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Items: 27

1.

Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase.

Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, Burke JE, Diedrich JK, Cooke S, Shea T, Gienger E, Lintner R, Yates JR 3rd, Hajkova P, Narlikar GJ, Cuomo CA, Pritchard JK, Madhani HD.

Cell. 2020 Feb 20;180(4):816. doi: 10.1016/j.cell.2020.02.006. No abstract available.

PMID:
32084344
2.

Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase.

Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, Burke JE, Diedrich JK, Cooke S, Shea T, Gienger E, Lintner R, Yates JR 3rd, Hajkova P, Narlikar GJ, Cuomo CA, Pritchard JK, Madhani HD.

Cell. 2020 Jan 23;180(2):263-277.e20. doi: 10.1016/j.cell.2019.12.012. Epub 2020 Jan 16. Erratum in: Cell. 2020 Feb 20;180(4):816.

PMID:
31955845
3.

Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay.

Anderson CM, Laeremans A, Wang XM, Wu X, Zhang B, Doolittle E, Kim J, Li N, Pimentel HXY, Park E, Ma XJ.

J Vis Exp. 2018 Aug 14;(138). doi: 10.3791/58097.

4.

Intron retention is a source of neoepitopes in cancer.

Smart AC, Margolis CA, Pimentel H, He MX, Miao D, Adeegbe D, Fugmann T, Wong KK, Van Allen EM.

Nat Biotechnol. 2018 Dec;36(11):1056-1058. doi: 10.1038/nbt.4239. Epub 2018 Aug 16.

5.

Gene-level differential analysis at transcript-level resolution.

Yi L, Pimentel H, Bray NL, Pachter L.

Genome Biol. 2018 Apr 12;19(1):53. doi: 10.1186/s13059-018-1419-z.

6.

Differential analysis of RNA-seq incorporating quantification uncertainty.

Pimentel H, Bray NL, Puente S, Melsted P, Pachter L.

Nat Methods. 2017 Jul;14(7):687-690. doi: 10.1038/nmeth.4324. Epub 2017 Jun 5.

PMID:
28581496
7.

Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways.

Yi L, Pimentel H, Pachter L.

PLoS One. 2017 Apr 27;12(4):e0175744. doi: 10.1371/journal.pone.0175744. eCollection 2017.

8.

Pseudoalignment for metagenomic read assignment.

Schaeffer L, Pimentel H, Bray N, Melsted P, Pachter L.

Bioinformatics. 2017 Jul 15;33(14):2082-2088. doi: 10.1093/bioinformatics/btx106.

9.

The Lair: a resource for exploratory analysis of published RNA-Seq data.

Pimentel H, Sturmfels P, Bray N, Melsted P, Pachter L.

BMC Bioinformatics. 2016 Dec 1;17(1):490.

10.

Erratum: Near-optimal probabilistic RNA-seq quantification.

Bray NL, Pimentel H, Melsted P, Pachter L.

Nat Biotechnol. 2016 Aug 9;34(8):888. doi: 10.1038/nbt0816-888d. No abstract available.

PMID:
27504780
11.

Near-optimal probabilistic RNA-seq quantification.

Bray NL, Pimentel H, Melsted P, Pachter L.

Nat Biotechnol. 2016 May;34(5):525-7. doi: 10.1038/nbt.3519. Epub 2016 Apr 4. Erratum in: Nat Biotechnol. 2016 Aug 9;34(8):888.

PMID:
27043002
12.

A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis.

Pimentel H, Parra M, Gee SL, Mohandas N, Pachter L, Conboy JG.

Nucleic Acids Res. 2016 Jan 29;44(2):838-51. doi: 10.1093/nar/gkv1168. Epub 2015 Nov 3.

13.

Unusually large anterior fontanellar bone and diffuse capillary malformation with overgrowth in a three-month-old child - a computed tomography case report.

Gonzalez-Reinoso M, Pimentel H, Fermin-Delgado R, Stoeter P.

Neuroradiol J. 2014 Oct;27(5):613-5. doi: 10.15274/NRJ-2014-10063. Epub 2014 Sep 25.

14.

Neuronal deletion of GSK3β increases microtubule speed in the growth cone and enhances axon regeneration via CRMP-2 and independently of MAP1B and CLASP2.

Liz MA, Mar FM, Santos TE, Pimentel HI, Marques AM, Morgado MM, Vieira S, Sousa VF, Pemble H, Wittmann T, Sutherland C, Woodgett JR, Sousa MM.

BMC Biol. 2014 Jun 12;12:47. doi: 10.1186/1741-7007-12-47.

15.

A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis.

Pimentel H, Parra M, Gee S, Ghanem D, An X, Li J, Mohandas N, Pachter L, Conboy JG.

Nucleic Acids Res. 2014 Apr;42(6):4031-42. doi: 10.1093/nar/gkt1388. Epub 2014 Jan 17.

16.

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL.

Genome Biol. 2013 Apr 25;14(4):R36. doi: 10.1186/gb-2013-14-4-r36.

17.

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L.

Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016. Erratum in: Nat Protoc. 2014 Oct;9(10):2513.

18.

Identification of novel transcripts in annotated genomes using RNA-Seq.

Roberts A, Pimentel H, Trapnell C, Pachter L.

Bioinformatics. 2011 Sep 1;27(17):2325-9. doi: 10.1093/bioinformatics/btr355. Epub 2011 Jun 21.

