Bibliography

Major publications by the team in recent years

1B. Batut, D. Parsons, S. Fischer, G. Beslon, C. Knibbe.

In silico experimental evolution: a tool to test evolutionary scenarios, in: BMC Bioinformatics, October 2013, vol. 14, n^o Suppl 15, S11 p.

http://hal.inria.fr/hal-00856813
2G. Beslon, B. Batut, D. P. Parsons, D. Schneider, C. Knibbe.

An alife game to teach evolution of antibiotic resistance, in: ECAL - 12th European Conference on Artificial Life - 2013, Taormina, Italy, MIT Press, 2013.

http://hal.inria.fr/hal-00849345
3A.-S. Coquel, J.-P. Jacob, M. Primet, A. Demarez, M. Dimiccoli, T. Julou, L. Moisan, A. Lindner, H. Berry.

Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect, in: PLoS Computational Biology, 2013, vol. 9, n^o 4. [ DOI : 10.1371/journal.pcbi.100303 ]

http://hal.inria.fr/hal-00798053
4M. De Pittà, V. Volman, H. Berry, E. Ben-Jacob.

A tale of two stories: astrocyte regulation of synaptic depression and facilitation, in: PLoS Computational Biology, 2011, vol. 7, n^o 12.
5T. Hindré, C. Knibbe, G. Beslon, D. Schneider.

New insights into bacterial adaptation through in vivo and in silico experimental evolution, in: Nature Reviews Microbiology, 2012, vol. 10, pp. 352-365.

http://hal.inria.fr/hal-00696231
6P.-N. Mougel, C. Rigotti, M. Plantevit, O. Gandrillon.

Finding maximal homogeneous clique sets, in: Knowledge and Information Systems, March 2013, vol. 35, n^o 1, pp. 1-30. [ DOI : 10.1007/s10115-013-0625-y ]

http://hal.inria.fr/hal-00827164
7J. Naudé, J. T. Paz, H. Berry, B. Delord.

A theory of rate coding control by intrinsic plasticity effects, in: PLoS Computational Biology, 2012, vol. 8, n^o 1. [ DOI : 10.1371/ journal.pcbi.1002349 ]

http://hal.inria.fr/hal-00645336
8M. Patterson, G. Szöllősi, V. Daubin, E. Tannier.

Lateral gene transfer, rearrangement, reconciliation, in: BMC Bioinformatics, 2013, vol. 14, n^o Suppl 15, S4 p.

http://hal.inria.fr/hal-00873233
9A. Rajaraman, E. Tannier, C. Chauve.

FPSAC: Fast Phylogenetic Scaffolding of Ancient Contigs, in: Bioinformatics, December 2013, vol. 29, n^o 23, pp. 2987-2994.

http://hal.inria.fr/hal-00859185
10H. Soula, B. Caré, G. Beslon, H. Berry.

Anomalous versus slowed-down Brownian diffusion in the ligand-binding equilibrium, in: Biophysical Journal, 2013, vol. 105, n^o 9, pp. 2064-2073. [ DOI : 10.1016/j.bpj.2013.07.023 ]

http://hal.inria.fr/hal-00720515
11G. J. Szöllosi, B. Boussau, S. S. Abby, E. Tannier, V. Daubin.

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations., in: Proceedings- National Academy of Sciences Usa, October 2012, vol. 109, n^o 43, pp. 17513-17518. [ DOI : 10.1073/pnas.1202997109 ]

http://hal.inria.fr/hal-00740292
12J. Viñuelas, G. Kaneko, A. Coulon, E. Vallin, V. Morin, C. Mejia-Pous, J.-J. Kupiec, G. Beslon, O. Gandrillon.

Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts, in: BMC Biology, February 2013, vol. 11, n^o 1, 15 p. [ DOI : 10.1186/1741-7007-11-15 ]

http://hal.inria.fr/inserm-00817963

Publications of the year

Doctoral Dissertations and Habilitation Theses

13S. Fischer.

Modélisation de l'évolution de la taille des génomes et de leur densité en gènes par mutations locales et grands réarrangements chromosomiques, INSA de Lyon, December 2013.

http://hal.inria.fr/tel-00924831
14G. Kaneko.

