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Matrix and analysis metadata standards (MAMS) to facilitate harmonization and reproducibility of single-cell data.
Wang Y, Sarfraz I, Teh WK, Sokolov A, Herb BR, Creasy HH, Virshup I, Dries R, Degatano K, Mahurkar A, Schnell DJ, Madrigal P, Hilton J, Gehlenborg N, Tickle T, Campbell JD. Wang Y, et al. Among authors: gehlenborg n. bioRxiv [Preprint]. 2023 Mar 7:2023.03.06.531314. doi: 10.1101/2023.03.06.531314. bioRxiv. 2023. Update in: Genome Biol. 2024 Aug 1;25(1):205. doi: 10.1186/s13059-024-03349-w PMID: 36945543 Free PMC article. Updated. Preprint.
Potential pitfalls in the use of real-world data for studying long COVID.
Zhang HG, Honerlaw JP, Maripuri M, Samayamuthu MJ, Beaulieu-Jones BR, Baig HS, L'Yi S, Ho YL, Morris M, Panickan VA, Wang X, Weber GM, Liao KP, Visweswaran S, Tan BWQ, Yuan W, Gehlenborg N, Muralidhar S, Ramoni RB; Consortium for Clinical Characterization of COVID-19 by EHR (4CE); Kohane IS, Xia Z, Cho K, Cai T, Brat GA. Zhang HG, et al. Among authors: gehlenborg n. Nat Med. 2023 May;29(5):1040-1043. doi: 10.1038/s41591-023-02274-y. Nat Med. 2023. PMID: 37055567 Free PMC article. No abstract available.
Clinical phenotypes and outcomes in children with multisystem inflammatory syndrome across SARS-CoV-2 variant eras: a multinational study from the 4CE consortium.
Sperotto F, Gutiérrez-Sacristán A, Makwana S, Li X, Rofeberg VN, Cai T, Bourgeois FT, Omenn GS, Hanauer DA, Sáez C, Bonzel CL, Bucholz E, Dionne A, Elias MD, García-Barrio N, González TG, Issitt RW, Kernan KF, Laird-Gion J, Maidlow SE, Mandl KD, Ahooyi TM, Moraleda C, Morris M, Moshal KL, Pedrera-Jiménez M, Shah MA, South AM, Spiridou A, Taylor DM, Verdy G, Visweswaran S, Wang X, Xia Z, Zachariasse JM; Consortium for Clinical Characterization of COVID-19 by EHR (4CE); Newburger JW, Avillach P. Sperotto F, et al. EClinicalMedicine. 2023 Sep 14;64:102212. doi: 10.1016/j.eclinm.2023.102212. eCollection 2023 Oct. EClinicalMedicine. 2023. PMID: 37745025 Free PMC article.
Long-term kidney function recovery and mortality after COVID-19-associated acute kidney injury: An international multi-centre observational cohort study.
Tan BWL, Tan BWQ, Tan ALM, Schriver ER, Gutiérrez-Sacristán A, Das P, Yuan W, Hutch MR, García Barrio N, Pedrera Jimenez M, Abu-El-Rub N, Morris M, Moal B, Verdy G, Cho K, Ho YL, Patel LP, Dagliati A, Neuraz A, Klann JG, South AM, Visweswaran S, Hanauer DA, Maidlow SE, Liu M, Mowery DL, Batugo A, Makoudjou A, Tippmann P, Zöller D, Brat GA, Luo Y, Avillach P, Bellazzi R, Chiovato L, Malovini A, Tibollo V, Samayamuthu MJ, Serrano Balazote P, Xia Z, Loh NHW, Chiudinelli L, Bonzel CL, Hong C, Zhang HG, Weber GM, Kohane IS, Cai T, Omenn GS, Holmes JH, Ngiam KY; Consortium for Clinical Characterization of COVID-19 by EHR (4CE). Tan BWL, et al. EClinicalMedicine. 2022 Nov 7;55:101724. doi: 10.1016/j.eclinm.2022.101724. eCollection 2023 Jan. EClinicalMedicine. 2022. PMID: 36381999 Free PMC article.
Characterization of long COVID temporal sub-phenotypes by distributed representation learning from electronic health record data: a cohort study.
Dagliati A, Strasser ZH, Hossein Abad ZS, Klann JG, Wagholikar KB, Mesa R, Visweswaran S, Morris M, Luo Y, Henderson DW, Samayamuthu MJ, Tan BWQ, Verdy G, Omenn GS, Xia Z, Bellazzi R; Consortium for Clinical Characterization of COVID-19 by EHR (4CE),; Murphy SN, Holmes JH, Estiri H; Consortium for Clinical Characterization of COVID-19 by EHR (4CE). Dagliati A, et al. EClinicalMedicine. 2023 Sep 14;64:102210. doi: 10.1016/j.eclinm.2023.102210. eCollection 2023 Oct. EClinicalMedicine. 2023. PMID: 37745021 Free PMC article.
An integrated view of the structure and function of the human 4D nucleome.
4D Nucleome Consortium; Dekker J, Oksuz BA, Zhang Y, Wang Y, Minsk MK, Kuang S, Yang L, Gibcus JH, Krietenstein N, Rando OJ, Xu J, Janssens DH, Henikoff S, Kukalev A, Willemin A, Winick-Ng W, Kempfer R, Pombo A, Yu M, Kumar P, Zhang L, Belmont AS, Sasaki T, van Schaik T, Brueckner L, Peric-Hupkes D, van Steensel B, Wang P, Chai H, Kim M, Ruan Y, Zhang R, Quinodoz SA, Bhat P, Guttman M, Zhao W, Chien S, Liu Y, Venev SV, Plewczynski D, Azcarate II, Szabó D, Thieme CJ, Szczepińska T, Chiliński M, Sengupta K, Conte M, Esposito A, Abraham A, Zhang R, Wang Y, Wen X, Wu Q, Yang Y, Liu J, Boninsegna L, Yildirim A, Zhan Y, Chiariello AM, Bianco S, Lee L, Hu M, Li Y, Barnett RJ, Cook AL, Emerson DJ, Marchal C, Zhao P, Park P, Alver BH, Schroeder A, Navelkar R, Bakker C, Ronchetti W, Ehmsen S, Veit A, Gehlenborg N, Wang T, Li D, Wang X, Nicodemi M, Ren B, Zhong S, Phillips-Cremins JE, Gilbert DM, Pollard KS, Alber F, Ma J, Noble WS, Yue F. 4D Nucleome Consortium, et al. Among authors: gehlenborg n. bioRxiv [Preprint]. 2024 Oct 27:2024.09.17.613111. doi: 10.1101/2024.09.17.613111. bioRxiv. 2024. PMID: 39484446 Free PMC article. Preprint.
214 results