Papers

Publications/preprints can be found on Google Scholar and ResearchGate.

Intradisciplinary mathematics research crosses cultures and boundaries, which means authorship conventions can range from alphabetical authorship (traditional mathematics conventions), independent authorship (students or postdocs demonstrate independence from supervisor and those papers not listed here), first/last authorship placement (where science conventions have joint first authorship, here denoted by *).

Manuscripts

  1. Grounded persistent path homology: a stable, topological descriptor for weighted digraphs

    Chaplin T, Harrington HA, Tillmann U

    Submitted. arXiv:2210.11274
  2. Hypergraphs for multiscale cycles in structured data

    Barbensi A, Yoon HR, Madsen CD, Ajayi DO, Stumpf MPH, Harrington HA

    Submitted. arXiv:2210.07545
  3. Topological descriptors for coral reef resilience using a stochastic spatial model

    McDonald RA, Neuhausler R, Robinson M, Larsen LG, Harrington HA, Bruna M

    Submitted. arXiv:2209.08974
  4. Brain Chains as Topological Signatures for Alzheimer’s Disease

    Goodbrake C, Beers D, Thompson TB, Harrington HA, Goriely A

    Submitted. arXiv:2208.12748
  5. Homology of homologous proteins

    Benjamin K, Mukta L, Moryoussef G, Uren C, Harrington HA, Tillmann U, Barbensi A

    Submitted. arXiv:2201.07709
  6. Barcodes distinguish morphology of neuronal tauopathy

    Beers D, Goniotaki D, Hanger DP, Goriely A, Harrington HA

    Submitted.

    7. Publications

  7. Continuous Indexing of Fibrosis (CIF): Improving the Assessment and Classification of MPN Patients

    H Ryou, Sirinukunwattana K, Aberdeen A, Grindstaff G, Stolz B, Byrne HM, Harrington HA, Sousos N, Godfrey AL, Harrison CN, Psaila B, Mead AJ, Rees G, Turner GDH, Rittscher J, Royston D

    Accepted, Leukemia. medRxiv.
  8. Algebra, Geometry and Topology of ERK Kinetics

    Marsh L, Dufresne E, Byrne HM, Harrington HA

    Accepted, Bull Math Biol. arXiv:2112.00688.
  9. Computing input-output projections of dynamical models with applications to structural identifiability

    Dong R, Goodbrake C, Harrington HA, Pogudin G

    Accepted SIAM J Appl Alg Geom. arXiv:2111.00991.
  10. What are higher order networks?

    Bick C, Gross E, Harrington HA, Schaub MT

    Review article to appear SIAM Review. arXiv:2104.11329.
  11. Multiscale methods for signal selection in single-cell data

    Hoekzema RS, Marsh L, Sumray O, Carroll TM, Lu X, Byrne HM, Harrington HA

    Submitted.
  12. Multiscale Topology Characterises Dynamic Tumour Vascular Networks

    Stolz BJ, Kaeppler J, Markelc B, Mech F, Lipsmeier F, Muschel RJ, Byrne HM, Harrington HA

    Accepted, Sci Adv. arXiv:2008.08667.
  13. Principal Components along Quiver Representations

    Seigal A, Harrington HA, Nanda V

    In Press, Found Comut Math. arXiv:2104.10666.
  14. Quantification of vascular networks in photoacoustic mesoscopy

    Brown EL, Lefebvre TL, Sweeney PW, Stolz BJ, Gröhl J, Hacker L, Huang Z, Couturier D-L, Harrington HA, Byrne HM, Bohndiek SE

    In Press, Photoacoustics bioRXiv:2021.11.22.469541.
  15. Double branched covers of knotoids

    Barbensi A, Buck D, Harrington HA, Lackenby M

    In Press, Comm in Anal Geom. arXiv:1811.091216.
  16. Topological Approximate Bayesian Computation for Parameter Inference of an Angiogenesis Model

    Thorne T, Kirk PDW, Harrington HA

    Bioinformatics. 2022, 38(9):2529–2535. arXiv:2108.11640.
  17. A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

    COvid-19 Multi-omics Blood ATlas (COMBAT) Consortium (203 authors, HAH member of integrative data analysis team).

