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Interplay of motility and polymer-driven depletion forces in the initial stages of bacterial aggregation.

Porter MK, Preska Steinberg A, Ismagilov RF.

Soft Matter. 2019 Sep 21;15(35):7071-7079. doi: 10.1039/c9sm00791a. Epub 2019 Aug 23.


Microfluidic SlipChip device for multistep multiplexed biochemistry on a nanoliter scale.

Zhukov DV, Khorosheva EM, Khazaei T, Du W, Selck DA, Shishkin AA, Ismagilov RF.

Lab Chip. 2019 Oct 7;19(19):3200-3211. doi: 10.1039/c9lc00541b. Epub 2019 Aug 23.


Human-gut-microbiome on a chip.

Poceviciute R, Ismagilov RF.

Nat Biomed Eng. 2019 Jul;3(7):500-501. doi: 10.1038/s41551-019-0425-0. No abstract available.


Food Polyelectrolytes Compress the Colonic Mucus Hydrogel by a Donnan Mechanism.

Preska Steinberg A, Wang ZG, Ismagilov RF.

Biomacromolecules. 2019 Jul 8;20(7):2675-2683. doi: 10.1021/acs.biomac.9b00442. Epub 2019 Jun 19.


Multistep SlipChip for the Generation of Serial Dilution Nanoliter Arrays and Hepatitis B Viral Load Quantification by Digital Loop Mediated Isothermal Amplification.

Yu M, Chen X, Qu H, Ma L, Xu L, Lv W, Wang H, Ismagilov RF, Li M, Shen F.

Anal Chem. 2019 Jul 16;91(14):8751-8755. doi: 10.1021/acs.analchem.9b01270. Epub 2019 May 23.


High-molecular-weight polymers from dietary fiber drive aggregation of particulates in the murine small intestine.

Preska Steinberg A, Datta SS, Naragon T, Rolando JC, Bogatyrev SR, Ismagilov RF.

Elife. 2019 Jan 22;8. pii: e40387. doi: 10.7554/eLife.40387.


Real-Time, Digital LAMP with Commercial Microfluidic Chips Reveals the Interplay of Efficiency, Speed, and Background Amplification as a Function of Reaction Temperature and Time.

Rolando JC, Jue E, Schoepp NG, Ismagilov RF.

Anal Chem. 2019 Jan 2;91(1):1034-1042. doi: 10.1021/acs.analchem.8b04324. Epub 2018 Dec 19.


RNA markers enable phenotypic test of antibiotic susceptibility in Neisseria gonorrhoeae after 10 minutes of ciprofloxacin exposure.

Khazaei T, Barlow JT, Schoepp NG, Ismagilov RF.

Sci Rep. 2018 Aug 2;8(1):11606. doi: 10.1038/s41598-018-29707-w.


Rapid pathogen-specific phenotypic antibiotic susceptibility testing using digital LAMP quantification in clinical samples.

Schoepp NG, Schlappi TS, Curtis MS, Butkovich SS, Miller S, Humphries RM, Ismagilov RF.

Sci Transl Med. 2017 Oct 4;9(410). pii: eaal3693. doi: 10.1126/scitranslmed.aal3693.


Corrigendum: Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility after only 15 Minutes of Antibiotic Exposure.

Schoepp NG, Khorosheva EM, Schlappi TS, Curtis MS, Humphries RM, Hindler JA, Ismagilov RF.

Angew Chem Int Ed Engl. 2017 Sep 18;56(39):11675. doi: 10.1002/anie.201707742. No abstract available.


Conceptual and Experimental Tools to Understand Spatial Effects and Transport Phenomena in Nonlinear Biochemical Networks Illustrated with Patchy Switching.

Pompano RR, Chiang AH, Kastrup CJ, Ismagilov RF.

Annu Rev Biochem. 2017 Jun 20;86:333-356. doi: 10.1146/annurev-biochem-060815-014207. Review.


Instrument for Real-Time Digital Nucleic Acid Amplification on Custom Microfluidic Devices.

Selck DA, Ismagilov RF.

PLoS One. 2016 Oct 19;11(10):e0163060. doi: 10.1371/journal.pone.0163060. eCollection 2016.


