Publications

2022

Making change sustainable: Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) meeting review.

Toby I, Williams J, Lu G, Cai C, Crandall KA, Dinsdale EA, Drew J, Edgington NP, Goller CC, Grandgenett NF, Grant BJ, Hauser C, Johnson KA, Jones CJ, Jue NK, Jungck FR, Kerby J, Kleinschmit AJ, Miller KG, Morgan WR, Murdoch B, Noutsios G, Nunez-Castilla J, Pauley M, Pearson WR, Robertson SD, Robic S, Rosenwald A, Seah YM, Shofner M, Sierk M, Siltberg-Liberles J, Smith T, Stover NA, Tapprich W, Triplett EW, Ryder EF.

CourseSource. https://doi.org/10.24918/cs.2022.10. Meeting review.

Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins.

Nunez-Castilla J, Stebliankin V, Baral P, Balbin CA, Sobhan M, Cickovski T, Mondal AM, Narasimhan G, Chapagain P, Mathee K, Siltberg-Liberles J. 

Viruses. 2022; 14(7):1415. https://doi.org/10.3390/v14071415.

Comparative Analysis of Structural Features in SLiMs from Eukaryotes, Bacteria, and Viruses with Importance for Host-Pathogen Interactions.

Elkhaligy H, Balbin CA, Siltberg-Liberles J.

Pathogens. 2022; 11(5):583. https://doi.org/10.3390/pathogens11050583.

2021

Dynamic, but Not Necessarily Disordered, Human-Virus Interactions Mediated through SLiMs in Viral Proteins.

Elkhaligy H, Balbin CA, Gonzalez JL, Liberatore T, Siltberg-Liberles J.  

Viruses. 2021 Nov; 13(12):2369. https://doi.org/10.3390/v13122369.

 

2020

A Phylogenetic Rate Parameter Indicates Different Sequence Divergence Patterns in Orthologs and Paralogs.

Ahrens JB, Teufel AI, Siltberg-Liberles J.

J Mol Evol. 2020 Dec;88(10):720-730. doi: 10.1007/s00239-020-09969-7.

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 May;88(4):399-414. doi: 10.1007/s00239-020-09941-5.

An Easy Protocol for Evolutionary Analysis of Intrinsically Disordered Proteins.

Nunez-Castilla J, Siltberg-Liberles J.

Methods Mol Biol. 2020;2141:147-177. doi: 10.1007/978-1-0716-0524-0_7.

2018

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 (Basel). 2018 Nov 14;9(11):553. doi: 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 Oct;55(10):7758-7774. doi: 10.1007/s12035-018-0944-9.

2017

Evolution of intrinsic disorder in eukaryotic proteins.

Ahrens JB, Nunez-Castilla J, Siltberg-Liberles J.

Cell Mol Life Sci. 2017 Sep;74(17):3163-3174. doi: 10.1007/s00018-017-2559-0. Review.

2016

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 Dec 31;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 Sep 19;8(9):2806-25. 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 Sep;33(9):2248-56. 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 Mar 22;11(3):e0151961. doi: 10.1371/journal.pone.0151961. eCollection 2016.

2014

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.

Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):10167-72. doi: 10.1073/pnas.1324301111.

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):1074-84. doi: 10.1080/07391102.2013.809022.

2013

Metazoan innovation: from aromatic amino acids to extracellular signaling.

Kutchko KM, Siltberg-Liberles J.

Amino Acids. 2013 Aug;45(2):359-67. doi: 10.1007/s00726-013-1509-x.

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. doi: 10.1093/gbe/evt026.

2011

The evolution of protein structures and structural ensembles under functional constraint.

Siltberg-Liberles J, Grahnen JA, Liberles DA.

Genes (Basel). 2011 Oct 28;2(4):748-62. doi: 10.3390/genes2040748.

PMID: 24710290 Free PMC article.

Evolution of structurally disordered proteins promotes neostructuralization.

Siltberg-Liberles J.

Mol Biol Evol. 2011 Jan;28(1):59-62. doi: 10.1093/molbev/msq291.

2010

Natural and engineered photoactivated nucleotidyl cyclases for optogenetic applications.

Ryu MH, Moskvin OV, Siltberg-Liberles J, Gomelsky M.

J Biol Chem. 2010 Dec 31;285(53):41501-8. doi: 10.1074/jbc.M110.177600.

Piriform spider silk sequences reveal unique repetitive elements.

Perry DJ, Bittencourt D, Siltberg-Liberles J, Rech EL, Lewis RV.

Biomacromolecules. 2010 Nov 8;11(11):3000-6. doi: 10.1021/bm1007585.

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 Nov;39(5):1463-75. doi: 10.1007/s00726-010-0611-6.

2009

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.

Proc Natl Acad Sci U S A. 2009 Jun 16;106(24):9842-7. doi: 10.1073/pnas.0904464106.

Searching distant homologs of the regulatory ACT domain in phenylalanine hydroxylase.

Siltberg-Liberles J, Martinez A.

Amino Acids. 2009 Feb;36(2):235-49. doi: 10.1007/s00726-008-0057-2.

2008

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 Dec 31;427(1-2):86-92. doi: 10.1016/j.gene.2008.09.005.

2005

Allosteric mechanisms in ACT domain containing enzymes involved in amino acid metabolism.

Liberles JS, Thórólfsson M, Martínez A.

Amino Acids. 2005 Feb;28(1):1-12. doi: 10.1007/s00726-004-0152-y. Review.

2002

A simple covarion-based approach to analyse nucleotide substitution rates. 

Siltberg J, Liberles DA. 

J Evol Biol. 2002; 15(4):588-594. https://doi.org/10.1046/j.1420-9101.2002.00416.x