Using network structure to better understand dynamical processes

I am a recently graduated Ph.D. student from the department of Ecology & Evolution at the University of Chicago. Working in Stefano Allesina's lab, I was exposed to the powerful perspective of seeing the complexity of nature as a network of connected pieces. I have been particularly captivated by the interaction between the dynamics of ecological systems (i.e. the stability and feasibility of equilibria and the role of transient dynamics) and the structures (both local and global) found in network representations of those systems.

Though I have worked historically with ecological interaction networks, many of my projects exploit the extreme generality of mathematical models, and have applied network- and matrix-based methods to a host of systems. I am driven by the development of computational and statistical methods to enhance our ability to detect patterns in ecological data.

More recently, I have been moving more into the study of how diseases spread on networks, working as a postdoc with Meggan Craft on a variety of projects applying this network perspective to disease ecology and, more recently, the spread of COVID-19 in realistic human contact networks. I also work with Linda Kinkel, keeping my more ecological roots alive by looking at the relationship between the structures of microbial interaction networks, including those detailing resource niche overlap and direct antimicrobial competition in plant microbiomes.

Disease dynamics

Disease dynamics have long been modelled through the use of compartmental models which rely on an assumption of well-mixing. That is, the case where all individuals have an equal likelihood of infection at any given timepoint. But we know that this is not reflective of reality, where individuals are connected in complex social networks that dictate the paths of pathogens through a population. I am interested in the ways the structure of these social networks dictates the spread of disease, limiting or exacerbating epidemics.


More than 40 years ago, Robert May introduced random matrices to ecology in a famous demonstration of the relationship between complexity and stability which was counter to the prevailing view of the time (May 1972). Following a long hiatus, random matrices have recently re-emerged as the impetus behind several important advances in our understanding of complex ecological systems, spearheaded by Si Tang and Stefano Allesina (Allesina & Tang 2012; Tang & Allesina 2014; Tang, Pawar, & Allesina 2014). I am particularly interested in applying random matrix techniques to bipartite networks (i.e. networks for which the nodes can be divided into groups such that all links are between nodes of disparate groups).


Random matrices à la May look for patterns in matrix ensembles which randomize matrix elements. Advances since then have explored alternative modes of randomization (Tang, Pawar, & Allesina 2014), yet these still tend to focus on node degree and interaction strength correlation. An alternative form of randomization would be to preserve small network structures such as motifs or global network structures such as nestedness and modularity. I am interested in applying this technique to evaluate the importance and utility of small structures which are found at unexpected densities in empirical networks.

Science of Science

In addition to my central focus on ecology, I have also been interested in studying the process of doing science, especially aspects related to publication and evaluating performance. For instance, one project I have worked on looked at the influence of multinational affiliation lists on the success of publications. We confirmed a historical result that more countries improves both the quality of journal a paper is published into and the number of citations (compared to peer publications) it receives once published. Furthermore, we showed that the benefit differs according to which countries are in the affiliations -- some collaborations show much greater improvements than others and some actually decrease the expected number of citations!

