Epitope prediction
Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions
Yohan Kim, John Sidney, Søren Buus, Alessandro Sette, Morten Nielsen, and Bjoern Peters
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4111843/
Gapped sequence alignment using artificial neural networks: application to the MHC class I system.
Andreatta M, Nielsen M
Bioinformatics (2016) Feb 15;32(4):511-7
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations.
Nielsen M, Lundegaard C, Worning P, Lauemoller SL, Lamberth K, Buus S, Brunak S, Lund O.
Protein Sci., (2003) 12:1007-17
The immune epitope database (IEDB) 3.0.
Vita R1, Overton JA2, Greenbaum JA3, Ponomarenko J4, Clark JD5, Cantrell JR5, Wheeler DK5, Gabbard JL6, Hix D6, Sette A2, Peters B2.
Leishmania- macrophage interaction
1. Future Microbiol. 2015;10(1):111-29. doi: 10.2217/fmb.14.103.
Leishmania and the macrophage: a multifaceted interaction.
Trypanosomatidae evolution
Kinetoplastid Biol Dis. 2003 Oct 28;2(1):15.
Molecular phylogenetics of Trypanosomatidae: contrasting results from 18S rRNA and protein phylogenies.
GP63 gene family
2. Infect Immun. 2003 Oct;71(10):5739-49.
gp63 homologues in Trypanosoma cruzi: surface antigens with metalloprotease activity and a possible role in host cell infection.
3. J Biol Chem. 2002 Mar 15;277(11):8802-9. Epub 2002 Jan 2.
Extracellular release of the glycosylphosphatidylinositol (GPI)-linked Leishmania surface metalloprotease, gp63, is independent of GPI phospholipolysis: implications for parasite virulence.
4. Front Cell Infect Microbiol. 2012 May 16;2:72. doi: 10.3389/fcimb.2012.00072. eCollection 2012.
Impact of Leishmania metalloprotease GP63 on macrophage signaling.
Trans-sialidade gene family
Pathway evolution
Phys Life Rev. 2009 Mar;6(1):23-52. doi: 10.1016/j.plrev.2008.12.003. Epub 2009 Jan 8.
Origin and evolution of metabolic pathways.
Res Microbiol. 2009 Sep;160(7):502-12. doi: 10.1016/j.resmic.2009.05.001. Epub 2009 May 22.
Origin and evolution of operons and metabolic pathways.
The Origin and Evolution of Metabolic Pathways: Why and How did Primordial Cells Construct Metabolic Routes
Plant Physiol. 2015 Mar;167(3):872-86. doi: 10.1104/pp.114.247403. Epub 2015 Jan 5.
Insights into the origin and evolution of the plant hormone signaling machinery.
BMC Evol Biol. 2009 Oct 13;9:249. doi: 10.1186/1471-2148-9-249.
Origin and evolution of the Notch signalling pathway: an overview from eukaryotic genomes.
Gazave E1, Lapébie P, Richards GS, Brunet F, Ereskovsky AV, Degnan BM, Borchiellini C, Vervoort M, Renard E.
BMC Evol Biol. 2009 Feb 21;9:44. doi: 10.1186/1471-2148-9-44.
Phylogenetic diversity of stress signalling pathways in fungi.
The origin and evolution of the signaling pathway of the plant hormone cytokinin
http://www.diss.fu-berlin.de/diss/servlets/MCRFileNodeServlet/FUDISS_derivate_000000015330/Gruhn_Dissertation_online.pdf
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