* indicates joint first authorship
click on the article title for the PubMed abstract

[95]  M. Martins, A. M. D. Santos, C. H. S. da Costa, S. W. Canner, M. Chungyoun, J. J. Gray, M. S. Skaf, M. Ostermeier, R. Goldbeck
Thermostability enhancement of GH 62 ɑ-l-arabinofuranosidase by directed evolution and rational design
J. Agric. Food Chem. 40, 72, 4225-4236 (2024) [full text]

[94]  R. Weeks, M. Ostermeier
Fitness and functional landscapes of the E. coli RNase III gene rnc
Mol. Bio. Evol. 40, msad047 (2023) [full text]

[93]  J. D. Mehlhoff, M. Ostermeier
Genes vary greatly in their propensity for collateral fitness effects of mutations
Mol. Bio. Evol. 40, msad038 (2023) [full text]

[92]  P. Hauk, R. Weeks, M. Ostermeier
A CRISPR/dCas9 system for assaying and selecting for RNase III activity in vivo in E. coli
CRISPR J. 6, 43-51 (2023) [full text]

[91]  S. Spisak, B. O'Brien, M. Ostermeier
A bacterial dual positive and negative selection system for dCas9 activity
PLoS One 17(6), e0269270 (2022) [full text]

[90]  S. Spisak, M. Ostermeier
Engineered protein switches for exogenous control of gene expression
Biochem. Soc. Trans. 48, 2205-2212 (2020) [full text]

[89]  J. D. Mehlhoff, F. W. Stearns, D. Rohm, B. Wang, E.-Y. Tsou, N. Dutta, M.-H. Hsiao, C. E. Gonzalez, A. F. Rubin, M. Ostermeier
Collateral fitness effects of mutations
Proc. Nat. Acad. Sci. USA 117, 11597-11607 (2020) [full text]  

[88]  J. D. Mehlhoff, M. Ostermeier
Biological fitness landscapes by deep mutational scanning
Methods Enzymol. 643, 203-224 (2020) [full text]

[87]  T. Sagara, M. Debeljak, C. Hu, C. M. Wright, N. Anders, H. Liang, A. Maitra, M. Rudek, M. Ostermeier, J. R. Eshleman, Y. Matsushita
Successful gene therapy requires targeting the vast majority of cancer cells
Cancer Biology & Therapy, 21, 946-953 (2020)

[86]  T. D. Warren, K. Patel, J. L. Rivera, J. R. Eshleman, M. Ostermeier
Comprehensive mutagenesis on yeast cytosine deaminase yields improvements in 5-fluorocytosine toxicity in HT1080 cells
AIChE Journal, 66:e16688 (2020) [full text]

[85]  J. P. Fuenzalida, T. Xiong, B. M. Moerschbacher, M. Ostermeier, F. M. Goycoolea
Protein-surfactant-polysaccharide nanoparticles increase the catalytic activity of an engineered β-lactamase maltose-activated switch enzyme
bioRxiv, doi:10.1101/746560 (2019)

[84]  T. D. Warren, K. Patel, J. R. Eshleman, M. Ostermeier
Protein-programmed accumulation of yeast cytosine deaminase in cancer cells in response to mock-hypoxia
ACS Synth. Biol., 17, 948-954 (2019) [full text]

[83]  C. E. Gonzalez, P. Roberts, M. Ostermeier
Fitness effects of single amino acid insertions and deletions in TEM-1 β-lactamase
J. Mol. Biol., 431, 2320-2330 (2019) [full text]

[82]  C. E. Gonzalez, M. Ostermeier
Pervasive pairwise intragenic epistasis among sequential mutations in TEM-1 β-lactamase
J. Mol. Biol., 431, 1981-1992 (2019) [full text]

