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Items: 23

1.

Mitochondrial Aging Defects Emerge in Directly Reprogrammed Human Neurons due to Their Metabolic Profile.

Kim Y, Zheng X, Ansari Z, Bunnell MC, Herdy JR, Traxler L, Lee H, Paquola ACM, Blithikioti C, Ku M, Schlachetzki JCM, Winkler J, Edenhofer F, Glass CK, Paucar AA, Jaeger BN, Pham S, Boyer L, Campbell BC, Hunter T, Mertens J, Gage FH.

Cell Rep. 2018 May 29;23(9):2550-2558. doi: 10.1016/j.celrep.2018.04.105.

2.

Efficient Generation of CA3 Neurons from Human Pluripotent Stem Cells Enables Modeling of Hippocampal Connectivity In Vitro.

Sarkar A, Mei A, Paquola ACM, Stern S, Bardy C, Klug JR, Kim S, Neshat N, Kim HJ, Ku M, Shokhirev MN, Adamowicz DH, Marchetto MC, Jappelli R, Erwin JA, Padmanabhan K, Shtrahman M, Jin X, Gage FH.

Cell Stem Cell. 2018 May 3;22(5):684-697.e9. doi: 10.1016/j.stem.2018.04.009.

PMID:
29727680
3.

Author Correction: L1-associated genomic regions are deleted in somatic cells of the healthy human brain.

Erwin JA, Paquola ACM, Singer T, Gallina I, Novotny M, Quayle C, Bedrosian TA, Alves FIA, Butcher CR, Herdy JR, Sarkar A, Lasken RS, Muotri AR, Gage FH.

Nat Neurosci. 2018 Jul;21(7):1016. doi: 10.1038/s41593-018-0131-3.

PMID:
29703932
4.

Horizontal Gene Transfer Building Prokaryote Genomes: Genes Related to Exchange Between Cell and Environment are Frequently Transferred.

Paquola ACM, Asif H, Pereira CAB, Feltes BC, Bonatto D, Lima WC, Menck CFM.

J Mol Evol. 2018 Apr;86(3-4):190-203. doi: 10.1007/s00239-018-9836-x. Epub 2018 Mar 19.

PMID:
29556740
5.

Insights into the role of somatic mosaicism in the brain.

Paquola ACM, Erwin JA, Gage FH.

Curr Opin Syst Biol. 2017 Feb;1:90-94. doi: 10.1016/j.coisb.2016.12.004. Epub 2016 Dec 9.

6.

Corrigendum: L1-associated genomic regions are deleted in somatic cells of the healthy human brain.

Erwin JA, Paquola ACM, Singer T, Gallina I, Novotny M, Quayle C, Bedrosian TA, Alves FIA, Butcher CR, Herdy JR, Sarkar A, Lasken RS, Muotri AR, Gage FH.

Nat Neurosci. 2017 Sep 28;20(10):1427. doi: 10.1038/nn1017-1427a. No abstract available.

PMID:
28949329
7.

Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network.

McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, Mills RE, Paquola ACM, Rodin RE, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub RE, Thorpe J, Weinberger DR, Urban AE, Zhou B, Gage FH, Lehner T, Senthil G, Walsh CA, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FM; Brain Somatic Mosaicism Network.

Science. 2017 Apr 28;356(6336). pii: eaal1641. doi: 10.1126/science.aal1641. Epub 2017 Apr 27. Review.

8.

Corrigendum: Nuclear RNA-seq of single neurons reveals molecular signatures of activation.

Lacar B, Linker SB, Jaeger BN, Krishnaswami SR, Barron JJ, Kelder MJ, Parylak SL, Paquola AC, Venepally P, Novotny M, O'Connor C, Fitzpatrick C, Erwin JA, Hsu JY, Husband D, McConnell MJ, Lasken R, Gage FH.

Nat Commun. 2017 Mar 17;8:15047. doi: 10.1038/ncomms15047. No abstract available.

9.

L1-associated genomic regions are deleted in somatic cells of the healthy human brain.

Erwin JA, Paquola AC, Singer T, Gallina I, Novotny M, Quayle C, Bedrosian TA, Alves FI, Butcher CR, Herdy JR, Sarkar A, Lasken RS, Muotri AR, Gage FH.

Nat Neurosci. 2016 Dec;19(12):1583-1591. doi: 10.1038/nn.4388. Epub 2016 Sep 12. Erratum in: Nat Neurosci. 2017 Sep 28;20(10 ):1427. Nat Neurosci. 2018 Apr 27;:.

10.

Corrigendum: Nuclear RNA-seq of single neurons reveals molecular signatures of activation.

