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Items: 1 to 50 of 117

1.

Influence of BRCA1 Germline Mutations in the Somatic Mutational Burden of Triple-Negative Breast Cancer.

Ferreira EN, Brianese RC, de Almeida RVB, Drummond RD, de Souza JE, da Silva IT, de Souza SJ, Carraro DM.

Transl Oncol. 2019 Aug 13;12(11):1453-1460. doi: 10.1016/j.tranon.2019.07.016. [Epub ahead of print]

2.

Essential Saccharomyces cerevisiae genome instability suppressing genes identify potential human tumor suppressors.

Srivatsan A, Li B, Sanchez DN, Somach SB, da Silva VL, de Souza SJ, Putnam CD, Kolodner RD.

Proc Natl Acad Sci U S A. 2019 Aug 27;116(35):17377-17382. doi: 10.1073/pnas.1906921116. Epub 2019 Aug 13.

PMID:
31409704
3.

On the Impact of the Pangenome and Annotation Discrepancies While Building Protein Sequence Databases for Bacteria Proteogenomics.

Machado KCT, Fortuin S, Tomazella GG, Fonseca AF, Warren RM, Wiker HG, de Souza SJ, de Souza GA.

Front Microbiol. 2019 Jun 20;10:1410. doi: 10.3389/fmicb.2019.01410. eCollection 2019.

4.

A comprehensive analysis of core polyadenylation sequences and regulation by microRNAs in a set of cancer predisposition genes.

Vieira IA, Recamonde-Mendoza M, da Silva VL, Leão DP, Scheid MR, de Souza SJ, Ashton-Prolla P.

Gene. 2019 Sep 5;712:143943. doi: 10.1016/j.gene.2019.143943. Epub 2019 Jun 21.

PMID:
31229581
5.

Gain of transcription factor binding sites is associated to changes in the expression signature of human brain and testis and is correlated to genes with higher expression breadth.

da Silva VL, Dos Santos AMR, Blanco W, de Souza SJ.

Sci China Life Sci. 2019 Apr;62(4):526-534. doi: 10.1007/s11427-018-9454-7. Epub 2019 Mar 22.

PMID:
30919278
6.

Oral Health Impact Profile and Associated Variables in Southern Brazilian Drug Users.

DE Souza SJR, Dos Santos AC, Albini MB, Gabardo MCL, DE Lima AAS, Machado MÂN.

Iran J Public Health. 2018 Oct;47(10):1466-1475.

7.

Sex-biased gene expression in the frontal cortex of common marmosets (Callithrix jacchus) and potential behavioral correlates.

Nogueira VB, Imparato DO, de Souza SJ, de Sousa MBC.

Brain Behav. 2018 Dec;8(12):e01148. doi: 10.1002/brb3.1148. Epub 2018 Oct 30.

8.

Resveratrol decreases the expression of genes involved in inflammation through transcriptional regulation.

Pinheiro DML, de Oliveira AHS, Coutinho LG, Fontes FL, de Medeiros Oliveira RK, Oliveira TT, Faustino ALF, Lira da Silva V, de Melo Campos JTA, Lajus TBP, de Souza SJ, Agnez-Lima LF.

Free Radic Biol Med. 2019 Jan;130:8-22. doi: 10.1016/j.freeradbiomed.2018.10.432. Epub 2018 Oct 24.

PMID:
30366059
9.

Uncovering association networks through an eQTL analysis involving human miRNAs and lincRNAs.

Branco PR, de Araújo GS, Barrera J, Suarez-Kurtz G, de Souza SJ.

Sci Rep. 2018 Oct 9;8(1):15050. doi: 10.1038/s41598-018-33420-z.

10.

Mutation Detection in Tumor-Derived Cell Free DNA Anticipates Progression in a Patient With Metastatic Colorectal Cancer.

de Figueiredo Barros BD, Kupper BEC, Aguiar Junior S, de Mello CAL, Begnami MD, Chojniak R, de Souza SJ, Torrezan GT, Carraro DM.

Front Oncol. 2018 Aug 10;8:306. doi: 10.3389/fonc.2018.00306. eCollection 2018.

11.

Whole Genome Sequencing of the Pirarucu (Arapaima gigas) Supports Independent Emergence of Major Teleost Clades.

Vialle RA, de Souza JES, Lopes KP, Teixeira DG, Alves Sobrinho PA, Ribeiro-Dos-Santos AM, Furtado C, Sakamoto T, Oliveira Silva FA, Herculano Corrêa de Oliveira E, Hamoy IG, Assumpção PP, Ribeiro-Dos-Santos Â, Santos Lima JPM, Seuánez HN, de Souza SJ, Santos S.

