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Items: 1 to 50 of 156

1.

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors.

Young MD, Mitchell TJ, Vieira Braga FA, Tran MGB, Stewart BJ, Ferdinand JR, Collord G, Botting RA, Popescu DM, Loudon KW, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Del Castillo Velasco-Herrera M, Guzzo C, Richoz N, Mamanova L, Aho T, Armitage JN, Riddick ACP, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, Lisgo S, Maxwell PH, Lindsay S, Warren AY, Stewart GD, Sebire N, Coleman N, Haniffa M, Teichmann SA, Clatworthy M, Behjati S.

Science. 2018 Aug 10;361(6402):594-599. doi: 10.1126/science.aat1699.

PMID:
30093597
2.

Editorial overview: Sequences and topology: Dynamic sequences and topologies of proteins.

Marsh JA, Teichmann SA.

Curr Opin Struct Biol. 2018 Jun;50:vii-viii. doi: 10.1016/j.sbi.2018.07.005. No abstract available.

PMID:
30080482
3.

BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq.

Lindeman I, Emerton G, Mamanova L, Snir O, Polanski K, Qiao SW, Sollid LM, Teichmann SA, Stubbington MJT.

Nat Methods. 2018 Aug;15(8):563-565. doi: 10.1038/s41592-018-0082-3. No abstract available.

PMID:
30065371
4.

Unbiased classification of mosquito blood cells by single-cell genomics and high-content imaging.

Severo MS, Landry JJM, Lindquist RL, Goosmann C, Brinkmann V, Collier P, Hauser AE, Benes V, Henriksson J, Teichmann SA, Levashina EA.

Proc Natl Acad Sci U S A. 2018 Aug 7;115(32):E7568-E7577. doi: 10.1073/pnas.1803062115. Epub 2018 Jul 23.

5.

Tissue-Restricted Adaptive Type 2 Immunity Is Orchestrated by Expression of the Costimulatory Molecule OX40L on Group 2 Innate Lymphoid Cells.

Halim TYF, Rana BMJ, Walker JA, Kerscher B, Knolle MD, Jolin HE, Serrao EM, Haim-Vilmovsky L, Teichmann SA, Rodewald HR, Botto M, Vyse TJ, Fallon PG, Li Z, Withers DR, McKenzie ANJ.

Immunity. 2018 Jun 19;48(6):1195-1207.e6. doi: 10.1016/j.immuni.2018.05.003. Epub 2018 Jun 12.

6.

SpatialDE: identification of spatially variable genes.

Svensson V, Teichmann SA, Stegle O.

Nat Methods. 2018 May;15(5):343-346. doi: 10.1038/nmeth.4636. Epub 2018 Mar 19.

PMID:
29553579
7.

Exponential scaling of single-cell RNA-seq in the past decade.

Svensson V, Vento-Tormo R, Teichmann SA.

Nat Protoc. 2018 Apr;13(4):599-604. doi: 10.1038/nprot.2017.149. Epub 2018 Mar 1.

PMID:
29494575
8.

Mapping human development at single-cell resolution.

Behjati S, Lindsay S, Teichmann SA, Haniffa M.

Development. 2018 Feb 8;145(3). pii: dev152561. doi: 10.1242/dev.152561.

9.

Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins.

Natan E, Endoh T, Haim-Vilmovsky L, Flock T, Chalancon G, Hopper JTS, Kintses B, Horvath P, Daruka L, Fekete G, Pál C, Papp B, Oszi E, Magyar Z, Marsh JA, Elcock AH, Babu MM, Robinson CV, Sugimoto N, Teichmann SA.

Nat Struct Mol Biol. 2018 Mar;25(3):279-288. doi: 10.1038/s41594-018-0029-5. Epub 2018 Feb 12.

10.

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.

11.

The Human Cell Atlas: from vision to reality.

Rozenblatt-Rosen O, Stubbington MJT, Regev A, Teichmann SA.

Nature. 2017 Oct 18;550(7677):451-453. doi: 10.1038/550451a. No abstract available.

PMID:
29072289
12.

Establishment of mouse expanded potential stem cells.

