Chromosome-level genome assembly of the european green woodpecker picus viridis

Forest, T., Achaz, G., Marbouty, M., Bignaud, A., Thierry, A., Koszul, R., Milhes, M., Lledo, J., Pons, J., Fuchs, J.

G3 Genes Genomes Genetics 2024-27-03

Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies and demographic inferences

Guez, J., Achaz, G., Bienvenu, F. C., Cury, J., Toupance, B., Heyer, \., Jay, F., Austerlitz, F.

bioRxiv

Mold, a novel software to compile accurate and reliable dna diagnoses for taxonomic descriptions

Fedosov, A., Achaz, G., Gontchar, A., Puillandre, N.

Molecular Ecology Resources

The quiescent x, the replicative y and the autosomes

Achaz, G., Gangloff, S., Arcangioli, B.

Peer Community Journal 2

Simulation of bacterial populations with slim

Cury, J., Haller, B. C., Achaz, G., Jay, F.

Peer Community Journal 2

A minimal yet flexible likelihood framework to assess correlated evolution

Behdenna, A., Godfroid, M., Petot, P., Pothier, J., Lambert, A., Achaz, G.

Systematic Biology 71 823-838

The speed of vaccination rollout and the risk of pathogen adaptation

Gandon, S., Lambert, A., Day, T., Parsons, T. L.

medRxiv

Bottlenecks can constrain and channel evolutionary paths

Gamblin, J., Gandon, S., Blanquart, F., Lambert, A.

bioRxiv

Interpreting the pervasive observation of u-shaped site frequency spectra

Freund, F., Kerdoncuff, E., Matuszewski, S., Lapierre, M., Hildebrandt, M., Jensen, J. D., Ferretti, L., Lambert, A., Sackton, T. B., Achaz, G.

bioRxiv

An appeal for an objective, open, and transparent scientific debate about the origin of sars-cov-2

Van Helden, J., Butler, C. D., Achaz, G., Canard, B., Casane, D., Claverie, J., Colombo, F., Courtier, V., Ebright, R. H., Graner, F., others, .

The Lancet 398 1402-1404

Asap: assemble species by automatic partitioning

Puillandre, N., Brouillet, S., Achaz, G.

Molecular Ecology Resources 21 609-620

Exchangeable coalescents, ultrametric spaces, nested interval-partitions: a unifying approach

Foutel-Rodier, F., Lambert, A., Schertzer, E.

The Annals of Applied Probability 31 2046-2090

General epidemic models: law of large numbers and contact tracing

Duchamps, J., Foutel-Rodier, F., Schertzer, E.

arXiv:2106.13135

Combinatorial and stochastic properties of ranked tree-child networks

Bienvenu, F., Lambert, A., Steel, M.

arXiv:2007.09701

From individual-based epidemic models to mckendrick-von foerster pdes: a guide to modeling and inferring covid-19 dynamics

Foutel-Rodier, F., Blanquart, F., Courau, P., Czuppon, P., Duchamps, J., Gamblin, J., Kerdoncuff, E., Kulathinal, R., Régnier, L., Vuduc, L., Lambert, A., Schertzer, E.

arXiv:2007.09622

Predicted success of prophylactic antiviral therapy to block or delay sars-cov-2 infection depends on the targeted mechanism

Czuppon, P., Débarre, F., Gonçalves, A., Tenaillon, O., Perelson, A. S., Guedj, J., Blanquart, F.

medRxiv

A mathematical assessment of the efficiency of quarantining and contact tracing in curbing the covid-19 epidemic

Lambert, A.

medRxiv

The spatial muller's ratchet: surfing of deleterious mutations during range expansion

Foutel-Rodier, F., Etheridge, A.

Theoretical Population Biology

Testing for population decline using maximal linkage disequilibrium blocks

Kerdoncuff, E., Lambert, A., Achaz, G.

Theoretical Population Biology 134 171 - 181

Kingman's coalescent with erosion

Foutel-Rodier, F., Lambert, A., Schertzer, E.

Electronic Journal of Probability 25 33 pp.

The effect of habitat choice on evolutionary rescue in subdivided populations

Czuppon, P., Blanquart, F., Uecker, H., Débarre, F.

bioRxiv

Invasion and extinction dynamics of mating types under facultative sexual reproduction

Czuppon, P., Constable, G. W. A.

Genetics 213 567-580

Evolution of mating types in finite populations: the precarious advantage of being rare

Czuppon, P., Rogers, D.

