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Publications

Joint first authorship is indicated by *

It is Ismagilov Group policy to include a detailed statement of author contributions within each publication; for convenience these statements are also linked below.

Preprints

Yixuan Zhou, Macy R. Komnick, Fabiola Sepulveda, Grace Liu, Elida Nieves-Ortiz, Kelsey Meador, Ornella Ndatabaye, Aliia Fatkhullina, Natalie J. Wu-Woods, Paulina M. Naydenkov, Johnathan Kent, Nathaniel Christiansen, Maria L Madariaga, Piotr Witkowski, Rustem F. Ismagilov, Daria Esterházy. 2024. "Inducible, but not constitutive, pancreatic REG/Reg isoforms are regulated by intestinal microbiota and pancreatic diseases" bioRxiv doi:10.1101/2024.10.18.619139.

*See bottom of this page for Archived Preprints / Other Documents

Publications

2025

178. Wioletta Lisicka, Zachary M. Early, Joseph J. Sifakis, Steven A. Erickson, Jonathan R. Mattingly, Natalie J. Wu-Woods, Siddharth R. Krishnamurthy, Yasmine Belkaid, Rustem F. Ismagilov, Jason G. Cyster, Samatha J. Riensenfeld, Albert Bendelac, and Bana Jabri. "Immunoglobulin A controls intestinal virus colonization to preserve immune homeostasis" Cell Host & Microbe. 2025. doi: 10.1016/j.chom.2025.03.004. Manuscript.

177. Alexander Viloria Winnett, Natasha Shelby, Rustem F. Ismagilov. 2025. "Letter to the Editor: COVID-19 study quantifying daily viral loads confirms throat samples are key to early diagnosis." Diagnostic Microbiology & Infectious Disease. 111(2025) 116742. Manuscript.

176. Michael K. Porter, Alexander Viloria Winnett, Linhui Hao, Natasha Shelby, Jessica A. Reyes, Noah W. Schlenker, Anna E. Romano, Colton Tognazzini, Matthew Feaster, Ying-Ying Goh, Michael Gale, Jr., and Rustem F. Ismagilov. 2023. "The ratio between SARS-CoV-2 RNA viral load and culturable viral titer differs depending on stage of infection: a case study of household transmission in an adult male." Access Microbiology 7:000732.v3. doi: 10.1099/acmi.0.000732.v1. medRxiv doi:10.1101/2023.07.06.23292300. Manuscript; Author contributions.

2024

175. Alexander Viloria Winnett, Timothy Stenzel, and Rustem F. Ismagilov. 2024. "Validating Combination Throat-Nasal Swab Specimens for Coronavirus Disease 2019 Tests Would Improve Early Detection, Especially for the Most Vulnerable." Clinical Infectious Diseases (Invited Commentary), ciae381, doi: 10.1093/cid/ciae381. Manuscript; Supplement.

2023

174. Natalie J. Wu-Woods, Jacob T. Barlow, Florian Trigodet, Dustin G. Shaw, Anna E. Romano, Bana Jabri, A. Murat Eren, and Rustem F. Ismagilov. 2023. "Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples." Nature Methods 20: 1672–1682. doi: 10.1038/s41592-023-02025-4. Manuscript; Supplement; Author contributions.

173. Jenny Ji*, Alexander Viloria Winnett*, Natasha Shelby, Jessica A. Reyes, Noah W. Schlenker, Hannah Davich, Saharai Caldera, Colten Tognazzini, Ying-Ying Goh, Matt Feaster, and Rustem F. Ismagilov. 2023. "Index Cases First Identified by Nasal-Swab Rapid COVID-19 Tests Had More Transmission to Household Contacts than Cases Identified by Other Test Types." PLoS ONE 18(10): e0292389. doi: 10.1371/journal.pone.0292389. Manuscript; Supplement; Author Contributions. medRxiv doi: 10.1101/2023.03.09.23286855.

172. Roberta Poceviciute, Said R. Bogatyrev, Anna E. Romano, Amanda H. Dilmore, Octavio Mondragón-Palomino, Heli Takko, Ojas Pradhan, and Rustem F. Ismagilov. 2023. "Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa." npj Biofilms and Microbiomes 9, 64. doi: 10.1038/s41522-023-00423-2. Manuscript; Supplement; Author Contributions. Springer Nature. bioRxiv doi: 10.1101/2022.06.17.496478.

