2014
167. De Vlaminck I, Valantine HA, Snyder TM, Strehl C, Cohen G, Luikart H, Neff NF, Okamoto J, Bernstein D, Weisshaar D, Quake SR, Khush KK.Circulating cell-free DNA enables noninvasive diagnosis of heart transplant rejection. Sci Transl Med. 2014 Jun 18;6(241):241ra77. doi: 10.1126/scitranslmed.3007803.PMID:24944192 [PubMed - in process] pdf
166. Koh W, Pan W, Gawad C, Fan HC, Kerchner GA, Wyss-Coray T, Blumenfeld YJ, El-Sayed YY, Quake SR. Noninvasive in vivo monitoring of tissue-specific global gene expression in humans. Proc Natl Acad Sci U S A. 2014 May 20;111(20):7361-6. doi: 10.1073/pnas.1405528111. Epub 2014 May 5. PubMed PMID: 24799715; PubMed Central PMCID: PMC4034220. pdf
165. Treutlein B, Brownfield DG, Wu AR, Neff NF, Mantalas GL, Espinoza FH, Desai TJ, Krasnow MA, Quake SR.Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq.Nature. 2014 May 15;509(7500):371-5. doi:10.1038/nature13173. Epub 2014 Apr 13.PubMed [citation] PMID: 24739965 pdf
164. Treutlein B, Gokce O, Quake SR, Südhof TC.Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing. Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):E1291-9. doi: 10.1073/pnas.1403244111. Epub 2014 Mar 17.PubMed [citation] PMID: 24639501, PMCID: PMC3977267 pdf
163. Underhill PA, Poznik GD, Rootsi S; et al. The phylogenetic and geographic structure of Y-chromosome haplogroup R1a. European Journal of Human Genetics. 2014 March 26. doi:10.1038/ejhg.2014.50. pdf
162. Bates SR, Quake SR.Mapping of protein-protein interactions of E. coli RNA polymerase with microfluidic mechanical trapping.PLoS One. 2014 March 18;9(3):e91542. doi: 10.1371/journal.pone.0091542.PubMed [citation] PMID: 24643045, PMCID: PMC3958368 pdf
161. Georgiou G, Ippolito GC, Beausang J, Busse CE, Wardemann H, Quake SR.The promise and challenge of high-throughput sequencing of the antibody repertoire.Nat Biotechnol. 2014 Feb;32(2):158-68. doi: 10.1038/nbt.2782. Epub 2014 Jan 19.PubMed [citation] PMID: 24441474pdf
160. Blainey PC, Quake SR. Dissecting genomic diversity, one cell at a time. Nat Methods. 2014 Jan; 11(1):19-21. PMC 2014 March 09. PMCID: PMC3947563 pdf
159. Gu W, Koh W, Blumenfeld YJ, El-Sayed YY, Hudgins L, Hintz SR, Quake SR.Noninvasive prenatal diagnosis in a fetus at risk for methylmalonic acidemia.Genet Med. 2014 Jan 9. doi: 10.1038/gim.2013.194. [Epub ahead of print]PubMed [citation] PMID: 24406457 pdf
158. Wu AR, Neff NF, Kalisky T, Dalerba P, Treutlein B, Rothenberg ME, Mburu FM, Mantalas GL, Sim S, Clarke MF, Quake SR. Quantitative assessment of single-cell RNA-sequencing methods.Nat Methods. 2014 Jan;11(1):41-6. doi: 10.1038/nmeth.2694. Epub 2013 Oct 20.PubMed [citation] PMID: 24141493, PMCID: PMC4022966 pdf
2013
157. De Vlaminck I, Khush KK, Strehl C, Kohli B, Luikart H, Neff NF, Okamoto J, Snyder TM, Cornfield DN, Nicolls MR, Weill D, Bernstein D, Valantine HA, Quake SR. Temporal response of the human virome to immunosuppression and antiviral therapy.Cell. 2013 Nov 21;155(5):1178-87. doi: 10.1016/j.cell.2013.10.034. PubMed PMID: 24267896. pdf
156. VLorthongpanich C, Cheow LF, Balu S, Quake SR, Knowles BB, Burkholder WF, Solter D, Messerschmidt DM. Single-cell DNA-methylation analysis reveals epigenetic chimerism in preimplantation embryos. Science. 2013 Sep 6;341(6150):1110-2. doi: 10.1126/science.1240617. PubMed PMID: 24009393. pdf
155. Vollmers C, Sit RV, Weinstein JA, Dekker CL, Quake SR. Genetic measurement of memory B-cell recall using antibody repertoire sequencing. Proc Natl Acad Sci USA. 2013 Aug 13; 110(33):13463-8. doi: 10.1073/pnas. 1312146110. Epub 2013 Jul 29. PMID: 23898164 pdf
154. Voskoboynik A, Newman AM, Corey DM, Sahoo D, Pushkarev D, Neff NF, Passarelli B, Koh W, Ishizuka KJ, Palmeri KJ, Dimov IK, Keasar C, Fan HC, Mantalas GL, Sinha R, Penland L, Quake SR, Weissman IL. Identification of a colonial chordate histocompatibility gene. Science. 2013 Jul 26; 341 (6144); 384-7. doi: 10.1126/science. 1238036. PMID: 23888037 pdf
153. Voskoboynik A, Neff NF, Sahoo D, Newman AM, Pushkarev D, Koh W, Passarelli B, Fan HC, Mantalas GL, Palmeri KJ, Ishizuka KJ, Gissi C, Griggio F, Ben-Shlomo R, Corey DM, Penland L, White RA, Weissman IL, Quake SR. The genome sequence of the colonial chordate, Botryllus schlosseri. Elife. 2013 Jul 2; 2:e00569. doi: 10.7554/eLife. 00569. Print 2013. PMCID: PMC3699833 pdf
