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Items: 1 to 50 of 214

1.

Donor-derived cell-free DNA predicts allograft failure and mortality after lung transplantation.

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, Grimm D, Goodwin N, Yang Y, Patel K, Zhu J, Iacono A, Orens JB, Nathan SD, Marboe C, Berry GJ, Quake SR, Khush K, Valantine HA.

EBioMedicine. 2019 Jan 25. pii: S2352-3964(18)30606-6. doi: 10.1016/j.ebiom.2018.12.029. [Epub ahead of print]

2.

Signatures of selection in the human antibody repertoire: Selective sweeps, competing subclones, and neutral drift.

Horns F, Vollmers C, Dekker CL, Quake SR.

Proc Natl Acad Sci U S A. 2019 Jan 22;116(4):1261-1266. doi: 10.1073/pnas.1814213116. Epub 2019 Jan 8.

3.

Developmental Heterogeneity of Microglia and Brain Myeloid Cells Revealed by Deep Single-Cell RNA Sequencing.

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.

Neuron. 2019 Jan 16;101(2):207-223.e10. doi: 10.1016/j.neuron.2018.12.006. Epub 2018 Dec 31.

PMID:
30606613
4.

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy.

Ghaemi MS, DiGiulio DB, Contrepois K, Callahan B, Ngo TTM, Lee-McMullen B, Lehallier B, Robaczewska A, Mcilwain D, Rosenberg-Hasson Y, Wong RJ, Quaintance C, Culos A, Stanley N, Tanada A, Tsai A, Gaudilliere D, Ganio E, Han X, Ando K, McNeil L, Tingle M, Wise P, Maric I, Sirota M, Wyss-Coray T, Winn VD, Druzin ML, Gibbs R, Darmstadt GL, Lewis DB, Partovi Nia V, Agard B, Tibshirani R, Nolan G, Snyder MP, Relman DA, Quake SR, Shaw GM, Stevenson DK, Angst MS, Gaudilliere B, Aghaeepour N.

Bioinformatics. 2019 Jan 1;35(1):95-103. doi: 10.1093/bioinformatics/bty537.

5.

Understanding health disparities.

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, Relman DA, Shaw GM, Snyder MP, Wang X, Wise PH.

J Perinatol. 2018 Dec 18. doi: 10.1038/s41372-018-0298-1. [Epub ahead of print]

PMID:
30560947
6.

High-affinity allergen-specific human antibodies cloned from single IgE B cell transcriptomes.

Croote D, Darmanis S, Nadeau KC, Quake SR.

Science. 2018 Dec 14;362(6420):1306-1309. doi: 10.1126/science.aau2599.

PMID:
30545888
7.

Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue.

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.

Proc Natl Acad Sci U S A. 2018 Dec 26;115(52):E12363-E12369. doi: 10.1073/pnas.1813819115. Epub 2018 Dec 7.

8.

Complex mammalian-like haematopoietic system found in a colonial chordate.

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, Neff NF, Nolan GP, Quake SR, Weissman IL, Voskoboynik A.

Nature. 2018 Dec;564(7736):425-429. doi: 10.1038/s41586-018-0783-x. Epub 2018 Dec 5.

PMID:
30518860
9.

Single-nucleotide-resolution sequencing of human N6-methyldeoxyadenosine reveals strand-asymmetric clusters associated with SSBP1 on the mitochondrial genome.

Koh CWQ, Goh YT, Toh JDW, Neo SP, Ng SB, Gunaratne J, Gao YG, Quake SR, Burkholder WF, Goh WSS.

Nucleic Acids Res. 2018 Dec 14;46(22):11659-11670. doi: 10.1093/nar/gky1104.

10.

Neutral and selective dynamics in a synthetic microbial community.

Cira NJ, Pearce MT, Quake SR.

Proc Natl Acad Sci U S A. 2018 Oct 16;115(42):E9842-E9848. doi: 10.1073/pnas.1808118115. Epub 2018 Sep 28.

11.

Surgical and molecular characterization of primary and metastatic disease in a neuroendocrine tumor arising in a tailgut cyst.

Erdrich J, Schaberg KB, Khodadoust MS, Zhou L, Shelton AA, Visser BC, Ford JM, Alizadeh AA, Quake SR, Kunz PL, Beausang JF.

Cold Spring Harb Mol Case Stud. 2018 Oct 1;4(5). pii: a003004. doi: 10.1101/mcs.a003004. Print 2018 Oct.

12.

Noninvasive blood tests for fetal development predict gestational age and preterm delivery.