Flow-through Capture and in Situ Amplification Can Enable Rapid Detection of a Few Single Molecules of Nucleic Acids from Several Milliliters of Solution.

Schlappi TS, McCalla SE, Schoepp NG, Ismagilov RF.

Anal Chem. 2016 Aug 2;88(15):7647-53. doi: 10.1021/acs.analchem.6b01485. Epub 2016 Jul 18.


Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility after only 15 Minutes of Antibiotic Exposure.

Schoepp NG, Khorosheva EM, Schlappi TS, Curtis MS, Humphries RM, Hindler JA, Ismagilov RF.

Angew Chem Int Ed Engl. 2016 Aug 8;55(33):9557-61. doi: 10.1002/anie.201602763. Epub 2016 Jun 30. Erratum in: Angew Chem Int Ed Engl. 2017 Sep 18;56(39):11675.


Polymers in the gut compress the colonic mucus hydrogel.

Datta SS, Preska Steinberg A, Ismagilov RF.

Proc Natl Acad Sci U S A. 2016 Jun 28;113(26):7041-6. doi: 10.1073/pnas.1602789113. Epub 2016 Jun 14.


Evaluating 3D printing to solve the sample-to-device interface for LRS and POC diagnostics: example of an interlock meter-mix device for metering and lysing clinical urine samples.

Jue E, Schoepp NG, Witters D, Ismagilov RF.

Lab Chip. 2016 May 21;16(10):1852-60. doi: 10.1039/c6lc00292g. Epub 2016 Apr 28.


Reading Out Single-Molecule Digital RNA and DNA Isothermal Amplification in Nanoliter Volumes with Unmodified Camera Phones.

Rodriguez-Manzano J, Karymov MA, Begolo S, Selck DA, Zhukov DV, Jue E, Ismagilov RF.

ACS Nano. 2016 Mar 22;10(3):3102-13. doi: 10.1021/acsnano.5b07338. Epub 2016 Feb 22.


High-Throughput Single-Cell Cultivation on Microfluidic Streak Plates.

Jiang CY, Dong L, Zhao JK, Hu X, Shen C, Qiao Y, Zhang X, Wang Y, Ismagilov RF, Liu SJ, Du W.

Appl Environ Microbiol. 2016 Feb 5;82(7):2210-8. doi: 10.1128/AEM.03588-15.


A biochemical network can control formation of a synthetic material by sensing numerous specific stimuli.

Hun Yeon J, Chan KY, Wong TC, Chan K, Sutherland MR, Ismagilov RF, Pryzdial EL, Kastrup CJ.

Sci Rep. 2015 May 15;5:10274. doi: 10.1038/srep10274.


Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis.

Yano JM, Yu K, Donaldson GP, Shastri GG, Ann P, Ma L, Nagler CR, Ismagilov RF, Mazmanian SK, Hsiao EY.

Cell. 2015 Apr 9;161(2):264-76. doi: 10.1016/j.cell.2015.02.047. Erratum in: Cell. 2015 Sep 24;163:258.


Advancing the speed, sensitivity and accuracy of biomolecular detection using multi-length-scale engineering.

Kelley SO, Mirkin CA, Walt DR, Ismagilov RF, Toner M, Sargent EH.

Nat Nanotechnol. 2014 Dec;9(12):969-80. doi: 10.1038/nnano.2014.261. Review.


Digital, ultrasensitive, end-point protein measurements with large dynamic range via Brownian trapping with drift.

Ge S, Liu W, Schlappi T, Ismagilov RF.

J Am Chem Soc. 2014 Oct 22;136(42):14662-5. doi: 10.1021/ja507849b. Epub 2014 Oct 7.


Rapid fucosylation of intestinal epithelium sustains host-commensal symbiosis in sickness.

Pickard JM, Maurice CF, Kinnebrew MA, Abt MC, Schenten D, Golovkina TV, Bogatyrev SR, Ismagilov RF, Pamer EG, Turnbaugh PJ, Chervonsky AV.

Nature. 2014 Oct 30;514(7524):638-41. doi: 10.1038/nature13823. Epub 2014 Oct 1.