    Cell 2022 185:916-938. medRXiv.
  18. Multiparameter persistent homology landscapes identify immune cell spatial patterns in tumors

    Vipond O, Bull JA, Macklin PS, Tillmann U, Pugh CW, Byrne HM, Harrington HA

    Proc Nat Acad Sci. 2021. 118 (41) e210216611.
  19. Topological data analysis of task-based fMRI data from experiments on schizophrenia

    Stolz BJ, Emerson T, Nahkuri S, Porter MA, Harrington HA

    J Phys Complexity 2021 2(3) arXiv:1809.08504.
  20. On some configurations of opositely charged trapped vortices in the plane

    Dufresne E, Harrington HA, Kevrekidis PG, Tripoli P

    Adv in Appl Math. 2021 124: 102099 arXiv:1810.11529.
  21. Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis

    Nardini JT, Stolz BJ, Flores KB, Harrington HA, Byrne HM

    PLoS Comput Biol. 2021. 17(6) e1009094 arXiv:2101.00523.
  22. Geometric anomaly detection in data

    Stolz BJ, Tanner J, Harrington HA, Nanda V

    Proc Nat Acad Sci.Aug 2020. 202001741 arXiv:1908.09397.
  23. Coloured noise from stochastic inflows in reaction-diffusion systems

    Adamer MF, Harrington HA, Gaffney EA, Woolley TE

    Bull Math Biol 2020. 82(4):44 arXiv:1810.12663.
  24. Joining and decomposing reaction networks

    Gross E, Harrington HA, Meshkat N and Shiu A

    J Math Biol 2020. 30:1683-1731. arXiv:1810.05575.
  25. Inference of Multisite Phosphorylation Rate Constants and their Modulation via Pathogenic Mutations

    Yeung E, McFann S, Marsh L, Dufresne E, Filippi S, Harrington HA, Shvartsman SY, Wuhr M

    Curr Biol, 2020. 30 (5):877-882. DOI:10.1016/j.cub.2019.12.052.
  26. Grid diagrams as tools to investigate knots space and topoisomerases-mediated simplification of DNA topology

    Barbensi A, Celoria D, Harrington HA, Stasiak A, Buck D

    Sci Adv, 2020 6(9) arXiv:1909.05937.
  27. Sampling real algebraic varieties for topological data analysis

    Dufresne E, Edwards PB, Harrington HA, Hauenstein JD

    2019 18th IEEE International Conference On Machine Learning And Applications (ICMLA) 2020 1531-1536. arXiv:1802.07716.
  28. Decomposing the parameter space of biological networks via a numerical discriminant approach

    Harrington HA, Mehta D, Byrne HM, Hauenstein JD

    MC 2019: Maple in Mathematics Education and Research 2020 (114-131) arXiv:1604.02623.
  29. Stratifying multiparameter persistent homology

    Harrington HA, Otter N, Schenck H, Tillmann U

    SIAM J Appl Algebr and Geom 2019 3(3):439–471arXiv:1708.07390 .
  30. Linear compartmental models: input-output equations and operations that preserve identifiability

    Gross E, Harrington HA, Meshkat N, Shiu A

    SIAM J Appl Math. 2019 79(4):1423-1447. arXiv:1808.00335.
  31. Tensors and algebra give interpretable groups for crosstalk mechanisms in breast cancer

    *Seigal A, *Beguerisse-Díaz M, Schoeberl B, Niepel M, Harrington HA

    J R Soc Interface 2019 16(151):20180661. arXiv:1612.08116.
  32. Differential algebra for model comparison

