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2019 1
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Page 1
Best practices for single-cell analysis across modalities.
Heumos L, Schaar AC, Lance C, Litinetskaya A, Drost F, Zappia L, Lücken MD, Strobl DC, Henao J, Curion F; Single-cell Best Practices Consortium; Schiller HB, Theis FJ. Heumos L, et al. Nat Rev Genet. 2023 Aug;24(8):550-572. doi: 10.1038/s41576-023-00586-w. Epub 2023 Mar 31. Nat Rev Genet. 2023. PMID: 37002403 Free PMC article. Review.
An integrated cell atlas of the lung in health and disease.
Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, Markov NS, Zaragosi LE, Ji Y, Ansari M, Arguel MJ, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung MI, Collin A, Gay ACA, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos TS, Kole TM, Leroy S, Mayr CH, Oliver AJ, von Papen M, Peter L, Taylor CJ, Walzthoeni T, Xu C, Bui LT, De Donno C, Dony L, Faiz A, Guo M, Gutierrez AJ, Heumos L, Huang N, Ibarra IL, Jackson ND, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini KJ, Wilbrey-Clark A, Worlock KB, Yoshida M; Lung Biological Network Consortium; van den Berge M, Bossé Y, Desai TJ, Eickelberg O, Kaminski N, Krasnow MA, Lafyatis R, Nikolic MZ, Powell JE, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold MA, Sheppard D, Shepherd DP, Sin DD, Timens W, Tsankov AM, Whitsett J, Xu Y, Banovich NE, Barbry P, Duong TE, Falk CS, Meyer KB, Kropski JA, Pe'er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis FJ. Sikkema L, et al. Among authors: heumos l. Nat Med. 2023 Jun;29(6):1563-1577. doi: 10.1038/s41591-023-02327-2. Epub 2023 Jun 8. Nat Med. 2023. PMID: 37291214 Free PMC article.
Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis.
Lang NJ, Gote-Schniering J, Porras-Gonzalez D, Yang L, De Sadeleer LJ, Jentzsch RC, Shitov VA, Zhou S, Ansari M, Agami A, Mayr CH, Hooshiar Kashani B, Chen Y, Heumos L, Pestoni JC, Molnar ES, Geeraerts E, Anquetil V, Saniere L, Wögrath M, Gerckens M, Lehmann M, Yildirim AÖ, Hatz R, Kneidinger N, Behr J, Wuyts WA, Stoleriu MG, Luecken MD, Theis FJ, Burgstaller G, Schiller HB. Lang NJ, et al. Among authors: heumos l. Sci Transl Med. 2023 Dec 6;15(725):eadh0908. doi: 10.1126/scitranslmed.adh0908. Epub 2023 Dec 6. Sci Transl Med. 2023. PMID: 38055803
The scverse project provides a computational ecosystem for single-cell omics data analysis.
Virshup I, Bredikhin D, Heumos L, Palla G, Sturm G, Gayoso A, Kats I, Koutrouli M; Scverse Community; Berger B, Pe'er D, Regev A, Teichmann SA, Finotello F, Wolf FA, Yosef N, Stegle O, Theis FJ. Virshup I, et al. Among authors: heumos l. Nat Biotechnol. 2023 May;41(5):604-606. doi: 10.1038/s41587-023-01733-8. Nat Biotechnol. 2023. PMID: 37037904 No abstract available.
mlf-core: a framework for deterministic machine learning.
Heumos L, Ehmele P, Kuhn Cuellar L, Menden K, Miller E, Lemke S, Gabernet G, Nahnsen S. Heumos L, et al. Bioinformatics. 2023 Apr 3;39(4):btad164. doi: 10.1093/bioinformatics/btad164. Bioinformatics. 2023. PMID: 37004171 Free PMC article.
A Mutation-Agnostic Hematopoietic Stem Cell Gene Therapy for Metachromatic Leukodystrophy.
Antony JS, Daniel-Moreno A, Lamsfus-Calle A, Raju J, Kaftancioglu M, Ureña-Bailén G, Rottenberger J, Hou Y, Santhanakumaran V, Lee JH, Heumos L, Böhringer J, Krägeloh-Mann I, Handgretinger R, Mezger M. Antony JS, et al. Among authors: heumos l. CRISPR J. 2022 Feb;5(1):66-79. doi: 10.1089/crispr.2021.0075. Epub 2021 Dec 8. CRISPR J. 2022. PMID: 34882002
MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics.
Bichmann L, Nelde A, Ghosh M, Heumos L, Mohr C, Peltzer A, Kuchenbecker L, Sachsenberg T, Walz JS, Stevanović S, Rammensee HG, Kohlbacher O. Bichmann L, et al. Among authors: heumos l. J Proteome Res. 2019 Nov 1;18(11):3876-3884. doi: 10.1021/acs.jproteome.9b00313. Epub 2019 Oct 22. J Proteome Res. 2019. PMID: 31589052
The AIMe registry for artificial intelligence in biomedical research.
Matschinske J, Alcaraz N, Benis A, Golebiewski M, Grimm DG, Heumos L, Kacprowski T, Lazareva O, List M, Louadi Z, Pauling JK, Pfeifer N, Röttger R, Schwämmle V, Sturm G, Traverso A, Van Steen K, de Freitas MV, Villalba Silva GC, Wee L, Wenke NK, Zanin M, Zolotareva O, Baumbach J, Blumenthal DB. Matschinske J, et al. Among authors: heumos l. Nat Methods. 2021 Oct;18(10):1128-1131. doi: 10.1038/s41592-021-01241-0. Nat Methods. 2021. PMID: 34433960 Free article. No abstract available.
Sfaira accelerates data and model reuse in single cell genomics.
Fischer DS, Dony L, König M, Moeed A, Zappia L, Heumos L, Tritschler S, Holmberg O, Aliee H, Theis FJ. Fischer DS, et al. Among authors: heumos l. Genome Biol. 2021 Aug 25;22(1):248. doi: 10.1186/s13059-021-02452-6. Genome Biol. 2021. PMID: 34433466 Free PMC article.
OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data.
Pfeuffer J, Bielow C, Wein S, Jeong K, Netz E, Walter A, Alka O, Nilse L, Colaianni PD, McCloskey D, Kim J, Rosenberger G, Bichmann L, Walzer M, Veit J, Boudaud B, Bernt M, Patikas N, Pilz M, Startek MP, Kutuzova S, Heumos L, Charkow J, Sing JC, Feroz A, Siraj A, Weisser H, Dijkstra TMH, Perez-Riverol Y, Röst H, Kohlbacher O, Sachsenberg T. Pfeuffer J, et al. Among authors: heumos l. Nat Methods. 2024 Mar;21(3):365-367. doi: 10.1038/s41592-024-02197-7. Nat Methods. 2024. PMID: 38366242 No abstract available.
12 results