetects,
      title={Topological Data Analysis Detects Percolation Thresholds in Arctic Melt-Pond Evolution}, 
      author={Wilfred Offord and Michael Coughlan and Ian J. Hewitt and Heather A. Harrington and Gillian Grindstaff},
      year={2022},
      eprint={2212.07961},
      archivePrefix={arXiv},
      primaryClass={physics.data-an},
      url={https://arxiv.org/abs/2212.07961}, 
}

@misc{beers2022stabilitytopologicaldescriptorsneuronal,
      title={Stability of topological descriptors for neuronal morphology}, 
      author={David Beers and Heather A. Harrington and Alain Goriely},
      year={2022},
      eprint={2211.09058},
      archivePrefix={arXiv},
      primaryClass={q-bio.NC},
      url={https://arxiv.org/abs/2211.09058}, 
}

@misc{barbensi2022hypergraphsmultiscalecyclesstructured,
      title={Hypergraphs for multiscale cycles in structured data}, 
      author={Agnese Barbensi and Iris H. R. Yoon and Christian Degnbol Madsen and Deborah O. Ajayi and Michael P. H. Stumpf and Heather A. Harrington},
      year={2022},
      eprint={2210.07545},
      archivePrefix={arXiv},
      primaryClass={math.AT},
      url={https://arxiv.org/abs/2210.07545}, 
}

@misc{barbensi2019doublebranchedcoversknotoids,
      title={Double branched covers of knotoids}, 
      author={Agnese Barbensi and Dorothy Buck and Heather A. Harrington and Marc Lackenby},
      year={2019},
      eprint={1811.09121},
      archivePrefix={arXiv},
      primaryClass={math.GT},
      url={https://arxiv.org/abs/1811.09121}, 
}

@misc{stolz2016topologicalshapebrexit,
      title={The Topological "Shape" of Brexit}, 
      author={Bernadette J. Stolz and Heather A. Harrington and Mason A. Porter},
      year={2016},
      eprint={1610.00752},
      archivePrefix={arXiv},
      primaryClass={cs.CG},
      url={https://arxiv.org/abs/1610.00752}, 
}

@article{harrington2026algebraic,
  title={Algebraic aspects of homogeneous Kuramoto oscillators},
  author={Harrington, Heather and Schenck, Hal and Stillman, Mike},
  journal={Mathematics of Computation},
  volume={95},
  number={358},
  pages={1023--1047},
  year={2026}
}

@article{everall2026comprehensive,
  title={Comprehensive repertoire of the chromosomal alteration and mutational signatures across 16 cancer types},
  author={Everall, Andrew and Tapinos, Avraam and Hawari, Aliah and Cornish, Alex J and Sud, Amit and Chubb, Daniel and Kinnersley, Ben and Frangou, Anna and Barquin, Miguel and Jung, Josephine and others},
  journal={Nature Genetics},
  pages={1--12},
  year={2026},
  publisher={Nature Publishing Group US New York}
}

@article{culliford2026contrasting,
  title={Contrasting features of papillary and chromophobe renal cell carcinoma revealed by whole genome sequencing.},
  author={Culliford, Richard and Mills, Charlie and Chubb, Daniel and Kinnersley, Ben and Sud, Amit and Cornish, Alex J and Browning, Lisa and Lawrence, Samuel ED and Bentham, Robert and Frangou, Anna and others},
  journal={Molecular Cancer Research},
  year={2026},
  publisher={American Association for Cancer Research}
}

@article{abiad2026hypergraphs,
  title={Hypergraphs and simplicial complexes in focus: A roadmap for future research in higher-order interactions},
  author={Abiad, Aida and Arenas, Alex and Backhausz, Agnes and Balogh, Jozsef and Banerji, Christopher RS and Barbarossa, Sergio and Bianconi, Ginestra and Bick, Christian and Botnan, Magnus Bakke B and Carletti, Timoteo and others},
  journal={Journal of Physics: Complexity},
  year={2026}
}

@article{spector2026persistent,
  title={Persistent homology classifies parameter dependence of patterns in Turing systems},
  author={Spector, Reemon and Harrington, Heather A and Gaffney, Eamonn A},
  journal={Bulletin of Mathematical Biology},
  volume={88},
  number={1},
  pages={10},
  year={2026},
  publisher={Springer}
}

@article{safey2026probabilistic,
  title={Probabilistic algorithm for computing all local minimizers of Morse functions on a compact domain},
  author={Safey El Din, Mohab and Scholten, Georgy and Tr{\'e}lat, Emmanuel},
  journal={Mathematics of Control, Signals, and Systems},
  pages={1--37},
  year={2026},
  publisher={Springer}
}

@article{mcdonald2026topological,
  title={Topological model selection: a case-study in tumour-induced angiogenesis},
  author={McDonald, Robert A and Byrne, Helen M and Harrington, Heather A and Thorne, Thomas and Stolz, Bernadette J},
  journal={Bioinformatics},
  volume={42},
  number={3},
  pages={btag065},
  year={2026},
  publisher={Oxford University Press}
}