22 More than the Sum of its Parts: Unlocking the Power of Network Structure for Understanding Organization and Function in Microbiomes
J.P. Dundore-Arias*, M.J. Michalska-Smith*, M. Millican*, L.L. Kinkel; 2023
21 The illusion of personal health decisions for infectious disease management: disease spread in social contact networks
M. Michalska-Smith, E.A. Enns, L.A. White, M.L.J. Gilbertson, M.E. Craft; 2023
20 Shortcomings of reusing species interaction networks created by different sets of researchers
C. Brimacombe, K. Bodner, M. Michalska-Smith, T. Poisot, M. Fortin; 2023
19 Network structure of resource use and niche overlap within the endophytic microbiome
M.J. Michalska-Smith, Z. Song, S. Spawn, Z. Hansen, M. Johnson, G. May, E. Borer, E. Seabloom, L.L. Kinkel; 2022
18 Asymmetric host movement reshapes local disease dynamics in metapopulations
M. Michalska-Smith, K. VanderWaal, M.E. Craft; 2022
17 Ecological and evolutionary dynamics of multi-strain RNA viruses
D. Makau, S. Lycett, M. Michalska-Smith, I. Paploski, M. Cheeran, M. Craft, R. Kao, D. Schroeder, A. Doeschl-Wilson; 2022
16 No strong evidence that modularity, specialization, or nestedness are linked to seasonal climatic variability in bipartite networks across large spatial extents
C. Brimacombe, K. Bodner, M. Michalska-Smith, D. Gravel, M. Fortin; 2022
15 Consequences of ignoring dispersal variation in network models for landscape connectivity
L.L. Sullivan, M.J. Michalska-Smith, K.P. Sperry, D.A. Moeller, A.K. Shaw; 2021
14 Lessons from movement ecology for the return to work: modeling contacts and the spread of COVID-19
A.K. Shaw, L.A. White, M. Michalska-Smith, E.T. Borer, M.E. Craft, E.W. Seabloom, E. Snell-Rood, M. Travisano; 2021
13 Broadening Participation in Scientific Conferences during the Era of Social Distancing
M.R. Fulcher, M.L. Bolton, M.D. Millican, M.J. Michalska-Smith, J.P. Dundore-Arias, J. Handelsman, J.L. Klassen, K.C. Milligan-Myhre, A. Shade, B.E. Wolfe, L.L. Kinkel; 2020
12 Telling ecological networks apart by their structure: A computational challenge
M.J. Michalska-Smith, S. Allesina; 2019
11 Manipulating Wild and Tamed Phytobiomes: Challenges and Opportunities
T.H. Bell, K.L. Hockett, R.I. Alcalá-Briseño, M. Barbercheck, G.A. Beattie, M.A. Bruns, J.E. Carlson, T. Chung, A. Collins, B. Emmett, P. Esker, K.A. Garrett, L. Glenna, B.K. Gugino, M.d.M. Jiménez-Gasco, L. Kinkel, J. Kovac, K.P. Kowalski, G. Kuldau, J.H.J. Leveau, M. Michalska-Smith, J. Myrick, K. Peter, M.F.V. Salazar, A. Shade, N. Stopnisek, X. Tan, A.T. Welty, K. Wickings, E. Yergeau; 2019
10 Understanding the role of parasites in food webs using the group model
M.J. Michalska-Smith*, E.L. Sander*, M. Pascual, S. Allesina; 2018
9 Self-regulation and the stability of large ecological networks
G. Barabás, M.J. Michalska-Smith, S. Allesina; 2017
8 Higher-order interactions stabilize dynamics in competitive network models
J. Grilli, G. Barabás, M.J. Michalska-Smith, S. Allesina; 2017
7 And, not or: Quality, quantity in scientific publishing
M.J. Michalska-Smith, S. Allesina; 2017
6 The Effect of Intra- and Interspecific Competition on Coexistence in Multispecies Communities
G. Barabás*, M.J. Michalska-Smith*, S. Allesina; 2016
5 Stability and feedback levels in food web models
M.J. Smith, E. Sander, G. Barabás, S. Allesina; 2015
4 The Scientific Impact of Nations: Journal Placement and Citation Performance
M.J. Smith, C. Weinberger, E.M. Bruna, S. Allesina; 2014
3 Selecting food web models using normalized maximum likelihood
P.P.A. Staniczenko, M.J. Smith, S. Allesina; 2014
2 Whirling disease dynamics: An analysis of intervention strategies
K.G. Turner, M.J. Smith, B.J. Ridenhour; 2014
1 Superelliptical laws for complex networks
S. Allesina, E. Sander, M.J. Smith, S. Tang; 2013
  • Why vaccination strategy is not as simple as it seems

    September 14, 2021

    When vaccination just started getting underway in the U.S., many people were confused and angered at the fact that many localities were pursuing vaccination strategies that didn’t just boil down to vaccinating the most vulnerable. On the other hand, there was a significant movement to vaccinate front-line workers which often cited equity and racial justice as motivations. What didn’t seem to make the news as often is the mathematics that make this a reasonable alternative to consider.

