Stephen Quake, D.Phil. - Publications

Affiliations: 
Bioengineering Stanford University, Palo Alto, CA 
Area:
biophysics, genomics
Website:
http://thebigone.stanford.edu/people.htm

223 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Schmidt ST, Yu FB, Blainey PC, May AP, Quake SR. Nucleic acid cleavage with a hyperthermophilic Cas9 from an uncultured Ignavibacterium. Proceedings of the National Academy of Sciences of the United States of America. PMID 31659048 DOI: 10.1073/pnas.1904273116  0.44
2019 Ren J, Isakova A, Friedmann D, Zeng J, Grutzner SM, Pun A, Zhao GQ, Kolluru SS, Wang R, Lin R, Li P, Li A, Raymond JL, Luo Q, Luo M, ... Quake SR, et al. Single-cell transcriptomes and whole-brain projections of serotonin neurons in the mouse dorsal and median raphe nuclei. Elife. 8. PMID 31647409 DOI: 10.7554/eLife.49424  0.52
2019 Segal JM, Kent D, Wesche DJ, Ng SS, Serra M, Oulès B, Kar G, Emerton G, Blackford SJI, Darmanis S, Miquel R, Luong TV, Yamamoto R, Bonham A, Jassem W, ... ... Quake SR, et al. Single cell analysis of human foetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors. Nature Communications. 10: 3350. PMID 31350390 DOI: 10.1038/s41467-019-11266-x  0.52
2019 Liu R, Mignardi M, Jones R, Enge M, Kim SK, Quake SR, Zou J. Modeling Spatial Correlation of Transcripts with Application to Developing Pancreas. Scientific Reports. 9: 5592. PMID 30944357 DOI: 10.1038/s41598-019-41951-2  0.52
2019 Agbor-Enoh S, Wang Y, Tunc I, Jang MK, Davis A, De Vlaminck I, Luikart H, Shah PD, Timofte I, Brown AW, Marishta A, Bhatti K, Gorham S, Fideli U, Wylie J, ... ... Quake SR, et al. Donor-derived cell-free DNA predicts allograft failure and mortality after lung transplantation. Ebiomedicine. PMID 30692045 DOI: 10.1016/j.ebiom.2018.12.029  0.36
2019 Horns F, Vollmers C, Dekker CL, Quake SR. Signatures of selection in the human antibody repertoire: Selective sweeps, competing subclones, and neutral drift. Proceedings of the National Academy of Sciences of the United States of America. 116: 1261-1266. PMID 30622180 DOI: 10.1073/pnas.1814213116  0.32
2018 Li Q, Cheng Z, Zhou L, Darmanis S, Neff NF, Okamoto J, Gulati G, Bennett ML, Sun LO, Clarke LE, Marschallinger J, Yu G, Quake SR, Wyss-Coray T, Barres BA. Developmental Heterogeneity of Microglia and Brain Myeloid Cells Revealed by Deep Single-Cell RNA Sequencing. Neuron. PMID 30606613 DOI: 10.1016/j.neuron.2018.12.006  0.52
2018 Stevenson DK, Wong RJ, Aghaeepour N, Angst MS, Darmstadt GL, DiGiulio DB, Druzin ML, Gaudilliere B, Gibbs RS, B Gould J, Katz M, Li J, Moufarrej MN, Quaintance CC, Quake SR, et al. Understanding health disparities. Journal of Perinatology : Official Journal of the California Perinatal Association. PMID 30560947 DOI: 10.1038/s41372-018-0298-1  0.32
2018 Croote D, Darmanis S, Nadeau KC, Quake SR. High-affinity allergen-specific human antibodies cloned from single IgE B cell transcriptomes. Science (New York, N.Y.). 362: 1306-1309. PMID 30545888 DOI: 10.1126/science.aau2599  0.52
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, ... ... Quake SR, et al. Noninvasive blood tests for fetal development predict gestational age and preterm delivery. Science (New York, N.Y.). 360: 1133-1136. PMID 29880692 DOI: 10.1126/science.aar3819  0.32
2017 Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell PJ, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, ... ... Quake SR, et al. Science Forum: The Human Cell Atlas. Elife. 6. PMID 29206104 DOI: 10.7554/eLife.27041  0.44
2017 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. 171: 1206-1220.e22. PMID 29149607 DOI: 10.1016/j.cell.2017.10.019  0.52
2017 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, ... ... Quake SR, et al. Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma. Cell Reports. 21: 1399-1410. PMID 29091775 DOI: 10.1016/j.celrep.2017.10.030  0.52
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. PMID 28965763 DOI: 10.1016/j.cell.2017.09.004  0.52
2017 de Bourcy CFA, Dekker CL, Davis MM, Nicolls MR, Quake SR. Dynamics of the human antibody repertoire after B cell depletion in systemic sclerosis. Science Immunology. 2. PMID 28963118 DOI: 10.1126/sciimmunol.aan8289  0.36
2017 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. Clinical Chemistry. PMID 28904056 DOI: 10.1373/clinchem.2017.273888  0.32
2017 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, ... ... Quake SR, et al. Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA. Proceedings of the National Academy of Sciences of the United States of America. PMID 28830999 DOI: 10.1073/pnas.1707009114  0.36
2017 Sloan SA, Darmanis S, Huber N, Khan TA, Birey F, Caneda C, Reimer R, Quake SR, Barres BA, Paşca SP. Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells. Neuron. 95: 779-790.e6. PMID 28817799 DOI: 10.1016/j.neuron.2017.07.035  0.52
2017 Schmidt ST, Zimmerman SM, Wang J, Kim SK, Quake SR. Quantitative analysis of synthetic cell lineage tracing using nuclease barcoding. Acs Synthetic Biology. PMID 28264564 DOI: 10.1021/acssynbio.6b00309  1
2017 Chakravarthy H, Gu X, Enge M, Dai X, Wang Y, Damond N, Downie C, Liu K, Wang J, Xing Y, Chera S, Thorel F, Quake S, Oberholzer J, MacDonald PE, et al. Converting Adult Pancreatic Islet α Cells into β Cells by Targeting Both Dnmt1 and Arx. Cell Metabolism. PMID 28215845 DOI: 10.1016/j.cmet.2017.01.009  1
2017 Beausang JF, Fan HC, Sit R, Hutchins MU, Jirage K, Curtis R, Hutchins E, Quake SR, Yabu JM. B cell repertoires in HLA-sensitized kidney transplant candidates undergoing desensitization therapy. Journal of Translational Medicine. 15: 9. PMID 28086979 DOI: 10.1186/s12967-017-1118-7  0.6
2016 Horns F, Vollmers C, Croote D, Mackey SF, Swan GE, Dekker CL, Davis MM, Quake SR. Correction: Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching. Elife. 5. PMID 27828776 DOI: 10.7554/eLife.23066  0.32
