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Bold: Members of the Serohijos lab
*Corresponding author #Equal contribution |
2022
40. Gencel M, Cofino GM, Hui C, Sahaf Z, Gauthier L, Tsang D, Philpott D, Ramathan S, Menendez A, Bershtein S, Serohijos AWR*
Intra- and inter-species interactions drive early phases of invasion in mice gut microbiota
(2022) Submitted.
Biorxiv
Intra- and inter-species interactions drive early phases of invasion in mice gut microbiota
(2022) Submitted.
Biorxiv
2021
39. N'Guessan A, Brito IL, Serohijos AWR*, Shapiro BJ*
Mobile gene sequence evolution within individual human gut microbiomes is better explained by gene-specific than host-specific selective pressures.
(2021) Genome Biol Evol., in press doi: 10.1093/gbe/evab142.
Mobile gene sequence evolution within individual human gut microbiomes is better explained by gene-specific than host-specific selective pressures.
(2021) Genome Biol Evol., in press doi: 10.1093/gbe/evab142.
38. Razban RM, Dasmeh P, Serohijos AWR, Shakhnovich EI*
Avoidance of protein unfolding constrains protein stability in long-term evolution
(2021) Biophys J. 120(12):2413-2424. doi: 10.1016/j.bpj.2021.03.042.
Avoidance of protein unfolding constrains protein stability in long-term evolution
(2021) Biophys J. 120(12):2413-2424. doi: 10.1016/j.bpj.2021.03.042.
2020
37. J Lerner, M Manhart, W Jasinska, L Gauthier, A Serohijos, S Bershtein*
Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution
(2020) Nature Eco & Evol. doi: 10.1038/s41559-020-1103-z. (PDF)
Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution
(2020) Nature Eco & Evol. doi: 10.1038/s41559-020-1103-z. (PDF)
36. L Gauthier, Stynen B, A Serohijos*, SW Michnick*
Genetics’ piece of the PI: Inferring the origin of complex traits and diseases from proteome-wide protein-protein interaction dynamics
(2020) Bioessays , 42(2):e1900169. (PDF)
Genetics’ piece of the PI: Inferring the origin of complex traits and diseases from proteome-wide protein-protein interaction dynamics
(2020) Bioessays , 42(2):e1900169. (PDF)
2019
35. M Mariani , P Dasmeh , A Fortin , E Caron , M Kalamujic , AN Harrison , DM Kasumba , S Cervantes-Ortiz , E Mukawera , A Serohijos , N Grandvaux*
The Combination of IFN β and TNF Induces an Antiviral and Immunoregulatory Program via Non-Canonical Pathways Involving STAT2 and IRF9
(2019) Cells 8(8). pii: E919. (PDF)
The Combination of IFN β and TNF Induces an Antiviral and Immunoregulatory Program via Non-Canonical Pathways Involving STAT2 and IRF9
(2019) Cells 8(8). pii: E919. (PDF)
34. S Khoury, M Piltonen, A-T Ton, T Cole, A Samoshkin, S Smith, I Belfer, G Slade, R Fillingim, J Greenspan, R Ohrbach, W Maixner, G Neely, A Serohijos, L Diatchenko*
A functional missense substitution in Dopa Decarboxylase worsens somatic symptoms through the serotonin pathway
(2019) Ann Neurol. 86(2):168-180. (PDF)
A functional missense substitution in Dopa Decarboxylase worsens somatic symptoms through the serotonin pathway
(2019) Ann Neurol. 86(2):168-180. (PDF)
33. L Gauthier, R Di Franco, A Serohijos*,
SodaPop: A computational suite for simulating the dynamics of asexual populations on protein fitness landscapes
(2019) Bioinformatics 35 (20), 4053-4062
SodaPop: A computational suite for simulating the dynamics of asexual populations on protein fitness landscapes
(2019) Bioinformatics 35 (20), 4053-4062
2018
32. P Dasmeh, A Serohijos*
Estimating the contribution of folding stability to non-specific epistasis in protein evolution
(2018) Proteins. 86(12):1242-1250. doi: 10.1002/prot.25588.
Estimating the contribution of folding stability to non-specific epistasis in protein evolution
(2018) Proteins. 86(12):1242-1250. doi: 10.1002/prot.25588.