Lacar B, Linker SB, Jaeger BN, Krishnaswami SR, Barron JJ, Kelder MJ, Parylak SL, Paquola AC, Venepally P, Novotny M, O'Connor C, Fitzpatrick C, Erwin JA, Hsu JY, Husband D, McConnell MJ, Lasken R, Gage FH.

Nat Commun. 2016 Jun 14;7:12020. doi: 10.1038/ncomms12020. No abstract available.

11.

Nuclear RNA-seq of single neurons reveals molecular signatures of activation.

Lacar B, Linker SB, Jaeger BN, Krishnaswami SR, Barron JJ, Kelder MJE, Parylak SL, Paquola ACM, Venepally P, Novotny M, O'Connor C, Fitzpatrick C, Erwin JA, Hsu JY, Husband D, McConnell MJ, Lasken R, Gage FH.

Nat Commun. 2016 Apr 19;7:11022. doi: 10.1038/ncomms11022. Erratum in: Nat Commun. 2016 Jun 14;7:12020. Nat Commun. 2017 Mar 17;8:15047.

12.

Directly Reprogrammed Human Neurons Retain Aging-Associated Transcriptomic Signatures and Reveal Age-Related Nucleocytoplasmic Defects.

Mertens J, Paquola ACM, Ku M, Hatch E, Böhnke L, Ladjevardi S, McGrath S, Campbell B, Lee H, Herdy JR, Gonçalves JT, Toda T, Kim Y, Winkler J, Yao J, Hetzer MW, Gage FH.

Cell Stem Cell. 2015 Dec 3;17(6):705-718. doi: 10.1016/j.stem.2015.09.001. Epub 2015 Oct 8.

13.

Differential L1 regulation in pluripotent stem cells of humans and apes.

Marchetto MCN, Narvaiza I, Denli AM, Benner C, Lazzarini TA, Nathanson JL, Paquola ACM, Desai KN, Herai RH, Weitzman MD, Yeo GW, Muotri AR, Gage FH.

Nature. 2013 Nov 28;503(7477):525-529. doi: 10.1038/nature12686. Epub 2013 Oct 23.

14.

LINE-1 retrotransposition in the nervous system.

Thomas CA, Paquola AC, Muotri AR.

Annu Rev Cell Dev Biol. 2012;28:555-73. doi: 10.1146/annurev-cellbio-101011-155822. Review.

PMID:
23057747
15.

Laterally transferred genomic islands in Xanthomonadales related to pathogenicity and primary metabolism.

Lima WC, Paquola AC, Varani AM, Van Sluys MA, Menck CF.

FEMS Microbiol Lett. 2008 Apr;281(1):87-97. doi: 10.1111/j.1574-6968.2008.01083.x.

16.

Characterization of the SOS regulon of Caulobacter crescentus.

da Rocha RP, Paquola AC, Marques Mdo V, Menck CF, Galhardo RS.

J Bacteriol. 2008 Feb;190(4):1209-18. Epub 2007 Dec 14.

17.

Large-scale transcriptome analyses reveal new genetic marker candidates of head, neck, and thyroid cancer.

Reis EM, Ojopi EP, Alberto FL, Rahal P, Tsukumo F, Mancini UM, Guimarães GS, Thompson GM, Camacho C, Miracca E, Carvalho AL, Machado AA, Paquola AC, Cerutti JM, da Silva AM, Pereira GG, Valentini SR, Nagai MA, Kowalski LP, Verjovski-Almeida S, Tajara EH, Dias-Neto E, Bengtson MH, Canevari RA, Carazzolle MF, Colin C, Costa FF, Costa MC, Estécio MR, Esteves LI, Federico MH, Guimarães PE, Hackel C, Kimura ET, Leoni SG, Maciel RM, Maistro S, Mangone FR, Massirer KB, Matsuo SE, Nobrega FG, Nóbrega MP, Nunes DN, Nunes F, Pandolfi JR, Pardini MI, Pasini FS, Peres T, Rainho CA, dos Reis PP, Rodrigus-Lisoni FC, Rogatto SR, dos Santos A, dos Santos PC, Sogayar MC, Zanelli CF; Head and Neck Annotation Consortium.

Cancer Res. 2005 Mar 1;65(5):1693-9.

18.

Antisense intronic non-coding RNA levels correlate to the degree of tumor differentiation in prostate cancer.

Reis EM, Nakaya HI, Louro R, Canavez FC, Flatschart AV, Almeida GT, Egidio CM, Paquola AC, Machado AA, Festa F, Yamamoto D, Alvarenga R, da Silva CC, Brito GC, Simon SD, Moreira-Filho CA, Leite KR, Camara-Lopes LH, Campos FS, Gimba E, Vignal GM, El-Dorry H, Sogayar MC, Barcinski MA, da Silva AM, Verjovski-Almeida S.