2016 Lee J, Boutz DR, Chromikova V, Joyce MG, Vollmers C, Leung K, Horton AP, DeKosky BJ, Lee CH, Lavinder JJ, Murrin EM, Chrysostomou C, Hoi KH, Tsybovsky Y, Thomas PV, ... ... Quake SR, et al. Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination. Nature Medicine. PMID 27820605 DOI: 10.1038/nm.4224  0.52
2016 Priest JR, Gawad C, Kahlig KM, Yu JK, O'Hara T, Boyle PM, Rajamani S, Clark MJ, Garcia ST, Ceresnak S, Harris J, Boyle S, Dewey FE, Malloy-Walton L, Dunn K, ... ... Quake SR, et al. Early somatic mosaicism is a rare cause of long-QT syndrome. Proceedings of the National Academy of Sciences of the United States of America. PMID 27681629 DOI: 10.1073/pnas.1607187113  1
2016 Földy C, Darmanis S, Aoto J, Malenka RC, Quake SR, Südhof TC. Single-cell RNAseq reveals cell adhesion molecule profiles in electrophysiologically defined neurons. Proceedings of the National Academy of Sciences of the United States of America. 113: E5222-31. PMID 27531958 DOI: 10.1073/pnas.1610155113  0.52
2016 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. Nature Methods. PMID 27525975 DOI: 10.1038/nmeth.3961  1
2016 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. 5. PMID 27481325 DOI: 10.7554/eLife.16578  0.32
2016 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. PMID 27281220 DOI: 10.1038/nature18323  1
2016 Song CX, Diao J, Brunger AT, Quake SR. Simultaneous single-molecule epigenetic imaging of DNA methylation and hydroxymethylation. Proceedings of the National Academy of Sciences of the United States of America. PMID 27035984 DOI: 10.1073/pnas.1600223113  1
2016 Amit I, Baker D, Barker R, Berger B, Bertozzi C, Bhatia S, Biffi A, Demichelis F, Doudna J, Dowdy SF, Endy D, Helmstaedter M, Junca H, June C, Kamb S, ... ... Quake S, et al. Voices of biotech. Nature Biotechnology. 34: 270-275. PMID 26963549 DOI: 10.1038/nbt.3502  1
2016 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. Journal of Neuro-Oncology. PMID 26961773 DOI: 10.1007/s11060-016-2081-5  1
2016 Gawad C, Koh W, Quake SR. Single-cell genome sequencing: current state of the science. Nature Reviews. Genetics. PMID 26806412 DOI: 10.1038/nrg.2015.16  0.36
2015 Wu AR, Quake SR. Microfluidics Technologies for Low Cell Number Chromatin Immunoprecipitation. Cold Spring Harbor Protocols. PMID 26700100 DOI: 10.1101/pdb.prot084996  1
2015 Becraft ED, Dodsworth JA, Murugapiran SK, Ohlsson JI, Briggs BR, Kanbar J, De Vlaminck I, Quake SR, Dong H, Hedlund BP, Swingley WD. Single-cell Genomics-Facilitated Read-first Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes. Applied and Environmental Microbiology. PMID 26637598 DOI: 10.1128/AEM.03140-15  0.36
2015 Kellogg RA, Tian C, Lipniacki T, Quake SR, Tay S. Digital signaling decouples activation probability and population heterogeneity. Elife. 4. PMID 26488364 DOI: 10.7554/eLife.08931  0.4
2015 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 Medicine. 12: e1001890. PMID 26466143 DOI: 10.1371/journal.pmed.1001890  1
2015 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, et al. Noninvasive monitoring of infection and rejection after lung transplantation. Proceedings of the National Academy of Sciences of the United States of America. 112: 13336-41. PMID 26460048 DOI: 10.1073/pnas.1517494112  1
2015 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. Proceedings of the National Academy of Sciences of the United States of America. 112: 7285-90. PMID 26060301 DOI: 10.1073/pnas.1507125112  0.52
2015 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, et al. Clonal Deletion Prunes but Does Not Eliminate Self-Specific αβ CD8(+) T Lymphocytes. Immunity. 42: 929-41. PMID 25992863 DOI: 10.1016/j.immuni.2015.05.001  1
2015 Nair N, Newell EW, Vollmers C, Quake SR, Morton JM, Davis MM, He XS, Greenberg HB. High-dimensional immune profiling of total and rotavirus VP6-specific intestinal and circulating B cells by mass cytometry. Mucosal Immunology. PMID 25899688 DOI: 10.1038/mi.2015.36  0.4
2015 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 Biology. 13: e1002110. PMID 25807212 DOI: 10.1371/journal.pbio.1002110  1
2015 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. 10: e0117050. PMID 25611855 DOI: 10.1371/journal.pone.0117050  0.36
2015 Pan W, Gu W, Nagpal S, Gephart MH, Quake SR. Brain tumor mutations detected in cerebral spinal fluid. Clinical Chemistry. 61: 514-22. PMID 25605683 DOI: 10.1373/clinchem.2014.235457  1
2015 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 (New York, N.Y.). 21: 135-43. PMID 25411354 DOI: 10.1261/rna.047803.114  1
2015 Underhill PA, Poznik GD, Rootsi S, Järve M, Lin AA, Wang J, Passarelli B, Kanbar J, Myres NM, King RJ, Di Cristofaro J, Sahakyan H, Behar DM, Kushniarevich A, Sarac J, ... ... Quake SR, et al. The phylogenetic and geographic structure of Y-chromosome haplogroup R1a. European Journal of Human Genetics : Ejhg. 23: 124-31. PMID 24667786 DOI: 10.1038/ejhg.2014.50  1
2015 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. 10. DOI: 10.1371/journal.pone.0117050  1
2015 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. 16. DOI: 10.1186/s12864-015-1700-4  1
2015 Darmanis S, Sloan SA, Zhang Y, Enge M, Caneda C, Shuer LM, Gephart MGH, Barres BA, Quake SR. A survey of human brain transcriptome diversity at the single cell level Proceedings of the National Academy of Sciences of the United States of America. 112: 7285-7290. DOI: 10.1073/pnas.1507125112  1
2015 Cheow LF, Quake SR, Burkholder WF, Messerschmidt DM. Multiplexed locus-specific analysis of DNA methylation in single cells Nature Protocols. 10: 619-631. DOI: 10.1038/nprot.2015.041  1
2015 Zambon A, Zoso A, Gagliano O, Magrofuoco E, Fadini GP, Avogaro A, Foletto M, Quake S, Elvassore N. High Temporal Resolution Detection of Patient-Specific Glucose Uptake from Human ex Vivo Adipose Tissue On-Chip Analytical Chemistry. 87: 6535-6543. DOI: 10.1021/ac504730r  1
