Publications

2020

Peng H and Chen IA. Phage engineering and the evolutionary arms race. Curr. Opin. Biotech. 68:23-29.

Blanco C*, Verbanic S, Seelig B, Chen IA. EasyDIVER: a pipeline for assembling and counting high-throughput sequencing data from in vitro evolution of nucleic acids or peptides.  J. Mol. Evol. 88(6): 477-481.

Peng H, Borg RE, Nguyen A, Chen IA. Chimeric phage-nanoparticles for rapid characterization of bacterial pathogens: detection in complex biological samples and determination of antibiotic sensitivity. ACS Sensors, 5:5, 1491–1499.

Lai Y-C and Chen IA. Protocells. Curr. Biol. 30, R451–R520. [pdf]

Verbanic S, Shen Y, Lee J, Deacon JM, Chen IA. Microbial predictors of healing and short-term effect of debridement on the microbiome of chronic wounds: the role of facultative anaerobes. npj Biofilms Microbiomes, 6:21.

Janzen E, Blanco C, Peng H, Kenchel J, Chen IA. Promiscuous ribozymes and their proposed role in prebiotic evolution. Chem. Rev. [pdf]

Blanco C, Verbanic S, Seelig B, Chen IA. High-throughput sequencing of in vitro selections of mRNA-displayed peptides: data analysis and applications. Phys. Chem. Chem. Phys. 22: 6492-6506. DOI: 10.1039/C9CP05912A. ‘HOT PCCP article’

Peng H, Borg RE, Dow LP, Pruitt BL, Chen IA. Controlled phage therapy by photothermal ablation of specific bacterial species using gold nanorods targeted by chimeric phages. Proc. Natl. Acad. Sci USA, DOI: 10.1073/pnas.1913234117. [pdf]

2019

Verbanic S, Kim CY, Deacon JM, Chen IA. Improved single-swab sample preparation for recovering bacterial and phage DNA from human skin and wound microbiomes. BMC Microbiology, 19:214 [pdf]

Pascal R and Chen IA. From soup to peptides. Nat. Chem., 11:763-764 [pdf]

Blanco C and Chen IA. Phage therapy administered noninvasively could be effective in thin tubes subject to episodic flow despite washout: a simulation study. Phys. Biol., 16(5):054001.

Saha R and Chen IA. Effect of UV radiation on functional and templating ability of fluorescent RNA aptamers. ChemBioChem, 20.

Pressman A, Liu Z, Janzen E, Blanco C, Muller UF, Joyce GF, Pascal R, Chen IA. Mapping a systematic ribozyme fitness landscape reveals a frustrated evolutionary network for self-aminoacylating RNA. J. Am. Chem. Soc., 141(15), 6213-6223.

Peng H and Chen IA. Rapid colorimetric detection of bacterial species through capture of gold nanoparticles by chimeric phages. ACS Nano, 13 (2), 1244–1252

Blanco C, Janzen E, Pressman A, Saha R, Chen IA. Molecular fitness landscapes from high coverage sequence profiling. Ann. Rev. Biophys. 48:1-18 [pdf]

2018

Blanco C and Chen IA. Connections between mathematical models of prebiotic evolution and homochirality. In Prebiotic Chemistry and Chemical Evolution of Nucleic Acids, Menor-Salvan C, ed. Springer. [pdf]

Saha R, Verbanic S, Chen IA. Lipid vesicles chaperone an encapsulated RNA aptamer. Nat. Commun. 9:2313

Blanco C, Bayas M, Yan F, Chen IA. Analysis of evolutionarily independent protein-RNA complexes yields a criterion to evaluate the relevance of prebiotic scenarios. Curr. Biol. 28, 526-537. [pdf] [dispatch perspective]

2017

Pressman A, Moretti JE, Campbell GW, Muller UF*, Chen IA*. Analysis of in vitro evolution reveals the underlying distribution of catalytic activity among random sequences. Nucleic Acids Res. 45: 8167-8179. ‘Breakthrough’ article. [pdf] [data on SRA]

