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Molecular Fitness Landscapes from High-Coverage Sequence Profiling.

Blanco C, Janzen E, Pressman A, Saha R, Chen IA.

Annu Rev Biophys. 2019 Jan 2. doi: 10.1146/annurev-biophys-052118-115333. [Epub ahead of print]


Rapid Colorimetric Detection of Bacterial Species through Capture of Gold Nanoparticles by Chimeric Phages.

Peng H, Chen IA.

ACS Nano. 2018 Dec 26. doi: 10.1021/acsnano.8b06395. [Epub ahead of print]


Thymectomy may not be associated with clinical improvement in MuSK myasthenia gravis.

Clifford KM, Hobson-Webb LD, Benatar M, Burns TM, Barnett C, Silvestri NJ, Howard JF Jr, Visser A, Crum BA, Nowak R, Beekman R, Kumar A, Ruzhansky K, Chen IA, Pulley MT, Laboy SM, Fellman MA, Howard DB, Kolb NA, Greene SM, Pasnoor M, Dimachkie MM, Barohn RJ, Hehir MK.

Muscle Nerve. 2018 Dec 21. doi: 10.1002/mus.26404. [Epub ahead of print]


Draft Genome Sequences of New Isolates and the Known Species of the Family Microbacteriaceae Associated with Plants.

Vasilenko OV, Starodumova IP, Dorofeeva LV, Tarlachkov SV, Prisyazhnaya NV, Chizhov VN, Subbotin SA, Huntemann M, Clum A, Duffy K, Pillay M, Palaniappan K, Varghese N, Chen IA, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Whitman WB, Evtushenko LI.

Microbiol Resour Announc. 2018 Sep 20;7(11). pii: e01051-18. doi: 10.1128/MRA.01051-18. eCollection 2018 Sep.


IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes.

Paez-Espino D, Roux S, Chen IA, Palaniappan K, Ratner A, Chu K, Huntemann M, Reddy TBK, Pons JC, Llabrés M, Eloe-Fadrosh EA, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2019 Jan 8;47(D1):D678-D686. doi: 10.1093/nar/gky1127.


The association between Type 1 diabetes mellitus and periodontal diseases.

Sun KT, Chen SC, Lin CL, Hsu JT, Chen IA, Wu IT, Palanisamy K, Shen TC, Li CY.

J Formos Med Assoc. 2018 Oct 31. pii: S0929-6646(18)30594-1. doi: 10.1016/j.jfma.2018.10.012. [Epub ahead of print]


Genomes OnLine database (GOLD) v.7: updates and new features.

Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Katta HY, Mojica A, Chen IA, Kyrpides NC, Reddy T.

Nucleic Acids Res. 2019 Jan 8;47(D1):D649-D659. doi: 10.1093/nar/gky977.


IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes.

Chen IA, Chu K, Palaniappan K, Pillay M, Ratner A, Huang J, Huntemann M, Varghese N, White JR, Seshadri R, Smirnova T, Kirton E, Jungbluth SP, Woyke T, Eloe-Fadrosh EA, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2019 Jan 8;47(D1):D666-D677. doi: 10.1093/nar/gky901.


Lipid vesicles chaperone an encapsulated RNA aptamer.

Saha R, Verbanic S, Chen IA.

Nat Commun. 2018 Jun 13;9(1):2313. doi: 10.1038/s41467-018-04783-8.


Analysis of Evolutionarily Independent Protein-RNA Complexes Yields a Criterion to Evaluate the Relevance of Prebiotic Scenarios.

Blanco C, Bayas M, Yan F, Chen IA.

Curr Biol. 2018 Feb 19;28(4):526-537.e5. doi: 10.1016/j.cub.2018.01.014. Epub 2018 Feb 1.


Analysis of in vitro evolution reveals the underlying distribution of catalytic activity among random sequences.

Pressman A, Moretti JE, Campbell GW, Müller UF, Chen IA.

