The reprints of articles are provided for personal and educational use only, and are subject to the copyright of their respective publishers.

[2017][2016][2015][2014] [2013] [2012] [2011] [2010] [2009] [2008] [2007] [2006] [2005] [2004] [2003]

Joint first authorship is indicated by *

It is Ismagilov Group policy to include a detailed statement of author contributions within each publication; for easy reference, these statements are also provided below as PDFs.


Emily S. Savela*, Alexander Winnett*, Anna E. Romano*, Michael K. Porter, Natasha Shelby, Reid Akana, Jenny Ji, Matthew M. Cooper, Noah W. Schlenker, Jessica A. Reyes, Alyssa M. Carter, Jacob T. Barlow, Colten Tognazzini, Matthew Feaster, Ying-Ying Goh, Rustem F. Ismagilov. 2021. "Quantitative SARS-CoV-2 viral-load curves in paired saliva and nasal swabs inform appropriate respiratory sampling site and analytical test sensitivity required for earliest viral detection." Posted 8/26/21. medRxiv doi:10.1101/2021.04.02.21254771

PRIOR VERSION: "SARS-CoV-2 is detectable using sensitive RNA saliva testing days before viral load reaches detection range of low-sensitivity nasal swab tests." Posted 4/7/21. medrxiv doi: 10.1101/2021.04.02.21254771

Alexander Winnett*, Matthew M. Cooper*, Natasha Shelby*, Anna E. Romano, Jessica A. Reyes, Jenny Ji, Michael K. Porter, Emily S. Savela, Jacob T. Barlow, Reid Akana, Colten Tognazzini, Matthew Feaster, Ying-Ying Goh, Rustem F. Ismagilov. 2020. "SARS-CoV-2 Viral Load in Saliva Rises Gradually and to Moderate Levels in Some Humans." medRxiv. doi:10.1101/2020.12.09.20239467

Erik Jue and Rustem F. Ismagilov. 2020. “Commercial stocks of SARS-CoV-2 RNA may report low concentration values, leading to artificially increased apparent sensitivity of diagnostic assays” medRxiv. medRxiv doi: 10.1101/2020.04.28.20077602

Said R. Bogatyrev and Rustem F. Ismagilov. 2020. "Quantitative microbiome profiling in lumenal and tissue samples with broad coverage and dynamic range via a single-step 16S rRNA gene DNA copy quantification and amplicon barcoding." bioRxiv. doi:10.1101/2020.01.22.914705


164. Jacob Barlow, Gabriela Leite, Anna E. Romano, Rashin Sedighi, Christine Chang, Shreya Celly, Ali Rezaie, Ruchi Mathur, Mark Pimentel, Rustem F. Ismagilov. 2021. "Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome." Accepted Microbiome. doi:pending

163. Mary V. Arrastia*, Joanna W. Jachowicz*, Noah Ollikainen, Matthew S. Curtis, Charlotte Lai, Sofia Quinodoz, David A. Selck, Rustem F. Ismagilov, Mitchell Guttman. 2021. "Single-cell measurement of higher-order 3D genome organization with scSPRITE." Nature Biotechnology. Manuscript (15MB)

PREPRINT: Mary V. Arrastia*, Joanna W. Jachowicz*, Noah Ollikainen, Matthew S. Curtis, Charlotte Lai, Sofia Quinodoz, David A. Selck, Mitchell Guttman, Rustem F. Ismagilov. 2020. A single-cell method to map higher-order 3D genome organization in thousands of individual cells reveals structural heterogeneity in mouse ES cells. bioRxiv. Posted 8/12/20. biorxiv doi: 10.1101/2020.08.11.242081v1

162. Christine A. Olson, Alonso J. Iniguez, Grace E. Yang, Ping Fang, Geoffrey N. Pronovost, Kelly G. Jameson, Tomiko K. Rendon, Jorge Paramo, Jacob T. Barlow, Rustem F. Ismagilov, and Elaine Y. Hsiao. "Alterations in the gut microbiota contribute to cognitive impairment induced by the ketogenic diet and hypoxia." Cell, Host & Microbe. doi:10.1016/j.chom.2021.07.004 Manuscript (3MB)

161. Wei-Li Wu, Mark D. Adame, Chia-Wei Liou, Jacob T. Barlow, Tzu-Ting Lai, Gil Sharon, Catherine E. Schretter, Brittany D. Needham, Madelyn I. Wang, Weiyi Tang, James Ousey, Yuan-Yuan Lin, Tzu-Hsuan Yao, Reem Abdel-Haq, Keith Beadle, Viviana Gradinaru, Rustem F. Ismagilov & Sarkis K. Mazmanian. "Microbiota regulate social behavior via stress response neurons in the brain." Nature 595:409–414. Manuscript (12MB)


160. Tahmineh Khazaei, Rory L. Williams, Said R. Bogatyrev, John C. Doyle, Christopher S. Henry, Rustem F. Ismagilov. 2020. "Metabolic multi-stability and hysteresis in a model aerobe-anaerobe microbiome community." Science Advances 6:eaba0353. Manuscript (1MB) SI (2MB) Author Contributions

PREPRINT: Posted 2/29/20. bioRxiv. doi: 10.1101/2020.02.28.968941

159. Jacob T. Barlow, Said R. Bogatyrev, and Rustem F. Ismagilov. 2020. "A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities." Nature Communications 11:2590. Manuscript (1.5MB) SI (2.4MB) Author Contributions

PREPRINT: Posted 2/28/20. bioRxiv. doi: 10.1101/2020.02.28.970087v1

158. Emily S. Savela*, Nathan G. Schoepp*, Matthew M. Cooper, Justin C. Rolando, Jeffrey D. Klausner, Olusegun O. Soge, and Rustem F. Ismagilov. 2020. "Surfactant-enhanced DNA accessibility to nuclease accelerates phenotypic β-lactam antibiotic susceptibility testing of Neisseria gonorrhoeae." PLoS Biology. 18(3):e3000651. Manuscript (2MB) Author Contributions

