Publications (peer-reviewed)
16. B.C. Haller, P.W. Messer. (2019). Evolutionary modeling in SLiM 3 for beginners. Molecular Biology and Evolution 36(5), 1101–1109. doi:10.1093/molbev/msy237
15. B.C. Haller, J. Galloway, J. Kelleher, P.W. Messer, P.L. Ralph. (2019). Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes. Molecular Ecology Resources 19(2), 552–566. doi:10.1111/1755-0998.12968
14. B.C. Haller, P.W. Messer. (2019). SLiM 3: Forward genetic simulations beyond the Wright–Fisher Model. Molecular Biology and Evolution 36(3), 632–637. doi:10.1093/molbev/msy228
13. B.C. Haller, P.W. Messer. (2017). asymptoticMK: A web-based tool for the asymptotic McDonald–Kreitman test. G3: Genes, Genomes, Genetics 7(5), 1569–1575. doi:10.1534/g3.117.039693
12. B.C. Haller, P.W. Messer. (2017). SLiM 2: Flexible, interactive forward genetic simulations. Molecular Biology and Evolution 34(1), 230–240. doi:10.1093/molbev/msw211
11. L.-M. Chevin, B.C. Haller. (2014). The temporal distribution of linear gradients under selection for an optimum. Evolution 68(12), 3381–3394. doi:10.1111/evo.12532
10. B.C. Haller, J.M. de Vos, B. Keller, A.P. Hendry, E. Conti. (2014). A tale of two morphs: Modeling pollen transfer, magic traits, and reproductive isolation in parapatry. PLoS ONE 9(9), e106512. doi:10.1371/journal.pone.0106512
9. B.C. Haller. (2014). Theoretical and empirical perspectives in ecology and evolution: A survey. BioScience 64(10), 907–916. doi:10.1093/biosci/biu131
8. M.D. Nowak, B.C. Haller, A.D. Yoder. (2014). The founding of Mauritian endemic coffee trees by a synchronous long-distance dispersal event. Journal of Evolutionary Biology 27(6), 1229–1239. doi:10.1111/jeb.12396
7. B.C. Haller, A.P. Hendry. (2013). Solving the paradox of stasis: Squashed stabilizing selection and the limits of detection. Evolution 68(2), 483–500. doi:10.1111/evo.12275
6. B.C. Haller, R. Mazzucco, U. Dieckmann. (2013). Evolutionary branching in complex landscapes. American Naturalist 182(4), E127–E141. doi:10.1086/671907
5. B.C. Haller, L.F. De Léon, G. Rolshausen, K.M. Gotanda, A.P. Hendry. (2012). Magic traits: distinguishing the important from the trivial [letter]. Trends in Ecology & Evolution 27(1), 4–5. doi:10.1016/j.tree.2011.09.005
4. M. Tum, M. Buchhorn, K.P. Günther, B.C. Haller. (2011). Validation of modelled forest biomass in Germany using BETHY/DLR. Geoscientific Model Development 4, 1019–1034. doi:10.5194/gmd-4-1019-2011
3. E. Crispo, J.-S. Moore, J. Lee-Yaw, S.M. Gray, B.C. Haller. (2011). Human impacts on gene flow and introgression and the consequences for biodiversity. BioEssays 33(7), 508–518. doi:10.1002/bies.201000154
2. B.C. Haller, D. Chambers, R. Cheng, V. Chemistruck, T.F. Hom, Z. Li, J. Nguyen, A. Ichimura, D.J.R. Brook. (2015). Oxidation of electron donor-substituted verdazyls: Building blocks for molecular switches. Journal of Physical Chemistry A 119(43), 10750–10760. doi:10.1021/acs.jpca.5b09295
1. D.J.R. Brook, C.J. Richardson, B.C. Haller, M. Hundley, G.T. Yee. (2010). Strong ferromagnetic metal-ligand exchange in a nickel bis(3,5-dipyridylverdazyl) complex. Chemical Communications 46(35), 6590–6592. doi:10.1039/C0CC02233K
B.C. Haller. (2013). The role of heterogeneity in adaptation and speciation [Ph.D. thesis]. McGill University, Montreal, Quebec, Canada. 309 pp. URL.
Not peer-reviewed (books)
2. B.C. Haller, P.W. Messer. (2016–2019). SLiM: An Evolutionary Simulation Framework. 517 pp. URL.
1. B.C. Haller. (2016–2019). Eidos: A Simple Scripting Language. 104 pp. URL.
Not peer-reviewed (software)
2. B.C. Haller, P.W. Messer. (2016–2019). SLiM [version 3.2.1]. Home page: http://messerlab.org/slim/. GitHub repository: https://github.com/MesserLab/SLiM.
SLiM is a software framework for making forward genetic simulations. It uses the Eidos scripting language to provide highly flexible scriptability, and provides an interactive GUI environment called SLiMgui for simulation development and testing.
1. B.C. Haller. (2016–2019). Eidos [version 2.2.1]. Home page: http://benhaller.com/eidos.html. GitHub repository: https://github.com/MesserLab/SLiM.
Eidos is a general-purpose scripting language. It was developed for the SLiM project, but can be used in other contexts too. It is designed for tight scripting integration with application code, including exposing application objects directly as objects in script.
Not peer-reviewed (blog posts)
The Hendry lab at McGill hosts a blog about eco-evolutionary dynamics called eco-evo evo-eco. In addition, I have kept two blogs so far about science-related travel, one for a class I took in the Amazon, and one related to research collaborations in Europe, particularly my participation in the Young Scientists Summer Program at IIASA in Austria.
See those blogs for many more posts; I've put only the relatively science-focused posts here.
17. B.C. Haller. (2017). Simulating continuous space in SLiM 2
16. B.C. Haller. (2016). Flexible, interactive simulations: SLiM 2 published in MBE
15. B.C. Haller. (2016). Announcing SLiM 2.0: flexible, fast, interactive forward genetic simulations
14. B.C. Haller. (2014). The Divide: a survey about interactions between theoretical and empirical researchers
13. B.C. Haller. (2014). Coffee, long-distance dispersal, and self-incompatibility: Baker's Rule explored
12. B.C. Haller. (2013). Solving the paradox of stasis
11. B.C. Haller. (2013). Evolutionary branching in complex landscapes
10. B.C. Haller. (2013). Academic dispersal
9. B.C. Haller. (2012). Saunas & speciation
8. B.C. Haller, K.M. Gotanda, K. Oke, S. Muttalib. (2012). A biological refugium
7. B.C. Haller. (2012). Adaptation at the margins
6. B.C. Haller. (2011). Magic traits, muggle traits and squib traits
5. K.M. Gotanda, B.C. Haller. (2011). Conferences, meme-sex and some science for good measure...
4. B.C. Haller. (2011). Eco-evolutionary modeling north of the Arctic circle
3. B.C. Haller. (2010). Speciation 2010
2. B.C. Haller. (2010). How does evolution work?
1. B.C. Haller. (2008). Global climate and the Amazon
Not peer-reviewed (other)
2. B.C. Haller. (2012). Programming in R [workshop]. Biology Graduate Students Association, McGill University.
1. E. Meir, B.C. Haller. (1991). Fractal Mountain Climbing. MacTutor 7(5).