Genome Biol Evol. 2018 Sep 1;10(9):2366-2379. doi: 10.1093/gbe/evy130.

12.

Complex Landscape of Germline Variants in Brazilian Patients With Hereditary and Early Onset Breast Cancer.

Torrezan GT, de Almeida FGDSR, Figueiredo MCP, Barros BDF, de Paula CAA, Valieris R, de Souza JES, Ramalho RF, da Silva FCC, Ferreira EN, de Nóbrega AF, Felicio PS, Achatz MI, de Souza SJ, Palmero EI, Carraro DM.

Front Genet. 2018 May 7;9:161. doi: 10.3389/fgene.2018.00161. eCollection 2018.

13.

Genome-wide identification of cancer/testis genes and their association with prognosis in a pan-cancer analysis.

da Silva VL, Fonseca AF, Fonseca M, da Silva TE, Coelho AC, Kroll JE, de Souza JES, Stransky B, de Souza GA, de Souza SJ.

Oncotarget. 2017 Oct 10;8(54):92966-92977. doi: 10.18632/oncotarget.21715. eCollection 2017 Nov 3.

14.
15.

The impact of dark chocolate intake on arterial elasticity in individuals with HIV/AIDS undergoing ART: a randomized, double-blind, crossover trial.

Teixeira AMNDC, Luzia LA, de Souza SJ, de Almeida Petrilli A, Pontilho PM, de Souza JMP, Segurado AAC, Efraim P, Picone CM, Rondo PHC.

Food Funct. 2017 Jun 21;8(6):2212-2219. doi: 10.1039/c6fo01681b.

PMID:
28513635
16.

Bioinformatics Analysis of the Human Surfaceome Reveals New Targets for a Variety of Tumor Types.

Fonseca AL, da Silva VL, da Fonsêca MM, Meira IT, da Silva TE, Kroll JE, Ribeiro-Dos-Santos AM, Freitas CR, Furtado R, de Souza JE, Stransky B, de Souza SJ.

Int J Genomics. 2016;2016:8346198. doi: 10.1155/2016/8346198. Epub 2016 Nov 14.

17.

A genomic case study of desmoplastic small round cell tumor: comprehensive analysis reveals insights into potential therapeutic targets and development of a monitoring tool for a rare and aggressive disease.

Ferreira EN, Barros BD, de Souza JE, Almeida RV, Torrezan GT, Garcia S, Krepischi AC, Mello CA, Cunha IW, Pinto CA, Soares FA, Dias-Neto E, Lopes A, de Souza SJ, Carraro DM.

Hum Genomics. 2016 Nov 18;10(1):36.

18.

NFAT1 transcription factor regulates cell cycle progression and cyclin E expression in B lymphocytes.

Teixeira LK, Carrossini N, Sécca C, Kroll JE, DaCunha DC, Faget DV, Carvalho LD, de Souza SJ, Viola JP.

Cell Cycle. 2016 Sep;15(17):2346-59. doi: 10.1080/15384101.2016.1203485. Epub 2016 Jul 11.

19.

A genetic network that suppresses genome rearrangements in Saccharomyces cerevisiae and contains defects in cancers.

Putnam CD, Srivatsan A, Nene RV, Martinez SL, Clotfelter SP, Bell SN, Somach SB, de Souza JE, Fonseca AF, de Souza SJ, Kolodner RD.

Nat Commun. 2016 Apr 13;7:11256. doi: 10.1038/ncomms11256.

20.

Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data.

Kroll JE, Kim J, Ohno-Machado L, de Souza SJ.

PeerJ. 2015 Nov 19;3:e1419. doi: 10.7717/peerj.1419. eCollection 2015.

21.

Effect of temperature and humidity on post-gel shrinkage, cusp deformation, bond strength and shrinkage stress - Construction of a chamber to simulate the oral environment.

Bicalho AA, de Souza SJ, de Rosatto CM, Tantbirojn D, Versluis A, Soares CJ.

Dent Mater. 2015 Dec;31(12):1523-32. doi: 10.1016/j.dental.2015.09.023. Epub 2015 Oct 28.

PMID:
26518338
22.

Populational landscape of INDELs affecting transcription factor-binding sites in humans.

Ribeiro-dos-Santos AM, da Silva VL, de Souza JE, de Souza SJ.

BMC Genomics. 2015 Jul 22;16:536. doi: 10.1186/s12864-015-1744-5.

23.

A New Approach for Identification of Cancer-related Pathways using Protein Networks and Genomic Data.

Fonseca A, Gubitoso MD, Reis MS, de Souza SJ, Barrera J.

Cancer Inform. 2016 May 2;14(Suppl 5):139-49. doi: 10.4137/CIN.S30800. eCollection 2015.

