Publications
A phylogenetic rate parameter indicates different sequence divergence patterns in orthologs and paralogs
Ahrens, JB, Teufel AI, Siltberg-Liberles, J.
J Mol Evol. Accepted
Potential RNA-dependent RNA polymerase inhibitors as prospective therapeutics against
SARS-CoV-2.
Pokhrel R, Chapagain P, Siltberg-Liberles J.
J Med Microbiol. 2020 Jun;69(6):864-873. doi: 10.1099/jmm.0.001203
Exploring evolutionary constraints in the proteomes of Zika, Dengue and other flaviviruses to find fitness critical sites
Nunez-Castilla J, Rahaman, J, Ahrens, JB, Balbin, CA, Siltberg-Liberles, J.
J Mol Evol. 2020; 88(4):399-414. doi: 10.1007/s00239-020-09941-5
An easy protocol for evolutionary analysis of IDPs
Nunez-Castilla, J & Siltberg-Liberles, J.
Methods Mol Biol. 2020;2141:147-177. doi: 10.1007/978-1-0716-0524-0_7
Large-scale Analyses of Site-specific Evolutionary Rates across Eukaryote Proteomes Reveal Confounding Interactions between Intrinsic Disorder, Secondary Structure and Functional Domains
Ahrens, JB, Rahaman, J, Siltberg-Liberles, J.
Genes. 2018; 9(11), 553. doi.org/10.3390/genes9110553
Interaction of Peptide Aptamers with Prion Protein Central Domain Promotes α-Cleavage of PrPC
Corda, E, Du, X, Shim, SY, Klein AN, Siltberg-Liberles J, Gilch S.
Mol Neurobiol. 2018; 55: 7758. doi.org/10.1007/s12035-018-0944-9
Evolution of Intrinsic Disorder in Eukaryotic Proteins
Ahrens JB, Nunez-Castilla J, Siltberg-Liberles J.
Cell Mol Life Sci. 2017; 74(17):3163-3174. doi: 10.1007/s00018-017-2559-0
Avoiding regions symptomatic of conformational and functional flexibility to identify antiviral targets in current and future coronaviruses.
Rahaman J, Siltberg-Liberles J.
Genome Biol Evol. 2016; 8 (11): 3471-3484. doi: 10.1093/gbe/evw246
Paralog-specific Patterns of Structural Disorder and Phosphorylation in the Vertebrate SH3-SH2-Tyrosine Kinase Protein Family.
Dos Santos HG, Siltberg-Liberles J.
Genome Biol Evol. 2016; 8 (9):2806-2825. doi: 10.1093/gbe/evw194
The Nuanced Interplay of Intrinsic Disorder and other Structural Properties Driving Protein Evolution.
Ahrens J, Dos Santos HG, Siltberg-Liberles J.
Mol Biol Evol. 2016; 33 (9): 2248-2256. doi: 10.1093/molbev/msw092
Functional diversification after gene duplication: paralog specific regions of structural disorder and phosphorylation in p53, p63, and p73.
Dos Santos HG, Nunez-Castilla J, Siltberg-Liberles J.
PLoS ONE. 2016; 11(3): e0151961. doi: 10.1371/journal.pone.0151961
Engineering adenylate cyclases regulated by near-infrared window light.
Ryu MH, Kang IH, Nelson MD, Jensen TM, Lyuksyutova AI, Siltberg-Liberles J, Raizen DM, Gomelsky M.
PNAS. 2014; 111(28):10167-10172.
Did the prion protein become vulnerable to misfolding after an evolutionary divide and conquer event?
Richmond K, Masterson P, Ortiz JF, Siltberg-Liberles J.
J Biomol Struct Dyn. 2014; 32(7):1074-1084.
Metazoan innovation: from aromatic amino acids to extracellular signaling.
Kutchko KM, Siltberg-Liberles J.
Amino Acids. 2013; 45(2):359-67.
Rapid evolutionary dynamics of structural disorder as a potential driving force for biological divergence in flaviviruses.
Ortiz JF, MacDonald ML, Masterson P, Uversky VN, Siltberg-Liberles J.
Genome Biol Evol. 2013; 5(3):504-13.
Evolution of structurally disordered proteins promotes neostructuralization.
Siltberg-Liberles J.
Mol Biol Evol. 2011; 28(1):59-62.
Natural and engineered photoactivated nucleotidyl cyclases for optogenetic applications.
Ryu MH, Moskvin OV, Siltberg-Liberles J, Gomelsky M.
J Biol Chem. 2010; 285(53):41501-8.
Piriform Spider Silk Sequences Reveal Unique Repetitive Elements.
Perry DJ, Bittencourt D, Siltberg-Liberles J, Rech EL, Lewis RV.
Biomacromolecules. 2010; 11(11) :3000-06.
Superstoichiometric binding of L-Phe to phenylalanine hydroxylase from Caenorhabditis elegans: evolutionary implications.
Flydal MI, Mohn TC, Pey AL, Siltberg-Liberles J, Teigen K, Martinez A.
Amino Acids. 2010; 39(5):1463-75.
Formyl peptide receptors are candidate chemosensory receptors in the vomeronasal organ.
Liberles SD, Horowitz LF, Kuang D, Contos JJ, Wilson KL, Siltberg-Liberles J, Liberles DA, Buck LB.
PNAS. 2009; 106(24):9842-7.
Searching distant homologs of the regulatory ACT domain in phenylalanine hydroxylase.
Siltberg-Liberles J, Martinez A.
Amino Acids. 2009; 36(2):235-49.
The phylogeny of the aromatic amino acid hydroxylases revisited by characterizing phenylalanine hydroxylase from Dictyostelium discoideum.
Siltberg-Liberles J, Steen IH, Svebak RM, Martinez A.
Gene. 2008; 427(1-2):86-92.
Allosteric mechanisms in ACT domain containing enzymes involved in amino acid metabolism.
Liberles JS, Thórólfsson M, Martínez A.
Amino Acids. 2005; 28(1):1-12.
A simple covarion-based approach to analyse nucleotide substitution rates.
Siltberg J and Liberles DA.
J. Evol. Biol. 2001; 15(4) :588-94.