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Quake Lab Publications

Koh CWQ, Goh YT, Toh JDW, Neo SO, Ng SB, Gunaratne J, Gao YG, Quake SR, Burkholder WF, Goh WSS. Single-nucleotide-resolution sequencing of human N6-methyldeoxyadenosine reveals strand-asymmetric clusters associated with SSBP1 on the mitochondrial genome. Nucleic Acids Res. 2018 Nov 9.

Tabula Muris Consortium; Overall coordination; Logistical coordination; Organ collection and processing; Library preparation and sequencing; Computational data analysis; Cell type annotation; Writing group; Supplemental text writing group; Principal investitgators.  Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature. 2018 Oct;562(7727):367-372.

Cira NJ, Pearce MT, Quake SR. Neutral and selective dynamics in a synthetic microbial community. Proc Natl Acad Sci U S A. 2018 Oct 16;115(42)E9842-E9848.

Collin F, Ning Y, Phillips T, McCarthy E, Scott A, Ellison C, Ku CJ, Guler GD, Chau K, Ashworth A, Quake SR, Levy S. Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA. Posted to Biorxiv on September 26, 2018.

Qingyun L, Zuolin C, Zhou L, Darmanis S, Neff N, Okamoto J, Gulati G, Bennett ML, Sun LO, Clarke LE, Marschallinger J, Yu G, Quake SR, Wyss-Coray t, Barres B. Developmental heterogeneity of microglia and brain myeloid cells revealed by deep single-cell RNA sequencing. Posted to Biorxiv on September 1, 2018.

Liu R, Mignardi M, Jones R, Enge M, Kim SK, Quake SR, Zou J. Modeling Spatial Correlation of Transcripts With Application to Developing Pancreas. Posted to Biorxiv on August 14, 2018.

Erdrich J, Schaberg K, Khodadoust MS, Zhou L, Shelton AA, VisserBC, Ford JM, Alizadeh AA, Quake SR, Kunz PL, Beausang JF. Surgical and molecular characterization of primary and metastatic disease in a neuroendocrine tumor arising in a tailgut cyst. Cold Spring Harb Mol Case Stud. 2018 Aug 7. pii: mcs.a003004. [Epub ahead of print].

Tarashansky AJ, Xue Y, Quake SR, Wang B. Self-assembling Manifolds in Single-cell RNA Sequencing Data. Posted to Biorxiv on July 7, 2018.

Ngo TTM, Moufarrej MN, Rasmussen MH, Camunas-Soler J, Pan W, Okamoto J, Neff NF, Liu K, Wong RJ, Downes K, Tibshirani R, Shaw GM, Skotte L, Stevenson DK, Biggio JR, Elovitz MA, Melbye M, Quake SR. Noninvasive blood tests for fetal development predict gestational age and preterm delivery. Science. 2018 Jun 8;360(6393):1133-1136.

Wang W, Vilella F, Moreno I, Pan W, Simon C, Quake SR. Single cell RNAseq provides a molecular and cellular cartography of changes to the human endometrium through the mentstrual cycle. Posted to Biorxiv on June 19, 2018.

Croote D, Darmanis S, Nadeau KC, Quake SR. Human IgE producing B cells have a unique transcriptional program and generate high affinity, allergen-specific antibodies. Posted to Biorxiv on May 22, 2018.

Dougan T, Quake SR. Viral Taxonomy Derived From Evolutionary Genome Relationships. Posted to Biorxiv on May 15, 2018.

Segal JM, Wesche DJ, Serra MP, Oules B, Kent D, Ng SS, Kar G, Emerton G, Blackford S, Darmanis S, Miquel R, Vinh T, Yamamoto R, Bonham A, Vigilante A, Teichmann S, Quake SR, Nakauchi H, Rashid ST. Single-cell analysis identifies EpCAM+/CDH6+/TROP-2 cells as human liver progenitors. Posted to Biorxiv on April 4, 2018.