152. Weinstein JA, Zeng X, Chien YH, Quake SR. "Correlation of gene expression and genome mutation in single B-cells." PLoS One. 2013 June 28; 8 (6):e67624. doi: 10.1371/journal.pone.0067624. Print 2013. PMCID: PMC3695916. pdf
151. Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, Ross CA, Tringe SG, Chain PS, Scholz MB, Lo CC, Raymond J, Quake SR, Hedlund BP. Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage.Nat Commun. 2013; 4:1854. doi: 10.1038/ncomms2884. PMCID: PMC3878185. pdf
150. Yu F, Horowitz MA, Quake SR. "Microfluidic serial digital to analog pressure converter for arbitrary pressure generation and contamination-free flow control" Lab Chip. 2013 Mar 25. [Epub ahead of print] PMID: 23529280. pdf
149. Jiang N, He J, Weinstein JA, Penland L, Sasaki S, He XS, Dekker CL, Zheng NY, Huang M, Sullivan M, Wilson PC, Greenberg HB, Davis MM, Fisher DS, Quake SR. "Lineage structure of the human antibody repertoire in response to influenza vaccination" Sci Transl Med. 2013 Feb 6;5(171):171ra19. doi: 10.1126/scitranslmed.3004794. PMCID: PMC3699344. pdf
148. Streets AM, Sourigues Y, Kopito RR, Melki R, Quake SR. "Simultaneous measurement of amyloid fibril formation by dynamic light scattering and fluorescence reveals complex aggregation kinetics" PLoS One. 2013;8(1):e54541. doi: 10.1371/journal.pone.0054541. Epub 2013 Jan 17. PMCID: PMC3547910 pdf
147. Meier M, Sit RV, Quake SR. "Proteome-wide protein interaction measurements of bacterial proteins of unknown function" Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):477-82. doi: 10.1073/pnas.1210634110. Epub 2012 Dec 24. PMID: 23267104 PMCID: PMC3545810. pdf
146. Vedel S, Tay S, Johnston DM, Bruus H, Quake SR. "Migration of cells in a social context."Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):129-34. doi: 10.1073/pnas.1204291110. Epub 2012 Dec 18. PMID: 23251032. PMCID: PMC3538227. pdf
2012
145. Martin, Lance; Meier, Matthias; Lyons, Shawn M.; et al. "Systematic reconstruction of RNA functional motifs with high-throughput microfluidics" NATURE METHODS Volume:9 Issue:12 Pages:1192-U85 DOI: 10.1038/NMETH.2225 Published: Dec 2012. PMID: 23142872; PMCID: PMC3863600. pdf
144. Marshall, Ian P. G.; Blainey, Paul C.; Spormann, Alfred M.; et al. "A Single-Cell Genome for Thiovulum sp." APPLIED AND ENVIRONMENTAL MICROBIOLOGY Volume:78 Issue:24 Pages:8555-8563 DOI: 10.1128/AEM.02314-12 Published: Dec 2012. PMID: 23023751; PMCID: PMC3502928. pdf
143. Meier, Matthias; Sit, Rene; Pan, Wenying; et al. "High-Performance Binary Protein Interaction Screening in a Microfluidic Format" ANALYTICAL CHEMISTRY Volume:84 Issue:21 Pages: 9572-9578 DOI: 10.1021/ac302436y Published: Nov 6, 2012. PMID: 23051662; PMCID: PMC3533494. pdf
142. Blainey, Paul C.; Milla, Carlos E.; Cornfield, David N.; et al. "Quantitative Analysis of the Human Airway Microbial Ecology Reveals a Pervasive Signature for Cystic Fibrosis" SCIENCE TRANSLATIONAL MEDICINE Volume:4 Issue:153 DOI: 10.1126/scitranslmed.3004458 Published: Sept 26, 2012. PMID: 23019655; PMCID: PMC3898170. pdf
141. Jan, Max; Snyder, Thomas M.; Corces-Zimmerman, M. Ryan; et al. "Clonal Evolution of Preleukemic Hematopoietic Stem Cells Precedes Human Acute Myeloid Leukemia" SCIENCE TRANSLATIONAL MEDICINE Volume:4 Issue:149 Article Number: 149ra118 DOI: 10.1126/scitranslmed.3004315 Published: August 29, 2012. PMID: 22932223; PMCID: PMC4045621. pdf
140. Wang, Jianbin; Fan, H. Christina; Behr, Barry; et al. "Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm" CELL Volume: 150 Issue: 2 Pages: 402-412 DOI: 10.1016/j.cell.2012.06.030 Published: July 20, 2012. PMID: 22817899; PMCID: PMC3525523. pdf
139. Fan, H. Christina; Gu, Wei; Wang, Jianbin; et al. "Non-invasive prenatal measurement of the fetal genome" NATURE Volume: 487 Issue: 7407 Pages: 320-+ DOI: 10.1038/nature11251 Published: July 19, 2012. PMID: 22763444; PMCID: PMC3561905. pdf
138. Pamp, Suenje J.; Harrington, Eoghan D.; Quake, Stephen R.; et al. "Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB)" GENOME RESEARCH Volume: 22 Issue: 6 Pages: 1107-1119 DOI: 10.1101/gr.131482.111 Published: June 2012. PMID: 22434425; PMCID: PMC3371716. pdf