Journal of Evolutionary Biology

Statistical inference for the evolutionary history of cancer genomes

Dinh, K., Jaksik, R., Kimmel, M., Lambert, A., Tavaré, S.

bioRxiv 722033

Population persistence under high mutation rate: from evolutionary rescue to lethal mutagenesis

Anciaux, Y., Lambert, A., Ronce, O., Roques, L., Martin, G.

Evolution

Fragmentations with self-similar branching speeds

Duchamps, J.

arXiv:1907.04712

The moran forest

Bienvenu, F., Duchamps, J., Foutel-Rodier, F.

arXiv:1906.08806

Recovering the brownian coalescent point process from the kingman coalescent by conditional sampling

Lambert, A., Schertzer, E.

Bernoulli 25 148-173

The equivocal mean age of parents in a cohort

Bienvenu, F.

The American Naturalist 194 276-284

Positive association of the oriented percolation cluster in randomly oriented graphs

Bienvenu, F.

Combinatorics, Probability and Computing 28 811-815

The split-and-drift random graph, a null model for speciation

Bienvenu, F., Débarre, F., Lambert, A.

Stochastic Processes and their Applications 129 2010-2048

The species problem from the modeler’s point of view

Manceau, M., Lambert, A.

Bulletin of mathematical biology 81 878-898

Clade diversification dynamics and the biotic and abiotic controls of speciation and extinction rates

Aguilée*, R., Gascuel*, F., Lambert**, A., Ferriere**, R.

Nature communications 9 3013

The genomic view of diversification

Marin, J., Achaz, G., Crombach, A., Lambert, A.

bioRxiv

The sequential loss of allelic diversity

Achaz, G., Lambert, A., Schertzer, E.

Advances in Applied Probability 50 13-29

Totally ordered measured trees and splitting trees with infinite variation ii: prolific skeleton decomposition

Lambert, A., Uribe Bravo, G.

arXiv:1803.05421

Exchangeable coalescents, ultrametric spaces, nested interval-partitions: a unifying approach

Foutel-Rodier, F., Lambert, A., Schertzer, E.

arXiv:1807.05165

Coagulation-transport equations and the nested coalescents

Lambert, A., Schertzer, E.

Probability Theory and Related Fields 1-71

Ranked tree shapes, nonrandom extinctions, and the loss of phylogenetic diversity

Maliet, O., Gascuel, F., Lambert, A.

Systematic biology 67 1025-1040

Branching processes seen from their extinction time via path decompositions of reflected lévy processes

Dávila Felipe, M., Lambert, A.

Electronic Journal of Probability 23

Chromosome painting

Lambert, A., Miró Pina, V., Schertzer, E.

arXiv:1807.09116

The coalescent of a sample from a binary branching process

Lambert, A.

Theoretical population biology 122 30-35

Pathogen evolution in finite populations: slow and steady spreads the best

Parsons, T. L., Lambert, A., Day, T., Gandon, S.

Journal of The Royal Society Interface 15 20180135

Trees within trees ii: nested fragmentations

Duchamps, J.

arXiv:1807.05951

Trees within trees: simple nested coalescents

Blancas, A., Duchamps, J., Lambert, A., Siri-Jégousse, A.

Electron. J. Probab. 1-27

Mutations on a random binary tree with measured boundary

Duchamps, J., Lambert, A.

Ann. Appl. Probab. 28 2141-2187

Totally ordered measured trees and splitting trees with infinite variation

Lambert, A., Uribe Bravo, G.

Electronic Journal of Probability 23

The comb representation of compact ultrametric spaces

Lambert, A., Uribe Bravo, G.

p-Adic Numbers, Ultrametric Analysis and Applications 9 22-38

Random ultrametric trees and applications

Lambert, A.

ESAIM: Proceedings and Surveys 60 70-89

Role of stem-cell divisions in cancer risk

Tomasetti, C., Durrett, R., Kimmel, M., Lambert, A., Parmigiani, G., Zauber, A., Vogelstein, B.

Nature 548

Renewal sequences and record chains related to multiple zeta sums

Duchamps, J., Pitman, J., Tang, W.

Transactions of the American Mathematical Society

How does geographical distance translate into genetic distance?

Miró Pina, V., Schertzer, E.

arXiv preprint arXiv:1703.00357

Probabilistic models for the (sub)tree(s) of life

Lambert, A.