171. Alexander Viloria Winnett*, Reid Akana*, Natasha Shelby*, Hannah Davich, Saharai Caldera, Taikun Yamada, John Raymond B. Reyna, Anna E. Romano, Alyssa M. Carter, Mi Kyung Kim, Matt Thomson, Colten Tognazzini, Matthew Feaster, Ying-Ying Goh, Yap Ching Chew, and Rustem F. Ismagilov. 2023. "Daily SARS-CoV-2 Nasal Antigen Tests Miss Infected and Presumably Infectious People Due to Viral-Load Differences Among Specimen Types." Microbiology Spectrum 11(4): e01295-23. doi: 10.1128/spectrum.01295-23. Manuscript; Supplement; Author Contributions. PREPRINT: V1: 7/15/22; V2: 1/11/23. medRxiv doi:10.1101/2022.07.13.22277513

170. Alexander Viloria Winnett*, Reid Akana*, Natasha Shelby*, Hannah Davich, Saharai Caldera, Taikun Yamada, John Raymond B. Reyna, Anna E. Romano, Alyssa M. Carter, Mi Kyung Kim, Matt Thomson, Colten Tognazzini, Matthew Feaster, Ying-Ying Goh, Yap Ching Chew, and Rustem F. Ismagilov. 2023. "Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods." PNAS Nexus 2(3): pgad033. doi:10.1093/pnasnexus/pgad033. Manuscript; Supplement (zip); Author Contributions. PREPRINT: V1: 7/15/22; V2: 1/11/23 medRxiv doi:10.1101/2022.07.13.22277113

169. Alyssa M. Carter*, Alexander Viloria Winnett*, Anna E. Romano, Reid Akana, Natasha Shelby, Rustem F. Ismagilov. 2023. "Laboratory Evaluation Links Some False-Positive COVID-19 Antigen Test Results Observed in a Field Study to a Specific Lot of Test Strips." Open Forum Infectious Diseases 10(1): ofac701. Manuscript; Supplement; Author Contributions.

168. Z.M. Earley, Lisicka, W., Sifakis, J.J., Gamboa, R.A., Kowalczyk, A., Barlow, J., Shaw, D.G., Discepolo, V., Tan, I.L., Gona, S., Ernest, J., Matzinger, P., Barreiro, L.B., Morgun, A., Bendelac, A., Ismagilov, R.F., Shulzhenko, N., Riesenfeld, S.J., and Jabri, B. 2023. "GATA4 controls regionalization of tissue immunity and commensal-driven immunopathology." Immunity 56(1): 43-57.e10. Manuscript; Supplement. PREPRINT: Posted 10/28/21. bioRxiv. doi:2021.2010.2028.466194

2022

167. Alexander Viloria Winnett*, Michael K. Porter*, Anna E. Romano, Emily S. Savela, Reid Akana, Natasha Shelby, Jessica A. Reyes, Noah W. Schlenker, Matthew M. Cooper, Alyssa M. Carter, Jenny Ji, Jacob T. Barlow, Colten Tognazzini, Matthew Feaster, Ying-Ying Goh, and Rustem F. Ismagilov. 2022. "Morning SARS-CoV-2 testing yields better detection of infection due to higher viral loads in saliva and nasal swabs upon waking." Microbiology Spectrum 10(6): e03873-22. doi: 10.1128/spectrum.03873-22 Manuscript; Supplementary information; Author Contributions. PREPRINT: Posted 3/2/22. medRxiv. doi:10.1101/2022.03.02.22271724

166. Octavio Mondragón-Palomino, Roberta Poceviciute, Antti Lignell, Jessica A. Griffiths, Heli Takko, Rustem F. Ismagilov. 2022. "Three-dimensional imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa." PNAS 119(18): e2118483119. doi: 10.1073/pnas.2118483119. Manuscript; Supplementary information; Supplementary movies; Author Contributions. PREPRINT: Posted 10/8/21. bioRxiv. doi:10.1101/2021.10.07.463215

2021

165. Emily S. Savela*, Alexander Viloria 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, and 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." Journal of Clinical Microbiology 60(2): e01785-21. doi:10.1128/JCM.01785-21. Manuscript; Supplementary Information; Author Contributions. PREPRINT V2: Posted 8/26/21. medRxiv doi:10.1101/2021.04.02.21254771v2. PREPRINT V1: Posted 4/7/21. medRxiv doi: 10.1101/2021.04.02.21254771v1

164. Jacob Barlow*, Gabriela Leite*, Anna E. Romano, Rashin Sedighi, Christine Chang, Shreya Celly, Ali Rezaie, Ruchi Mathur, Mark Pimentel, and Rustem F. Ismagilov. 2021. "Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome." Microbiome 9: 214. Manuscript; Supplementary Information; Author Contributions.

163. Mary V. Arrastia*, Joanna W. Jachowicz*, Noah Ollikainen, Matthew S. Curtis, Charlotte Lai, Sofia Quinodoz, David A. Selck, Rustem F. Ismagilov, and Mitchell Guttman. 2021. "Single-cell measurement of higher-order 3D genome organization with scSPRITE." Nature Biotechnology. doi:10.1038/s41587-021-00998-1. Manuscript; Supplementary information. PREPRINT: 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. 2021. "Alterations in the gut microbiota contribute to cognitive impairment induced by the ketogenic diet and hypoxia." Cell, Host & Microbe 29: 1–15. doi:10.1016/j.chom.2021.07.004. Manuscript.

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.

2020

160. Tahmineh Khazaei, Rory L. Williams, Said R. Bogatyrev, John C. Doyle, Christopher S. Henry, and Rustem F. Ismagilov. 2020. "Metabolic multi-stability and hysteresis in a model aerobe-anaerobe microbiome community." Science Advances 6: eaba0353. Manuscript; Supplementary Information; 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; Supplementary Information; 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; 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; 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 48(7): e42. doi:10.1093/nar/gkaa099. Manuscript; Supplements available at NAR; 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 155. 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; Supplementary Information; 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; Supplementary Information; Author Contributions.

