Publications

In review and/or preprint

114. Reduction of native VHH aggregation using interpretable machine learning, in review (2025).

113. Antibody brain shuttles targeting CD98hc with broad species cross-reactivity, in review (2025).

112. Multi-objective antibody design and optimization using machine learning, in review (2025).

111. In vivo auto-tuning of antibody-drug conjugate delivery for effective immunotherapy using high-avidity, low-affinity antibodies, preprint (2025). [link]

Published or in press

110. Flow cytometric isolation of drug-like conformational antibodies specific for amyloid fibrils, Nat Chem Biol (2025). [link]

109. Maximizing activity and selectivity of antibody-mediated effector functions using antibody mixtures, mAbs (2025). [link]

108. Comparative radiotracing quantifies brain cellular uptake and catabolism for bispecific antibodies targeting transferrin receptor and CD98hc, ACS Chem Neurosci (2025). [link]

107. Deep learning-based design and experimental validation of a medicine-like human antibody library, Brief Bioinform (2025). [link]

106. TDP43 autoregulation gives rise to shortened isoforms that are tightly controlled by both transcriptional and post-translational mechanisms, Cell Rep (2025). [link]

105. Ultra-dilute developability analysis of antibody self-association and non-specific binding, Methods Mol Biol, in press (2025).

104. AIntibody: an experimentally validated in silico antibody discovery design challenge, Nat Biotechnol (2024). [link]

103. Generation of nanobodies with conformational specificity for tau oligomers that recognize tau aggregates from human Alzheimer’s disease samples, Biomat Sci (2024). [link]

102. Human antibody polyreactivity is governed primarily by the heavy chain complementarity-determining regions, Cell Rep (2024). [link]

101. Monoclonal antibody generation using single B-cell screening for treating infectious diseases, BioDrugs (2024). [link]

100. Native ion mobility-mass spectrometry reveals the binding mechanisms of anti-amyloid therapeutic antibodies, Protein Sci (2024). [link]

99. Development of a pan-tau multivalent nanobody that binds tau aggregation motifs and recognizes pathological tau aggregates, Biotechnol Prog (2024). [link]

98. Reduction of monoclonal antibody viscosity using interpretable machine learning, mAbs (2024). [link]

97. Facile generation of biepitopic antibodies with intrinsic agonism for activating receptors in the tumor necrosis factor superfamily, Cell Chem Biol (2024). [link]

96. Bispecific antibody shuttles targeting CD98hc mediate efficient and long-lived brain delivery of IgGs, Cell Chem Biol (2024). [link] [news story]

95. Quantitative flow cytometric selection of tau conformational nanobodies specific for pathological aggregates, Front Immunol  (2023). [link]

94. Optimization of therapeutic antibodies for reduced self-association and non-specific binding using interpretable machine learning, Nat Biomed Eng (2024). [link] [news story] 

93. Simplifying complex antibody engineering using machine learning, Cell Systems (2023). [link]

92. Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data, Bioinformatics (2023). [link]

91. Computational optimization of antibody humanness and stability by systematic energy-based ranking, Nat Biomed Eng (2023). [link]

90. Characterization of pairs of toxic and nontoxic misfolded protein oligomers elucidates the structural determinants of oligomer toxicity in protein misfolding diseases, Acc Chem Res (2023). [link]

89. Assessing developability early in the discovery process for novel biologics, mAbs (2023). [link]

88. Approaches to expand the conventional toolbox for discovery and selection of drug-like antibodies, mAbs (2023). [link]

87. Unlocking the potential of agonist antibodies for treating cancer using antibody engineering, Trends Mol Med (2023). [link]

86. Editorial overview: Nanobiotechnology, Curr Opin Biotech (2022). [link]

85. Reduction of therapeutic antibody self-association using yeast-display selections and machine learning, mAbs (2022). [link] [press release]

84. Co-optimization of therapeutic antibody affinity and specificity using machine learning models that generalize to novel mutational space, Nat Commun (2022). [link] [blog] [press release]

83. Mutational analysis of SARS-CoV-2 Variants of Concern reveals key tradeoffs between receptor affinity and antibody escape, PLOS Comput Biol (2022). [link]

82. Isolating anti-amyloid antibodies from yeast-displayed libraries, Methods Mol Biol (2022). [link]

81. Rapid and quantitative in-vitro evaluation of SARS-CoV-2 neutralizing antibodies and nanobodies, Anal Chem (2022). [link]

80. Antibodies with weakly basic isoelectric points minimize trade-offs between formulation and physiological colloidal properties, Mol Pharm (2022). [link]

79. Facile isolation of high-affinity nanobodies from synthetic libraries using CDR-swapping mutagenesis, STAR Protoc (2022). [link]

78. Improving antibody drug development using bionanotechnology, Curr Opin Biotech (2022). [link]

77. Agonist antibody discovery: experimental, computational and rational engineering approaches, Drug Discov Today (2022). [link]