Nucleic Acids Res. 2017 Oct 13;45(18):10922. doi: 10.1093/nar/gkx816. No abstract available.


Rituximab as treatment for anti-MuSK myasthenia gravis: Multicenter blinded prospective review.

Hehir MK, Hobson-Webb LD, Benatar M, Barnett C, Silvestri NJ, Howard JF Jr, Howard D, Visser A, Crum BA, Nowak R, Beekman R, Kumar A, Ruzhansky K, Chen IA, Pulley MT, LaBoy SM, Fellman MA, Greene SM, Pasnoor M, Burns TM.

Neurology. 2017 Sep 5;89(10):1069-1077. doi: 10.1212/WNL.0000000000004341. Epub 2017 Aug 11.


Analysis of in vitro evolution reveals the underlying distribution of catalytic activity among random sequences.

Pressman A, Moretti JE, Campbell GW, Müller UF, Chen IA.

Nucleic Acids Res. 2017 Aug 21;45(14):8167-8179. doi: 10.1093/nar/gkx540.


IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes.

Hadjithomas M, Chen IA, Chu K, Huang J, Ratner A, Palaniappan K, Andersen E, Markowitz V, Kyrpides NC, Ivanova NN.

Nucleic Acids Res. 2017 Jan 4;45(D1):D560-D565. doi: 10.1093/nar/gkw1103. Epub 2016 Nov 29.


IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

Paez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Szeto E, Pillay M, Huang J, Markowitz VM, Nielsen T, Huntemann M, K Reddy TB, Pavlopoulos GA, Sullivan MB, Campbell BJ, Chen F, McMahon K, Hallam SJ, Denef V, Cavicchioli R, Caffrey SM, Streit WR, Webster J, Handley KM, Salekdeh GH, Tsesmetzis N, Setubal JC, Pope PB, Liu WT, Rivers AR, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D457-D465. doi: 10.1093/nar/gkw1030. Epub 2016 Oct 30.


IMG/M: integrated genome and metagenome comparative data analysis system.

Chen IA, Markowitz VM, Chu K, Palaniappan K, Szeto E, Pillay M, Ratner A, Huang J, Andersen E, Huntemann M, Varghese N, Hadjithomas M, Tennessen K, Nielsen T, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D507-D516. doi: 10.1093/nar/gkw929. Epub 2016 Oct 13.


From underwear to non-equilibrium thermodynamics: physical chemistry informs the origin of life.

Chen IA, de Vries MS.

Phys Chem Chem Phys. 2016 Jul 27;18(30):20005-6. doi: 10.1039/c6cp90169g. No abstract available.


What motivates individuals with sickle cell disease to talk with others about their illness? Reasons for and against sickle cell disease disclosure.

Derlega VJ, Maduro RS, Janda LH, Chen IA, Goodman BM 3rd.

J Health Psychol. 2018 Jan;23(1):103-113. doi: 10.1177/1359105316649786. Epub 2016 May 26.


Computational analysis of fitness landscapes and evolutionary networks from in vitro evolution experiments.

Xulvi-Brunet R, Campbell GW, Rajamani S, Jiménez JI, Chen IA.

Methods. 2016 Aug 15;106:86-96. doi: 10.1016/j.ymeth.2016.05.012. Epub 2016 May 19.


Size-dependent dielectrophoretic crossover frequency of spherical particles.

Weng PY, Chen IA, Yeh CK, Chen PY, Juang JY.

Biomicrofluidics. 2016 Feb 11;10(1):011909. doi: 10.1063/1.4941853. eCollection 2016 Jan.


Origin of Life: Protocells Red in Tooth and Claw.

Saha R, Chen IA.

Curr Biol. 2015 Dec 21;25(24):R1175-7. doi: 10.1016/j.cub.2015.11.007.


The RNA World as a Model System to Study the Origin of Life.

Pressman A, Blanco C, Chen IA.