2014 Gawad C, Koh W, Quake SR. Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics. Proceedings of the National Academy of Sciences of the United States of America. 111: 17947-52. PMID 25425670 DOI: 10.1073/pnas.1420822111  1
2014 Hong LZ, Hong S, Wong HT, Aw PP, Cheng Y, Wilm A, de Sessions PF, Lim SG, Nagarajan N, Hibberd ML, Quake SR, Burkholder WF. BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads. Genome Biology. 15: 517. PMID 25406369 DOI: 10.1186/PREACCEPT-6768001251451949  0.4
2014 Huang Q, Briggs BR, Dong H, Jiang H, Wu G, Edwardson C, De Vlaminck I, Quake S. Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China. Plos One. 9: e111681. PMID 25365331 DOI: 10.1371/journal.pone.0111681  1
2014 Scheeren FA, Kuo AH, van Weele LJ, Cai S, Glykofridis I, Sikandar SS, Zabala M, Qian D, Lam JS, Johnston D, Volkmer JP, Sahoo D, van de Rijn M, Dirbas FM, Somlo G, ... ... Quake SR, et al. A cell-intrinsic role for TLR2-MYD88 in intestinal and breast epithelia and oncogenesis. Nature Cell Biology. 16: 1238-48. PMID 25362351 DOI: 10.1038/ncb3058  1
2014 Cheow LF, Viswanathan R, Chin CS, Jennifer N, Jones RC, Guccione E, Quake SR, Burkholder WF. Multiplexed analysis of protein-ligand interactions by fluorescence anisotropy in a microfluidic platform. Analytical Chemistry. 86: 9901-8. PMID 25207435 DOI: 10.1021/ac502605f  1
2014 Wang J, Quake SR. RNA-guided endonuclease provides a therapeutic strategy to cure latent herpesviridae infection. Proceedings of the National Academy of Sciences of the United States of America. 111: 13157-62. PMID 25157128 DOI: 10.1073/pnas.1410785111  1
2014 Araci IE, Su B, Quake SR, Mandel Y. An implantable microfluidic device for self-monitoring of intraocular pressure. Nature Medicine. 20: 1074-8. PMID 25150497 DOI: 10.1038/nm.3621  1
2014 de Bourcy CF, De Vlaminck I, Kanbar JN, Wang J, Gawad C, Quake SR. A quantitative comparison of single-cell whole genome amplification methods. Plos One. 9: e105585. PMID 25136831 DOI: 10.1371/journal.pone.0105585  1
2014 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. Science Translational Medicine. 6: 241ra77. PMID 24944192 DOI: 10.1126/scitranslmed.3007803  1
2014 Kuhn A, Ong YM, Cheng CY, Wong TY, Quake SR, Burkholder WF. Linkage disequilibrium and signatures of positive selection around LINE-1 retrotransposons in the human genome Proceedings of the National Academy of Sciences of the United States of America. 111: 8131-8136. PMID 24847061 DOI: 10.1073/pnas.1401532111  1
2014 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. Proceedings of the National Academy of Sciences of the United States of America. 111: 7361-6. PMID 24799715 DOI: 10.1073/pnas.1405528111  1
2014 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. 509: 371-5. PMID 24739965 DOI: 10.1038/nature13173  1
2014 Blainey PC, Quake SR. Dissecting genomic diversity, one cell at a time Nature Methods. 11: 19-21. PMID 24524132 DOI: 10.1038/nmeth.2783  1
2014 Georgiou G, Ippolito GC, Beausang J, Busse CE, Wardemann H, Quake SR. The promise and challenge of high-throughput sequencing of the antibody repertoire. Nature Biotechnology. 32: 158-68. PMID 24441474 DOI: 10.1038/nbt.2782  1
2014 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. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 16: 564-7. PMID 24406457 DOI: 10.1038/gim.2013.194  1
2014 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 Nature Methods. 11: 41-46. PMID 24141493 DOI: 10.1038/nmeth.2694  1
2014 Bates SR, Quake SR. Mapping of protein-protein interactions of E. coli RNA polymerase with microfluidic mechanical trapping Plos One. 9. DOI: 10.1371/journal.pone.0091542  1
2014 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 (Proceedings of the National Academy of Sciences of the United States of America (2014) 111 (7361-7366) DOI: 10.1073/pnas.1405528111) Proceedings of the National Academy of Sciences of the United States of America. 111: 11223. DOI: 10.1073/pnas.1412162111  1
2014 Wang J, Quake SR. RNA-guided endonuclease provides a therapeutic strategy to cure latent herpesviridae infection Proceedings of the National Academy of Sciences of the United States of America. 111: 13157-13162. DOI: 10.1073/pnas.1410785111  1
2013 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. 155: 1178-87. PMID 24267896 DOI: 10.1016/j.cell.2013.10.034  1
2013 Landry ZC, Giovanonni SJ, Quake SR, Blainey PC. Optofluidic cell selection from complex microbial communities for single-genome analysis Methods in Enzymology. 531: 61-90. PMID 24060116 DOI: 10.1016/B978-0-12-407863-5.00004-6  1
2013 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 (New York, N.Y.). 341: 1110-2. PMID 24009393 DOI: 10.1126/science.1240617  1
2013 Vollmers C, Sit RV, Weinstein JA, Dekker CL, Quake SR. Genetic measurement of memory B-cell recall using antibody repertoire sequencing. Proceedings of the National Academy of Sciences of the United States of America. 110: 13463-8. PMID 23898164 DOI: 10.1073/pnas.1312146110  1
2013 Tan SJ, Phan H, Gerry BM, Kuhn A, Hong LZ, Min Ong Y, Poon PS, Unger MA, Jones RC, Quake SR, Burkholder WF. A microfluidic device for preparing next generation DNA sequencing libraries and for automating other laboratory protocols that require one or more column chromatography steps. Plos One. 8: e64084. PMID 23894273 DOI: 10.1371/journal.pone.0064084  1
2013 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, ... ... Quake SR, et al. Identification of a colonial chordate histocompatibility gene. Science (New York, N.Y.). 341: 384-7. PMID 23888037 DOI: 10.1126/science.1238036  1
2013 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, ... ... Quake SR, et al. The genome sequence of the colonial chordate, Botryllus schlosseri. Elife. 2: e00569. PMID 23840927 DOI: 10.7554/eLife.00569  1
2013 Weinstein JA, Zeng X, Chien YH, Quake SR. Correlation of gene expression and genome mutation in single B-cells. Plos One. 8: e67624. PMID 23840752 DOI: 10.1371/journal.pone.0067624  1