31. A Rotem#, A Serohijos#, C Chang, J Wolfe, A Fischer, T Mehoke, H Zhang, Y Tao, L Ung, J-M Choi, A Kolawole, S Koehler, S Wu, P Thielen, N Cui, P Demirev, N Giacobbi, T Julian, K Schwab, J Lin, T Smith, J Pipas, C Wobus, A Feldman, D Weitz*, E Shakhnovich*
“Evolution on the biophysical fitness landscape of an RNA virus”
(2018) Mol Biol Evol. , 35(10):2390-2400. doi: 10.1093/molbev/msy131.
30. E Klein, D Blumenkrantz, A Serohijos, E Shakhnovich, J-M Choi, J Rodrigues, B Smith, A Lane, A Feldman, A Pekosz*,
“Stability of the influenza hemagglutinin protein correlates with fitness and seasonal evolutionary dynamics"
(2018) mSphere 3:e00554-17. doi.org/10.1128/mSphereDirect.00554-17
2017
29. P. Dasmeh#, E. Girard#, A Serohijos*
"Highly expressed genes evolve under strong epistasis from a proteome-wide scan in E. coli"
(2017) Scientific Reports 7: 15844 | DOI:10.1038/s41598-017-16030-z . (PDF)
"Highly expressed genes evolve under strong epistasis from a proteome-wide scan in E. coli"
(2017) Scientific Reports 7: 15844 | DOI:10.1038/s41598-017-16030-z . (PDF)
28. G Desrochers, L Cappadocia, M Lussier-Price, A-T Ton, R Ayoubi, A Serohijos, JG Omichinski, A Angers*,
"Molecular Basis of Interactions Between SH3 Domain-Containing Proteins and the Proline-Rich Region of the Ubiquitin Ligase Itch"
(2017) J. Biol. Chem. 292(15):6325-6338. (PDF)
"Molecular Basis of Interactions Between SH3 Domain-Containing Proteins and the Proline-Rich Region of the Ubiquitin Ligase Itch"
(2017) J. Biol. Chem. 292(15):6325-6338. (PDF)
27. S Bershtein, A Serohijos, EI Shakhnovich*,
"Bridging the physical scales in evolutionary biology: From protein sequence space to fitness of organisms and populations"
(2017) Curr. Opin. Struct. Biol. 42: 31-40. (PDF)
"Bridging the physical scales in evolutionary biology: From protein sequence space to fitness of organisms and populations"
(2017) Curr. Opin. Struct. Biol. 42: 31-40. (PDF)
2016
26. N Cheron#, A Serohijos#, D Lucarelli, S Murphy, J Lin, AB Feldman and EI Shakhnovich,
“Evolutionary dynamics of viral escape under antibody stress: A biophysical model”
(2016) Protein Sci. doi: 10.1002/pro.2915. [#Equal contribution] (PDF)
“Evolutionary dynamics of viral escape under antibody stress: A biophysical model”
(2016) Protein Sci. doi: 10.1002/pro.2915. [#Equal contribution] (PDF)
2015
25. S Bershtein#, A Serohijos#, S Bhattacharyya, M Manhart, J-M Choi, W. Mu, J Zhou, EI Shakhnovich,
"Protein homeostasis imposes a barrier to the functional integration of horizontally transferred genes in bacteria"
(2015) PLoS Genetics 11(10): e1005612. [#Equal contribution] (PDF)
"Protein homeostasis imposes a barrier to the functional integration of horizontally transferred genes in bacteria"
(2015) PLoS Genetics 11(10): e1005612. [#Equal contribution] (PDF)
24. H Zhang, SK Cockrell, AO Kolawole, Assaf Rotem, A Serohijos, TS Mehoke, JS Lin, NS Giacobbi, EI Shakhnovich, AB Feldman, DA Weitz, CE Wobus, and JM Pipas
“Isolation and analysis of rare norovirus recombinants from co-infected mice using droplet-based microfluidics”
(2015) J Virology 89(15):7722-34. (PDF)
“Isolation and analysis of rare norovirus recombinants from co-infected mice using droplet-based microfluidics”
(2015) J Virology 89(15):7722-34. (PDF)
23. J.M. Choi, A Serohijos, S. Murphy, D. Lucarelli, L. Lofranco, A.B. Feldman and E.I. Shakhnovich,
“Minimalistic Predictor of Protein Binding Energy: Contribution of Solvation Factor to Protein Binding”
(2015) Biophys J. 108(4):795-8. (PDF)
“Minimalistic Predictor of Protein Binding Energy: Contribution of Solvation Factor to Protein Binding”
(2015) Biophys J. 108(4):795-8. (PDF)
2014
22. P. Dasmeh*,#, A Serohijos*,#, K. Kepp, E.I. Shakhnovich,
"The influence of selection for folding stability on dN/dS estimations"