2016

Chen IA, de Vries MS. From underwear to non-equilibrium thermodynamics: physical chemistry informs the origin of life. Phys. Chem. Chem. Phys. 18, 20005-20006. [pdf]

Xulvi-Brunet R*, Campbell GW*, Rajamani S, Jimenez JI, and Chen IA. Computational analysis of fitness landscapes and evolutionary networks from in vitro evolution experiments. Methods 106, 86-96. [source code on Github] [pdf] 

Xulvi-Brunet R, Campbell GW, Rajamani S, Jimenez JI, and Chen IA. Quantitative analysis of synthesized nucleic acid pools. In Nonlinear Dynamics in Biological Systems, Carballido-Landeira J and Escribano B, ed. Springer, 2016.

2015

Saha R, Chen IA. Origin of Life: Protocells red in tooth and claw. Curr. Biol. 201; 25(24):R1175-7. [pdf]

*Pressman A, *Blanco C, Chen IA. The RNA World as a model system to study the origin of life. Curr. Biol. 2015, 25, R953–R963. *co-first author [pdf] 

Chen IA. Replicating toward complexity. Nat. Chem. 2015, 7, 191-192. [pdf]

Saha R, Pohorille A, Chen IA. Molecular crowding and early evolution. Orig. Life Evol. Biosph. 2015, 44(4):319-24. [pdf]

2014

Athavale SS, Spicer B, Chen IA. Experimental fitness landscapes to understand the molecular evolution of RNA-based life. Curr. Opin. Chem. Biol. 2014, 22:35-39. [pdf]

Freese PD, Korolev KS, Jimenez JI, Chen IA. Genetic drift suppresses bacterial conjugation in spatially structured populations. Biophys. J., 2014, 106(4):944-954. [pdf]

2013

Ivica NA, Obermayer B, Campbell GW, Rajamani S, Gerland U, Chen IA. The paradox of dual roles in the RNA World: Resolving the conflict between stable folding and templating ability. J. Mol. Evol. 2013, 77(3):55-63. [pdf]

Jimenez JI, Xulvi-Brunet R, Campbell G, Turk-MacLeod R, Chen IA. Comprehensive experimental fitness landscape and evolutionary network for small RNA. Proc. Natl. Acad. Sci. USA, 2013 110(37):14984-9. [Data on Dryad: doi:10.5061/dryad.3rq8q88] [pdf]

Bianconi G, Zhao K, Chen IA, Nowak MA. Selection for replicases in protocells. PLoS Comp. Biol. 2013, 9(5):e1003051.

Leconte A, Dickinson B, Yang D, Chen IA, Allen B, Liu DR. A population-based experimental model for protein evolution: effects of mutation rate and selection stringency on evolutionary outcomes. Biochemistry 2013, 52:1490-1499.

Leu K, Kervio E, Obermayer B, Turk-MacLeod R, Yuan C, Luevano J-M, Chen E, Gerland U, Richert C, Chen IA. Cascade of reduced speed and accuracy after errors in enzyme-free copying of nucleic acid sequences. J. Am. Chem. Soc. 2013. 135(1):354-366. [pdf]

2012

Vaidya N, Manapat ML, Chen IA, Xulvi-Brunet R, Hayden EJ, Lehman N. Spontaneous network formation among cooperative RNA replicators. Nature 2012, 491:72-77. [pdf]

Derr J, Manapat ML, Rajamani S, Leu K, Xulvi-Brunet R, Joseph I, Nowak MA, Chen IA. Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences. Nuc. Acids Res. 2012, 40(10):4711-22. (Chosen by editors as Featured Article.)

Chen IA and Nowak MA. From prelife to life: how chemical kinetics become evolutionary dynamics. Acc. Chem. Res. 2012, 45(12):2088-2096. [pdf]

Turk-MacLeod R, Gerland U, Chen IA. Life: the physical underpinnings of replication. In Astrochemistry and Astrobiology: Physical Chemistry in Action. Smith I, Leach S, Cockell C., eds. Springer 2013.