2019

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; SI; 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; SI; Author Contributions.

150. Roberta Poceviciute and Rustem F. Ismagilov. 2019. "Human-gut-microbiome on a chip." Nature Biomedical Engineering 3: 500–501. doi:10.1038/s41551-019-0425-0. Manuscript.

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; Author Contributions.

148. Mengchao Yu, Xiaoying Chen, Haijun Qu, Liang Ma, Lei Xu, Weiyuan Lv, Hua Wang, Rustem F. Ismagilov, Min Li, and 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; SI; 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. Data files at eLife; 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; Author Contributions.

2018

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; SI; Author Contributions.

2017

144. *Nathan G. Schoepp, *Travis S. Schlappi, Matthew S. Curtis, Slava S. Butkovich, Shelley Miller, Romney M. Humphries, and 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; SI; 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.

2016

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; SI; 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; SI; 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; SI ; 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 ; Author Contributions.

138. Erik Jue, Nathan G. Schoepp, Daan Witters, and Rustem F. Ismagilov. 2016. "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." Lab on a Chip 16: 1852–1860. doi: 10.1039/c6lc00292g. Manuscript; Movie.

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; SI.

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; SI.

2015

135. *Eugenia M. Khorosheva, *Mikhail A. Karymov, David A. Selck and Rustem F. Ismagilov. 2015. "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; SI.

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. Manuscript; SI.

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. Manuscript; SI.

2014

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

131. *Shencheng Ge, *Weishan Liu, Travis Schlappi, and Rustem F. Ismagilov. 2014. "Digital, Ultrasensitive, End-Point Protein Measurements with Large Dynamic Range via Brownian Trapping with Drift." JACS 136: 14662–14665. DOI: 10.1021/ja507849b. Manuscript; SI.

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. 2014. "Rapid fucosylation of intestinal epithelium sustains host–commensal symbiosis in sickness." Nature 514: 638–641. DOI: 10.1038/nature13823. Manuscript; SI.

129. *Stefano Begolo, *Dmitriy V. Zhukov, David A. Selck, Liang Li, and Rustem F. Ismagilov. 2014. "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 14(24): 4616–4628. DOI: 10.1039/C4LC00910J. Manuscript; SI.

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

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

126. Daan Witters, Bing Sun, Stefano Begolo, Jesus Rodriguez-Manzano, Whitney Robles, and Rustem F. Ismagilov. 2014. "Digital Biology and Chemistry." Lab on a Chip 14 (17): 3225–3232. DOI: 10.1039/C4LC00248B. Manuscript; Video S1, Video S2.

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

2013

124. *David A. Selck, *Mikhail A. Karymov, Bing Sun, and Rustem F. Ismagilov. 2013. "Increased Robustness of Single-Molecule Counting with Microfluidics, Digital Isothermal Amplification, and a Mobile Phone versus Real-Time Kinetic Measurements." Analytical Chemistry 85: 11129–11136. Manuscript; SI; Video S1.

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

122. Stefano Begolo, Feng Shen, and Rustem F. Ismagilov. 2013. "A Microfluidic Device for Dry Sample Preservation in Remote Settings." Lab on a Chip 13: 4331–4342. Manuscript; SI; 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. 2013. "A Genetically Encoded AND Gate for Cell-Targeted Metabolic Labeling of Proteins." JACS 135: 2979–2982. Manuscript; SI.

120. Bing Sun, Feng Shen, Stephanie E. McCalla, Jason E. Kreutz, Mikhail A. Karymov, and Rustem F. Ismagilov. 2013. "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 85: 1540–1546. Manuscript; SI.

2012

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

2011

118. Feng Shen, Bing Sun, Jason E. Kreutz, Elena K. Davydova, Wenbin Du, Poluru L. Reddy, Loren J. Joseph, and Rustem F. Ismagilov. 2011. "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 133: 17705–17712. Manuscript; SI.

117. Jason E. Kreutz, Todd Munson, Toan Huynh, Feng Shen, Wenbin Du, and Rustem F. Ismagilov. 2011. "Theoretical Design and Analysis of Multivolume Digital Assays with Wide Dynamic Range Validated Experimentally with Microfluidic Digital PCR." Analytical Chemistry 83: 8158–8168. Manuscript; SI; Software zip.

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

115. Maryna I. Bodnarchuk, Liang Li, Alice Fok, Sigrid Nachtergaele, Rustem F. Ismagilov, and Dmitri V. Talapin. 2011. "Three-Dimensional Nanocrystal Superlattices Grown in Nanoliter Microfluidic Plugs." JACS 133: 8956–8960. Manuscript; SI; Movie.

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

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

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

2010

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. 2010. "Molecular Mechanism of MLL PHD3 and RNA Recognition by the Cyp33 RRM Domain." J. Mol. Biol. 400: 145–154. Manuscript.

