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A proteomics sample metadata representation for multiomics integration and big data analysis.
Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky LI, Perez-Riverol Y. Dai C, et al. Among authors: gruning b. Nat Commun. 2021 Oct 6;12(1):5854. doi: 10.1038/s41467-021-26111-3. Nat Commun. 2021. PMID: 34615866 Free PMC article. Review.
"Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling.
David R, Rybina A, Burel JM, Heriche JK, Audergon P, Boiten JW, Coppens F, Crockett S, Exter K, Fahrner S, Fratelli M, Goble C, Gormanns P, Grantner T, Grüning B, Gurwitz KT, Hancock JM, Harmse H, Holub P, Juty N, Karnbach G, Karoune E, Keppler A, Klemeier J, Lancelotti C, Legras JL, Lister AL, Longo DL, Ludwig R, Madon B, Massimi M, Matser V, Matteoni R, Mayrhofer MT, Ohmann C, Panagiotopoulou M, Parkinson H, Perseil I, Pfander C, Pieruschka R, Raess M, Rauber A, Richard AS, Romano P, Rosato A, Sánchez-Pla A, Sansone SA, Sarkans U, Serrano-Solano B, Tang J, Tanoli Z, Tedds J, Wagener H, Weise M, Westerhoff HV, Wittner R, Ewbank J, Blomberg N, Gribbon P. David R, et al. Among authors: gruning b. EMBO J. 2023 Dec 1;42(23):e115008. doi: 10.15252/embj.2023115008. Epub 2023 Nov 15. EMBO J. 2023. PMID: 37964598 Free PMC article.
BioContainers: an open-source and community-driven framework for software standardization.
da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y. da Veiga Leprevost F, et al. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. Bioinformatics. 2017. PMID: 28379341 Free PMC article.
An Accessible Proteogenomics Informatics Resource for Cancer Researchers.
Chambers MC, Jagtap PD, Johnson JE, McGowan T, Kumar P, Onsongo G, Guerrero CR, Barsnes H, Vaudel M, Martens L, Grüning B, Cooke IR, Heydarian M, Reddy KL, Griffin TJ. Chambers MC, et al. Among authors: gruning b. Cancer Res. 2017 Nov 1;77(21):e43-e46. doi: 10.1158/0008-5472.CAN-17-0331. Cancer Res. 2017. PMID: 29092937 Free PMC article.
Software engineering for scientific big data analysis.
Grüning BA, Lampa S, Vaudel M, Blankenberg D. Grüning BA, et al. Gigascience. 2019 May 1;8(5):giz054. doi: 10.1093/gigascience/giz054. Gigascience. 2019. PMID: 31121028 Free PMC article.
The omics discovery REST interface.
Dass G, Vu MT, Xu P, Audain E, Hitz MP, Grüning BA, Hermjakob H, Perez-Riverol Y. Dass G, et al. Nucleic Acids Res. 2020 Jul 2;48(W1):W380-W384. doi: 10.1093/nar/gkaa326. Nucleic Acids Res. 2020. PMID: 32374843 Free PMC article.
A single-cell RNA-sequencing training and analysis suite using the Galaxy framework.
Tekman M, Batut B, Ostrovsky A, Antoniewski C, Clements D, Ramirez F, Etherington GJ, Hotz HR, Scholtalbers J, Manning JR, Bellenger L, Doyle MA, Heydarian M, Huang N, Soranzo N, Moreno P, Mautner S, Papatheodorou I, Nekrutenko A, Taylor J, Blankenberg D, Backofen R, Grüning B. Tekman M, et al. Among authors: gruning b. Gigascience. 2020 Oct 20;9(10):giaa102. doi: 10.1093/gigascience/giaa102. Gigascience. 2020. PMID: 33079170 Free PMC article.
User-friendly, scalable tools and workflows for single-cell RNA-seq analysis.
Moreno P, Huang N, Manning JR, Mohammed S, Solovyev A, Polanski K, Bacon W, Chazarra R, Talavera-López C, Doyle MA, Marnier G, Grüning B, Rasche H, George N, Fexova SK, Alibi M, Miao Z, Perez-Riverol Y, Haeussler M, Brazma A, Teichmann S, Meyer KB, Papatheodorou I. Moreno P, et al. Among authors: gruning b. Nat Methods. 2021 Apr;18(4):327-328. doi: 10.1038/s41592-021-01102-w. Nat Methods. 2021. PMID: 33782609 Free PMC article. No abstract available.
124 results