2013 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. Nature Communications. 4: 1854. PMID 23673639 DOI: 10.1038/ncomms2884  1
2013 Yu F, Horowitz MA, Quake SR. Microfluidic serial digital to analog pressure converter for arbitrary pressure generation and contamination-free flow control Lab On a Chip - Miniaturisation For Chemistry and Biology. 13: 1911-1918. PMID 23529280 DOI: 10.1039/c3lc41394b  1
2013 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. Science Translational Medicine. 5: 171ra19. PMID 23390249 DOI: 10.1126/scitranslmed.3004794  1
2013 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. 8. PMID 23349924 DOI: 10.1371/journal.pone.0054541  1
2013 Meier M, Sit RV, Quake SR. Proteome-wide protein interaction measurements of bacterial proteins of unknown function Proceedings of the National Academy of Sciences of the United States of America. 110: 477-482. PMID 23267104 DOI: 10.1073/pnas.1210634110  1
2013 Vedel S, Tay S, Johnston DM, Bruus H, Quake SR. Migration of cells in a social context. Proceedings of the National Academy of Sciences of the United States of America. 110: 129-34. PMID 23251032 DOI: 10.1073/pnas.1204291110  1
2013 Yu F, Horowitz MA, Quake SR. Robust layout techniques decrease volume injection and capacitive mismatch due to alignment errors 17th International Conference On Miniaturized Systems For Chemistry and Life Sciences, Microtas 2013. 2: 940-942.  1
2013 Yu F, Song K, Horowitz MA, Quake SR. Single cell tracking of Synechocystis growth in a microfluidic culture device using a probabilistic automated image analysis technique 17th International Conference On Miniaturized Systems For Chemistry and Life Sciences, Microtas 2013. 3: 1689-1691.  1
2012 Martin L, Meier M, Lyons SM, Sit RV, Marzluff WF, Quake SR, Chang HY. Systematic reconstruction of RNA functional motifs with high-throughput microfluidics Nature Methods. 9: 1192-1194. PMID 23142872 DOI: 10.1038/nmeth.2225  1
2012 Meier M, Sit R, Pan W, Quake SR. High-performance binary protein interaction screening in a microfluidic format Analytical Chemistry. 84: 9572-9578. PMID 23051662 DOI: 10.1021/ac302436y  1
2012 Marshall IPG, Blainey PC, Spormann AM, Quake SR. A single-cell genome for Thiovulum sp. Applied and Environmental Microbiology. 78: 8555-8563. PMID 23023751 DOI: 10.1128/AEM.02314-12  1
2012 Blainey PC, Milla CE, Cornfield DN, Quake SR. Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis. Science Translational Medicine. 4: 153ra130. PMID 23019655 DOI: 10.1126/scitranslmed.3004458  1
2012 Jan M, Snyder TM, Corces-Zimmerman MR, Vyas P, Weissman IL, Quake SR, Majeti R. Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia. Science Translational Medicine. 4: 149ra118. PMID 22932223 DOI: 10.1126/scitranslmed.3004315  1
2012 Wang J, Fan HC, Behr B, Quake SR. Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm Cell. 150: 402-412. PMID 22817899 DOI: 10.1016/j.cell.2012.06.030  1
2012 Grossmann G, Meier M, Cartwright HN, Sosso D, Quake SR, Ehrhardt DW, Frommer WB. Time-lapse fluorescence imaging of Arabidopsis root growth with rapid manipulation of the root environment using the RootChip. Journal of Visualized Experiments : Jove. PMID 22805296 DOI: 10.3791/4290  1
2012 Christina Fan H, Gu W, Wang J, Blumenfeld YJ, El-Sayed YY, Quake SR. Non-invasive prenatal measurement of the fetal genome Nature. 487: 320-324. PMID 22763444 DOI: 10.1038/nature11251  1
2012 Araci IE, Quake SR. Microfluidic very large scale integration (mVLSI) with integrated micromechanical valves Lab On a Chip - Miniaturisation For Chemistry and Biology. 12: 2803-2806. PMID 22714259 DOI: 10.1039/c2lc40258k  1
2012 Powell AA, Talasaz AH, Zhang H, Coram MA, Reddy A, Deng G, Telli ML, Advani RH, Carlson RW, Mollick JA, Sheth S, Kurian AW, Ford JM, Stockdale FE, Quake SR, et al. Single cell profiling of circulating tumor cells: transcriptional heterogeneity and diversity from breast cancer cell lines. Plos One. 7: e33788. PMID 22586443 DOI: 10.1371/journal.pone.0033788  1
2012 Wu AR, Kawahara TLA, Rapicavoli NA, Riggelen JV, 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 - Miniaturisation For Chemistry and Biology. 12: 2190-2198. PMID 22566096 DOI: 10.1039/c2lc21290k  1
2012 Sanchez-Freire V, Ebert AD, Kalisky T, Quake SR, Wu JC. Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns Nature Protocols. 7: 829-838. PMID 22481529 DOI: 10.1038/nprot.2012.021  1
2012 Pamp SJ, Harrington ED, Quake SR, Relman DA, Blainey PC. Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB). Genome Research. 22: 1107-19. PMID 22434425 DOI: 10.1101/gr.131482.111  1
2012 Dewey FE, Pan S, Wheeler MT, Quake SR, Ashley EA. DNA sequencing clinical applications of new DNA sequencing technologies Circulation. 125: 931-944. PMID 22354974 DOI: 10.1161/CIRCULATIONAHA.110.972828  1
2012 Rothenberg ME, Nusse Y, Kalisky T, Lee JJ, Dalerba P, Scheeren F, Lobo N, Kulkarni S, Sim S, Qian D, Beachy PA, Pasricha PJ, Quake SR, Clarke MF. Identification of a cKit(+) colonic crypt base secretory cell that supports Lgr5(+) stem cells in mice. Gastroenterology. 142: 1195-1205.e6. PMID 22333952 DOI: 10.1053/j.gastro.2012.02.006  1
2012 Quake S. Sizing up cell-free DNA Clinical Chemistry. 58: 489-490. PMID 22235102 DOI: 10.1373/clinchem.2011.174250  1
2012 White RA, Quake SR, Curr K. Digital PCR provides absolute quantitation of viral load for an occult RNA virus Journal of Virological Methods. 179: 45-50. PMID 21983150 DOI: 10.1016/j.jviromet.2011.09.017  1
2012 Tan SJ, Kee MZL, Mathuru AS, Quake SR, Jesuthasan SJ, Burkholder WF. Sorting single cells based on dynamic assessment of signaling Proceedings of the 16th International Conference On Miniaturized Systems For Chemistry and Life Sciences, Microtas 2012. 1690-1692.  1