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

109. Feng Shen, Wenbin Du, Jason E. Kreutz, Alice Fok, and Rustem F. Ismagilov. 2010. "Digital PCR on a SlipChip." Lab on a Chip 10: 2666–2672. Manuscript; SI; Cover.

108. Liang Li, Mikhail A. Karymov, Kevin P. Nichols, and Rustem F. Ismagilov. 2010. "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 26: 12465–12471. Manuscript; SI; Movie S1.

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 82: 4606–4612. Manuscript; SI.

106. Weishan Liu, Delai Chen, Wenbin Du, Kevin P. Nichols, and Rustem F. Ismagilov. 2010. "SlipChip for Immunoassays in Nanoliter Volumes." Analytical Chemistry 82: 3276–3282. Manuscript; SI.

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

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

103. Jason E. Kreutz, Anton Shukhaev, Wenbin Du, Sasha Druskin, Olafs Daugulis, and Rustem F. Ismagilov. 2010. "Evolution of Catalysts Directed by Genetic Algorithms in a Plug-Based Microfluidic Device Tested with Oxidation of Methane by Oxygen." JACS 132: 3128–3132. Manuscript; SI; Movie S1.

102. Liang Li, Wenbin Du, and Rustem F. Ismagilov. 2010. "Multiparameter Screening on SlipChip Used for Nanoliter Protein Crystallization Combining Free Interface Diffusion and Microbatch Methods." JACS 132: 112–119. Manuscript; SI; Movie S1.

101. Liang Li, Wenbin Du, and Rustem F. Ismagilov. 2010. "User-Loaded SlipChip for Equipment-Free Multiplexed Nanoliter-Scale Experiments." JACS 132: 106–111. Manuscript; SI; Movie S1, Movie S2.

100. Liang Li, Qiang Fu, Christopher A. Kors, Lance Stewart, Peter Nollert, Philip D. Laible, and Rustem F. Ismagilov. 2010. "A Plug-Based Microfluidic System for Dispensing Lipidic Cubic Phase (LCP) Material Validated by Crystallizing Membrane Proteins in Lipidic Mesophases." Microfluidics and Nanofluidics 8: 789–798. Manuscript; SI.

2009

99. Feng Shen, Rebecca R. Pompano, Christian J. Kastrup, and Rustem F. Ismagilov. 2009. "Confinement Regulates Complex Biochemical Networks: Initiation of Blood Clotting by ‘Diffusion Acting'." Biophysical Journal 97(8): 2137–2145. Manuscript; Supporting information.

98. Elena M. Lucchetta,Richard W. Carthew, and Rustem F. Ismagilov. 2009. "The Endo-siRNA Pathway Is Essential for Robust Development of the DrosophilaEmbryo." PLoS ONE 4: e7576. Manuscript; Supporting information.

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. 2009. "Structural and spectropotentiometric analysis of Blastochloris viridis heterodimer mutant reaction center." Biochimica et Biophysica Acta 1788: 1822–1831. Manuscript.

96. Delai Chen, Wenbin Du, and Rustem F. Ismagilov. 2009. "Using TIRF microscopy to quantify and confirm efficient mass transfer at the substrate surface of the chemistrode." New Journal of Physics 11: 075017. Manuscript; MovieS1, MovieS2.

95. James Q. Boedicker, Meghan E. Vincent, and Rustem F. Ismagilov. 2009. "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. 48: 5908–5911. Manuscript; Supporting information.

94. Wenbin Du, Liang Li, Kevin P. Nichols, and Rustem F. Ismagilov. 2009. "SlipChip." Lab on a Chip 9: 2286–2292. Manuscript; Supporting information; MovieS1.

93. Weishan Liu, Hyun Jung Kim , Elena M. Lucchetta , Wenbin Du, and Rustem F. Ismagilov. 2009. "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 on a Chip 9: 2153–2162. Manuscript; Supporting information.

92. Jason E. Kreutz, Liang Li, L. Spencer Roach, Takuji Hatakeyama, and Rustem F. Ismagilov. 2009. "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 131: 6042–6043. Manuscript; Supporting information.

91. Ying Liu and Rustem F. Ismagilov. 2009. "Dynamics of Coalescence of Plugs with a Hydrophilic Wetting Layer Induced by Flow in a Microfluidic Chemistrode." Langmuir 25: 2854–2859. Manuscript.

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

2008

89. *Hyun Jung Kim, *James Q. Boedicker, Jang Wook Choi, and Rustem F. Ismagilov. 2008. "Defined spatial structure stabilizes a synthetic multispecies bacterial community." PNAS 105: 18188– 18193. Manuscript; Supporting information.

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. 2008. "Spatial localization of bacteria controls coagulation of human blood by 'quorum acting'." Nature Chemical Biology 4: 742–750. Manuscript; Supporting information.

87. Elena M. Lucchetta, Meghan E. Vincent, and Rustem F. Ismagilov. 2008. "A Precise Bicoid Gradient Is Nonessential during Cycles 11-13 for Precise Patterning in the Drosophila Blastoderm." PLoS ONE 3: e3651. Manuscript; Supporting information; MovieS1, MovieS2, MovieS3, MovieS4, MovieS5, MovieS6.