157. Nathan G. Schoepp, Eric J. Liaw, Alexander Winnett, Emily S. Savela, Omai B. Garner, and Rustem F. Ismagilov. 2020. "Differential DNA Accessibility to Polymerase during Nucleic Acid Amplification Enables 30-Minute Phenotypic Beta-lactam Antibiotic Susceptibility Testing of Carbapenem-resistant Enterobacteriaceae (CRE)." PLoS Biology. 18(3):e3000652. Manuscript (2MB) Author Contributions

156. Justin C. Rolando, Erik Jue, Jacob T. Barlow, and Rustem F. Ismagilov. 2020. "Real-time kinetics and high-resolution melt curves in single-molecule digital LAMP to differentiate and study specific and nonspecific amplification." Nucleic Acids Research. gkaa099 doi:10.1093/nar/gkaa099. Manuscript (1.2MB) Supplements (zip). Author Contributions

155. Ziqing Yu, Weiyuan Lyu, Mengchao Yu, Qian Wang, Haijun Qu, Rustem F. Ismagilov, Xu Han, Dongmei Lai, and Feng Shen. 2020. "Self-partitioning SlipChip for slip-induced droplet formation and human papillomavirus viral load quantification with digital LAMP." Biosensors and Bioelectronics. doi:10.1016/j.bios.2020.112107. Manuscript

154. Said R. Bogatyrev, Justin C. Rolando, and Rustem F. Ismagilov. 2020. "Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine." Microbiome. 8(19):1-22. doi:10.1186/s40168-020-0785-4. Manuscript (2MB) SI (1MB) Author Contributions

153. Erik Jue, Daan Witters, and Rustem F. Ismagilov. 2020. "Two-phase wash to solve the ubiquitous contaminant-carryover problem in commercial nucleic-acid extraction kits." Scientific Reports. 10(1940). doi:10.1038/s41598-020-58586-3. Manuscript (3MB) SI (2MB). Author Contributions


152. Michael Porter, Asher Preska Steinberg, and Rustem F. Ismagilov. 2019. "Interplay of motility and polymer-driven depletion forces in the initial stages of bacterial aggregation.” Soft Matter. 15:7071-7079. doi:10.1039/C9SM00791A. Manuscript (4MB). SI (526KB). Author Contributions

151. Dmitriy V. Zhukov, Eugenia M. Khorosheva, Tahmineh Khazaei, Wenbin Du, David A. Selck, Alexander Shishkin, and Rustem F. Ismagilov. 2019. "Microfluidic SlipChip device for multistep multiplexed biochemistry on a nanoliter scale." Lab on a Chip. 19(19):3200-3211. doi:10.1039/C9LC00541B. Manuscript (5MB) SI (1MB). Author Contributions

150. Roberta Poceviciute and Rustem F. Ismagilov. 2019. NEWS & VIEWS "Human-gut-microbiome on a chip." Nature Biomedical Engineering. doi:10.1038/s41551-019-0425-0

149. Asher Preska Steinberg, Zhen-Gang Wang, and Rustem F. Ismagilov. 2019. "Food polyelectrolytes compress the colonic mucus hydrogel by a Donnan mechanism." Biomacromolecules. 20(7):2675-2683. doi:10.1021/acs.biomac.9b00442 Manuscript (2MB). Author Contributions

148. Mengchao Yu, Xiaoying Chen, Haijun Qu, Liang Ma, Lei Xu, Weiyuan Lv, Hua Wang, Rustem F. Ismagilov, Min Li, Feng Shen. 2019. "Multistep SlipChip for the Generation of Serial Dilution Nanoliter Arrays and Hepatitis B Viral Load Quantification by Digital Loop Mediated Isothermal Amplification." Analytical Chemistry. 91(14):8751-8755. doi:10.1021/acs.analchem.9b01270. Manuscript (2MB) SI (323KB). Author Contributions

147. Asher Preska Steinberg, Sujit S. Datta, Thomas Naragon, Justin C. Rolando, Said R. Bogatyrev, and Rustem F. Ismagilov. 2019. "High-molecular-weight polymers from dietary fiber drive aggregation of particulates in the murine small intestine." eLife. 8:e40387. Manuscript (15MB) Data (direct link). Author Contributions

PREPRINT: Posted 12/10/18. bioRxiv. doi: 10.1101/490920

146. Justin C. Rolando, Erik Jue, Nathan G. Schoepp, and Rustem F. Ismagilov. 2019. "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." Analytical Chemistry. 91(1):1034–1042. Manuscript (2.5MB) SI (380KB). Author Contributions


145. Tahmineh Khazaei, Jacob T. Barlow, Nathan G. Schoepp, and Rustem F. Ismagilov. 2018. "RNA markers enable phenotypic test of antibiotic susceptibility in Neisseria gonorrhoeae after 10 minutes of ciprofloxacin exposure." Scientific Reports. 8:11606. doi:10.1038/s41598-018-29707-w. Manuscript (2MB) + SI (77KB). Author Contributions


144. *Nathan G. Schoepp, *Travis S. Schlappi, Matthew S. Curtis, Slava S. Butkovich, Shelley Miller, Romney M. Humphries, Rustem F. Ismagilov. 2017. "Rapid pathogen-specific phenotypic antibiotic susceptibility testing using digital LAMP quantification in clinical samples." Science Translational Medicine. 9(410): eaal3693. doi:10.1126/scitranslmed.aal3693 Manuscript (1.4MB) SI (1.2MB). Author Contributions

143. Rebecca R. Pompano, Andrew H. Chiang, Christian J. Kastrup, and Rustem F. Ismagilov. 2017. "Conceptual and Experimental Tools to Understand Spatial Effects and Transport Phenomena in Nonlinear Biochemical Networks Illustrated with Patchy Switching." Annual Review of Biochemistry. 86:20.1–20.24. doi:10.1146/annurev-biochem-060815-014207 Manuscript (3MB).


