Data and software can be found on our GitHub site 

  • Diaz Rodriguez JR, Lu W, Papadopoulos J, Venturelli OS, Romero PA. Engineered lysins to modulate human gut microbiome communities. Submitted. [BioRxiv]

  • Gelman S, Johnson B,  Freschlin CR, D'Costa S, Gitter A*, Romero PA *. Biophysics-based protein language models for protein engineering. Submitted. [BioRxiv]

  • Freschlin CR, Fahlberg, SA, Heinzelman P, Romero PA. Neural network extrapolation to distant regions of the protein fitness landscape. Nature Communications (2024). [Publisher] [pdf]

  • Rapp JT, Bremer BJ, Romero PA. Self-driving laboratories to autonomously navigate the protein fitness landscape. Nature Chemical Engineering (2024) 1. [Publisher] [pdf]

  • D’Costa S, Hinds EC, Freschlin CR, Song H, Romero PA. Inferring protein fitness landscapes from laboratory evolution experiments. PLoS Comp Biol (2023). [Publisher] [pdf]

  • Heinzelman P, Romero PA. Directed evolution of angiotensin-converting enzyme 2 (ACE2) peptidase activity profiles for therapeutic applications. Protein Science (2023) e4597. [Publisher] [pdf]

  • Hyman LB, Christopher CR, Romero PA. Competitive SNP-LAMP probes for rapid and robust single-nucleotide polymorphism detection. Cell Reports Methods (2022) 2, 100242. [Publisher] [pdf]

  • Freschlin CR, Fahlberg SA, Romero PA. Machine learning to navigate fitness landscapes for protein engineering. Curr Opin Biotechnol (2022) 75. [Publisher] [pdf]

  • Heinzelman P, Greenhalgh JC, Romero PA. Yeast surface display-based identification of ACE2 mutations that modulate SARS-CoV-2 spike binding across multiple mammalian species. Prot Eng Des Sel (2022) 35. [Publisher] [pdf]

  • Roychowdhury H, Romero PA. Microfluidic deep mutational scanning of the human executioner caspases reveals differences in structure and regulation. Cell Death Discov (2022) 8. [Publisher] [pdf]

  • Gelman S, Fahlberg SA, Heinzelman P, Romero PA*, Gitter A*. Neural networks to learn protein sequence-function relationships from deep mutational scanning data. Proc Natl Acad Sci USA (2021) 118, e2104878118. [Publisher] [pdf]

  • Greenhalgh JC, Fahlberg SA, Pfleger BF*, Romero PA*. Machine learning-guided acyl-ACP reductase engineering for improved in vivo fatty alcohol production. Nature Comm (2021) 5825. [Publisher] [pdf]

  • Kumar P, Adamczyk P, Zhang X, Bonela R, Romero PA, Ramanathan P, Reed JL. Active and machine learning-based approaches to rapidly enhance microbial chemical production. Metabolic Engineering (2021) [Publisher] [pdf]

  • Hyman LB, Christopher CR, Romero PA. Single-cell nucleic acid profiling in droplets (SNAPD) enables high-throughput analysis of heterogeneous cell populations. Nucleic Acids Research (2021) gkab577 [Publisher] [pdf]

  • Heinzelman P, Romero PA. Discovery of human ACE2 variants with altered recognition by the SARS-CoV-2 spike protein. PLoS ONE (2021) 16, e0251585. [Publisher] [pdf]

  • Song H, Bremer BJ, Hinds EC, Raskutti G, Romero PA. Inferring protein sequence-function relationships with large-scale positive-unlabeled learning. Cell Systems (2021). [Publisher] [pdf]

  • Greenhalgh JH, Saraogee A, Romero PA. Data-driven protein engineering. In Protein Engineering: Tools and Applications, Wiley-VCH (2020) [pdf]

  • Gupta S, Ross TD, Gomez MM, Grant JL, Romero PA, Venturelli OS. Investigating the dynamics of microbial consortia in spatially structured environments. Nature Comm (2020) 2418. [Publisher] [pdf]