2012 Yu F, Kibardin V, Horowitz MA, Quake SR. Microfluidic serial DAC for analog pressure generation Proceedings of the 16th International Conference On Miniaturized Systems For Chemistry and Life Sciences, Microtas 2012. 70-72.  1
2011 Grossmann G, Guo WJ, Ehrhardt DW, Frommer WB, Sit RV, Quake SR, Meier M. The Rootchip: An integrated microfluidic chip for plant Science Plant Cell. 23: 4234-4240. PMID 22186371 DOI: 10.1105/tpc.111.092577  1
2011 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, ... ... Quake SR, et al. Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nature Biotechnology. 29: 1120-7. PMID 22081019 DOI: 10.1038/nbt.2038  1
2011 Lu R, Neff NF, Quake SR, Weissman IL. Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding. Nature Biotechnology. 29: 928-33. PMID 21964413 DOI: 10.1038/nbt.1977  1
2011 Kalisky T, Blainey P, Quake SR. Genomic analysis at the single-cell level Annual Review of Genetics. 45: 431-445. PMID 21942365 DOI: 10.1146/annurev-genet-102209-163607  1
2011 Youssef NH, Blainey PC, Quake SR, Elshahed MS. Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone spring, Oklahoma) Applied and Environmental Microbiology. 77: 7804-7814. PMID 21908640 DOI: 10.1128/AEM.06059-11  1
2011 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, ... ... Quake SR, et al. The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nature Biotechnology. 29: 735-41. PMID 21804562 DOI: 10.1038/nbt.1932  1
2011 Kawahara TLA, Rapicavoli NA, Wu AR, Qu K, Quake SR, Chang HY. Dynamic chromatin localization of sirt6 shapes stress- and aging-related transcriptional networks Plos Genetics. 7. PMID 21738489 DOI: 10.1371/journal.pgen.1002153  1
2011 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. 6. PMID 21731674 DOI: 10.1371/journal.pone.0021211  1
2011 Kalisky T, Quake SR. Single-cell genomics Nature Methods. 8: 311-314. PMID 21451520 DOI: 10.1038/nmeth0411-311  1
2011 Snyder TM, Khush KK, Valantine HA, Quake SR. Universal noninvasive detection of solid organ transplant rejection Proceedings of the National Academy of Sciences of the United States of America. 108: 6229-6234. PMID 21444804 DOI: 10.1073/pnas.1013924108  1
2011 Jiang N, Weinstein JA, Penland L, White RA, Fisher DS, Quake SR. Determinism and stochasticity during maturation of the zebrafish antibody repertoire. Proceedings of the National Academy of Sciences of the United States of America. 108: 5348-53. PMID 21393572 DOI: 10.1073/pnas.1014277108  1
2011 Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR. Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. Plos One. 6: e16626. PMID 21364937 DOI: 10.1371/journal.pone.0016626  0.6
2011 Kim S, Streets AM, Lin RR, Quake SR, Weiss S, Majumdar DS. High-throughput single-molecule optofluidic analysis Nature Methods. 8: 242-245. PMID 21297618 DOI: 10.1038/nmeth.1569  1
2011 Fan HC, Wang J, Potanina A, Quake SR. Whole-genome molecular haplotyping of single cells Nature Biotechnology. 29: 51-59. PMID 21170043 DOI: 10.1038/nbt.1739  1
2011 Blainey PC, Quake SR. Digital MDA for enumeration of total nucleic acid contamination Nucleic Acids Research. 39: e19. PMID 21071419 DOI: 10.1093/nar/gkq1074  1
2011 Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR. Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis Plos One. 6. DOI: 10.1371/journal.pone.0016626  1
2011 Quake S. LOC out of the box: Design, engineering and utility of biotic games Lab On a Chip - Miniaturisation For Chemistry and Biology. 11: 13. DOI: 10.1039/c0lc90076a  1
2011 Quake SR. Genomic analysis at the single cell level 15th International Conference On Miniaturized Systems For Chemistry and Life Sciences 2011, Microtas 2011. 1: 1-2.  1
2010 Bao XR, Fraser ID, Wall EA, Quake SR, Simon MI. Variability in G-protein-coupled signaling studied with microfluidic devices. Biophysical Journal. 99: 2414-22. PMID 20959081 DOI: 10.1016/j.bpj.2010.08.043  1
2010 Fordyce PM, Gerber D, Tran D, Zheng J, Li H, DeRisi JL, Quake SR. De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nature Biotechnology. 28: 970-5. PMID 20802496 DOI: 10.1038/nbt.1675  1
2010 Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW. Single-cell NF-B dynamics reveal digital activation and analogue information processing Nature. 466: 267-271. PMID 20581820 DOI: 10.1038/nature09145  1
2010 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 Clinical Chemistry. 56: 1279-1286. PMID 20558635 DOI: 10.1373/clinchem.2010.144188  1
2010 Streets AM, Quake SR. Ostwald ripening of clusters during protein crystallization. Physical Review Letters. 104: 178102. PMID 20482145 DOI: 10.1103/PhysRevLett.104.178102  0.76
2010 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. PMID 20454671 DOI: 10.1371/journal.pone.0010439  1
2010 Lee CC, Snyder TM, Quake SR. A microfluidic oligonucleotide synthesizer Nucleic Acids Research. 38: 2514-2521. PMID 20176572 DOI: 10.1093/nar/gkq092  1
2010 Wilding P, Verpoorte S, Allen Northrup M, Yager P, Quake S, Landers J. Microtechnology in the clinical laboratory: Will it solve analytical problems, and when will it make an impact? Clinical Chemistry. 56: 508-514. PMID 20167692 DOI: 10.1373/clinchem.2009.138719  1
2010 Schwartz JJ, Stavrakis S, Quake SR. Colloidal lenses allow high-temperature single-molecule imaging and improve fluorophore photostability Nature Nanotechnology. 5: 127-132. PMID 20023643 DOI: 10.1038/nnano.2009.452  1
2010 Streets AM, Quake SR. Ostwald ripening of clusters during protein crystallization Physical Review Letters. 104. DOI: 10.1103/PhysRevLett.104.178102  1
2010 Schwartz JJ, Quake SR. Single molecule measurement of the 'speed limit' of DNA polymerase (Proceedings of the National Academy of Sciences of the United States of America (2009) 106, 48, (20294-20299) DOI:10.1073/pnas.0907404106) Proceedings of the National Academy of Sciences of the United States of America. 107: 1254. DOI: 10.1073/pnas.0913884107  1
2010 Weaver JA, Melin J, Stark D, Quake SR, Horowitz MA. Static control logic for microfluidic devices using pressure-gain valves Nature Physics. 6: 218-223. DOI: 10.1038/nphys1513  1
