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Items: 37


Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution.

Jasinska W, Manhart M, Lerner J, Gauthier L, Serohijos AWR, Bershtein S.

Nat Ecol Evol. 2020 Mar;4(3):437-452. doi: 10.1038/s41559-020-1103-z. Epub 2020 Feb 24.


Genetics' Piece of the PI: Inferring the Origin of Complex Traits and Diseases from Proteome-Wide Protein-Protein Interaction Dynamics.

Gauthier L, Stynen B, Serohijos AWR, Michnick SW.

Bioessays. 2020 Feb;42(2):e1900169. doi: 10.1002/bies.201900169. Epub 2019 Dec 18.


The Combination of IFN β and TNF Induces an Antiviral and Immunoregulatory Program via Non-Canonical Pathways Involving STAT2 and IRF9.

Mariani MK, Dasmeh P, Fortin A, Caron E, Kalamujic M, Harrison AN, Hotea DI, Kasumba DM, Cervantes-Ortiz SL, Mukawera E, Serohijos AWR, Grandvaux N.

Cells. 2019 Aug 17;8(8). pii: E919. doi: 10.3390/cells8080919.


A functional substitution in the L-aromatic amino acid decarboxylase enzyme worsens somatic symptoms via a serotonergic pathway.

Khoury S, Piltonen MH, Ton AT, Cole T, Samoshkin A, Smith SB, Belfer I, Slade GD, Fillingim RB, Greenspan JD, Ohrbach R, Maixner W, Neely GG, Serohijos AWR, Diatchenko L.

Ann Neurol. 2019 Aug;86(2):168-180. doi: 10.1002/ana.25521. Epub 2019 Jun 8.


SodaPop: a forward simulation suite for the evolutionary dynamics of asexual populations on protein fitness landscapes.

Gauthier L, Di Franco R, Serohijos AWR.

Bioinformatics. 2019 Oct 15;35(20):4053-4062. doi: 10.1093/bioinformatics/btz175.


Estimating the contribution of folding stability to nonspecific epistasis in protein evolution.

Dasmeh P, Serohijos AWR.

Proteins. 2018 Dec;86(12):1242-1250. doi: 10.1002/prot.25588. Epub 2018 Nov 9.


Evolution on the Biophysical Fitness Landscape of an RNA Virus.

Rotem A, Serohijos AWR, Chang CB, Wolfe JT, Fischer AE, Mehoke TS, Zhang H, Tao Y, Lloyd Ung W, Choi JM, Rodrigues JV, Kolawole AO, Koehler SA, Wu S, Thielen PM, Cui N, Demirev PA, Giacobbi NS, Julian TR, Schwab K, Lin JS, Smith TJ, Pipas JM, Wobus CE, Feldman AB, Weitz DA, Shakhnovich EI.

Mol Biol Evol. 2018 Oct 1;35(10):2390-2400. doi: 10.1093/molbev/msy131.


Stability of the Influenza Virus Hemagglutinin Protein Correlates with Evolutionary Dynamics.

Klein EY, Blumenkrantz D, Serohijos A, Shakhnovich E, Choi JM, Rodrigues JV, Smith BD, Lane AP, Feldman A, Pekosz A.

mSphere. 2018 Jan 3;3(1). pii: e00554-17. doi: 10.1128/mSphereDirect.00554-17. eCollection 2018 Jan-Feb.


Highly expressed genes evolve under strong epistasis from a proteome-wide scan in E. coli.

Dasmeh P, Girard É, Serohijos AWR.

Sci Rep. 2017 Nov 20;7(1):15844. doi: 10.1038/s41598-017-16030-z.


Molecular basis of interactions between SH3 domain-containing proteins and the proline-rich region of the ubiquitin ligase Itch.

Desrochers G, Cappadocia L, Lussier-Price M, Ton AT, Ayoubi R, Serohijos A, Omichinski JG, Angers A.

J Biol Chem. 2017 Apr 14;292(15):6325-6338. doi: 10.1074/jbc.M116.754440. Epub 2017 Feb 24.


Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations.

Bershtein S, Serohijos AW, Shakhnovich EI.

Curr Opin Struct Biol. 2017 Feb;42:31-40. doi: 10.1016/ Epub 2016 Oct 31. Review.


Evolutionary dynamics of viral escape under antibodies stress: A biophysical model.

Chéron N, Serohijos AW, Choi JM, Shakhnovich EI.

Protein Sci. 2016 Jul;25(7):1332-40. doi: 10.1002/pro.2915. Epub 2016 Mar 24.


Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria.

Bershtein S, Serohijos AW, Bhattacharyya S, Manhart M, Choi JM, Mu W, Zhou J, Shakhnovich EI.

PLoS Genet. 2015 Oct 20;11(10):e1005612. doi: 10.1371/journal.pgen.1005612. eCollection 2015 Oct.


Isolation and Analysis of Rare Norovirus Recombinants from Coinfected Mice Using Drop-Based Microfluidics.

Zhang H, Cockrell SK, Kolawole AO, Rotem A, Serohijos AW, Chang CB, Tao Y, Mehoke TS, Han Y, Lin JS, Giacobbi NS, Feldman AB, Shakhnovich E, Weitz DA, Wobus CE, Pipas JM.

J Virol. 2015 Aug;89(15):7722-34. doi: 10.1128/JVI.01137-15. Epub 2015 May 13.


Minimalistic predictor of protein binding energy: contribution of solvation factor to protein binding.

Choi JM, Serohijos AWR, Murphy S, Lucarelli D, Lofranco LL, Feldman A, Shakhnovich EI.

Biophys J. 2015 Feb 17;108(4):795-798. doi: 10.1016/j.bpj.2015.01.001.


The influence of selection for protein stability on dN/dS estimations.

Dasmeh P, Serohijos AW, Kepp KP, Shakhnovich EI.

Genome Biol Evol. 2014 Oct 28;6(10):2956-67. doi: 10.1093/gbe/evu223.


Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics.

Serohijos AW, Shakhnovich EI.

Curr Opin Struct Biol. 2014 Jun;26:84-91. doi: 10.1016/ Epub 2014 Jun 19. Review.


Influenza A H1N1 pandemic strain evolution--divergence and the potential for antigenic drift variants.

Klein EY, Serohijos AW, Choi JM, Shakhnovich EI, Pekosz A.

PLoS One. 2014 Apr 3;9(4):e93632. doi: 10.1371/journal.pone.0093632. eCollection 2014.


Contribution of selection for protein folding stability in shaping the patterns of polymorphisms in coding regions.

Serohijos AW, Shakhnovich EI.

Mol Biol Evol. 2014 Jan;31(1):165-76. doi: 10.1093/molbev/mst189. Epub 2013 Oct 11.


Positively selected sites in cetacean myoglobins contribute to protein stability.

Dasmeh P, Serohijos AW, Kepp KP, Shakhnovich EI.

PLoS Comput Biol. 2013;9(3):e1002929. doi: 10.1371/journal.pcbi.1002929. Epub 2013 Mar 7.


Highly abundant proteins favor more stable 3D structures in yeast.

Serohijos AW, Lee SY, Shakhnovich EI.

Biophys J. 2013 Feb 5;104(3):L1-3. doi: 10.1016/j.bpj.2012.11.3838.


Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness.

Bershtein S, Mu W, Serohijos AW, Zhou J, Shakhnovich EI.

Mol Cell. 2013 Jan 10;49(1):133-44. doi: 10.1016/j.molcel.2012.11.004. Epub 2012 Dec 6.


Protein biophysics explains why highly abundant proteins evolve slowly.

Serohijos AW, Rimas Z, Shakhnovich EI.

Cell Rep. 2012 Aug 30;2(2):249-56. doi: 10.1016/j.celrep.2012.06.022. Epub 2012 Aug 2.


The Streptomyces-produced antibiotic fosfomycin is a promiscuous substrate for archaeal isopentenyl phosphate kinase.

Mabanglo MF, Serohijos AW, Poulter CD.

