Publications

2015

Manceau, M., Lambert, A., & Morlon, H. (2015). Phylogenies support out-of-equilibrium models of biodiversity. Ecology Letters, 18(4), 347‑356.

2014

Achaz, G., Rodriguez-Verdugo, A., Gaut, B. S., & Tenaillon, O. (2014). The reproducibility of adaptation in the light of experimental evolution with whole genome sequencing. Advances in Experimental Medicine and Biology, 781, 211‑231.

Delaporte, C. (2014). Lévy processes with marked jumps I: Limit theorems. Journal of Theoretical Probability.

Etienne, R. S., Morlon, H., & Lambert, A. (2014). Estimating the duration of speciation from phylogenies. Evolution, 68(8), 2430‑2440.

Ferretti, L., Cortelezzi, M., & Mamino, M. (2014). Duality between preferential attachment and hyperbolic networks. Eur. Phys. Lett, 105(3), 38001.

Ferretti, L., Mamino, M., & Bianconi, G. (2014). Condensation and topological phase transitions in a dynamical network model with rewiring of the links. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics, 89(4), 042810.

Lambert, A. (2014). Vers une approche formelle des origines évolutives de la simplexité ? In J.-L. Petit & A. Berthoz (Éd.), Complexité-Simplexité. Paris: Collège de France.

Lambert, A., Alexander, H. K., & Stadler, T. (2014). Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics. Journal of Theoretical Biology, 352, 60‑70.

Lambert, A., Morlon, H., & Etienne, R. S. (2014). The reconstructed tree in the lineage-based model of protracted speciation. Journal of Mathematical Biology, 70(1-2), 367‑397.

Lambert, A., & Simatos, F. (2014). The weak convergence of regenerative processes using some excursion path decompositions. Ann. Inst. Henri Poincaré, 50(2), 492‑511.

Lechner, S., Ferretti, L., Schöning, C., Kinuthia, W., Willemsen, D., & Hasselmann, M. (2014). Nucleotide variability at its limit? Insights into the number and evolutionary dynamics of the sex-determining specificities of the honey bee Apis mellifera. Molecular Biology and Evolution, 31(2), 272‑287.

Moen, D., & Morlon, H. (2014). From dinosaurs to modern bird diversity – Extending the time-scale of adaptive radiation. PLoS Biology, 12(5), e1001854.

Moen, D., & Morlon, H. (2014). Why does diversification slow down? Trends in Ecology & Evolution, 29(4), 190‑197.

Morlon, H. (2014). Phylogenetic approaches for studying diversification. Ecology Letters, 17(4), 508‑525.

Rolland, J., Condamine, F. L., Jiguet, F., & Morlon, H. (2014). Faster speciation and reduced extinction in the tropics contribute to the Mammalian latitudinal diversity gradient. PLoS Biology, 12(1), e1001775.

Rolland, J., Jiguet, F., Jønsson, K. A., Condamine, F. L., & Morlon, H. (2014). Settling down of seasonal migrants promotes bird diversification. Proceedings. Biological Sciences / The Royal Society, 281(1784), 20140473.

Schertzer, E., Staver, A. C., & Levin, S. A. (2014). Implications of the spatial dynamics of fire spread for the bistability of savanna and forest. Journal of Mathematical Biology.

Schertzer, E., Sun, R., & Swart, J. (2014). Stochastic flows in the Brownian web and net. Memoirs of the American Mathematical Society, 160.

2013

Aguilée, R., Claessen, D., & Lambert, A. (2013). Adaptive radiation driven by the interplay of eco-evolutionary and landscape dynamics. Evolution, 67(5), 1291‑1306.

Bansaye, V., & Lambert, A. (2013). Past, growth and persistence of source-sink metapopulations, 88, 31‑46.

Champagnat, N., & Lambert, A. (2013). Splitting trees with neutral Poissonian mutations II: Largest and oldest families. Stochastic Processes and Their Applications, 123(4), 1368‑1414.

Chapron, G., Wielgus, R., & Lambert, A. (2013). Overestimates of maternity and population growth rates in multi-annual breeders, 59, 237‑243.

Condamine, F. L., Rolland, J., & Morlon, H. (2013). Macroevolutionary perspectives to environmental change. Ecology Letters, 16 Suppl 1, 72‑85.

Dornelas, M., Magurran, A. E., Buckland, S. T., Chao, A., Chazdon, R. L., Colwell, R. K., … Vellend, M. (2013). Quantifying temporal change in biodiversity: challenges and opportunities. Proceedings. Biological Sciences / The Royal Society, 280(1750), 20121931.

Duhalde, X., Foucart, C., & Ma, C. (2013). On the hitting times of continuous-state branching processes with immigration. arXiv, 1310, 7401.

