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Items: 1 to 50 of 178

1.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Björne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Šmuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O'Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I.

Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8.

2.

Ground and excited state properties of furanoflavylium derivatives.

Alejo-Armijo A, Basílio N, Freitas AA, Maçanita AL, Lima JC, Parola AJ, Pina F.

Phys Chem Chem Phys. 2019 Oct 14;21(38):21651-21662. doi: 10.1039/c9cp04917g. Epub 2019 Sep 24.

PMID:
31549705
3.

Draft Genome Sequence of Multidrug-Resistant Enterococcus faecium Strain E1298, with a Sequence Type 1274 Profile, Recovered from the Cloacal Microbiome of a Tropical Screech Owl (Megascops choliba) in Rio de Janeiro, Brazil.

Freitas AAR, Souza SSR, Faria AR, Planet PJ, Merquior VLC, Teixeira LM.

Microbiol Resour Announc. 2019 Apr 18;8(16). pii: e00168-19. doi: 10.1128/MRA.00168-19.

4.

Comparing enrichment analysis and machine learning for identifying gene properties that discriminate between gene classes.

Fabris F, Palmer D, de Magalhães JP, Freitas AA.

Brief Bioinform. 2019 Mar 20. pii: bbz028. doi: 10.1093/bib/bbz028. [Epub ahead of print]

PMID:
30895300
5.

Investigating the role of Simpson's paradox in the analysis of top-ranked features in high-dimensional bioinformatics datasets.

Freitas AA.

Brief Bioinform. 2019 Jan 9. doi: 10.1093/bib/bby126. [Epub ahead of print]

PMID:
30629111
6.

Structure and dynamics of mica-confined films of [C10C1Pyrr][NTf2] ionic liquid.

Freitas AA, Shimizu K, Smith AM, Perkin S, Canongia Lopes JN.

J Chem Phys. 2018 May 21;148(19):193808. doi: 10.1063/1.5007809.

PMID:
30307208
7.

High-Level Multidrug-Resistant Escherichia coli Isolates from Wild Birds in a Large Urban Environment.

Batalha de Jesus AA, Freitas AAR, de Souza JC, Martins N, Botelho LAB, Girão VBC, Teixeira LM, Riley LW, Moreira BM.

Microb Drug Resist. 2019 Mar;25(2):167-172. doi: 10.1089/mdr.2018.0180. Epub 2018 Sep 19.

PMID:
30234422
8.

Triplet Excited States and Singlet Oxygen Production by Analogs of Red Wine Pyranoanthocyanins.

Silva GTM, Thomas SS, Silva CP, Schlothauer JC, Baptista MS, Freitas AA, Bohne C, Quina FH.

Photochem Photobiol. 2019 Jan;95(1):176-182. doi: 10.1111/php.12973. Epub 2018 Aug 2.

PMID:
29978920
9.

Designing the ammonium cation to achieve a higher hydrophilicity of bistriflimide-based ionic liquids.

de Ferro AM, Reis PM, Soromenho MRC, Bernardes CES, Shimizu K, Freitas AA, Esperança JMSS, Canongia Lopes JN, Rebelo LPN.

Phys Chem Chem Phys. 2018 Jul 25;20(29):19307-19313. doi: 10.1039/c8cp03398f.

PMID:
29900442
10.

In situ T regulatory cells and Th17 cytokines in paired samples of leprosy type 1 and type 2 reactions.

Costa MB, Hungria EM, Freitas AA, Sousa ALOM, Jampietro J, Soares FA, Stefani MMA.

PLoS One. 2018 Jun 8;13(6):e0196853. doi: 10.1371/journal.pone.0196853. eCollection 2018.

11.

Ground- and Excited-State Acidity of Analogs of Red Wine Pyranoanthocyanins.

Freitas AA, Silva CP, Silva GTM, Maçanita AL, Quina FH.

Photochem Photobiol. 2018 Nov;94(6):1086-1091. doi: 10.1111/php.12944. Epub 2018 Jun 22.

PMID:
29806973
12.

Mast cell heterogeneity and anti-inflammatory annexin A1 expression in leprosy skin lesions.

Costa MB, Mimura KKO, Freitas AA, Hungria EM, Sousa ALOM, Oliani SM, Stefani MMA.

