Eric Goolsby, Jorn Bruggeman and C. Ané (2016). Rphylopars: Phylogenetic comparative methods for missing data and within-species variation. Methods in Ecology and Evolution.
R package on GitHub (more current): Rphylopars and on CRAN.

Cécile Ané, Lam S.T. Ho and Sebastien Roch (2016). Phase transition on the convergence rate of parameter estimation under an Ornstein-Uhlenbeck diffusion on a tree. Journal of Mathematical Biology, doi:10.1007/s00285-016-1029-x. (earlier on arXiv).

Bret Larget, Cécile Ané, Martin Bontrager, Steven J. Hunter, Noah Stenz and David A. Baum. Statistical evidence for common ancestry: New tests of universal ancestry. bioRxiv

Martin Bontrager, Bret Larget, Cécile Ané and David A. Baum. Statistical Evidence of Common Ancestry: Testing for Signal in Silent Sites. bioRxiv

David A. Baum, Cécile Ané, Bret Larget, Claudia Solís-Lemus, Lam Si Tung Ho, Peggy Boone, Chloe P. Drummond, Martin Bontrager, Steve Hunter and William Saucier (2016). Statistical evidence for common ancestry: Application to primates. Evolution, 70(6):1354–1363.

Claudia Solís-Lemus, Mengyao Yang and Cécile Ané. Inconsistency of species-tree methods under gene flow (2016). Systematic Biology, 65(5):843-851. pdf.

George Tiley, Cécile Ané and Gordon Burleigh (2016). Evaluating and characterizing ancient whole genome duplications in plants with gene count data. Genome Biology and Evolution, 8(4):1023-1037.

Claudia Solís-Lemus and Cécile Ané (2016). Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting. PLoS Genetics, 12(3):e1005896. (earlier on arXiv 2015). SNaQ logo
Software on GitHub: SNaQ (Julia package).

Mohammad Khabbazian, Ricardo Kriebel, Karl Rohe and Cécile Ané (2016). Fast and accurate detection of evolutionary shifts in Ornstein-Uhlenbeck models. Methods in Ecology and Evolution, 7(7):811–824.
Software on GitHub: ℓ1ou


Noah W. M. Stenz, Bret Larget, David A. Baum, and Cécile Ané (2015). Exploring tree-like and non-tree-like patterns using genome sequences: An example using the inbreeding plant species Arabidopsis thaliana (L.) Heynh. Systematic Biology, 64(5):809-823. abstract, pdf.
Software, including TICR, available on GitHub, and data available from the Dryad digital repository.

Claudia Solís-Lemus, L. Lacey Knowles and Cécile Ané (2015). Bayesian species delimitation combining multiple genes and traits in a unified framework. Evolution, 69(2):492-507.
Software iBPP on GitHub, scripts available on Dryad, and lizard data available on Dryad as well.
Featured in the Molecular Ecologist blog here and here.


Lam Ho and Cécile Ané (2014). Intrinsic inference difficulties for trait evolution with Ornstein-Uhlenbeck models. Methods in Ecology and Evolution, 5(11):1133-1146. Tools available in the R package phylolm (v2.2).

Lam Ho and Cécile Ané (2014). A linear-time algorithm for Gaussian and non-Gaussian trait evolution models. Systematic Biology, 63(3):397-408, abstract.
R package: phylolm is on CRAN.

Charles-Elie Rabier, Tram Ta and Cécile Ané (2014). Detecting and locating whole genome duplications on a phylogeny: a probabilistic approach. Molecular Biology and Evolution, 31(3):750-762, abstract.
R package: WGDgc


Yujin Chung, Nicole T. Perna and Cécile Ané (2013). Computing the joint distribution of tree shape and tree distance for gene tree inference and recombination detection. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(5):1263-1274. preprint and pdf

Aaron W. Kolb, Cécile Ané and Curtis R. Brandt (2013). Using HSV-1 genome phylogenetics to track past human migrations. PLoS ONE, 8(10):e76267. Press release from University News and NBCNews.

Richard J. Wang, Cécile Ané and Bret A. Payseur (2013). The Evolution of hybrid incompatibilities along a phylogeny. Evolution, 67(10):2905-2922.