@article{puente2025absolute,
  title={Absolute concentration robustness: Algebra and geometry},
  author={Puente, Luis David Garc{\'\i}a and Gross, Elizabeth and Harrington, Heather A and Johnston, Matthew and Meshkat, Nicolette and Mill{\'a}n, Mercedes P{\'e}rez and Shiu, Anne},
  journal={Journal of Symbolic Computation},
  volume={128},
  pages={102398},
  year={2025},
  publisher={Elsevier}
}

@article{byrne2025algebraic,
  title={Algebraic identifiability of partial differential equation models},
  author={Byrne, Helen M and Harrington, Heather A and Ovchinnikov, Alexey and Pogudin, Gleb and Rahkooy, Hamid and Soto, Pedro},
  journal={Nonlinearity},
  volume={38},
  number={2},
  pages={025022},
  year={2025},
  publisher={IOP Publishing}
}

@article{coons2025combinatorial,
  title={Combinatorial geometry of rational quasi-independence models as toric fiber products},
  author={Coons, Jane Ivy and Harrington, Heather A and Paul, Niharika Chakrabarty},
  journal={Algebraic Statistics},
  volume={17},
  number={1},
  pages={1--31},
  year={2025},
  publisher={Mathematical Sciences Publishers}
}

@article{kinnersley2025genomic,
  title={Genomic landscape of diffuse glioma revealed by whole genome sequencing},
  author={Kinnersley, Ben and Jung, Josephine and Cornish, Alex J and Chubb, Daniel and Laxton, Ross and Frangou, Anna and Gruber, Andreas J and Sud, Amit and Caravagna, Giulio and Sottoriva, Andrea and others},
  journal={Nature communications},
  volume={16},
  number={1},
  pages={4233},
  year={2025},
  publisher={Nature Publishing Group UK London}
}

@article{chaplin2025grounded,
  title={Grounded persistent path homology: a stable, topological descriptor for weighted digraphs},
  author={Chaplin, Thomas and Harrington, Heather A and Tillmann, Ulrike},
  journal={Foundations of Computational Mathematics},
  volume={25},
  number={5},
  pages={1711--1776},
  year={2025},
  publisher={Springer}
}

@article{dowbaj2025mouse,
  title={Mouse liver assembloids model periportal architecture and biliary fibrosis},
  author={Dowbaj, Anna M and Sljukic, Aleksandra and Niksic, Armin and Landerer, Cedric and Delpierre, Julien and Yang, Haochen and Lahree, Aparajita and K{\"u}hn, Ariane C and Beers, David and Byrne, Helen M and others},
  journal={Nature},
  volume={644},
  number={8076},
  pages={473--482},
  year={2025},
  publisher={Nature Publishing Group UK London}
}

@article{gafvert2025hidden,
  title={On the hidden layer-to-layer topology of the representations of reality realised within neural networks},
  author={Gafvert, Oliver and Grindrod, Peter and Harrington, Heather A and Higham, Catherine F and Higham, Desmond J and Yim, Ka Man},
  journal={Engineering Computations},
  year={2025},
  publisher={Emerald Publishing Limited}
}

@article{ward2025replication,
  title={Replication-associated mechanisms contribute to an increased CpG> TpG mutation burden in mismatch repair-deficient cancers},
  author={Ward, Joseph C and Soriano, Ignacio and Thorn, Steve and Fern{\'a}ndez-Tajes, Juan and Sherwood, Kitty and G{\"u}l, G{\"u}ler and Scheffers, Joost and Frangou, Anna and Kinnersley, Ben and Kafetzopoulos, Ioannis and others},
  journal={Genome medicine},
  volume={17},
  number={1},
  pages={95},
  year={2025},
  publisher={Springer}
}

@article{yang2025topological,
  title={Topological classification of tumour-immune interactions and dynamics: J. Yang et al.},
  author={Yang, Jingjie and Fang, Heidi and Dhesi, Jagdeep and Yoon, Iris HR and Bull, Joshua A and Byrne, Helen M and Harrington, Heather A and Grindstaff, Gillian},
  journal={Journal of mathematical biology},
  volume={91},
  number={3},
  pages={25},
  year={2025},
  publisher={Springer}
}

@article{TorrasPrez2025,
  title = {Topology across scales on heterogeneous cell data},
  volume = {21},
  ISSN = {1553-7358},
  url = {http://dx.doi.org/10.1371/journal.pcbi.1013460},
  DOI = {10.1371/journal.pcbi.1013460},
  number = {10},
  journal = {PLOS Computational Biology},
  publisher = {Public Library of Science (PLoS)},
  author = {Torras-Pérez,  Maria and Yoon,  Iris H. R. and Weeratunga,  Praveen and Ho,  Ling-Pei and Byrne,  Helen M. and Tillmann,  Ulrike and Harrington,  Heather A.},
  editor = {Copos,  Calina},
  year = {2025},
  month = oct,
  pages = {e1013460}
}