Curr Biol. 2015 Oct 5;25(19):R953-63. doi: 10.1016/j.cub.2015.06.016. Review.


Ten years of maintaining and expanding a microbial genome and metagenome analysis system.

Markowitz VM, Chen IA, Chu K, Pati A, Ivanova NN, Kyrpides NC.

Trends Microbiol. 2015 Nov;23(11):730-741. doi: 10.1016/j.tim.2015.07.012. Epub 2015 Oct 14. Review.


Prebiotic chemistry: Replicating towards complexity.

Chen IA.

Nat Chem. 2015 Mar;7(3):191-2. doi: 10.1038/nchem.2188. No abstract available.


Molecular crowding and early evolution.

Saha R, Pohorille A, Chen IA.

Orig Life Evol Biosph. 2014 Dec;44(4):319-24. doi: 10.1007/s11084-014-9392-3. Epub 2015 Jan 14.


Experimental fitness landscapes to understand the molecular evolution of RNA-based life.

Athavale SS, Spicer B, Chen IA.

Curr Opin Chem Biol. 2014 Oct;22:35-9. doi: 10.1016/j.cbpa.2014.09.008. Epub 2014 Sep 29. Review.


How patients' self-disclosure about sickle cell pain episodes to significant others relates to living with sickle cell disease.

Derlega VJ, Janda LH, Miranda J, Chen IA, Goodman BM 3rd, Smith W.

Pain Med. 2014 Sep;15(9):1496-507. doi: 10.1111/pme.12535. Epub 2014 Aug 26.


Genetic drift suppresses bacterial conjugation in spatially structured populations.

Freese PD, Korolev KS, Jiménez JI, Chen IA.

Biophys J. 2014 Feb 18;106(4):944-54. doi: 10.1016/j.bpj.2014.01.012.


The paradox of dual roles in the RNA world: resolving the conflict between stable folding and templating ability.

Ivica NA, Obermayer B, Campbell GW, Rajamani S, Gerland U, Chen IA.

J Mol Evol. 2013 Sep;77(3):55-63.


Comprehensive experimental fitness landscape and evolutionary network for small RNA.

Jiménez JI, Xulvi-Brunet R, Campbell GW, Turk-MacLeod R, Chen IA.

Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):14984-9. doi: 10.1073/pnas.1307604110. Epub 2013 Aug 26.


Selection for replicases in protocells.

Bianconi G, Zhao K, Chen IA, Nowak MA.

PLoS Comput Biol. 2013;9(5):e1003051. doi: 10.1371/journal.pcbi.1003051. Epub 2013 May 9.


Primary adrenal de novo CD5-positive diffuse large B cell lymphoma.

Rashidi A, Bergeron CW, Fisher SI, Chen IA.

Ann Hematol. 2013 Sep;92(9):1281-2. doi: 10.1007/s00277-013-1690-8. Epub 2013 Feb 14. No abstract available.


A population-based experimental model for protein evolution: effects of mutation rate and selection stringency on evolutionary outcomes.

Leconte AM, Dickinson BC, Yang DD, Chen IA, Allen B, Liu DR.

Biochemistry. 2013 Feb 26;52(8):1490-9. doi: 10.1021/bi3016185. Epub 2013 Feb 14.


Cascade of reduced speed and accuracy after errors in enzyme-free copying of nucleic acid sequences.

Leu K, Kervio E, Obermayer B, Turk-MacLeod RM, Yuan C, Luevano JM Jr, Chen E, Gerland U, Richert C, Chen IA.

J Am Chem Soc. 2013 Jan 9;135(1):354-66. doi: 10.1021/ja3095558. Epub 2012 Dec 21.


Infectious disease emergencies: frontline clinical pearls.

Goodman BM 3rd, Boggs JP, Tahhan SG, Ryal JL, Chen IA.