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  • The case against "herd immunity" through infection

    December 21, 2020

    As COVID-19 cases continue to spike and governments implement stronger and stronger restrictions, I thought it might be worth visiting an argument that I have encountered on and off over the past year. In its most basic form, the argument goes “why not simply let the pandemic run its course while protecting the vulnerable as best we can, but not worrying overly much (indeed, perhaps even encouraging) those young and healthy individuals to contract the virus in a push toward herd immunity?”

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  • Interpreting graphs: the red-blue coronavirus divide

    June 28, 2020

    I recently saw this graph floating about the internet, and it has some interesting properties that I thought might warrant a new type of post, where I dive into interpreting a particular figure and see where it takes me.

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  • Comparing COVID-19 Responses

    May 4, 2020

    There has been a lot of talk about different countries’ responses to the ongoing COVID-19 pandemic, but how can we tell which responses are better than others? Even if one country has fewer cases/deaths/etc. than another, does that mean their approach is transferable?

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  • Resources for Tracking the COVID-19 Epidemic

    April 9, 2020

    this post was inspired by this recent blogpost

    It is easy to succumb to number overload when faced with the incredible volume of data available detailing the spread of the SARS-CoV-2 virus around the globe. As of the writing of this post, more than 1.5 million individuals have been confirmed to have contracted COVID-19 and nearly 90 thousand individuals have died. As the pandemic has progressed, dozens of dashboardsand even tutorials on how to make your own have been created to track the climbing numbers each day. With so many to choose from, how does one pick a trustworthy source? and what are the most important numbers to consider anyway?

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  • Rethinking poster sessions? (Post associated with EEID 2019)

    June 7, 2019

    Get the full paper pre-print here (pdf) or read online on AUTHOREA.

    I confess, I am not a huge fan of posters.

    I find them to be inefficient in their production, ineffective in their communication, and awkward for both presenter and viewer during poster sessions themselves. In part because of this, before this week, I hadn’t made a poster since undergrad. In spite of my prejudice, I tried to dive into the task, telling myself it was a valuable skill to condense information into a single infographic. Yet, I found myself struggling with the same issue I have expounded on before with regards to presentations: namely there is a two-use-case problem. On one hand, you want something aesthetic that compliments (without distracting from) the more important part—what you are saying—but on the other hand, you want this to have some shelf-life and be useful to viewers after you are no longer physically standing in front of them.

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  • 5 Tips for Early Career ESA Attendees

    August 20, 2018

    When I first went to the annual meeting of the Ecological Society of America (ESA), I was overwhelmed. The conference is huge by the standards of most ecological conferences, boasting around 3000 ecologists in attendance each year. It stretches on for five and a half days with dozens of concurrent sessions, hundreds of posters, and mixers most evenings.

    As a newcomer, especially if you are not traveling with someone who is both social and conference savvy, this can make for a lonely experience which is only amplified by the swirling masses of people around you. It is tempting to disengage, to either pack your schedule with talks or to give up and just spend some time seeing the city in which the conference is hosted that particular yearNot that you shouldn’t make some time for that too!.

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  • ESA2016 & HTML presentations

    August 19, 2016

    Welcome to the site!

    Last week, I attended the 101st Annual Meeting of the Ecological Society of America in Ft. Lauderdale, FL. While there I was able to meet up with several colleagues I hadn’t seen in a long time and see many interesting talks. I also gave a talk of my own, where I presented some recently submitted work on distinguishing ecological categorizations or roles (e.g. parasites vs predators) using a purely statistical consideration of the network structure. For this, we utilized (and enhanced) the group model which was introduced to Ecology by my adviser (Stefano Allesina) and committee member (Mercedes Pascual) back in 2009.

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