Harris K, Chen IA. Mathematical models of prebiotic replication of informational molecules. In Genesis – in the beginning: Precursors of Life, Chemical Models and Early Biological Evolution. Seckbach, J, ed. Springer, 2012.

2011

Leu K, Obermayer B, Rajamani S, Gerland U, Chen IA. The prebiotic evolutionary advantage of transferring information from RNA to DNA. Nuc. Acids Res. 2011. 39(18):8135-47. 

Lin A, Jimenez J, Derr J, Vera P, Manapat ML, Esvelt KM, Villanueva L, Liu DR, Chen IA. Inhibition of bacterial conjugation by phage M13 and its protein g3p: quantitative analysis and model. PLoS One 2011, 6(5): e19991.

2010

Chen IA. An RNA Whirl. Science 2010. 330:758 (book review) [pdf]

Chen IA, Walde P. From self-assembled vesicles to protocells. Cold Spring Harb Perspect Biol 2010 Jul 1;2(7):a002170. Epub 2010 Jun 2. [pdf]

Rajamani S, Ichida JK, Antal T, Treco DA, Leu K, Nowak MA, Szostak JW, Chen IA. Effect of stalling after mismatches on the error catastrophe in non-enzymatic nucleic acid replication. J. Am. Chem. Soc. 2010, 132, 5880–5885. [pdf]

Chen IA, Schindlinger M. Quadruplet codons: One small step for a ribosome, one giant leap for proteins. BioEssays, 2010, 32: 650–654. [pdf]

Manapat ML, Chen IA, Nowak MA. The basic reproductive ratio of life. J. Theor. Biol. 2010, 263(3): 317-327. [pdf]

2009

Chen IA. Cell division: breaking up is easy to do. Current Biology 2009, 19(8), R327-R328. [pdf]

<2009

Hanczyc MM, Chen IA, Sazani P, Szostak JW. 2008. Steps towards a synthetic protocell. In Protocells: Bridging Nonliving and Living Matter. Rasmussen S, Bedau MA, Chen L, Deamer D, Krakauer DC, Packard NH, Stadler PF, eds. MIT Press.

Chen, IA. The emergence of cells during the origin of life. Science 2006, 314: 1558-1559. [pdf]

Chen IA, Hanczyc MM, Sazani PL, Szostak JW. Protocells: Genetic polymers inside membrane vesicles. In RNA World, 3rd ed. Gesteland RF, Cech TR, Atkins JF, eds. Cold Spring Harbor Laboratory Press. 2006.

Chen IA, Salehi-Ashtiani K, Szostak JW. 2005. RNA catalysis in model protocell vesicles. J. Am. Chem. Soc. 2005, 127(38):13213-9. [pdf]

Fujikawa SM, Chen IA, Szostak JW. Vesicle shrink-wrap. Langmuir 2005, 21(12124 – 12129). [pdf]

Chen IA, Roberts RW, Szostak JW. The emergence of competition between model protocells. Science 2004, 305(5689):1474-1476. [pdf]

Chen IA, Szostak JW. A kinetic study of the growth of fatty acid vesicles. Biophys. J. 2004, 87(2):988-98. [pdf]

Chen IA, Szostak JW. Membrane growth can generate a transmembrane pH gradient in fatty acid vesicles. Proc. Natl. Acad. Sci. 2004, 101(21): 7965-7970. [pdf]

Straight AF, Cheung A, Limouze J, Chen I, Westwood NJ, Sellers JR, Mitchison TJ. Dissecting temporal and spatial control of cytokinesis with a myosin II inhibitor. Science 2003, 299 (5613): 1743-1747.

Kast P, Grisostomi C, Chen IA, Li S, Krengel U, Xue Y, Hilvert D. A strategically positioned cation is crucial for efficient catalysis by chorismate mutase.  J. Biol. Chem. 2000, 275 (47): 36832-36838.