2009 Schwartz JJ, Quake SR. Single molecule measurement of the "speed limit" of DNA polymerase. Proceedings of the National Academy of Sciences of the United States of America. 106: 20294-9. PMID 19906998 DOI: 10.1073/pnas.0907404106  1
2009 Maerkl SJ, Quake SR. Experimental determination of the evolvability of a transcription factor. Proceedings of the National Academy of Sciences of the United States of America. 106: 18650-5. PMID 19841254 DOI: 10.1073/pnas.0907688106  1
2009 Bates SR, Quake SR. Highly parallel measurements of interaction kinetic constants with a microfabricated optomechanical device. Applied Physics Letters. 95: 73705. PMID 19777091 DOI: 10.1063/1.3211382  1
2009 Pushkarev D, Neff NF, Quake SR. Single-molecule sequencing of an individual human genome. Nature Biotechnology. 27: 847-50. PMID 19668243 DOI: 10.1038/nbt.1561  1
2009 Weinstein JA, Jiang N, White RA, Fisher DS, Quake SR. High-throughput sequencing of the zebrafish antibody repertoire. Science (New York, N.Y.). 324: 807-10. PMID 19423829 DOI: 10.1126/science.1170020  1
2009 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: 1365-70. PMID 19417902 DOI: 10.1039/b819648f  1
2009 Fan HC, Blumenfeld YJ, El-Sayed YY, Chueh J, Quake SR. Microfluidic digital PCR enables rapid prenatal diagnosis of fetal aneuploidy. American Journal of Obstetrics and Gynecology. 200: 543.e1-7. PMID 19375573 DOI: 10.1016/j.ajog.2009.03.002  1
2009 Melin J, Lee A, Foygel K, Leong DE, Quake SR, Yao MW. In vitro embryo culture in defined, sub-microliter volumes. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 238: 950-5. PMID 19301395 DOI: 10.1002/dvdy.21918  1
2009 White RA, Blainey PC, Fan HC, Quake SR. Digital PCR provides sensitive and absolute calibration for high throughput sequencing. Bmc Genomics. 10: 116. PMID 19298667 DOI: 10.1186/1471-2164-10-116  1
2009 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 FM, Somlo G, ... ... Quake SR, et al. Association of reactive oxygen species levels and radioresistance in cancer stem cells. Nature. 458: 780-3. PMID 19194462 DOI: 10.1038/nature07733  1
2009 Gerber D, Maerkl SJ, Quake SR. An in vitro microfluidic approach to generating protein-interaction networks Nature Methods. 6: 71-74. PMID 19098921 DOI: 10.1038/nmeth.1289  1
2008 Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood Proceedings of the National Academy of Sciences of the United States of America. 105: 16266-16271. PMID 18838674 DOI: 10.1073/pnas.0808319105  1
2008 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 Biotechnology. 26: 1019-27. PMID 18758449 DOI: 10.1038/nbt.1490  1
2008 Balagaddé FK, Song H, Ozaki J, Collins CH, Barnet M, Arnold FH, Quake SR, You L. A synthetic Escherichia coli predator-prey ecosystem. Molecular Systems Biology. 4: 187. PMID 18414488 DOI: 10.1038/msb.2008.24  1
2008 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, ... ... Quake SR, et al. Single-molecule DNA sequencing of a viral genome. Science (New York, N.Y.). 320: 106-9. PMID 18388294 DOI: 10.1126/science.1150427  0.8
2008 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. PMID 18094763 DOI: 10.1039/b712116d  1
2007 Kartalov EP, Scherer A, Quake SR, Taylor CR, Anderson WF. Experimentally validated quantitative linear model for the device physics of elastomeric microfluidic valves. Journal of Applied Physics. 101: 64505. PMID 19381353 DOI: 10.1063/1.2511688  1
2007 Gómez-Sjöberg R, Leyrat AA, Pirone DM, Chen CS, Quake SR. Versatile, fully automated, microfluidic cell culture system. Analytical Chemistry. 79: 8557-63. PMID 17953452 DOI: 10.1021/ac071311w  1
2007 Warren LA, Rossi DJ, Schiebinger GR, Weissman IL, Kim SK, Quake SR. Transcriptional instability is not a universal attribute of aging. Aging Cell. 6: 775-82. PMID 17925006 DOI: 10.1111/j.1474-9726.2007.00337.x  1
2007 Marcy Y, Ishoey T, Lasken RS, Stockwell TB, Walenz BP, Halpern AL, Beeson KY, Goldberg SM, Quake SR. Nanoliter reactors improve multiple displacement amplification of genomes from single cells. Plos Genetics. 3: 1702-8. PMID 17892324 DOI: 10.1371/journal.pgen.0030155  1
2007 Fan HC, Quake SR. Detection of aneuploidy with digital polymerase chain reaction Analytical Chemistry. 79: 7576-7579. PMID 17715994 DOI: 10.1021/ac0709394  1
2007 Quake S. At the interface of physics and biology Biotechniques. 43: 19. PMID 17695250 DOI: 10.2144/000112501  1
2007 Spletter ML, Liu J, Liu J, Su H, Giniger E, Komiyama T, Quake S, Luo L. Lola regulates Drosophila olfactory projection neuron identity and targeting specificity. Neural Development. 2: 14. PMID 17634136 DOI: 10.1186/1749-8104-2-14  1
2007 Marcy Y, Ouverney C, Bik EM, Lösekann 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. Proceedings of the National Academy of Sciences of the United States of America. 104: 11889-94. PMID 17620602 DOI: 10.1073/pnas.0704662104  1
2007 Anderson MJ, DeLabarre B, Raghunathan A, Palsson BO, Brunger AT, Quake SR. Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices. Biochemistry. 46: 5722-31. PMID 17441732 DOI: 10.1021/bi700096p  1
2007 Melin J, Quake SR. Microfluidic large-scale integration: The evolution of design rules for biological automation Annual Review of Biophysics and Biomolecular Structure. 36: 213-231. PMID 17269901 DOI: 10.1146/annurev.biophys.36.040306.132646  1
2007 Maerkl SJ, Quake SR. A systems approach to measuring the binding energy landscapes of transcription factors Science. 315: 233-237. PMID 17218526 DOI: 10.1126/science.1131007  1
2007 Huang Y, Castrataro P, Lee CC, Quake SR. Solvent resistant microfluidic DNA synthesizer Lab On a Chip - Miniaturisation For Chemistry and Biology. 7: 24-26. PMID 17180201 DOI: 10.1039/b613923j  1
2007 Schwartz JJ, Quake SR. High density single molecule surface patterning with colloidal epitaxy Applied Physics Letters. 91. DOI: 10.1063/1.2772762  1