Analyse et modélisation de la stochasticité de l'expression génique dans des cellules eucaryotes, INSA de Lyon, September 2013.

http://hal.inria.fr/tel-00926607

Articles in International Peer-Reviewed Journals

15B. Batut, D. Parsons, S. Fischer, G. Beslon, C. Knibbe.

In silico experimental evolution: a tool to test evolutionary scenarios, in: BMC Bioinformatics, October 2013, vol. 14, n^o Suppl 15, S11 p.

http://hal.inria.fr/hal-00856813
16H. Berry, H. Chaté.

Anomalous diffusion due to hindering by mobile obstacles undergoing Brownian motion or Orstein-Ulhenbeck processes, in: Physical Review E, 2014.

http://hal.inria.fr/inria-00575651
17B. Boussau, G. J. Szöllosi, L. Duret, M. Gouy, E. Tannier, V. Daubin.

Genome-scale coestimation of species and gene trees, in: Genome Research, February 2013, vol. 23, pp. 323-330. [ DOI : 10.1101/gr.141978.112 ]

http://hal.inria.fr/hal-00750148
18B. R. Caré, H. A. Soula.

Receptor clustering affects signal transduction at the membrane level in the reaction-limited regime, in: Physical Review E, January 2013, vol. 87, n^o 1. [ DOI : 10.1103/PhysRevE.87.012720 ]

http://hal.inria.fr/hal-00858439
19A.-S. Coquel, J.-P. Jacob, M. Primet, A. Demarez, M. Dimiccoli, T. Julou, L. Moisan, A. Lindner, H. Berry.

Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect, in: PLoS Computational Biology, 2013, vol. 9, n^o 4. [ DOI : 10.1371/journal.pcbi.100303 ]

http://hal.inria.fr/hal-00798053
20M. L. Croze, R. E. Vella, N. J. Pillon, H. A. Soula, L. Hadji, M. Guichardant, C. O. Soulage.

Chronic treatment with myo-inositol reduces white adipose tissue accretion and improves insulin sensitivity in female mice, in: The Journal of Nutritional Biochemistry, February 2013, vol. 24, n^o 2, pp. 457-66. [ DOI : 10.1016/j.jnutbio.2012.01.008 ]

http://hal.inria.fr/hal-00759518
21L. Koppe, N. J. Pillon, R. E. Vella, M. L. Croze, C. C. Pelletier, S. Chambert, Z. Massy, G. Glorieux, R. Vanholder, Y. Dugenet, H. A. Soula, D. Fouque, C. O. Soulage.

p-Cresyl sulfate promotes insulin resistance associated with CKD, in: Journal of the American Society of Nephrology, January 2013, vol. 24, n^o 1, pp. 88-99. [ DOI : 10.1681/ASN.2012050503 ]

http://hal.inria.fr/hal-00850482
22M. Lafond, M. Semeria, K. Swenson, E. Tannier, N. El-Mabrouk.

Gene tree correction guided by orthology, in: BMC Bioinformatics, 2013, vol. 14, n^o Suppl 15, S5 p.

http://hal.inria.fr/hal-00873235
23P.-N. Mougel, C. Rigotti, M. Plantevit, O. Gandrillon.

Finding maximal homogeneous clique sets, in: Knowledge and Information Systems, March 2013, vol. 35, n^o 1, pp. 1-30. [ DOI : 10.1007/s10115-013-0625-y ]

http://hal.inria.fr/hal-00827164
24J. Naudé, B. Cessac, H. Berry, B. Delord.

Effects of Cellular Homeostatic Intrinsic Plasticity on Dynamical and Computational Properties of Biological Recurrent Neural Networks, in: Journal of Neuroscience, 2013, vol. 33, n^o 38, pp. 15032-15043. [ DOI : 10.1523/JNEUROSCI.0870-13.2013 ]

http://hal.inria.fr/hal-00844218
25M. Patterson, G. Szöllősi, V. Daubin, E. Tannier.

Lateral gene transfer, rearrangement, reconciliation, in: BMC Bioinformatics, 2013, vol. 14, n^o Suppl 15, S4 p.

http://hal.inria.fr/hal-00873233
26A. Rajaraman, E. Tannier, C. Chauve.

