- 2014 Dec 8 - Boston Area Parasitology Symposium.
- Deep origins of P. falciparum var genes in the ape-infecting Plasmodium Laverania subgenus. FXB 301.
- 2014 Nov 7 - Western New England University Mathematics Colloquium.
- Complex networks, rapid genetic recombination, and tricky malaria antigens. 3PM in Herman 312.
- 2014 Nov 3-6 - I'll be presenting at the ASTMH meeting in New Orleans.
- Deep origins of P. falciparum var genes in the ape-infecting Plasmodium Laverania clade.
- 2014 Oct 31 - Presenting at the Harvard Med Channing Network Science Seminar.
- A complex networks approach to understanding genetic recombination in malaria antigens.
- 3-4 PM, 5th floor conference room, 181 Longwood Ave, Boston, MA.
- 2014 July 29 - biSBM code now available for C++, MATLAB, and R.
- Code and info about the bipartite stochastic block model here.
- 2014 July 24 and 31 - Teaching at a HSPH summer nanocourse on Modeling Infectious Disease.
- 2014 July 10 - "Efficiently inferring community structure in bipartite networks" published in Physical Review E, with Aaron Clauset and Abigail Z. Jacobs
- [PDF][PRE][code and data]
Software and Code
- [Download webweb]
- PercoVIS is a free software tool, created to visualize the process of percolation on a network. It was developed with much inspiration and feedback from my collaborator, Dane Taylor. It includes Erdos-Renyi and Adjacent Edge decision rules for link addition, as well as the Social Climber attachment model. Documentation about these processes can be found on the download page. If you are interested in a similar tool to visualize Kuramoto oscillators, please check out Sebastian Skardal's Synched software.
- [Download PercoVIS]
- biSBM is free and open-source code, created to apply the method described in the paper "Efficiently inferring community structure in bipartite networks". The code finds communities in a bipartite network using a maximum-likelihood approach stochastic block model. The code requires MATLAB as well as a C++ compiler. Details, and the publication on which this code is based, can be found through the link below.
- [Download biSBM]
- MATLAB Codes
- findNetworkComponents - take an undirected network adjacency matrix and return the number of components, their sizes, and their membership lists.
- [MATLAB File Exchange]
Networks - I am interested in the development of mathematical and statistical methods to understand complex processes on complex networks. This includes the dynamics of human populations, environment, economics, education, health, and disease. But it also includes block models, generative models, and other network descriptors. Collaborators for this work are Abigail Z. Jacobs, Leto Peel, Aaron Clauset, Johan Ugander, Bailey Fosdick, and Joel Nishimura.
Malaria - I work with Caroline Buckee, and Aaron Clauset on the development of robust and principled methods to understand genetic recombination among a subset of genes of Plasmodium falciparum, the parasite that causes a majority of malaria deaths each year.
Neuronal Networks - I investigate the role of network topology on the dynamics of excitable systems. A nice example of an excitable system that can be understood in this light is a neuronal network—a network of brain cells—where excitations may be passed from cell to cell via electrochemical impulses. Collaborators for this work are Juan G. Restrepo, Woodrow L. Shew, Ed Ott, Marshall Y. Carpenter, and Francesco Sorrentino.
- 2014 "Prestige hierarchies predict placement in faculty hiring networks"
- Aaron Clauset, Samuel Arbesman, and Daniel B. Larremore.
- 2014 "Ape origins of human malaria virulence genes"
- Daniel B. Larremore, William R. Proto, Aaron Clauset, Sesh A. Sundararaman, Weimin Liu, Dorothy E. Loy, Paul M. Sharp, Beatrice H. Hahn, Julian C. Rayner*, and Caroline O. Buckee*.
- 2014 "Immune characterization of P. falciparum parasites with a shared genetic signature in a region of decreasing transmission"
- Amy K. Bei, Ababacar Diouf, Kazutoyo Miura, Daniel B. Larremore, Ulf Ribacke, Gregory Tullo, Eli L. Moss, Daniel E. Neafsey, Rachel F. Daniels, Amir E. Zeituni, Iguosadolo Nosamiefan, Sarah K. Volkman, Ambroise D. Ahouidi, Daouda Ndiaye, Tandakha Dieye, Souleymane Mboup, Caroline O. Buckee, Carole Long, and Dyann F. Wirth.