137. Powell, Ashley A.; Talasaz, AmirAli H.; Zhang, Haiyu; et al. "Single Cell Profiling of Circulating Tumor Cells: Transcriptional Heterogeneity and Diversity from Breast Cancer Cell Lines" PLOS ONE, Volume: 7 Issue:5 Article Number: e33788 DOI: 10.1371/journal.pone.0033788 Published: May 7, 2012. PMID: 22586443; PMCID: PMC3346739. pdf
136. Rothenberg, Michael E.; Nusse, Ysbrand; Kalisky, Tomer; et al. "Identification of a cKit(+) Colonic Crypt Base Secretory Cell That Supports Lgr5(+) Stem Cells in Mice" Gastroenterology, Volume:142 Issue:5 Pages:1195-+ DOI:10.1053/j.gastro.2012.02.006 Published: May 2012.PMID: 22333952; PMCID: PMC3911891. pdf
135. Sanchez-Freire, Veronica; Ebert, Antje D.; Kalisky, Tomer; et al. "Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns" Nature Protocols Volume:7 Issue:5 Pages:829-838 DOI:10.1038/nprot.2012.021 Published: April 2012. PMID: 22481529; PMCID: PMC3657501. pdf
134. Dewey, Frederick E., Pan, Stephen; Wheeler, Matthew T.; et al. "DNA Sequencing Clinical Applications of New DNA Sequencing Technologies" Circulation, Volume:125 Issue:7 Pages:931-944 DOI:10.1161/CIRCULATIONAHA.110.972828 Published Feb 21, 2012. PMID: 22354974; PMCID: PMC3364518. pdf
133. Araci, Ismail Emre; Quake, Stephen R. "Microfluidic very lage scale integration (mVLSI) with integrated micromechnical valves" Lab on a Chip, Volume:12 Issue:16 Pages:2803-2806 DOI:10.1029/c21c40258k Published:2012 Aug 21;12(16):2803-6. doi: 10.1039/c2lc40258k. PMID: 22714259. pdf
132. White, Richard Allen, III; Quake, Stephen R.; Curr, Kenneth. "Digital PCR provides absolute quantitation of viral load for an occult RNA virus" Journal of Virological Methods, Volume:179 Issue:1 Pages:45-50 DOI:10.1016/j.jviromet.2011.09.017 Published Jan 2012. pdf
131. Wang J, Fan CH, Behr B, Quake SR. "Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm" Cell, 20 July 2012; 150(402-412). pdf
130. Fan CH, Gu W, Wang J, Blumenfeld YJ, El0Sayed YY, Quake SR. "Non-invasive prenatal measurement of the fetal genome" Nature, 19 July 2012; 487(320-324). DOI:10.1038/nature11251. pdf
129. Wu AR, Kawahara TLA, Rapicavoli NA, van Riggelen J, Shroff EH, Xu L, Felsher DW, Chang HY, Quake SR. "High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation" Lab on a Chip, 19 March 2012; 12(2190-2198). DOI:10.1039/c21c21290k. pdf
2011
128. Dalerba P, Kalisky T, Sahoo D, Rajendran PS, Rothenberg ME, Leyrat AA, Sim S, Okamoto J, Johnston DM, Qian D, Zabala M, Bueno J, Neff NF, Wang J, Shelton AA, Visser B, Hisamori S, Shimono Y, van de Wetering M, Clevers H, Clarke MF, Quake SR. "Single-cell dissection of transcriptional heterogeneity in human colon tumors" Nat Biotechnol. 2011;  29 (12):  1120-7. pdf
127. Kalisky T, Blainey P, Quake S, "Genomic Analysis at the Single-Cell Level" Annu.Rev.Genet., 2011 45: 431-45 pdf
126. White RA, Quake SR, Curr K, "Digital PCR provides absolute quantitation of viral load for an occult RNA virus" J Virol Methods, 2011 Sep 29 pdf
125. Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W, Hammond S, Andersen MR, Neff N, Passarelli B, Koh W, Fan, HC, Wang J, Gui Y, Lee KH, Betenbaugh MJ, Quake, SR, Famili I, Palsson BO, Wang J., "The Genomic Sequence of the Chinese Hamster Ovary (CHO)-K1 Cell Line" Nat Biotechnology, 2011; 29(8). pdf
124. Glotzbach JP, Januszyk M, Vial IN, Wong VW, Gelbard A, Kalisky T, Thangarajah H, Longaker MT, Quake SR, Chu G, Gurtner GC., "An Information Theoretic, Microfluidic-Based Single Cell Analysis Permits Identification of Subpopulations among Putatively Homogeneous Stem Cells" PLOS One, 2011; 6(6). pdf
123. Kawahara TL, Rapicavoli NA, Wu AR, Qu K, Quake SR, Chang HY. "Dynamic Chromatin Localization of Sirt6 Shapes Stress - and aging - related Transcriptional Networks" PLoS Genet, June 2011, 7(6). pdf
122. Kalisky T, Quake SR."Single-cell Genomics" Nat. Methods, 2011 Apr;8(4). pdf
121. Snyder TM, Khush KK, Calantine HA, Quake SR."Universal Noninvasive Detection of Solid Organ Transplant Rejection" Pro Natl Acad Sci USA, 2011 Apr 12;108(15). pdf
120. Jiang N, Weinstein JA, Penland L, White III RA, Fisher DS, Quake SR. "Determinism and stochasticity during maturation of the zebrafish antibody repertoire" Proc Natl Acad Sci USA. March 29, 2011, 108(13) 5348-5353. pdf