FPSAC: Fast Phylogenetic Scaffolding of Ancient Contigs, in: Bioinformatics, September 2013, vol. 29, n^o 23, pp. 2987-2994. [ DOI : 10.1093/bioinformatics/btt527 ]

http://hal.inria.fr/hal-00859185
27H. Soula, B. Caré, G. Beslon, H. Berry.

Anomalous versus slowed-down Brownian diffusion in the ligand-binding equilibrium, in: Biophysical Journal, 2013, vol. 105, n^o 9, pp. 2064-2073. [ DOI : 10.1016/j.bpj.2013.07.023 ]

http://hal.inria.fr/hal-00720515
28H. A. Soula, H. Julienne, C. O. Soulage, A. Géloën.

Modelling adipocytes size distribution, in: J Theor Biol, Journal-Full = Journal of theoretical biology, September 2013, vol. 332, pp. 89-95. [ DOI : 10.1016/j.jtbi.2013.04.025 ]

http://hal.inria.fr/hal-00850474
29G. J. Szöllosi, W. Rosikiewicz, B. Boussau, E. Tannier, V. Daubin.

Efficient Exploration of the Space of Reconciled Gene Trees, in: Systematic Biology, August 2013, epub ahead of print. [ DOI : 10.1093/sysbio/syt054 ]

http://hal.inria.fr/hal-00856826
30G. J. Szöllosi, E. Tannier, N. Lartillot, V. Daubin.

Lateral Gene Transfer from the Dead, in: Systematic Biology, January 2013, epub ahead of print. [ DOI : 10.1093/sysbio/syt003 ]

http://hal.inria.fr/hal-00784662
31J. Viñuelas, G. Kaneko, A. Coulon, E. Vallin, V. Morin, C. Mejia-Pous, J.-J. Kupiec, G. Beslon, O. Gandrillon.

Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts, in: BMC Biology, February 2013, vol. 11, n^o 1, 15 p. [ DOI : 10.1186/1741-7007-11-15 ]

http://hal.inria.fr/inserm-00817963

Articles in Non Peer-Reviewed Journals

32V. Daubin, S. Penel, E. Tannier.

L'ADN, mémoire numérique du vivant, in: Pour la Science, October 2013, pp. 102-108.

http://hal.inria.fr/hal-00878875

International Conferences with Proceedings

33G. Beslon, B. Batut, D. P. Parsons, D. Schneider, C. Knibbe.

An alife game to teach evolution of antibiotic resistance, in: ECAL - 12th European Conference on Artificial Life - 2013, Taormina, Italy, MIT Press, 2013.

http://hal.inria.fr/hal-00849345
34Y. Cui, V. Paille, B. Delord, S. Genet, E. Fino, L. Venance, H. Berry.

Endocannabinoids mediate spike-timing dependent potentiation and depression: a model-based experimental approach, in: the Twenty Second Annual Computational Neuroscience Meeting: CNS*2013, Paris, France, G. S. Cymbalyuk, A. A. Prinz (editors), Biomed Central, 2013, vol. 14, O1 p. [ DOI : 10.1186/1471-2202-14-S1-O1 ]

http://hal.inria.fr/inserm-00842298

Scientific Books (or Scientific Book chapters)

35H. Berry.

Modélisation de la diffusion-réaction dans les milieux intracellulaires encombrés, in: Le vivant discret et continu, N. Glade, A. Stéphanou (editors), Editions Matériologiques, September 2013, pp. 241-266.

http://hal.inria.fr/hal-00858738
36H. Berry, G. Beslon.

De la modélisation comme poésie. La modélisation de systèmes biologiques complexes vue par deux modélisateurs, in: Modéliser & simuler. Epistémologies et pratiques de la modélisation et de la simulation, F. Varenne, M. Silberstein (editors), Editions Matériologiques, Paris, April 2013, vol. 1.

http://hal.inria.fr/hal-00815550
37C. Chauve, N. El-Mabrouk, E. Tannier.

Models and Algorithms for Genome Evolution, Springer, 2013, 318 p.

http://hal.inria.fr/hal-00847154
38C. Chauve, N. El-Mabrouk, L. Gueguen, M. Semeria, E. Tannier.

