Jack Chen, Professor

Ortholog: identification and analysis

Review articles

1. Sonnhammer et al., 2014. Big data and other challenges in the quest for orthologs. (Bioinformatics)
2. Gabaldon and Koonin, 2013. Functional and evolutionary implications of gene ortholog.(Nature Reviews Genetics)
   Notes: Discussed "generalized orthology conjecture".
   
3. Dessimoz et al., 2012. Toward community standards in the quest for orthologs. (Bioinformatics)
4. Kristensen et al., 2011. Computational methods for gene orthology inference. (Briefings in Bioinformatics)
5. Trachana et al., 2011. Orthology prediction methods: a quality assessment using curated protein families. (Bioessays)
6. Fang et al., 2010. Getting started in gene orthology and functional analysis. (PLoS Computational Biology)
7. Gabaldon et al., 2009. Joining forces in the quest for orthologs. (Genome Biology)
8. Gabaldon, 2008. Large-scale assignment of orthology: back to phylogenetics? (Genome Biology)
9. Kuzniar et al., 2008. The quest for orthologs: finding the corresponding gene across genomes. (TIGs)
10. Koonin, 2005. Orthologs, paralogs, and evolutionary genomics. (Annual Review. Genet.)
11. Theiben, 2002. Orthology: Secret life of genes. (Nature)
12. Sonnhammer and Koonin, 2002. Orthology, paralogy and proposed classification for paralog subtypes. (TIGs)
13. Fitch, 2000. Homology: a personal view of some of the problems. (TIGs)

1. Hellmuth et al., 2015. Phylogenomics with paralogs. (PNAS)
2. Ostlund et al., 2010. InParanoid 7: new algorithms and tools for eukaryotic orthology analsyis. (NAR)
3. Peterson et al., 2009. Evolutionary constraints on structural similarity in orthologs and paralogs. (Protein Science)
4. Altenhoff and Dessimoz, 2009. Phylogenetic and functional assessment of orthologs inference projects and methods. (PLoS Computational Biology)
5. Chen et al., 2007. Assessing performance of orthology detection strategies applied to eukaryotic genomes. (PLoS ONE)
6. Hulsen et al., 2005. Benchmarking ortholog identification methods using functional genomics data. (Genome Biology)
7. Li et al., 2003. OrthoMCL: Indentificaiotn of ortholog groups for eukaryotic genomes. (Genome Research)

1. Powell et al., 2014. eggNOG v4.0: nested orhtolog inference across 3686 organisms. (NARs)
2. Nehrt et al., 2011. Testing teh ortholog conjecture with comparative functional genomic data from mammals. (PLoS Computational Biology)