  • Hsu RH, Clark RL, Tan JW, Gupta S, Romero PA, Venturelli OS. Microbial Interaction Network Inference in Microfluidic Droplets. Cell Systems (2019) 9, 1-14. [Publisher] [pdf]

  • Ojala DS, Sun S, Santiago-Ortiz JL, Shapiro MG, Romero PA, and Schaffer DV. In Vivo Selection of a Computationally Designed SCHEMA AAV Library Yields a Novel Variant for Infection of Adult Neural Stem Cells in the Subventricular Zone. Molecular Therapy (2018) 26, 304-319. [PubMed] [pdf]

  • Romero PA, Tran TM, and Abate AR. Dissecting enzyme function with microfluidic-based deep mutational scanning. Proc Natl Acad Sci USA (2015) 112, 7159-64. [PubMed] [pdf]

  • Romero PA*, Shapiro MG*, Arnold FH, and Jasanoff A. Directed evolution of protein-based neurotransmitter sensors for MRI. Meth. Mol. Biol. (2013) 955, 193-205. [PubMed]

  • Heinzelman P, Romero PA, and Arnold FH. Efficient sampling of SCHEMA chimera families to identify useful sequence elements. Meth. Enzymol. (2013) 523, 351-368. [PubMed] [pdf]

  • Smith MA, Romero PA, Wu T, Brustad EM, Arnold FH. Chimeragenesis of distantly-related proteins by non-contiguous recombination. Protein Sci. (2013) 22, 231-238. [PubMed] [pdf]

  • Romero PA, Krause A, and Arnold FH. Navigating the protein fitness landscape with Gaussian processes. Proc. Natl. Acad. Sci. USA (2013) 110, E193- E201. [PubMed] [pdf]

  • Romero PA and Abate AR. Flow focusing geometry generates droplets through a plug and squeeze mechanism. Lab Chip (2012) 12, 5130-2. [PubMed] [pdf]

  • Romero PA and Arnold FH. Random field model reveals structure of the protein recombinational landscape. PLoS Comp. Biol. (2012) 8, e1002713. [PubMed] [pdf]

  • Komor R, Romero PA, Xie C, and Arnold FH. Highly thermostable fungal cellobiohydrolase I (Cel7A) engineered using predictive methods. Protein Eng. Des. Sel. (2012) 25, 1-7. [PubMed] [pdf]

  • Romero PA*, Stone E*, Lamb C, Chantranupong L, Krause A, Miklos AE, Hughes RA, Fechtel B, Ellington AD, Arnold FH, and Georgiou G. SCHEMA designed variants of human arginase I and II reveal sequence elements important to stability and catalysis. ACS Synth. Biol. (2012) 1, 221-228. [PubMed] [pdf]

  • Heinzelman P, Komor RS, Kanaan A, Romero PA, Yu X, Mohler S, Snow CD and Arnold FH. Efficient screening of fungal cellobiohydrolase class I enzymes for thermostabilizing sequence blocks by SCHEMA structure-guided recombination. Protein Eng. Des. Sel. (2010) 23, 871-880. [PubMed] [pdf]

  • Shapiro MG*, Westmeyer GG*, Romero PA, Szablowski JO, Kster B, Shah A, Otey CR, Langer R, Arnold FH and Jasanoff A. Directed evolution of a magnetic resonance imaging contrast agent for noninvasive imaging of dopamine. Nat. Biotechnol. (2010) 28, 264-272. [PubMed] [pdf]

  • Romero PA and Arnold FH. Exploring protein fitness landscapes by directed evolution. Nat. Rev. Mol. Cell Biol. (2009) 10, 866-876. [PubMed] [pdf]

  • Bloom JD, Romero PA, Lu Z, and Arnold FH. Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution. Biol. Direct (2007) 2, 1-19. [PubMed] [pdf]