142. David A. Selck and Rustem F. Ismagilov. 2016 "Instrument for Real-Time Digital Nucleic Acid Amplification on Custom Microfluidic Devices" PLoS One. 11(10): e0163060. doi:10.1371/journal.pone.0163060 Manuscript (4.1MB) SI files. Author Contributions

141. *Travis S. Schlappi, *Stephanie E. McCalla, Nathan G. Schoepp, and Rustem F. Ismagilov. 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." Analytical Chemistry. 88 (15): 7647–765. doi: 10.1021/acs.analchem.6b01485 Manuscript (3MB) SI (812KB). Author Contributions

140. *Nathan G. Schoepp, *Eugenia M. Khorosheva, Travis S. Schlappi, Matthew S. Curtis, Romney M. Humphries, Janet A. Hindler and Rustem F. Ismagilov. 2016. "Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility After Only 15 Minutes of Antibiotic Exposure." Angewandte Chemie. 55(33):9557–9561. doi: 10.1002/anie.201602763 Manuscript (2.3MB) SI (664KB). Author Contributions

139. Sujit S. Datta, Asher Preska Steinberg, and Rustem F. Ismagilov. 2016 "Polymers in the gut compress the colonic mucus hydrogel." PNAS 113(26):7041-7046. doi: 10.1073/pnas.1602789113 Manuscript+SI (2.3MB). Author Contributions

138. Erik Jue, Nathan G. Schoepp, Daan Witters, and Rustem F. Ismagilov. 2016 "Evaluating 3D printing to solve the sample-todevice interface for LRS and POC diagnostics: example of an interlock meter-mix device for metering and lysing clinical urine samples." Lab on a Chip. 16:1852-1860. doi: 10.1039/c6lc00292g Manuscript (2.6MB) movie (5.6MB).

137. *Jesus Rodriguez-Manzano,*Mikhail A. Karymov, Stefano Begolo, David A. Selck, Dmitriy V. Zhukov, Erik Jue, and Rustem F. Ismagilov. 2016 "Reading Out Single-Molecule Digital RNA and DNA Isothermal Amplification in Nanoliter Volumes with Unmodified Camera Phones." ACS NANO. 10(3): 3102-3113. doi: 10.1021/acsnano.5b07338 Manuscript (7.5MB) SI (3MB).

136. Cheng-Ying Jiang, Libing Dong, Jian-Kang Zhao, Xiaofang Hu, Chaohua Shen, Yuxin Qiao, Xinyue Zhang, Yapei Wang, Rustem F. Ismagilov, Shuang-Jiang Liu and Wenbin Du. 2016 "High throughput Single-cell Cultivation on Microfluidic Streak Plates." Applied and Environmental Microbiology. 82(7):2210-2218. doi: 10.1128/AEM.03588-15. Manuscript (3.7MB) SI (1.8MB).

135. *Eugenia M. Khorosheva, *Mikhail A. Karymov, David A. Selck and Rustem F. Ismagilov. 2016 "Lack of correlation between reaction speed and analytical sensitivity in isothermal amplification reveals the value of digital methods for optimization: validation using digital real-time RT-LAMP." Nucleic Acids Research. 44(2):e10. doi: 10.1093/nar/gkv877 Manuscript (2.8MB) SI (1.7MB).


134. *Ju Hun Yeon, *Karen, Y. T. Chan, Ting-Chia Wong, Kelvin Chan, Michael R. Sutherland, Rustem F. Ismagilov, Edward L. G. Pryzdial and Christian J. Kastrup. 2015 "A biochemical network can control formation of a synthetic material by sensing numerous specific stimuli." Scientific Reports, 5:10274 pdf (1,309 KB) SI (371 KB).

133. Jessica M. Yano, Kristie Yu, Gregory P. Donaldson, Gauri G. Shastri, Phoebe Ann Liang Ma, Cathryn R. Nagler, Rustem F. Ismagilov, Sarkis K. Mazmanian and Elaine Y. Hsiao. 2015 "Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis." Cell, 161 (2):264-276. pdf (2,980 KB) SI (1,606 KB)


132. Shana O. Kelley, Chad A. Mirkin, David R. Walt, Rustem F. Ismagilov, Mehmet Toner, and Edward H. Sargent. "Advancing the speed, sensitivity and accuracy of biomolecular detection using multi-length-scale engineering." Nature Nanotechnology 2014 9:969-980. DOI: 0.1038/NNANO.2014.261. pdf (1,799 KB).

131. *Shencheng Ge, *Weishan Liu, Travis Schlappi, and Rustem F. Ismagilov. "Digital, Ultrasensitive, End-Point Protein Measurements with Large Dynamic Range via Brownian Trapping with Drift" JACS 2014 136:14662-14665. DOI: 10.1021/ja507849b. pdf (2,182 KB) SI (4,180KB).

130. Joseph M. Pickard, Corinne F. Maurice, Melissa A. Kinnebrew, Michael C. Abt, Dominik Schenten, Tatyana V. Golovkina, Said R. Bogatyrev, Rustem F. Ismagilov, Eric G. Pamer, Peter J. Turnbaugh, and Alexander V. Chervonsky. "Rapid fucosylation of intestinal epithelium sustains host–commensal symbiosis in sickness." Nature. 2014 514:638–641. DOI: 10.1038/nature13823. pdf (5,236 KB) SI (1,095 KB).
Featured in Nature News and Views pdf (991 KB).

129. *Stefano Begolo, *Dmitriy V. Zhukov, David A. Selck, Liang Li, and Rustem F. Ismagilov. "The Pumping Lid: investigating multi-material 3D Printing for Equipment-Free, Programmable Generation of Positive and Negative Pressures for Microfluidic Applications." Lab on a Chip. 2014 14(24):4616-4628. DOI: 10.1039/C4LC00910J, pdf (6,224 KB), SI (844 KB).

128. Liang Ma, Jungwoo Kim, Roland Hatzenpichler, Mikhail A. Karymov, Nathaniel Hubert, Ira M. Hanan, Eugene B. Chang, and Rustem F. Ismagilov. "Gene-targeted Microfluidic Cultivation Validated by Isolation of a Gut Bacterium Listed in Human Microbiome Project's Most Wanted taxa." PNAS 2014 111(27):9768-9773, pdf (1,330 KB), full text with SI (3,550 KB).