Ngo TTM, Moufarrej MN, Rasmussen MH, Camunas-Soler J, Pan W, Okamoto J, Neff NF, Liu K, Wong RJ, Downes K, Tibshirani R, Shaw GM, Skotte L, Stevenson DK, Biggio JR, Elovitz MA, Melbye M, Quake SR.

Science. 2018 Jun 8;360(6393):1133-1136. doi: 10.1126/science.aar3819.

PMID:
29880692
13.

Single-cell transcriptional dynamics of flavivirus infection.

Zanini F, Pu SY, Bekerman E, Einav S, Quake SR.

Elife. 2018 Feb 16;7. pii: e32942. doi: 10.7554/eLife.32942.

14.

High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis.

Wang W, Penland L, Gokce O, Croote D, Quake SR.

BMC Genomics. 2018 Feb 13;19(1):140. doi: 10.1186/s12864-018-4512-5.

15.

Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes.

Gee MH, Han A, Lofgren SM, Beausang JF, Mendoza JL, Birnbaum ME, Bethune MT, Fischer S, Yang X, Gomez-Eerland R, Bingham DB, Sibener LV, Fernandes RA, Velasco A, Baltimore D, Schumacher TN, Khatri P, Quake SR, Davis MM, Garcia KC.

Cell. 2018 Jan 25;172(3):549-563.e16. doi: 10.1016/j.cell.2017.11.043. Epub 2017 Dec 21.

16.

Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress.

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.

PLoS Biol. 2017 Dec 14;15(12):e2004050. doi: 10.1371/journal.pbio.2004050. eCollection 2017 Dec.

17.

High-throughput full-length single-cell mRNA-seq of rare cells.

Ooi CC, Mantalas GL, Koh W, Neff NF, Fuchigami T, Wong DJ, Wilson RJ, Park SM, Gambhir SS, Quake SR, Wang SX.

PLoS One. 2017 Nov 29;12(11):e0188510. doi: 10.1371/journal.pone.0188510. eCollection 2017.

18.

Risky Business: Meeting the Structural Needs of Transdisciplinary Science.

Wise PH, Shaw GM, Druzin ML, Darmstadt GL, Quaintance C, Mäkinen E, Relman DA, Quake SR, Butte AJ, Angst MS, Muglia LJ, Macones G, Driscoll D, Ober C, Simpson JL, Katz M, Howse J, Stevenson DK.

J Pediatr. 2017 Dec;191:255-258. doi: 10.1016/j.jpeds.2017.08.072. No abstract available.

PMID:
29173314
19.

Role of epithelial to mesenchymal transition associated genes in mammary gland regeneration and breast tumorigenesis.

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.

Nat Commun. 2017 Nov 21;8(1):1669. doi: 10.1038/s41467-017-01666-2.

20.

Classifying Drosophila Olfactory Projection Neuron Subtypes by Single-Cell RNA Sequencing.

Li H, Horns F, Wu B, Xie Q, Li J, Li T, Luginbuhl DJ, Quake SR, Luo L.

Cell. 2017 Nov 16;171(5):1206-1220.e22. doi: 10.1016/j.cell.2017.10.019.

21.

T cell receptor sequencing of early-stage breast cancer tumors identifies altered clonal structure of the T cell repertoire.

Beausang JF, Wheeler AJ, Chan NH, Hanft VR, Dirbas FM, Jeffrey SS, Quake SR.

Proc Natl Acad Sci U S A. 2017 Nov 28;114(48):E10409-E10417. doi: 10.1073/pnas.1713863114. Epub 2017 Nov 14.

22.

Noninvasive Prenatal Diagnosis of Single-Gene Disorders by Use of Droplet Digital PCR.

Camunas-Soler J, Lee H, Hudgins L, Hintz SR, Blumenfeld YJ, El-Sayed YY, Quake SR.

Clin Chem. 2018 Feb;64(2):336-345. doi: 10.1373/clinchem.2017.278101. Epub 2017 Nov 2.

23.

Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma.

Darmanis S, Sloan SA, Croote D, Mignardi M, Chernikova S, Samghababi P, Zhang Y, Neff N, Kowarsky M, Caneda C, Li G, Chang SD, Connolly ID, Li Y, Barres BA, Gephart MH, Quake SR.

Cell Rep. 2017 Oct 31;21(5):1399-1410. doi: 10.1016/j.celrep.2017.10.030.

24.

Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns.

Enge M, Arda HE, Mignardi M, Beausang J, Bottino R, Kim SK, Quake SR.

Cell. 2017 Oct 5;171(2):321-330.e14. doi: 10.1016/j.cell.2017.09.004. Epub 2017 Sep 28.

25.