2006 Ma Z, Gerton JM, Wade LA, Quake SR. Fluorescence near-field microscopy of DNA at sub-10 nm resolution. Physical Review Letters. 97: 260801. PMID 17280412 DOI: 10.1103/PhysRevLett.97.260801  1
2006 Ottesen EA, Jong WH, Quake SR, Leadbetter JR. Microfluidic digital PCR enables multigene analysis of individual environmental bacteria Science. 314: 1464-1467. PMID 17138901 DOI: 10.1126/science.1131370  1
2006 Warren L, Bryder D, Weissman IL, Quake SR. Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR Proceedings of the National Academy of Sciences of the United States of America. 103: 17807-17812. PMID 17098862 DOI: 10.1073/pnas.0608512103  1
2006 Anderson MJ, Hansen CL, Quake SR. Phase knowledge enables rational screens for protein crystallization. Proceedings of the National Academy of Sciences of the United States of America. 103: 16746-51. PMID 17075056 DOI: 10.1073/pnas.0605293103  1
2006 Psaltis D, Quake SR, Yang C. Developing optofluidic technology through the fusion of microfluidics and optics. Nature. 442: 381-6. PMID 16871205 DOI: 10.1038/nature05060  1
2006 Marcus JS, Anderson WF, Quake SR. Microfluidic single-cell mRNA isolation and analysis Analytical Chemistry. 78: 3084-3089. PMID 16642997 DOI: 10.1021/ac0519460  1
2006 Liu J, Williams BA, Gwirtz RM, Wold BJ, Quake S. Enhanced signals and fast nucleic acid hybridization by microfluidic chaotic mixing. Angewandte Chemie (International Ed. in English). 45: 3618-23. PMID 16639763 DOI: 10.1002/anie.200503830  1
2006 Polin M, Grier DG, Quake SR. Anomalous vibrational dispersion in holographically trapped colloidal arrays. Physical Review Letters. 96: 088101. PMID 16606228 DOI: 10.1103/PhysRevLett.96.088101  1
2006 Hansen CL, Classen S, Berger JM, Quake SR. A microfluidic device for kinetic optimization of protein crystallization and in situ structure determination. Journal of the American Chemical Society. 128: 3142-3. PMID 16522084 DOI: 10.1021/ja0576637  1
2006 Kartalov EP, Zhong JF, Scherer A, Quake SR, Taylor CR, Anderson WF. High-throughput multi-antigen microfluidic fluorescence immunoassays. Biotechniques. 40: 85-90. PMID 16454045 DOI: 10.2144/000112071  1
2006 Marcus JS, Anderson WF, Quake SR. Parallel picoliter RT-PCR assays using microfluidics Analytical Chemistry. 78: 956-958. PMID 16448074 DOI: 10.1021/ac0513865  1
2006 Lacenere C, Garg MK, Stoltz BM, Quake SR. Effects of a modified dye-labeled nucleotide spacer arm on incorporation by thermophilic DNA polymerases. Nucleosides, Nucleotides & Nucleic Acids. 25: 9-15. PMID 16440981 DOI: 10.1080/15257770500377714  1
2006 Hong JW, Chen Y, Anderson WF, Quake SR. Molecular biology on a microfluidic chip Journal of Physics Condensed Matter. 18: S691-S701. DOI: 10.1088/0953-8984/18/18/S14  1
2006 Phillips R, Quake SR. The biological frontier of physics Physics Today. 59: 38-43. DOI: 10.1063/1.2216960  1
2006 Gambin Y, Legrand O, Quake SR. Microfabricated rubber microscope using soft solid immersion lenses Applied Physics Letters. 88. DOI: 10.1063/1.2194477  1
2005 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, et al. Multistep synthesis of a radiolabeled imaging probe using integrated microfluidics. Science (New York, N.Y.). 310: 1793-6. PMID 16357255 DOI: 10.1126/science.1118919  1
2005 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 (Cambridge, England). 4551-3. PMID 16158111 DOI: 10.1039/b505737j  1
2005 Balagaddé FK, You L, Hansen CL, Arnold FH, Quake SR. Long-term monitoring of bacteria undergoing programmed population control in a microchemostat. Science (New York, N.Y.). 309: 137-40. PMID 15994559 DOI: 10.1126/science.1109173  1
2005 Wu HM, Sui G, Lee CC, Ladno W, Quake SR, Tseng HR, Huang SC. An integrated microfluidic blood sampler for determination of blood input function in quantitative mouse microPET studies Ieee Nuclear Science Symposium Conference Record. 3: 1658-1661. DOI: 10.1109/NSSMIC.2005.1596638  1
2005 Squires TM, Quake SR. Microfluidics: Fluid physics at the nanoliter scale Reviews of Modern Physics. 77: 977-1026. DOI: 10.1103/RevModPhys.77.977  1
2005 Adams ML, Johnston ML, Scherer A, Quake SR. Polydimethylsiloxane based microfluidic diode Journal of Micromechanics and Microengineering. 15: 1517-1521. DOI: 10.1088/0960-1317/15/8/020  1
2005 Erickson D, Li B, Adleman JR, Vyawahare S, Quake S, Psaltis D. Spectrographic microfluidic memory Proceedings of the 3rd International Conference On Microchannels and Minichannels, 2005. 563-568.  1
2004 Gerton JM, Wade LA, Lessard GA, Ma Z, Quake SR. Tip-enhanced fluorescence microscopy at 10 nanometer resolution. Physical Review Letters. 93: 180801. PMID 15525147 DOI: 10.1103/PhysRevLett.93.180801  1
2004 Hansen CL, Sommer MO, Quake SR. Systematic investigation of protein phase behavior with a microfluidic formulator. Proceedings of the National Academy of Sciences of the United States of America. 101: 14431-6. PMID 15452343 DOI: 10.1073/pnas.0405847101  1
2004 Kartalov EP, Quake SR. Microfluidic device reads up to four consecutive base pairs in DNA sequencing-by-synthesis. Nucleic Acids Research. 32: 2873-9. PMID 15155856 DOI: 10.1093/nar/gkh613  1
2004 Hong JW, Studer V, Hang G, Anderson WF, Quake SR. A nanoliter-scale nucleic acid processor with parallel architecture. Nature Biotechnology. 22: 435-9. PMID 15024389 DOI: 10.1038/nbt951  1
2004 Rolland JP, Van Dam RM, Schorzman DA, Quake SR, DeSimone JM. Solvent-resistant photocurable liquid fluoropolymers for microfluidic device fabrication [corrected]. Journal of the American Chemical Society. 126: 2322-3. PMID 14982433 DOI: 10.1021/ja031657y  1
2004 Groisman A, Quake SR. A microfluidic rectifier: Anisotropic flow resistance at low Reynolds numbers Physical Review Letters. 92: 094501-1. DOI: 10.1103/PhysRevLett.92.094501  1
2004 Studer V, Hang G, Pandolfi A, Ortiz M, Anderson WF, Quake SR. Scaling properties of a low-actuation pressure microfluidic valve Journal of Applied Physics. 95: 393-398. DOI: 10.1063/1.1629781  1