[81]  L. Ribeiro, C. Chelius, K. Boppidi, N. Naik, S. Hossain, J. Ramsey, J. Kumar, L. Riberio, M. Ostermeier, B. Tran, Y. Goo, L. deAssis, M. Ulas, Ö. Bayram, G. Goldman, S. Lincoln, R. Srivastava, S. Harris, M. Marten
Comprehensive analysis of A. nidulans PKA phosphorylome identifies a novel mode of CreA regulation
mBio, 10:e02825-18 (2019)

[80]  T. Xiong, D. Rohm, R. E. Workman, L. Roundtree, C. D. Novina, W. Timp, M. Ostermeier
Protein engineering strategies for improving the selective methylation of target CpG sites by a dCas9-directed cytosine methyltransferase in bacteria
PLoS One, 13(12): e0209408 (2018) [full text]

[79]  C.-C. Ko, M. Ostermeier, S.-C. Lin
Dual column approach for the purification of zinc finger proteins by immobilized metal affinity chromatography
Process Biochem., 73: 204 (2018) [full text]

[78]  T. Xiong*, G. E. Meister*, R. E. Workman, N. C. Kato, M. J. Spellberg, T. Fulya, W. Timp, M. Ostermeier, C. D. Novina
Targeted DNA methylation in human cells using engineered dCas9-methyltransferases
Sci. Rep., 7: 6732 (2017) [full text]

[77]  L. F. Ribeiro, T. D. Warren, M. Ostermeier
Construction of protein switches by domain insertion and directed evolution
Methods Mol. Biol., 1596, 43-55 (2017)

[76]  N. Y. Shelat, S. Parhi, M. Ostermeier
Development of a cancer-marker activated enzymatic switch from the herpes simplex virus thymidine kinase
Protein Eng. Des. Sel., 30, 95-103 (2017) [full text]

[75]  P. Hauk, K. Stephens, R. McKay, C. Virgile, H. Ueda, M. Ostermeier, K.-S. Ryu, H. Sintim, W. Bentley
Directed evolution of Escherichia coli quorum sensing promoter region of the lsrACDBFG operon: a tool for synthetic biology systems and protein expression
Nucleic Acids Res., 44, 10515-10525 (2016) [full text]

[74]  N. Y. Shelat, S. Parhi, M. Ostermeier
A positive selection for nucleoside kinases in E. coli
PLoS One, 11(9):e0162921 (2016) [full text]

[73]  J. H. Choi, T. Xiong, M. Ostermeier
The interplay between effector binding and allostery in an engineered protein switch
Protein Sci., 25, 1605–1616 (2016) [full text]

[72]  L. F. Ribeiro, J. Tullman, N. Nicholes, S. R. B. Silva, D. S. Vieira, M. Ostermeier, R. J. Ward
A xylose-stimulated xylanase-xylose binding protein chimera created by random nonhomologous recombination
Biotechnol. Biofuels, 9:119 (2016) [full text]

[71]  B. Steinberg, M. Ostermeier
Shifting fitness and epistatic landscapes reflect tradeoffs along an evolutionary pathway
J. Mol. Biol., 428, 2730–2743 (2016) [full text]

[70]  B. Steinberg, M. Ostermeier
Environmental changes bridge evolutionary valleys
Sci. Adv., 2(1):e1500921 (2016) [full text]

[69]  N. Nicholes, A. Date, P. Beaujean, P. Hauk, M. Kanwar, M. Ostermeier
Modular protein switches derived from antibody mimetic proteins
Protein Eng. Des. Sel., 29, 77-85 (2016) [full text]

[68]  J. Tullman*, N. Nicholes*, M. R. Dumont, L. F. Ribeiro, M. Ostermeier
Enzymatic protein switches built from paralogous input domains
Biotechnol. Bioeng. 113, 852-858 (2016) [full text]

[67]  J. H. Choi*, M. Zayats*, P. C. Searson, M. Ostermeier
Electrochemical activation of engineered protein switches
Biotechnol. Bioeng., 113, 453-456 (2016) [full text]