@article{oliveri2024active,
  title={Active shape control by plants in dynamic environments},
  author={Oliveri, Hadrien and Moulton, Derek E and Harrington, Heather A and Goriely, Alain},
  journal={Physical Review E},
  volume={110},
  number={1},
  pages={014405},
  year={2024},
  publisher={APS}
}

@article{harrington2024algebraic,
  title={Algebraic network reconstruction of discrete dynamical systems},
  author={Harrington, Heather A and Stillman, Mike and Veliz-Cuba, Alan},
  journal={Advances in Applied Mathematics},
  volume={161},
  pages={102760},
  year={2024},
  publisher={Elsevier}
}

@article{goodbrake2024brain,
  title={Brain chains as topological signatures for Alzheimer’s disease},
  author={Goodbrake, Christian and Beers, David and Thompson, Travis B and Harrington, Heather A and Goriely, Alain},
  journal={Journal of Applied and Computational Topology},
  volume={8},
  number={5},
  pages={1257--1298},
  year={2024},
  publisher={Springer}
}

@article{marsh2024detecting,
  title={Detecting temporal shape changes with the Euler characteristic transform},
  author={Marsh, Lewis and Zhou, Felix Y and Qin, Xiao and Lu, Xin and Byrne, Helen M and Harrington, Heather A},
  journal={Transactions of Mathematics and its Applications},
  volume={8},
  number={2},
  pages={tnae002},
  year={2024},
  publisher={Oxford University Press}
}

@article{ni2024genomic,
  title={Genomic landscape of adult testicular germ cell tumours in the 100,000 Genomes Project},
  author={N{\'\i} Leathlobhair, M{\'a}ire and Frangou, Anna and Kinnersley, Ben and Cornish, Alex J and Chubb, Daniel and Lakatos, Eszter and Arumugam, Prabhu and Gruber, Andreas J and Law, Philip and Tapinos, Avraam and others},
  journal={Nature communications},
  volume={15},
  number={1},
  pages={9247},
  year={2024},
  publisher={Nature Publishing Group UK London}
}

@article{benjamin2024multiscale,
  title={Multiscale topology classifies cells in subcellular spatial transcriptomics},
  author={Benjamin, Katherine and Bhandari, Aneesha and Kepple, Jessica D and Qi, Rui and Shang, Zhouchun and Xing, Yanan and An, Yanru and Zhang, Nannan and Hou, Yong and Crockford, Tanya L and others},
  journal={Nature},
  volume={630},
  number={8018},
  pages={943--949},
  year={2024},
  publisher={Nature Publishing Group UK London}
}

@article{stolz2024relational,
  title={Relational persistent homology for multispecies data with application to the tumor microenvironment},
  author={Stolz, Bernadette J and Dhesi, Jagdeep and Bull, Joshua A and Harrington, Heather A and Byrne, Helen M and Yoon, Iris HR},
  journal={Bulletin of mathematical biology},
  volume={86},
  number={11},
  pages={128},
  year={2024},
  publisher={Springer}
}

@inproceedings{oliveri2024robust,
  title={Robust posture control by plants in dynamic gravity field},
  author={Oliveri, Hadrien and Moulton, Derek and Harrington, Heather and Goriely, Alain},
  booktitle={APS March Meeting Abstracts},
  volume={2024},
  pages={T36--008},
  year={2024}
}

@article{cornish2024genomic,
  title={The genomic landscape of 2,023 colorectal cancers},
  author={Cornish, Alex J and Gruber, Andreas J and Kinnersley, Ben and Chubb, Daniel and Frangou, Anna and Caravagna, Giulio and Noyvert, Boris and Lakatos, Eszter and Wood, Henry M and Thorn, Steve and others},
  journal={Nature},
  volume={633},
  number={8028},
  pages={127--136},
  year={2024},
  publisher={Nature Publishing Group UK London}
}

@article{reise2024topological,
  title={Topological fingerprints for audio identification},
  author={Reise, Wojciech and Fern{\'a}ndez, Ximena and Dominguez, Maria and Harrington, Heather A and Beguerisse-D{\'\i}az, Mariano},
  journal={SIAM Journal on Mathematics of Data Science},
  volume={6},
  number={3},
  pages={815--841},
  year={2024},
  publisher={SIAM}
}

@article{culliford2024whole,
  title={Whole genome sequencing refines stratification and therapy of patients with clear cell renal cell carcinoma},
  author={Culliford, Richard and Lawrence, Samuel ED and Mills, Charlie and Tippu, Zayd and Chubb, Daniel and Cornish, Alex J and Browning, Lisa and Kinnersley, Ben and Bentham, Robert and Sud, Amit and others},
  journal={Nature communications},
  volume={15},
  number={1},
  pages={5935},
  year={2024},
  publisher={Nature Publishing Group UK London}
}

@article{beers2023barcodes,
  title={Barcodes distinguishing morphology of neuronal tauopathy},
  author={Beers, David and Goniotaki, Despoina and Hanger, Diane P and Goriely, Alain and Harrington, Heather A},
  journal={Physical Review Research},
  volume={5},
  number={4},
  pages={043006},
  year={2023},
  publisher={APS}
}