Zanini F, Pu SY, Bekerman E, Einav S, Quake SR. Single-cell transcriptional dynamics of flavivirus infection. Elife. 2018 Feb 16;7. pii: e32942.

Wang W, Penland L, Gokce O, Croote D, Quake SR. High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis. BMC Genomics. 2018 Feb 13;19(1):140.


Gee MH, Han A, Lofgren SM, Beausang JF, Mendoza JL, Birnbaum ME, Bethune MT, Fischer S, Yang X, Gomez-Eerland R, Bingham DB, Sibener LV, Fernandes RA, Velasco A, Baltimore D, Schumacher TN, Khatri P, Quake SR, Davis MM, Garcia KC. Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes. Cell. 2017 Dec 20. pii: S0092-8674(17)31433-2.

Gasch AP, Yu FB, Hose J, Escalante LE, Place M, Bacher R, Kanbar J, Ciobanu D, Sandor L, Grigoriev IV, Kendziorski C, Quake SR, McClean MN. Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. PLoS Biol. 2017 Dec 14;15(12):e2004050.

Ooi CC, Mantalas GL, Koh W, Neff N, Fuchigami T, Wong DJ, Wilson RJ, Park SM, Gambhir SS, Quake SR, Wang SX. High-throughput full-length single-cell mRNA-seq of rare cells. PLoS One. 2017 Nov 29; 12(11):e0188510

Wise PH, Shaw GM, Druzin ML, Darmstadt GL, Quaintance C, Makinen E, Relman DA, Quake SR, Butte AJ, Angst, MS, Muglia, LJ, Macones G, Driscoll D, Ober C, Simpson JL, Katz M, Howse J, Stevenson DK. Risky Business: Meeting the Structural Needs of Transdisciplinary Science. J Pediatr. 2017 Dec; 191:255-258.

Sikandar SS, Kuo AH, Kalisky T, Cai S, Zabala M, Hsieh RW, Lobo NA, Scheeren FA, Sim S, Qian D, Dirbas FM, Somlo G, Quake SR, Clarke MF. Role of epithelial to mesenchymal transition associated genes in mammary gland regeneration and breast tumorigenesis. Nat Commun. 2017 Nov 21;8(1):1669.


Li H, Horns F, Wu B, Xie Q, Li J, Li T, Luginbuhl DJ, Quake SR, Luo L. Classifying Drosophila olfactory projection neuron subtypes by single-cell RNA sequencing. Cell. 2017 Nov 16;171(5):1206-1220.e22

Beausang JF, Wheeler AJ, Chan NH, Hanft VR, Dirbas FM, Jeffrey SS, Quake SR. T cell receptor sequencing of early-stage breast cancer tumors identifies altered clonal structure of the T cell repertoire. Proc Natl Acad Sci U S A. 2017 Nov 14. pii: 201713863. [Epub ahead of print]

Camunas-Soler J, Lee H, Hudgins L, Hintz SR, Blumenfeld YJ, El-Sayed YY, Quake SR. Noninvasive prenatal diagnosis of single-gene disorders by use of droplet digital PCR. Clin Chem. 2017 Nov 2. pii: clinchem.2017.278101. [Epub ahead of print]

Darmanis S, Sloan SA, Croote D, Mignardi M, Chernikova S, Samghababi P, Zhang Y, Neff N, Kowarsky M, Caneda C, Li G, Chang SD, Connolly ID, Li Y, Barres BA, Gephart MH, Quake SR. Single-cell RNA-Seq analysis of infiltrating neoplastic cells at the migrating front of human glioblastoma. Cell Rep. 2017 Oct 31;21(5):1399-1410.

Zanini F, Pu Szu-Yuan, Bekerman E, Einav S, Quake SR. Single-cell transcriptional dynamics of flavivirus infection. Posted to Biorxiv on Oct. 14, 2017.