Esteve-Codina, A., Paudel, Y., Ferretti, L., Raineri, E., Megens, H.-J., Silió, L., … Pérez-Enciso, M. (2013). Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs. BMC Genomics, 14, 148.

Ferretti, L., Disanto, F., & Wiehe, T. (2013). The effect of single recombination events on coalescent tree height and shape. PloS One, 8(4), e60123.

Ferretti, L., Ramos-Onsins, S. E., & Pérez-Enciso, M. (2013). Population genomics from pool sequencing. Molecular Ecology, 22(22), 5561‑5576.

Ishida, S., Picard, F., Rudolf, G., Noé, E., Achaz, G., Thomas, P., … Baulac, S. (2013). Mutations of DEPDC5 cause autosomal dominant focal epilepsies. Nature Genetics, 45(5), 552‑555.

Jaunatre, R., Buisson, E., Muller, I., Morlon, H., Meslard, F., & Dutoit, T. (2013). New synthetic indicators to assess community resilience and restoration success. Ecological Indicators, 29, 468‑477.

Lambert, A., & Ma, C. (2013). The peripatric coalescent. arXiv, 1303.3277.

Lambert, A., & Popovic, L. (2013). The coalescent point process of branching trees. Ann. Appl. Prob., 23(1), 99‑144.

Lambert, A., & Simatos, F. (2013). Asymptotic behavior of local times of compound poisson processes with drift in the infinite variance case. Journal of Theoretical Probability.

Lambert, A., Simatos, F., & Zwart, B. (2013). Scaling limits via excursion theory: Interplay between Crump-Mode-Jagers branching processes and Processor-Sharing queues, 23(6), 2357‑2381.

Lambert, A., & Stadler, T. (2013). Birth-death models and coalescent point processes: the shape and probability of reconstructed phylogenies. Theoretical Population Biology, 90, 113‑128.

Lambert, A., & Steel, M. (2013). Predicting the loss of phylogenetic diversity under non-stationary diversification models. Journal of Theoretical Biology, 337, 111‑124.

Lambert, A., & Trapman, P. (2013). Splitting trees stopped when the first clock rings and Vervaat’s transformation. Journal of Applied Probability, 50(1), 208‑227.

Loire, E., Higuet, D., Netter, P., & Achaz, G. (2013). Evolution of coding microsatellites in primate genomes. Genome Biology and Evolution, 5(2), 283‑295.

Richard, M. (2013). Lévy processes conditioned on having a large height process. Annales de l’Institut Henri Poincaré, 49(4), 982‑1013.

Segura, J., Ferretti, L., Ramos-Onsins, S., Capilla, L., Farré, M., Reis, F., … Ruiz-Herrera, A. (2013). Evolution of recombination in eutherian mammals: Insights into mechanisms that affect recombination rates and crossover interference. Proceedings. Biological Sciences / The Royal Society, 280(1771), 20131945.

2012

Champagnat, N., & Lambert, A. (2012). Splitting trees with neutral Poissonian mutations I: Small families. Stochastic Processes and Their Applications, 122(3), 1003‑1033.

Champagnat, N., Lambert, A., & Richard, M. (2012). Birth and Death Processes with Neutral Mutations. International Journal of Stochastic Analysis, 2012, 1‑20.

Ferretti, L., Cortelezzi, M., Yang, B., Marmorini, G., & Bianconi, G. (2012). Features and heterogeneities in growing network models. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics, 85(6 Pt 2), 066110.

Ferretti, L., Raineri, E., & Ramos-Onsins, S. (2012). Neutrality tests for sequences with missing data. Genetics, 191(4), 1397‑1401.

Halu, A., Ferretti, L., Vezzani, A., & Bianconi, G. (2012). Phase diagram of the Bose-Hubbard Model on Complex Networks, 99, 18001.

Morlon, H. (2012). Microbiology. Microbial cooperative warfare. Science (New York, N.Y.), 337(6099), 1184‑1185.

Morlon, H., Kemps, B. D., Plotkin, J. B., & Brisson, D. (2012). Explosive radiation of a bacterial species group. Evolution, 66(8), 2577‑2586.

Pirino, D., Rigosa, J., Ledda, A., & Ferretti, L. (2012). Detecting correlations among functional-sequence motifs. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics, 85(6 Pt 2), 066124.

Puillandre, N., Lambert, A., Brouillet, S., & Achaz, G. (2012). ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular Ecology, 21(8), 1864‑1877.

Raineri, E., Ferretti, L., Esteve-Codina, A., Nevado, B., Heath, S., & Pérez-Enciso, M. (2012). SNP calling by sequencing pooled samples. BMC Bioinformatics, 13, 239.