76. A hybridoma-derived monoclonal antibody with high homology to the aberrant myeloma light chain, PLoS One (2021). [link]

75. Discovery and characterization of high-affinity, potent SARS-CoV-2 neutralizing antibodies via single B cell screening, Sci Rep (2021). [link]

74. Systematic engineering of optimized autonomous heavy-chain variable domains, J Mol Biol (2021). [link]

73. Engineered multivalent nanobodies potently and broadly neutralize SARS-CoV-2 variants, Adv Ther (2021). [link]

72. Highly sensitive detection of antibody non-specific interactions using flow cytometry, mAbs (2021). [link]

71. Discovery-stage identification of drug-like antibodies using emerging experimental and computational methods, mAbs (2021). [link]

70. Ultra-dilute measurements of self-association for the identification of antibodies with favorable high concentration solution properties, Mol Pharm (2021). [link]

69. Directed evolution of potent neutralizing nanobodies against SARS-CoV-2 using CDR-swapping mutagenesis, Cell Chem Biol (2021). [link][news story]

68. Rational affinity maturation of anti-amyloid antibodies with high conformational and sequence specificity, J Biol Chem (2021). [link]

67. Directed evolution of conformation-specific antibodies for sensitive detection of polypeptide aggregates in therapeutic drug formulations, Biotech Biogen (2021). [link]

66. Toward in silico CMC: An industrial collaborative approach to model‐based process development, Biotech Biogen (2020). [link]

65. Toward drug-like multispecific antibodies by design, Int J Mol Sci (2020). [link]

64. Physicochemical rules for identifying monoclonal antibodies with drug-like specificity, Mol Pharm (2020). [link]

63. Directed evolution methods for overcoming trade-offs between protein activity and stability, AIChE Journal (special issue honoring Frances Arnold's Nobel Prize) (2020). [link]

62. Unique impacts of methionine oxidation, tryptophan oxidation and asparagine deamidation on antibody stability and aggregation, J Pharm Sci (2020). [link]

61. An engineered, pH-toggle switch, human Fc domain for ultra-long circulation persistence , Nat Commun (2019). [link] 

60. Sensitive detection of glucagon aggregation using amyloid fibril-specific antibodies, Biotech Bioeng,  (2019). [link]

59. Nature-inspired design and evolution of anti-amyloid antibodies, J Biol Chem (2019). [link]

58. Deamidation compromises antibody colloidal stability and enhances aggregation in a pH-dependent manner, Mol Pharm (2019). [link]

57. Selecting and engineering monoclonal antibodies with drug-like specificity, Current Opin Biotech (2019). [link]

56. Net charge of the complementarity-determining regions is a key predictor of antibody specificity, Protein Eng Des Sel (2018). [link]

55. Understanding and overcoming trade-offs between antibody affinity, specificity, stability and solubility, Biochem Eng J (2018). [link]

54. Biophysical and sequence-based methods for identifying monovalent and bivalent antibodies with high colloidal stability, Mol Pharm (2018). [link]

53. Facile affinity maturation of antibody variable domains using natural diversity mutagenesis, Front Immunol (2017). [link]

52. Arginine mutations in antibody complementarity-determining regions display context-dependent affinity/specificity trade-offs, J Biol Chem (2017). [link]

51. Efficient affinity maturation of antibody variable domains requires co-selection of compensatory mutations to maintain thermodynamic stability, Sci Rep (2017). [link]

50. Glycan determinants of heparin-tau interaction, Biophys J (2017). [link]

49. Engineered autonomous human variable domains, Curr Pharm Des (2016). [link]

48. Facile preparation of stable antibody-gold conjugates and application to affinity-capture self-interaction nanoparticle spectroscopy, Bioconjug Chem (2016). [link]

47. Measurements of monoclonal antibody self-association are correlated with complex biophysical properties, Mol Pharm (2016). [link]

46. Intrahippocampal administration of a domain antibody that binds aggregated amyloid-β reverses cognitive deficits produced by diet-induced obesity, Biochim Biophys Acta (2016). [link]

45. Design and optimization of anti-amyloid domain antibodies specific for Aβ and IAPP, J Biol Chem (2016). [link]

44. Advances in antibody design, Ann Rev Biomed Eng (2015). [link] 

43. Co-evolution of affinity and stability of grafted amyloid-motif domain antibodies, Protein Eng Des Sel (2015). [link]

42. Discovery of highly soluble antibodies prior to purification using affinity-capture self-interaction nanoparticle spectroscopy, Protein Eng Des Sel (2015). [link]

41. Comparison of human and bovine insulin amyloidogenesis under uniform shear, J Phys Chem B (2015). [link]

40. An alternative assay to hydrophobic interaction chromatography for high-throughput characterization of monoclonal antibodies, mAbs (2015). [link]

39. High-throughput assay for measuring monoclonal antibody self-association and aggregation in serum, Bioconjug Chem (2015). [link] 