Brazilian Journal of Probability and Statistics 31 415-475

The genealogical decomposition of a matrix population model with applications to the aggregation of stages

Bienvenu, F., Akcay, E., Legendre, S., McCandlish, D.

Theoretical Population Biology 115 69-80

Perturbations of the voter model in one-dimension

Newman, C., Ravishankar, K., Schertzer, E.

arXiv preprint arXiv:1607.06058

Height and contour processes of crump-mode-jagers forests (i): general distribution and scaling limits in the case of short edges

Schertzer, E., Simatos, F.

arXiv preprint arXiv:1506.03192

Renewal structure of the brownian taut string

Schertzer, E.

Stochastic Processes and their Applications

Heterogeneous preference and local nonlinearity in consensus decision making

Hartnett, A. T., Schertzer, E., Levin, S. A., Couzin, I. D.

Physical review letters 116

A unifying comparative phylogenetic framework including traits coevolving across interacting lineages

Manceau, M., Lambert, A., Morlon, H.

Systematic biology 66 551-568

Fidelity of parent-offspring transmission and the evolution of social behavior in structured populations

Débarre, F.

Accuracy of demographic inferences from site frequency spectrum: the case of the yoruba population

Lapierre, M., Lambert, A., Achaz, G.

Measuring epistasis in fitness landscapes: the correlation of fitness effects of mutations

Ferretti, L., Schmiegelt, B., Weinreich, D., Yamauchi, A., Kobayashi, Y., Tajima, F., Achaz, G.

Journal of theoretical biology 396 132-143

Testing for independence between evolutionary processes

Behdenna, A., Pothier, J., Abby, S. S., Lambert, A., Achaz, G.

Systematic biology 65 812-823

The impact of selection, gene conversion, and biased sampling on the assessment of microbial demography

Lapierre, M., Blin, C., Lambert, A., Achaz, G., Rocha, E. P. C.

Evolutionary dynamics of a quantitative trait in a finite asexual population

Débarre, F., Otto, S. P.

Theoretical Population Biology 108 75-88

Mutational pattern of a sample from a critical branching population

Delaporte, C., Achaz, G., Lambert, A.

Journal of Mathematical Biology 1-38

Quantifying age-dependent extinction from species phylogenies

Alexander, H. K., Lambert, A., Stadler, T.

65 35-50

A simple, semi-deterministic approximation to the distribution of selective sweeps in large populations

Martin, G., Lambert, A.

Theoretical Population Biology 101 40-46

The brownian web, the brownian net, and their universality

Schertzer, E., Sun, R., Swart, J. M.

arXiv preprint arXiv:1506.00724

Trimming a tree and the two-sided skorohod reflection

Schertzer, E.

ALEA 12 811-834

Decomposing the site frequency spectrum: the impact of tree topology on neutrality tests

Ledda, A., Achaz, G., Wiehe, T., Ferretti, L.

arXiv preprint arXiv:1510.06748

Magellan: a tool to explore small fitness landscapes

Brouillet, S., Annoni, H., Ferretti, L., Achaz, G.

A new approach to the generation time in matrix population models

Bienvenu, F., Legendre, S.

The American Naturalist 185 834-843

Brownian net with killing

Newman, C. M., Ravishankar, K., Schertzer, E.

Stochastic Processes and their Applications 125 1148-1194

Mass extinction in poorly known taxa

Regnier, C., Achaz, G., Lambert, A., Cowie, R. H., Bouchet, P., Fontaine, B.

Proceedings of the National Academy of Sciences of the United States of America 112 7761-7766

Presence in mediterranean hotspots and floral symmetry affect speciation and extinction rates in proteaceae

Reyes, E., Morlon, H., Sauquet, H.

New Phytologist 207 401-410

Dispersal is a major driver of the latitudinal diversity gradient of carnivora

Rolland, J., Condamine, F. L., Beeravolu, C. R., Jiguet, F., Morlon, H.

Global Ecology and Biogeography 24 1059-1071

Micness: genotyping microsatellite loci from a collection of (ngs) reads

Suez, M., Behdenna, A., Brouillet, S., Graça, P., Higuet, D., Achaz, G.

Molecular Ecology Resources

How ecology and landscape dynamics shape phylogenetic trees

Gascuel, F., Ferrière, R., Aguilée, R., Lambert, A.

Systematic Biology 64 590-607

The coalescent in peripatric metapopulations

Lambert, A., Ma, C.

Journal of Applied Probability 52 538-557

The reconstructed tree in the lineage-based model of protracted speciation

Lambert, A., Morlon, H., Etienne, R. S.

