Pre-prints and Manuscripts in preparation
Syrlybaeva R, Strauch EM#, "One-sided design of protein-protein interaction motifs using deep learning", (biorxiv, in revision)
Publications
* contributed equally, # corresponding author
2024
Gonzalez KJ, Yim K, Boukhvalova MS, Kim S, Strauch EM#, Systematic computer-aided disulfide design as a general strategy to stabilize prefusion class I fusion proteins, Front Immunol. 2024 Jul 24;15:1406929. doi: 10.3389/fimmu.2024.1406929. eCollection 2024.PMID: 39114655
Gonzalez KJ, Criado M, Huang J, Lei Y, Mousa JJ, Tompkins SM, Strauch EM#, "A general computational design strategy for stabilizing class I viral fusion proteins", Nat Commun. 2024 Feb 13;15(1):1335. doi: 10.1038/s41467-024-45480-z., PMID: 38351001
2023
Bunkofske ME, Perumal N, White BE, Strauch EM, Tarleton RL, "Epitopes in the GPI signal peptide of Trypanosoma cruzi mucin proteins generate robust but delayed, nonprotective CD8+ T cell responses", J Immunol. 2023 Jan 4:ji2200723. doi: 10.4049/jimmunol.2200723. Online ahead of print.
2022
Linsky T*, Noble K*, Tobin A*, Crow R*, Carter L, Urbauer J, Baker D, Strauch EM#, “Sampling Structure and Sequence Space of Small Folds”, Nat Commun, 2022 Nov 22;13(1):7151. doi: 10.1038/s41467-022-34937-8.
Syrlybaeva R, Strauch EM#, "Deep learning of Protein Sequence Design of Protein-protein Interactions", Bioinformatics. 2022 Nov 15:btac733. doi: 10.1093/bioinformatics/btac733. Online ahead of print.
Tobin A*, Crow R*, Urusova D, Salinas ND, Carter L, Tolia NH, Strauch EM#, “Inhibition of a critical malaria host-pathogen interaction by a computationally designed inhibitor targeting Plasmodium vivax DBP”, Protein Sci. 2022 Nov 11;e4507. doi: 10.1002/pro.4507. Online ahead of print.
Cao L*, Coventry B*, Goreshnik I, Huang B, Lee S, Jude K, Markovic I, Walsh STR, Bennett N, Phal AA, Yang A, Kozodoy L, DeWitt M, Picton L, Miller L, Strauch EM, Halabiya S, Yang W, Hammerson B, Kadam R, Benard S, Stewart L, Wilson IA, Ruohola-Baker H, Schlessinger J, Savvides S, Garcia C, Baker D#, “Robust de novo design of protein binding proteins from target structural information alone” (Nature. 2022 Mar 24. doi: 10.1038/s41586-022-04654-9. Online ahead of print)
Singer JD#, Novotney S, Strickland D, Haddox HK, Leiby N, Rocklin GJ, Chow CM, Roy A, Bera AK, Motta FC, Cao L, Strauch EM, Chidyausiku T, Ford A, Ho E, Mackenzie CO, Eramian H, DiMaio F, Grigoryan G, Vaughn M, Stewart LJ, Baker D, Klavins E, "Large-scale design and refinement of stable proteins using sequence-only models", (PLoS One. 2022 Mar 14;17(3):e0265020. doi: 10.1371/journal.pone.0265020. eCollection 2022)
2021
Gonzalez KJ, Strauch EM#, "Decreased vaccine protection of egg-based influenza vaccine in the elderly could be associated with a non-hemagglutinin focused immunity", J Clin Invest. 2021 Aug 2;131(15):e151732. doi: 10.1172/JCI151732
Narkhede YB*, Gonzalez KJ*, Strauch EM#, Targeting viral surface proteins through structure-based design Viruses 2021, 13(7), 1320; https://doi.org/10.3390/v13071320
2020
Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, Chen RE, Carter L, Walls AC, Park YJ, Strauch EM, Stewart L, Diamond MS, Veesler D, Baker D. De novo design of picomolar SARS-CoV-2 miniprotein inhibitors., Science. 2020 Sep 9; eabd9909. doi: 10.1126/science.abd9909. Online ahead of print
Kim HW*, Alexander EletskyA*, Gonzales KJ, van der Wel H, Strauch EM, James H. Prestegard JH, West CM, “Skp1 Dimerization Conceals its F-box Protein Binding Site”, Biochemistry. 2020 Apr 13. doi: 10.1021/acs.biochem.0c00094. [Epub ahead of print]
2019
Dou J, Goreshnik I, Bryan C, Baker D, Strauch EM#, “Parallelized Identification of On- and Off-Target Protein Interaction”, Molecular Systems Design & Engineering, 2019, DOI: 10.1039/C9ME00118B
Anderson CE1, Buser JR, Fleming AM, Strauch EM, Ladd PD, Englund J, Baker D, Yager P., "An integrated device for the rapid and sensitive detection of the influenza hemagglutinin", Lab Chip. 2019 Feb 26;19(5):885-896.
