Stephen R Quake, D.Phil. - Publications

Affiliations: 
1995-2005 California Institute of Technology, Pasadena, CA 
 2005- Bioengineering Stanford University, Palo Alto, CA 
Area:
biophysics, genomics
Website:
http://thebigone.stanford.edu/people.htm

143 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
2021 Phansalkar R, Krieger J, Zhao M, Kolluru SS, Jones RC, Quake SR, Weissman I, Bernstein D, Winn VD, D'Amato G, Red-Horse K. Coronary blood vessels from distinct origins converge to equivalent states during mouse and human development. Elife. 10. PMID 34910626 DOI: 10.7554/eLife.70246  0.358
2021 Xue Y, Braslavsky I, Quake SR. Temperature Effect on Polymerase Fidelity. The Journal of Biological Chemistry. 101270. PMID 34695416 DOI: 10.1016/j.jbc.2021.101270  0.547
2021 Kowarsky M, Anselmi C, Hotta K, Burighel P, Zaniolo G, Caicci F, Rosental B, Neff NF, Ishizuka KJ, Palmeri KJ, Okamoto J, Gordon T, Weissman IL, Quake SR, Manni L, et al. Sexual and asexual development: two distinct programs producing the same tunicate. Cell Reports. 34: 108681. PMID 33503429 DOI: 10.1016/j.celrep.2020.108681  0.772
2020 Travaglini KJ, Nabhan AN, Penland L, Sinha R, Gillich A, Sit RV, Chang S, Conley SD, Mori Y, Seita J, Berry GJ, Shrager JB, Metzger RJ, Kuo CS, Neff N, ... ... Quake SR, et al. A molecular cell atlas of the human lung from single-cell RNA sequencing. Nature. PMID 33208946 DOI: 10.1038/s41586-020-2922-4  0.428
2020 Chen MB, Jiang X, Quake SR, Südhof TC. Persistent transcriptional programmes are associated with remote memory. Nature. PMID 33177708 DOI: 10.1038/s41586-020-2905-5  0.351
2020 Zanini F, Berghuis BA, Jones RC, Nicolis di Robilant B, Nong RY, Norton JA, Clarke MF, Quake SR. Northstar enables automatic classification of known and novel cell types from tumor samples. Scientific Reports. 10: 15251. PMID 32943655 DOI: 10.1038/S41598-020-71805-1  0.353
2020 Wang W, Vilella F, Alama P, Moreno I, Mignardi M, Isakova A, Pan W, Simon C, Quake SR. Single-cell transcriptomic atlas of the human endometrium during the menstrual cycle. Nature Medicine. PMID 32929266 DOI: 10.1038/S41591-020-1040-Z  0.328
2020 Horns F, Quake SR. Cloning antibodies from single cells in pooled sequence libraries by selective PCR. Plos One. 15: e0236477. PMID 32756607 DOI: 10.1371/Journal.Pone.0236477  0.325
2020 Schaum N, Lehallier B, Hahn O, Pálovics R, Hosseinzadeh S, Lee SE, Sit R, Lee DP, Losada PM, Zardeneta ME, Fehlmann T, Webber JT, McGeever A, Calcuttawala K, Zhang H, ... ... Quake SR, et al. Ageing hallmarks exhibit organ-specific temporal signatures. Nature. PMID 32669715 DOI: 10.1038/S41586-020-2499-Y  0.313
2020 Rastogi S, Xue Y, Quake SR, Boothroyd JC. Differential Impacts on Host Transcription by ROP and GRA Effectors from the Intracellular Parasite Toxoplasma gondii. Mbio. 11. PMID 32518180 DOI: 10.1128/Mbio.00182-20  0.314
2020 Jerison ER, Quake SR. Heterogeneous T cell motility behaviors emerge from a coupling between speed and turning in vivo. Elife. 9. PMID 32427565 DOI: 10.7554/Elife.53933  0.337
2020 Camunas-Soler J, Dai XQ, Hang Y, Bautista A, Lyon J, Suzuki K, Kim SK, Quake SR, MacDonald PE. Patch-Seq Links Single-Cell Transcriptomes to Human Islet Dysfunction in Diabetes. Cell Metabolism. PMID 32302527 DOI: 10.1016/J.Cmet.2020.04.005  0.346
2020 Kim S, Whitener RL, Peiris H, Gu X, Chang CA, Lam JY, Camunas-Soler J, Park I, Bevacqua RJ, Tellez K, Quake SR, Lakey JRT, Bottino R, Ross PJ, Kim SK. Molecular and genetic regulation of pig pancreatic islet cell development. Development (Cambridge, England). PMID 32108026 DOI: 10.1242/Dev.186213  0.324
2020 Xue Y, Theisen TC, Rastogi S, Ferrel A, Quake SR, Boothroyd JC. A single-parasite transcriptional atlas of reveals novel control of antigen expression. Elife. 9. PMID 32065584 DOI: 10.7554/Elife.54129  0.356
2020 Li J, Han S, Li H, Udeshi ND, Svinkina T, Mani DR, Xu C, Guajardo R, Xie Q, Li T, Luginbuhl DJ, Wu B, McLaughlin CN, Xie A, Kaewsapsak P, ... Quake SR, et al. Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators. Cell. PMID 31955847 DOI: 10.1016/J.Cell.2019.12.029  0.341
2020 Domingo-Gonzalez R, Zanini F, Che X, Liu M, Jones RC, Swift MA, Quake SR, Cornfield DN, Alvira CM. Author response: Diverse homeostatic and immunomodulatory roles of immune cells in the developing mouse lung at single cell resolution Elife. DOI: 10.7554/Elife.56890.Sa2  0.311
2019 Stanley G, Gokce O, Malenka RC, Südhof TC, Quake SR. Continuous and Discrete Neuron Types of the Adult Murine Striatum. Neuron. PMID 31813651 DOI: 10.1016/J.Neuron.2019.11.004  0.687