The pumping lid: investigating multi-material 3D printing for equipment-free, programmable generation of positive and negative pressures for microfluidic applications.

Begolo S, Zhukov DV, Selck DA, Li L, Ismagilov RF.

Lab Chip. 2014 Dec 21;14(24):4616-28. doi: 10.1039/c4lc00910j. Epub 2014 Sep 18.


Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa.

Ma L, Kim J, Hatzenpichler R, Karymov MA, Hubert N, Hanan IM, Chang EB, Ismagilov RF.

Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9768-73. doi: 10.1073/pnas.1404753111. Epub 2014 Jun 25.


Individually addressable arrays of replica microbial cultures enabled by splitting SlipChips.

Ma L, Datta SS, Karymov MA, Pan Q, Begolo S, Ismagilov RF.

Integr Biol (Camb). 2014 Aug;6(8):796-805. doi: 10.1039/c4ib00109e.


Digital biology and chemistry.

Witters D, Sun B, Begolo S, Rodriguez-Manzano J, Robles W, Ismagilov RF.

Lab Chip. 2014 Sep 7;14(17):3225-32. doi: 10.1039/c4lc00248b. Review.


Measuring fate and rate of single-molecule competition of amplification and restriction digestion, and its use for rapid genotyping tested with hepatitis C viral RNA.

Sun B, Rodriguez-Manzano J, Selck DA, Khorosheva E, Karymov MA, Ismagilov RF.

Angew Chem Int Ed Engl. 2014 Jul 28;53(31):8088-8092. doi: 10.1002/anie.201403035. Epub 2014 Jun 2.


Increased robustness of single-molecule counting with microfluidics, digital isothermal amplification, and a mobile phone versus real-time kinetic measurements.

Selck DA, Karymov MA, Sun B, Ismagilov RF.

Anal Chem. 2013 Nov 19;85(22):11129-36. doi: 10.1021/ac4030413. Epub 2013 Nov 7.


Chemical analog-to-digital signal conversion based on robust threshold chemistry and its evaluation in the context of microfluidics-based quantitative assays.

Huynh T, Sun B, Li L, Nichols KP, Koyner JL, Ismagilov RF.

J Am Chem Soc. 2013 Oct 2;135(39):14775-83. doi: 10.1021/ja4062882. Epub 2013 Sep 24.


A microfluidic device for dry sample preservation in remote settings.

Begolo S, Shen F, Ismagilov RF.

Lab Chip. 2013 Nov 21;13(22):4331-42. doi: 10.1039/c3lc50747e.


A genetically encoded and gate for cell-targeted metabolic labeling of proteins.

Mahdavi A, Segall-Shapiro TH, Kou S, Jindal GA, Hoff KG, Liu S, Chitsaz M, Ismagilov RF, Silberg JJ, Tirrell DA.

J Am Chem Soc. 2013 Feb 27;135(8):2979-82. doi: 10.1021/ja400448f. Epub 2013 Feb 18.


Mechanistic evaluation of the pros and cons of digital RT-LAMP for HIV-1 viral load quantification on a microfluidic device and improved efficiency via a two-step digital protocol.

Sun B, Shen F, McCalla SE, Kreutz JE, Karymov MA, Ismagilov RF.

Anal Chem. 2013 Feb 5;85(3):1540-6. doi: 10.1021/ac3037206. Epub 2013 Jan 16.


Control of initiation, rate, and routing of spontaneous capillary-driven flow of liquid droplets through microfluidic channels on SlipChip.

Pompano RR, Platt CE, Karymov MA, Ismagilov RF.

Langmuir. 2012 Jan 24;28(3):1931-41. doi: 10.1021/la204399m. Epub 2012 Jan 10.


Multiplexed quantification of nucleic acids with large dynamic range using multivolume digital RT-PCR on a rotational SlipChip tested with HIV and hepatitis C viral load.

Shen F, Sun B, Kreutz JE, Davydova EK, Du W, Reddy PL, Joseph LJ, Ismagilov RF.

J Am Chem Soc. 2011 Nov 9;133(44):17705-12. doi: 10.1021/ja2060116. Epub 2011 Oct 13.