Microb Pathog. 2018 May;118:277-284. doi: 10.1016/j.micpath.2018.03.050. Epub 2018 Mar 29.

PMID:
29605649
13.

Warfarin Safety: A Cross-Sectional Study of the Factors Associated with the Consumption of Medicinal Plants in a Brazilian Anticoagulation Clinic.

Leite PM, de Freitas AA, Mourão AOM, Martins MAP, Castilho RO.

Am J Cardiovasc Drugs. 2018 Jun;18(3):231-243. doi: 10.1007/s40256-018-0268-1.

PMID:
29476459
14.

A new approach for interpreting Random Forest models and its application to the biology of ageing.

Fabris F, Doherty A, Palmer D, de Magalhães JP, Freitas AA.

Bioinformatics. 2018 Jul 15;34(14):2449-2456. doi: 10.1093/bioinformatics/bty087.

15.

Distribution of species and antimicrobial resistance among enterococci isolated from the fecal microbiota of captive blue-fronted parrot (Amazona aestiva) in Rio de Janeiro, Brazil.

Freitas AAR, Faria AR, Pinto TCA, Merquior VLC, Neves DM, Costa RCD, Teixeira LM.

Sci Total Environ. 2018 Feb 15;615:1428-1437. doi: 10.1016/j.scitotenv.2017.09.004. Epub 2017 Oct 19.

PMID:
29055593
16.

A rapid simultaneous determination of methylxanthines and proanthocyanidins in Brazilian guaraná (Paullinia cupana Kunth.).

Machado KN, Freitas AA, Cunha LH, Faraco AAG, Pádua RM, Braga FC, Vianna-Soares CD, Castilho RO.

Food Chem. 2018 Jan 15;239:180-188. doi: 10.1016/j.foodchem.2017.06.089. Epub 2017 Jun 16.

17.

Machine learning for predicting lifespan-extending chemical compounds.

Barardo DG, Newby D, Thornton D, Ghafourian T, de Magalhães JP, Freitas AA.

Aging (Albany NY). 2017 Jul 18;9(7):1721-1737. doi: 10.18632/aging.101264.

18.

Assessment of the accuracy of a new tool for the screening of smartphone addiction.

Khoury JM, de Freitas AAC, Roque MAV, Albuquerque MR, das Neves MCL, Garcia FD.

PLoS One. 2017 May 17;12(5):e0176924. doi: 10.1371/journal.pone.0176924. eCollection 2017.

19.

The S(c)ensory Immune System Theory.

Veiga-Fernandes H, Freitas AA.

Trends Immunol. 2017 Oct;38(10):777-788. doi: 10.1016/j.it.2017.02.007. Epub 2017 Mar 7. Review.

PMID:
28283352
20.

A review of supervised machine learning applied to ageing research.

Fabris F, Magalhães JP, Freitas AA.

Biogerontology. 2017 Apr;18(2):171-188. doi: 10.1007/s10522-017-9683-y. Epub 2017 Mar 6. Review.

21.

Antigen-specific secretion of IFNγ and CXCL10 in whole blood assay detects Mycobacterium leprae infection but does not discriminate asymptomatic infection from symptomatic leprosy.

Hungria EM, Freitas AA, Pontes MA, Gonçalves HS, Sousa AL, Costa MB, Castilho ML, Duthie MS, Stefani MM.

Diagn Microbiol Infect Dis. 2017 Apr;87(4):328-334. doi: 10.1016/j.diagmicrobio.2017.01.002. Epub 2017 Jan 5.

PMID:
28126361
22.

Regulation and Maintenance of an Adoptive T-Cell Dependent Memory B Cell Pool.

Anson M, Amado I, Mailhé MP, Donnadieu E, Garcia S, Huetz F, Freitas AA.

PLoS One. 2016 Nov 23;11(11):e0167003. doi: 10.1371/journal.pone.0167003. eCollection 2016.

23.

Simultaneous Prediction of four ATP-binding Cassette Transporters' Substrates Using Multi-label QSAR.

Aniceto N, Freitas AA, Bender A, Ghafourian T.

Mol Inform. 2016 Oct;35(10):514-528. doi: 10.1002/minf.201600036.

PMID:
27582431
24.