86. *Delai Chen, *Wenbin Du, Ying Liu, Weishan Liu, Andrey Kuznetsov, Felipe E. Mendez, Louis H. Philipson, and Rustem F. Ismagilov. 2008. "The chemistrode: A droplet-based microfluidic device for stimulation and recording with high temporal, spatial, and chemical resolution." PNAS 105: 16843–16848. Manuscript; Supporting information; MovieS1, MovieS2, MovieS3, MovieS4.

85. Liang Li, Sigrid Nachtergaele, Annela M. Seddon, Valentina Tereshko, Nina Ponomarenko, and Rustem F. Ismagilov. 2008. "Simple Host-Guest Chemistry to Modulate the Process of Concentration and Crystallization of Membrane Proteins by Detergent Capture in a Microfluidic Device." JACS 130: 14324–14328. Manuscript; Supporting information.

84. Feng Shen, Christian J. Kastrup, and Rustem F. Ismagilov. 2008. "Using microfluidics to understand the effect of spatial distribution of tissue factor on blood coagulation." Thromb. Res. 122: S27–S30. Manuscript.

83. Feng Shen, Christian J. Kastrup, Ying Liu, and Rustem F. Ismagilov. 2008. "Threshold Response of Initiation of Blood Coagulation by Tissue Factor in Patterned Microfluidic Capillaries Is Controlled by Shear Rate." Arterioscler. Thromb. Vasc. Biol. 28: 2035–2041. Manuscript; Supporting information.

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

81. James Q. Boedicker, Liang Li, Timothy R. Kline, and Rustem F. Ismagilov. 2008. "Detecting bacteria and determining their susceptibility to antibiotics by stochastic confinement in nanoliter droplets using plug-based microfluidics." Lab on a Chip 8: 1265–1272. Manuscript; Supporting information.

80. Rebecca R. Pompano, Hung-Wing Li, and Rustem F. Ismagilov. 2008. "Rate of mixing controls rate and outcome of autocatalytic processes theory and microfluidic experiments with chemical reactions and blood coagulation." Biophysical Journal 95: 1531–1543. Manuscript; Supporting information.

79. Matthew K. Runyon, Christian J. Kastrup,Bethany L. Johnson-Kerner, Thuong G, Van Ha, and Rustem F. Ismagilov. 2008. "Effects of Shear Rate on Propagation of Blood Clotting Determined Using Microfluidics and Numerical Simulations." JACS 130: 3458–3464. Manuscript; Supporting information.

78. Christian J. Kastrup, Matthew K. Runyon, Elena M. Lucchetta, Jessica M. Price, and Rustem F. Ismagilov. 2008. "Using Chemistry and Microfluidics to Understand the Spatial Dynamics of Complex Biological Networks." Acc. Chem. Res. 41: 449–558. Manuscript.

2007

77. Rustem F. Ismagilov, and Michel M. Maharbiz. 2007. "Can we build synthetic, multicellular systems by controlling developmental signaling in space and time?" Current Opinion in Chemical Biology 11: 604–611. Manuscript.

76. Rafe T. Petty; Hung-Wing Li; Jane H. Maduram; Rustem F. Ismagilov; and Milan Mrksich. 2007. "Attachment of Cells to Islands Presenting Gradients of Adhesion Ligands." J. Am. Chem. Soc. 129: 8966–8967. Manuscript; Supporting information.

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

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

73. Matthew K. Runyon, Bethany L. Johnson-Kerner, Christian J. Kastrup, Thuong G. Van Ha, and Rustem F. Ismagilov. 2007. "Propagation of Blood Clotting in the Complex Biochemical Network of Hemostasis Is Described by a Simple Mechanism." JACS 129: 7014–7015. Manuscript; Supporting information; Movie.

72. Christian J. Kastrup, Feng Shen, and Rustem F. Ismagilov. 2007. "Response to Shape Emerges in a Complex Biochemical Network and Its Simple Chemical Analogue." Angew. Chem. Int. Ed. 46: 3660–3662. Manuscript; Supporting information.

71. Liang Li, James Q. Boedicker, and Rustem F. Ismagilov. 2007. "Using a Multijunction Microfluidic Device to Inject Substrate into an Array of Preformed Plugs without Cross-Contamination: Comparing Theory and Experiments." Anal. Chem. 79: 2756–2761. Manuscript; Supporting information.

70. Delai L. Chen, Liang Li, Sebastian Reyes, David N. Adamson, and Rustem F. Ismagilov. 2007. "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 23: 2255–2260. Manuscript.

2006

69. Liang Li, Debarshi Mustafi, Qiang Fu, Valentina Tereshko, Delai L. Chen, Joshua D. Tice, and Rustem F. Ismagilov. 2006. "Nanoliter microfluidic hybrid method for simultaneous screening and optimization validated with crystallization of membrane proteins." PNAS 103: 19243–19248. Manuscript; Supporting information.

