Stephen Beckett

31/03/2017:	The algorithms I advocate using for computing modularity for weighted bipartite networks are now the default behaviour in the latest version of the R bipartite package (v2.08) on CRAN.
08/03/2017:	Hosted David Talmy (MIT) in the WeitzLab and worked on problems relating to grazers and viruses.
03/03/2017:	I attended the ASLO Ocean sciences meeting and presented work on the dilution method in Hawai`i.
18/07/2016:	I presented a poster related to our dilution method work at Viruses of Microbes 2016 in Liverpool.
11/07/2016:	I spoke at the 8th Viral Aquatic Workshop in Plymouth about the theoretical underpinnings of the dilution method for estimating plankton mortality.
23/01/2016:	I attended my graduation ceremony at the University of Exeter, where I was duly hooded, gowned and embraced!
20/01/2016:	My paper on weighted modularity in bipartite networks is now up at RSOS. I wrote a short blog post about it.
19/09/2015:	Spoke at the "Living systems: from interaction patterns to critical behavior" workshop in Venice about phage-bacteria coevolutionary dynamics.
07/09/2015:	Completed my first review for the journal: Methods in Ecology and Evolution.
17/08/2015:	I have joined the Weitz lab @ Georgia Tech as a PostDoc.
29/07/2015:	My degree has been officially conferred - I am now Dr. Stephen Beckett!
19/07/2015:	New website is being designed (quite excited by how this is turning out!)

I am a postdoctoral researcher in the Weitz lab at Georgia Tech. I am interested in using mathematical and computational methods to investigate and solve ecological and environmental problems. In this sense, I can be termed a computational ecologist. I was awarded my PhD from the University of Exeter where I was a part of the Earth Systems Science Group. Thank you to Hywel Williams for supervising me! Previously I've studied at the University of Leeds, University of York and with the Computational Science Lab at Microsoft Research.

I believe one step towards making science more available in general, is to provide free and open access to research materials. I do not agree with the predominantly expensive open access options provided by many publishers, but am a strong advocate of making pre/post-prints of my research available. If I write a paper, I would sure like to make it as easy as possible, for as many people as possible, to be able to read and use the information discovered! Specific journal policies on this matter can be found using SHERPA/RoMEO.

In my spare time I enjoy being in the great outdoors, especially on the coast. Some of the other things I like to do are playing the harmonica (badly), reading books and playing computer games. Chances are, I am thinking about the sea right now.

Marine Viruses

There are estimated to be over 10³⁰ viruses of prokaryotic bacteria, known as bacteriophage or just phage, in the worlds oceans (Suttle, 2005) which makes them an important component of the global marine ecosystem and ocean biogeochemistry. However, much is unknown about the strengths of these interactions and the coevolutionary processes that mediate community structure and dynamics of microbial ecosystems. Better understanding of how these processes influence one another on the small scale e.g. in chemostats or flasks, may lay down the foundations for embedding virus population models into circulation models of oceanic sizes - which may further inform about how viruses can control biogeochemical cycling.

Bipartite network analysis

The infection pattern between phage and bacteria is an example of a bipartite (two mode) network. Finding and attempting to understand the structures in these types of networks can help explain how communities organise and behave. I have a keen interest in the patterns of nestedness (a generalist to specialist gradient of overlapping range) and modularity (communities formed between the two sets of nodes). These concepts have been largely applied to ecological datasets - but there are many other types of bipartite networks out there where these analyses could prove useful.

The categories below highlight my publications, software and other research outputs. Click on a category to expand or contract it. I try my best to provide open access to all my research. You may also be interested in viewing my Google Scholar and ResearchGate profiles.

>Publications >

		Beckett S.J., Weitz J.S. Disentangling niche competition from grazing mortality in phytoplankton dilution experiments 2017. PLOS ONE 12(5): e0177517.       [see the preprint]
		Beckett S.J. Improved community detection in weighted bipartite networks 2016. Royal Society Open Science 3: 140536.       [code] [blog]
		Beckett S.J. Nestedness and modularity in bipartite networks 2015. PhD Thesis, University of Exeter, UK.
		Cowley L.A., Beckett S.J., Chase-Topping M., Perry N., Dallman T.J., Gally D.L., Jenkins C. Analysis of whole genome sequencing for the Escherichia coli O157:H7 typing phages 2015. BMC Genomics 16: 271.
		Beckett S.J., Boulton C.A., Williams H.T.P. FALCON: a software package for analysis of nestedness in bipartite networks 2014. [v1; ref status: indexed, http://f1000r.es/3z8] F1000Research 3: 185.       [code]
		Watts A.J.R., Lewis C., Goodhead R.M., Beckett S.J., Moger J., Tyler C.R., Galloway T.S. Uptake and retention of microplastics by the shore crab Carcinus maenas 2014. Environmental Science & Technology 48(15): 8823-8830.
		Beckett S.J., Williams H.T.P. Coevolutionary diversification creates nested-modular structure in phage-bacteria interaction networks 2013. Interface Focus 3: 20130033.       [blog]

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>Software >

	Beckett S.J. weighted-modularity-LPAwbPLUS: Improved community detection in weighted bipartite networks 2015. Zenodo.
	Beckett S.J., Boulton C.A., Williams H.T.P. FALCON: nestedness statistics for bipartite networks 2014. figshare.

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>Data >

Beckett S.J., Williams H.T.P. Synthetic matrix ensemble for nestedness analysis 2015. figshare.

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>Posters >

	Beckett S.J., Williams H.T.P. Coevolved nestedness and modularity in phage-bacteria infection networks 2013. figshare.
	Beckett S.J., Williams H.T.P. Towards trait-based models for aquatic virology 2012. figshare.

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>Miscellaneous >

Beckett S.J. Online tools for researchers 2013. figshare.

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>In progress >

	Beckett S.J., Weitz J.S. The effect of strain level diversity on robust inference of virus-induced mortality via the modified dilution method In prep.
	Weitz J.S., Beckett S.J., Brum J.R., Cael B.B., Dushoff J. Lysis, Lysogeny, and Virus-Microbe Ratios In review.       [see the preprint]
	Beckett S.J., Williams H.T.P. Brooding on nestedness: nestedness analyses are confounded by sensitivity to measurement choices and network properties In prep.       [see chapter 5 of my thesis]

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