    Harrington HA, Ho KL, Meshkat N

    Complexity 2019 6041981arXiv:1603.09730.
  33. The geometry of sloppiness

    Dufresne E, Harrington HA, Raman DV

    Journal of Algebraic Statistics 2018 9(1) arXiv:1608.05697.
  34. Topological data analysis of continuum percolation with disks

    Speidel L, Harrington HA, Chapman SJ, Porter MA

    Phys Rev E 2018 98 012318 arXiv:1804.07733.
  35. Graph-Facilitated Resonant Mode Counting in Stochastic Interaction Networks

    Adamer MF, Woolley TE, Harrington HA

    J R Soc Interface 2017 14 20170447 arXiv:1702.08747.
  36. Roadmap for the computation of persistent homology

    Otter N, Porter MA, Tillmann U, Grindrod P, Harrington HA.

    EP J Data Science 2017 6(1) 17 arXiv:1506.08903.
  37. Nanog fluctuations in Embryonic Stem cells highlight the problem of measurement in cell biology

    Smith RCG, Stumpf PS, Ridden SJ, Sim A, Filippi S, Harrington HA, MacArthur BD

    Biophys J 2017 112(12):2641-265 biorxiv. doi.
  38. Persistent homology of time-dependent functional networks constructed from coupled time series

    Stolz BJ, Harrington HA, Porter MA

    Chaos 2017 27, 047410 arXiv:1506.00562. doi.
  39. The Role of the Hes1 Crosstalk Hub in Notch-Wnt Interactions of the Intestinal Crypt

    Kay SK, Harrington HA, Shepherd S, Brennan K, Dale T, Osborne JM, Gavaghan DJ, Byrne HM

    PLoS Comput Biol 2017 13(2): e1005400 arXiv:1608.06146. doi.
  40. Reduction of dimension for nonlinear dynamical systems

    Harrington HA and Van Gorder R.

    Nonlinear Dynamics 2017 88(1):715-734 arXiv:1508.05921.
  41. Numerical algebraic geometry for model selection and its application to the life sciences

    Gross E, Davis B, Ho KL, Bates DJ, Harrington HA.

    J R Soc Interface 2016 13:20160256 arXiv:1507.04331. doi.
  42. Role of seasonality on predator-prey-subsidy population dynamics

    Levy D, Harrington HA and Van Gorder R.

    J Theor Biol 2016 396:163-181. doi.
  43. Algebraic systems biology: a case study for the Wnt pathway

    Gross E, Harrington HA, Rosen Z, Sturmfels B.

    Bull Math Biol 2016 87(1):21-51. arXiv:1502.03188. doi.
  44. Topological data analysis of contagion maps for examining spreading processes on networks

    *Taylor D, *Klimm F, Harrington HA, Kramar M, Mischaikow K, Porter MA, Mucha PJ.

    Nat Commun 2015 6:7723. arXiv:1408:1168. doi.

  45. Phosphorelay in non-orthodox two component systems in-vivo functions through a bi-molecular mechanism: the case of ArcB

    Jonanovic G, Sheng X, Ale A, Feliu E, Harrington HA, Kirk P, Wiuf C, Buck M, Stumpf MPH.

    Molecular BioSystems 2015. doi.
  46. Parameter-free methods distinguish Wnt pathway models and guide design of experiments

    MacLean AL, Rosen Z, Byrne HM, Harrington HA.

    Proc Nat Acad Sci. 2015 Mar;112(9):2652-2657.arXiv:1409.0269. doi.
  47. Epithelial-Mesenchymal Transition in Metastatic Cancer Cell Populations Affects Tumor Dormancy in a Simple Mathematical Model

    MacLean AL, Harrington HA, Stumpf MPH, Hansen M.

    Biomedicines 2014 2(4):384-403. doi.
  48. Nuclear-cytoplasmic shuttling of ERK provides a switch-like transition between proliferation and differentiation of muscle progenitors

    Michailovici I, Harrington H, Azogui HH, Yahalom-Ronen Y, Plotnikov A, Ching S, Stumpf MPH, Klein OD, Seger R, Tzahor E.

