- Jensen RA (2001) Orthologs and paralogs - we
need to get it right. Genome Biol 2(8):inter-
actions1002.1–interactions1002.3. https://
doi.org/10.1186/gb-2001-2-8-
interactions1002
- Baldauf SL (2003) Phylogeny for the faint of
heart: a tutorial. Trends Genet 19:345–351.
https://doi.org/10.1016/S0168-9525(03)
00112-4
- Koonin EV (2005) Orthologs, paralogs, and
evolutionary genomics. Annu Rev Genet
39:309–338. https://doi.org/10.1146/
annurev.genet.39.073003.114725
- Dolinski K, Botstein D (2007) Orthology and
functional conservation in eukaryotes. Annu
Rev Genet 41:465–507.https://doi.org/10.
1146/annurev.genet.40.110405.090439
- Studer RA, Robinson-Rechavi M (2009) How
confident can we be that orthologs are similar,
but paralogs differ? Trends Genet 25:210–216.
https://doi.org/10.1016/j.tig.2009.03.004
- Nehrt NL, Clark WT, Radivojac P, Hahn MW
(2011) Testing the ortholog conjecture with
comparative functional genomic data from
mammals. PLoS Comput Biol 7(6):
e1002073.https://doi.org/10.1371/journal.
pcbi.1002073
- Gabaldo ́n T, Koonin EV (2013) Functional
and evolutionary implications of gene orthol-
ogy. Nat Rev Genet 14:360–366.https://doi.
org/10.1038/nrg3456
- Roustan V, Jain A, Teige M et al (2016) An
evolutionary perspective of AMPK-TOR sig-
naling in the three domains of life. J Exp Bot
67:3897–3907. https://doi.org/10.1093/
jxb/erw211
- Kanehisa M, Goto S (2000) KEGG: kyoto
encyclopaedia of genes and genomes. Nucleic
Acids Res 28:27–30. https://doi.org/10.
1093/nar/28.1.27
- Nordberg H, Cantor M, Dusheyko S et al
(2014) The genome portal of the department
of energy joint genome institute: 2014
updates. Nucleic Acids Res 42(Database
issue):D26–D31. https://doi.org/10.1093/
nar/gkt1069
- Bateman A, Martin MJ, O’Donovan C et al
(2015) UniProt: a hub for protein informa-
tion. Nucleic Acids Res 43:D204–D212.
https://doi.org/10.1093/nar/gku989
- Herrero J, Muffato M, Beal K et al (2016)
Ensembl comparative genomics resources.
Database 2016:baw053.https://doi.org/10.
1093/database/bav096
- Sonnhammer ELL, Gabaldon T, Sousa Da
Silva AW et al (2014) Big data and other chal-
lenges in the quest for orthologs.
Bioinformatics 30:2993–2998. https://doi.
org/10.1093/bioinformatics/btu492
- Kelder T, Van Iersel MP, Hanspers K et al
(2012) WikiPathways: building research com-
munities on biological pathways. Nucleic Acids
Res 40(Database issue):D1301–D1307.
https://doi.org/10.1093/nar/gkr1074
- Fabregat A, Sidiropoulos K, Garapati P et al
(2016) The reactome pathway knowledgebase.
Nucleic Acids Res 44:D481–D487.https://
doi.org/10.1093/nar/gkv1351
- Cerami EG, Gross BE, Demir E et al (2011)
Pathway commons, a web resource for
biological pathway data. Nucleic Acids Res 39
(Database):D685–D690.https://doi.org/10.
1093/nar/gkq1039
- Sonnhammer ELL, O ̈stlund G (2015) InPara-
noid 8: orthology analysis between 273 pro-
teomes, mostly eukaryotic. Nucleic Acids Res
43:D234–D239. https://doi.org/10.1093/
nar/gku1203
- Altenhoff AM, Boeckmann B, Capella-
Gutierrez S et al (2016) Standardized bench-
marking in the quest for orthologs. Nat Meth-
ods 13:425–430.https://doi.org/10.1038/
nmeth.3830
- Altenhoff AM, Sˇunca N, Glover N et al (2015)
The OMA orthology database in 2015: func-
tion predictions, better plant support, synteny
view and other improvements. Nucleic Acids
Res 43:D240–D249. https://doi.org/10.
1093/nar/gku1158
- Zdobnov EM, Tegenfeldt F, Kuznetsov D et al
(2016) OrthoDB v9.1: cataloging evolution-
ary and functional annotations for animal, fun-
gal, plant, archaeal, bacterial and viral
orthologs. Nucleic Acids Res 45(D1):
D744–D749.https://doi.org/10.1093/nar/
gkw1119
- Ebersberger I, Strauss S, von Haeseler A
(2009) HaMStR: profile hidden markov
model based search for orthologs in ESTs.
BMC Evol Biol 9:157.https://doi.org/10.
1186/1471-2148-9-157
- Ebersberger I, Simm S, Leisegang MS et al
(2014) The evolution of the ribosome biogen-
esis pathway from a yeast perspective. Nucleic
Acids Res 42:1509–1523.https://doi.org/10.
1093/nar/gkt1137
- Jones P, Binns D, Chang HYet al (2014) Inter-
ProScan 5: genome-scale protein function clas-
sification. Bioinformatics 30:1236–1240.
https://doi.org/10.1093/bioinformatics/
btu031
- Finn RD, Mistry J, Tate J et al (2010) The
Pfam protein families database. Nucleic Acids
Res 38:D211–D222. https://doi.org/10.
1093/nar/gkm960
Tracing AMPK Evolution 141