# = corresponding author
* = author contributed equally
Selected publications from Eva's postdoctoral work
Strauch EM, Bernard S, La D, Bohn A, Nieusma T, Lee P, Garcia NK, Holstein C, Anderson CE, Hooper KA, Trenant M, Sheffler W, Bloom JD, Yager P, Lee KK, Ward A, Fuller D, Wilson IA, Baker D, “Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site”, Nat Biotechnol. 2017 Jul;35(7):667-671. doi: 10.1038/nbt.3907
Special reports in:
Holstein CA*, Anderson CE*, Strauch EM, Bennett S, Chevalier A, Nelson J, Fu E, Baker D, Yager P; Development of a Paper-Based Assay for Whole Influenza Virus Detection using a Computationally Designed Hemagglutinin Head Region Binder, Anal Chem. 2017 Jun 20;89(12):6608-6615. doi: 10.1021/acs.analchem.7b00769
Klein JC, Lajoie MJ, Schwartz JJ, Strauch EM, Nelson J, Baker B, Shendure J, “Multiplex pairwise assembly of array-derived DNA oligonucleotides”, Nucleic Acids Res. 2016 Mar 18;44(5):e43. doi: 10.1093
Strauch EM, Fleishman SJ, Baker D, ” Computational Design of a pH-sensitive IgG Binding Protein”, Proc Natl Acad Sci U S A., 2014 Jan 14;111(2):675-80, PMID: 24381156
For the complete list check on Pubmed
* = contributed equally
2024
Gonzalez KJ, Yim K, Boukhvalova MS, Kim S, Strauch EM#, Systematic computer-aided disulfide design as a general strategy to stabilize prefusion class I fusion proteins, Front Immunol. 2024 Jul 24;15:1406929. doi: 10.3389/fimmu.2024.1406929. eCollection 2024.PMID: 39114655
Gonzalez KJ, Criado M, Huang J, Lei Y, Mousa JJ, Tompkins SM, Strauch EM#, "A general computational design strategy for stabilizing class I viral fusion proteins", Nat Commun. 2024 Feb 13;15(1):1335. doi: 10.1038/s41467-024-45480-z., PMID: 38351001
- paper of the month by the International Society for Vaccines
2023
Bunkofske ME, Perumal N, White BE, Strauch EM, Tarleton RL, "Epitopes in the GPI signal peptide of Trypanosoma cruzi mucin proteins generate robust but delayed, nonprotective CD8+ T cell responses", J Immunol. 2023 Jan 4:ji2200723. doi: 10.4049/jimmunol.2200723. Online ahead of print.
2022
Linsky T*, Noble K*, Tobin A*, Crow R*, Carter L, Urbauer J, Baker D, Strauch EM#, “Sampling Structure and Sequence Space of Small Folds”, Nat Commun, 2022 Nov 22;13(1):7151. doi: 10.1038/s41467-022-34937-8.
Syrlybaeva R, Strauch EM#, "Deep learning of Protein Sequence Design of Protein-protein Interactions", Bioinformatics. 2022 Nov 15:btac733. doi: 10.1093/bioinformatics/btac733. Online ahead of print.
Tobin A*, Crow R*, Urusova D, Salinas ND, Carter L, Tolia NH, Strauch EM#, “Inhibition of a critical malaria host-pathogen interaction by a computationally designed inhibitor targeting Plasmodium vivax DBP”, Protein Sci. 2022 Nov 11;e4507. doi: 10.1002/pro.4507. Online ahead of print.