Dynamics of the human antibody repertoire after B cell depletion in systemic sclerosis.

de Bourcy CFA, Dekker CL, Davis MM, Nicolls MR, Quake SR.

Sci Immunol. 2017 Sep 29;2(15). pii: eaan8289. doi: 10.1126/sciimmunol.aan8289.

26.

Rapid Chromatin Switch in the Direct Reprogramming of Fibroblasts to Neurons.

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, Chang HY.

Cell Rep. 2017 Sep 26;20(13):3236-3247. doi: 10.1016/j.celrep.2017.09.011.

27.

Simultaneously Monitoring Immune Response and Microbial Infections during Pregnancy through Plasma cfRNA Sequencing.

Pan W, Ngo TTM, Camunas-Soler J, Song CX, Kowarsky M, Blumenfeld YJ, Wong RJ, Shaw GM, Stevenson DK, Quake SR.

Clin Chem. 2017 Nov;63(11):1695-1704. doi: 10.1373/clinchem.2017.273888. Epub 2017 Sep 13.

28.

Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA.

Kowarsky M, Camunas-Soler J, Kertesz M, De Vlaminck I, Koh W, Pan W, Martin L, Neff NF, Okamoto J, Wong RJ, Kharbanda S, El-Sayed Y, Blumenfeld Y, Stevenson DK, Shaw GM, Wolfe ND, Quake SR.

Proc Natl Acad Sci U S A. 2017 Sep 5;114(36):9623-9628. doi: 10.1073/pnas.1707009114. Epub 2017 Aug 22.

29.

5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages.

Song CX, Yin S, Ma L, Wheeler A, Chen Y, Zhang Y, Liu B, Xiong J, Zhang W, Hu J, Zhou Z, Dong B, Tian Z, Jeffrey SS, Chua MS, So S, Li W, Wei Y, Diao J, Xie D, Quake SR.

Cell Res. 2017 Oct;27(10):1231-1242. doi: 10.1038/cr.2017.106. Epub 2017 Aug 18.

30.

Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells.

Sloan SA, Darmanis S, Huber N, Khan TA, Birey F, Caneda C, Reimer R, Quake SR, Barres BA, Paşca SP.

Neuron. 2017 Aug 16;95(4):779-790.e6. doi: 10.1016/j.neuron.2017.07.035.

31.

Food allergen detection by mass spectrometry: the role of systems biology.

Croote D, Quake SR.

NPJ Syst Biol Appl. 2016 Sep 29;2:16022. doi: 10.1038/npjsba.2016.22. eCollection 2016. Review.

32.

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples.

Yu FB, Blainey PC, Schulz F, Woyke T, Horowitz MA, Quake SR.

Elife. 2017 Jul 5;6. pii: e26580. doi: 10.7554/eLife.26580.

33.

Single Cell Restriction Enzyme-Based Analysis of Methylation at Genomic Imprinted Regions in Preimplantation Mouse Embryos.

Ling KY, Cheow LF, Quake SR, Burkholder WF, Messerschmidt DM.

Methods Mol Biol. 2017;1605:171-189. doi: 10.1007/978-1-4939-6988-3_12.

PMID:
28456965
34.

Quantitative Analysis of Synthetic Cell Lineage Tracing Using Nuclease Barcoding.

Schmidt ST, Zimmerman SM, Wang J, Kim SK, Quake SR.

ACS Synth Biol. 2017 Jun 16;6(6):936-942. doi: 10.1021/acssynbio.6b00309. Epub 2017 Mar 10.

35.

Long-term microfluidic tracking of coccoid cyanobacterial cells reveals robust control of division timing.

Yu FB, Willis L, Chau RM, Zambon A, Horowitz M, Bhaya D, Huang KC, Quake SR.

BMC Biol. 2017 Feb 14;15(1):11. doi: 10.1186/s12915-016-0344-4.

36.

Sanativo Wound Healing Product Does Not Accelerate Reepithelialization in a Mouse Cutaneous Wound Healing Model.

Marshall CD, Hu MS, Leavitt T, Barnes LA, Cheung AT, Malhotra S, Lorenz HP, Delp SL, Quake SR, Longaker MT.

Plast Reconstr Surg. 2017 Feb;139(2):343-352. doi: 10.1097/PRS.0000000000003013.

PMID:
28121865
37.

Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging.

de Bourcy CF, Angel CJ, Vollmers C, Dekker CL, Davis MM, Quake SR.

Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):1105-1110. doi: 10.1073/pnas.1617959114. Epub 2017 Jan 17.

38.

B cell repertoires in HLA-sensitized kidney transplant candidates undergoing desensitization therapy.