Oncogene. 2004 Aug 26;23(39):6684-92.

PMID:
15221013
19.

RASL11A, member of a novel small monomeric GTPase gene family, is down-regulated in prostate tumors.

Louro R, Nakaya HI, Paquola AC, Martins EA, da Silva AM, Verjovski-Almeida S, Reis EM.

Biochem Biophys Res Commun. 2004 Apr 9;316(3):618-27.

PMID:
15033445
20.

The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags.

Brentani H, Caballero OL, Camargo AA, da Silva AM, da Silva WA Jr, Dias Neto E, Grivet M, Gruber A, Guimaraes PE, Hide W, Iseli C, Jongeneel CV, Kelso J, Nagai MA, Ojopi EP, Osorio EC, Reis EM, Riggins GJ, Simpson AJ, de Souza S, Stevenson BJ, Strausberg RL, Tajara EH, Verjovski-Almeida S, Acencio ML, Bengtson MH, Bettoni F, Bodmer WF, Briones MR, Camargo LP, Cavenee W, Cerutti JM, Coelho Andrade LE, Costa dos Santos PC, Ramos Costa MC, da Silva IT, Estécio MR, Sa Ferreira K, Furnari FB, Faria M Jr, Galante PA, Guimaraes GS, Holanda AJ, Kimura ET, Leerkes MR, Lu X, Maciel RM, Martins EA, Massirer KB, Melo AS, Mestriner CA, Miracca EC, Miranda LL, Nobrega FG, Oliveira PS, Paquola AC, Pandolfi JR, Campos Pardini MI, Passetti F, Quackenbush J, Schnabel B, Sogayar MC, Souza JE, Valentini SR, Zaiats AC, Amaral EJ, Arnaldi LA, de Araújo AG, de Bessa SA, Bicknell DC, Ribeiro de Camaro ME, Carraro DM, Carrer H, Carvalho AF, Colin C, Costa F, Curcio C, Guerreiro da Silva ID, Pereira da Silva N, Dellamano M, El-Dorry H, Espreafico EM, Scattone Ferreira AJ, Ayres Ferreira C, Fortes MA, Gama AH, Giannella-Neto D, Giannella ML, Giorgi RR, Goldman GH, Goldman MH, Hackel C, Ho PL, Kimura EM, Kowalski LP, Krieger JE, Leite LC, Lopes A, Luna AM, Mackay A, Mari SK, Marques AA, Martins WK, Montagnini A, Mourão Neto M, Nascimento AL, Neville AM, Nobrega MP, O'Hare MJ, Otsuka AY, Ruas de Melo AI, Paco-Larson ML, Guimarães Pereira G, Pereira da Silva N, Pesquero JB, Pessoa JG, Rahal P, Rainho CA, Rodrigues V, Rogatto SR, Romano CM, Romeiro JG, Rossi BM, Rusticci M, Guerra de Sá R, Sant' Anna SC, Sarmazo ML, Silva TC, Soares FA, Sonati Mde F, de Freitas Sousa J, Queiroz D, Valente V, Vettore AL, Villanova FE, Zago MA, Zalcberg H; Human Cancer Genome Project/Cancer Genome Anatomy Project Annotation Consortium; Human Cancer Genome Project Sequencing Consortium.

Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13418-23. Epub 2003 Oct 30.

21.

Transcriptome analysis of the acoelomate human parasite Schistosoma mansoni.

Verjovski-Almeida S, DeMarco R, Martins EA, Guimarães PE, Ojopi EP, Paquola AC, Piazza JP, Nishiyama MY Jr, Kitajima JP, Adamson RE, Ashton PD, Bonaldo MF, Coulson PS, Dillon GP, Farias LP, Gregorio SP, Ho PL, Leite RA, Malaquias LC, Marques RC, Miyasato PA, Nascimento AL, Ohlweiler FP, Reis EM, Ribeiro MA, Sá RG, Stukart GC, Soares MB, Gargioni C, Kawano T, Rodrigues V, Madeira AM, Wilson RA, Menck CF, Setubal JC, Leite LC, Dias-Neto E.

Nat Genet. 2003 Oct;35(2):148-57. Epub 2003 Sep 14.

PMID:
12973350
22.

ESTWeb: bioinformatics services for EST sequencing projects.

Paquola AC, Nishyiama MY Jr, Reis EM, da Silva AM, Verjovski-Almeida S.

Bioinformatics. 2003 Aug 12;19(12):1587-8.

PMID:
12912845
23.

Zerg: a very fast BLAST parser library.

Paquola AC, Machado AA, Reis EM, Da Silva AM, Verjovski-Almeida S.

Bioinformatics. 2003 May 22;19(8):1035-6.

PMID:
12761068

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