Theoretical design and analysis of multivolume digital assays with wide dynamic range validated experimentally with microfluidic digital PCR.

Kreutz JE, Munson T, Huynh T, Shen F, Du W, Ismagilov RF.

Anal Chem. 2011 Nov 1;83(21):8158-68. doi: 10.1021/ac201658s. Epub 2011 Oct 7.


Toward mechanistic understanding of nuclear reprocessing chemistries by quantifying lanthanide solvent extraction kinetics via microfluidics with constant interfacial area and rapid mixing.

Nichols KP, Pompano RR, Li L, Gelis AV, Ismagilov RF.

J Am Chem Soc. 2011 Oct 5;133(39):15721-9. doi: 10.1021/ja206020u. Epub 2011 Sep 2.


Three-dimensional nanocrystal superlattices grown in nanoliter microfluidic plugs.

Bodnarchuk MI, Li L, Fok A, Nachtergaele S, Ismagilov RF, Talapin DV.

J Am Chem Soc. 2011 Jun 15;133(23):8956-60. doi: 10.1021/ja201129n. Epub 2011 May 17.


Digital isothermal quantification of nucleic acids via simultaneous chemical initiation of recombinase polymerase amplification reactions on SlipChip.

Shen F, Davydova EK, Du W, Kreutz JE, Piepenburg O, Ismagilov RF.

Anal Chem. 2011 May 1;83(9):3533-40. doi: 10.1021/ac200247e. Epub 2011 Apr 8.


Microfluidics using spatially defined arrays of droplets in one, two, and three dimensions.

Pompano RR, Liu W, Du W, Ismagilov RF.

Annu Rev Anal Chem (Palo Alto Calif). 2011;4:59-81. doi: 10.1146/annurev.anchem.012809.102303. Review.


Complex function by design using spatially pre-structured synthetic microbial communities: degradation of pentachlorophenol in the presence of Hg(ii).

Kim HJ, Du W, Ismagilov RF.

Integr Biol (Camb). 2011 Feb;3(2):126-33. doi: 10.1039/c0ib00019a. Epub 2010 Aug 17.


Digital PCR on a SlipChip.

Shen F, Du W, Kreutz JE, Fok A, Ismagilov RF.

Lab Chip. 2010 Oct 21;10(20):2666-72. doi: 10.1039/c004521g. Epub 2010 Jul 1.


Chemical stimulation of the Arabidopsis thaliana root using multi-laminar flow on a microfluidic chip.

Meier M, Lucchetta EM, Ismagilov RF.

Lab Chip. 2010 Aug 21;10(16):2147-53. doi: 10.1039/c004629a. Epub 2010 Jun 11.


A Plug-Based Microfluidic System for Dispensing Lipidic Cubic Phase (LCP) Material Validated by Crystallizing Membrane Proteins in Lipidic Mesophases.

Li L, Fu Q, Kors CA, Stewart L, Nollert P, Laible PD, Ismagilov RF.

Microfluid Nanofluidics. 2010 Jun;8(6):789-798.


Molecular mechanism of MLL PHD3 and RNA recognition by the Cyp33 RRM domain.

Hom RA, Chang PY, Roy S, Musselman CA, Glass KC, Selezneva AI, Gozani O, Ismagilov RF, Cleary ML, Kutateladze TG.

J Mol Biol. 2010 Jul 9;400(2):145-54. doi: 10.1016/j.jmb.2010.04.067. Epub 2010 May 8.


Nanoliter multiplex PCR arrays on a SlipChip.

Shen F, Du W, Davydova EK, Karymov MA, Pandey J, Ismagilov RF.

Anal Chem. 2010 Jun 1;82(11):4606-12. doi: 10.1021/ac1007249.


SlipChip for immunoassays in nanoliter volumes.

Liu W, Chen D, Du W, Nichols KP, Ismagilov RF.

Anal Chem. 2010 Apr 15;82(8):3276-82. doi: 10.1021/ac100044c.


Protein crystallization using microfluidic technologies based on valves, droplets, and SlipChip.

Li L, Ismagilov RF.

Annu Rev Biophys. 2010;39:139-58. doi: 10.1146/annurev.biophys.050708.133630. Review.


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