127. Liang Ma, Sujit S. Datta, Mikhail A. Karymov, Qichao Pan, Stefano Begolo, Rustem F. Ismagilov. "Individually addressable arrays of  replica microbial cultures enabled by splitting SlipChips." Integr. Biol. 2014 6(8):796-805, DOI: 10.1039/C4IB00109E. 
pdf (2,700 KB) SI (2,300 KB).

126. Daan Witters, Bing Sun, Stefano Begolo, Jesus Rodriguez-Manzano, Whitney Robles, and Rustem F. Ismagilov, "Digital Biology and Chemistry," Lab on a Chip 2014 14 (17): 3225-3232, DOI: 10.1039/C4LC00248B, pdf (3,300 KB) video s1 link, video s2 link.

125. *Bing Sun, *Jesus Rodriguez-Manzano, David A. Selck, Eugenia Khorosheva, Mikhail A. Karymov and Rustem F. Ismagilov, "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," Angewandte Chemie 2014 53(31):8088-8092, DOI: 10.1002/anie.201403035; pdf (1,200 KB) SI (872 KB).


124. *David A. Selck, *Mikhail A. Karymov, Bing Sun, and Rustem F. Ismagilov, "Increased Robustness of Single-Molecule Counting with Microfluidics, Digital Isothermal Amplification, and a Mobile Phone versus Real-Time Kinetic Measurements," Analytical Chemistry 2013 85: 11129-11136, pdf (3,061 KB), SI (2,355 KB), video s1 link.

123. Toan Huynh, Bing Sun, Liang Li, Kevin P. Nichols, Jay L. Koyner, and Rustem F. Ismagilov, "Chemical Analog-to-Digital Signal Conversion Based on Robust Threshold Chemistry and Its Evaluation in the Context of Microfluidics-Based Quantitative Assays," JACS 2013 135: 14775–14783, pdf (2,471 KB), SI (175 KB).

122. Stefano Begolo, Feng Shen, and Rustem F. Ismagilov, "A Microfluidic Device for Dry Sample Preservation in Remote Settings," Lab Chip 2013 13: 4331-4342, pdf (8,188 KB), supporting information (28,487 KB), movie S1, movie S2, movie S3.

121. Alborz Mahdavi, Thomas H. Segall-Shapiro, Songzi Kou, Granton A. Jindal, Kevin G. Hoff, Shirley Liu, Mohsen Chitsaz, Rustem F. Ismagilov, Jonathan J. Silberg, and David A. Tirrell, "A Genetically Encoded AND Gate for Cell-Targeted Metabolic Labeling of Proteins," JACS 2013 135: 2979-2982, pdf (1,788 KB), SI (2,030 KB).

120. Bing Sun, Feng Shen, Stephanie E. McCalla, Jason E. Kreutz, Mikhail A. Karymov, and Rustem F. Ismagilov, "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," Analytical Chemistry 2013 85: 1540-1546, pdf (1,295 KB), SI (403 KB).

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119. Rebecca R. Pompano, Carol E. Platt, Mikhail A. Karymov, and Rustem F. Ismagilov, "Control of Initiation, Rate, and Routing of Spontaneous Capillary-Driven Flow of Liquid Droplets through Microfluidic Channels on SlipChip," Langmuir 2012 28: 1931-1941, pdf (3,230 KB), supporting information (1,224 KB), supporting movie 1 (670 KB), supporting movie 2 (391 KB), supporting movie 3 (1,260 KB)

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118. Feng Shen, Bing Sun, Jason E. Kreutz, Elena K. Davydova, Wenbin Du, Poluru L. Reddy, Loren J. Joseph, and Rustem F. Ismagilov, "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," JACS 2011 133: 17705-17712, pdf (4,870 KB), SI (105 KB)

117. Jason E. Kreutz, Todd Munson, Toan Huynh, Feng Shen, Wenbin Du, and Rustem F. Ismagilov, "Theoretical Design and Analysis of Multivolume Digital Assays with Wide Dynamic Range Validated Experimentally with Microfluidic Digital PCR," Analytical Chemistry 2011 83: 8158-8168, pdf (3,280 KB), SI (199 KB), software .zip (117 KB)

116. Kevin P. Nichols, Rebecca R. Pompano, Liang Li, Artem V. Gelis, and Rustem F. Ismagilov, "Toward Mechanistic Understanding of Nuclear Reprocessing Chemistries by Quantifying Lanthanide Solvent Extraction Kinetics via Microfluidics with Constant Interfacial Area and Rapid Mixing," JACS 2011 133: 15721-15729, pdf (1,040 KB), SI (112 KB)

115. Maryna I. Bodnarchuk, Liang Li, Alice Fok, Sigrid Nachtergaele, Rustem F. Ismagilov, Dmitri V. Talapin, "Three-Dimensional Nanocrystal Superlattices Grown in Nanoliter Microfluidic Plugs," JACS 2011 133: 8956-8960, pdf (2,777 KB), SI (9,335 KB), Movie (138,246 KB)

114. Rebecca R. Pompano, Weishan Liu, Wenbin Du, and Rustem F. Ismagilov, "Microfluidics Using Spatially Defined Arrays of Droplets in One, Two, and Three Dimensions," Annual Review of Analytical Chemistry 2011 4:59-81, pdf (1,860 KB)

113. Feng Shen, Elena K. Davydova, Wenbin Du, Jason E. Kreutz, Olaf Piepenburg, and Rustem F. Ismagilov, "Digital Isothermal Quantification of Nucleic Acids via Simultaneous Chemical Initiation of Recombinase Polymerase Amplification Reactions on SlipChip," Analytical Chemistry 2011 83:3533-3540, pdf (4,190 KB), SI (519 KB)

112. Hyun Jung Kim, Wenbin Du and Rustem F. Ismagilov, "Complex function by design using spatially pre-structured synthetic microbial communities: degradation of pentachlorophenol in the presence of Hg(II)," Integrative Biology 2011 3: 126-133 pdf (1,566 KB), SI (112 KB)