24.

Identification of rare alternative splicing events in MS/MS data reveals a significant fraction of alternative translation initiation sites.

Kroll JE, de Souza SJ, de Souza GA.

PeerJ. 2014 Nov 13;2:e673. doi: 10.7717/peerj.673. eCollection 2014.

25.

S-score: a scoring system for the identification and prioritization of predicted cancer genes.

de Souza JE, Fonseca AF, Valieris R, Carraro DM, Wang JY, Kolodner RD, de Souza SJ.

PLoS One. 2014 Apr 7;9(4):e94147. doi: 10.1371/journal.pone.0094147. eCollection 2014.

26.

High-throughput sequencing of a South American Amerindian.

Ribeiro-dos-Santos AM, de Souza JE, Almeida R, Alencar DO, Barbosa MS, Gusmão L, Silva WA Jr, de Souza SJ, Silva A, Ribeiro-dos-Santos Â, Darnet S, Santos S.

PLoS One. 2013 Dec 30;8(12):e83340. doi: 10.1371/journal.pone.0083340. eCollection 2013.

27.

"Extended Fitness" hypothesis: a link between individual and group selection.

de Souza SJ.

Genet Mol Res. 2013 Oct 17;12(4):4625-9. doi: 10.4238/2013.October.17.5.

28.

The human cell surfaceome of breast tumors.

da Cunha JP, Galante PA, de Souza JE, Pieprzyk M, Carraro DM, Old LJ, Camargo AA, de Souza SJ.

Biomed Res Int. 2013;2013:976816. doi: 10.1155/2013/976816. Epub 2013 Sep 9.

29.

Testing for natural selection in human exonic splicing regulators associated with evolutionary rate shifts.

Ramalho RF, Gelfman S, de Souza JE, Ast G, de Souza SJ, Meyer D.

J Mol Evol. 2013 Apr;76(4):228-39. doi: 10.1007/s00239-013-9555-2. Epub 2013 Mar 26.

PMID:
23529588
30.

Modeling tumor evolutionary dynamics.

Stransky B, de Souza SJ.

Front Physiol. 2013 Feb 14;3:480. doi: 10.3389/fphys.2012.00480. eCollection 2012.

31.

SurfaceomeDB: a cancer-orientated database for genes encoding cell surface proteins.

de Souza JE, Galante PA, de Almeida RV, da Cunha JP, Ohara DT, Ohno-Machado L, Old LJ, de Souza SJ.

Cancer Immun. 2012;12:15. Epub 2012 Dec 28.

32.

Gene copy-number polymorphism caused by retrotransposition in humans.

Schrider DR, Navarro FC, Galante PA, Parmigiani RB, Camargo AA, Hahn MW, de Souza SJ.

PLoS Genet. 2013;9(1):e1003242. doi: 10.1371/journal.pgen.1003242. Epub 2013 Jan 24.

33.

SPLOOCE: a new portal for the analysis of human splicing variants.

Kroll JE, Galante PA, Ohara DT, Navarro FC, Ohno-Machado L, de Souza SJ.

RNA Biol. 2012 Nov;9(11):1339-43. doi: 10.4161/rna.22182. Epub 2012 Oct 12.

34.

Evolutionary history of exon shuffling.

França GS, Cancherini DV, de Souza SJ.

Genetica. 2012 Jun;140(4-6):249-57. Epub 2012 Sep 5.

PMID:
22948334
35.

Domain shuffling and the increasing complexity of biological networks.

de Souza SJ.

Bioessays. 2012 Aug;34(8):655-7. doi: 10.1002/bies.201200006. Epub 2012 Apr 23.

PMID:
22528879
36.

Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual.

Galante PA, Parmigiani RB, Zhao Q, Caballero OL, de Souza JE, Navarro FC, Gerber AL, Nicolás MF, Salim AC, Silva AP, Edsall L, Devalle S, Almeida LG, Ye Z, Kuan S, Pinheiro DG, Tojal I, Pedigoni RG, de Sousa RG, Oliveira TY, de Paula MG, Ohno-Machado L, Kirkness EF, Levy S, da Silva WA Jr, Vasconcelos AT, Ren B, Zago MA, Strausberg RL, Simpson AJ, de Souza SJ, Camargo AA.

Nucleic Acids Res. 2011 Aug;39(14):6056-68. doi: 10.1093/nar/gkr221. Epub 2011 Apr 14.

37.

Alternative splicing and genetic diversity: silencers are more frequently modified by SNVs associated with alternative exon/intron borders.

de Souza JE, Ramalho RF, Galante PA, Meyer D, de Souza SJ.