Biochemistry. 2012 Jan 31;51(4):917-25. doi: 10.1021/bi201662k. Epub 2012 Jan 11.


Structural basis for μ-opioid receptor binding and activation.

Serohijos AW, Yin S, Ding F, Gauthier J, Gibson DG, Maixner W, Dokholyan NV, Diatchenko L.

Structure. 2011 Nov 9;19(11):1683-90. doi: 10.1016/j.str.2011.08.003.


A physical model reveals the mechanochemistry responsible for dynein's processive motion.

Tsygankov D, Serohijos AW, Dokholyan NV, Elston TC.

Biophys J. 2011 Jul 6;101(1):144-50. doi: 10.1016/j.bpj.2011.05.043.


Molecular modeling tools and approaches for CFTR and cystic fibrosis.

Serohijos AW, Thibodeau PH, Dokholyan NV.

Methods Mol Biol. 2011;741:347-63. doi: 10.1007/978-1-61779-117-8_23.


Multiscale approaches for studying energy transduction in dynein.

Serohijos AW, Tsygankov D, Liu S, Elston TC, Dokholyan NV.

Phys Chem Chem Phys. 2009 Jun 28;11(24):4840-50. doi: 10.1039/b902028d. Epub 2009 May 15. Review.


A structural model of the pore-forming region of the skeletal muscle ryanodine receptor (RyR1).

Ramachandran S, Serohijos AW, Xu L, Meissner G, Dokholyan NV.

PLoS Comput Biol. 2009 Apr;5(4):e1000367. doi: 10.1371/journal.pcbi.1000367. Epub 2009 Apr 24.


Kinetic models for the coordinated stepping of cytoplasmic dynein.

Tsygankov D, Serohijos AW, Dokholyan NV, Elston TC.

J Chem Phys. 2009 Jan 14;130(2):025101. doi: 10.1063/1.3050098.


Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers.

Hao J, Serohijos AW, Newton G, Tassone G, Wang Z, Sgroi DC, Dokholyan NV, Basilion JP.

PLoS Comput Biol. 2008 Aug 1;4(8):e1000138. doi: 10.1371/journal.pcbi.1000138.


Multiple membrane-cytoplasmic domain contacts in the cystic fibrosis transmembrane conductance regulator (CFTR) mediate regulation of channel gating.

He L, Aleksandrov AA, Serohijos AW, Hegedus T, Aleksandrov LA, Cui L, Dokholyan NV, Riordan JR.

J Biol Chem. 2008 Sep 26;283(39):26383-90. doi: 10.1074/jbc.M803894200. Epub 2008 Jul 25.


Diminished self-chaperoning activity of the DeltaF508 mutant of CFTR results in protein misfolding.

Serohijos AW, Hegedus T, Riordan JR, Dokholyan NV.

PLoS Comput Biol. 2008 Feb 29;4(2):e1000008. doi: 10.1371/journal.pcbi.1000008.


Computational studies reveal phosphorylation-dependent changes in the unstructured R domain of CFTR.

Hegedus T, Serohijos AW, Dokholyan NV, He L, Riordan JR.

J Mol Biol. 2008 May 16;378(5):1052-63. doi: 10.1016/j.jmb.2008.03.033. Epub 2008 Mar 26.


Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function.

Serohijos AW, Hegedus T, Aleksandrov AA, He L, Cui L, Dokholyan NV, Riordan JR.

Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3256-61. doi: 10.1073/pnas.0800254105. Epub 2008 Feb 27.


Protein folding: then and now.

Chen Y, Ding F, Nie H, Serohijos AW, Sharma S, Wilcox KC, Yin S, Dokholyan NV.

Arch Biochem Biophys. 2008 Jan 1;469(1):4-19. Epub 2007 Jun 8.


A structural model reveals energy transduction in dynein.

Serohijos AW, Chen Y, Ding F, Elston TC, Dokholyan NV.

Proc Natl Acad Sci U S A. 2006 Dec 5;103(49):18540-5. Epub 2006 Nov 22.

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