Beausang JF, Fan HC, Sit R, Hutchins MU, Jirage K, Curtis R, Hutchins E, Quake SR, Yabu JM.

J Transl Med. 2017 Jan 13;15(1):9. doi: 10.1186/s12967-017-1118-7.

39.

Transcriptomic Profiling Maps Anatomically Patterned Subpopulations among Single Embryonic Cardiac Cells.

Li G, Xu A, Sim S, Priest JR, Tian X, Khan T, Quertermous T, Zhou B, Tsao PS, Quake SR, Wu SM.

Dev Cell. 2016 Nov 21;39(4):491-507. doi: 10.1016/j.devcel.2016.10.014. Epub 2016 Nov 10.

40.

Correction: Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching.

Horns F, Vollmers C, Croote D, Mackey SF, Swan GE, Dekker CL, Davis MM, Quake SR.

Elife. 2016 Nov 9;5. pii: e23066. doi: 10.7554/eLife.23066. No abstract available.

41.

Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination.

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, Druz A, Zhang B, Zhang Y, Wang L, Kong WP, Park D, Popova LI, Dekker CL, Davis MM, Carter CE, Ross TM, Ellington AD, Wilson PC, Marcotte EM, Mascola JR, Ippolito GC, Krammer F, Quake SR, Kwong PD, Georgiou G.

Nat Med. 2016 Dec;22(12):1456-1464. doi: 10.1038/nm.4224. Epub 2016 Nov 7.

42.

Early somatic mosaicism is a rare cause of long-QT syndrome.

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, Grove M, Perez MV, Neff NF, Chen R, Maeda K, Dubin A, Belardinelli L, West J, Antolik C, Macaya D, Quertermous T, Trayanova NA, Quake SR, Ashley EA.

Proc Natl Acad Sci U S A. 2016 Oct 11;113(41):11555-11560. Epub 2016 Sep 28.

43.

Single-cell RNAseq reveals cell adhesion molecule profiles in electrophysiologically defined neurons.

Földy C, Darmanis S, Aoto J, Malenka RC, Quake SR, Südhof TC.

Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):E5222-31. doi: 10.1073/pnas.1610155113. Epub 2016 Aug 16.

44.

Single-cell multimodal profiling reveals cellular epigenetic heterogeneity.

Cheow LF, Courtois ET, Tan Y, Viswanathan R, Xing Q, Tan RZ, Tan DS, Robson P, Loh YH, Quake SR, Burkholder WF.

Nat Methods. 2016 Oct;13(10):833-6. doi: 10.1038/nmeth.3961. Epub 2016 Aug 15.

PMID:
27525975
45.

Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching.

Horns F, Vollmers C, Croote D, Mackey SF, Swan GE, Dekker CL, Davis MM, Quake SR.

Elife. 2016 Aug 2;5. pii: e16578. doi: 10.7554/eLife.16578. Erratum in: Elife. 2016 Nov 09;5:.

46.

Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq.

Gokce O, Stanley GM, Treutlein B, Neff NF, Camp JG, Malenka RC, Rothwell PE, Fuccillo MV, Südhof TC, Quake SR.

Cell Rep. 2016 Jul 26;16(4):1126-1137. doi: 10.1016/j.celrep.2016.06.059. Epub 2016 Jul 14.

47.

Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq.

Treutlein B, Lee QY, Camp JG, Mall M, Koh W, Shariati SA, Sim S, Neff NF, Skotheim JM, Wernig M, Quake SR.

Nature. 2016 Jun 16;534(7607):391-5. doi: 10.1038/nature18323. Epub 2016 Jun 8.

48.

Developmental cell death programs license cytotoxic cells to eliminate histocompatible partners.

Corey DM, Rosental B, Kowarsky M, Sinha R, Ishizuka KJ, Palmeri KJ, Quake SR, Voskoboynik A, Weissman IL.

Proc Natl Acad Sci U S A. 2016 Jun 7;113(23):6520-5. doi: 10.1073/pnas.1606276113. Epub 2016 May 23.

49.

A reusable microfluidic device provides continuous measurement capability and improves the detection limit of digital biology.

Araci IE, Robles M, Quake SR.

Lab Chip. 2016 Apr 26;16(9):1573-8. doi: 10.1039/c6lc00194g.

PMID:
27072314
50.

Simultaneous single-molecule epigenetic imaging of DNA methylation and hydroxymethylation.

Song CX, Diao J, Brunger AT, Quake SR.

Proc Natl Acad Sci U S A. 2016 Apr 19;113(16):4338-43. doi: 10.1073/pnas.1600223113. Epub 2016 Mar 28.

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