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111. Robert A. Hom, Pei-Yun Chang, Siddhartha Roy, Catherine A. Musselman, Karen C. Glass, Anna I. Selezneva, Or Gozani, Rustem F. Ismagilov, Michael L. Cleary and Tatiana G. Kutateladze, "Molecular Mechanism of MLL PHD3 and RNA Recognition by the Cyp33 RRM Domain," J. Mol. Biol. 2010 400: 145-154 pdf (1,280 KB)

110. Matthias Meier, Elena M. Lucchetta, and Rustem F. Ismagilov, "Chemical stimulation of the Arabidopsis thaliana root using multi-laminar flow on a microfluidic chip," Lab Chip 2010 10: 2147-2153 pdf (281 KB)

109. Feng Shen, Wenbin Du, Jason E. Kreutz, Alice Fok, and Rustem F. Ismagilov, "Digital PCR on a SlipChip," Lab Chip 2010 10: 2666-2672 pdf (536 KB) SI (285 KB) cover (291 KB)

108. Liang Li, Mikhail A. Karymov, Kevin P. Nichols, and Rustem F. Ismagilov, "Dead-End Filling of SlipChip Evaluated Theoretically and Experimentally as a Function of the Surface Chemistry and the Gap Size between the Plates for Lubricated and Dry SlipChips," Langmuir 2010 26:12465-12471 pdf (4,584 KB) SI (369 KB) movieS1 (3,773 KB)

107. Feng Shen, Wenbin Du, Elena K. Davydova, Mikhail A. Karymov, Janmajay Pandey, and
Rustem F. Ismagilov, "Nanoliter Multiplex PCR Arrays on a SlipChip," Analytical Chemistry 2010 82:4606-4612 pdf (4,656 KB) SI (88 KB)

106. Weishan Liu, Delai Chen, Wenbin Du, Kevin P. Nichols, and Rustem F. Ismagilov, "SlipChip for Immunoassays in Nanoliter Volumes," Analytical Chemistry 2010 82:3276-3282 pdf (4,735 KB) SI (94 KB)

105. Liang Li and Rustem F. Ismagilov, "Protein Crystallization Using Microfluidic Technologies Based on Valves, Droplets, and SlipChip," Annu. Rev. Biophys 2010 39: 139-158 link

104. Meghan E. Vincent, Weishan Liu, Elizabeth B. Haney , and Rustem F. Ismagilov, "Microfluidic stochastic confinement enhances analysis of rare cells by isolating cells and creating high density environments for control of diffusible signals," Chem. Soc. Rev. 2010 39: 974-984 pdf (2,476 KB)

103. Jason E. Kreutz, Anton Shukhaev, Wenbin Du, Sasha Druskin, Olafs Daugulis, and Rustem F. Ismagilov, "Evolution of Catalysts Directed by Genetic Algorithms in a Plug-Based Microfluidic Device Tested with Oxidation of Methane by Oxygen," JACS 2010 132:3128-3132 pdf (2,203 KB) SI (793 KB) movie S1 (12,896 KB)

102. Liang Li, Wenbin Du, and Rustem F. Ismagilov, "Multiparameter Screening on SlipChip Used for Nanoliter Protein Crystallization Combining Free Interface Diffusion and Microbatch Methods," JACS 2010 132: 112-119 pdf (5,943 KB) SI (368 KB)movieS1 (6,932 KB)

101. Liang Li, Wenbin Du, and Rustem F. Ismagilov, "User-Loaded SlipChip for Equipment-Free Multiplexed Nanoliter-Scale Experiments," JACS 2010 132: 106-111 pdf (4,116 KB) SI (215 KB) movieS1 (3,100 KB) movieS2 (12,630 KB)

100. Liang Li, Qiang Fu, Christopher A. Kors, Lance Stewart, Peter Nollert, Philip D. Laible, and Rustem F. Ismagilov, "A Plug-Based Microfluidic System for Dispensing Lipidic Cubic Phase (LCP) Material Validated by Crystallizing Membrane Proteins in Lipidic Mesophases," Microfluidics and Nanofluidics 20108:789-798 pdf (549 KB) SI (21 KB)

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99. Feng Shen, Rebecca R. Pompano, Christian J. Kastrup, and Rustem F. Ismagilov, "Confinement Regulates Complex Biochemical Networks: Initiation of Blood Clotting by ‘Diffusion Acting’," Biophysical Journal 2009 97: 2137-2145 pdf (712 KB) supporting information (794 KB)

98. Elena M. Lucchetta,Richard W. Carthew, and Rustem F. Ismagilov, "The Endo-siRNA Pathway Is Essential for Robust Development of the DrosophilaEmbryo,” PLoS ONE. 2009 4: e7576 pdf (626 KB) supporting information (2,698 KB)

97. Nina S. Ponomarenko, Liang Li, Antony R. Marino, Valentina Tereshko, Agnes Ostafin, Julia A. Popova, Edward J. Bylina, Rustem F. Ismagilov, and James R. Norris Jr., "Structural and spectropotentiometric analysis of Blastochloris viridis heterodimer mutant reaction center," Biochimica et Biophysica Acta 2009 1788:1822-1831 pdf (1,645 KB)

96. Delai Chen, Wenbin Du, and Rustem F. Ismagilov, "Using TIRF microscopy to quantify and confirm efficient mass transfer at the substrate surface of the chemistrode," New Journal of Physics 2009 11: 075017 pdf (603 KB) movieS1 (2,606 KB) movieS2 (337 KB)

95. James Q. Boedicker, Meghan E. Vincent, and Rustem F. Ismagilov, "Microfluidic Confinement of Single Cells of Bacteria in Small Volumes Initiates High-Density Behavior of Quorum Sensing and Growth and Reveals Its Variability," Angew. Chem. Int. Ed. 2009 48: 5908-5911 pdf (774 KB) supporting information (1,586 KB)

94. Wenbin Du, Liang Li, Kevin P. Nichols, and Rustem F. Ismagilov, "SlipChip," Lab Chip 2009 9: 2286-2292 pdf (418 KB) supporting information (78 KB) movieS1 (3,206 KB)