Application of Mycobacterium Leprae-specific cellular and serological tests for the differential diagnosis of leprosy from confounding dermatoses.

Freitas AA, Hungria EM, Costa MB, Sousa AL, Castilho ML, Gonçalves HS, Pontes MA, Duthie MS, Stefani MM.

Diagn Microbiol Infect Dis. 2016 Oct;86(2):163-8. doi: 10.1016/j.diagmicrobio.2016.07.024. Epub 2016 Jul 27.

PMID:
27506457
25.

IFN-gamma role in granuloma formation in experimental subcutaneous cysticercosis.

Freitas AA, Moura VB, Irusta VR, Vinaud MC, Oliveira MA, Lino-Júnior RS.

Exp Parasitol. 2016 Sep;168:1-8. doi: 10.1016/j.exppara.2016.06.004. Epub 2016 Jun 19.

PMID:
27334396
26.

New KEGG pathway-based interpretable features for classifying ageing-related mouse proteins.

Fabris F, Freitas AA.

Bioinformatics. 2016 Oct 1;32(19):2988-95. doi: 10.1093/bioinformatics/btw363. Epub 2016 Jun 17.

PMID:
27318209
27.

IL-15-dependent balance between Foxp3 and RORγt expression impacts inflammatory bowel disease.

Tosiek MJ, Fiette L, El Daker S, Eberl G, Freitas AA.

Nat Commun. 2016 Mar 11;7:10888. doi: 10.1038/ncomms10888.

28.

Extracting kinetic information from literature with KineticRE.

Freitas AA, Costa H, Rocha M, Rocha I.

J Integr Bioinform. 2015 Nov 3;12(4):282. doi: 10.2390/biecoll-jib-2015-282.

PMID:
26673933
29.

An Extensive Empirical Comparison of Probabilistic Hierarchical Classifiers in Datasets of Ageing-Related Genes.

Fabris F, Freitas AA, Tullet JM.

IEEE/ACM Trans Comput Biol Bioinform. 2016 Nov-Dec;13(6):1045-1058. doi: 10.1109/TCBB.2015.2505288. Epub 2015 Dec 3.

PMID:
26661786
30.

Multibacillary leprosy patients with high and persistent serum antibodies to leprosy IDRI diagnostic-1/LID-1: higher susceptibility to develop type 2 reactions.

Mizoguti Dde F, Hungria EM, Freitas AA, Oliveira RM, Cardoso LP, Costa MB, Sousa AL, Duthie MS, Stefani MM.

Mem Inst Oswaldo Cruz. 2015 Nov;110(7):914-20. doi: 10.1590/0074-02760150198.

31.

Predicting the Pro-Longevity or Anti-Longevity Effect of Model Organism Genes with New Hierarchical Feature Selection Methods.

Wan C, Freitas AA, de Magalhães JP.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Mar-Apr;12(2):262-75. doi: 10.1109/TCBB.2014.2355218.

PMID:
26357215
32.

Structural and aggregate analyses of (Li salt + glyme) mixtures: the complex nature of solvate ionic liquids.

Shimizu K, Freitas AA, Atkin R, Warr GG, FitzGerald PA, Doi H, Saito S, Ueno K, Umebayashi Y, Watanabe M, Canongia Lopes JN.

Phys Chem Chem Phys. 2015 Sep 14;17(34):22321-35. doi: 10.1039/c5cp03414k. Epub 2015 Aug 6.

PMID:
26245295
33.

Alterations to antigen-specific immune responses before and after multidrug therapy of leprosy.

Freitas AA, Oliveira RM, Hungria EM, Cardoso LP, Sousa AL, Costa MB, Reed SG, Duthie MS, Stefani MM.

Diagn Microbiol Infect Dis. 2015 Oct;83(2):154-61. doi: 10.1016/j.diagmicrobio.2015.06.021. Epub 2015 Jul 2.

PMID:
26233487
34.

From lime to silica and alumina: systematic modeling of cement clinkers using a general force-field.

Freitas AA, Santos RL, Colaço R, Bayão Horta R, Canongia Lopes JN.

Phys Chem Chem Phys. 2015 Jul 28;17(28):18477-94. doi: 10.1039/c5cp02823j.

PMID:
26109081
35.

