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Items: 1 to 50 of 250

1.

A single-parasite transcriptional atlas of Toxoplasma gondii reveals novel control of antigen expression.

Xue Y, Theisen TC, Rastogi S, Ferrel A, Quake SR, Boothroyd JC.

Elife. 2020 Feb 17;9. pii: e54129. doi: 10.7554/eLife.54129. [Epub ahead of print]

PMID:
32065584
2.

Single-Cell Transcriptomes Reveal Diverse Regulatory Strategies for Olfactory Receptor Expression and Axon Targeting.

Li H, Li T, Horns F, Li J, Xie Q, Xu C, Wu B, Kebschull JM, McLaughlin CN, Kolluru SS, Jones RC, Vacek D, Xie A, Luginbuhl DJ, Quake SR, Luo L.

Curr Biol. 2020 Feb 3. pii: S0960-9822(20)30093-2. doi: 10.1016/j.cub.2020.01.049. [Epub ahead of print]

PMID:
32059767
3.

Multiomic immune clockworks of pregnancy.

Peterson LS, Stelzer IA, Tsai AS, Ghaemi MS, Han X, Ando K, Winn VD, Martinez NR, Contrepois K, Moufarrej MN, Quake S, Relman DA, Snyder MP, Shaw GM, Stevenson DK, Wong RJ, Arck P, Angst MS, Aghaeepour N, Gaudilliere B.

Semin Immunopathol. 2020 Feb 4. doi: 10.1007/s00281-019-00772-1. [Epub ahead of print] Review.

PMID:
32020337
4.

Enabling Technologies for Personalized and Precision Medicine.

Ho D, Quake SR, McCabe ERB, Chng WJ, Chow EK, Ding X, Gelb BD, Ginsburg GS, Hassenstab J, Ho CM, Mobley WC, Nolan GP, Rosen ST, Tan P, Yen Y, Zarrinpar A.

Trends Biotechnol. 2020 Jan 21. pii: S0167-7799(19)30316-6. doi: 10.1016/j.tibtech.2019.12.021. [Epub ahead of print] Review.

PMID:
31980301
5.

Memory B Cell Activation, Broad Anti-influenza Antibodies, and Bystander Activation Revealed by Single-Cell Transcriptomics.

Horns F, Dekker CL, Quake SR.

Cell Rep. 2020 Jan 21;30(3):905-913.e6. doi: 10.1016/j.celrep.2019.12.063.

6.

Non-invasive characterization of human bone marrow stimulation and reconstitution by cell-free messenger RNA sequencing.

Ibarra A, Zhuang J, Zhao Y, Salathia NS, Huang V, Acosta AD, Aballi J, Toden S, Karns AP, Purnajo I, Parks JR, Guo L, Mason J, Sigal D, Nova TS, Quake SR, Nerenberg M.

Nat Commun. 2020 Jan 21;11(1):400. doi: 10.1038/s41467-019-14253-4.

7.

Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators.

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, Carr SA, Ting AY, Luo L.

Cell. 2020 Jan 23;180(2):373-386.e15. doi: 10.1016/j.cell.2019.12.029. Epub 2020 Jan 16.

PMID:
31955847
8.

Broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics.

Durham ND, Agrawal A, Waltari E, Croote D, Zanini F, Fouch M, Davidson E, Smith O, Carabajal E, Pak JE, Doranz BJ, Robinson M, Sanz AM, Albornoz LL, Rosso F, Einav S, Quake SR, McCutcheon KM, Goo L.

Elife. 2019 Dec 10;8. pii: e52384. doi: 10.7554/eLife.52384.

9.

Continuous and Discrete Neuron Types of the Adult Murine Striatum.

Stanley G, Gokce O, Malenka RC, Südhof TC, Quake SR.

Neuron. 2019 Dec 5. pii: S0896-6273(19)30967-5. doi: 10.1016/j.neuron.2019.11.004. [Epub ahead of print]

PMID:
31813651
10.

c-Jun overexpression in CAR T cells induces exhaustion resistance.

Lynn RC, Weber EW, Sotillo E, Gennert D, Xu P, Good Z, Anbunathan H, Lattin J, Jones R, Tieu V, Nagaraja S, Granja J, de Bourcy CFA, Majzner R, Satpathy AT, Quake SR, Monje M, Chang HY, Mackall CL.

Nature. 2019 Dec;576(7786):293-300. doi: 10.1038/s41586-019-1805-z. Epub 2019 Dec 4.

PMID:
31802004
11.