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. 2006. "Time-Controlled Microfluidic Seeding in nL-Volume Droplets to Separate Nucleation and Growth Stages of Protein Crystallization." Angew. Chem. Int. Ed. 45: 8156–8160. Manuscript; Supporting information.

67. Helen Song, Delai L. Chen, and Rustem F. Ismagilov. 2006. "Reactions in droplets in microfluidic channels." Angew. Chem. Int. Ed. 45: 7336–7356. Manuscript.

66. Christian J. Kastrup, Matthew K. Runyon, Feng Shen, and Rustem F. Ismagilov. 2006. "Modular chemical mechanism predicts spatiotemporal dynamics of initiation in the complex network of hemostasis." PNAS 103: 15747–15752. Manuscript; Supporting information.

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

64. Helen Song, Hung-Wing Li, Matthew S. Munson, Thuong G. Van Ha, and Rustem F. Ismagilov. 2006. "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. 78: 4839–4849. Manuscript; Supporting information.

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

62. Takuji Hatakeyama, Delai L. Chen, and Rustem F. Ismagilov. 2006. "Microgram-Scale Testing of Reaction Conditions in Solution Using Nanoliter Plugs in Microfluidics with Detection by MALDI-MS." JACS 128: 2518–2519. Manuscript; Supporting information.

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

2005

60. Stephen F. Nelsen, Asgeir E. Konradsson, Rustem F. Ismagilov, and Ilia A. Guzei. 2005. "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 5(6): 2344–2347. Manuscript; Supporting information.

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

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

57. Delai L. Chen, Cory J. Gerdts, and Rustem F. Ismagilov. 2005. "Using Microfluidics to Observe the Effect of Mixing on Nucleation of Protein Crystals." JACS 127: 9672–9673. Manuscript; Supporting information.

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

55. Elena M. Lucchetta, Ji Hwan Lee, Lydia A. Fu, Nipam H. Patel, and Rustem F. Ismagilov. 2005. "Dynamics of Drosophila Embryonic Patterning Network Perturbed in Space and Time with Microfluidics." Nature 434: 1134–1138. Manuscript; Supporting information.

54. Bo Zheng and Rustem F. Ismagilov. 2005. "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. 44 (17): 2520–2523. Manuscript; Supporting information.

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

2004

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

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

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

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

48. Bo Zheng, Joshua D. Tice, L. Spencer Roach, and Rustem F. Ismagilov. 2004. "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. 43: 2508–2511. Manuscript; Supporting information.

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

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

45. Joshua D. Tice, Adam D. Lyon, and Rustem F. Ismagilov. 2004. "Effect of Viscosity on Droplet Formation and Mixing in Microfluidic Channels." Anal. Chim. Acta 507: 73–77. Manuscript.

2003

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

43. Helen Song, and Rustem F. Ismagilov. 2003. "Millisecond Kinetics on a Microfluidic Chip Using Nanoliters of Reagents." JACS 125: 14613–14619. Manuscript.