- [In press at Infection and Immunity]
- 2014 "Efficiently inferring community structure in bipartite networks"
- Daniel B. Larremore, Aaron Clauset, and Abigail Z. Jacobs, Physical Review E 90(1), 012805 (2014).
- [PDF][PRE][code and data]
- 2014 "Inhibition Causes Ceaseless Dynamics in Networks of Excitable Nodes"
- Daniel B. Larremore, Woodrow L. Shew, Edward Ott, Francesco Sorrentino, and Juan G. Restrepo, Physical Review Letters 112, 138103.
- [PDF] [PRL]
- 2013 "A network approach to analyzing highly recombinant malaria parasite genes"
- Daniel B. Larremore, Aaron Clauset, and Caroline O. Buckee. PLoS Computational Biology 9(10), e1003268.
- [PDF] [PLoS Comp Bio] [interactive figures] [sequence data adapted from Rask et al.]
- 2012 "Social Climber attachment in forming networks produces phase transition in a measure of connectivity"
- Dane Taylor*, Daniel B. Larremore*. Physical Review E 86, 031140.
- 2012 "Statistical properties of avalanches in networks"
- Daniel B. Larremore, Marshall Y. Carpenter, Edward Ott, and Juan G. Restrepo. Physical Review E 85, 066131.
- [PDF] [PRE]
- 2011 "Effects of network topology, transmission delays, and refractoriness on the response of coupled excitable systems to a stochastic stimulus"
- Daniel B. Larremore, Woodrow L. Shew, Edward Ott, and Juan G. Restrepo. Chaos 21, 025117.
- [PDF] [Chaos]
- 2011 "Predicting criticality and dynamic range in complex networks: effects of topology"
- Daniel B. Larremore, Woodrow L. Shew, and Juan G. Restrepo. Physical Review Letters 106, p. 058101.
- [PDF] [PRL]
* denotes equal contribution.
- 2014 Critical Dynamics in Complex Networks, chapter in Criticality in Neural Systems.
- Daniel B. Larremore, Woodrow L. Shew, Juan G. Restrepo. Wiley, 365-392, 2014.
- 2012 "Progess Is Infectious"
- Daniel E. Geer Jr., Daniel B. Larremore. IEEE Security & Privacy, 10(6), p. 94-95.
- [PDF] [IEEE S&P]
- 2013 PercoVIS featured in Franco Landriscina's textbook, Simulation and Learning (2013)
- 2012 PercoVIS called "a lovely visualization tool." in Daniel E. Geer's column, "Power. Law."
- IEEE Security and Privacy, 10(1), 94 (2012)
- [IEEE S&P]
- 2010 My notes "David's Lawnmowing Efficiency Hierarchy" on NPR's Planet Money.'
- [NPR's' Planet Money Blog]
Teaching and WorkshopsWorkshops and Guest Lecturing
- University of Colorado at Boulder
- 2014 Oct 9, CSCI 5352. Network Analysis and Modeling
- 2013 Nov 5-7, PHYS 7810 / CHEM 6711 / MCDB 6400. Foundations of Quantitative Biology
- HSPH summer nanocourse: Modeling Infectious Disease
- 2014 July 24 and 27. [details]
- AMS Mathematics Research Community
- 2014 June 24-30, Network Science. [details]
- Oxford Tropical Disease Network Meeting, Kilifi, Kenya
- 2013 Oct 3, Network Analysis Workshop.
I am not doing any teaching at this time.
Previous courses are listed below. See my FCQ evaluations.
- University of Colorado at Boulder
- 2012 Spring APPM 2350, Calculus III (Instructor)
- 2011 Fall APPM 2350, Calculus III (Instructor)
- 2009 - 2010 Applied Mathematics Lead TA
- 2009 Fall - APPM 1360, Calculus II (TA)
- 2009 Spring - APPM 2360, Ordinary Differential Equations (TA)
- 2008 Fall - APPM 2350, Calculus III (TA)
- 2008 Summer - APPM 2350, Calculus III (TA)
- 2008 Spring - APPM 2360, Ordinary Differential Equations (TA)
- 2007 Fall - APPM 2350, Calculus III (TA)