@article{ryou2023continuous,
  title={Continuous Indexing of Fibrosis (CIF): improving the assessment and classification of MPN patients},
  author={Ryou, Hosuk and Sirinukunwattana, Korsuk and Aberdeen, Alan and Grindstaff, Gillian and Stolz, Bernadette J and Byrne, Helen and Harrington, Heather A and Sousos, Nikolaos and Godfrey, Anna L and Harrison, Claire N and others},
  journal={Leukemia},
  volume={37},
  number={2},
  pages={348--358},
  year={2023},
  publisher={Nature Publishing Group UK London}
}

@article{dong2023differential,
  title={Differential elimination for dynamical models via projections with applications to structural identifiability},
  author={Dong, Ruiwen and Goodbrake, Christian and Harrington, Heather A and Pogudin, Gleb},
  journal={SIAM Journal on Applied Algebra and Geometry},
  volume={7},
  number={1},
  pages={194--235},
  year={2023},
  publisher={SIAM}
}

@article{gao2023dynamics,
  title={Dynamics on networks with higher-order interactions},
  author={Gao, Z and Ghosh, D and Harrington, HA and Restrepo, JG and Taylor, D},
  journal={Chaos: An Interdisciplinary Journal of Nonlinear Science},
  volume={33},
  number={4},
  year={2023},
  publisher={AIP Publishing}
}

@article{benjamin2023Homology,
 title = {Homology of homologous knotted proteins},
 volume = {20},
 url = {https://royalsocietypublishing.org/doi/full/10.1098/rsif.2022.0727},
 doi = {10.1098/rsif.2022.0727},
 number = {201},
 journal = {Journal of the Royal Society Interface},
 author = {Benjamin, Katherine and Mukta, Lamisah and Moryoussef, Gabriel and Uren, Christopher and Harrington, Heather A. and Tillmann, Ulrike and Barbensi, Agnese},
 month = apr,
 year = {2023},
 keywords = {62R40, 55N31, 57K10, Quantitative Biology - Biomolecules, algebraic topology, geometric topology},
}

@article{seigal2023principal,
  title={Principal components along quiver representations},
  author={Seigal, Anna and Harrington, Heather A and Nanda, Vidit},
  journal={Foundations of Computational Mathematics},
  volume={23},
  number={4},
  pages={1129--1165},
  year={2023},
  publisher={Springer}
}

@article{bull2023topological,
  title={Topological Analysis of High-Resolution Spatial Transcriptomics Reveals Immune Glomerular Architecture of Lupus Nephritis: TH-PO533},
  author={Bull, Katherine R and Benjamin, Katherine and Bhandari, Aneesha and Shang, Zhouchun and Xing, Yanan and An, Yanru and Zhang, Nannan and Tillmann, Ulrike and Harrington, Heather A},
  journal={Journal of the American Society of Nephrology},
  volume={34},
  number={11S},
  pages={239--239},
  year={2023}
}

@article{carroll2023tumor,
  title={Tumor monocyte content predicts immunochemotherapy outcomes in esophageal adenocarcinoma},
  author={Carroll, Thomas M and Chadwick, Joseph A and Owen, Richard P and White, Michael J and Kaplinsky, Joseph and Peneva, Iliana and Frangou, Anna and Xie, Phil F and Chang, Jaeho and Roth, Andrew and others},
  journal={Cancer Cell},
  volume={41},
  number={7},
  pages={1222--1241},
  year={2023},
  publisher={Elsevier}
}

@article{bick2023higher,
  title={What are higher-order networks?},
  author={Bick, Christian and Gross, Elizabeth and Harrington, Heather A and Schaub, Michael T},
  journal={SIAM review},
  volume={65},
  number={3},
  pages={686--731},
  year={2023},
  publisher={SIAM}
}

@article{mcdonald2023zigzag,
  title={Zigzag persistence for coral reef resilience using a stochastic spatial model},
  author={McDonald, Robert A and Neuhausler, Rosanna and Robinson, Martin and Larsen, Laurel G and Harrington, Heather A and Bruna, Maria},
  journal={Journal of The Royal Society Interface},
  volume={20},
  number={205},
  year={2023},
  publisher={The Royal Society}
}

@article{ahern2022blood,
  title={A blood atlas of COVID-19 defines hallmarks of disease severity and specificity},
  author={Ahern, David J and Ai, Zhichao and Ainsworth, Mark and Allan, Chris and Allcock, Alice and Angus, Brian and Ansari, M Azim and Arancibia-C{\'a}rcamo, Carolina V and Aschenbrenner, Dominik and Attar, Moustafa and others},
  journal={Cell},
  volume={185},
  number={5},
  pages={916--938},
  year={2022},
  publisher={Elsevier}
}

@article{marsh2022algebra,
  title={Algebra, geometry and topology of ERK kinetics},
  author={Marsh, Lewis and Dufresne, Emilie and Byrne, Helen M and Harrington, Heather A},
  journal={Bulletin of Mathematical Biology},
  volume={84},
  number={12},
  pages={137},
  year={2022},
  publisher={Springer}
}