93. Weishan Liu, Hyun Jung Kim , Elena M. Lucchetta , Wenbin Du, and Rustem F. Ismagilov, "Isolation, incubation, and parallel functional testing and identification by FISH of rare microbial single-copy cells from multi-species mixtures using the combination of chemistrode and stochastic confinement," Lab Chip Lab Chip 2009 9: 2153-2162 pdf (446 KB) supporting information (205 KB)

92. Jason E. Kreutz, Liang Li, L. Spencer Roach, Takuji Hatakeyama, and Rustem F. Ismagilov, "Laterally Mobile, Functionalized Self-Assembled Monolayers at the Fluorous-Aqueous Interface in a Plug-Based Microfluidic System: Characterization and Testing with Membrane Protein Crystallization," JACS 2009 131: 6042 - 6043 pdf (528 KB) supporting information (1,043 KB)

91. Ying Liu, and Rustem F. Ismagilov, "Dynamics of Coalescence of Plugs with a Hydrophilic Wetting Layer Induced by Flow in a Microfluidic Chemistrode," Langmuir 2009 25: 2854-2859 pdf (380 KB)

90. Matthias Meier, Julia Kennedy-Darling, Se Hoon Choi, Eric M. Norstrom, Sangram S. Sisodia, and Rustem F. Ismagilov, "Plug-Based Microfluidics with Defined Surface Chemistry to Miniaturize and Control Aggregation of Amyloidogenic Peptides," Angew. Chem. Int. Ed.2009 48: 1487 - 1489 pdf (630 KB) supporting information (201 KB)

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89. *Hyun Jung Kim, *James Q. Boedicker, Jang Wook Choi, and Rustem F. Ismagilov, "Defined spatial structure stabilizes a synthetic multispecies bacterial community," PNAS 2008 105:18188- 18193 pdf (1,138 KB) supporting information (1,970 KB)

88. Christian J. Kastrup, James Q. Boedicker, Andrei P. Pomerantsev, Mahtab Moayeri, Yao Bian, Rebecca R. Pompano, Timothy R. Kline, Patricia Sylvestre, Feng Shen, Stephen H. Leppla, Wei-Jen Tang, and Rustem F. Ismagilov, "Spatial localization of bacteria controls coagulation of human blood by 'quorum acting'," Nature Chemical Biology 2008 4:742-750 pdf (611 KB) supporting information (2,049 KB)

87. Elena M. Lucchetta, Meghan E. Vincent, and Rustem F. Ismagilov, "A Precise Bicoid Gradient Is Nonessential during Cycles 11-13 for Precise Patterning in the Drosophila Blastoderm,” PLoS ONE. 2008 3: e3651 pdf (1,042 KB) supporting information (2,199 KB) movieS1 (102,875 KB) movieS2 (31,131 KB) movieS3 (14,175 KB) movieS4 (28,945KB) movieS5 (54,574 KB) movieS6 (18,938 KB)

86. *Delai Chen, *Wenbin Du, Ying Liu, Weishan Liu, Andrey Kuznetsov, Felipe E. Mendez, Louis H. Philipson, and Rustem F. Ismagilov, "The chemistrode: A droplet-based microfluidic device for stimulation and recording with high temporal, spatial, and chemical resolution," PNAS 2008 105: 16843-16848 pdf (1,633 KB) supporting information (4,419 KB) movieS1 (4,296 KB) movieS2 (4,058 KB) movieS3 (406 KB) movieS4 (451 KB)

85. Liang Li, Sigrid Nachtergaele, Annela M. Seddon, Valentina Tereshko, Nina Ponomarenko, and Rustem F. Ismagilov, "Simple Host-Guest Chemistry To Modulate the Process of Concentration and Crystallization of Membrane Proteins by Detergent Capture in a Microfluidic Device," JACS 2008 130: 14324-14328 pdf (1,000 KB) supporting information (9,569 KB)

84. Feng Shen, Christian J. Kastrup and Rustem F. Ismagilov, Using microfluidics to understand the effect of spatial distribution of tissue factor on blood coagulation. Thromb. Res. 2008 122, S27-S30. pdf (124 KB)

83. Feng Shen, Christian J. Kastrup, Ying Liu, and Rustem F. Ismagilov, "Threshold Response of Initiation of Blood Coagulation by Tissue Factor in Patterned Microfluidic Capillaries Is Controlled by Shear Rate," Arterioscler. Thromb. Vasc. Biol. 2008 28: 2035-2041 pdf (997 KB) supporting information (180 KB)

82. Timothy R. Kline, Matthew K. Runyon, Mohammad Pothiawala, and Rustem F. Ismagilov, "ABO, D Blood Typing and Subtyping Using Plug-Based Microfluidics," Anal Chem 2008 80: 6190-6197 pdf (1,734 KB)

81. James Q. Boedicker, Liang Li, Timothy R. Kline, and Rustem F. Ismagilov, "Detecting bacteria and determining their susceptibility to antibiotics by stochastic confinement in nanoliter droplets using plug-based microfluidics," Lab Chip 2008 8: 1265-1272 pdf (500 KB) supporting information (352 KB)

80. Rebecca R. Pompano, Hung-Wing Li, and Rustem F. Ismagilov, "Rate of mixing controls rate and outcome of autocatalytic processes theory and microfluidic experiments with chemical reactions and blood coagulation,” Biophysical Journal 2008 95: 1531-1543 pdf (1,187 KB) supporting information (608 KB)

79. Matthew K. Runyon, Christian J. Kastrup,Bethany L. Johnson-Kerner, Thuong G, Van Ha, and Rustem F. Ismagilov, "Effects of Shear Rate on Propagation of Blood Clotting Determined Using Microfluidics and Numerical Simulations,” JACS 2008 130: 3458-3464 pdf (292 KB) supporting information (786 KB)

78. Christian J. Kastrup, Matthew K. Runyon, Elena M. Lucchetta, Jessica M. Price, and Rustem F. Ismagilov, “Using Chemistry and Microfluidics to Understand the Spatial Dynamics of Complex Biological Networks,” Acc. Chem. Res. 2008 41:449-558 pdf (2,773 KB) supporting information (2,058 KB)