[66]  J. P. Fuenzalida, P. K. Nareddy, I. Moreno-Villoslada, B. M. Moerschbacher, M. J. Swamy, S. Pan, M. Ostermeier, F. M. Goycoolea
On the role of alginate structure in complexing with lysozyme and application for enzyme delivery.
Food Hydrocolloids, 53, 239-248 (2016) [full text]

[65]  J. H. Choi, A. H. Laurent, V. J. Hilser, M. Ostermeier
Design of protein switches based on an ensemble model of allostery
Nat. Commun., 6:6968 (2015) [full text]

[64]  J. H. Choi, M. Ostermeier
Rational design of a fusion protein to exhibit disulfide-mediated logic gate behavior
ACS Synth. Biol., 4, 400-406 (2015) [full text]

[63]  L. F. Ribeiro, N. Nicholes, J. Tullman, L. F. C. Ribeiro, C. A. Fuzo, D. S. Vieira, G. P. Furtado, M. Ostermeier, and R. J. Ward
Insertion of a xylanase in xylose binding protein results in a xylose-stimulated xylanase
Biotechnol. Biofuels, 8:118 (2015) [full text]

[62]  L. S.-L. Cheung*, D. J. Shea*, N. Nicholes, A. Date, M. Ostermeier, K. Konstantopoulos
Characterization of monobody scaffold interactions with ligand via force spectroscopy and steered molecular dynamics
Sci. Rep., 5: 8247 (2015) [full text]

[61]  R. C. Wright, A. Khakhar, J. R. Eshleman, M. Ostermeier
Advancements in the development of HIF-1α-activated protein switches for use in enzyme prodrug therapy
PLoS One, 9(11): e114032 (2014) [full text]

[60]  J. H. Russell, M. Ostermeier
The thymidylate kinase genes from Mycobacterium tuberculosis and methicillin resistant Staphylococcus auerus confer 3'-azido-3'-deoxythymidine resistance to Escherichia coli
FEMS Microbiol. Lett., 361, 158-165 (2014) [full text]

[59]  B.Chaikind, M. Ostermeier
Directed evolution of improved zinc finger methyltransferases
PLoS One, 9(5): e96931 (2014) [full text]

[58]  E. Firnberg, J. W. Labonte, J. J. Gray, M. Ostermeier
A comprehensive, high-resolution map of a gene's fitness landscape
Mol. Bio. Evol., 31, 1581-1592 (2014) [PDF]

[57]  G. Valdes, R. W. Schulte, M. Ostermeier, K. S. Iwamoto
The high-affinity maltose switch MBP317-347 has low affinity for glucose: implications for targeting tumors with metabolically-directed enzyme prodrug therapy
Chem. Biol. Drug Des., 83, 266-271 (2014)

[56]  E. Firnberg, M. Ostermeier
The genetic code constrains yet facilitates Darwinian evolution
Nucleic Acids Res., 41, 7420-7428 (2013) [full text]

[55]  J. H. Choi, A. San, M. Ostermeier
Non-allosteric enzyme switches possess larger effector-induced changes in thermodynamic stability than their non-switch analogs
Protein Sci., 22, 475-485 (2013) [PDF]

[54]  M. Kanwar, R. C. Wright, A. Date, J. Tullman, M. Ostermeier
Protein switch engineering by domain insertion
Methods Enzymol., 523, 369-388 (2013)

[53]  E. Firnberg, M. Ostermeier
PFunkel: efficient, expansive, user-defined mutagenesis
PLoS One, 7(12): e52031 (2012) [PDF]

[52]  B.Chaikind, K. P. Kilambi, J. J. Gray, M. Ostermeier
Targeted DNA methylation using an artificially bisected M.HhaI fused to zinc fingers
PLoS One, 7(9): e44852 (2012) [PDF]