Lam Ho and Cécile Ané (2013). Asymptotic theory with hierarchical autocorrelation: Ornstein-Uhlenbeck tree models. Annals of Statistics, 41(2):957-981, pdf.


Tom D. Mand, D. Döpfer, B. Ingham, C. Ané, C.W. Kaspar (2012). Growth and survival parameter estimates and relation to RpoS levels in serotype O157:H7 and non-O157 Shiga toxin-producing Escherichia coli. Journal of Applied Microbiology. 114(1):242-255.

B. Marazzi, C. Ané, M.F. Simon, A. Delgado-Salinas, M. Luckow, M.J. Sanderson (2012). Locating evolutionary precursors on a phylogenetic tree Evolution, 66(12):3918-3930.

K.W. Broman, S. Kim, S. Sen, C. Ané, B.A. Payseur (2012). Mapping quantitative trait loci onto a phylogenetic tree. Genetics, 192:267-279 (issue highlights)

D. Cai, F. Rodríguez, Y. Teng, C. Ané, M. Bonierbale, L.A. Mueller, D. Spooner. Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota) (2012). BMC Evolutionary Biology, 12:70 (highly accessed), ScienceOpen.


Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kuback A, Narro M, Hopkins N, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH, Grene R, Noutsos C, Gendler K, Feng X, Tang C, Lent M, Kim S, Tannen V, Stamatakis A, Sanderson M, Welch SM, Cranston K, Soltis P, Soltis D, O'Meara B, Ané C, Brutnell T, Kleibenstein DJ, White JW, Leebens-Mack J, Donoghue MJ, Spalding EP, Kvilekval K, Manjunath B, Vision TJ, Enquist BJ, Boyle B, Lowenthal D, Akoglu A, Micklos D, Andrews G, Ram S, Ware D, Stein L and Stanzione D (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers in Plant Genetics and Genomics. 2:34

S.C. Ingham, Y. Hu and C. Ané (2011). Comparison of bulk-tank standard plate count and somatic cell count for Wisconsin dairy farms in three size categories. Journal of Dairy Science, 94(8):4237-4241.

C. Ané (2011). Detecting phylogenetics breakpoints and discordance from genome-wide alignments for species tree reconstruction. Genome Biology and Evolution, 3:246-258.
Program download: tarball

Y. Chung, C. Ané (2011). Comparing two Bayesian methods for gene tree / species tree reconstruction: A simulation with incomplete lineage sorting and horizontal gene transfer. Systematic Biology. 60(3): 261-275 abstract, pdf.


B. Larget, S.K. Kotha, C.N. Dewey, C. Ané (2010). BUCKy: Gene tree / species tree reconciliation with Bayesian concordance analysis. Bioinformatics 26(22): 2910-2911. cover
Program available here: BUCKy

C. Ané (2010). Reconstructing concordance trees and testing the coalescent model from genome-wide data sets. Chapter 3, p.35-52 in "Estimating species trees: Practical and theoretical aspects", L. Knowles and L. Kubatko, eds. Wiley-Blackwell.

S.C. Ingham, D.L. Borneman, C. Ané and B.H. Ingham (2010). Predicting growth-no growth of Listeria monocytogenes on vacuum-packaged ready-to-eat meats. Journal of Food Protection 73(4):708-714.


M.A. White, C. Ané, C.N. Dewey, B.R. Larget, B.A. Payseur (2009). Fine scale phylogenetic discordance across the house mouse genome. PloS Genetics. 5(11):e1000729.

S.D. Smith, C. Ané, D.A. Baum (2009). Macroevolutionary tests of pollination syndromes: A reply to Fenster et al. Evolution. 63(10):2763-2767.

F. Rodriguez, F. Wu, C. Ané, S. Tanksley, D.M. Spooner (2009). Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history? BMC Evolutionary Biology 9:191.

D.L. Borneman, S.C. Ingham, C. Ané (2009). Mathematical approaches to estimating lag-phase duration and growth rate for predicting growth of Salmonella serovars, Escherichia coli O157:H7, and Staphylococcus aureus in raw beef, bratwurst, and poultry. Journal of Food Protection 72(6):1190-1200.