Rolland, J., Cadotte, M. W., Davies, J., Devictor, V., Lavergne, S., Mouquet, N., … Morlon, H. (2012). Using phylogenies in conservation: new perspectives. Biology Letters, 8(5), 692‑694.

Stewart, A., Parsons, T., & Plotkin, J. (2012). Environmental robustness and the evolvability of populations. Evolution, 66 (5), 1598‑1612.

2011

Aguilée, R., de Becdelièvre, B., Lambert, A., & Claessen, D. (2011). Under which conditions is character displacement a likely outcome of secondary contact? Journal of Biological Dynamics, 5(2), 135‑146.

Aguilée, R., Lambert, A., & Claessen, D. (2011). Ecological speciation in dynamic landscapes. Journal of Evolutionary Biology, 24(12), 2663‑2677.

Amaral, A. J., Ferretti, L., Megens, H.-J., Crooijmans, R. P. M. A., Nie, H., Ramos-Onsins, S. E., … Groenen, M. A. M. (2011). Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA. PloS One, 6(4), e14782.

Draghi, J. A., Parsons, T. L., & Plotkin, J. B. (2011). Epistasis increases the rate of conditionally neutral substitution in an adapting population. Genetics, 187(4), 1139‑1152.

Esteve-Codina, A., Kofler, R., Himmelbauer, H., Ferretti, L., Vivancos, A. P., Groenen, M. a. M., … Pérez-Enciso, M. (2011). Partial short-read sequencing of a highly inbred Iberian pig and genomics inference thereof. Heredity, 107(3), 256‑264.

Ferretti, L., & Cortelezzi, M. (2011). Preferential attachment in growing spatial networks. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics, 84(1 Pt 2), 016103.

Kobayashi, Y., Achaz, G., & Telschow, A. (2011). Effect of parasitic sex-ratio distorters on host gene frequencies in a mainland-island context. Journal of Evolutionary Biology, 24(8), 1695‑1705.

Lambert, A. (2011). Species abundance distributions in neutral models with immigration or mutation and general lifetimes. Journal of Mathematical Biology, 63(1), 57‑72.

McInnes, L., Baker, W. J., Barraclough, T. G., Dasmahapatra, K. K., Goswami, A., Harmon, L. J., … Phillimore, A. B. (2011). Integrating ecology into macroevolutionary research. Biology Letters, 7(5), 644‑646.

Morlon, H., Parsons, T. L., & Plotkin, J. B. (2011a). Reconciling molecular phylogenies with the fossil record. Proceedings of the National Academy of Sciences of the United States of America, 108(39), 16327‑16332.

Morlon, H., Schwilk, D. W., Bryant, J. A., Marquet, P. A., Rebelo, A. G., Tauss, C., … Green, J. L. (2011). Spatial patterns of phylogenetic diversity. Ecology Letters, 14(2), 141‑149.

Tully, T., & Lambert, A. (2011). The evolution of post-reproductive lifespan as an insurance against developmental indeterminacy. Evolution, 65, 3013‑3020.

2010

Draghi, J. A., Parsons, T. L., Wagner, G. P., & Plotkin, J. B. (2010). Mutational robustness can facilitate adaptation. Nature, 463(7279), 353‑355.

Ferretti, L., Perez-Enciso, M., & Ramos-Onsins, S. (2010). Optimal neutrality tests based on the frequency spectrum. Genetics, 186(1), 353‑365.

Kutty, G., Achaz, G., Maldarelli, F., Varma, A., Shroff, R., Becker, S., … Kovacs, J. A. (2010). Characterization of the meiosis-specific recombinase Dmc1 of pneumocystis. The Journal of Infectious Diseases, 202(12), 1920‑1929.

Lambert, A. (2010). Population genetics, ecology and the size of populations. Journal of Mathematical Biology, 60(3), 469‑472.

Lambert, A. (2010). The contour of splitting trees is a Lévy process. Ann. Probab, 38, 348–395.

Newman, C., Ravishankar, K., & Schertzer, E. (2010). Marking (1, 2) points of the Brownian web and applications. Annales de l’Institut Henri Poincaré, Probabilités et Statistique, 46(2), 537‑574.

Parsons, T., Quince, C., & Plotkin, J. (2010). Some Consequences of demographic stochasticity in population genetics. Genetics, 185(4), 1345‑1354.

Pellet, J., Tafforeau, L., Lucas-Hourani, M., Navratil, V., Meyniel, L., Achaz, G., … Vidalain, P. O. (2010). ViralORFeome: an integrated database to generate a versatile collection of viral ORFs. Nucleic Acids Research, 38(Database issue), D371‑378.