@article{kotanidis2022constructing,
  title={Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19},
  author={Kotanidis, Christos P and Xie, Cheng and Alexander, Donna and Rodrigues, Jonathan CL and Burnham, Katie and Mentzer, Alexander and O’Connor, Daniel and Knight, Julian and Siddique, Muhammad and Lockstone, Helen and others},
  journal={The Lancet Digital Health},
  volume={4},
  number={10},
  pages={e705--e716},
  year={2022},
  publisher={Elsevier}
}

@article{hoekzema2022multiscale,
  title={Multiscale methods for signal selection in single-cell data},
  author={Hoekzema, Renee S and Marsh, Lewis and Sumray, Otto and Carroll, Thomas M and Lu, Xin and Byrne, Helen M and Harrington, Heather A},
  journal={Entropy},
  volume={24},
  number={8},
  pages={1116},
  year={2022},
  publisher={MDPI}
}

@article{stolz2022multiscale,
  title={Multiscale topology characterizes dynamic tumor vascular networks},
  author={Stolz, Bernadette J and Kaeppler, Jakob and Markelc, Bostjan and Braun, Franziska and Lipsmeier, Florian and Muschel, Ruth J and Byrne, Helen M and Harrington, Heather A},
  journal={Science Advances},
  volume={8},
  number={23},
  pages={eabm2456},
  year={2022},
  publisher={American Association for the Advancement of Science}
}

@article{brown2022quantification,
  title={Quantification of vascular networks in photoacoustic mesoscopy},
  author={Brown, Emma L and Lefebvre, Thierry L and Sweeney, Paul W and Stolz, Bernadette J and Gr{\"o}hl, Janek and Hacker, Lina and Huang, Ziqiang and Couturier, Dominique-Laurent and Harrington, Heather A and Byrne, Helen M and others},
  journal={Photoacoustics},
  volume={26},
  pages={100357},
  year={2022},
  publisher={Elsevier}
}

@article{thorne2022topological,
  title={Topological approximate Bayesian computation for parameter inference of an angiogenesis model},
  author={Thorne, Thomas and Kirk, Paul DW and Harrington, Heather A},
  journal={Bioinformatics},
  volume={38},
  number={9},
  pages={2529--2535},
  year={2022},
  publisher={Oxford University Press}
}

@article{vipond2021multiparameter,
  title={Multiparameter persistent homology landscapes identify immune cell spatial patterns in tumors},
  author={Vipond, Oliver and Bull, Joshua A and Macklin, Philip S and Tillmann, Ulrike and Pugh, Christopher W and Byrne, Helen M and Harrington, Heather A},
  journal={Proceedings of the National Academy of Sciences},
  volume={118},
  number={41},
  pages={e2102166118},
  year={2021},
  publisher={National Academy of Sciences}
}

@article{dufresne2021some,
  title={On some configurations of oppositely charged trapped vortices in the plane},
  author={Dufresne, Emilie and Harrington, Heather A and Hauenstein, Jonathan D and Kevrekidis, Panayotis G and Tripoli, Paolo},
  journal={Advances in Applied Mathematics},
  volume={124},
  pages={102099},
  year={2021},
  publisher={Elsevier}
}

@article{nardini2021topological,
  title={Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis},
  author={Nardini, John T and Stolz, Bernadette J and Flores, Kevin B and Harrington, Heather A and Byrne, Helen M},
  journal={PLOS Computational Biology},
  volume={17},
  number={6},
  pages={e1009094},
  year={2021},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article{stolz2021topological,
  title={Topological data analysis of task-based fMRI data from experiments on schizophrenia},
  author={Stolz, Bernadette J and Emerson, Tegan and Nahkuri, Satu and Porter, Mason A and Harrington, Heather A},
  journal={Journal of Physics: Complexity},
  volume={2},
  number={3},
  pages={035006},
  year={2021},
  publisher={IOP Publishing}
}

@article{adamer2020coloured,
  title={Coloured noise from stochastic inflows in reaction--diffusion systems},
  author={Adamer, Michael F and Harrington, Heather A and Gaffney, Eamonn A and Woolley, Thomas E},
  journal={Bulletin of Mathematical Biology},
  volume={82},
  number={4},
  pages={44},
  year={2020},
  publisher={Springer}
}

@article{stolz2020geometric,
  title={Geometric anomaly detection in data},
  author={Stolz, Bernadette J and Tanner, Jared and Harrington, Heather A and Nanda, Vidit},
  journal={Proceedings of the national academy of sciences},
  volume={117},
  number={33},
  pages={19664--19669},
  year={2020},
  publisher={National Academy of Sciences}
}

@article{barbensi2020grid,
  title={Grid diagrams as tools to investigate knot spaces and topoisomerase-mediated simplification of DNA topology},
  author={Barbensi, Agnese and Celoria, Daniele and Harrington, Heather A and Stasiak, Andrzej and Buck, Dorothy},
  journal={Science advances},
  volume={6},
  number={9},
  pages={eaay1458},
  year={2020},
  publisher={American Association for the Advancement of Science}
}