(2014), Genome Biology and Evolution. 6 (10): 2956-2967. [*Equal contribution; #Corresponding authors] (PDF)
"The influence of selection for folding stability on dN/dS estimations"
(2014), Genome Biology and Evolution. 6 (10): 2956-2967. [*Equal contribution; #Corresponding authors] (PDF)
21. A Serohijos and E.I. Shakhnovich,
“Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics”
(2014), Curr. Opin. Struct. Biol., 26: 84–91. (PDF)
“Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics”
(2014), Curr. Opin. Struct. Biol., 26: 84–91. (PDF)
20. E.Y. Klein, A Serohijos, J.M. Choi, E.I. Shakhnovich, and A. Pekoz,
“Influenza A H1N1 Pandemic Strain Evolution – divergence and the potential for antigenic drift variants”
(2014) PLoS One 9(4):e93632. (PDF)
“Influenza A H1N1 Pandemic Strain Evolution – divergence and the potential for antigenic drift variants”
(2014) PLoS One 9(4):e93632. (PDF)
19. A Serohijos and E.I. Shakhnovich,
“Contribution of selection for protein folding stability in shaping the patterns of polymorphisms in coding regions”
(2014) Mol. Biol & Evol., 31(1):165-76. (PDF)
“Contribution of selection for protein folding stability in shaping the patterns of polymorphisms in coding regions”
(2014) Mol. Biol & Evol., 31(1):165-76. (PDF)
2013
18. P. Dasmeh, A Serohijos, K. Kepp, E.I. Shakhnovich,
“Positively selected sites in cetacean myoglobin increase folding stability”
(2013) PLoS Computational Biology, 9 (3), e1002929. (PDF)
“Positively selected sites in cetacean myoglobin increase folding stability”
(2013) PLoS Computational Biology, 9 (3), e1002929. (PDF)
17. A Serohijos, S.Y.R. Lee, E.I. Shakhnovich,
“Highly abundant proteins favor more stable 3D structures in yeast”
(2013), Biophysical J, 104: L01-L03 (2013) [Cover Article]. (PDF)
“Highly abundant proteins favor more stable 3D structures in yeast”
(2013), Biophysical J, 104: L01-L03 (2013) [Cover Article]. (PDF)
16. S. Bershtein, W. Mu, A Serohijos, E.I. Shakhnovich,
“Protein quality control shapes the fitness effects of mutations in E. coli.”
(2013) Molecular Cell, 49: 1-12. (PDF)
“Protein quality control shapes the fitness effects of mutations in E. coli.”
(2013) Molecular Cell, 49: 1-12. (PDF)
2012
15. A Serohijos, Z. Rimas, E.I. Shakhnovich,
“Protein biophysics explains why highly abundant proteins evolve slowly”
(2012) Cell Reports, 2(2): 249-256. (PDF)
“Protein biophysics explains why highly abundant proteins evolve slowly”
(2012) Cell Reports, 2(2): 249-256. (PDF)
14. M.F. Mabanglo, A Serohijos, C.D. Poulter,
“The Streptomyces-produced antibiotic fosfomycin is a promiscuous substrate of Archaeal isopentenyl phosphate kinase”
(2012) Biochemistry, 51(4): 917-25. (PDF)
“The Streptomyces-produced antibiotic fosfomycin is a promiscuous substrate of Archaeal isopentenyl phosphate kinase”
(2012) Biochemistry, 51(4): 917-25. (PDF)
2011
13. A Serohijos, S. Yin, F. Ding, J. Gauthier, D.G. Gibson, W. Maixner, N.V. Dokholyan, L. Diatchenko,
“Structural basis for μ-opioid receptor binding and activation”
(2011) Structure, 19: 1-8. (PDF)
“Structural basis for μ-opioid receptor binding and activation”
(2011) Structure, 19: 1-8. (PDF)
12. D. Tsygankov, A Serohijos, N.V. Dokholyan, and T.C. Elston,
"A physical model reveals the mechanochemistry responsible for dynein’s processive motion"
(2011) Biophysical J, 101(1): 144-50. (PDF)
"A physical model reveals the mechanochemistry responsible for dynein’s processive motion"
(2011) Biophysical J, 101(1): 144-50. (PDF)
11. A Serohijos, P.H. Thibodeau, and N.V. Dokholyan,
“Molecular modeling tools and approaches for CFTR and cystic fibrosis.”
(2011) Methods Mol Biol. 741: 347-63. (PDF)
“Molecular modeling tools and approaches for CFTR and cystic fibrosis.”