[51]  W. Ke, A. H. Laurent, M. D. Armstrong, Y. Chen, W. E. Smith, J. Liang, C. M. Wright, M. Ostermeier, F. van den Akker
Structure of an engineered β-lactamase maltose binding protein fusion protein: insights into heterotropic allosteric regulation
PLoS One, 7(6): e39168 (2012) [PDF]

[50]  G.Guntas, M. Kanwar, M. Ostermeier
Circular permutation in the Ω-loop of TEM1 β-lactamase results in improved activity and altered substrate specificity
PLoS One, 7(4): e35998 (2012) [PDF]

[49]  L. S.-L. Cheung*, M. Kanwar*, M. Ostermeier, K. Konstantopoulos
A hot-spot motif characterizes the interface between a designed ankyrin-repeat protein and its target ligand
Biophys. J., 102, 407-416 (2012) [PDF]

[48]  R. A. Heins*, J. H. Choi*, T. Sohka, M. Ostermeier
In vitro recombination of non-homologous genes can result in gene fusions that confer a switching phenotype to cells
PLoS One, 6(11): e27302 (2011) [PDF]

[47]  C. M. Wright, R. C. Wright, J. R. Eshleman, M. Ostermeier
A protein therapeutic modality founded on molecular regulation
Proc. Nat. Acad. Sci. USA, 108, 16206-16211 (2011) [PDF]

[46]  M. Zayats, M. Kanwar, M. Ostermeier, P. C. Searson.
Molecular Imprinting of maltose binding protein: tuning protein recognition at the molecular level
Macromolecules, 44, 3966-3972 (2011) [PDF]

[45]  J. Tullman, G. Guntas, M. Dumont, M. Ostermeier
Protein switches identified from diverse insertion libraries created using S1 nuclease digestion of supercoiled-form plasmid DNA
Biotechnol. Bioeng., 108, 2535-2543 (2011) [PDF]

[44]  M. Zayats, M. Kanwar, M. Ostermeier, P. C. Searson
Surface-tethered protein switches
Chem. Commun., 47, 3398-3400 (2011) [PDF]

[43]  K. Hida, S. Y. Won, G. Di Pasquale, J. Hanes, J. A. Chiorini, M. Ostermeier
Sites in the AAV5 capsid tolerant to deletions and tandem duplications
Arch. Biochem. Biophys. 496, 1-8 (2010) [PDF]

[42]  G. E. Meister, S. Chandrasegaran, M. Ostermeier
Heterodimeric DNA methyltransferases as a platform for creating designer zinc finger methyltransferases for targeted DNA methylation in cells
Nucleic Acids Res., 38, 1749-1759 (2010) [PDF]

[41]  C. M. Wright, A. Majumdar, J. R. Tolman, M. Ostermeier
NMR characterization of an engineered domain fusion between maltose binding protein and TEM1 β-lactamase provides insight into its structure and allosteric mechanism
Proteins, 78, 1423-1430 (2010) [PDF]

[40]  T. Sohka, R. A. Heins, M. Ostermeier
Morphogen-defined patterning of Escherichia coli enabled by an externally tunable band-pass filter
J. Biol. Eng., 3, 10 (2009) [PDF]

[39]  C. Kim, B. Pierre, M. Ostermeier, L. L. Looger, J. R. Kim
Enzyme stabilization by domain insertion into a thermophilic protein
Protein Eng. Des. Sel., 22, 615-623 (2009) [PDF]

[38]  M. Ostermeier
Designing switchable enzymes
Curr. Opin. Struct. Biol., 19, 442-448 (2009) [PDF]

[37]  T. Sohka*, R. A. Heins*, R. M. Phelan, J. M. Greisler, C. A. Townsend, M. Ostermeier
An externally-tunable bacterial band-pass filter
Proc. Nat. Acad. Sci. USA, 106, 10135-10140 (2009) [PDF]

[36]  R. M. Phelan, M. Ostermeier, C. A. Townsend
Design and synthesis of a β-lactamase activated 5-fluorouracil prodrug
Bioorg. Med. Chem. Let., 19, 1261-1263 (2009) [PDF]

[35]  G. E. Meister, M. Kanwar, M. Ostermeier
Circular permutation of proteins
In: S. Lutz and U. Bornscheuer (eds) Protein Engineering Handbook, Wiley (2009).