Duplication, Rearrangement and Reconciliation, in: Models and Algorithms for Genome Evolution, Springer, 2013.

http://hal.inria.fr/hal-00847155
39J.-G. Dumas, J.-L. Roch, E. Tannier, S. Varette.

Foundations of Coding: Compression, Encryption, Error-Correction, –, 2014, A paraître.

http://hal.inria.fr/hal-00765802
40J.-G. Dumas, J.-L. Roch, E. Tannier, S. Varrette.

Théorie des Codes : compression, cryptage, correction, 2e edition, Sciences Sup, Dunod, August 2013, 384 p.

http://hal.inria.fr/hal-00932851
41C. Knibbe.

L'évolution expérimentale in silico, in: Modéliser et simuler - Epistémologies et pratiques de la modélisation et de la simulation - Tome 1, F. Varenne, M. Silberstein (editors), Editions Matériologiques, April 2013, pp. 581-610.

http://hal.inria.fr/hal-00850175

Other Publications

42C. Chauve, M. Patterson, A. Rajaraman.

Hypergraph covering problems motivated by genome assembly questions, 2013, 13 pages+3 page appendix A short version will appear in the proceedings of IWOCA 2013.

http://hal.inria.fr/hal-00849753
43Y. Cui, V. Paille, B. Delord, S. Genet, E. Fino, L. Venance, H. Berry.

Endocannabinoids mediate spike-timing dependent potentiation and depression: a model-based experimental approach, in: Twenty Second Annual Computational Neuroscience Meeting : CNS 2013, Paris, France, July 2013, 01 p. [ DOI : 10.1186/1471-2202-14-S1-O1 ]

http://hal.inria.fr/hal-00842299
44A. Rajaraman, E. Tannier, C. Chauve.

The genome of the medieval Black Death agent (extended abstract), 2013, Extended abstract of a talk presented at the conference JOBIM 2013. Full paper submitted.

https://colloque.inra.fr/jobim2013_eng/, http://hal.inria.fr/hal-00849754
45G. Szöllősi, E. Tannier, V. Daubin, B. Boussau.

The inference of gene trees with species trees, 2013, arXiv:1311.0651.

http://hal.inria.fr/hal-00915301

References in notes

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47J.-M. Aury, O. Jaillon, L. Duret, B. Noel, C. Jubin, B. M. Porcel, B. Ségurens, V. Daubin, V. Anthouard, N. Aiach, O. Arnaiz, A. Billaut, J. Beisson, I. Blanc, K. Bouhouche, F. Câmara, S. Duharcourt, R. Guigó, D. Gogendeau, M. Katinka, A.-M. Keller, R. Kissmehl, C. Klotz, F. Koll, A. Le Mouël, G. Lepère, S. Malinsky, M. Nowacki, J. K. Nowak, H. Plattner, J. Poulain, F. Ruiz, V. Serrano, M. Zagulski, P. Dessen, M. Bétermier, J. Weissenbach, C. Scarpelli, V. Schächter, L. Sperling, E. Meyer, J. Cohen, P. Wincker.

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48J. A. Bailey, R. Baertsch, W. J. Kent, D. Haussler, E. E. Eichler.

Hotspots of mammalian chromosomal evolution, in: Genome Biol, 2004, vol. 5, n^o 4, R23 p.

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49H. Berry.

Monte Carlo simulations of enzyme reactions in two dimensions: fractal kinetics and spatial segregation., in: Biophys J, 2002, vol. 83, n^o 4, pp. 1891–1901.
50G. Beslon, D. P. Parsons, Y. Sanchez-Dehesa, J.-M. Peña, C. Knibbe.

Scaling Laws in Bacterial Genomes: A Side-Effect of Selection of Mutational Robustness, in: BioSystems, 2010, vol. 102, n^o 1, pp. 32-40.
51G. Beslon, Y. Sanchez-Dehesa, D. P. Parsons, J.-M. Peña, C. Knibbe.

Scaling Laws in Digital Organisms, in: Proceedings of Information Processing in Cells and Tissues (IPCAT'09), 2009, pp. 111-114.
52G. Beslon, Y. Sanchez-Dehesa, D. P. Parsons, C. Rigotti, J.-M. Peña.