Yang J, Ryan DJ, Wang W, Tsang JC, Lan G, Masaki H, Gao X, Antunes L, Yu Y, Zhu Z, Wang J, Kolodziejczyk AA, Campos LS, Wang C, Yang F, Zhong Z, Fu B, Eckersley-Maslin MA, Woods M, Tanaka Y, Chen X, Wilkinson AC, Bussell J, White J, Ramirez-Solis R, Reik W, Göttgens B, Teichmann SA, Tam PPL, Nakauchi H, Zou X, Lu L, Liu P.

Nature. 2017 Oct 19;550(7676):393-397. doi: 10.1038/nature24052. Epub 2017 Oct 11.

13.

Single-cell transcriptomics to explore the immune system in health and disease.

Stubbington MJT, Rozenblatt-Rosen O, Regev A, Teichmann SA.

Science. 2017 Oct 6;358(6359):58-63. doi: 10.1126/science.aan6828. Review.

14.

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications.

Haque A, Engel J, Teichmann SA, Lönnberg T.

Genome Med. 2017 Aug 18;9(1):75. doi: 10.1186/s13073-017-0467-4. Review.

15.

Circulating and Tissue-Resident CD4+ T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function Is Altered During Inflammation.

Hegazy AN, West NR, Stubbington MJT, Wendt E, Suijker KIM, Datsi A, This S, Danne C, Campion S, Duncan SH, Owens BMJ, Uhlig HH, McMichael A; Oxford IBD Cohort Investigators, Bergthaler A, Teichmann SA, Keshav S, Powrie F.

Gastroenterology. 2017 Nov;153(5):1320-1337.e16. doi: 10.1053/j.gastro.2017.07.047. Epub 2017 Aug 4.

16.

Single cell transcriptomics of pluripotent stem cells: reprogramming and differentiation.

Natarajan KN, Teichmann SA, Kolodziejczyk AA.

Curr Opin Genet Dev. 2017 Oct;46:66-76. doi: 10.1016/j.gde.2017.06.003. Epub 2017 Jul 1. Review.

PMID:
28675884
17.

Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.

Kar G, Kim JK, Kolodziejczyk AA, Natarajan KN, Torlai Triglia E, Mifsud B, Elderkin S, Marioni JC, Pombo A, Teichmann SA.

Nat Commun. 2017 Jun 26;8(1):36. doi: 10.1038/s41467-017-00052-2.

18.

Computational approaches for interpreting scRNA-seq data.

Rostom R, Svensson V, Teichmann SA, Kar G.

FEBS Lett. 2017 Aug;591(15):2213-2225. doi: 10.1002/1873-3468.12684. Epub 2017 Jun 12. Review.

19.

Wounding induces dedifferentiation of epidermal Gata6+ cells and acquisition of stem cell properties.

Donati G, Rognoni E, Hiratsuka T, Liakath-Ali K, Hoste E, Kar G, Kayikci M, Russell R, Kretzschmar K, Mulder KW, Teichmann SA, Watt FM.

Nat Cell Biol. 2017 Jun;19(6):603-613. doi: 10.1038/ncb3532. Epub 2017 May 15.

20.

Aging increases cell-to-cell transcriptional variability upon immune stimulation.

Martinez-Jimenez CP, Eling N, Chen HC, Vallejos CA, Kolodziejczyk AA, Connor F, Stojic L, Rayner TF, Stubbington MJT, Teichmann SA, de la Roche M, Marioni JC, Odom DT.

Science. 2017 Mar 31;355(6332):1433-1436. doi: 10.1126/science.aah4115.

21.

Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.

Lönnberg T, Svensson V, James KR, Fernandez-Ruiz D, Sebina I, Montandon R, Soon MS, Fogg LG, Nair AS, Liligeto U, Stubbington MJ, Ly LH, Bagger FO, Zwiessele M, Lawrence ND, Souza-Fonseca-Guimaraes F, Bunn PT, Engwerda CR, Heath WR, Billker O, Stegle O, Haque A, Teichmann SA.

Sci Immunol. 2017 Mar 3;2(9). pii: eaal2192. doi: 10.1126/sciimmunol.aal2192. Erratum in: Sci Immunol. 2018 Mar 9;3(21):.

22.

Are cells from a snowman realistic? Cryopreserved tissues as a source for single-cell RNA-sequencing experiments.

Vieira Braga FA, Teichmann SA, Stubbington MJ.

Genome Biol. 2017 Mar 24;18(1):54. doi: 10.1186/s13059-017-1192-4. Review.

23.

Power analysis of single-cell RNA-sequencing experiments.