Journal of Mathematical Biology 70 367-397

Asymptotic behavior of local times of compound poisson processes with drift in the infinite variance case

Lambert, A., Simatos, F.

Journal of Theoretical Probability 28 41-91

Phylogenies support out-of-equilibrium models of biodiversity

Manceau, M., Lambert, A., Morlon, H.

Ecology Letters 18 347-356

A simple, semi-deterministic approximation to the distribution of selective sweeps in large populations

Martin, G., Lambert, A.

Theoretical Population Biology 101 40-46

Evolution of dispersal in spatially and temporally variable environments: the importance of life cycles

Massol, F., Débarre, F.

Evolution; International Journal of Organic Evolution 69 1925-1937

The biogeography of putative microbial antibiotic production

Morlon, H., O'Connor, T. K., Bryant, J. A., Charkoudian, L. K., Docherty, K. M., Jones, E., Kembel, S. W., Green, J. L., Bohannan, B. J. M.

PloS One 10

On the evolutionary interplay between dispersal and local adaptation in heterogeneous environments

Berdahl, A., Torney, C. J., Schertzer, E., Levin, S. A.

Evolution 69 1390-1405

On computer-intensive simulation and estimation methods for rare-event analysis in epidemic models

Clémençon, S., Cousien, A., Dávila Felipe, M., Tran, V.

Statistics in Medicine 34 3696-3713

Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in bayesian molecular dating

Condamine, F. L., Nagalingum, N. S., Marshall, C. R., Morlon, H.

BMC evolutionary biology 15

Time reversal dualities for some random forests

Dávila Felipe, M., Lambert, A.

ALEA Latin American Journal of Probability and Mathematical Statistics 12 399-426

Fitness costs in spatially structured environments

Débarre, F.

Evolution 69 1329-1335

Evolution of quantitative traits under a migration-selection balance: when does skew matter?*

Débarre, F., Yeaman, S., Guillaume, F.

The American Naturalist 186

Faster speciation and reduced extinction in the tropics contribute to the mammalian latitudinal diversity gradient

Rolland, J., Condamine, F. L., Jiguet, F., Morlon, H.

PLoS biology 12

Settling down of seasonal migrants promotes bird diversification

Rolland, J., Jiguet, F., Jønsson, K. A., Condamine, F. L., Morlon, H.

Proceedings. Biological Sciences / The Royal Society 281

Stochastic flows in the brownian web and net

Schertzer, E., Sun, R., Swart, J.

Memoirs of the American Mathematical Society

Implications of the spatial dynamics of fire spread for the bistability of savanna and forest

Schertzer, E., Staver, A. C., Levin, S. A.

Journal of Mathematical Biology 70 329-41

The availability of research data declines rapidly with article age

Vines, T. H., Albert, A. Y. K., Andrew, R. L., Débarre, F., Bock, D. G., Franklin, M. T., Gilbert, K. J., Moore, J., Renaut, S., Rennison, D. J.

Current biology: CB 24 94-97

Duality between preferential attachment and hyperbolic networks

Ferretti, L., Cortelezzi, M., Mamino, M.

EPL (Europhysics Letters) 105

Condensation and topological phase transitions in a dynamical network model with rewiring of the links

Ferretti, L., Mamino, M., Bianconi, G.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics 89

Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics

Lambert, A., Alexander, H. K., Stadler, T.

Journal of Theoretical Biology 352 60-70

The weak convergence of regenerative processes using some excursion path decompositions

Lambert, A., Simatos, F.

Ann. Inst. Henri Poincaré 50 492-511

Nucleotide variability at its limit? insights into the number and evolutionary dynamics of the sex-determining specificities of the honey bee apis mellifera

Lechner, S., Ferretti, L., Schöning, C., Kinuthia, W., Willemsen, D., Hasselmann, M.

Molecular Biology and Evolution 31 272-287

Why does diversification slow down?

Moen, D., Morlon, H.

Trends in Ecology \& Evolution 29 190-197

From dinosaurs to modern bird diversity: extending the time scale of adaptive radiation

Moen, D., Morlon, H.

PLoS biology 12

From dinosaurs to modern bird diversity -- extending the time-scale of adaptive radiation

Moen, D., Morlon, H.

PLoS Biology 12

Phylogenetic approaches for studying diversification

Morlon, H.

Ecology Letters 17 508-525

Effects of trophic similarity on community composition

Morlon, H., Kefi, S., Martinez, N. D.