119. Kim S, Streets AM, Lin RR, Quake SR, Weiss S, Majumdar DS. "High-Throughput Single Molecule Optofluidic Analysis" Nature Methods, March 2011 8:3, 242-245 pdf
118. Blainey PC, Mosier AC, Potanina A, Franics CA, Quake SR. "Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis" 6(2): e16626. 2011 pdf
2010
117. Fan HC, Wang J, Potanina A, Quake SR. "Whole Genome Molecular Haplotyping of Single Cells" Nature Biotechnology. 2010 Epub Dec 19 pdf
116. Blainey PC, Quake SR. "Digital MDA for enumeration of total nucleic acid contamination" Nucleic Acids Research Advance Access. 2010 Nov;1-9. pdf
115. Bao XR, Fraser IDC, Wall EA, Quake SR, Simon MI "Variability in G-Protein-Coupled Signaling Studied with Microfluidic Devices" Biophysical Journal Volume 99 October 2010 2414–2422. pdf
114. Gomez-Sjoberg R, Leyrat AA, Houseman BT, Shokat K, Quake SR. "Niocompatibility and Reduced Drug Absorption of Sol-Gel-Treated Poly(dimethyl siloxane) for Microfluidic Cell Culture Applications" Ana Chem., 2010 Oct 11 pdf
113. Fordyce PM, Gerber D, Tran D, Zheng J, Li H5, DeRisi JL, Quake SR. "De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis" NatureBiotechnology. 2010 Sep ;28(9):970-976. Epub 2010 Aug 29. pdf
112. Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW. "Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing." Nature. 2010 Jul 8;466(7303):267-71. Epub 2010 Jun 27. pdf
111. Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR. "Analysis of the size distributions of fetal and maternal cell-free DNA by paired-end sequencing." Clin Chem. 2010 Aug;56(8):1279-86. Epub 2010 Jun 17. pdf
110. Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Morgan AA, Pushkarev D, Neff NF, Hudgins L, Gong L, Hodges LM, Berlin DS, Thorn CF, Sangkuhl K, Herbert JM, Woon M, Sagreiya H, Whaley R, Knowles JW, Chou MF, Thakuria JV, Rosenbaum AM, Zaranek AW, Church GM, Greely HT, Quake SR, Altman RB."Clinical Assessment Incorporating a Personal Genome" Lancet 2010 May 1;375(9725). pdf
109. Streets AM, Quake SR "Ostwald ripening of clusters during protein crystallization" Physical Reveiw Letters. 2010 April 104;178102. pdf
108. Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Morgan AA, Pushkarev D, Neff NF, Hudgins L, Gong L, Hodges LM, Berlin DS, Thorn CF, Sangkuhl K, Hebert JM, Woon M, Sagreiya H, Whaley R, Knowles JW, Chou MF, Thakuria JV, Rosenbaum AM, Zaranek AW, Church GM, Greely HT, Quake SR, Altman RB " Clinical assessment incorportating a personal genome" Lancet 2010: 375 (9725) 1525:1535 pdf
107. Fan HC, Quake SR "Sensitivity of Noninvasive Prenatal Detection of Fetal Aneuploidy from Maternal Plasma Using Shotgun Sequencing is Limited Only by Counting Statistics" PLOS ONE 5 (5) pdf
106. Lee CC, Snyder TM, Quake SR."A microfluidic oligonucleotide synthesizer." Nucleic Acids Res. 2010 May;38(8):2514-21. Epub 2010 Feb 21. pdf
105. Schwartz JJ, Stavrakis S, Quake SR.."Colloidal lenses allow high-temperature single-molecule imaging and improve fluorophore photostability." Nat Nanotechnol. 2010 Feb;5(2):127-32. Epub 2009 Dec 20. pdf
2009
104. Bates SR, Quake SR "Highly parallel measurements of interaction kinetic constants with a microfabricated optomechanical device" Applied Physics Letters 95 August 2009: 073705 pdf
103. Schwartz JJ, Quake SR"Single molecule measurement of the "speed limit" of DNA polymerase." Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20294-9. Epub 2009 Nov 11. Erratum in: Proc Natl Acad Sci U S A. 2010 Jan 19;107(3):1254. pdf
102. Maerkl SJ, Quake SR."Experimental determination of the evolvability of a transcription factor."Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18650-5. Epub 2009 Oct 19. pdf
101. Pushkarev D, Neff NF, Quake SR.."Single-molecule sequencing of an individual human genome." Nat Biotechnol. 2009 Sep;27(9):847-52. Epub 2009 Aug 10. pdf
100. Weinstein JA, Jian N, White III RA, Fisher DS, Quake SR "High-Throughput Sequencing of the Zebrafish Antibody Repertoire" Science 8 May 2009: 807-810 pdf
99. Wu AR, Hiatt JB, Lu R, Attema JL, Lobo NA, Weissman IL, Clarke MF, Quake SR "Automated microfluidic chromatin immunoprecipitation from 2,000 cells" Lab on a Chip 9, 1365-1370, 2009 pdf