PMID:
21697122
19.

Mucopolysaccharidosis I, II, and VI: Brief review and guidelines for treatment.

Giugliani R, Federhen A, Rojas MV, Vieira T, Artigalás O, Pinto LL, Azevedo AC, Acosta A, Bonfim C, Lourenço CM, Kim CA, Horovitz D, Bonfim D, Norato D, Marinho D, Palhares D, Santos ES, Ribeiro E, Valadares E, Guarany F, de Lucca GR, Pimentel H, de Souza IN, Correa J Sr, Fraga JC, Goes JE, Cabral JM, Simionato J, Llerena J Jr, Jardim L, Giuliani L, da Silva LC, Santos ML, Moreira MA, Kerstenetzky M, Ribeiro M, Ruas N, Barrios P, Aranda P, Honjo R, Boy R, Costa R, Souza C, Alcantara FF, Avilla SG, Fagondes S, Martins AM.

Genet Mol Biol. 2010 Oct;33(4):589-604. Epub 2010 Dec 1.

20.

[Enzyme replacement therapy for mucopolysaccharidoses I, II and VI: recommendations from a group of Brazilian F experts].

Giugliani R, Federhen A, Muñoz Rojas MV, Vieira TA, Artigalás O, Pinto LL, Azevedo AC, Acosta AX, Bomfim C, Lourenço CM, Kim CA, Horovitz D, Souza DB, Norato D, Marinho D, Palhares D, Santos ES, Ribeiro E, Valadares ER, Guarany F, De Lucca GR, Pimentel H, Souza IN, Corrêa Neto J, Fraga JC, Góes JE, Cabral JM, Simeonato J, Llerena JC Jr, Jardim LB, Giuliani Lde R, Silva LC, Santos M, Moreira MA, Kerstenetzky M, Ribeiro M, Ruas N, Barrios P, Aranda P, Honjo R, Boy R, Costa R, Souza CF, Alcântara FF, Avilla SG, Fagondes S, Martins AM.

Rev Assoc Med Bras (1992). 2010 May-Jun;56(3):271-7. Portuguese.

21.

Guidelines for the management of mucopolysaccharidosis type I.

Martins AM, Dualibi AP, Norato D, Takata ET, Santos ES, Valadares ER, Porta G, de Luca G, Moreira G, Pimentel H, Coelho J, Brum JM, Semionato Filho J, Kerstenetzky MS, Guimarães MR, Rojas MV, Aranda PC, Pires RF, Faria RG, Mota RM, Matte U, Guedes ZC.

J Pediatr. 2009 Oct;155(4 Suppl):S32-46. doi: 10.1016/j.jpeds.2009.07.005. Review. No abstract available.

PMID:
19765409
22.

Guidelines to diagnosis and monitoring of Fabry disease and review of treatment experiences.

Martins AM, D'Almeida V, Kyosen SO, Takata ET, Delgado AG, Gonçalves AM, Benetti Filho CC, Martini Filho D, Biagini G, Pimentel H, Abensur H, Guimarães HC, Gomes JG, Sobral Neto J, D'Almeida LO, Carvalho LR, Harouche MB, Maldonado MC, Nascimento OJ, Montoril PS, Bastos RV.

J Pediatr. 2009 Oct;155(4 Suppl):S19-31. doi: 10.1016/j.jpeds.2009.07.003. Review. No abstract available.

PMID:
19765408
23.

Poor zinc and selenium status in phenylketonuric children and adolescents in Brazil.

Barretto JR, Silva LR, Leite ME, Boa-Sorte N, Pimentel H, Purificação AC, Carvalho G, Fontes MI, Amorim T.

Nutr Res. 2008 Mar;28(3):208-11. doi: 10.1016/j.nutres.2007.12.009.

PMID:
19083409
24.

Daily use of phosphodiesterase 5 inhibitors for erectile dysfunction and lower urinary tract symptoms.

Pimentel H, Wald M, Niederberger C.

Int J Impot Res. 2008 Mar-Apr;20(2):145-9. Epub 2007 Dec 13. Review.

PMID:
18075506
25.

Use of medications or devices for erectile dysfunction among long-term prostate cancer treatment survivors: potential influence of sexual motivation and/or indifference.

Miller DC, Wei JT, Dunn RL, Montie JE, Pimentel H, Sandler HM, McLaughlin PW, Sanda MG.

Urology. 2006 Jul;68(1):166-71.

PMID:
16844457
26.

Preparation of alpha-diazocarbonyl compounds from beta-lapachone derivatives and other 1,2-naphthoquinones: use of the 2D NMR 1H,15N and 1H,13C HMBC techniques in assigning regiochemistry.

Ferreira VF, Jorqueira A, Leal KZ, Pimentel HR, Seidl PR, da Silva MN, da Souza MC, Pinto AV, Wardell JL, Wardell SM.

Magn Reson Chem. 2006 Apr;44(4):481-90.

PMID:
16489549
27.

Long-term outcomes among localized prostate cancer survivors: health-related quality-of-life changes after radical prostatectomy, external radiation, and brachytherapy.

Miller DC, Sanda MG, Dunn RL, Montie JE, Pimentel H, Sandler HM, McLaughlin WP, Wei JT.

J Clin Oncol. 2005 Apr 20;23(12):2772-80.

PMID:
15837992

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