Cao L*, Coventry B*, Goreshnik I, Huang B, Lee S, Jude K, Markovic I, Walsh STR, Bennett N, Phal AA, Yang A, Kozodoy L, DeWitt M, Picton L, Miller L, Strauch EM, Halabiya S, Yang W, Hammerson B, Kadam R, Benard S, Stewart L, Wilson IA, Ruohola-Baker H, Schlessinger J, Savvides S, Garcia C, Baker D#, “Robust de novo design of protein binding proteins from target structural information alone” (Nature. 2022 Mar 24. doi: 10.1038/s41586-022-04654-9. Online ahead of print)
Singer JD#, Novotney S, Strickland D, Haddox HK, Leiby N, Rocklin GJ, Chow CM, Roy A, Bera AK, Motta FC, Cao L, Strauch EM, Chidyausiku T, Ford A, Ho E, Mackenzie CO, Eramian H, DiMaio F, Grigoryan G, Vaughn M, Stewart LJ, Baker D, Klavins E, "Large-scale design and refinement of stable proteins using sequence-only models", (PLoS One. 2022 Mar 14;17(3):e0265020. doi: 10.1371/journal.pone.0265020. eCollection 2022)
2021
Gonzalez KJ, Strauch EM#, "Decreased vaccine protection of egg-based influenza vaccine in the elderly could be associated with a non-hemagglutinin focused immunity", J Clin Invest. 2021 Aug 2;131(15):e151732. doi: 10.1172/JCI151732
Narkhede YB*, Gonzalez KJ*, Strauch EM#, Targeting viral surface proteins through structure-based design Viruses 2021, 13(7), 1320; https://doi.org/10.3390/v13071320
2020
Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, Chen RE, Carter L, Walls AC, Park YJ, Strauch EM, Stewart L, Diamond MS, Veesler D, Baker D. De novo design of picomolar SARS-CoV-2 miniprotein inhibitors., Science. 2020 Sep 9; eabd9909. doi: 10.1126/science.abd9909. Online ahead of print
Kim HW*, Alexander EletskyA*, Gonzales KJ, van der Wel H, Strauch EM, James H. Prestegard JH, West CM, “Skp1 Dimerization Conceals its F-box Protein Binding Site”, Biochemistry. 2020 Apr 13. doi: 10.1021/acs.biochem.0c00094. [Epub ahead of print]
2019
Dou J, Goreshnik I, Bryan C, Baker D, Strauch EM#, “Parallelized Identification of On- and Off-Target Protein Interaction”, Molecular Systems Design & Engineering, 2019, DOI: 10.1039/C9ME00118B
Anderson CE1, Buser JR, Fleming AM, Strauch EM, Ladd PD, Englund J, Baker D, Yager P., "An integrated device for the rapid and sensitive detection of the influenza hemagglutinin", Lab Chip. 2019 Feb 26;19(5):885-896.
# = corresponding author
* = author contributed equally
Selected publications from Eva's postdoctoral work
Strauch EM, Bernard S, La D, Bohn A, Nieusma T, Lee P, Garcia NK, Holstein C, Anderson CE, Hooper KA, Trenant M, Sheffler W, Bloom JD, Yager P, Lee KK, Ward A, Fuller D, Wilson IA, Baker D, “Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site”, Nat Biotechnol. 2017 Jul;35(7):667-671. doi: 10.1038/nbt.3907
Special reports in:
- Science: “Designer protein halts flu”, DOI: 10.1126/science.aan6958
- Scientific American: “ Designing Antiviral Proteins Via Computer Could Help Halt the Next Pandemic ”
- ACS Chemical and Engineering News : ”Three-pronged designed peptide neutralizes influenza”, Volume 95 Issue 26 | p. 8 | Concentrates
- the Conversation and LiveScience
Holstein CA*, Anderson CE*, Strauch EM, Bennett S, Chevalier A, Nelson J, Fu E, Baker D, Yager P; Development of a Paper-Based Assay for Whole Influenza Virus Detection using a Computationally Designed Hemagglutinin Head Region Binder, Anal Chem. 2017 Jun 20;89(12):6608-6615. doi: 10.1021/acs.analchem.7b00769
Klein JC, Lajoie MJ, Schwartz JJ, Strauch EM, Nelson J, Baker B, Shendure J, “Multiplex pairwise assembly of array-derived DNA oligonucleotides”, Nucleic Acids Res. 2016 Mar 18;44(5):e43. doi: 10.1093
Strauch EM, Fleishman SJ, Baker D, ” Computational Design of a pH-sensitive IgG Binding Protein”, Proc Natl Acad Sci U S A., 2014 Jan 14;111(2):675-80, PMID: 24381156
For the complete list check on Pubmed
* = contributed equally