Pérez-Enciso, M., & Ferretti, L. (2010). Massive parallel sequencing in animal genetics: wherefroms and wheretos. Animal Genetics, 41(6), 561‑569.

Picard, N., & Oudraogo, D. (2010). Choosing classes for size projection matrix models. Ecological Modelling, 221, 2270‑2279.

2009

Achaz, G. (2009). Frequency spectrum neutrality tests: one for all and all for one. Genetics, 183(1), 249‑258.

Aguilée, R., Claessen, D., & Lambert, A. (2009). Allele fixation in a dynamic metapopulation: founder effects vs refuge effects. Theoretical Population Biology, 76(2), 105‑117.

Bianconi, G., Ferretti, L., & Franz, S. (2009). Non-neutral theory of biodiversity, 87, 28001.

Caballero, M., Lambert, A., & Uribe Bravo, G. (2009). Proof(s) of the Lamperti representation of continuous-state branching processes Probab. Surveys, 6, 62‑89.

Calibbi, L., Ferretti, L., Romanino, A., & Ziegler, R. (2009a). Consequences of a unified, anarchical model of fermion masses and mixings, 0903, 031.

Calibbi, L., Ferretti, L., Romanino, A., & Ziegler, R. (2009b). Gauge coupling unification, the GUT scale, and magic fields, B 672, 152.

Cattiaux, P., Collet, P., Lambert, A., Martinez, S., Méléard, S., & San Martin, J. (2009). Quasi-stationary distributions and diffusion models in population dynamics, 37, 1926‑1969.

Fontes, L., Newman, C., Ravishankar, K., & Schertzer, E. (2009). Exceptional times for the dynamical discrete web. Stochastic Processes and their Application, 119, 2832‑2858.

Lambert, A. (2009). The allelic partition for coalescent point processes. Markov Proc. Relat. Fields, 15, 359‑386.

Loire, E., Praz, F., Higuet, D., Netter, P., & Achaz, G. (2009). Hypermutability of genes in Homo sapiens due to the hosting of long mono-SSR. Molecular Biology and Evolution, 26(1), 111‑121.

Schertzer, E., Sun, R., & Swart, J. (2009). Special points of the brownian net. Electronic Journal of Probability, 14, 805‑864.

Treangen, T. J., Darling, A. E., Achaz, G., Ragan, M. A., Messeguer, X., & Rocha, E. P. C. (2009). A novel heuristic for local multiple alignment of interspersed DNA repeats. Transactions on Computational Biology and Bioinformatics, 6(2), 180‑189.

2008

Achaz, G. (2008). Testing for neutrality in samples with sequencing errors. Genetics, 179(3), 1409‑1424.

Champagnat, N., & Lambert, A. (2008). Adaptive dynamics in logistic branching populations (p. 235‑235). Institute of Mathematics Polish Academy of Sciences.

Chapron, G., Miquelle, D., Lambert, A., Goodrich, J., Legendre, S., & Clobert, J. (2008). The impact on tigers of poaching versus prey depletion. J. Appl. Ecology, 45, 1667‑1674.

Ferretti, L., & Bianconi, G. (2008). Dynamics of condensation in growing complex networks. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics, 78(5 Pt 2), 056102.

Ferretti, L., Gudnason, S., & Konishi, K. (2008). Non-Abelian vortices and monopoles in SO(N) theories, 789, 84.

Gonzalez, A., Lambert, A., & Ricciardi, A. (2008). When does ecosystem engineering cause invasion and species replacement? Oikos, 117, 1247‑1257.

Kutty, G., Maldarelli, F., Achaz, G., & Kovacs, J. A. (2008). Variation in the major surface glycoprotein genes in Pneumocystis jirovecii. The Journal of Infectious Diseases, 198(5), 741‑749.

Lambert, A. (2008a). Population Dynamics and Random Genealogies. Stoch. Models, 24, 45‑163.

Lambert, A. (2008b). Population genetics, ecology and the size of populations. J. Math. Biol, 60, 469‑472.

Nicolas, P., Mondot, S., Achaz, G., Bouchenot, C., Bernardet, J.-F., & Duchaud, E. (2008). Population structure of the fish-pathogenic bacterium Flavobacterium psychrophilum. Applied and Environmental Microbiology, 74(12), 3702‑3709.

Parsons, T. L., Quince, C., & Plotkin, J. B. (2008). Absorption and fixation times for neutral and quasi-neutral populations with density dependence. Theoretical Population Biology, 74(4), 302‑310.

Raquin, A.-L., Depaulis, F., Lambert, A., Galic, N., Brabant, P., & Goldringer, I. (2008). Experimental estimation of mutation rates in a wheat population with a gene genealogy approach. Genetics, 179(4), 2195‑2211.

 
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