Enge M, Arda HE, Mignardi M, Beausang J, Bottino R, Kim SK, Quake SR. Single-cell analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns. Cell. 2017 Oct5; 17(12): doi: 10.1016/j.cell.2017.09.004

deBourcy CFA, Dekker CL, Davis MM, Nicolls MR, Quake SR. Dynamics of the human antibody repertoire after B cell depletion in systemic sclerosis. Science Immunol. 2017 Sep 29; 2(15): doi: 10.1126/sciimmunol.aan8289

Pan W, Ngo TTM, Camunas-Soler J, Song CX, Kowarsky M, Blumenfeld YJ, Wong RJ, Shaw GM, Stevenson DK, Quake SR. Simultaneously monitoring immune response and microbial infections during pregnancy through plasma cfRNA sequencing. Clin Chem. 2017 Sep 13; doi: 10.1373/clinchem.2017.273888. [Epub ahead of print]

Kowarsky M, Camunas-Soler J, Kertesz M, De Vlaminck I, Koh W, Pan W, Martin L, Neff NF, Okamoto J, Wong RJ, Kharbanda S, El-Sayed Y, Blumenfeld Y, Stevenson DK, Shaw GM, Wolfe ND, Quake SR. Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA. PNAS. 2017 Sep 5;114(36):9623-9628. doi: 10.1073/pnas.1707009114

Camunas-Soler J, Lee H, Hudgins L, Hintz SR, Blumenfeld YJ, El-Sayed YY, Quake SR. Nonivasive prenatal diagnosis of single-gene disorders using droplet digital PCR. Posted to Biorxiv on Aug 23, 2017. doi: 10.1101/179804

Deaton J, Yu FB, Quake SR. PhaMers identifies novel bacteriophage sequences from thermophilic hot springs. Posted to Biorxiv on Jul 28, 2017. doi: 10.1101/169672

Song CX, Yin S, Ma L, Wheeler A, Chen Y, Zhang Y, Liu B, Xiong J, Zhang W, Hu J, Zhou Z, Dong B, Tian Z, Jeffrey SS, Chua MS, So S, Li W, Wei Y, Diao J, Xie D, Quake SR. 5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages. Cell Res. 2017 Aug 18. doi: 10.1038/cr.2017.106

Yu FB, Blainey PC, Schulz F, Woyke T, Horowitz MA, Quake SR. Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples. eLife. 2017 Jul 5; 6 pii: e26580. doi: 10.7554/eLife.26580

Schmidt ST, Zimmerman SM, Wang J, Kim SK, Quake SR. Quantitative Analysis of Synthetic Cell Lineage Tracing Using Nuclease Barcoding. ACS Synth Biol. 2017 Mar 10 [Epub ahead of print]. doi: 10.1021/acssynbio.6b00309.

Wang W, Penland L, Gokce O, Croote D, Quake SR. High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis. Posted to Biorxiv on Mar 10, 2017. doi: 10.1101/115733

Yu FB, Blainey PC, Schulz F, Woyke T, Horowitz MA, Quake SR. Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples. Posted to Bioarxiv on Mar 7, 2017. doi: 10.1101/114496

Yu FB, Willis L, Chau RM, Zambon A, Horowitz M, Bhaya D, Huang KC, Quake SR. Long-term microfluidic tracking of coccoid cyanobacterial cells reveals robust control of division timing. BMC Biol. 2017 Feb 14; 15(1): 11. doi: 10.1186/s12915-016-0344-4

Enge M, Arda HE, Mignardi M, Beausang J, Bottino R, Kim SK, Quake SR. Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns. Posted to Biorxiv on Feb 13, 2017. doi: 10.1101/108043.

Cira NJ, Pearce MT, Quake SR.  Neutral and niche dynamics in a synthetic microbial community. Posted to Biorxiv on Feb 12, 2017. doi: 10.1101/107896.

de Bourcy CF, Angel CJ, Vollmers C, Dekker CL, Davis MM, Quake SR.  Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging. PNAS. 2017 Jan 31; 114(5):1105-1110. doi: 10.1073/pnas.1617959114.


