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


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.

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.

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.