Publications

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1.           Ahrens JB, Teufel AI, & Siltberg-Liberles J. A Phylogenetic Rate Parameter Indicates Different Sequence Divergence Patterns in Orthologs and Paralogs. J Mol Evol. 2020;1–11.

2.           Pokhrel R, Chapagain P, & Siltberg-Liberles J. Potential RNA-dependent RNA polymerase inhibitors as prospective therapeutics against SARS-CoV-2. J Med Microbiol. 2020;69(6).

3.           Nunez-Castilla J, Rahaman J, Ahrens JB, Balbin CA, & Siltberg-Liberles J. Exploring Evolutionary Constraints in the Proteomes of Zika, Dengue, and Other Flaviviruses to Find Fitness-Critical Sites. J Mol Evol. 2020;88(4).

4.           Nunez-Castilla J, Siltberg-Liberles J. An easy protocol for evolutionary analysis of intrinsically disordered proteins. In: Methods in Molecular Biology. Humana Press Inc.; 2020. p. 147–77. (Book chapter)

5.           Ahrens JB, Rahaman J, & Siltberg-Liberles J. Large-scale analyses of site-specific evolutionary rates across eukaryote proteomes reveal confounding interactions between intrinsic disorder, secondary structure, and functional domains. Genes (Basel). 2018;9(11).

6.           Corda E, Du X, Shim SY, Klein AN, Siltberg-Liberles J, & Gilch S. Interaction of Peptide Aptamers with Prion Protein Central Domain Promotes α-Cleavage of PrPC. Mol Neurobiol. 2018;55(10).

7.           Ahrens JB, Nunez-Castilla J, & Siltberg-Liberles J. Evolution of intrinsic disorder in eukaryotic proteins. Cell Mol Life Sci. 2017;74(17). (Review)

8.           Rahaman J & Siltberg-Liberles J. Avoiding regions symptomatic of conformational and functional flexibility to identify antiviral targets in current and future coronaviruses. Genome Biol Evol. 2016;8(11):3471–84.

9.           Dos Santos HG & Siltberg-Liberles J. Paralog-Specific Patterns of Structural Disorder and Phosphorylation in the Vertebrate SH3–SH2–Tyrosine Kinase Protein Family. Genome Biol Evol. 2016 Sep;8(9):2806–25.

10.        Ahrens J, Dos Santos HG, & Siltberg-Liberles J. The Nuanced Interplay of Intrinsic Disorder and Other Structural Properties Driving Protein Evolution. Mol Biol Evol. 2016;33(9).

11.        Dos Santos HG, Nunez-Castilla J, & Siltberg-Liberles J. Functional Diversification after Gene Duplication: Paralog Specific Regions of Structural Disorder and Phosphorylation in p53, p63, and p73. PLoS One. 2016;11(3):e0151961.

12.        Ryu M-H, Kang I-H, Nelson MD, Jensen TM, Lyuksyutova AI, Siltberg-Liberles J, Raizen DM & Gomelsky M. Engineering adenylate cyclases regulated by near-infrared window light. Proc Natl Acad Sci U S A. 2014;111(28).

13.        Richmond K, Masterson P, Ortiz JF, & Siltberg-Liberles J. Did the prion protein become vulnerable to misfolding after an evolutionary divide and conquer event? J Biomol Struct Dyn. 2014;32(7).

14.        Kutchko KM & Siltberg-Liberles J. Metazoan innovation: From aromatic amino acids to extracellular signaling. Amino Acids. 2013;45(2).

15.        Ortiz JF, MacDonald ML, Masterson P, Uversky VN & Siltberg-Liberles J. Rapid evolutionary dynamics of structural disorder as a potential driving force for biological divergence in flaviviruses. Genome Biol Evol. 2013 Jan;5(3):504–13.

16.        Siltberg-Liberles J, Grahnen JA & Liberles DA. The Evolution of Protein Structures and Structural Ensembles Under Functional Constraint. Genes (Basel). 2011 Oct;2(4):748–62.  (Review)

17.        Siltberg-Liberles J. Evolution of structurally disordered proteins promotes neostructuralization. Mol Biol Evol. 2011 Jan;28(1):59–62.

18.        Ryu M-H, Moskvin OV, Siltberg-Liberles J & Gomelsky M. Natural and engineered photoactivated nucleotidyl cyclases for optogenetic applications. J Biol Chem. 2010;285(53).

19.        Perry DJ, Bittencourt D, Siltberg-Liberles J, Rech EL & Lewis R V. Piriform spider silk sequences reveal unique repetitive elements. Biomacromolecules. 2010 Nov 8;11(11):3000–6.

20.        Flydal MI, Mohn TC, Pey AL, Siltberg-Liberles J, Teigen K & Martinez A. Superstoichiometric binding of L-Phe to phenylalanine hydroxylase from Caenorhabditis elegans: Evolutionary implications. Amino Acids. 2010;39(5).

21.        Liberles SD, Horowitz LF, Kuang D, Contos JJ, Wilson KL, Siltberg-Liberles J, Liberles DA & Buck LB. Formyl peptide receptors are candidate chemosensory receptors in the vomeronasal organ. Proc Natl Acad Sci U S A. 2009;106(24).

22.        Siltberg-Liberles J & Martinez A. Searching distant homologs of the regulatory ACT domain in phenylalanine hydroxylase. Amino Acids. 2009;36(2).

23.        Siltberg-Liberles J, Steen IH, Svebak RM & Martinez A. The phylogeny of the aromatic amino acid hydroxylases revisited by characterizing phenylalanine hydroxylase from Dictyostelium discoideum. Gene. 2008;427(1–2).

24.        Liberles JS, Thórólfsson M & Martínez A. Allosteric mechanisms in ACT domain containing enzymes involved in amino acid metabolism. Amino Acids; 2005; 28(1):1-12.

25.        Siltberg J & Liberles DA. A simple covarion-based approach to analyse nucleotide substitution rates. J Evol Biol. 2002;15(4):588–94.