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77. Rustem F. Ismagilov; and Michel M. Maharbiz, "Can we build synthetic, multicellular systems by controlling developmental signaling in space and time?", Current Opinion in Chemical Biology 2007 11: 604-611 pdf (996 KB)

76. Rafe T. Petty; Hung-Wing Li; Jane H. Maduram; Rustem F. Ismagilov; and Milan Mrksich, "Attachment of Cells to Islands Presenting Gradients of Adhesion Ligands," J. Am. Chem. Soc. 2007 129: 8966-8967 pdf (1305 KB) supporting information (112 KB)

75. Christian J. Kastrup, and Rustem F.Ismagilov, "A physical organic mechanistic approach to understanding the complex reaction network of hemostasis (blood clotting)," J. Phys. Org. Chem. 2007 20:711-715 pdf (383 KB)

74. Christian J. Kastrup, Feng Shen, Matthew K. Runyon, and Rustem F.Ismagilov, "Characterization of the Threshold Response of Initiation of Blood Clotting to Stimulus Patch Size," Biophysical Journal 2007 93:2969-2977 pdf (1215 KB)

73. Matthew K. Runyon, Bethany L. Johnson-Kerner, Christian J. Kastrup, Thuong G. Van Ha, and Rustem F.Ismagilov, "Propagation of Blood Clotting in the Complex Biochemical Network of Hemostasis Is Described by a Simple Mechanism," JACS 2007 129: 7014-7015 pdf (93 KB) supporting information (165 KB) movie (3690 KB)

72. Christian J. Kastrup, Feng Shen, and Rustem F. Ismagilov, "Response to Shape Emerges in a Complex Biochemical Network and Its Simple Chemical Analogue," Angew. Chem. Int. Ed. 2007 46: 3660-3662 pdf (255 KB) supporting information (74 KB)

71. Liang Li, James Q. Boedicker, and Rustem F. Ismagilov, "Using a Multijunction Microfluidic Device To Inject Substrate into an Array of Preformed Plugs without Cross-Contamination: Comparing Theory and Experiments," Anal. Chem. 2007 79: 2756-2761 pdf (321 KB) supporting information (248 KB)

70. Delai L. Chen, Liang Li, Sebastian Reyes, David N. Adamson, and Rustem F. Ismagilov, "Using Three-Phase Flow of Immiscible Liquids To Prevent Coalescence of Droplets in Microfluidic Channels: Criteria To Identify the Third Liquid and Validation with Protein Crystallizations," Langmuir 2007 23: 2255-2260 pdf (175 KB)

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69. Liang Li, Debarshi Mustafi, Qiang Fu, Valentina Tereshko, Delai L. Chen, Joshua D. Tice,
and Rustem F. Ismagilov, "Nanoliter microfluidic hybrid method for simultaneous screening and optimization validated with crystallization of membrane proteins," PNAS 2006 103: 19243-19248 pdf (1.5 MB) supporting information (124 KB)

68. Cory J. Gerdts, Valentina Tereshko, Maneesh K. Yadav, Irina Dementieva, Frank Collart, Andrzej Joachimiak, Raymond C. Stevens, Peter Kuhn, Anthony Kossiakoff, and Rustem F. Ismagilov, "Time-Controlled Microfluidic Seeding in nL-Volume Droplets To Separate Nucleation and Growth Stages of Protein Crystallization," Angew. Chem. Int. Ed. 2006 45: 8156-8160 pdf (352 KB) supporting information (332 KB)

67. Helen Song, Delai L. Chen, and Rustem F. Ismagilov, "Reactions in droplets in microfluidic channels," Angew. Chem. Int. Ed. 2006 45:7336-7356 pdf (2.33 MB)

66. Christian J. Kastrup, Matthew K. Runyon, Feng Shen, and Rustem F. Ismagilov, "Modular chemical mechanism predicts spatiotemporal dynamics of initiation in the complex network of hemostasis," PNAS 2006 103:15747-15752 pdf (1.15 MB) supporting information (143 KB)

65. David N. Adamson, Debarshi Mustafi, John X.J. Zhang, Bo Zheng and Rustem F. Ismagilov, "Production of arrays of chemically distinct nanolitre plugs via repeated splitting in microfluidic devices," Lab on a Chip, 2006 6: 1178- 1186 pdf (517KB)

64. Helen Song, Hung-Wing Li, Matthew S. Munson, Thuong G. Van Ha and Rustem F. Ismagilov, "On-chip Titration of an Anticoagulant Argatroban and Determination of the Activated Partial Thromboplastin Time for Clotting within Whole Blood or Plasma Using a Plug-based Microfluidic System," Anal. Chem. 2006 78: 4839-4849 pdf (666KB) supporting information (320 KB)

63. Delai L. Chen and Rustem F. Ismagilov, "Microfluidic Cartridges Preloaded with Nanoliter Plugs of Reagents: an Alternative to 96-well Plates for Screening," COCB 2006 10: 226-231 pdf (304KB)

62. Takuji Hatakeyama, Delai L. Chen and Rustem F. Ismagilov, "Microgram-Scale Testing of Reaction Conditions in Solution Using Nanoliter Plugs in Microfluidics with Detection by MALDI-MS," JACS 2006 128: 2518-2519 pdf (540KB) supporting information (940 KB)

61. Elena M. Lucchetta, Matthew S. Munson and Rustem F. Ismagilov, "Characterization of the Local Temperature in Space and Time around a Developing Drosophila Embryo in a Microfluidic Device," Lab on a Chip 2006 6: 185-190 pdf (600KB)

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60. Stephen F. Nelsen, Asgeir E. Konradsson, Rustem F. Ismagilov, andIlia A. Guzei. "Crystallographic characterization of the geometry changes upon electron loss from 2-tert-butyl-3-aryl-2,3-diazabicyclo 2.2.2 octanes." Crystal Growth and Design, 20055(6):2344-2347 pdf (147 KB) supporting information (301 KB)

59. Bo Zheng, Cory J. Gerdts and Rustem F. Ismagilov, "Using nanoliter plugs in microfluidics to facilitate and understand protein crystallization," Current Opinion in Structural Biology 2005 15: 548-555 pdf (468 KB)