42. Rustem F. Ismagilov. 2003. "Integrated Microfluidic Systems." Angew. Chem. Int. Edit. 42: 4130–4132. Manuscript.

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

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

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

Pre-2003 Publications

  1. Troyansky, E. I.; Demchuk, D. V.; Ismagilov, R. F.; Lazareva, M. I.; Strelenko, Y. A.; Nikishin, G. I. "Homolytic Macrocyclization of Alkynes with Propane-1,3-Dithiol as a Route to 14-Membered and 21-Membered Crown Thioethers", Mendeleev Commun. 1993, 112-114.
  2. Demchuk, D. V.; Lazareva, M. I.; Lindeman, S. V.; Khrustalyov, V. N.; Struchkov, Y. T.; Ismagilov, R. F.; Troyansky, E. I.; Nikishin, G. I. "Synthesis of 12-Membered and 13-Membered Sulfur-Containing Lactones by Homolytic Macrocyclization of Mercaptoacetic Esters with Alkynes", Synthesis 1995, 307-311
  3. Troyansky, E. I.; Ismagilov, R. F.; Samoshin, V. V.; Strelenko, Y. A.; Demchuk, D. V.; Nikishin, G. I.; Lindeman, S. V.; Khrustalyov, V. N.; Struchkov, Y. T. "Stereoselective Free-Radical Cycloaddition-Macrocyclization in Facile Synthesis of Trans-Cyclohexano-Fused 12-Membered Crown Thioethers", Tetrahedron 1995, 51, 11431-11444.
  4. Troyansky, E. I.; Ismagilov, R. F.; Strelenko, Y. A.; Samoshin, V. V.; Demchuk, D. V.; Nikishin, G. I.; Lindeman, S. V.; Khrustalyov, V. V.; Struchkov, Y. T. "Remote Asymmetric Induction in Free-Radical Cycloaddition Leading to Trans-Cyclohexano-Fused 12-Membered Crown Thioethers", Tetrahedron Lett. 1995, 36, 2293-2294.
  5. Troyansky, E.; Ismagilov, R. F.; Korneeva, E. N.; Pogosyan, M. S.; Nikishin, G. I. "An Approach to 8-Membered, 16-Membered and 24-Membered Sulfur- Containing Heterocycles Via Homolytic Cycloaddition of Alkynes with Butane-1,4-Dithiol", Mendeleev Commun. 1995, 18-20.
  6. Nelsen, S. F.; Ismagilov, R. F.; Powell, D. R. "Charge localization in a dihydrazine analogue of tetramethyl-p- phenylenediamine radical cation", J. Am. Chem. Soc. 1996, 118, 6313-6314.
  7. Nelsen, S. F.; Ismagilov, R. F.; Chen, L. J.; Brandt, J. L.; Chen, X.; Pladziewicz, J. R. "Slow electron transfer reactions involving tetraisopropylhydrazine", J. Am. Chem. Soc. 1996, 118, 1555-1556.
  8. Nelsen, S. F.; Ismagilov, R. F.; Powell, D. R. "Charge-localized p-phenylenedihydrazine radical cations: ESR and optical studies of intramolecular electron transfer rates", J. Am. Chem. Soc. 1997, 119, 10213-10222.
  9. Nelsen, S. F.; Klein, S. J.; Trieber, D. A.; Ismagilov, R. F.; Powell, D. R. "sigma,pi Interaction in halogen-substituted biadamantylidene radical cations", J. Org. Chem. 1997, 62, 6539-6546.
  10. Nelsen, S. F.; Ramm, M. T.; Ismagilov, R. F.; Nagy, M. A.; Trieber, D. A.; Powell, D. R.; Chen, X.; Gengler, J. J.; Qu, Q. L.; Brandt, J. L.; Pladziewicz, J. R. "Estimation of self-exchange electron transfer rate constants for organic compounds from stopped-flow studies", J. Am. Chem. Soc. 1997, 119, 5900-5907.
  11. Troyansky, E. I.; Ismagilov, R. F.; Samoshin, V. V. "Homolytic cycloaddition of dithiols to alkynes leading to sulfur-containing heterocycles and crown thioethers: new comments to the mechanism." Sulfur Letters 1997, 20, 219.
  12. Nelsen, S. F.; Ismagilov, R. F.; Trieber, D. A. "Adiabatic electron transfer: Comparison of modified theory with experiment", Science 1997, 278, 846-849.
  13. Ismagilov, R. F. "Mathematical description of kinetic resolution with an enantiomerically impure catalyst and nonracemic substrate", J. Org. Chem. 1998, 63, 3772-3774.
  14. Nelsen, S. F.; Ismagilov, R. F.; Gentile, K. E.; Nagy, M. A.; Tran, H. Q.; Qu, Q. L.; Halfen, D. T.; Odegard, A. L.; Pladziewicz, J. R. "Indirect determination of self-exchange electron transfer rate constants", J. Am. Chem. Soc. 1998, 120, 8230-8240.
  15. Nelsen, S. F.; Tran, H. Q.; Ismagilov, R. F.; Ramm, M. T.; Chen, L. J.; Powell, D. R. "Structural information from hydrazine radical cation optical absorption spectra", J. Org. Chem. 1998, 63, 2536-2543.
  16. Nelsen, S. F.; Ismagilov, R. F.; Teki, Y. "Comparison of the singlet, triplet energy gap of a symmetrical diradical dication with ET parameters derived from its optical spectrum", J. Am. Chem. Soc. 1998, 120, 2200-2201.
  17. Nelsen, S. F.; Ismagilov, R. F.; Powell, D. R. "Effects of bridge redox state levels on the electron transfer and optical properties of intervalence compounds with hydrazine charge-bearing units", J. Am. Chem. Soc. 1998, 120, 1924-1925.
  18. Samoshin, V. V.; Troyansky, E. I.; Demchuk, D. V.; Ismagilov, R. F.; Chertkov, V. A.; Lindeman, S. V.; Khrustalyov, V. N.; Struchkov, Y. T. "Conformational analysis of a 12-membered crown dithioether in the solid state and in solution", J. Phys. Org. Chem. 1998, 11, 241-253.