98. Fan HC, Blumenfeld YJ, El-Sayed YY, Chueh J, Quake SR "Microfluidic digital PCR enables rapid prenatal diagnosis of fetal aneuploidy." Am J Obstet Gynecol. 2009 May;200(5):543.e1-7. pdf
97. Melin J, Lee A, Foygel K, Leong DE, Quake SR, Yao MWM "In Vitro Embryo Culture in Defined, Sub-microliter Volumes" Dev. Dynamics. 238:950-955, 2009 pdf
96. White III RA, Blainey PC, Fan CH, Quake SR. "Digital PCR provides sensitive and absolute calibration for high throughput sequencing" BMC Genomics 10:116 doi:10.1186/1471-2164-10-116 pdf
95. Diehn M, Cho RW, Lobo NA, Kalisky T, Dorie MJ, Kulp AN, Qian D, Lam JS, Ailles LE, Wong M, Joshua B, Kaplan MJ, Wapnir I, Dirbas F, Somlo G, Garberoglio C, Paz B, Shen J, Lau SK, Quake SR, Brown JM, Weissman IL, Clarke MF "Association of reactive oxygen species levels and radioresistance in cancer stem cells" Nature Feb 2009 doi:10.1038/nature07733 pdf
94. Gerber D, Maerkl SJ, Quake SR. "An in vitro microfluidic approach to generating protein-interaction networks" Nature Methods 6:1 Jan 2009 10.1038/NMET.1289 pdf
2008
93. Fan CH, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR. "Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood " Proc. Nat. Acad. Sci. 10.1073/pnas.0808319105 pdf
92. Einav S, Gerber D, Bryson PD, Sklan EH, Elazar M, Maerkl SJ, Glenn JS, Quake SR. "Discovery of a hepatitis C target and its pharmacological inhibitors by microfluidic affinity analysis" Nature Biotech. 26:9, 1019-1027 pdf
91. Balagadde FK, Song H, Collins CH, Barnet M, Arnold FH, Quake SR, You L. "A synthetic Escherichia coli predator-prey ecosystem" Mol. Sys. Biol. 4:187, 1-8 pdf
90. Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, DiMeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. "Single-Molecule DNA Sequencing of a Viral Genome" Science. 4 April 2008 Vol. 320 pdf
89. Zhong JF, Chen Y, Marcus JS, Scherer A, Quake SR, Taylor CR, Weiner LP. "A microfluidic processor for gene expression profiling of single human embryonic stem cells" Lab on a Chip. 8, 68-74 pdf
2007
88. Warren LA, Rossi DJ, Schiebinger GR, Weissman IL, Kim SK, Quake SR. "Transcriptional instability is not a universal attribute of aging" Aging Cell. 6:6 775-782 pdf
87. Gomez-Sjoberg R, Leyrat AA, Pirone DM, Chen CS, Quake SR. "Versatile, Fully Automated, Microfluidic Cell Culture System" Anal. Chem. 10.1021/ac071311w pdf
86. Marcy Y, Oshoey T, Lasken RS, Stockwell TB, Walenz BP, Halpern AL, Beeson KY, Goldberg SMD, Quake SR. "Nanoliter reactors improve multiple displacement amplification of genomes from single cells" PLoS Genet 3(9): e155. doi:10.1371/journal.pgen.0030155 pdf
85. Fan HC , Quake SR. "Detection of aneuploidy with digital polymerase chain reaction" Anal. Chem. 10.1021/ac0709394 pdf
84. Schwartz JJ, Quake SR. "High density single molecule surface patterning with colloidal epitaxy" Appl. Phys. Lett. 91, 083902 2007 pdf
83. Spletter ML, Liu J, Liu J, Su H, Giniger E, Komiyama T, Quake SR, Luo L. "Lola regulates Drosophila olfactory projection meuron identity and targeting specificity" Neural. Develop. 2:14 2007 pdf
82. Marcy Y, Ouverney C, Blik EM, Losekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz P, Relman DA, Quake SR. "Dissecting biological "dark matter" with single cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth" Proc. Nat. Acad. Sci. July 9, 2007, 10.1073/pnas.0704662104 pdf
81. Kartalov EP, Scherer A, Quake SR, Taylor CR, Anderson WF. "Experimentally validated quantitative linear model for the device physics of elastomeric microfluidic valves" J. Appl. Phys. 101 (6) Mar 15 2007 pdf
80. Anderson MJ, DeLaBarre B, Raghunathan A, Palsson BO, Brunger AT, Quake SR. "Crystal Structure of a Hyperactive Escherichia coli Gylcerol Kinase Mutand Gly230Asp Obtained Using Microfluidic Crystallization Devices" Biochemistry 2007, 46, 5277-5731. pdf
79. Melin J, Quake SR. "Microfluidic Large-Scale Integration: The Evolution of Design Rules for Biological Automation" Annu. Rev. Biophys. Biomol. Struct. 36:213-31 pdf
78. Warren LA, Weinstein JA, Quake SR. "The Digital Array Response Curve" Preprint. pdf
77. Huang Y, Castrataro P, Lee CC, Quake SR. "Solvent resistant microfluidic DNA synthesizer" Lab on a Chip . 2007, 7, 1 DOI: 10.1039/b613923j pdf
