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UCSC Cell Browser: visualize your single-cell data.
Speir ML, Bhaduri A, Markov NS, Moreno P, Nowakowski TJ, Papatheodorou I, Pollen AA, Raney BJ, Seninge L, Kent WJ, Haeussler M. Speir ML, et al. Among authors: papatheodorou i. Bioinformatics. 2021 Dec 7;37(23):4578-4580. doi: 10.1093/bioinformatics/btab503. Bioinformatics. 2021. PMID: 34244710 Free PMC article.
Diagnosis of Multisystem Inflammatory Syndrome in Children by a Whole-Blood Transcriptional Signature.
Jackson HR, Miglietta L, Habgood-Coote D, D'Souza G, Shah P, Nichols S, Vito O, Powell O, Davidson MS, Shimizu C, Agyeman PKA, Beudeker CR, Brengel-Pesce K, Carrol ED, Carter MJ, De T, Eleftheriou I, Emonts M, Epalza C, Georgiou P, De Groot R, Fidler K, Fink C, van Keulen D, Kuijpers T, Moll H, Papatheodorou I, Paulus S, Pokorn M, Pollard AJ, Rivero-Calle I, Rojo P, Secka F, Schlapbach LJ, Tremoulet AH, Tsolia M, Usuf E, Van Der Flier M, Von Both U, Vermont C, Yeung S, Zavadska D, Zenz W, Coin LJM, Cunnington A, Burns JC, Wright V, Martinon-Torres F, Herberg JA, Rodriguez-Manzano J, Kaforou M, Levin M. Jackson HR, et al. Among authors: papatheodorou i. J Pediatric Infect Dis Soc. 2023 Jun 30;12(6):322-331. doi: 10.1093/jpids/piad035. J Pediatric Infect Dis Soc. 2023. PMID: 37255317 Free PMC article.
High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A; PCAWG Transcriptome Working Group; PCAWG Structural Variation Working Group; Creighton CJ; PCAWG Consortium. Zhang Y, et al. Nat Commun. 2020 Feb 5;11(1):736. doi: 10.1038/s41467-019-13885-w. Nat Commun. 2020. PMID: 32024823 Free PMC article.
The landscape of viral associations in human cancers.
Zapatka M, Borozan I, Brewer DS, Iskar M, Grundhoff A, Alawi M, Desai N, Sültmann H, Moch H; PCAWG Pathogens; Cooper CS, Eils R, Ferretti V, Lichter P; PCAWG Consortium. Zapatka M, et al. Nat Genet. 2020 Mar;52(3):320-330. doi: 10.1038/s41588-019-0558-9. Epub 2020 Feb 5. Nat Genet. 2020. PMID: 32025001 Free PMC article.
Expression Atlas update: from tissues to single cells.
Papatheodorou I, Moreno P, Manning J, Fuentes AM, George N, Fexova S, Fonseca NA, Füllgrabe A, Green M, Huang N, Huerta L, Iqbal H, Jianu M, Mohammed S, Zhao L, Jarnuczak AF, Jupp S, Marioni J, Meyer K, Petryszak R, Prada Medina CA, Talavera-López C, Teichmann S, Vizcaino JA, Brazma A. Papatheodorou I, et al. Nucleic Acids Res. 2020 Jan 8;48(D1):D77-D83. doi: 10.1093/nar/gkz947. Nucleic Acids Res. 2020. PMID: 31665515 Free PMC article.
Putative cell type discovery from single-cell gene expression data.
Miao Z, Moreno P, Huang N, Papatheodorou I, Brazma A, Teichmann SA. Miao Z, et al. Among authors: papatheodorou i. Nat Methods. 2020 Jun;17(6):621-628. doi: 10.1038/s41592-020-0825-9. Epub 2020 May 18. Nat Methods. 2020. PMID: 32424270
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: papatheodorou i. 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: papatheodorou i. 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.
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: papatheodorou i. Nat Commun. 2021 Oct 6;12(1):5854. doi: 10.1038/s41467-021-26111-3. Nat Commun. 2021. PMID: 34615866 Free PMC article. Review.
116 results