    Development 2014 Jul;141(13):2611-20. doi.
  49. Cellular compartments cause multistability and allow cells to process more information

    *Harrington HA, *Feliu E, Wiuf C, Stumpf MPH.

    Biophys J. 2013 April;104:1824-1831. arXiv:1210.2993. doi.
  50. Clinical drug resistance linked to inter-convertible phenotypic and functional states of tumor-propagating cells in multiple myeloma

    Chaidos A, Barnes C, Cowan G, May P, Melo V, Hatjiharissi E, Papaioannou M, Harrington H, Doolittle H, Terpos E, Abdalla S, Yarranton H, Naresh K, Foroni L, Reid A, Rahemtulla A, Stumpf M, Roberts I, Karadimitris A.

    Blood. 2012 Nov 20. doi.
  51. A parameter-free model selection criterion based on steady-state coplanarity

    *Harrington HA, *Ho K, Thorne T, Stumpf MPH.

    Proc Nat Acad Sci. 2012 Sept;109(39):15746-15751.arXiv:1109.3670. doi.
  52. Mathematical modeling reveals the functional implications of the different nuclear shuttling rates of Erk1 and Erk2.

    Harrington HA, Komorowski M, Beguerisse-Díaz M, Ratto GM, Stumpf MPH.

    Physical Biology. 2012 9(3):036001.arXiv:1110.3742. doi.
  53. Skin barrier homeostasis in atopic dermatitis: feedback regulation of kallikrein activity.

    Tanaka RJ, Ono M, Harrington HA.

    PLoS One. 2011 6(5):e19895. doi.
  54. Bistability in apoptosis by receptor clustering

    Ho KL, Harrington HA.

    PLoS Comput Biol. 2010 6(10): e1000956.arXiv:0912.1548. doi.
  55. Coronary intraplaque hemorrhage evokes a novel atheroprotective macrophage phenotype

    Boyle J, Harrington HA, Piper E, Elderfield K, Stark J, Landis RC, Haskard DO.

    Am J Pathol. 2009 Mar;174(3):1097-108.doi.
  56. Construction and analysis of a modular model of caspase activation in apoptosis

    Harrington HA, Ho KL, Ghosh S, Tung KC.

    Theor Biol Med Model. 2008 5:26. doi.
  57. A hybrid model for tumor-induced angiogenesis in the cornea in the presence of inhibitors

    Harrington HA, Maier M, Naidoo L, Whitaker N, Kevrekidis PG.

    Math and Comput Model. 2007 Aug;46(3-4):513-524. doi.

    58. Peer-reviewed book chapters

  58. Geometric combinatorics and computational molecular biology: Branching polytopes for RNA sequences

    Drellich E, Gainer-Dewar A, Harrington HA, He Q, Heitsch C, Poznanovic S.

    Accepted (to appear AMS Contemporary Mathematics Volume). arXiv:1509.04090.
  59. Mathematical and Statistical Techniques for Systems Medicine: The Wnt Signaling Pathway as a Case Study

    MacLean AL, Harrington HA, Stumpf MPH, Byrne HM.

    Systems Medicine. Editors: U Schmitz and and O Wolkenhauer, (2016) Springer. arXiv:1502.01902. doi.

    60. Outreach

  60. The topological "shape" of Brexit

    Stolz BJ, Harrington HA, Porter MA

    Submitted. SSRN:2843662. arxiv:1610.00752.
  61. Topology characterises spatial networks of tumour vasculature

    Byrne HM, Harrington HA,Muschel R, Reinert G, Stolz BJ, Tillmann U

    Mathematics Today, 2019 55(5):206-210. arXiv:1907.08711.
  62. Teach Network Science to Teenagers

    Harrington HA, Beguerisse Díaz M, Rombach, MP, Keating LM, Porter AP.

    Network Science 2013 Sept;2:1-22.arXiv:1302.6567. doi.
    * = joint first authors