76. Maerkl SJ, Quake SR. "A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors" Science . 12 January 2007, 315:233-237 pdf
2006
75. Ma Z, Gerton JM, Wade LA, Quake SR. "Fluorescence Near-Field Microscopy of DNA at Sub-10nm Resolution" Phys. Rev. Lett. 31 December 2006 97:26 (260801) pdf
74. Ottesen EA, Hong JW, Quake SR, Leadbetter JR. "Microfluidic Digital PCR Enables Multigene Analysis of Individual Environmental Bacteria" Science. 1 December 2006, 314:1464-67 pdf
73. Warren L, Bryder D, Weissman IL, Quake SR. "Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR" Proc. Nat. Acad. Sci. 2006 10.1073/pnas.0608512103 pdf
72. Anderson MJ, Hansen CL, Quake SR. "Phase knowledge enables rational screens for protein crystallization " Proc. Nat. Acad. Sci. 2006 103: 16746-16751 pdf
71. Psaltis D, Quake SR, Yang CH. "Developing optofluidic technology through the fusion of microfluidics and optics" Nature 442 (7101): 381-386 pdf
70. Hong JW, Chen Y, Anderson WF, Quake SR. "Molecular Biology on a Microfluidic Chip" J. Cond. Matt. Phys . 2006 18 (18):S691-S701 May 10 2006 pdf
69. Phillips R, Quake SR. "The Biological Frontier of Physics" Physics Today 2006 59 (5): 38-43 May 2006 pdf
68. Liu J, Williams BA, Gwirtz RM, Wolf BJ, Quake SR. "Enhanced Signals and Fast Nucleic Acid Hybridization By Microfluidic Chaotic Mixing" Angew. Chem. 2006 45:3618-3623 pdf
67. Gambin Y, Legrand O, Quake SR. "Microfabricated rubber microscope using soft solid immersion lenses" Appl. Phys. Lett . 88 (17) Art. No. 174102 pdf
66. Marcus JS, Anderson WF, Quake SR. "Microfluidic Single-Cell mRNA Isolation and Analysis" Anal. Chem. 2006 Mar 31;10.1021/ac0518506. pdf
65. Hansen CL, Classen S, Berger JM, Quake SR. "A microfluidic device for kinetic optimization of protein crystallization and in situ structure determination" J. Am. Chem. Soc. 2006 Mar 15;128(10):3142-3. pdf
64. Polin M, Grier DG, Quake SR. "Anomalous Vibrational Dispersion in Holographically Trapped Colloidal Arrays" Phys. Rev. Lett. 2006 Mar 3;96(8):088101 pdf
63. Marcus JS, Anderson WF, Quake SR. " Parallel Picoliter rt-PCR Assays Using Microfluidics." Anal. Chem. 2006 Feb 1;78(3):956-8. pdf
62. Kartalov EP, Zhong JF, Scherer A, Quake SR, Taylor CR, Anderson WF. " High-throughput multi-antigen microfluidic fluorescence immunoassays" Biotechniques . 2006 Jan;40(1):85-90. pdf
61. Lacenere CJ, Garg NK, Stoltz BM, Quake SR. "Effects of a Modified Dye-Labeled Nucleotide Spacer Arm on Incorporation Thermophilic DNA Polymerases" Nucleosides, Nucleotides & Nucleic Acids . 25:9-15, 2006. pdf
2005
60. Lee CC, Sui G, Elizarov A, Shu CJ, Shin YS, Dooley AN, Huang J, Daridon A, Wyatt P, Stout D, Kolb HC, Witte ON, Satyamurthy N, Heath JR, Phelps ME, Quake SR, Tseng HR. "Multistep Synthesis of a Radiolabeled Imaging Probe Using Integrated Microfluidics" Science. 16 December 2005: 1793-1796. pdf
59. Squires TM, Quake SR. "Microfluidics: Fluid physics at the nanoliter scale" Rev. Mod. Phys. July 2005, 7:3 pp. 977-1026. pdf
58. Adams ML, Johnston ML, Scherer A, Quake SR. "Polydimethylsiloxane based microfluidic diode" J. MicroMech. MicroEng. June 2005 15: 1517-1521 pdf
57. Garg NK, Woodroofe CC, Lacenere CJ, Quake SR, Stoltz BM. "A ligand-free solid-supported system for Sonogashira couplings: applications in nucleoside chemistry" Chemical Communications. 2005, (36), 4551-4553. pdf
56. Balagadde FK, You L, Hansen CL, Arnold FH, Quake SR. "Long-term monitoring of bacteria undergoing programmed population control in a microchemostat." Science . 2005 Jul 1;309(5731):137-40. pdf
2004
55. Gerton JM, Wade LA, Lessard GA, Ma Z, Quake SR. "Tip-enhanced fluorescence microscopy at 10 nanometer resolution." Phys Rev Lett . 2004 Oct 29;93(18):180801. pdf
54. Hansen CL, Sommer MO, Quake SR. "Systematic investigation of protein phase behavior with a microfluidic formulator." Proc. Natl. Acad. Sci . 2004 Oct 5;101(40):14431-6. pdf
53. Kartalov EP, Quake SR. "Microfluidic device reads up to four consecutive base pairs in DNA sequencing-by-synthesis." Nucleic Acids Res . 2004 May 20;32(9):2873-9. pdf
52. Hong JW, Studer V, Hang G, Anderson WF, Quake SR. "A nanoliter-scale nucleic acid processor with parallel architecture" Nat Biotechnol . 2004 Apr;22(4):435-9. pdf