Nucleic acid cleavage with a hyperthermophilic Cas9 from an uncultured Ignavibacterium.

Schmidt ST, Yu FB, Blainey PC, May AP, Quake SR.

Proc Natl Acad Sci U S A. 2019 Nov 12;116(46):23100-23105. doi: 10.1073/pnas.1904273116. Epub 2019 Oct 28.

12.

Single-cell transcriptomes and whole-brain projections of serotonin neurons in the mouse dorsal and median raphe nuclei.

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, Luo L.

Elife. 2019 Oct 24;8. pii: e49424. doi: 10.7554/eLife.49424.

13.

Self-assembling manifolds in single-cell RNA sequencing data.

Tarashansky AJ, Xue Y, Li P, Quake SR, Wang B.

Elife. 2019 Sep 16;8. pii: e48994. doi: 10.7554/eLife.48994.

14.

Viral taxonomy derived from evolutionary genome relationships.

Dougan TJ, Quake SR.

PLoS One. 2019 Aug 14;14(8):e0220440. doi: 10.1371/journal.pone.0220440. eCollection 2019.

15.

Single cell analysis of human foetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors.

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, Heaton N, Vigilante A, King A, Sancho R, Teichmann S, Quake SR, Nakauchi H, Rashid ST.

Nat Commun. 2019 Jul 26;10(1):3350. doi: 10.1038/s41467-019-11266-x.

16.

Addressing Complex Matrix Interference Improves Multiplex Food Allergen Detection by Targeted LC-MS/MS.

Croote D, Braslavsky I, Quake SR.

Anal Chem. 2019 Aug 6;91(15):9760-9769. doi: 10.1021/acs.analchem.9b01388. Epub 2019 Jul 24.

PMID:
31339301
17.

Aged blood impairs hippocampal neural precursor activity and activates microglia via brain endothelial cell VCAM1.

Yousef H, Czupalla CJ, Lee D, Chen MB, Burke AN, Zera KA, Zandstra J, Berber E, Lehallier B, Mathur V, Nair RV, Bonanno LN, Yang AC, Peterson T, Hadeiba H, Merkel T, Körbelin J, Schwaninger M, Buckwalter MS, Quake SR, Butcher EC, Wyss-Coray T.

Nat Med. 2019 Jun;25(6):988-1000. doi: 10.1038/s41591-019-0440-4. Epub 2019 May 13.

18.

Modeling Spatial Correlation of Transcripts with Application to Developing Pancreas.

Liu R, Mignardi M, Jones R, Enge M, Kim SK, Quake SR, Zou J.

Sci Rep. 2019 Apr 3;9(1):5592. doi: 10.1038/s41598-019-41951-2.

19.

Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens.

Berghuis BA, Yu FB, Schulz F, Blainey PC, Woyke T, Quake SR.

Proc Natl Acad Sci U S A. 2019 Mar 12;116(11):5037-5044. doi: 10.1073/pnas.1815631116. Epub 2019 Feb 27.

20.

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 Feb;40:541-553. doi: 10.1016/j.ebiom.2018.12.029. Epub 2019 Jan 26.

21.

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.

22.

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.

23.

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.

24.

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. 2019 Mar;39(3):354-358. doi: 10.1038/s41372-018-0298-1. Epub 2018 Dec 18.

PMID:
30560947
25.

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
26.

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.

27.

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.

28.

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.

29.

Identifying deer antler uhrf1 proliferation and s100a10 mineralization genes using comparative RNA-seq.

Ker DFE, Wang D, Sharma R, Zhang B, Passarelli B, Neff N, Li C, Maloney W, Quake S, Yang YP.

Stem Cell Res Ther. 2018 Oct 31;9(1):292. doi: 10.1186/s13287-018-1027-6.

30.

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.

31.

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.

32.

Single-cell analysis of early progenitor cells that build coronary arteries.

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, Miquerol L, Butcher EC, Weissman I, Quake S, Red-Horse K.

Nature. 2018 Jul;559(7714):356-362. doi: 10.1038/s41586-018-0288-7. Epub 2018 Jul 4.

33.

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
34.

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.

35.

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.

36.

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.

37.

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.

38.

The Human Cell Atlas.

Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N; Human Cell Atlas Meeting Participants.

Elife. 2017 Dec 5;6. pii: e27041. doi: 10.7554/eLife.27041.

39.

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.

40.

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
41.

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.

42.

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.

43.

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.

44.

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.

PMID:
29097507
45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

PMID:
28904056
50.

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.

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