D.L. Borneman, S.C. Ingham, C. Ané (2009). Predicting growth-no growth of Staphylococcus aureus on vacuum-packaged ready-to-eat meats. Journal of Food Protection 72(3):539-548.

C. Ané, O. Eulenstein, R. Piaggio-Talice and M.J. Sanderson (2009). Groves of phylogenetic trees. Annals of Combinatorics 13(2):139-167. Technical report available here (2006).


C. Ané (2008). Analysis of comparative data with hierarchical autocorrelation. Annals of Applied Statistics 2(3):1078-1102. arXiv

S. Martin, E.L. Epperson,J. Rose,C. Kurtz, C. Ané, H. Carey (2008). Proteomic analysis of the winter-protected phenotype of hibernating ground squirrel intestine. AJP- Regulatory, Integrative and Comparative Physiology, 295:316-328. cover

J.P. Huelsenbeck, C. Ané, B. Larget and F. Ronquist (2008). A Bayesian perspective on a non-parsimonious parsimony model. Systematic Biology, 57(3):406-419.

S.D. Smith, C. Ané and D.A. Baum (2008). The role of pollinator shifts in the floral diversification of Iochroma (Solanaceae). Evolution 62(4):793-806.

E.S. Allman, C. Ané, J.A. Rhodes (2008). Identifiability of a Markovian model of molecular evolution with Gamma-distributed rates. Advances in Applied Probability 40(1), 229-249. Abstract or preprint.

≤ 2007

M.J. Sanderson, C. Ané, O. Eulenstein, D. Fernández-Baca, J. Kim, M.M. McMahon, R. Piaggio-Talice (2007). Fragmentation of large data sets in phylogenetic analyses. Chapter 7 (p. 199-216) in Reconstructing Evolution: New Mathematical and Computational Advances. Olivier Gascuel and Mike Steel, editors. Oxford University Press.

C. Ané, B. Larget, D.A. Baum, S.D. Smith, A. Rokas (2007). Bayesian estimation of concordance among gene trees. Molecular Biology and Evolution 24(2), 412-426. Abstract and Erratum. Software available here.

B.C. O'Meara, C. Ané, M.J. Sanderson, P.C. Wainwright (2006). Testing for different rates of continuous trait evolution using likelihood. Evolution 60(5), 922-933.

C. Ané, J.G. Burleigh, M.M. McMahon, M.J. Sanderson (2005). Covarion structure in plastid genome evolution: A new statistical test. Molecular Biology and Evolution 22(4), 914-924. Abstract, full text and supplemental data.

C. Ané and M.J. Sanderson (2005). Missing the forest for the trees: phylogenetic compression and its implication for inferring complex evolutionary histories. Systematic Biology, 54(1), 146-157. and supplemental data

C. Ané, O. Eulenstein, and R. Piaggio-Talice (2005). Phylogenetic compression and model selection: an improved encoding scheme. Technical report here.

A.C. Driskell, C. Ané, J.G. Burleigh, M.M. McMahon, B.C. O'Meara, M.J. Sanderson (2004). Prospects for building the tree of life from large sequence databases. Science, 306(5699), 1172-1174.

D. Concordet, F. Léger, C. Ané (2004). Population PK/PD Analysis. In Encyclopedia of Biopharmaceutical Statistics, 2nd Ed.; S. Chow, Ed.; Marcel Dekker, Inc.: New York.

C. Ané and D. Concordet (2003). Population pharmacokinetics - pharmacodynamics relationships of an anticancer drug. Statistics in Medicine 22(6), 833-846.

C. Ané and D. Chafai (2000). Entropy inequalities in information theory (in french). Chapter 10 of the book Sur les ingalités de Sobolev logarithmiques, Panoramas et Syntheses no 10, SMF. Mathematical Review report. More here.

C. Ané (2001). Clark-Ocone formulas and Poincaré inequalities on the discrete cube. Annales de l'Institut Henri Poincaré, Probab. Statist. 37(1), 101-137.

C. Ané and M. Ledoux (2000). On logarithmic Sobolev inequalities for continuous time random walks on graphs Probability Theory and Related Fields, 116(4), 573-602.

C. Ané (1997). Large deviations in small time for a Markov process with countable state space (in french). C. R. Acad. Sc. Paris, I 325, 1025-1028.