51. Vyawahare, S. Eyal, S. Mathews, K. D. Quake, S. R. " Nanometer-scale Fluorescence Resonance Optical Waveguides" Nano Lett. ; (Comm.); 2004; 4 (6); 1035-1039. pdf
50. Groisman A, Quake SR. "A microfluidic rectifier: anisotropic flow resistance at low Reynolds numbers." Phys Rev Lett . 2004 Mar 5;92(9):094501. pdf
49. Rolland JP, Van Dam RM, Schorzman DA, Quake SR, DeSimone JM. "Solvent-resistant photocurable liquid fluoropolymers for microfluidic device fabrication" J. Am. Chem. Soc. 2004 Mar 3;126(8):2322-3. pdf
48. Wade, LA, Shaprio IR, Ma Z, Quake SR, Collier PC. "Correlating AFM Probe Morphology to Image Resolution for Single-Wall Carbon Nanotube Tips" Nano Lett. ; 2004; 4 (4); 725-731 pdf
47. Studer V, Hang G, Pandolfi A, Ortiz M, Anderson WF, Quake SR. "Scaling properties of a low-actuation pressure microfluidic valve" J. Appl. Phys. ; 95 (1) 393-398 pdf
2003
46. Bao XR, Lee HJ, Quake SR. "Behavior of complex knots in single DNA molecules." Phys Rev Lett. 2003 Dec 31;91(26 Pt 1):265506. pdf
45. Hong JW, Quake SR. "Integrated nanoliter systems." Nat Biotechnol. 2003 Oct;21(10):1179-83. Review. pdf
44. Hansen C, Quake SR. "Microfluidics in structural biology: smaller, faster ... better." Curr Opin Struct Biol. 2003 Oct;13(5):538-44. Review. pdf
43. Reese MO, van Dam RM, Scherer A, Quake SR. "Microfabricated fountain pens for high-density DNA arrays." Genome Res. 2003 Oct;13(10):2348-52. pdf
42. Liu J, Hansen C, Quake SR. "Solving the "world-to-chip" interface problem with a microfluidic matrix." Anal Chem. 2003 Sep 15;75(18):4718-23. pdf
41. Yi GR, Jeon SJ, Thorsen T, Manoharan VN, Quake SR, Pine DJ, Yang SM. "Generation of uniform photonic balls by template-assisted colloidal crystallization" Synth. Mat. 139 (3) 803-806 pdf
40. Yi GR, Thorsen T, Manoharan VN, Hwang MJ, Jeon SJ, Pine DJ, Quake SR, Yang SM. "Generation of uniform colloidal assemblies in soft microfluidic devices" Adv. Mat . 2003 15 (15) 1300+ pdf
39. Groisman A, Enzelberger M, Quake SR. "Microfluidic memory and control devices" Science . 2003 May 9;300(5621):955-8. pdf
38. Wade LA, Shapiro I, Ma Z, Quake SR, Collier CP. "Single Molecule Fluorescence and Force Microscopy Employing Carbon Nanotubes" Nanotech 2003 Vol. 3 317-320 pdf
37. Braslavsky I, Hebert B, Kartalov E, Quake SR, "Sequence Information can be obtained from Single DNA Molecules", Proc. Nat'l Acad. Sci. 100: 3960-3964 (2003). pdf
36. Kartalov EP, Unger MA, Quake SR. "Polyelectrolyte surface interface for single-molecule fluorescence studies of DNA polymerase." Biotechniques . 2003 Mar;34(3):505-10. pdf
35. Adams, ML, Enzelberger M, Quake SR, Scherer A. "Microfluidic integration on detector arrays for absorption and fluorescence micro-spectrometers" Sens. and Act. A . 104 (1):25-31 pdf
34. Filippova EM, Monteleone DC, Trunk JG, Sutherland BM, Quake SR, Sutherland JC. "Quantifying double-strand breaks and clustered damages in DNA by single-molecule laser fluorescence sizing." Biophys. J . 2003 Feb;84(2 Pt 1):1281-90. pdf
2002
33. Chiu CS, Jensen K, Sokolova I, Wang D, Li M, Deshpande P, Davidson N, Mody I, Quick MW, Quake SR, and Lester HA. "Number, density, and surface/cytoplasmic distribution of GABA transporters at presynaptic structures of knock-in mice carrying GABA transporter subtype 1-green fluorescent protein fusions." J Neurosci . 2002 Dec 1; 22 (23): 10251-66. pdf
32. Hansen CL, Skordalakes E, Berger JM, Quake SR, "A Robust and Scalable Microfluidic Metering Method that Allows Protein Crystal Growth by Free Interface Diffusion", Proc. Nat'l Acad. Sci. 99: 16531-6 (2002). pdf
31. Thorsen T, Maerkl SJ, Quake SR, "Microfluidic Large Scale Integration", Science 298: 580-584 (2002). pdf
30. Brody JP, Williams BA, Wold BJ, Quake SR, "Significance and Statistical Errors in the Analysis of DNA Microarray Data", Proc. Nat'l Acad. Sci. 99: 12975-12978 (2002). pdf
29. Thompson HGR, Harris JW, Wold BJ, Quake SR, Brody JP, "Identification and Confirmation of a Module of Coexpressed Genes", Genome Research 12: 1517-1522 (2002). pdf
28. Adams M, DeRose G, Quake SR, Scherer A. "Fundamental approach for optoelectronic and microfluidic integration for miniaturizing spectroscopic devices", Proceedings of SPIE Vol. 4647 1-6 (2002). pdf