@article{yeung2020inference,
  title={Inference of multisite phosphorylation rate constants and their modulation by pathogenic mutations},
  author={Yeung, Eyan and McFann, Sarah and Marsh, Lewis and Dufresne, Emilie and Filippi, Sarah and Harrington, Heather A and Shvartsman, Stanislav Y and W{\"u}hr, Martin},
  journal={Current Biology},
  volume={30},
  number={5},
  pages={877--882},
  year={2020},
  publisher={Elsevier}
}

@article{gross2020joining,
  title={Joining and decomposing reaction networks},
  author={Gross, Elizabeth and Harrington, Heather and Meshkat, Nicolette and Shiu, Anne},
  journal={Journal of mathematical biology},
  volume={80},
  number={6},
  pages={1683--1731},
  year={2020},
  publisher={Springer}
}

@article{harrington2019parameter,
  title={A Parameter-Free Model Comparison Test Using Differential Algebra},
  author={Harrington, Heather A and Ho, Kenneth L and Meshkat, Nicolette},
  journal={Complexity},
  volume={2019},
  number={1},
  pages={6041981},
  year={2019},
  publisher={Wiley Online Library}
}

@inproceedings{harrington2019decomposing,
  title={Decomposing the parameter space of biological networks via a numerical discriminant approach},
  author={Harrington, Heather A and Mehta, Dhagash and Byrne, Helen M and Hauenstein, Jonathan D},
  booktitle={Maple Conference},
  pages={114--131},
  year={2019},
  organization={Springer}
}

@article{gross2019linear,
  title={Linear compartmental models: input-output equations and operations that preserve identifiability},
  author={Gross, Elizabeth and Harrington, Heather and Meshkat, Nicolette and Shiu, Anne},
  journal={SIAM Journal on Applied Mathematics},
  volume={79},
  number={4},
  pages={1423--1447},
  year={2019},
  publisher={SIAM}
}

@inproceedings{dufresne2019sampling,
  title={Sampling real algebraic varieties for topological data analysis},
  author={Dufresne, Emilie and Edwards, Parker and Harrington, Heather and Hauenstein, Jonathan},
  booktitle={2019 18th IEEE International Conference On Machine Learning And Applications (ICMLA)},
  pages={1531--1536},
  year={2019},
  organization={IEEE}
}

@article{harrington2019stratifying,
  title={Stratifying multiparameter persistent homology},
  author={Harrington, Heather A and Otter, Nina and Schenck, Hal and Tillmann, Ulrike},
  journal={SIAM Journal on Applied Algebra and Geometry},
  volume={3},
  number={3},
  pages={439--471},
  year={2019},
  publisher={SIAM}
}

@article{seigal2019tensor,
  title={Tensor clustering with algebraic constraints gives interpretable groups of crosstalk mechanisms in breast cancer},
  author={Seigal, Anna and Beguerisse-D{\'\i}az, Mariano and Schoeberl, Birgit and Niepel, Mario and Harrington, Heather A},
  journal={Journal of the Royal Society Interface},
  volume={16},
  number={151},
  year={2019},
  publisher={The Royal Society}
}

@article{byrne2019topology,
  title={Topology characterises tumour vasculature},
  author={Byrne, Helen M and Harrington, Heather A and Muschel, Ruth and Reinert, Gesine and Stolz, Bernadette J and Tillmann, Ulrike},
  journal={Mathematics Today},
  volume={55},
  number={5},
  pages={206--210},
  year={2019},
  publisher={Institute of Mathematics and its Applications}
}

@article{speidel2018topological,
  title={Topological data analysis of continuum percolation with disks},
  author={Speidel, Leo and Harrington, Heather A and Chapman, S Jonathan and Porter, Mason A},
  journal={Physical Review E},
  volume={98},
  number={1},
  pages={012318},
  year={2018},
  publisher={APS}
}

@article{otter2017roadmap,
  title={A roadmap for the computation of persistent homology},
  author={Otter, Nina and Porter, Mason A and Tillmann, Ulrike and Grindrod, Peter and Harrington, Heather A},
  journal={EPJ data science},
  volume={6},
  number={1},
  pages={17},
  year={2017},
  publisher={Springer}
}

@book{harrington2017algebraic,
  title={Algebraic and geometric methods in discrete mathematics},
  author={Harrington, Heather A and Omar, Mohamed and Wright, Matthew},
  volume={685},
  year={2017},
  publisher={American mathematical society Providence}
}

@article{drellich2017geometric,
  title={Geometric combinatorics and computational molecular biology: Branching polytopes for RNA sequences},
  author={Drellich, Elizabeth and Gainer-Dewar, Andrew and Harrington, H and He, Qijun and Heitsch, CE and Poznanovi{\'c}, S},
  journal={Algebraic and Geometric Methods in Applied Discrete Mathematics. Contemporary Mathematics},
  volume={685},
  pages={137--154},
  year={2017}
}