2019 Tarashansky AJ, Xue Y, Li P, Quake SR, Wang B. Self-assembling manifolds in single-cell RNA sequencing data. Elife. 8. PMID 31524596 DOI: 10.7554/Elife.48994  0.379
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  0.303
2019 Croote D, Braslavsky I, Quake SR. Addressing Complex Matrix Interference Improves Multiplex Food Allergen Detection by Targeted LC-MS/MS. Analytical Chemistry. PMID 31339301 DOI: 10.1021/Acs.Analchem.9B01388  0.558
2019 Tarashansky AJ, Xue Y, Li P, Quake SR, Wang B. Author response: Self-assembling manifolds in single-cell RNA sequencing data Elife. DOI: 10.7554/Elife.48994.126  0.302
2019 Wang W, Mas A, Monleón J, Quake S, Simon C. Single cell RNAseq analyses of uterine fibroids and fibroid-free myometria reveal previously unidentified cell type and state Fertility and Sterility. 112: e348. DOI: 10.1016/J.Fertnstert.2019.07.1001  0.333
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  0.307
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  0.321
2018 Zanini F, Robinson ML, Croote D, Sahoo MK, Sanz AM, Ortiz-Lasso E, Albornoz LL, Rosso F, Montoya JG, Goo L, Pinsky BA, Quake SR, Einav S. Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue. Proceedings of the National Academy of Sciences of the United States of America. PMID 30530648 DOI: 10.1073/Pnas.1813819115  0.351
2018 Rosental B, Kowarsky M, Seita J, Corey DM, Ishizuka KJ, Palmeri KJ, Chen SY, Sinha R, Okamoto J, Mantalas G, Manni L, Raveh T, Clarke DN, Tsai JM, Newman AM, ... ... Quake SR, et al. Complex mammalian-like haematopoietic system found in a colonial chordate. Nature. PMID 30518860 DOI: 10.1038/S41586-018-0783-X  0.779
2018 Su T, Stanley G, Sinha R, D'Amato G, Das S, Rhee S, Chang AH, Poduri A, Raftrey B, Dinh TT, Roper WA, Li G, Quinn KE, Caron KM, Wu S, ... ... Quake S, et al. Single-cell analysis of early progenitor cells that build coronary arteries. Nature. PMID 29973725 DOI: 10.1038/S41586-018-0288-7  0.431
2018 Zanini F, Pu SY, Bekerman E, Einav S, Quake SR. Single-cell transcriptional dynamics of flavivirus infection. Elife. 7. PMID 29451494 DOI: 10.7554/Elife.32942  0.314
2018 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. 19: 140. PMID 29439658 DOI: 10.1186/S12864-018-4512-5  0.659
2018 Wang W, Vilella F, Moreno I, Pan W, Quake S, Simon C. Single cell RNAseq provides a molecular and cellular cartography of changes to the human endometrium through the menstrual cycle Fertility and Sterility. 110: e2. DOI: 10.1016/J.Fertnstert.2018.07.027  0.317
2017 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 Biology. 15: e2004050. PMID 29240790 DOI: 10.1371/Journal.Pbio.2004050  0.345
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  0.354
2017 Ooi CC, Mantalas GL, Koh W, Neff NF, 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. 12: e0188510. PMID 29186152 DOI: 10.1371/Journal.Pone.0188510  0.366
2017 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. Nature Communications. 8: 1669. PMID 29162812 DOI: 10.1038/S41467-017-01666-2  0.3
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  0.306
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  0.78
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  0.361
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  0.311
2017 Wapinski OL, Lee QY, Chen AC, Li R, Corces MR, Ang CE, Treutlein B, Xiang C, Baubet V, Suchy FP, Sankar V, Sim S, Quake SR, Dahmane N, Wernig M, et al. Rapid Chromatin Switch in the Direct Reprogramming of Fibroblasts to Neurons. Cell Reports. 20: 3236-3247. PMID 28954238 DOI: 10.1016/J.Celrep.2017.09.011  0.31
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  0.762
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  0.775
2017 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, ... ... Quake SR, et al. 5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages. Cell Research. PMID 28820176 DOI: 10.1038/Cr.2017.106  0.317
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  0.324
2017 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. 6. PMID 28678007 DOI: 10.7554/Elife.26580  0.322
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  0.359
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  0.301
2017 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 Biology. 15: 11. PMID 28196492 DOI: 10.1186/S12915-016-0344-4  0.305