[34]  G. E. Meister, S. Chandrasegaran, M. Ostermeier
An engineered split M.HhaI-zinc finger fusion lacks the intended methyltransferase specificity
Biochem. Biophys. Res. Commun., 377, 226-230 (2008) [PDF]

[33]  M. Berrondo, M. Ostermeier, J. J. Gray
Structure prediction of domain insertion proteins from structures of the individual domains
Structure, 16, 513-527 (2008) [PDF]

[32]  K. Hida, J. Hanes, M. Ostermeier
Directed evolution for drug and nucleic acid delivery
Adv. Drug Deliv. Rev., 59, 1562-1578 (2007) [PDF]

[31]  C. M. Wright, R. A. Heins, M. Ostermeier
As easy as flipping a switch?
Curr. Opin. Chem. Biol., 11, 342-346 (2007) [PDF]

[30]  J. Liang, J. R. Kim, J. T. Boock, T. J. Mansell, M. Ostermeier
Ligand binding and allostery can emerge simultaneously
Protein Sci., 16, 929-937 (2007) [PDF]

[29]  M. Ostermeier
Beyond cataloging the Library of Babel
Chem. Biol. 14, 237-238 (2007) [PDF]

[28]  S. Durai*, A. D. Bosley*, A. B. Abulencia, S. Chandrasegaran, M. Ostermeier
A bacterial one-hybrid selection system for interrogating zinc finger-DNA interactions
Combinatorial Chemistry and High Throughput Screening, 9, 301-311 (2007) [PDF]

[27]  J. R. Kim, M. Ostermeier
Modulation of effector affinity by hinge region mutations also modulates switching activity in an engineered allosteric TEM1 β-lactamase
Arch. Biochem. Biophys., 446, 44-51 (2006) [PDF]

[26]  D. Paschon, Z. S. Patel, M. Ostermeier
Enhanced catalytic efficiency of aminoglycoside phosphotransferase (3')-IIa achieved through protein fragmentation and reassembly
J. Mol. Biol., 353, 26-37 (2005) [PDF]

[25]  M. Ostermeier
Engineering allosteric protein switches by domain insertion
Protein Eng. Des. Sel., 18, 359-364 (2005) [PDF]

[24]  G. Guntas, T. J. Mansell, J. R. Kim, M. Ostermeier
Directed evolution of protein switches and their application to the creation of ligand-binding proteins
Proc. Nat. Acad. Sci. USA, 102, 11224-11229 (2005) [PDF]

[23]  W. Choe, S. Chandrasegaran, M. Ostermeier
Protein fragment complementation in M.HhaI DNA methyltransferase
Biochem. Biophys. Res. Commun., 334, 1233-1240 (2005) [PDF]

[22]  A. D. Bosley, M. Ostermeier
Mathematical expressions useful in the construction, description and evaluation of protein libraries
Biomol. Eng., 22, 57-61 (2005) [PDF]

[21]  G. Guntas, S. F. Mitchell, M. Ostermeier
A molecular switch created by in vitro recombination of non-homologous genes
Chem. Biol., 11, 1483-1487 (2004) [PDF]

[20]  D. E. Paschon, M. Ostermeier
Construction of protein fragment complementation libraries using incremental truncation
Methods Enzymol., 388, 103-116 (2004) [PDF]

[19]  G. Guntas, M. Ostermeier
Creation of an allosteric enzyme by domain insertion
J. Mol. Biol., 336, 263-273 (2004) [PDF]

[18]  M. Ostermeier
Synthetic gene libraries: in search of the optimal diversity
Trends Biotechnol., 21, 244-247 (2003) [PDF]