Ecology Letters 17 1495-1506

The reproducibility of adaptation in the light of experimental evolution with whole genome sequencing

Achaz, G., Rodriguez-Verdugo, A., Gaut, B. S., Tenaillon, O.

Advances in Experimental Medicine and Biology 781 211-231

Properties of selected mutations and genotypic landscapes under fisher’s geometric model

Blanquart, F., Achaz, G., Bataillon, T., Tenaillon, O.

Evolution; international journal of organic evolution 68 3537-3554

Lévy processes with marked jumps i: limit theorems

Delaporte, C.

Journal of Theoretical Probability 28 1468-1499

On the hitting times of continuous-state branching processes with immigration

Duhalde, X., Foucart, C., Ma, C.

Stochastic Processes and their Applications 124 4182-4201

Social evolution in structured populations

Débarre, F., Hauert, C., Doebeli, M.

Nature Communications 5

Multidimensional (co)evolutionary stability

Débarre, F., Nuismer, S. L., Doebeli, M.

The American Naturalist 184 158-171

Estimating the duration of speciation from phylogenies

Etienne, R. S., Morlon, H., Lambert, A.

Evolution; International Journal of Organic Evolution 68 2430-2440

Lévy processes conditioned on having a large height process

Richard, M.

Annales de l'Institut Henri Poincaré 49 982-1013

Evolution of recombination in eutherian mammals: insights into mechanisms that affect recombination rates and crossover interference

Segura, J., Ferretti, L., Ramos-Onsins, S., Capilla, L., Farré, M., Reis, F., Oliver-Bonet, M., Fernández-Bellón, H., Garcia, F., Garcia-Caldés, M., Robinson, T. J., Ruiz-Herrera, A.

Proceedings. Biological Sciences / The Royal Society 280

The effect of single recombination events on coalescent tree height and shape

Ferretti, L., Disanto, F., Wiehe, T.

PloS One 8

Population genomics from pool sequencing

Ferretti, L., Ramos-Onsins, S. E., Pérez-Enciso, M.

Molecular Ecology 22 5561-5576

Host resistance, population structure and the long-term persistence of bubonic plague: contributions of a modelling approach in the malagasy focus

Gascuel, F., Choisy, M., Duplantier, J., Débarre, F., Brouat, C.

PLoS computational biology 9

Mutations of depdc5 cause autosomal dominant focal epilepsies

Ishida, S., Picard, F., Rudolf, G., Noé, E., Achaz, G., Thomas, P., Genton, P., Mundwiller, E., Wolff, M., Marescaux, C., Miles, R., Baulac, M., Hirsch, E., Leguern, E., Baulac, S.

Nature Genetics 45 552-555

New synthetic indicators to assess community resilience and restoration success

Jaunatre, R., Buisson, E., Muller, I., Morlon, H., Meslard, F., Dutoit, T.

Ecological Indicators 29 468-477

The coalescent point process of branching trees

Lambert, A., Popovic, L.

Ann. Appl. Prob. 23 99-144

Scaling limits via excursion theory: interplay between crump-mode-jagers branching processes and processor-sharing queues

Lambert, A., Simatos, F., Zwart, B.

Ann. Appl. Probab. 23 2357-2381

Birth–death models and coalescent point processes: the shape and probability of reconstructed phylogenies

Lambert, A., Stadler, T.

Theoretical Population Biology 90 113-128

Predicting the loss of phylogenetic diversity under non-stationary diversification models

Lambert, A., Steel, M.

Journal of Theoretical Biology 337 111-124

Splitting trees stopped when the first clock rings and vervaat's transformation

Lambert, A., Trapman, P.

Journal of Applied Probability 50 208-227

Evolution of coding microsatellites in primate genomes

Loire, E., Higuet, D., Netter, P., Achaz, G.

Genome Biology and Evolution 5 283-295

Adaptive radiation driven by the interplay of eco-evolutionary and landscape dynamics

Aguilée, R., Claessen, D., Lambert, A.

Evolution 67 1291-1306

Past, growth and persistence of source-sink metapopulations

Bansaye, V., Lambert, A.

Theoretical Population Biology 88 31-46

Splitting trees with neutral poissonian mutations ii: largest and oldest families

Champagnat, N., Lambert, A.

Stochastic Processes and their Applications 123 1368-1414

Overestimates of maternity and population growth rates in multi-annual breeders

Chapron, G., Wielgus, R., Lambert, A.