Croote D, Quake SR. Food allergen detection by mass spectrometry: the role of systems biology. NPJ Syst Biol Appl. 2016 Sep 29; 2: 16022. doi: 10.1038/npjsba.2016.22

Földy C, Darmanis S, Aoto J, Malenka RC, Quake SR, Südhof TC.  Single-cell RNAseq reveals cell adhesion molecule profiles in electrophysiologically defined neurons. PNAS. 2016 Aug 30; 113(35): E5222-31. doi: 10.1073/pnas.1610155113.

Cheow LF, Courtois ET, Tan Y, Viswanathan R, Xing Q, Tan RZ, Tan DS, Robson P, Loh YH, Quake SR, Burkholder WF. Single-cell multimodal profiling reveals cellular epigenetic heterogeneity. Nat Methods. 2016 Aug 15. doi: 10.1038/nmeth.3961.

Horns F, Vollmers C, Croote D, Mackey SF, Swan GE, Dekker CL, Davis MM, Quake SR. Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching. Elife. 2016 Aug 2; 5 pii: e16578. doi: 10.7554/eLife.16578.

Gokce O, Stanley GM, Treutlein B, Neff NF, Camp JG, Malenka RC, Rothwell PE, Fuccillo MV, Südhof TC, Quake SR. Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq. Cell Rep. 2016 Jul 14; 16:1-12. doi: 10.1016/j.celrep.2016.06.059.

Treutlein B, Lee QY, Camp JG, Mall M, Koh W, Shariati SA, Sim S, Neff NF, Skotheim JM, Wernig M, Quake SR. Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq. Nature. 2016 Jun 8;534(7607):391-5. doi: 10.1038/nature18323.

Corey DM, Rosental B, Kowarsky M, Sinha R, Ishizuka KJ, Palmeri KJ, Quake SR, Voskoboynik A, Weissman IL. Developmental cell death programs license cytotoxic cells to eliminate histocompatible partners. Proc Natl Acad Sci U S A. 2016 Jun 7;113(23):6520-5. doi: 10.1073/pnas.1606276113.

Araci IE, Robles M, Quake SR. A reusable microfluidic device provides continuous measurement capability and improves the detection limit of digital biology. Lab Chip. 2016 Apr 26;16(9):1573-8. doi: 10.1039/c6lc00194g.

Song CX, Diao J, Brunger AT, Quake SR. Simultaneous single-molecule epigenetic imaging of DNA methylation and hydroxymethylation. Proc Natl Acad Sci U S A. 2016 Apr 19;113(16):4338-43. doi: 10.1073/pnas.1600223113.

Li Y, Pan W, Connolly ID, Reddy S, Nagpal S, Quake S, Gephart MH. Tumor DNA in cerebral spinal fluid reflects clinical course in a patient with melanoma leptomeningeal brain metastases. J Neurooncol. 2016 May;128(1):93-100. doi: 10.1007/s11060-016-2081-5.

Gawad C, Koh W, Quake SR. Single-cell genome sequencing: current state of the science. Nat Rev Genet. 2016 Mar; 17(3):175-88. doi: 10.1038/nrg.2015.16.


Wu AR, Quake SR. Microfluidics Technologies for Low Cell Number Chromatin Immunoprecipitation. Cold Spring Harb Protoc. 2015 Dec 23. doi: 10.1101/pdb.prot084996.

Kellogg RA, Tian C, Lipniacki T, Quake SR, Tay S. Digital signaling decouples activation probability and population heterogeneity. Elife 2015 Oct 21; 4:e08931. doi: 10.7554/eLife.08931.