@article{adamer2017graph,
  title={Graph-facilitated resonant mode counting in stochastic interaction networks},
  author={Adamer, Michael F and Woolley, Thomas E and Harrington, Heather A},
  journal={Journal of The Royal Society Interface},
  volume={14},
  number={137},
  year={2017},
  publisher={The Royal Society}
}

@article{smith2017nanog,
  title={Nanog fluctuations in embryonic stem cells highlight the problem of measurement in cell biology},
  author={Smith, Rosanna CG and Stumpf, Patrick S and Ridden, Sonya J and Sim, Aaron and Filippi, Sarah and Harrington, Heather A and MacArthur, Ben D},
  journal={Biophysical journal},
  volume={112},
  number={12},
  pages={2641--2652},
  year={2017},
  publisher={Elsevier}
}

@article{stolz2017persistent,
  title={Persistent homology of time-dependent functional networks constructed from coupled time series},
  author={Stolz, Bernadette J and Harrington, Heather A and Porter, Mason A},
  journal={Chaos: An Interdisciplinary Journal of Nonlinear Science},
  volume={27},
  number={4},
  year={2017},
  publisher={AIP Publishing}
}

@article{harrington2017reduction,
  title={Reduction of dimension for nonlinear dynamical systems},
  author={Harrington, Heather A and Van Gorder, Robert A},
  journal={Nonlinear Dynamics},
  volume={88},
  number={1},
  pages={715--734},
  year={2017},
  publisher={Springer}
}

@article{kay2017role,
  title={The role of the Hes1 crosstalk hub in Notch-Wnt interactions of the intestinal crypt},
  author={Kay, Sophie K and Harrington, Heather A and Shepherd, Sarah and Brennan, Keith and Dale, Trevor and Osborne, James M and Gavaghan, David J and Byrne, Helen M},
  journal={PLoS computational biology},
  volume={13},
  number={2},
  pages={e1005400},
  year={2017},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article{gross2016algebraic,
  title={Algebraic systems biology: a case study for the Wnt pathway},
  author={Gross, Elizabeth and Harrington, Heather A and Rosen, Zvi and Sturmfels, Bernd},
  journal={Bulletin of mathematical biology},
  volume={78},
  number={1},
  pages={21--51},
  year={2016},
  publisher={Springer}
}

@article{maclean2016mathematical,
  title={Mathematical and statistical techniques for systems medicine: the Wnt signaling pathway as a case study},
  author={MacLean, Adam L and Harrington, Heather A and Stumpf, Michael PH and Byrne, Helen M},
  journal={Systems Medicine},
  pages={405--439},
  year={2016},
  publisher={Springer}
}

@article{gross2016numerical,
  title={Numerical algebraic geometry for model selection and its application to the life sciences},
  author={Gross, Elizabeth and Davis, Brent and Ho, Kenneth L and Bates, Daniel J and Harrington, Heather A},
  journal={Journal of The Royal Society Interface},
  volume={13},
  number={123},
  pages={20160256},
  year={2016},
  publisher={The Royal Society}
}

@article{levy2016role,
  title={Role of seasonality on predator--prey--subsidy population dynamics},
  author={Levy, Dorian and Harrington, Heather A and Van Gorder, Robert A},
  journal={Journal of theoretical biology},
  volume={396},
  pages={163--181},
  year={2016},
  publisher={Elsevier}
}

@article{dufresne2016geometry,
  title={The geometry of sloppiness},
  author={Dufresne, Emilie and Harrington, Heather A and Raman, Dhruva V},
  journal={arXiv preprint arXiv:1608.05679},
  year={2016}
}

@article{maclean2015parameter,
  title={Parameter-free methods distinguish Wnt pathway models and guide design of experiments},
  author={MacLean, Adam L and Rosen, Zvi and Byrne, Helen M and Harrington, Heather A},
  journal={Proceedings of the National Academy of Sciences},
  volume={112},
  number={9},
  pages={2652--2657},
  year={2015},
  publisher={National Academy of Sciences}
}

@article{jovanovic2015phosphorelay,
  title={Phosphorelay of non-orthodox two component systems functions through a bi-molecular mechanism in vivo: the case of ArcB},
  author={Jovanovic, Goran and Sheng, Xia and Ale, Angelique and Feliu, Elisenda and Harrington, Heather A and Kirk, Paul and Wiuf, Carsten and Buck, Martin and Stumpf, Michael PH},
  journal={Molecular BioSystems},
  volume={11},
  number={5},
  pages={1348--1359},
  year={2015},
  publisher={The Royal Society of Chemistry Oxford, UK}
}

@article{taylor2015topological,
  title={Topological data analysis of contagion maps for examining spreading processes on networks},
  author={Taylor, Dane and Klimm, Florian and Harrington, Heather A and Kram{\'a}r, Miroslav and Mischaikow, Konstantin and Porter, Mason A and Mucha, Peter J},
  journal={Nature communications},
  volume={6},
  number={1},
  pages={7723},
  year={2015},
  publisher={Nature Publishing Group UK London}
}