Nucleic Acids Res. 2011 Jul;39(12):4942-8. doi: 10.1093/nar/gkr081. Epub 2011 Mar 11.

38.

Analysis of allelic differential expression in the human genome using allele-specific serial analysis of gene expression tags.

Vidal DO, de Souza JE, Pires LC, Masotti C, Salim AC, Costa MC, Galante PA, de Souza SJ, Camargo AA.

Genome. 2011 Feb;54(2):120-7. doi: 10.1139/G10-103.

PMID:
21326368
39.

Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts.

Ferreira EN, Rangel MC, Galante PF, de Souza JE, Molina GC, de Souza SJ, Carraro DM.

BMC Genomics. 2010 Dec 22;11 Suppl 5:S4. doi: 10.1186/1471-2164-11-S5-S4.

40.

The role of exon shuffling in shaping protein-protein interaction networks.

Cancherini DV, França GS, de Souza SJ.

BMC Genomics. 2010 Dec 22;11 Suppl 5:S11. doi: 10.1186/1471-2164-11-S5-S11.

41.

Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing.

Zhao Q, Kirkness EF, Caballero OL, Galante PA, Parmigiani RB, Edsall L, Kuan S, Ye Z, Levy S, Vasconcelos AT, Ren B, de Souza SJ, Camargo AA, Simpson AJ, Strausberg RL.

Genome Biol. 2010;11(11):R114. doi: 10.1186/gb-2010-11-11-r114. Epub 2010 Nov 25.

42.

PVALB, a new Hürthle adenoma diagnostic marker identified through gene expression.

Cerutti JM, Oler G, Delcelo R, Gerardt R, Michaluart P Jr, de Souza SJ, Galante PA, Huang P, Riggins GJ.

J Clin Endocrinol Metab. 2011 Jan;96(1):E151-60. doi: 10.1210/jc.2010-1318. Epub 2010 Oct 6.

43.

Insights into gliomagenesis: systems biology unravels key pathways.

de Souza SJ, Stransky B, Camargo AA.

Genome Med. 2009 Oct 27;1(10):101. doi: 10.1186/gm101.

44.

Bioinformatics construction of the human cell surfaceome.

da Cunha JP, Galante PA, de Souza JE, de Souza RF, Carvalho PM, Ohara DT, Moura RP, Oba-Shinja SM, Marie SK, Silva WA Jr, Perez RO, Stransky B, Pieprzyk M, Moore J, Caballero O, Gama-Rodrigues J, Habr-Gama A, Kuo WP, Simpson AJ, Camargo AA, Old LJ, de Souza SJ.

Proc Natl Acad Sci U S A. 2009 Sep 29;106(39):16752-7. doi: 10.1073/pnas.0907939106. Epub 2009 Sep 15.

45.

Identification of FAM46D as a novel cancer/testis antigen using EST data and serological analysis.

Bettoni F, Filho FC, Grosso DM, Galante PA, Parmigiani RB, Geraldo MV, Henrique-Silva F, Oba-Shinjo SM, Marie SK, Soares FA, Brentani HP, Simpson AJ, de Souza SJ, Camargo AA.

Genomics. 2009 Sep;94(3):153-60. doi: 10.1016/j.ygeno.2009.06.001. Epub 2009 Jun 18.

46.

A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling.

Pinheiro DG, Galante PA, de Souza SJ, Zago MA, Silva WA Jr.

BMC Bioinformatics. 2009 Jun 6;10:170. doi: 10.1186/1471-2105-10-170.

47.

A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue: Identification of potential players in tumor formation.

Galante PA, Sandhu D, de Sousa Abreu R, Gradassi M, Slager N, Vogel C, de Souza SJ, Penalva LO.

RNA Biol. 2009 Sep-Oct;6(4):426-33. Epub 2009 Sep 24.

48.

Exploiting ESTs in human health.

de Souza SJ.

Methods Mol Biol. 2009;533:311-24. doi: 10.1007/978-1-60327-136-3_15.

PMID:
19277565
49.

Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line.

Zhao Q, Caballero OL, Levy S, Stevenson BJ, Iseli C, de Souza SJ, Galante PA, Busam D, Leversha MA, Chadalavada K, Rogers YH, Venter JC, Simpson AJ, Strausberg RL.

Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1886-91. doi: 10.1073/pnas.0812945106. Epub 2009 Jan 30.

50.

AMIN domains have a predicted role in localization of diverse periplasmic protein complexes.

de Souza RF, Anantharaman V, de Souza SJ, Aravind L, Gueiros-Filho FJ.

Bioinformatics. 2008 Nov 1;24(21):2423-6. doi: 10.1093/bioinformatics/btn449. Epub 2008 Aug 21.

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