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A cellular census of human lungs identifies novel cell states in health and in asthma.
Vieira Braga FA, Kar G, Berg M, Carpaij OA, Polanski K, Simon LM, Brouwer S, Gomes T, Hesse L, Jiang J, Fasouli ES, Efremova M, Vento-Tormo R, Talavera-López C, Jonker MR, Affleck K, Palit S, Strzelecka PM, Firth HV, Mahbubani KT, Cvejic A, Meyer KB, Saeb-Parsy K, Luinge M, Brandsma CA, Timens W, Angelidis I, Strunz M, Koppelman GH, van Oosterhout AJ, Schiller HB, Theis FJ, van den Berge M, Nawijn MC, Teichmann SA. Vieira Braga FA, et al. Among authors: theis fj. Nat Med. 2019 Jul;25(7):1153-1163. doi: 10.1038/s41591-019-0468-5. Epub 2019 Jun 17. Nat Med. 2019. PMID: 31209336
Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios.
Hoppe PS, Schwarzfischer M, Loeffler D, Kokkaliaris KD, Hilsenbeck O, Moritz N, Endele M, Filipczyk A, Gambardella A, Ahmed N, Etzrodt M, Coutu DL, Rieger MA, Marr C, Strasser MK, Schauberger B, Burtscher I, Ermakova O, Bürger A, Lickert H, Nerlov C, Theis FJ, Schroeder T. Hoppe PS, et al. Among authors: theis fj. Nature. 2016 Jul 14;535(7611):299-302. doi: 10.1038/nature18320. Nature. 2016. PMID: 27411635
Diffusion pseudotime robustly reconstructs lineage branching.
Haghverdi L, Büttner M, Wolf FA, Buettner F, Theis FJ. Haghverdi L, et al. Among authors: theis fj. Nat Methods. 2016 Oct;13(10):845-8. doi: 10.1038/nmeth.3971. Epub 2016 Aug 29. Nat Methods. 2016. PMID: 27571553
Prospective identification of hematopoietic lineage choice by deep learning.
Buggenthin F, Buettner F, Hoppe PS, Endele M, Kroiss M, Strasser M, Schwarzfischer M, Loeffler D, Kokkaliaris KD, Hilsenbeck O, Schroeder T, Theis FJ, Marr C. Buggenthin F, et al. Among authors: theis fj. Nat Methods. 2017 Apr;14(4):403-406. doi: 10.1038/nmeth.4182. Epub 2017 Feb 20. Nat Methods. 2017. PMID: 28218899 Free PMC article.
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. Regev A, et al. Among authors: theis fj. Elife. 2017 Dec 5;6:e27041. doi: 10.7554/eLife.27041. Elife. 2017. PMID: 29206104 Free PMC article.
Single-cell RNA-seq denoising using a deep count autoencoder.
Eraslan G, Simon LM, Mircea M, Mueller NS, Theis FJ. Eraslan G, et al. Among authors: theis fj. Nat Commun. 2019 Jan 23;10(1):390. doi: 10.1038/s41467-018-07931-2. Nat Commun. 2019. PMID: 30674886 Free PMC article.
381 results