@article{maclean2014epithelial,
  title={Epithelial-mesenchymal transition in metastatic cancer cell populations affects tumor dormancy in a simple mathematical model},
  author={MacLean, Adam L and Harrington, Heather A and Stumpf, Michael PH and Hansen, Marc DH},
  journal={Biomedicines},
  volume={2},
  number={4},
  pages={384--402},
  year={2014},
  publisher={MDPI}
}

@article{michailovici2014nuclear,
  title={Nuclear to cytoplasmic shuttling of ERK promotes differentiation of muscle stem/progenitor cells},
  author={Michailovici, Inbal and Harrington, Heather A and Azogui, Hadar Hay and Yahalom-Ronen, Yfat and Plotnikov, Alexander and Ching, Saunders and Stumpf, Michael PH and Klein, Ophir D and Seger, Rony and Tzahor, Eldad},
  journal={Development},
  volume={141},
  number={13},
  pages={2611--2620},
  year={2014},
  publisher={The Company of Biologists}
}

@article{harrington2013cellular,
  title={Cellular compartments cause multistability and allow cells to process more information},
  author={Harrington, Heather A and Feliu, Elisenda and Wiuf, Carsten and Stumpf, Michael PH},
  journal={Biophysical journal},
  volume={104},
  number={8},
  pages={1824--1831},
  year={2013},
  publisher={Elsevier}
}

@article{chaidos2013clinical,
  title={Clinical drug resistance linked to interconvertible phenotypic and functional states of tumor-propagating cells in multiple myeloma},
  author={Chaidos, Aristeidis and Barnes, Chris P and Cowan, Gillian and May, Philippa C and Melo, Valeria and Hatjiharissi, Evdoxia and Papaioannou, Maria and Harrington, Heather and Doolittle, Helen and Terpos, Evangelos and others},
  journal={Blood, The Journal of the American Society of Hematology},
  volume={121},
  number={2},
  pages={318--328},
  year={2013},
  publisher={American Society of Hematology Washington, DC}
}

@article{harrington2013commentary,
  title={Commentary: Teach network science to teenagers},
  author={Harrington, Heather A and Beguerisse-D{\'\i}az, Mariano and Rombach, M Puck and Keating, Laura M and Porter, Mason A},
  journal={Network Science},
  volume={1},
  number={2},
  pages={226--247},
  year={2013},
  publisher={Cambridge University Press}
}

@article{harrington2012mathematical,
  title={Mathematical modeling reveals the functional implications of the different nuclear shuttling rates of Erk1 and Erk2},
  author={Harrington, Heather A and Komorowski, Micha{\l} and Beguerisse-D{\'\i}az, Mariano and Ratto, Gian Michele and Stumpf, Michael PH},
  journal={Physical biology},
  volume={9},
  number={3},
  pages={036001},
  year={2012},
  publisher={IOP Publishing}
}

@article{harrington2012parameter,
  title={Parameter-free model discrimination criterion based on steady-state coplanarity},
  author={Harrington, Heather A and Ho, Kenneth L and Thorne, Thomas and Stumpf, Michael PH},
  journal={Proceedings of the National Academy of Sciences},
  volume={109},
  number={39},
  pages={15746--15751},
  year={2012},
  publisher={National Academy of Sciences}
}

@article{tanaka2011skin,
  title={Skin barrier homeostasis in atopic dermatitis: feedback regulation of kallikrein activity},
  author={Tanaka, Reiko J and Ono, Masahiro and Harrington, Heather A},
  journal={PLoS One},
  volume={6},
  number={5},
  pages={e19895},
  year={2011},
  publisher={Public Library of Science San Francisco, USA}
}

@article{ho2010bistability,
  title={Bistability in apoptosis by receptor clustering},
  author={Ho, Kenneth L and Harrington, Heather A},
  journal={PLoS computational biology},
  volume={6},
  number={10},
  pages={e1000956},
  year={2010},
  publisher={Public Library of Science San Francisco, USA}
}

@article{boyle2009coronary,
  title={Coronary intraplaque hemorrhage evokes a novel atheroprotective macrophage phenotype},
  author={Boyle, Joseph J and Harrington, Heather A and Piper, Emma and Elderfield, Kay and Stark, Jaroslav and Landis, Robert C and Haskard, Dorian O},
  journal={The American journal of pathology},
  volume={174},
  number={3},
  pages={1097--1108},
  year={2009},
  publisher={Elsevier}
}

@article{harrington2008construction,
  title={Construction and analysis of a modular model of caspase activation in apoptosis},
  author={Harrington, Heather A and Ho, Kenneth L and Ghosh, Samik and Tung, KC},
  journal={Theoretical Biology and Medical Modelling},
  volume={5},
  number={1},
  pages={26},
  year={2008},
  publisher={Springer}
}

@article{harrington2007hybrid,
  title={A hybrid model for tumor-induced angiogenesis in the cornea in the presence of inhibitors},
  author={Harrington, Heather A and Maier, M and Naidoo, L and Whitaker, Nathaniel and Kevrekidis, Panayotis G},
  journal={Mathematical and computer modelling},
  volume={46},
  number={3-4},
  pages={513--524},
  year={2007},
  publisher={Elsevier}
}