  19. Nelsen, S. F.; Ismagilov, R. F.; Gentile, K. E.; Powell, D. R. "Temperature effects on electron transfer within intervalence bis(hydrazine) radical cations", J. Am. Chem. Soc. 1999, 121, 7108-7114.
  20. Nelsen, S. F.; Ismagilov, R. F. "Ion pairing effects on bis(hydrazine) intervalence radical cations", J. Phys. Chem. A 1999, 103, 5373-5378.
  21. Teki, Y.; Ismagilov, R. F.; Nelsen, S. F. "Intra- and inter-molecular exchange on symmetrical hydrazine diradical dications and comparison of the magnetic exchange with ET parameters derived from their optical spectra", Mol. Cryst. Liq. Cryst. Sci. Technol. Sect. A-Mol. Cryst. Liq. Cryst. 1999, 334, 313-322.
  22. Kenis, P. J. A.; Ismagilov, R. F.; Whitesides, G. M. "Microfabrication inside capillaries using multiphase laminar flow patterning", Science 1999, 285, 83-85.
  23. Takayama, S.; McDonald, J. C.; Ostuni, E.; Liang, M. N.; Kenis, P. J. A.; Ismagilov, R. F.; Whitesides, G. M. "Patterning cells and their environments using multiple laminar fluid flows in capillary networks", Proc. Natl. Acad. Sci. U. S. A. 1999, 96, 5545-5548.
  24. Whitesides, G. M.; Ismagilov, R. F. "Complexity in chemistry", Science 1999, 284, 89-92.
  25. Deng, T.; Arias, F.; Ismagilov, R. F.; Kenis, P. J. A.; Whitesides, G. M. "Fabrication of metallic microstructures using exposed, developed silver halide-based photographic film", Anal. Chem. 2000, 72, 645-651.
  26. Hong, S. H.; Evans, D. H.; Nelsen, S. F.; Ismagilov, R. F. "Evidence for a two-step electron-transfer process in the electrode reactions of tetraisopropylhydrazine, tetracyclohexylhydrazine and their radical cation salts", J. Electroanal. Chem. 2000, 486, 75-84.
  27. Ismagilov, R. F.; Stroock, A. D.; Kenis, P. J. A.; Whitesides, G.; Stone, H. A. "Experimental and theoretical scaling laws for transverse diffusive broadening in two-phase laminar flows in microchannels", Appl. Phys. Lett. 2000, 76, 2376-2378.
  28. Stroock, A. D.; Weck, M.; Chiu, D. T.; Huck, W. T. S.; Kenis, P. J. A.; Ismagilov, R. F.; Whitesides, G. M. "Patterning electro-osmotic flow with patterned surface charge", Phys. Rev. Lett. 2000, 84, 3314-3317.
  29. Kenis, P. J. A.; Ismagilov, R. F.; Takayama, S.; Whitesides, G. M.; Li, S. L.; White, H. S. "Fabrication inside microchannels using fluid flow", Accounts Chem. Res. 2000, 33, 841-847.
  30. Holmlin, R. E.; Ismagilov, R. F.; Haag, R.; Mujica, V.; Ratner, M. A.; Rampi, M. A.; Whitesides, G. M. "Correlating electron transport and molecular structure in organic thin films", Angew. Chem.-Int. Edit. 2001, 40, 2316.
  31. Holmlin, R. E.; Haag, R.; Chabinyc, M. L.; Ismagilov, R. F.; Cohen, A. E.; Terfort, A.; Rampi, M. A.; Whitesides, G. M. "Electron transport through thin organic films in metal- insulator-metal junctions based on self-assembled monolayers", J. Am. Chem. Soc. 2001, 123, 5075-5085.
  32. Nelsen, S. F.; Trieber, D. A.; Ismagilov, R. F.; Teki, Y. "Solvent effects on charge transfer bands of nitrogen-centered intervalence compounds", J. Am. Chem. Soc. 2001, 123, 5684-5694.
  33. Ismagilov, R. F.; Ng, J. M. K.; Kenis, P. J. A.; Whitesides, G. M. "Microfluidic arrays of fluid-fluid diffusional contacts as detection elements and combinatorial tools", Anal. Chem. 2001, 73, 5207-5213.
  34. Ismagilov, R. F.; Rosmarin, D.; Kenis, P. J. A.; Chiu, D. T.; Zhang, W.; Stone, H. A.; Whitesides, G. M. "Pressure-driven laminar flow in tangential microchannels: an elastomeric microfluidic switch", Anal. Chem. 2001, 73, 4682-4687.
  35. Ismagilov, R. F.; Rosmarin, D.; Gracias, D. H.; Stroock, A. D.; Whitesides, G. M. "Competition of intrinsic and topographically imposed patterns in Benard-Marangoni convection", Appl. Phys. Lett. 2001, 79, 439-441.
  36. Ismagilov, R. F.; Schwartz, A.; Bowden, N.; Whitesides, G. M. "Autonomous movement and self-assembly", Angew. Chem.-Int. Edit. 2002, 41, 652.
  37. Chabinyc, M.L.; Holmin, R.E.; Haag, R.; Chen, X.X.; Ismagilov, R.F.; Rampi, M.A.; Whitesides, G.M.;Molecular Electronics with a Metal—Insulator—Metal Junction Based on Self-Assembled Monolayers In Molecules as Components of Electronic Devices Amer. Chem.Soc.: Washington, 2003; Vol. 844, pp 16-35.
  38. Stroock, A. D.; Ismagilov, R. F.; Stone, H. A.; Whitesides, G. M. "Fluidic ratchet based on Marangoni-Benard convection", Langmuir 2003, 19, 4358-4362 pdf.

ARCHIVED PREPRINTS / OTHER DOCUMENTS

Rustem F. Ismagilov. 2021. "Molnupiravir FDA Antimicrobial drugs advisory committee meeting (AMDAC) Virtual Meeting, November 30, 2021." Public Comment and Presentation. Video Recording (see 5:12) and Transcript (see p. 214).

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, and 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. Author Contributions.

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 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.