Bertl J, Ewing G, Kosiol C, and Futschik A, 2013.
Approximate Maximum Likelihood Inference for Coalescent Models.
In prep.
The Marmoset Genome Sequencing and Analysis Consortium, 2013.
The genome of the common marmoset: A comparative analysis of an extraordinary South American primate. Submitted to Nature.
De Maio N, Schlötterer C and Kosiol C, 2013.
Linking Great Apes Genome Evolution across Time Scales using Polymorphism-aware Phylogenetic Models. MBE Advanced access
Marek A, Kosiol C, Harrach B, Kaján GL, Schlötterer C, Hess M, 2013. The first whole genome sequence of a Fowl adenovirus B strain enables interspecies comparisons within the genus Aviadenovirus. Veterinary Microbiology Advanced access
De Maio N, Holmes I, Schlötterer C and Kosiol C, 2013.
Estimating Empirical Codon Hidden Markov Models. Mol Biol Evol 30 (3): 725-736. Webpage
Palmieri N, Nolte V, Suvorov A, Kosiol C and Schlötterer C, 2012.
Evaluation of different reference
based annotation strategies using RNA-Seq - A case study in Drosophila pseudoobscura. PLoS ONE 7(10): e46415. Webpage
Kosiol C and Anisimova M, 2012.
Selection on the protein coding genome.
Book chapter for "Evolutionary Genomics: statistical and computational methods", Part 2: 113-140, eds. M. Anisimova within Meth Mol Biol Series of Springer-Humana. Webpage
Kosiol C and Goldman N, 2011.
Markovian and non-Markovian sequence evolution: aggregated Markov process models.
JMB in press. doi:10.1016/j.jmb.2011.06.005. Webpage
Kofler R, Orozco-terWengel P, De Maio N, Vinay Pandey R, Nolte V, Futschik A,
Kosiol C, Schlötterer C, 2011.
PoPoolation: a toolbox for population genetic
analysis of 2nd generation sequencing data from pooled individuals.
PLoS One 6(1): e15925. Webpage
Orangutan Genome Sequencing and Analysis Consortium, 2011.
Comparative and demographic analysis of orang-utan genomes.
Nature: advance oneline. Webpage
Janssen R, Le Gouar M, Pechmann M, Poulin F, Bolognesi R, Schwager EE, Hopfen C,
Colbourne JK, Budd GE, Brown SJ, Prpic N, Kosiol C, Vervoort M, Damen WGM,
Balavoine G and McGregor, 2010.
Conservation, loss, and redeployment of Wnt
ligands in protostomes: implications for understanding the evolution of segment
formation.
BMC Evolutionary Biology 10:374. pdf
Da Fonseca RR, Kosiol C, Vinar T, Siepel A and Nielsen R, 2009.
Positive selection on apoptosis related genes.
doi:10.1016/j.febslet.2009.12.022.
pdf
Giant Panda Genome Project, 2009.
The sequence and de novo assembly of the giant panda genome.
Nature: advance oneline. Webpage
Anisimova M and Kosiol C, 2009.
Investigating protein-coding sequence evolution with probabilistic codon models.
Mol Biol Evol 26: 255-271.
pdf
Kosiol C, Vinar T, da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R and Siepel A, 2008.
Patterns of positive selection in six mammalian genomes. PLoS Genet 4(8): e1000144.
pdf
Blekhman R, Man O, Herrmann L, Boyko AR, Indap A, Kosiol C, Bustamante CD, Teshima KM and Przeworski M, 2008.
Natural selection on genes that underlie human disease susceptibility.
Current Biology 18: 883-889.
pdf
Rhesus Macaque Genome Sequencing and Analysis Consortium, 2007.
Evolutionary and biomedical insights from the rhesus macaque genome.
Science, 316: 222-234.
pdf
Kosiol C, Holmes I, and Goldman N, 2007.
An empirical codon model for protein sequence evolution.
Mol Biol Evol 24: 1464-1479.
pdf
Klosterman PS, Uzilov AV, Bendana YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I, 2006.
XRate: a fast prototyping, training and annotation tool for phylo-grammars.
BMC Bioinformatics 7 (1): 428.
pdf
Kosiol C, 2006.
Markov models for protein sequence evolution.
PhD Thesis. Cambridge University. Download from EBI
Kosiol C, Bofkin L and Whelan S, 2005.
Phylogenetics by likelihood: evolutionary modelling as a tool for understanding the genome.
J Biomed Info 39: 51-61.
pdf
Kosiol C and Goldman N, 2005.
Different versions of the Dayhoff rate matrix.
Mol Bio Evol 22: 193-199.
http://www.ebi.ac.uk/goldman/dayhoff/
pdf
Kosiol C, Goldman N, and Buttimore NH, 2004.
A new criterion and method for amino acid classification.
J Theor Biol 228: 97-106.
pdf
McCarthy LG, Kosiol C, Healy AM, Bradley G, Sexton JC and Corrigan OI, 2003.
Simulating the Hydrodynamic Conditions in the United States Pharmacopeia Paddle Dissolution Apparatus.
AAPS PharmSciTech 2003; 4(2): article 22.
pdf