Med Clin North Am. 2012 Nov;96(6):1033-66. doi: 10.1016/j.mcna.2012.09.001. Review.


Spontaneous network formation among cooperative RNA replicators.

Vaidya N, Manapat ML, Chen IA, Xulvi-Brunet R, Hayden EJ, Lehman N.

Nature. 2012 Nov 1;491(7422):72-7. doi: 10.1038/nature11549. Epub 2012 Oct 17.


White and blue fingers: a red flag in sickle cell disease.

Goodman BM 3rd, Chen IA.

J Gen Intern Med. 2013 Mar;28(3):477. doi: 10.1007/s11606-012-2238-7. Epub 2012 Oct 5. No abstract available.


From prelife to life: how chemical kinetics become evolutionary dynamics.

Chen IA, Nowak MA.

Acc Chem Res. 2012 Dec 18;45(12):2088-96. doi: 10.1021/ar2002683. Epub 2012 Feb 15.


Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences.

Derr J, Manapat ML, Rajamani S, Leu K, Xulvi-Brunet R, Joseph I, Nowak MA, Chen IA.

Nucleic Acids Res. 2012 May;40(10):4711-22. doi: 10.1093/nar/gks065. Epub 2012 Feb 7.


Comparing nurses' intent to leave or stay: differences of practice environment perceptions.

Lin SY, Chiang HY, Chen IaL.

Nurs Health Sci. 2011 Dec;13(4):463-7. doi: 10.1111/j.1442-2018.2011.00640.x. Epub 2011 Oct 20.


The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA.

Leu K, Obermayer B, Rajamani S, Gerland U, Chen IA.

Nucleic Acids Res. 2011 Oct;39(18):8135-47. doi: 10.1093/nar/gkr525. Epub 2011 Jun 30.


Inhibition of bacterial conjugation by phage M13 and its protein g3p: quantitative analysis and model.

Lin A, Jimenez J, Derr J, Vera P, Manapat ML, Esvelt KM, Villanueva L, Liu DR, Chen IA.

PLoS One. 2011;6(5):e19991. doi: 10.1371/journal.pone.0019991. Epub 2011 May 26.


Update in pain medicine.

Alford DP, Krebs EE, Chen IA, Nicolaidis C, Bair MJ, Liebschutz J.

J Gen Intern Med. 2010 Nov;25(11):1222-6. doi: 10.1007/s11606-010-1452-4. Epub 2010 Jul 15. No abstract available.


From self-assembled vesicles to protocells.

Chen IA, Walde P.

Cold Spring Harb Perspect Biol. 2010 Jul;2(7):a002170. doi: 10.1101/cshperspect.a002170. Epub 2010 Jun 2. Review.


Prevalence of vitamin D deficiency in adults with sickle cell disease.

Goodman BM 3rd, Artz N, Radford B, Chen IA.

J Natl Med Assoc. 2010 Apr;102(4):332-5.


Effect of stalling after mismatches on the error catastrophe in nonenzymatic nucleic acid replication.

Rajamani S, Ichida JK, Antal T, Treco DA, Leu K, Nowak MA, Szostak JW, Chen IA.

J Am Chem Soc. 2010 Apr 28;132(16):5880-5. doi: 10.1021/ja100780p.


The basic reproductive ratio of life.

Manapat ML, Chen IA, Nowak MA.

J Theor Biol. 2010 Apr 7;263(3):317-27. doi: 10.1016/j.jtbi.2009.12.020. Epub 2009 Dec 23.


Long-term video-EEG monitoring for paroxysmal events.

Lee YY, Lee MY, Chen IA, Tsai YT, Sung CY, Hsieh HY, Lim SN, Hung PW, Wu T.

Chang Gung Med J. 2009 May-Jun;32(3):305-12.


Cell division: breaking up is easy to do.

Chen IA.

Curr Biol. 2009 Apr 28;19(8):R327-8. doi: 10.1016/j.cub.2009.03.002.

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