(2011) Methods Mol Biol. 741: 347-63. (PDF)
2009
10. D. Tsygankov, A Serohijos, N.V. Dokholyan, and T.C. Elston,
“Kinetic models for the coordinated stepping of cytoplasmic dynein”
(2009) J. Chem. Phys., 130: 025101. (PDF)
“Kinetic models for the coordinated stepping of cytoplasmic dynein”
(2009) J. Chem. Phys., 130: 025101. (PDF)
9. A Serohijos, D. Tsygankov, S. Liu, T.C. Elston, and N.V. Dokholyan,
“Multiscale approaches for studying energy transduction in dynein”
(2009) Phys. Chem. Chem. Phys. 11:4840-4850. (PDF)
“Multiscale approaches for studying energy transduction in dynein”
(2009) Phys. Chem. Chem. Phys. 11:4840-4850. (PDF)
8. S. Ramachandran, A Serohijos, L. Xu, G. Meissner, and N.V. Dokholyan,
“A structural model of the pore-forming region of the skeletal muscle ryanodine receptor (RyR1)”
(2009) PLoS Computational Biology, 5:e1000367. (PDF)
“A structural model of the pore-forming region of the skeletal muscle ryanodine receptor (RyR1)”
(2009) PLoS Computational Biology, 5:e1000367. (PDF)
2008
7. Y. Chen*, F. Ding*, H. Nie*, A Serohijos*, S. Sharma*, K.C. Wilcox*, S. Yin*, and N.V. Dokholyan*,
"Protein folding: then and now"
(2008) Archives of Biochemistry and Biophysics, 469: 4-19. [*Equal contribution] (PDF)
"Protein folding: then and now"
(2008) Archives of Biochemistry and Biophysics, 469: 4-19. [*Equal contribution] (PDF)
6. A Serohijos*, T. Hegedus*, J. Riordan, and N.V. Dokholyan,
“Diminished self-chaperoning activity of the DF508 mutant CFTR results in protein misfolding”
(2008) PLoS Computational Biology, 4: e1000008. [*Equal contribution] (PDF)
“Diminished self-chaperoning activity of the DF508 mutant CFTR results in protein misfolding”
(2008) PLoS Computational Biology, 4: e1000008. [*Equal contribution] (PDF)
5. T. Hegedus, A Serohijos, N.V. Dokholyan, L. He, J.R. Riordan,
“Computational studies reveal phosphorylation dependent changes in the unstructured R domain of CFTR”
(2008) J. Mol. Biol., 378: 1052-1063. (PDF)
“Computational studies reveal phosphorylation dependent changes in the unstructured R domain of CFTR”
(2008) J. Mol. Biol., 378: 1052-1063. (PDF)
4. J. Hao*, A Serohijos*, G. Newton, G. Tassone, D.C. Sgroi, N.V. Dokholyan, and J.P. Basilion,
“Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers”
(2008) PLoS Computational Biology, 4: e1000138. [*Equal contribution] (PDF)
“Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers”
(2008) PLoS Computational Biology, 4: e1000138. [*Equal contribution] (PDF)
3. L. He, A.A. Aleksandrov, A Serohijos, T. Hegedus, L.A. Aleksandrov, L. Cui, N.V. Dokholyan J.R. Riordan,
“Multiple membrane-cytoplasmic domain contacts in the cystic fibrosis transmembrane conductance regulator (CFTR) mediate regulation of channel gating”
(2008) J. Biol. Chem., 283: 26383-26390. (PDF)
“Multiple membrane-cytoplasmic domain contacts in the cystic fibrosis transmembrane conductance regulator (CFTR) mediate regulation of channel gating”
(2008) J. Biol. Chem., 283: 26383-26390. (PDF)
2. A Serohijos, T. Hegedus, A.A. Aleksandrov, L. He, L. Cui, N.V. Dokholyan, J.R. Riordan, “Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function” (2008) Proc. Natl. Acad. Sci. USA, 105: 3256-3261. (PDF)
2006
1. A Serohijos, Y. Chen, F. Ding, T.C. Elston, and N.V. Dokholyan, “A structural model reveals energy transduction in dynein” (2006) Proc. Natl. Acad. Sci. USA, 103: 18540-18545. (PDF)
Patents
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“Mu-opioid receptor binding compounds” L Diatchenko, W Maixner, NV Dokholyan, F Ding, A Serohijos, S Yin, International Patent Application PCT/US12/40168 May 31, 2012; U.S. Provisional Patent Application No. 61/491,828 filed May 31, 2011
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