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Items: 11

1.

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.

PLoS One. 2018 Dec 26;13(12):e0209648. doi: 10.1371/journal.pone.0209648. eCollection 2018.

2.

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.

Nat Neurosci. 2018 Sep;21(9):1185-1195. doi: 10.1038/s41593-018-0205-2. Epub 2018 Aug 27.

3.

Cell type discovery using single-cell transcriptomics: implications for ontological representation.

Aevermann BD, Novotny M, Bakken T, Miller JA, Diehl AD, Osumi-Sutherland D, Lasken RS, Lein ES, Scheuermann RH.

Hum Mol Genet. 2018 May 1;27(R1):R40-R47. doi: 10.1093/hmg/ddy100.

4.

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.

BMC Bioinformatics. 2017 Dec 21;18(Suppl 17):559. doi: 10.1186/s12859-017-1977-1.

5.

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.

Pac Symp Biocomput. 2017;22:564-575. doi: 10.1142/9789813207813_0052.

6.

Influenza Research Database: An integrated bioinformatics resource for influenza virus research.

Zhang Y, Aevermann BD, Anderson TK, Burke DF, Dauphin G, Gu Z, He S, Kumar S, Larsen CN, Lee AJ, Li X, Macken C, Mahaffey C, Pickett BE, Reardon B, Smith T, Stewart L, Suloway C, Sun G, Tong L, Vincent AL, Walters B, Zaremba S, Zhao H, Zhou L, Zmasek C, Klem EB, Scheuermann RH.

Nucleic Acids Res. 2017 Jan 4;45(D1):D466-D474. doi: 10.1093/nar/gkw857. Epub 2016 Sep 26.

7.

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.

Nat Protoc. 2016 Mar;11(3):499-524. doi: 10.1038/nprot.2016.015. Epub 2016 Feb 18.

8.

Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans.

Lee AJ, Das SR, Wang W, Fitzgerald T, Pickett BE, Aevermann BD, Topham DJ, Falsey AR, Scheuermann RH.

J Virol. 2015 May;89(10):5427-40. doi: 10.1128/JVI.03636-14. Epub 2015 Mar 4.

9.

A comprehensive collection of systems biology data characterizing the host response to viral infection.

Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS, Bankhead A 3rd, Bolles M, Carter V, Chang J, Clauss TR, Dash P, Diercks AH, Eisfeld AJ, Ellis A, Fan S, Ferris MT, Gralinski LE, Green RR, Gritsenko MA, Hatta M, Heegel RA, Jacobs JM, Jeng S, Josset L, Kaiser SM, Kelly S, Law GL, Li C, Li J, Long C, Luna ML, Matzke M, McDermott J, Menachery V, Metz TO, Mitchell H, Monroe ME, Navarro G, Neumann G, Podyminogin RL, Purvine SO, Rosenberger CM, Sanders CJ, Schepmoes AA, Shukla AK, Sims A, Sova P, Tam VC, Tchitchek N, Thomas PG, Tilton SC, Totura A, Wang J, Webb-Robertson BJ, Wen J, Weiss JM, Yang F, Yount B, Zhang Q, McWeeney S, Smith RD, Waters KM, Kawaoka Y, Baric R, Aderem A, Katze MG, Scheuermann RH.

Sci Data. 2014 Oct 14;1:140033. doi: 10.1038/sdata.2014.33. eCollection 2014.

10.

Comparative analysis of the small heat shock proteins in three angiosperm genomes identifies new subfamilies and reveals diverse evolutionary patterns.

Waters ER, Aevermann BD, Sanders-Reed Z.

Cell Stress Chaperones. 2008 Summer;13(2):127-42. doi: 10.1007/s12192-008-0023-7. Epub 2008 Feb 26.

11.

A comparative genomic analysis of the small heat shock proteins in Caenorhabditis elegans and briggsae.

Aevermann BD, Waters ER.

Genetica. 2008 Jul;133(3):307-19. Epub 2007 Oct 17.

PMID:
17940840

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