From Digital Genetics to Knowledge Discovery: Perspectives in Genetic Network Understanding, in: Intelligent Data Analysis journal (IDAj), 2010, vol. 14, n^o 2, pp. 173-191.
53B. R. Caré, H. A. Soula.

Impact of receptor clustering on ligand binding, in: BMC Systems Biology, March 2011, vol. 5, n^o 1, 48 p, PMID: 21453460. [ DOI : 10.1186/1752-0509-5-48 ]

http://www.ncbi.nlm.nih.gov/pubmed/21453460
54C. Chauve, H. Gavranovic, A. Ouangraoua, E. Tannier.

Yeast ancestral genome reconstructions: the possibilities of computational methods II., in: J Comput Biol, Sep 2010, vol. 17, n^o 9, pp. 1097–1112.

http://dx.doi.org/10.1089/cmb.2010.0092
55A. Coulon, O. Gandrillon, G. Beslon.

On the spontaneous stochastic dynamics of a single gene: complexity of the molecular interplay at the promoter, in: BMC Systems Biology, 2010, vol. 4, n^o 1, 2 p.
56A. E. Darling, I. Miklós, M. A. Ragan.

Dynamics of genome rearrangement in bacterial populations, in: PLoS Genet, 2008, vol. 4, n^o 7, e1000128.

http://dx.doi.org/10.1371/journal.pgen.1000128
57V. Daubin, N. A. Moran, H. Ochman.

Phylogenetics and the cohesion of bacterial genomes, in: Science, Aug 2003, vol. 301, n^o 5634, pp. 829–832.

http://dx.doi.org/10.1126/science.1086568
58L. A. David, E. J. Alm.

Rapid evolutionary innovation during an Archaean genetic expansion, in: Nature, Jan 2011, vol. 469, n^o 7328, pp. 93–96. [ DOI : 10.1038/nature09649 ]
59M. Eigen.

Selforganization of matter and the evolution of biological macromolecules, in: Naturwissenschaften, 1971, vol. 58, n^o 10, pp. 465-523.
60M. Elowitz, A. Levine, E. Siggia, P. Swain.

Stochastic gene expression in a single cell, in: Science, 2002, vol. 297, n^o 5584, pp. 1183–1186.
61J. Felsenstein.

Inferring phylogenies, Sinauer Associates, 2004.
62P. Galison.

Image and Logic: A Material Culture of Microphysics, University Of Chicago Press, 1997.
63T. Hindré, C. Knibbe, G. Beslon, D. Schneider.

New insights into bacterial adaptation through in vivo and in silico experimental evolution, in: Nature Reviews Microbiology, 2012, vol. 10, pp. 352-365.

http://hal.inria.fr/hal-00696231
64International Aphid Genomics Consortium.

Genome sequence of the pea aphid Acyrthosiphon pisum, in: PLoS Biol, Feb 2010, vol. 8, n^o 2, e1000313.

http://dx.doi.org/10.1371/journal.pbio.1000313
65O. Jaillon, J.-M. Aury, F. Brunet, J.-L. Petit, N. Stange-Thomann, E. Mauceli, L. Bouneau, C. Fischer, C. Ozouf-Costaz, A. Bernot, S. Nicaud, D. Jaffe, S. Fisher, G. Lutfalla, C. Dossat, B. Ségurens, C. Dasilva, M. Salanoubat, M. Levy, N. Boudet, S. Castellano, V. Anthouard, C. Jubin, V. Castelli, M. Katinka, B. Vacherie, C. Biémont, Z. Skalli, L. Cattolico, J. Poulain, V. De Berardinis, C. Cruaud, S. Duprat, P. Brottier, J.-P. Coutanceau, J. Gouzy, G. Parra, G. Lardier, C. Chapple, K. J. McKernan, P. McEwan, S. Bosak, M. Kellis, J.-N. Volff, R. Guigó, M. C. Zody, J. Mesirov, K. Lindblad-Toh, B. Birren, C. Nusbaum, D. Kahn, M. Robinson-Rechavi, V. Laudet, V. Schächter, F. Quétier, W. Saurin, C. Scarpelli, P. Wincker, E. S. Lander, J. Weissenbach, H. R. Crollius.

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype., in: Nature, Oct 2004, vol. 431, n^o 7011, pp. 946–957.

http://dx.doi.org/10.1038/nature03025
66C. Knibbe, A. Coulon, J.-M. Fayard, G. Beslon.