Eur. J. Wildlife Res. 59 237-243

Macroevolutionary perspectives to environmental change

Condamine, F. L., Rolland, J., Morlon, H.

Ecology Letters 72-85

Quantifying temporal change in biodiversity: challenges and opportunities

Dornelas, M., Magurran, A. E., Buckland, S. T., Chao, A., Chazdon, R. L., Colwell, R. K., Curtis, T., Gaston, K. J., Gotelli, N. J., Kosnik, M. A., McGill, B., McCune, J. L., Morlon, H., Mumby, P. J., Ovreås, L., Studeny, A., Vellend, M.

Proceedings. Biological Sciences / The Royal Society 280

Quantifying the effects of migration and mutation on adaptation and demography in spatially heterogeneous environments

Débarre, F., Ronce, O., Gandon, S.

Journal of Evolutionary Biology 26 1185-1202

Dissecting structural and nucleotide genome-wide variation in inbred iberian pigs

Esteve-Codina, A., Paudel, Y., Ferretti, L., Raineri, E., Megens, H., Silió, L., Rodríguez, M. C., Groenen, M. A. M., Ramos-Onsins, S. E., Pérez-Enciso, M.

BMC genomics 14

Detecting correlations among functional-sequence motifs

Pirino, D., Rigosa, J., Ledda, A., Ferretti, L.

Physical Review E 85

Abgd automatic barcode gap discovery for primary species delimitation

Puillandre, N., Lambert, A., Brouillet, S., Achaz, G.

Molecular Ecology 21 1864-1877

Snp calling by sequencing pooled samples

Raineri, E., Ferretti, L., Esteve-Codina, A., Nevado, B., Heath, S., Pérez-Enciso, M.

BMC bioinformatics 13

Using phylogenies in conservation: new perspectives

Rolland, J., Cadotte, M. W., Davies, J., Devictor, V., Lavergne, S., Mouquet, N., Pavoine, S., Rodrigues, A., Thuiller, W., Turcati, L., Winter, M., Zupan, L., Jabot, F., Morlon, H.

Biology Letters 8 692-694

Environmental robustness and the evolvability of populations

Stewart, A., Parsons, T., Plotkin, J.

Evolution 66 1598-1612

Features and heterogeneities in growing network models

Ferretti, L., Cortelezzi, M., Yang, B., Marmorini, G., Bianconi, G.

Physical Review E 85

Neutrality tests for sequences with missing data

Ferretti, L., Raineri, E., Ramos-Onsins, S.

Genetics 191 1397-1401

Phase diagram of the bose-hubbard model on complex networks

Halu, A., Ferretti, L., Vezzani, A., Bianconi, G.

EPL (Europhysics Letters) 99

Microbiology. microbial cooperative warfare

Morlon, H.

Science (New York, N.Y.) 337 1184-1185

Explosive radiation of a bacterial species group

Morlon, H., Kemps, B. D., Plotkin, J. B., Brisson, D.

Evolution 66 2577-2586

Splitting trees with neutral poissonian mutations i: small families

Champagnat, N., Lambert, A.

Stochastic Processes and their Applications 122 1003-1033

Birth and death processes with neutral mutations

Champagnat, N., Lambert, A., Richard, M.

International Journal of Stochastic Analysis 2012 1-20

Refining the conditions for sympatric ecological speciation

Débarre, F.

Journal of Evolutionary Biology 25 2651-2660

Evolution of host life-history traits in a spatially structured host-parasite system

Débarre, F., Lion, S., van Baalen, M., Gandon, S.

The American Naturalist 179 52-63

The evolution of post-reproductive lifespan as an insurance against developmental indeterminacy

Tully, T., Lambert, A.

Evolution 65 3013-3020

Preferential attachment in growing spatial networks

Ferretti, L., Cortelezzi, M.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics 84

Effect of parasitic sex-ratio distorters on host gene frequencies in a mainland-island context

Kobayashi, Y., Achaz, G., Telschow, A.

Journal of Evolutionary Biology 24 1695-1705

Species abundance distributions in neutral models with immigration or mutation and general lifetimes

Lambert, A.

Journal of Mathematical Biology 63 57-72

Integrating ecology into macroevolutionary research

McInnes, L., Baker, W. J., Barraclough, T. G., Dasmahapatra, K. K., Goswami, A., Harmon, L. J., Morlon, H., Purvis, A., Rosindell, J., Thomas, G. H., Turvey, S. T., Phillimore, A. B.