Vollmers C, De Vlaminck I, Valantine HA, Penland L, Luikart H, Strehl C, Cohen G, Khush KK, Quake SR. Monitoring pharmacologically induced immunosuppression by immune repertoire sequencing to detect acute allograft rejection in heart transplant patients: a proof-of-concept diagnostic accuracy study. PLOS Med. 2015 Oct 14;12(10): e1001890. doi: 10.1371/journal.pmed.1001890. ]

De Vlaminck I, Martin L, Kertesz M, Patel K, Kowarsky M, Strehl C, Cohen G, Luikart H, Neff NF, Okamoto J, Nicolls MR, Cornfield D, Weill D, Valantine H, Khush KK, Quake SR. Noninvasive monitoring of infection and rejection after lung transplantation. Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):13336-41. doi: 10.1073/pnas.1517494112.

Kuhn A, Ong YM, Quake SR, Burkholder WF. Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants. BMC Genomics. 2015 Jul 8;16:508. doi: 10.1186/s12864-015-1700-4. 

Darmanis S, Sloan SA, Zhang Y, Enge M, Caneda C, Shuer LM, Hayden Gephart MG, Barres BA, Quake SR. A survey of human brain transcriptome diversity at the single cell level. Proc Natl Acad Sci U S A. 2015 Jun 9;112(23):7285-90. doi: 10.1073/pnas.1507125112.

Yu W, Jiang N, Ebert PJ, Kidd BA, Müller S, Lund PJ, Juang J, Adachi K, Tse T, Birnbaum ME, Newell EW, Wilson DM, Grotenbreg GM, Valitutti S, Quake SR, Davis MM. Clonal Deletion Prunes but Does Not Eliminate Self-Specific aß CD8(+) T Lymphocytes. Immunity. 2015 May 19; 42(5):929-41. doi: 10.1016/j.immuni.2015.05.001.

Cira NJ, Chung AM, Denisin AK, Rensi S, Sanchez GN, Quake SR, Riedel-Kruse IH. A biotic game design project for integrated life science and engineering education. PLoS Biol. 2015 Mar 25;13(3):e1002110. doi: 10.1371/journal.pbio.1002110.

Vollmers C, Penland L, Kanbar JN, Quake SR. Novel exons and splice variants in the human antibody heavy chain identified by single cell and single molecule sequencing. PLOS One. 2015 Jan 22;10(1):e0117050. doi: 10.1371/journal.pone.0117050. eCollection 2015.

Pan W, Gu W, Nagpal S, Gephart MH, Quake SR. Brain tumor mutations detected in cerebral spinal fluid. Clin Chem. 2015 Mar; 61(3):514-22. doi: 10.1373/clinchem.2014.235457.

Flynn RA, Martin L, Spitale RC, Do BT, Sagan SM, Zarnegar B, Qu K, Khavari PA, Quake SR, Sarnow P, Chang HY. Dissecting noncoding and pathogen RNA-protein interactomes. RNA. 2015 Jan; 21(1):135-43. doi: 10.1261/rna.047803.114.


Araci IE, Su B, Quake SR, Mandel Y (2014 Sept) An implantable microfluidic device for self-monitoring of intraocular pressure. Nat Med 20(9):1074-8. doi: 10.1038/nm.3621.

de Bourcy CFA, De Vlaminck I, Kanbar JN, Wang J, Gawad C, Quake SR. (2014 Aug 19) A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods. PLoS ONE 9(8): e105585. doi: 10.1371/journal.pone.0105585.

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.

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.

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.

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.

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.

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.

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.

Blainey PC, Quake SR. Dissecting genomic diversity, one cell at a time. Nat Methods. 2014 Jan; 11(1):19-21.

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.

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.


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.

Lorthongpanich 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.


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.

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 .

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

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.


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.

Kalisky T, Blainey P, Quake S, "Genomic Analysis at the Single-Cell Level" Annu.Rev.Genet., 2011 45: 431-45.

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.

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).

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).

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).

Kalisky T, Quake SR."Single-cell Genomics" Nat. Methods, 2011 Apr;8(4).

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).

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.

