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Page 1
A guide to the BRAIN Initiative Cell Census Network data ecosystem.
Hawrylycz M, Martone ME, Ascoli GA, Bjaalie JG, Dong HW, Ghosh SS, Gillis J, Hertzano R, Haynor DR, Hof PR, Kim Y, Lein E, Liu Y, Miller JA, Mitra PP, Mukamel E, Ng L, Osumi-Sutherland D, Peng H, Ray PL, Sanchez R, Regev A, Ropelewski A, Scheuermann RH, Tan SZK, Thompson CL, Tickle T, Tilgner H, Varghese M, Wester B, White O, Zeng H, Aevermann B, Allemang D, Ament S, Athey TL, Baker C, Baker KS, Baker PM, Bandrowski A, Banerjee S, Bishwakarma P, Carr A, Chen M, Choudhury R, Cool J, Creasy H, D'Orazi F, Degatano K, Dichter B, Ding SL, Dolbeare T, Ecker JR, Fang R, Fillion-Robin JC, Fliss TP, Gee J, Gillespie T, Gouwens N, Zhang GQ, Halchenko YO, Harris NL, Herb BR, Hintiryan H, Hood G, Horvath S, Huo B, Jarecka D, Jiang S, Khajouei F, Kiernan EA, Kir H, Kruse L, Lee C, Lelieveldt B, Li Y, Liu H, Liu L, Markuhar A, Mathews J, Mathews KL, Mezias C, Miller MI, Mollenkopf T, Mufti S, Mungall CJ, Orvis J, Puchades MA, Qu L, Receveur JP, Ren B, Sjoquist N, Staats B, Tward D, van Velthoven CTJ, Wang Q, Xie F, Xu H, Yao Z, Yun Z, Zhang YR, Zheng WJ, Zingg B. Hawrylycz M, et al. Among authors: aevermann b. PLoS Biol. 2023 Jun 30;21(6):e3002133. doi: 10.1371/journal.pbio.3002133. eCollection 2023 Jun. PLoS Biol. 2023. PMID: 37390046 Free PMC article.
Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons.
Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken RS. Krishnaswami SR, et al. Among authors: aevermann bd. Nat Protoc. 2016 Mar;11(3):499-524. doi: 10.1038/nprot.2016.015. Epub 2016 Feb 18. Nat Protoc. 2016. PMID: 26890679 Free PMC article.
PRODUCTION OF A PRELIMINARY QUALITY CONTROL PIPELINE FOR SINGLE NUCLEI RNA-SEQ AND ITS APPLICATION IN THE ANALYSIS OF CELL TYPE DIVERSITY OF POST-MORTEM HUMAN BRAIN NEOCORTEX.
Aevermann B, McCorrison J, Venepally P, Hodge R, Bakken T, Miller J, Novotny M, Tran DN, Diezfuertes F, Christiansen L, Zhang F, Steemers F, Lasken RS, Lein ED, Schork N, Scheuermann RH. Aevermann B, et al. Pac Symp Biocomput. 2017;22:564-575. doi: 10.1142/9789813207813_0052. Pac Symp Biocomput. 2017. PMID: 27897007 Free PMC article.
Cell type discovery and representation in the era of high-content single cell phenotyping.
Bakken T, Cowell L, Aevermann BD, Novotny M, Hodge R, Miller JA, Lee A, Chang I, McCorrison J, Pulendran B, Qian Y, Schork NJ, Lasken RS, Lein ES, Scheuermann RH. Bakken T, et al. Among authors: aevermann bd. BMC Bioinformatics. 2017 Dec 21;18(Suppl 17):559. doi: 10.1186/s12859-017-1977-1. BMC Bioinformatics. 2017. PMID: 29322913 Free PMC article.
Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type.
Boldog E, Bakken TE, Hodge RD, Novotny M, Aevermann BD, Baka J, Bordé S, Close JL, Diez-Fuertes F, Ding SL, Faragó N, Kocsis ÁK, Kovács B, Maltzer Z, McCorrison JM, Miller JA, Molnár G, Oláh G, Ozsvár A, Rózsa M, Shehata SI, Smith KA, Sunkin SM, Tran DN, Venepally P, Wall A, Puskás LG, Barzó P, Steemers FJ, Schork NJ, Scheuermann RH, Lasken RS, Lein ES, Tamás G. Boldog E, et al. Among authors: aevermann bd. Nat Neurosci. 2018 Sep;21(9):1185-1195. doi: 10.1038/s41593-018-0205-2. Epub 2018 Aug 27. Nat Neurosci. 2018. PMID: 30150662 Free PMC article.
Single-nucleus and single-cell transcriptomes compared in matched cortical cell types.
Bakken TE, Hodge RD, Miller JA, Yao Z, Nguyen TN, Aevermann B, Barkan E, Bertagnolli D, Casper T, Dee N, Garren E, Goldy J, Graybuck LT, Kroll M, Lasken RS, Lathia K, Parry S, Rimorin C, Scheuermann RH, Schork NJ, Shehata SI, Tieu M, Phillips JW, Bernard A, Smith KA, Zeng H, Lein ES, Tasic B. Bakken TE, et al. Among authors: aevermann b. PLoS One. 2018 Dec 26;13(12):e0209648. doi: 10.1371/journal.pone.0209648. eCollection 2018. PLoS One. 2018. PMID: 30586455 Free PMC article.
Conserved cell types with divergent features in human versus mouse cortex.
Hodge RD, Bakken TE, Miller JA, Smith KA, Barkan ER, Graybuck LT, Close JL, Long B, Johansen N, Penn O, Yao Z, Eggermont J, Höllt T, Levi BP, Shehata SI, Aevermann B, Beller A, Bertagnolli D, Brouner K, Casper T, Cobbs C, Dalley R, Dee N, Ding SL, Ellenbogen RG, Fong O, Garren E, Goldy J, Gwinn RP, Hirschstein D, Keene CD, Keshk M, Ko AL, Lathia K, Mahfouz A, Maltzer Z, McGraw M, Nguyen TN, Nyhus J, Ojemann JG, Oldre A, Parry S, Reynolds S, Rimorin C, Shapovalova NV, Somasundaram S, Szafer A, Thomsen ER, Tieu M, Quon G, Scheuermann RH, Yuste R, Sunkin SM, Lelieveldt B, Feng D, Ng L, Bernard A, Hawrylycz M, Phillips JW, Tasic B, Zeng H, Jones AR, Koch C, Lein ES. Hodge RD, et al. Among authors: aevermann b. Nature. 2019 Sep;573(7772):61-68. doi: 10.1038/s41586-019-1506-7. Epub 2019 Aug 21. Nature. 2019. PMID: 31435019 Free PMC article.
Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons.
Hodge RD, Miller JA, Novotny M, Kalmbach BE, Ting JT, Bakken TE, Aevermann BD, Barkan ER, Berkowitz-Cerasano ML, Cobbs C, Diez-Fuertes F, Ding SL, McCorrison J, Schork NJ, Shehata SI, Smith KA, Sunkin SM, Tran DN, Venepally P, Yanny AM, Steemers FJ, Phillips JW, Bernard A, Koch C, Lasken RS, Scheuermann RH, Lein ES. Hodge RD, et al. Nat Commun. 2020 Mar 3;11(1):1172. doi: 10.1038/s41467-020-14952-3. Nat Commun. 2020. PMID: 32127543 Free PMC article.
30 results