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Joint representation and visualization of derailed cell states with Decipher.
Nazaret A, Fan JL, Lavallée VP, Burdziak C, Cornish AE, Kiseliovas V, Bowman RL, Masilionis I, Chun J, Eisman SE, Wang J, Hong J, Shi L, Levine RL, Mazutis L, Blei D, Pe'er D, Azizi E. Nazaret A, et al. bioRxiv [Preprint]. 2024 Nov 5:2023.11.11.566719. doi: 10.1101/2023.11.11.566719. bioRxiv. 2024. PMID: 38014231 Free PMC article. Preprint.
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.
Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jané-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe'er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH; Human Tumor Atlas Network. Rozenblatt-Rosen O, et al. Cell. 2020 Apr 16;181(2):236-249. doi: 10.1016/j.cell.2020.03.053. Cell. 2020. PMID: 32302568 Free PMC article. Review.
Distinct tumor architectures for metastatic colonization of the brain.
Gan S, Macalinao DG, Shahoei SH, Tian L, Jin X, Basnet H, Muller JT, Atri P, Seffar E, Chatila W, Hadjantonakis AK, Schultz N, Brogi E, Bale TA, Pe'er D, Massagué J. Gan S, et al. bioRxiv [Preprint]. 2023 Jan 28:2023.01.27.525190. doi: 10.1101/2023.01.27.525190. bioRxiv. 2023. PMID: 37034672 Free PMC article. Preprint.
Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities.
Garg V, Yang Y, Nowotschin S, Setty M, Kuo YY, Sharma R, Polyzos A, Salataj E, Murphy D, Jang A, Pe'er D, Apostolou E, Hadjantonakis AK. Garg V, et al. bioRxiv [Preprint]. 2023 Mar 29:2023.03.28.534648. doi: 10.1101/2023.03.28.534648. bioRxiv. 2023. Update in: Dev Cell. 2024 Dec 19:S1534-5807(24)00722-6. doi: 10.1016/j.devcel.2024.11.022 PMID: 37034770 Free PMC article. Updated. Preprint.
Progressive plasticity during colorectal cancer metastasis.
Moorman AR, Cambuli F, Benitez EK, Jiang Q, Xie Y, Mahmoud A, Lumish M, Hartner S, Balkaran S, Bermeo J, Asawa S, Firat C, Saxena A, Luthra A, Sgambati V, Luckett K, Wu F, Li Y, Yi Z, Masilionis I, Soares K, Pappou E, Yaeger R, Kingham P, Jarnagin W, Paty P, Weiser MR, Mazutis L, D'Angelica M, Shia J, Garcia-Aguilar J, Nawy T, Hollmann TJ, Chaligné R, Sanchez-Vega F, Sharma R, Pe'er D, Ganesh K. Moorman AR, et al. bioRxiv [Preprint]. 2023 Aug 21:2023.08.18.553925. doi: 10.1101/2023.08.18.553925. bioRxiv. 2023. Update in: Nature. 2024 Oct 30. doi: 10.1038/s41586-024-08150-0 PMID: 37662289 Free PMC article. Updated. Preprint.
Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity.
Bui LT, Winters NI, Chung MI, Joseph C, Gutierrez AJ, Habermann AC, Adams TS, Schupp JC, Poli S, Peter LM, Taylor CJ, Blackburn JB, Richmond BW, Nicholson AG, Rassl D, Wallace WA, Rosas IO, Jenkins RG, Kaminski N, Kropski JA, Banovich NE; Human Cell Atlas Lung Biological Network. Bui LT, et al. bioRxiv [Preprint]. 2021 Jan 4:2020.10.20.347187. doi: 10.1101/2020.10.20.347187. bioRxiv. 2021. Update in: Nat Commun. 2021 Jul 14;12(1):4314. doi: 10.1038/s41467-021-24467-0 PMID: 33106805 Free PMC article. Updated. Preprint.
145 results