27. Eyal S and Quake SR, "Velocity Independent Microfluidic Flow Cytometry", Electrophoresis 23: 2653-2657 (2002). pdf
26. Liu J, Enzelberger M, Quake SR, "A Nanoliter Rotary Device for Polymerase Chain Reaction", Electrophoresis 23: 1531-1536 (2002). pdf
25. Fu AY, Chou HP, Spence C, Arnold FH, Quake SR, "An Integrated Microfabricated Cell Sorter", Anal. Chem. (2002). pdf
24. Van Dam RM, Quake SR, "Gene Expression Analysis with Universal n-mer Arrays", Genome Research 12: 145-152 (2002). pdf
2001
23. Chou HP, Unger MA, Quake SR, "A Microfabricated Rotary Pump", Biomedical Microdevices 3: 323-330 (2001). pdf
22. Thorsen T, Roberts RW, Arnold FH, Quake SR, "Dynamic Pattern Formation in a Vesicle-Generating Microfluidic Device", Phys. Rev. Lett. 86: 4163-6 (2001). pdf
21. Chiu CS, Kartalov E, Unger MA, Quake SR, Lester H, "Single molecule measurements calibrate green fluorescent protein surface densities on transparent beads for use in "knock-in" animals and other expression systems", Journal of Neuroscience Methods 105: 55-63 (2001). pdf
2000
20. Quake SR and Scherer A, "From Micro to Nano Fabrication with Soft Materials", Science 290: 1536-40 (2000). pdf
19. Chou HP, Unger MA, Scherer A, Quake SR, "Integrated Elastomer Fluidic Lab on a Chip - Surface Patterning and DNA diagnostics", in Proceedings of the Solid State Actuator and Sensor Workshop , Hilton Head, S.C. (2000). pdf
18. Meiners JC, Quake SR, "FemtoNewton Force Spectroscopy of Single Extended DNA Molecules", Phys. Rev. Lett. 84: 5014-7 (2000). pdf
17. Quake SR, Yang TJ, Lessard GA, Unger A, Kartalov E, "Fluorescence apertureless near-field microscope: a step towards imaging information in DNA", Proceedings of SPIE Vol. 3922 199-204 (2000). pdf
16. Unger MA, Chou HP, Thorsen T, Scherer A, Quake SR, "Monolithic Microfabricated Valves and Pumps by Multilayer Soft Lithography", Science 288: 113-116 (2000). pdf
15. Yang TJ, Lessard GA, Quake SR, "An Apertureless Near-Field Microscope for Fluorescence Imaging", Applied Physics Letters 76: 378-380 (2000). pdf
1999
14. Unger MA, Kartalov E, Chiu CS, Lester H, Quake SR, "Single Molecule Fluorescence Observed with Mercury Lamp Illumination", Biotechniques 27: 1008-1013 (1999). pdf
13. Fu AY, Spence C, Scherer A, Arnold FH, Quake SR, "A Microfabricated Fluorescence-Activated Cell Sorter", Nature Biotechnology 17: 1109-1111 (1999). pdf
12. Hatfield JW and Quake SR, "Dynamic Properties of an Extended Polymer in Solution", Phys Rev Lett 82: 3548-51 (1999). pdf
11. Lessard G, Yang TJ, Barritault P, Quake SR, "A Scanning Apertureless Fluorescence Microscope", Proceedings of the SPIE , Vol. 3607 158-165 (1999) pdf
10. Meiners JC and Quake SR, "A Direct Measurement of Hydrodynamic Cross Correlations Between Two Particles in an External Potential", Phys Rev Lett 82: 2211-2214 (1999). pdf
9. Brody JP and Quake SR, "A Self-Assembled Microlensing Rotational Probe", Appl Phys Lett. volume 74, no. 1, 4 January 1999. pdf
8. Chou HP, Spence C, Scherer A, Quake SR, "A Microfabricated Device for Sizing and Sorting DNA Molecules", Proc. Nat'l Acad. Sci. 96: 11-13 (1999). pdf
1998
7. Quake SR, Chou HP, Spence C, Fu AY, Scherer A, "Disposable Microdevices for DNA Analysis and Cell Sorting", Proc. Solid-State Sensor and Actuator Workshop , Hilton Head, SC, June 8-11, 1998, pp.11-14. pdf
6. Chou HP, Spence C, Scherer A, Quake SR, "Microfabricated devices for sizing DNA and sorting cells," in Micro- and Nanofabricated Structures and Devices for Biomedical Environmental Applications , Paul L. Gourley, Editor, Proceedings of SPIE Vol 3258, 181-7, (1998). pdf
1997
5. Quake SR, Babcock H, Chu S, "The dynamics of partially extended single molecules of DNA", Nature 388 : 151-154 (1997). pdf
4. Quake SR. "Fast Monte Carlo algorithms for knotted polymers" Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics. 1995 Jul; 52(1):1176-1180. pdf
3. Quake SR. "Topological effects of knots in polymers" Phys. Rev. Lett. 1994 Dec 12; 73(24): 3317-3320. pdf
2. Quake SR. "The Zimm model applied to extended single polymers" J. Chem Phys . 1994 Sept. 101 (5); 4307-4311 pdf
1. Perkins TT, Quake SR, Smith DE, Chu S. "Relaxation of a single DNA molecule observed by optical microscopy" Science . 1994 May 6; 264(5160):822-6. pdf