58. Maneesh K. Yadav, Cory J. Gerdts, Ruslan Sanishvili, Ward W. Smith, L. Spencer Roach, Rustem F. Ismagilov, Peter Kuhn and Raymond C. Stevens, "In Situ Data Collection and Structure Refinement from Microcapillary Protein Crystallization," Journal of Applied Crystallography 2005 38: 900-905 pdf (352 KB)

57. Delai L. Chen, Cory J. Gerdts, and Rustem F. Ismagilov, "Using Microfluidics to Observe the Effect of Mixing on Nucleation of Protein Crystals," JACS 2005 127: 9672-9673 pdf (106 KB) supporting information (124 KB)

56. Jing Su, Michelle R. Bringer, Rustem F. Ismagilov, and Milan Mrksich, "Combining Microfluidic Networks and Peptide Arrays for Multi-Enzyme Assays," JACS 2005 127: 7280-7281 pdf (100 KB)

55. Elena M. Lucchetta, Ji Hwan Lee, Lydia A. Fu, Nipam H. Patel, and Rustem F. Ismagilov, "Dynamics of Drosophila Embryonic Patterning Network Perturbed in Space and Time with Microfluidics," Nature 2005 434: 1134-1138 pdf (318 KB) supporting information (727 KB)

54. Bo Zheng and Rustem F. Ismagilov, "A Microfluidic Approach for Screening Submicroliter Volumes Against Multiple Reagents by Using Preformed Arrays of Nanoliter Plugs in a Three-Phase Liquid/Liquid/Gas Flow," Angew. Chem. Int. Ed. 2005 44 (17): 2520-2523 pdf (208 KB) supporting information (48 KB)

53. L. Spencer Roach, Helen Song, and Rustem F. Ismagilov, "Controlling Nonspecific Protein Adsorption in a Plug-Based Microfluidic System by Controlling Interfacial Chemistry Using Fluorous-Phase Surfactants," Anal. Chem. 2005 77 (3): 785-796 pdf (545 KB) supporting information (627 KB)

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52. Bo Zheng, Joshua D. Tice, and Rustem F. Ismagilov, "Formation of Arrayed Droplets by Soft Lithography and Two-Phase Fluid Flow, and Application in Protein Crystallization," Adv. Mater. 2004 16:1365-1368 pdf (168 KB)

51. Bo Zheng, Joshua D. Tice, and Rustem F. Ismagilov, "Formation of Droplets of Alternating Composition in Microfluidic Channels and Applications to Indexing of Concentrations in Droplet-Based Assays," Anal. Chem. 2004 76: 4977-4982 pdf (302 KB)

50. Ilya A. Shestopalov, Joshua D. Tice, and Rustem F. Ismagilov, "Multi-Step Synthesis of Nanoparticles Performed on Millisecond Time Scale in a Microfluidic Droplet-Based System," Lab on a Chip 2004 4: 316-321 pdf (1,027 KB)

49. Cory J. Gerdts, David E. Sharoyan, and Rustem F. Ismagilov, "A Synthetic Reaction Network: Chemical Amplification Using Nonequilibrium Autocatalytic Reactions Coupled in Time," JACS 2004 126: 6327-6331 pdf (154 KB)

48. Bo Zheng, Joshua D. Tice, L. Spencer Roach, and Rustem F. Ismagilov, "A Droplet-Based, Composite PDMS/Glass Capillary Microfluidic System for Evaluating Protein Crystallization Conditions by Microbatch and Vapor-Diffusion Methods with On-Chip X-Ray Diffraction," Angew. Chem. Int. Edit. 2004 43: 2508-2511 pdf (534 KB) supporting information (121 KB)

47. Michelle R. Bringer, Cory J. Gerdts, Helen Song, Joshua D. Tice, and Rustem F. Ismagilov, "Microfluidic Systems for Chemical Kinetics that Rely on Chaotic Mixing in Droplets," Philos. T. Roy. Soc. A 2004 362: 1087-1104 pdf (966 KB)

46. Matthew K. Runyon, Bethany L. Johnson-Kerner, and Rustem F. Ismagilov, "Minimal Functional Model of Hemostasis in a Biomimetic Microfluidic System," Angew. Chem. Int. Edit. 2004 43: 1531-1536 pdf (171KB)

45. Joshua D. Tice, Adam D. Lyon, and Rustem F. Ismagilov, "Effect of Viscosity on Droplet Formation and Mixing in Microfluidic Channels," Anal. Chim. Acta 2004 507: 73-77 pdf (228 KB)

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44. Helen Song, Michelle R. Bringer, Joshua D. Tice, Cory J. Gerdts, and Rustem F. Ismagilov, "Experimental Test of Scaling of Mixing by Chaotic Advection in Droplets Moving Through Microfluidic Channels," Appl. Phys. Lett. 2003 83: 4664-4666 pdf (168 KB)

43. Helen Song and Rustem F. Ismagilov, "Millisecond Kinetics on a Microfluidic Chip Using Nanoliters of Reagents," JACS 2003 125: 14613-14619 pdf (277 KB)

42. Rustem F. Ismagilov, "Integrated Microfluidic Systems", Angew. Chem. Int. Edit. 2003 42: 4130-4132 pdf (132 KB)

41. Joshua D. Tice, Helen Song, Adam D. Lyon, and Rustem F. Ismagilov, "Formation of Droplets and Mixing in Multiphase Microfludics at Low Values of the Reynolds and the Capillary Numbers," Langmuir. 2003 19 (22) 9127-9133 pdf (462 KB)

40. Bo Zheng, L. Spencer Roach, and Rustem F. Ismagilov, "Screening of Protein Crystallization Conditions on a Microfluidic Chip Using Nanoliter-Size Droplets," JACS 2003 125 (37): 11170-11171 pdf (156 KB)

39. Helen Song, Joshua D. Tice, and Rustem F. Ismagilov, "A Microfluidic System for Controlling Reaction Networks in Time," Angew. Chem. Int. Edit. 2003 42 (7): 768-772 pdf (315 KB)


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Additional publications: pre-2003 publications