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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: creasy h. 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.
The Neuroscience Multi-Omic Archive: a BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain.
Ament SA, Adkins RS, Carter R, Chrysostomou E, Colantuoni C, Crabtree J, Creasy HH, Degatano K, Felix V, Gandt P, Garden GA, Giglio M, Herb BR, Khajouei F, Kiernan E, McCracken C, McDaniel K, Nadendla S, Nickel L, Olley D, Orvis J, Receveur JP, Schor M, Sonthalia S, Tickle TL, Way J, Hertzano R, Mahurkar AA, White OR. Ament SA, et al. Among authors: creasy hh. Nucleic Acids Res. 2023 Jan 6;51(D1):D1075-D1085. doi: 10.1093/nar/gkac962. Nucleic Acids Res. 2023. PMID: 36318260 Free PMC article.
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex.
Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, Casper T, Colantuoni C, Crabtree J, Creasy H, Crichton K, Crow M, Dee N, Dougherty EL, Doyle WI, Dudoit S, Fang R, Felix V, Fong O, Giglio M, Goldy J, Hawrylycz M, Herb BR, Hertzano R, Hou X, Hu Q, Kancherla J, Kroll M, Lathia K, Li YE, Lucero JD, Luo C, Mahurkar A, McMillen D, Nadaf NM, Nery JR, Nguyen TN, Niu SY, Ntranos V, Orvis J, Osteen JK, Pham T, Pinto-Duarte A, Poirion O, Preissl S, Purdom E, Rimorin C, Risso D, Rivkin AC, Smith K, Street K, Sulc J, Svensson V, Tieu M, Torkelson A, Tung H, Vaishnav ED, Vanderburg CR, van Velthoven C, Wang X, White OR, Huang ZJ, Kharchenko PV, Pachter L, Ngai J, Regev A, Tasic B, Welch JD, Gillis J, Macosko EZ, Ren B, Ecker JR, Zeng H, Mukamel EA. Yao Z, et al. Among authors: creasy h. Nature. 2021 Oct;598(7879):103-110. doi: 10.1038/s41586-021-03500-8. Epub 2021 Oct 6. Nature. 2021. PMID: 34616066 Free PMC article.
HMPDACC: a Human Microbiome Project Multi-omic data resource.
Creasy HH, Felix V, Aluvathingal J, Crabtree J, Ifeonu O, Matsumura J, McCracken C, Nickel L, Orvis J, Schor M, Giglio M, Mahurkar A, White O. Creasy HH, et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D734-D742. doi: 10.1093/nar/gkaa996. Nucleic Acids Res. 2021. PMID: 33305317 Free PMC article.
Strains, functions and dynamics in the expanded Human Microbiome Project.
Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C. Lloyd-Price J, et al. Among authors: creasy hh. Nature. 2017 Oct 5;550(7674):61-66. doi: 10.1038/nature23889. Epub 2017 Sep 20. Nature. 2017. PMID: 28953883 Free PMC article.
The IGS Standard Operating Procedure for Automated Prokaryotic Annotation.
Galens K, Orvis J, Daugherty S, Creasy HH, Angiuoli S, White O, Wortman J, Mahurkar A, Giglio MG. Galens K, et al. Among authors: creasy hh. Stand Genomic Sci. 2011 Apr 29;4(2):244-51. doi: 10.4056/sigs.1223234. Epub 2011 Apr 25. Stand Genomic Sci. 2011. PMID: 21677861 Free PMC article.
Making Common Fund data more findable: catalyzing a data ecosystem.
Charbonneau AL, Brady A, Czajkowski K, Aluvathingal J, Canchi S, Carter R, Chard K, Clarke DJB, Crabtree J, Creasy HH, D'Arcy M, Felix V, Giglio M, Gingrich A, Harris RM, Hodges TK, Ifeonu O, Jeon M, Kropiwnicki E, Lim MCW, Liming RL, Lumian J, Mahurkar AA, Mandal M, Munro JB, Nadendla S, Richter R, Romano C, Rocca-Serra P, Schor M, Schuler RE, Tangmunarunkit H, Waldrop A, Williams C, Word K, Sansone SA, Ma'ayan A, Wagner R, Foster I, Kesselman C, Brown CT, White O. Charbonneau AL, et al. Among authors: creasy hh. Gigascience. 2022 Nov 21;11:giac105. doi: 10.1093/gigascience/giac105. Gigascience. 2022. PMID: 36409836 Free PMC article.
Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project.
Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C. Lloyd-Price J, et al. Among authors: creasy hh. Nature. 2017 Nov 9;551(7679):256. doi: 10.1038/nature24485. Epub 2017 Oct 12. Nature. 2017. PMID: 29022944 Free PMC article.
The Integrative Human Microbiome Project.
Integrative HMP (iHMP) Research Network Consortium. Integrative HMP (iHMP) Research Network Consortium. Nature. 2019 May;569(7758):641-648. doi: 10.1038/s41586-019-1238-8. Epub 2019 May 29. Nature. 2019. PMID: 31142853 Free PMC article.
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