My main project was about analysing disrupted co-evolution using presence/absence information of genes in Eukaryotes. Different explanations are possible for situations where in some genomes only certain but not all of a group of interacting proteins are lost. We were using phylogenetic profiles to identify such cases and also to identify genes that potentially take over the role of the lost interaction partner.
In another project, together with Stefan Zoller from the ETH Zürich, we developed semi-empirical codon substitution models. This was a continuation of my previous work on empirical codon models. We were trying to empirically find the relevant parameters for modelling codon evolution and to turn these findings into new codon substitution models.
And together with Gina Cannarozzi from the University of Bern, I have been editing a book entitled "Codon Evolution: Mechanisms and Models" with contributions from leading researchers working on modelling coding sequence evolution and analysing codon usage bias. The book is available from Oxford University Press.
⇒ See also my Google Scholar Citations.
MF Seidl, A Schneider, F Govers and B Snel (2013): A predicted functional gene network for the plant pathogen Phytophtera infestans as a framework for genomic biology. BMC Genomics 14: 483.
A Schneider, MF Seidl and B Snel (2013): Shared protein complex subunits contribute to explaining desrupted co-occurrence. PLoS Computational Biology 9(7): e1003124.
S Zoller and A Schneider (2013): Improving phylogenetic inference with a semiempirical amino acid substitution model. Molecular Biology and Evolution 30(2): 469–479.
S Zoller and A Schneider (2012): A new semiempirical codon substitution model based on principal component analysis of mammalian sequences. Molecular Biology and Evolution 29(1): 271–277.
A Schneider, B Charlesworth, A Eyre-Walker and PD Keightley (2011): A method for inferring the rate of occurrence and fitness effects of advantageous mutations. Genetics 189(4): 1427–1437.
BM Hallström, A Schneider, S Zoller and A Janke (2011): A genomic approach to examine the complex evolution of laurasiatherian mammals. PLoS ONE 6(12):e28199.
AM Altenhoff, A Schneider, GH Gonnet and C Dessimoz (2011): OMA 2011: Orthology inference among 1,000 complete genomes. Nucleic Acids Research 39(suppl 1):D289–D294.
S Zoller and A Schneider (2010): Empirical analysis of the most relevant parameters of codon substitution models. Journal of Molecular Evolution 70(6):605–612.
A Schneider, A Souvorov, N Sabath, G Landan, GH Gonnet and D Graur (2009): Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment. Genome Biology and Evolution 1(1):114–118.
A Gattiker, C Dessimoz, A Schneider, I Xenarios, M Pagni and J Rougemont (2009): The Microbe Browser for comparative genomics. Nucleic Acids Research 37(suppl 2):W296–W299.
A Schneider and GM Cannarozzi (2009): Support patterns from different outgroups provide a strong phylogenetic signal. Molecular Biology and Evolution 26(6):1259–1272.
A Schneider, C Dessimoz and GH Gonnet (2007): OMA Browser – exploring orthologous relations across 352 complete genomes. Bioinformatics 23(16):2180–2182.
A Schneider, GH Gonnet and GM Cannarozzi (2007): SynPAM – a distance measure based on synonymous codon substitutions. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 4(4):553–560.
GM Cannarozzi, A Schneider and GH Gonnet (2007): A phylogenomic study of human, dog and mouse. PLoS Computational Biology 3(1):e2.
C Dessimoz, M Gil, A Schneider and GH Gonnet (2006): Fast estimation of the difference between PAM/JTT evolutionary distances in triplets of homologous sequences. BMC Bioinformatics 7:529.
A Schneider, GH Gonnet and GM Cannarozzi (2006): Synonymous codon substitution matrices. Lecture Notes in Computer Science 3992:630–637.
C Dessimoz, GM Cannarozzi, M Gil, D Margadant, A Roth, A Schneider and GH Gonnet (2005): OMA, a comprehensive, automated project for the identification of orthologs from complete genome data: Introduction and first achievements. Lecture Notes in Computer Science 3678:61–72.
A Schneider, GM Cannarozzi and GH Gonnet (2005): Empirical codon substitution matrix. BMC Bioinformatics 6:134.
A Schneider and GM Cannarozzi: Background. In: GM Cannarozzi and A Schneider (editors): Codon Evolution: Mechanisms and Models, Oxford University Press, 2012.
A Schneider and GM Cannarozzi: Empirical and semi-empirical models of codon evolution. In: GM Cannarozzi and A Schneider (editors): Codon Evolution: Mechanisms and Models, Oxford University Press, 2012.
GM Cannarozzi, A Schneider and GH Gonnet: Probabilistic ancestral sequences based on the Markovian model of evolution – algorithms and applications. In: DA Liberles (editor): Ancestral Sequence Reconstruction, Oxford University Press, 2007.