A long term evolutionary pressure on the amount of noncoding DNA, in: Molecular Biology and Evolution, 2007, vol. 24, n^o 10, pp. 2344-2353.
67C. Knibbe, J.-M. Fayard, G. Beslon.

The topology of the protein network influences the dynamics of gene order : From systems biology to a systemic understanding of evolution, in: Artificial Life, 2008, vol. 14, n^o 1, pp. 149-156c.
68C. Knibbe.

Structuration de génomes par sélection indirecte de la variabilité mutationnelle, une approche par modélisation et simulation, PhD Thesis, Institut National des Sciences Appliquées de Lyon, 2006, 174 p.
69C. Knibbe, O. Mazet, F. Chaudier, J.-M. Fayard, G. Beslon.

Evolutionary coupling between the deleteriousness of gene mutations and the amount of non-coding sequences, in: Journal of Theoretical Biology, 2007, vol. 244, n^o 4, pp. 621–630.
70R. E. Lenski, C. Ofria, R. T. Pennock, C. Adami.

The evolutionary origin of complex features, in: Nature, 2003, vol. 423, pp. 139–144.
71D. A. Liberles.

Ancestral Sequence Reconstruction, Oxford University Press, 2007.
72J. Ma, L. Zhang, B. B. Suh, B. J. Raney, R. C. Burhans, W. J. Kent, M. Blanchette, D. Haussler, W. Miller.

Reconstructing contiguous regions of an ancestral genome, in: Genome Res, Dec 2006, vol. 16, n^o 12, pp. 1557–1565.

http://dx.doi.org/10.1101/gr.5383506
73G. A. B. Marais, A. Forrest, E. Kamau, J. Käfer, V. Daubin, D. Charlesworth.

Multiple nuclear gene phylogenetic analysis of the evolution of dioecy and sex chromosomes in the genus Silene., in: PLoS One, 2011, vol. 6, n^o 8, e21915.

http://dx.doi.org/10.1371/journal.pone.0021915
74I. Miklós, E. Tannier.

Bayesian sampling of genomic rearrangement scenarios via double cut and join., in: Bioinformatics, Dec 2010, vol. 26, n^o 24, pp. 3012–3019.

http://dx.doi.org/10.1093/bioinformatics/btq574
75M. Muffato, A. Louis, C.-E. Poisnel, H. R. Crollius.

Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes., in: Bioinformatics, Apr 2010, vol. 26, n^o 8, pp. 1119–1121.

http://dx.doi.org/10.1093/bioinformatics/btq079
76F. Murat, J.-H. Xu, E. Tannier, M. Abrouk, N. Guilhot, C. Pont, J. Messing, J. Salse.

Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution., in: Genome Res, Nov 2010, vol. 20, n^o 11, pp. 1545–1557. [ DOI : 10.1101/gr.109744.110 ]
77A. Ouangraoua, E. Tannier, C. Chauve.

Reconstructing the architecture of the ancestral amniote genome, in: Bioinformatics, Oct 2011, vol. 27, n^o 19, pp. 2664–2671.

http://dx.doi.org/10.1093/bioinformatics/btr461
78D. P. Parsons, C. Knibbe, G. Beslon.

Importance of the rearrangement rates on the organization of transcription, in: Proceedings of Artificial Life 12, MIT Press, 2010, pp. 479-486.
79D. P. Parsons, C. Knibbe, G. Beslon.

Homologous and nonhomologous rearrangements: Interactions and effects on evolvability, in: European Conference on Artificial Life (ECAL), MIT Press, 2011, pp. 622–629.
80M. Sémon, K. H. Wolfe.

Consequences of genome duplication, in: Curr Opin Genet Dev, Dec 2007, vol. 17, n^o 6, pp. 505–512.

http://dx.doi.org/10.1016/j.gde.2007.09.007
81A. Tofigh, M. Hallett, J. Lagergren.

Simultaneous identification of duplications and lateral gene transfers, in: IEEE/ACM Trans Comput Biol Bioinform, 2011, vol. 8, n^o 2, pp. 517–535.

http://dx.doi.org/10.1109/TCBB.2010.14

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