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.

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.


Fan HC, Wang J, Potanina A, Quake SR. "Whole Genome Molecular Haplotyping of Single Cells" Nature Biotechnology. 2010 Epub Dec 19.

Blainey PC, Quake SR. "Digital MDA for enumeration of total nucleic acid contamination" Nucleic Acids Research Advance Access. 2010 Nov;1-9.

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.

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.

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.

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.

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.

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)

Streets AM, Quake SR "Ostwald ripening of clusters during protein crystallization" Physical Reveiw Letters. 2010 April 104;178102.

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.

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).

Lee CC, Snyder TM, Quake SR."A microfluidic oligonucleotide synthesizer." Nucleic Acids Res. 2010 May;38(8):2514-21. Epub 2010 Feb 21.

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.


Bates SR, Quake SR "Highly parallel measurements of interaction kinetic constants with a microfabricated optomechanical device" Applied Physics Letters 95 August 2009: 073705.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.


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.

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.

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.

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.

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.


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.

Gomez-Sjoberg R, Leyrat AA, Pirone DM, Chen CS, Quake SR. "Versatile, Fully Automated, Microfluidic Cell Culture System" Anal. Chem. 10.1021/ac071311w .

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.

Fan HC , Quake SR. "Detection of aneuploidy with digital polymerase chain reaction" Anal. Chem. 10.1021/ac0709394.

Schwartz JJ, Quake SR. "High density single molecule surface patterning with colloidal epitaxy" Appl. Phys. Lett. 91, 083902 2007.

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.

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.

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.

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.

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

Warren LA, Weinstein JA, Quake SR. "The Digital Array Response Curve" Preprint.

Huang Y, Castrataro P, Lee CC, Quake SR. "Solvent resistant microfluidic DNA synthesizer" Lab on a Chip . 2007, 7, 1 doi: 10.1039/b613923j.

Maerkl SJ, Quake SR. "A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors" Science . 12 January 2007, 315:233-237.


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).

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.

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.

Anderson MJ, Hansen CL, Quake SR. "Phase knowledge enables rational screens for protein crystallization " Proc. Nat. Acad. Sci. 2006 103: 16746-16751.

Psaltis D, Quake SR, Yang CH. "Developing optofluidic technology through the fusion of microfluidics and optics" Nature 442 (7101): 381-386.

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.

Phillips R, Quake SR. "The Biological Frontier of Physics" Physics Today 2006 59 (5): 38-43 May 2006.

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

Gambin Y, Legrand O, Quake SR. "Microfabricated rubber microscope using soft solid immersion lenses" Appl. Phys. Lett . 88 (17) Art. No. 174102

Marcus JS, Anderson WF, Quake SR. "Microfluidic Single-Cell mRNA Isolation and Analysis" Anal. Chem. 2006 Mar 31;10.1021/ac0518506.

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.

Polin M, Grier DG, Quake SR. "Anomalous Vibrational Dispersion in Holographically Trapped Colloidal Arrays" Phys. Rev. Lett. 2006 Mar 3;96(8):088101.

Marcus JS, Anderson WF, Quake SR. " Parallel Picoliter rt-PCR Assays Using Microfluidics." Anal. Chem. 2006 Feb 1;78(3):956-8.

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.

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.


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.

Squires TM, Quake SR. "Microfluidics: Fluid physics at the nanoliter scale" Rev. Mod. Phys. July 2005, 7:3 pp. 977-1026.

Adams ML, Johnston ML, Scherer A, Quake SR. "Polydimethylsiloxane based microfluidic diode" J. MicroMech. MicroEng. June 2005 15: 1517-1521.

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.

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.


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.

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.

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.

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.

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

Groisman A, Quake SR. "A microfluidic rectifier: anisotropic flow resistance at low Reynolds numbers." Phys Rev Lett . 2004 Mar 5;92(9):094501.

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.

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.

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.


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.