2016 Cai S, Kalisky T, Sahoo D, Dalerba P, Feng W, Lin Y, Qian D, Kong A, Yu J, Wang F, Chen EY, Scheeren FA, Kuo AH, Sikandar SS, Hisamori S, ... ... Quake S, et al. A Quiescent Bcl11b High Stem Cell Population Is Required for Maintenance of the Mammary Gland. Cell Stem Cell. PMID 28041896 DOI: 10.1016/J.Stem.2016.11.007  0.351
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  0.32
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  0.519
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  0.356
2016 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 Reports. 16: 1126-37. PMID 27425622 DOI: 10.1016/J.Celrep.2016.06.059  0.723
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  0.384
2016 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 27217570 DOI: 10.1073/Pnas.1606276113  0.779
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  0.313
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  0.346
2016 Corey DM, Kowarsky M, Rosental B, Ishizuka K, Palmeri K, Sinha R, Voskoboynik A, Quake S, Weissman I. Developmental Regulated Cell Death Programs Account for Colony Elimination and Unstable Mixed-Chimerism in B. Schlosseri: Implications for Allogeneic Graft Survival Biology of Blood and Marrow Transplantation. 22: S310. DOI: 10.1016/J.Bbmt.2015.11.780  0.759
2015 Wu AR, Quake SR. Microfluidics Technologies for Low Cell Number Chromatin Immunoprecipitation. Cold Spring Harbor Protocols. PMID 26700100 DOI: 10.1101/Pdb.Prot084996  0.371
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  0.751
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  0.343
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  0.331
2015 Cheow LF, Quake SR, Burkholder WF, Messerschmidt DM. Multiplexed locus-specific analysis of DNA methylation in single cells. Nature Protocols. 10: 619-31. PMID 25811896 DOI: 10.1038/Nprot.2015.041  0.309
2015 He HM, Yu FB, Quake SR, Dorigo O. Abstract 3202: Single cell analysis of ascites macrophages in ovarian cancer Cancer Research. 75: 3202-3202. DOI: 10.1158/1538-7445.Am2015-3202  0.302
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  0.358
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  0.484
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  0.365
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  0.311
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  0.322
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  0.371
2014 Treutlein B, Gokce O, Quake SR, Südhof TC. Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing. Proceedings of the National Academy of Sciences of the United States of America. 111: E1291-9. PMID 24639501 DOI: 10.1073/Pnas.1403244111  0.689
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  0.33
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  0.34
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  0.367
2014 Quake S. Single Cell Genome Analysis Biophysical Journal. 106: 6a. DOI: 10.1016/J.Bpj.2013.11.071  0.331
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  0.37
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  0.304
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  0.43
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  0.459
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  0.344
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  0.346
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: 10.1016/J.Bpj.2012.11.834  0.769
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  0.342
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: 10.1182/Blood.V126.23.Sci-11.Sci-11  0.435
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  0.348
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  0.332
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  0.371
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  0.335
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  0.305
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  0.362
2012 Quake S. Sizing up cell-free DNA Clinical Chemistry. 58: 489-490. PMID 22235102 DOI: 10.1373/Clinchem.2011.174250  0.346
2012 Jan M, Snyder T, Corces-Zimmerman MR, Quake S, Weissman I, Majeti R. Abstract SY35-01: Clonal evolution of pre-leukemic hematopoietic stem cells precedes human acute myeloid leukemia Cancer Research. 72. DOI: 10.1158/1538-7445.Am2012-Sy35-01  0.439
2012 Jan M, Snyder TM, Corces-Zimmerman MR, Weissman IL, Quake SR, Majeti R. Abstract 3303: Clonal evolution of pre-leukemic hematopoietic stem cells precedes human acute myeloid leukemia Cancer Research. 72: 3303-3303. DOI: 10.1158/1538-7445.Am2012-3303  0.441