38. Improving monoclonal antibody selection and engineering using measurements of colloidal protein interactions, J Pharm Sci (2014). [link]

37. Plasmonic measurements of monoclonal antibody self-association using self-interaction nanoparticle spectroscopy, Biotech Bioeng (2014). [link]

36. Emerging methods for identifying monoclonal antibodies with low propensity to self-associate during the early discovery process, Expert Opin Drug Deliv (2014). [link]

35. Optimal charged mutations in the complementarity-determining regions that prevent domain antibody aggregation are dependent on the antibody scaffold, Protein Eng Des Sel (2014). [link]

34. High-throughput screening for developability during early-stage antibody discovery using self-interaction nanoparticle spectroscopy, mAbs (2014). [link]

33. Mechanisms of transthyretin inhibition of Aβ aggregation in vitro, J Neurosci (2013). [link]

32. Modulation of curli assembly and pellicle biofilm formation by chemical and protein chaperones, Chem Biol (2013). [link] 

31. Toward aggregation-resistant antibodies by design, Trends Biotechnol (2013). [link]

30. Lifting the veil on amyloid drug design, eLife (2013). [link]

29. Rapid analysis of antibody self-association in complex mixtures using immunogold conjugates, Mol Pharm (2013). [link]

28. Rational design of potent domain antibody inhibitors of amyloid fibril assembly, P Natl Acad Sci U S A (2012). [link]

27. Aggregation-resistant domain antibodies engineered with charged mutations near the edges of the complementarity-determining regions, Protein Eng Des Sel (2012). [link]

26. Conformational differences between two amyloid β oligomers of similar size and dissimilar toxicity, J Biol Chem (2012). [link]

25. Polyphenolic disaccharides endow proteins with unusual resistance to aggregation, Biotech Bioeng (2012). [link]

24. Engineering aggregation-resistant antibodies, Ann Rev Chem Biomol Eng (2012). [link]

23. Solution pH that minimizes self-association of three monoclonal antibodies is strongly dependent on ionic strength, Mol Pharm (2012). [link]

22. Structure-based design of conformation- and sequence-specific antibodies against amyloid β, P Natl Acad Sci U S A (2012). [link]

21. Removal versus fragmentation of amyloid-forming precursors via membrane filtration, Biotech Bioeng (2012). [link]

20. High-throughput analysis of concentration-dependent antibody self-association, Biophys J (2011). [link]

19. Site-specific structural analysis of a yeast prion strain with species-specific seeding activity, Prion (2011). [link]

18. Polyphenolic glycosides and aglycones utilize opposing pathways to selectively remodel and inactivate toxic oligomers of amyloid β, ChemBioChem (2011). [link]

17. Mutational analysis of domain antibodies reveals aggregation hotspots within and near the complementarity determining regions, Proteins (2011). [link]

16. Aromatic small molecules remodel toxic soluble oligomers of amyloid ß through three independent pathways, J Biol Chem (2011). [link]

15. Resveratrol selectively remodels soluble oligomers and fibrils of amyloid Aß into off-pathway conformers, J Biol Chem (2010). [link]

14. Unraveling molecular interactions and structures of self-perpetuating prions and amyloids, Nat Struct Mol Biol (2009). [link]

13. Biospecific immobilization of proteins for rapid analysis of weak protein interactions using self-interaction nanoparticle spectroscopy, Biotechnol Bioeng (2009). [link]

12. Self-interaction nanoparticle spectroscopy: A nanoparticle-based protein interaction assay, J Am Chem Soc (2008). [link]

11. Prion recognition elements govern nucleation, strain specificity and species barriers, Nature (2007). [link] *See accompanying commentaries in Nature (2007) [link],  Nat Methods (2007) [link] & J Cell Biol (2007) [link].

10. Direct measurement of protein osmotic second virial cross coefficients by cross-interaction chromatography, Protein Sci (2004). [link]

9. Predictive crystallization of ribonuclease A via rapid screening of osmotic second virial coefficients, Proteins (2003). [link]

8. Measurement of protein self-association as a guide to crystallization, Curr Opin Biotechnol (2003). [link]

7. Correlation of diafiltration sieving behavior of lysozyme-BSA mixtures with osmotic second virial cross coefficients, Biotechol Bioeng (2003). [link]

6. Rapid measurement of protein osmotic second virial coefficients by self-interaction chromatography, Biophys J (2002). [link]

5. Self-interaction chromatography: A novel screening method for rational protein crystallization, Acta Cryst D (2002). [link]

4. On-line spectroscopic characterization of sodium cyanide with nanostructured gold SERS substrates, Appl Spectrosc (2002). [link]

3. Structured metallic films for optical and spectroscopic applications via colloidal crystal templating, Adv Mater (2001). [link]

2. Assembly of gold nanostructured films templated by colloidal crystals and use in surface-enhanced Raman spectroscopy, J Am Chem Soc (2000). [link]

1. A class of porous metallic nanostructures, Nature (1999). [link]