Hong JW, Quake SR. "Integrated nanoliter systems." Nat Biotechnol. 2003 Oct;21(10):1179-83. Review.

Hansen C, Quake SR. "Microfluidics in structural biology: smaller, faster ... better." Curr Opin Struct Biol. 2003 Oct;13(5):538-44. Review.

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.

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.

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.

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.

Groisman A, Enzelberger M, Quake SR. "Microfluidic memory and control devices" Science . 2003 May 9;300(5621):955-8.

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.

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).

Kartalov EP, Unger MA, Quake SR. "Polyelectrolyte surface interface for single-molecule fluorescence studies of DNA polymerase." Biotechniques . 2003 Mar;34(3):505-10.

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

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.


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.

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).

Thorsen T, Maerkl SJ, Quake SR, "Microfluidic Large Scale Integration", Science 298: 580-584 (2002).

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).

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).

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).

Eyal S and Quake SR, "Velocity Independent Microfluidic Flow Cytometry", Electrophoresis 23: 2653-2657 (2002).

Liu J, Enzelberger M, Quake SR, "A Nanoliter Rotary Device for Polymerase Chain Reaction", Electrophoresis 23: 1531-1536 (2002).

Fu AY, Chou HP, Spence C, Arnold FH, Quake SR, "An Integrated Microfabricated Cell Sorter", Anal. Chem. (2002).

Van Dam RM, Quake SR, "Gene Expression Analysis with Universal n-mer Arrays", Genome Research 12: 145-152 (2002).


Chou HP, Unger MA, Quake SR, "A Microfabricated Rotary Pump", Biomedical Microdevices 3: 323-330 (2001).

Thorsen T, Roberts RW, Arnold FH, Quake SR, "Dynamic Pattern Formation in a Vesicle-Generating Microfluidic Device", Phys. Rev. Lett. 86: 4163-6 (2001).

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).


Quake SR and Scherer A, "From Micro to Nano Fabrication with Soft Materials", Science 290: 1536-40 (2000).

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).

Meiners JC, Quake SR, "FemtoNewton Force Spectroscopy of Single Extended DNA Molecules", Phys. Rev. Lett. 84: 5014-7 (2000).

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).

Unger MA, Chou HP, Thorsen T, Scherer A, Quake SR, "Monolithic Microfabricated Valves and Pumps by Multilayer Soft Lithography", Science 288: 113-116 (2000).

Yang TJ, Lessard GA, Quake SR, "An Apertureless Near-Field Microscope for Fluorescence Imaging", Applied Physics Letters 76: 378-380 (2000).


Unger MA, Kartalov E, Chiu CS, Lester H, Quake SR, "Single Molecule Fluorescence Observed with Mercury Lamp Illumination", Biotechniques 27: 1008-1013 (1999).

Fu AY, Spence C, Scherer A, Arnold FH, Quake SR, "A Microfabricated Fluorescence-Activated Cell Sorter", Nature Biotechnology 17: 1109-1111 (1999).

Hatfield JW and Quake SR, "Dynamic Properties of an Extended Polymer in Solution", Phys Rev Lett 82: 3548-51 (1999).

Lessard G, Yang TJ, Barritault P, Quake SR, "A Scanning Apertureless Fluorescence Microscope", Proceedings of the SPIE , Vol. 3607 158-165 (1999)

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).

Brody JP and Quake SR, "A Self-Assembled Microlensing Rotational Probe", Appl Phys Lett. volume 74, no. 1, 4 January 1999.

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).


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.

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).


Quake SR, Babcock H, Chu S, "The dynamics of partially extended single molecules of DNA", Nature 388 : 151-154 (1997).

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.

Quake SR. "Topological effects of knots in polymers" Phys. Rev. Lett. 1994 Dec 12; 73(24): 3317-3320.

Quake SR. "The Zimm model applied to extended single polymers" J. Chem Phys . 1994 Sept. 101 (5); 4307-4311

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.