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About

About

Apuā Paquola is a computer scientist and computational biologist, with main interest in genomics and machine learning. During his postdoc at the Salk Institute, in the Gage Lab, he developed computational approaches to identify somatic retrotransposition events in single cells, which led to the discovery of extensive somatic mosaicism in the healthy human brain. At the Lieber Institute, his goal is to develop and apply machine learning approaches on multiple types of biomedical data to gain insight on brain development and brain disorders. He has a B.Sc. in Computer Science at the State University of Campinas, and Ph.D. in Bioinformatics at the University of Sāo Paulo, Brazil, where he worked on gene regulation and horizontal gene transfer in prokaryotes.

Publications

Publications

Paquola, AC*, Erwin, JA*, Gage, FH. Insights into the role of somatic mosaicism in the brain. Current Opinion in Systems Biology 2017, 1:90–94. (*equal contribution, review article)

McConnell MJ, et al.,  Paquola, AC, et al., Brain Somatic Mosaicism Network. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. Science. 2017 Apr 28;356(6336).

Erwin, JA*, Paquola, AC*, Singer, T, Gallina, I, Novotny, M, Quayle, C, Bedrosian, T, Butcher, CR, Herdy, JR, Lasken, RS, Muotri, AR, Gage, FH. L1-Associated Genomic Regions are Deleted in Somatic Cells of the Healthy Human Brain. Nat Neurosci. 2016 Dec;19(12):1583-1591   (*equal contribution).

Han J, Kim HJ, Schafer ST, Paquola AC, Clemenson GD, Toda T, Oh J, Pankonin AR, Lee BS, Johnston ST, Sarkar A, Denli AM, Gage FH. Functional Implications of miR-19 in the Migration of Newborn Neurons in the Adult Brain. Neuron. 2016 Jul 6;91(1):79-89.

Paquola, AC, Erwin, JA, Gage, FH  A framework for collaborative computational research. bioRxiv 2015; 033654

Lacar, B, Linker, S, Jaeger, B, Krishnaswami, S, Barron, J, Kelder, M, Parylak, S, Paquola, AC, Venepally, P, Novotny, M, O’Connor, C, Fitzpatrick, C, Erwin, JA, Hsu, J, Husband, J, McConnell, MJ, Lasken, R, and Gage, FH. Nuclear RNA-seq of single neurons reveals molecular signatures of activation. Nat Commun. 2016 Jun 14;7:12020.

Vadodaria KC, Mertens J, Paquola AC, Bardy C, Li X, Jappelli R, Fung L, Marchetto MC, Hamm M, Gorris M, Koch P, Gage FH. Generation of functional human serotonergic neurons from fibroblasts. Mol Psychiatry. 2016 Jan;21(1):49-61.

Mertens J, Paquola AC, 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. Directly Reprogrammed Human Neurons Retain Aging-Associated Transcriptomic Signatures and Reveal Age-Related Nucleocytoplasmic Defects. Cell  Stem Cell. 2015 Dec 3;17(6):705-18.

Marchetto MC, Narvaiza I, Denli AM, Benner C, Lazzarini TA, Nathanson JL, Paquola AC, Desai KN, Herai RH, Weitzman MD, Yeo GW, Muotri AR, Gage FH. Differential L1 regulation in pluripotent stem cells of humans and apes. Nature.  2013 Nov 28;503(7477):525-9.

Lima WC, Paquola AC, Varani AM, Van Sluys MA, Menck CF. Laterally transferred  genomic islands in Xanthomonadales related to pathogenicity and primary metabolism. FEMS Microbiol Lett. 2008 Apr;281(1):87-97.

da Rocha RP, Paquola AC, Marques Mdo V, Menck CF, Galhardo RS. Characterization of the SOS regulon of Caulobacter crescentus. J Bacteriol. 2008  Feb;190(4):1209-18.

Ojopi EP, Oliveira PS, Nunes DN, Paquola AC, DeMarco R, Gregório SP, Aires KA,  Menck CF, Leite LC, Verjovski-Almeida S, Dias-Neto E. A quantitative view of the  transcriptome of Schistosoma mansoni adult-worms using SAGE. BMC Genomics. 2007 Jun 21;8:186.

Reis EM, et al., Paquola AC, et al.; Head and Neck Annotation Consortium. Large-scale transcriptome analyses reveal new genetic marker candidates of head, neck, and thyroid cancer. Cancer Res. 2005 Mar 1;65(5):1693-9.

da Costa RM, Riou L, Paquola AC, Menck CF, Sarasin A. Transcriptional profiles  of unirradiated or UV-irradiated human cells expressing either the cancer-prone XPB/CS allele or the noncancer-prone XPB/TTD allele. Oncogene. 2005 Feb 17;24(8):1359-74.

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. Antisense intronic non-coding RNA levels correlate to the degree of tumor differentiation in prostate cancer. Oncogene. 2004 Aug 26;23(39):6684-92.

Louro R, Nakaya HI, Paquola AC, Martins EA, da Silva AM, Verjovski-Almeida S, Reis EM. RASL11A, member of a novel small monomeric GTPase gene family, is down-regulated in prostate tumors. Biochem Biophys Res Commun. 2004 Apr 9;316(3):618-27.

Brentani H, et al., Paquola AC, et al., Human Cancer Genome Project/Cancer Genome Anatomy Project Annotation Consortium; Human Cancer Genome Project Sequencing Consortium. The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags. Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13418-23. Epub 2003 Oct 30.

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. Transcriptome analysis of the acoelomate human parasite Schistosoma mansoni. Nat Genet. 2003 Oct;35(2):148-57.  Epub 2003 Sep 14.

Paquola AC, Nishyiama MY Jr, Reis EM, da Silva AM, Verjovski-Almeida S. ESTWeb: bioinformatics services for EST sequencing projects. Bioinformatics. 2003 Aug 12;19(12):1587-8.

Paquola AC, Machado AA, Reis EM, Da Silva AM, Verjovski-Almeida S. Zerg: a very fast BLAST parser library. Bioinformatics. 2003 May 22;19(8):1035-6.