[17]  M. Ostermeier
Theoretical distribution of truncation lengths in incremental truncation libraries
Biotechnol. Bioeng., 82, 564-577 (2003) [PDF]

[16]  M. Ostermeier, S. Lutz
The creation of ITCHY hybrid protein libraries
Methods Mol. Biol., 231, 129-142 (2003) [PDF]

[15]  S. Lutz, M. Ostermeier
Preparation of SCRATCHY hybrid protein libraries: size- and in-frame selection of nucleic acid sequences
Methods Mol. Biol., 231, 143-152 (2003) [PDF]

Other publications by Marc Ostermeier

[14]  M. Ostermeier, S. Lutz, S. J. Benkovic
Generation of protein fragment libraries by incremental truncation
In: Golemis, E.A. (ed) Protein-Protein Interactions: A Molecular Cloning Manual, Cold Spring Harbor Laboratory Press (Cold Spring Harbor, NY, 2002).

[13]  S. Lutz, M. Ostermeier, G. L. Moore, C. D. Maranas, S. J. Benkovic
Creating multiple-crossover DNA libraries independent of sequence identity
Proc. Nat. Acad. Sci. USA, 98, 11248-11253 (2001) [PDF]

[12]  S. Lutz, M. Ostermeier, S. J. Benkovic
Rapid generation of incremental truncation libraries for protein engineering using alpha-phosphothioate nucleotides
Nucleic Acids Res., 29, e16 (2001) [PDF]

[11]  M. Ostermeier, S. J. Benkovic
Construction of hybrid gene libraries involving the circular permutation of DNA
Biotechnology Letters, 23, 303-310 (2001) [PDF]

[10]  M. Ostermeier, S. J. Benkovic
Evolution of protein function by domain swapping
Advances in Protein Chemistry, 55, 29-77 (2000) [PDF]

[9]  M. Ostermeier, S. J. Benkovic
A two-phagemid system for the creation of non-phage displayed antibody libraries approaching one trillion members
J. Immunol. Methods, 237, 175-186 (2000) [PDF]

[8]  M. Ostermeier, J. H. Shim, S. J. Benkovic
A combinatorial approach to hybrid enzymes independent of DNA homology
Nature Biotechnol., 17, 1205-1209 (1999) [PDF]

[7]  M. Ostermeier, A. E. Nixon, S. J. Benkovic
Incremental truncation as a strategy in the engineering of novel catalysts
Bioorg. Med. Chem., 7, 2139-2144 (1999) [PDF]

[6]  M. Ostermeier, S. J. Benkovic
Finding Cinderella's slipper - proteins that fit
Nature Biotechnol., 17, 639-640 (1999) [PDF]

[5]  M. Ostermeier, A. E. Nixon, J. H. Shim, S. J. Benkovic
Combinatorial protein engineering by incremental truncation
Proc. Nat. Acad. Sci. USA, 96, 3562-3567 (1999) [PDF]

[4]  A.E. Nixon, M. Ostermeier, S. J. Benkovic
Hybrid enzymes: manipulating enzyme design
Trends Biotechnol., 16, 258-264 (1998) [PDF]

[3]  M. Ostermeier, K. De Sutter, G. Georgiou
Eukaryotic protein disulfide isomerase complements Escherichia coli dsbA mutants and increases the yield of a heterologously secreted protein with disulfide bonds
J. Biol. Chem., 271, 10616-10622 (1996) [PDF]

[2]  G. Georgiou, P. Valax, M. Ostermeier, M., P. M. Horowitz
Folding and aggregation of TEM β-lactamase: analogies with the formation of inclusion bodies in Escherichia coli
Prot. Sci., 3, 1953-1960 (1994) [PDF]

[1]  M. Ostermeier, M., G. Georgiou
The folding of bovine pancreatic trypsin inhibitor in the Escherichia coli periplasm
J. Biol. Chem., 269, 21072-21077 (1994) [PDF]