2004 Wade LA, Shapiro IR, Ma Z, Quake SR, Collier CP. Correlating AFM probe morphology to image resolution for single-wall carbon nanotube tips Nano Letters. 4: 725-731. DOI: 10.1021/nl049976q  1
2004 Vyawahare S, Eyal S, Mathews KD, Quake SR. Nanometer-scale fluorescence resonance optical waveguides Nano Letters. 4: 1035-1039. DOI: 10.1021/nl049660i  1
2003 Bao XR, Lee HJ, Quake SR. Behavior of complex knots in single DNA molecules. Physical Review Letters. 91: 265506. PMID 14754067  1
2003 Hansen C, Quake SR. Microfluidics in structural biology: Smaller, faster... better Current Opinion in Structural Biology. 13: 538-544. PMID 14568607 DOI: 10.1016/j.sbi.2003.09.010  1
2003 Hong JW, Quake SR. Integrated nanoliter systems Nature Biotechnology. 21: 1179-1183. PMID 14520403 DOI: 10.1038/nbt871  1
2003 Reese MO, van Dam RM, Scherer A, Quake SR. Microfabricated fountain pens for high-density DNA arrays. Genome Research. 13: 2348-52. PMID 12975313 DOI: 10.1101/gr.623903  1
2003 Groisman A, Enzelberger M, Quake SR. Microfluidic memory and control devices Science. 300: 955-958. PMID 12738857 DOI: 10.1126/science.1083694  1
2003 Kartalov EP, Unger MA, Quake SR. Polyelectrolyte surface interface for single-molecule fluorescence studies of DNA polymerase. Biotechniques. 34: 505-10. PMID 12661156  1
2003 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 Biophysical Journal. 84: 1281-1290. PMID 12547808  1
2003 Liu J, Hansen C, Quake SR. Solving the "world-to-chip" interface problem with a microfluidic matrix Analytical Chemistry. 75: 4718-4723. DOI: 10.1021/ac0346407  1
2003 Adams ML, Enzelberger M, Quake S, Scherer A. Microfluidic integration on detector arrays for absorption and fluorescence micro-spectrometers Sensors and Actuators, a: Physical. 104: 25-31. DOI: 10.1016/S0924-4247(02)00477-6  1
2003 Yi GR, Jeon SJ, Thorsen T, Manoharan VN, Quake SR, Pine DJ, Yang SM. Generation of uniform photonic balls by template-assisted colloidal crystallization Synthetic Metals. 139: 803-806. DOI: 10.1016/S0379-6779(03)00246-7  1
2003 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 Advanced Materials. 15: 1300-1304. DOI: 10.1002/adma.200304890  1
2003 Gerton JM, Lessard GA, Wade LA, Quake SR. Apertureless near-field fluorescence microscope for biological imaging Conference On Quantum Electronics and Laser Science (Qels) - Technical Digest Series. 89: QMD2/1-QMD2/2.  1
2003 Wade LA, Shapiro I, Ma Z, Quake SR, Collier CP. Single-molecule fluorescence and force microscopy employing carbon nanotubes 2003 Nanotechnology Conference and Trade Show - Nanotech 2003. 3: 317-320.  1
2002 Hansen CL, Skordalakes E, Berger JM, Quake SR. A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion. Proceedings of the National Academy of Sciences of the United States of America. 99: 16531-6. PMID 12486223 DOI: 10.1073/pnas.262485199  1
2002 Chiu CS, Jensen K, Sokolova I, Wang D, Li M, Deshpande P, Davidson N, Mody I, Quick MW, Quake SR, 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. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 22: 10251-66. PMID 12451126  1
2002 Thompson HG, Harris JW, Wold BJ, Quake SR, Brody JP. Identification and confirmation of a module of coexpressed genes. Genome Research. 12: 1517-22. PMID 12368243 DOI: 10.1101/gr.418402  1
2002 Thorsen T, Maerkl SJ, Quake SR. Microfluidic large-scale integration. Science (New York, N.Y.). 298: 580-4. PMID 12351675 DOI: 10.1126/science.1076996  1
2002 Brody JP, Williams BA, Wold BJ, Quake SR. Significance and statistical errors in the analysis of DNA microarray data. Proceedings of the National Academy of Sciences of the United States of America. 99: 12975-8. PMID 12235357 DOI: 10.1073/pnas.162468199  1
2002 Eyal S, Quake SR. Velocity-independent microfluidic flow cytometry Electrophoresis. 23: 2653-2657. PMID 12210169 DOI: 10.1002/1522-2683(200208)23:16<2653::AID-ELPS2653>3.0.CO;2-H  1
2002 Liu J, Enzelberger M, Quake S. A nanoliter rotary device for polymerase chain reaction Electrophoresis. 23: 1531-1536. PMID 12116165 DOI: 10.1002/1522-2683(200205)23:10<1531::AID-ELPS1531>3.0.CO;2-D  1
2002 Fu AY, Chou HP, Spence C, Arnold FH, Quake SR. An integrated microfabricated cell sorter. Analytical Chemistry. 74: 2451-7. PMID 12069222 DOI: 10.1021/ac0255330  1
2002 Van Dam MR, Quake SR. Gene expression analysis with universal n-mer arrays Genome Research. 12: 145-152. PMID 11779839 DOI: 10.1101/gr.198901  1
2002 Adams ML, DeRose GA, Quake SR, Scherer A. Fundamental approach for optoelectronic and microfluidic integration for miniaturizing spectroscopic devices Proceedings of Spie - the International Society For Optical Engineering. 4647: 1-6. DOI: 10.1117/12.469818  1
2001 Chiu CS, Kartalov E, Unger M, Quake S, Lester HA. Single-molecule measurements calibrate green fluorescent protein surface densities on transparent beads for use with 'knock-in' animals and other expression systems. Journal of Neuroscience Methods. 105: 55-63. PMID 11166366 DOI: 10.1016/S0165-0270(00)00354-X  1
2001 Thorsen T, Roberts RW, Arnold FH, Quake SR. Dynamic pattern formation in a vesicle-generating microfluidic device Physical Review Letters. 86: 4163-4166. DOI: 10.1103/PhysRevLett.86.4163  1
2001 Chou HP, Unger MA, Quake SR. A microfabricated rotary pump Biomedical Microdevices. 3: 323-330. DOI: 10.1023/A:1012412916446  1
2000 Quake SR, Scherer A. From micro- to nanofabrication with soft materials Science. 290: 1536-1540. PMID 11090344  1
1997 Quake SR, Babcock H, Chu S. The dynamics of partially extended single molecules of DNA. Nature. 388: 151-4. PMID 9217154 DOI: 10.1038/40588  1
1994 Perkins TT, Quake SR, Smith DE, Chu S. Relaxation of a single DNA molecule observed by optical microscopy. Science (New York, N.Y.). 264: 822-6. PMID 8171336  1
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