Biology Letters 7 644-646

Reconciling molecular phylogenies with the fossil record

Morlon, H., Parsons, T. L., Plotkin, J. B.

Proceedings of the National Academy of Sciences of the United States of America 108 16327-16332

Spatial patterns of phylogenetic diversity

Morlon, H., Schwilk, D. W., Bryant, J. A., Marquet, P. A., Rebelo, A. G., Tauss, C., Bohannan, B. J. M., Green, J. L.

Ecology Letters 14 141-149

Ecological speciation in dynamic landscapes

Aguilée, R., Lambert, A., Claessen, D.

Journal of Evolutionary Biology 24 2663-2677

Under which conditions is character displacement a likely outcome of secondary contact?

Aguilée, R., de Becdelièvre, B., Lambert, A., Claessen, D.

Journal of Biological Dynamics 5 135-146

Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled dna

Amaral, A. J., Ferretti, L., Megens, H., Crooijmans, R. P. M. A., Nie, H., Ramos-Onsins, S. E., Perez-Enciso, M., Schook, L. B., Groenen, M. A. M.

PloS One 6

Epistasis increases the rate of conditionally neutral substitution in an adapting population

Draghi, J. A., Parsons, T. L., Plotkin, J. B.

Genetics 187 1139-1152

Evolution in heterogeneous environments: between soft and hard selection

Débarre, F., Gandon, S.

The American Naturalist 177

Distance-limited dispersal promotes coexistence at habitat boundaries: reconsidering the competitive exclusion principle

Débarre, F., Lenormand, T.

Ecology Letters 14 260-266

Partial short-read sequencing of a highly inbred iberian pig and genomics inference thereof

Esteve-Codina, A., Kofler, R., Himmelbauer, H., Ferretti, L., Vivancos, A. P., Groenen, M. A. M., Folch, J. M., Rodríguez, M. C., Pérez-Enciso, M.

Heredity 107 256-264

Marking (1, 2) points of the brownian web and applications

Newman, C., Ravishankar,, K., Schertzer, E.

Annales de l'Institut Henri Poincaré, Probabilités et Statistiques 46

Some consequences of demographic stochas- ticity in population genetics.

Parsons, T., Quince, C., Plotkin, J.

Genetics 185 1345-1354

Viralorfeome: an integrated database to generate a versatile collection of viral orfs

Pellet, J., Tafforeau, L., Lucas-Hourani, M., Navratil, V., Meyniel, L., Achaz, G., Guironnet-Paquet, A., Aublin-Gex, A., Caignard, G., Cassonnet, P., Chaboud, A., Chantier, T., Deloire, A., Demeret, C., Le Breton, M., Neveu, G., Jacotot, L., Vaglio, P., Delmotte, S., Gautier, C., Combet, C., Deleage, G., Favre, M., Tangy, F., Jacob, Y., Andre, P., Lotteau, V., Rabourdin-Combe, C., Vidalain, P. O.

Nucleic Acids Research 38

Massive parallel sequencing in animal genetics: wherefroms and wheretos

Pérez-Enciso, M., Ferretti, L.

Animal Genetics 41 561-569

Optimal neutrality tests based on the frequency spectrum

Ferretti, L., Perez-Enciso, M., Ramos-Onsins, S.

Genetics 186 353-365

Characterization of the meiosis-specific recombinase dmc1 of pneumocystis

Kutty, G., Achaz, G., Maldarelli, F., Varma, A., Shroff, R., Becker, S., Fantoni, G., Kovacs, J. A.

The Journal of Infectious Diseases 202 1920-1929

Population genetics, ecology and the size of populations

Lambert, A.

Journal of Mathematical Biology 60 469-472

The contour of splitting trees is a lévy process

Lambert, A.

The Annals of Probability 38 348-395

Mutational robustness can facilitate adaptation

Draghi, J. A., Parsons, T. L., Wagner, G. P., Plotkin, J. B.

Nature 463 353-355

Evolution of specialization in a spatially continuous environment

Débarre, F., Gandon, S.

Journal of Evolutionary Biology 23 1090-1099

Special points of the brownian net

Schertzer, E., Sun, R., Swart, J. M.

Electronic Journal of Probability 14 805-864

A novel heuristic for local multiple alignment of interspersed dna repeats

Treangen, T. J., Darling, A. E., Achaz, G., Ragan, M. A., Messeguer, X., Rocha, E. P. C.

IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 6 180-189

Exceptional times for the dynamical discrete web

Fontes, L., Newman, C., Ravishankar, K., Schertzer, E.

Stochastic Processes and their Applications 119 2832-2858

The allelic partition for coalescent point processes

Lambert, A.

Markov Proc. Relat. Fields 15 359-386

Hypermutability of genes in homo sapiens due to the hosting of long mono-ssr

Loire, E., Praz, F., Higuet, D., Netter, P., Achaz, G.

Molecular Biology and Evolution 26 111-121

Frequency spectrum neutrality tests: one for all and all for one

Achaz, G.

Genetics 183 249-258

Allele fixation in a dynamic metapopulation: founder effects vs refuge effects

Aguilée, R., Claessen, D., Lambert, A.

Theoretical Population Biology 76 105-117

Non-neutral theory of biodiversity

Bianconi, G., Ferretti, L., Franz, S.

EPL (Europhysics Letters) 87

Proof(s) of the lamperti representation of continuous-state branching processes

Caballero, M., Lambert, A., Uribe Bravo, G.

Probab. Surveys 6 62-89

Consequences of a unified, anarchical model of fermion masses and mixings

Calibbi, L., Ferretti, L., Romanino, A., Ziegler, R.

Journal of High Energy Physics 3

Gauge coupling unification, the gut scale, and magic fields

Calibbi, L., Ferretti, L., Romanino, A., Ziegler, R.

Physics Letters B 672 152-157

Quasi-stationary distributions and diffusion models in population dynamics

Cattiaux, P., Collet, P., Lambert, A., Martínez, S., Méléard, S., Martín, J. S.

The Annals of Probability 37 1926-1969

Evolutionary epidemiology of drug-resistance in space

Débarre, F., Lenormand, T., Gandon, S.

PLoS computational biology 5

Population structure of the fish-pathogenic bacterium flavobacterium psychrophilum

Nicolas, P., Mondot, S., Achaz, G., Bouchenot, C., Bernardet, J., Duchaud, E.

Applied and Environmental Microbiology 74 3702-3709

Absorption and fixation times for neutral and quasi-neutral populations with density dependence

Parsons, T. L., Quince, C., Plotkin, J. B.

Theoretical Population Biology 74 302-310

Experimental estimation of mutation rates in a wheat population with a gene genealogy approach

Raquin, A., Depaulis, F., Lambert, A., Galic, N., Brabant, P., Goldringer, I.

Genetics 179 2195-2211

When does ecosystem engineering cause invasion and species replacement?

Gonzalez, A., Lambert, A., Ricciardi, A.

Oikos 117 1247-1257

Variation in the major surface glycoprotein genes in pneumocystis jirovecii

Kutty, G., Maldarelli, F., Achaz, G., Kovacs, J. A.

The Journal of Infectious Diseases 198 741-749

Population dynamics and random genealogies

Lambert, A.

Stochastic Models 24 45-163

Testing for neutrality in samples with sequencing errors

Achaz, G.

Genetics 179 1409-1424

The impact on tigers of poaching versus prey depletion.

Chapron, G., Miquelle, D., Lambert, A., Goodrich, J., Legendre, S., Clobert, J.

J. Appl. Ecology 45 1667-1674

Non-abelian vortices and monopoles in so(n) theories

Ferretti, L., Gudnason, S., Konishi, K.

789

Dynamics of condensation in growing complex networks

Ferretti, L., Bianconi, G.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics 78

Fixation in haploid populations exhibiting density dependence i: the non-neutral case

Parsons, T. L., Quince, C.

Theoretical Population Biology 72 121-135

Fixation in haploid populations exhibiting density dependence ii: the quasi-neutral case

Parsons, T. L., Quince, C.

Theoretical Population Biology 72 468-479

Novel insights into rnai off-target effects using c. elegans paralogs

Rual, J., Klitgord, N., Achaz, G.

BMC genomics 8

Quasistationary distributions and the continuous-state branching process conditioned to be never extinct

Lambert, A.

Electronic Journal of Probability 12 420-446

Repseek, a tool to retrieve approximate repeats from large dna sequences

Achaz, G., Boyer, F., Rocha, E. P. C., Viari, A., Coissac, E.

Bioinformatics (Oxford, England) 23 119-121

The effect of population structure on the emergence of drug resistance during influenza pandemics

Débarre, F., Bonhoeffer, S., Regoes, R. R.

Journal of the Royal Society, Interface / the Royal Society 4 893-906