Svensson V, Natarajan KN, Ly LH, Miragaia RJ, Labalette C, Macaulay IC, Cvejic A, Teichmann SA.

Nat Methods. 2017 Apr;14(4):381-387. doi: 10.1038/nmeth.4220. Epub 2017 Mar 6.

24.

Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types.

Carmona SJ, Teichmann SA, Ferreira L, Macaulay IC, Stubbington MJ, Cvejic A, Gfeller D.

Genome Res. 2017 Mar;27(3):451-461. doi: 10.1101/gr.207704.116. Epub 2017 Jan 13.

25.

Intrinsic transcriptional heterogeneity in B cells controls early class switching to IgE.

Wu YL, Stubbington MJ, Daly M, Teichmann SA, Rada C.

J Exp Med. 2017 Jan;214(1):183-196. doi: 10.1084/jem.20161056. Epub 2016 Dec 19.

26.

Regulation, evolution and consequences of cotranslational protein complex assembly.

Natan E, Wells JN, Teichmann SA, Marsh JA.

Curr Opin Struct Biol. 2017 Feb;42:90-97. doi: 10.1016/j.sbi.2016.11.023. Epub 2016 Dec 12. Review.

27.

Single-cell analysis at the threshold.

Chen X, Love JC, Navin NE, Pachter L, Stubbington MJ, Svensson V, Sweedler JV, Teichmann SA.

Nat Biotechnol. 2016 Nov 8;34(11):1111-1118. doi: 10.1038/nbt.3721. No abstract available.

PMID:
27824834
28.

Single-cell RNA-seq identifies a PD-1hi ILC progenitor and defines its development pathway.

Yu Y, Tsang JC, Wang C, Clare S, Wang J, Chen X, Brandt C, Kane L, Campos LS, Lu L, Belz GT, McKenzie AN, Teichmann SA, Dougan G, Liu P.

Nature. 2016 Nov 3;539(7627):102-106. doi: 10.1038/nature20105. Epub 2016 Sep 29.

PMID:
27749818
29.

MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs.

Eckersley-Maslin MA, Svensson V, Krueger C, Stubbs TM, Giehr P, Krueger F, Miragaia RJ, Kyriakopoulos C, Berrens RV, Milagre I, Walter J, Teichmann SA, Reik W.

Cell Rep. 2016 Sep 27;17(1):179-192. doi: 10.1016/j.celrep.2016.08.087.

30.

Data on publications, structural analyses, and queries used to build and utilize the AlloRep database.

Sousa FL, Parente DJ, Hessman JA, Chazelle A, Teichmann SA, Swint-Kruse L.

Data Brief. 2016 Jul 9;8:948-57. doi: 10.1016/j.dib.2016.07.006. eCollection 2016 Sep.

31.

Genetics and immunity in the era of single-cell genomics.

Vieira Braga FA, Teichmann SA, Chen X.

Hum Mol Genet. 2016 Oct 1;25(R2):R141-R148. Epub 2016 Jul 12. Review.

32.

Erratum to: Single cell analysis of CD4+ T cell differentiation reveals three major cell states and progressive acceleration of proliferation.

Proserpio V, Piccolo A, Haim-Vilmovsky L, Kar G, Lönnberg T, Svensson V, Pramanik J, Natarajan KN, Zhai W, Zhang X, Donati G, Kayikci M, Kotar J, McKenzie AN, Montandon R, James KR, Fernandez-Ruiz D, Heath WR, Haque A, Billker O, Woodhouse S, Cicuta P, Nicodemi M, Teichmann SA.

Genome Biol. 2016 Jun 22;17(1):133. No abstract available.

33.

Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation.

Proserpio V, Piccolo A, Haim-Vilmovsky L, Kar G, Lönnberg T, Svensson V, Pramanik J, Natarajan KN, Zhai W, Zhang X, Donati G, Kayikci M, Kotar J, McKenzie AN, Montandon R, Billker O, Woodhouse S, Cicuta P, Nicodemi M, Teichmann SA.

Genome Biol. 2016 May 12;17:103. doi: 10.1186/s13059-016-0957-5. Erratum in: Genome Biol. 2016;17(1):133.

34.

Single-cell genomics: coming of age.

Linnarsson S, Teichmann SA.

Genome Biol. 2016 May 10;17:97. doi: 10.1186/s13059-016-0960-x. No abstract available.

35.