2012 Kim S, Streets AM, Lin RR, Quake SR, Weiss S, Majumdar DS. High-Throughput Single-Molecule Transcription Assay Biophysical Journal. 102: 600a. DOI: 10.1016/J.Bpj.2011.11.3268  0.337
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  0.329
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  0.487
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  0.349
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  0.323
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  0.324
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  0.382
2011 Kalisky T, Quake SR. Single-cell genomics Nature Methods. 8: 311-314. PMID 21451520 DOI: 10.1038/Nmeth0411-311  0.35
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  0.34
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  0.307
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  0.324
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  0.309
2011 Rothenberg ME, Kalisky T, Dalerba PD, Nusse Y, Quake S, Clarke MF. Single Cell Gene Expression Profiling of Adult Murine Colon Provides Novel Insight Into Both the Origin of Stem Cells and Their Supportive Cell Type Gastroenterology. 140: S-13-S-14. DOI: 10.1016/S0016-5085(11)60054-1  0.349
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  0.351
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  0.307
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  0.317
2010 Lee CC, Snyder TM, Quake SR. A microfluidic oligonucleotide synthesizer Nucleic Acids Research. 38: 2514-2521. PMID 20176572 DOI: 10.1093/Nar/Gkq092  0.301
2010 Tay S, Hughey J, Lee TK, Covert M, Quake SR. Cells Respond Digitally to Variation in Signal Intensity via Stochastic Activation of NF-κB Biophysical Journal. 98: 429a-430a. DOI: 10.1016/J.Bpj.2009.12.2328  0.312
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  0.303
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  0.32
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  0.488
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  0.301
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  0.447
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  0.312
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  0.759
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  0.361
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  0.31
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  0.47
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  0.374
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  0.361
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  0.523
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  0.468
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  0.501
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  0.342
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  0.507
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  0.333
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  0.54
2005 Bao XR, Lee HJ, Quake SR. Erratum: Behavior of Complex Knots in Single DNA Molecules [Phys. Rev. Lett. 91 , 265506 (2003)] Physical Review Letters. 95: 199901. DOI: 10.1103/Physrevlett.95.199901  0.552
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  0.519
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  0.304
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  0.332
2004 Liu J, Hansen C, Quake SR. Solving the "world-to-chip" interface problem with a microfluidic matrix. Analytical Chemistry. 75: 4718-23. PMID 14674446 DOI: 10.1021/ac0346407  0.446
2003 Bao XR, Lee HJ, Quake SR. Behavior of complex knots in single DNA molecules. Physical Review Letters. 91: 265506. PMID 14754067 DOI: 10.1103/Physrevlett.91.265506  0.553
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  0.529
2003 Braslavsky I, Hebert B, Kartalov E, Quake SR. Sequence information can be obtained from single DNA molecules. Proceedings of the National Academy of Sciences of the United States of America. 100: 3960-4. PMID 12651960 DOI: 10.1073/Pnas.0230489100  0.624
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  0.504
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  0.518
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  0.334
1999 Meiners J, Quake SR. Direct Measurement of Hydrodynamic Cross Correlations between Two Particles in an External Potential Physical Review Letters. 82: 2211-2214. DOI: 10.1103/Physrevlett.82.2211  0.704
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  0.723
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 DOI: 10.1126/Science.8171336  0.693
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