T cell fate and clonality inference from single-cell transcriptomes.

Stubbington MJT, Lönnberg T, Proserpio V, Clare S, Speak AO, Dougan G, Teichmann SA.

Nat Methods. 2016 Apr;13(4):329-332. doi: 10.1038/nmeth.3800. Epub 2016 Mar 7.

36.

Classification of low quality cells from single-cell RNA-seq data.

Ilicic T, Kim JK, Kolodziejczyk AA, Bagger FO, McCarthy DJ, Marioni JC, Teichmann SA.

Genome Biol. 2016 Feb 17;17:29. doi: 10.1186/s13059-016-0888-1.

37.

Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells.

Macaulay IC, Svensson V, Labalette C, Ferreira L, Hamey F, Voet T, Teichmann SA, Cvejic A.

Cell Rep. 2016 Feb 2;14(4):966-977. doi: 10.1016/j.celrep.2015.12.082. Epub 2016 Jan 21.

38.

Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.

Kim JK, Kolodziejczyk AA, Ilicic T, Teichmann SA, Marioni JC.

Nat Commun. 2016 Jan 11;7:10415. doi: 10.1038/ncomms10415. No abstract available.

39.

Principles of assembly reveal a periodic table of protein complexes.

Ahnert SE, Marsh JA, Hernández H, Robinson CV, Teichmann SA.

Science. 2015 Dec 11;350(6266):aaa2245. doi: 10.1126/science.aaa2245.

40.
41.

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.

Kolodziejczyk AA, Kim JK, Tsang JC, Ilicic T, Henriksson J, Natarajan KN, Tuck AC, Gao X, Bühler M, Liu P, Marioni JC, Teichmann SA.

Cell Stem Cell. 2015 Oct 1;17(4):471-85. doi: 10.1016/j.stem.2015.09.011.

42.

AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators.

Sousa FL, Parente DJ, Shis DL, Hessman JA, Chazelle A, Bennett MR, Teichmann SA, Swint-Kruse L.

J Mol Biol. 2016 Feb 22;428(4):671-678. doi: 10.1016/j.jmb.2015.09.015. Epub 2015 Sep 25.

43.

Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells.

Tsang JC, Yu Y, Burke S, Buettner F, Wang C, Kolodziejczyk AA, Teichmann SA, Lu L, Liu P.

Genome Biol. 2015 Sep 21;16:178. doi: 10.1186/s13059-015-0739-5.

44.

Computational assignment of cell-cycle stage from single-cell transcriptome data.

Scialdone A, Natarajan KN, Saraiva LR, Proserpio V, Teichmann SA, Stegle O, Marioni JC, Buettner F.

Methods. 2015 Sep 1;85:54-61. doi: 10.1016/j.ymeth.2015.06.021. Epub 2015 Jul 2.

45.

The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding.

Xie X, Stubbington MJ, Nissen JK, Andersen KG, Hebenstreit D, Teichmann SA, Betz AG.

PLoS Genet. 2015 Jun 24;11(6):e1005251. doi: 10.1371/journal.pgen.1005251. eCollection 2015 Jun.

46.

The technology and biology of single-cell RNA sequencing.

Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA.

Mol Cell. 2015 May 21;58(4):610-20. doi: 10.1016/j.molcel.2015.04.005. Review.

47.

An atlas of mouse CD4(+) T cell transcriptomes.

Stubbington MJ, Mahata B, Svensson V, Deonarine A, Nissen JK, Betz AG, Teichmann SA.

Biol Direct. 2015 Apr 3;10:14. doi: 10.1186/s13062-015-0045-x.

48.

Structural and evolutionary versatility in protein complexes with uneven stoichiometry.

Marsh JA, Rees HA, Ahnert SE, Teichmann SA.

Nat Commun. 2015 Mar 16;6:6394. doi: 10.1038/ncomms7394.

PMID:
25775164
49.

Computational and analytical challenges in single-cell transcriptomics.

Stegle O, Teichmann SA, Marioni JC.

Nat Rev Genet. 2015 Mar;16(3):133-45. doi: 10.1038/nrg3833. Epub 2015 Jan 28. Review.

PMID:
25628217
50.

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.

Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, Teichmann SA, Marioni JC, Stegle O.

Nat Biotechnol. 2015 Feb;33(2):155-60. doi: 10.1038/nbt.3102. Epub 2015 Jan 19.

PMID:
25599176

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