Improving the Interpretability of Classification Rules Discovered by an Ant Colony Algorithm: Extended Results.

Otero FE, Freitas AA.

Evol Comput. 2016 Fall;24(3):385-409. doi: 10.1162/EVCO_a_00155. Epub 2015 Jun 12.

PMID:
26066807
36.

Predicting volume of distribution with decision tree-based regression methods using predicted tissue:plasma partition coefficients.

Freitas AA, Limbu K, Ghafourian T.

J Cheminform. 2015 Feb 26;7:6. doi: 10.1186/s13321-015-0054-x. eCollection 2015.

37.

Decision trees to characterise the roles of permeability and solubility on the prediction of oral absorption.

Newby D, Freitas AA, Ghafourian T.

Eur J Med Chem. 2015 Jan 27;90:751-65. doi: 10.1016/j.ejmech.2014.12.006. Epub 2014 Dec 4.

PMID:
25528330
38.

Comparing multilabel classification methods for provisional biopharmaceutics class prediction.

Newby D, Freitas AA, Ghafourian T.

Mol Pharm. 2015 Jan 5;12(1):87-102. doi: 10.1021/mp500457t. Epub 2014 Dec 1.

PMID:
25397721
39.

microRNA-mediated regulation of mTOR complex components facilitates discrimination between activation and anergy in CD4 T cells.

Marcais A, Blevins R, Graumann J, Feytout A, Dharmalingam G, Carroll T, Amado IF, Bruno L, Lee K, Walzer T, Mann M, Freitas AA, Boothby M, Fisher AG, Merkenschlager M.

J Exp Med. 2014 Oct 20;211(11):2281-95. doi: 10.1084/jem.20132059. Epub 2014 Oct 13.

40.

Human hematopoietic reconstitution and HLA-restricted responses in nonpermissive alymphoid mice.

Serra-Hassoun M, Bourgine M, Boniotto M, Berges J, Langa F, Michel ML, Freitas AA, Garcia S.

J Immunol. 2014 Aug 1;193(3):1504-11. doi: 10.4049/jimmunol.1400412. Epub 2014 Jun 27.

41.

Femtosecond and temperature-dependent picosecond dynamics of ultrafast excited-state proton transfer in water-dioxane mixtures.

Freitas AA, Quina FH, Maçanita AA.

J Phys Chem A. 2014 Nov 13;118(45):10448-55. doi: 10.1021/jp504189m. Epub 2014 Jun 13.

PMID:
24925753
42.

A mathematical perspective on CD4(+) T cell quorum-sensing.

Reynolds J, Amado IF, Freitas AA, Lythe G, Molina-París C.

J Theor Biol. 2014 Apr 21;347:160-75. doi: 10.1016/j.jtbi.2013.12.019. Epub 2013 Dec 31.

PMID:
24389364
43.

IL-2 coordinates IL-2-producing and regulatory T cell interplay.

Amado IF, Berges J, Luther RJ, Mailhé MP, Garcia S, Bandeira A, Weaver C, Liston A, Freitas AA.

J Exp Med. 2013 Nov 18;210(12):2707-20. doi: 10.1084/jem.20122759.

44.

Development of a quantitative rapid diagnostic test for multibacillary leprosy using smart phone technology.

Paula Vaz Cardoso L, Dias RF, Freitas AA, Hungria EM, Oliveira RM, Collovati M, Reed SG, Duthie MS, Martins Araújo Stefani M.

BMC Infect Dis. 2013 Oct 23;13:497. doi: 10.1186/1471-2334-13-497.

45.

Pre-processing feature selection for improved C&RT models for oral absorption.

Newby D, Freitas AA, Ghafourian T.

J Chem Inf Model. 2013 Oct 28;53(10):2730-42. doi: 10.1021/ci400378j. Epub 2013 Oct 9.

PMID:
24050619
46.

Origin, trafficking, and intraepithelial fate of gut-tropic T cells.

Guy-Grand D, Vassalli P, Eberl G, Pereira P, Burlen-Defranoux O, Lemaitre F, Di Santo JP, Freitas AA, Cumano A, Bandeira A.

J Exp Med. 2013 Aug 26;210(9):1839-54. doi: 10.1084/jem.20122588. Epub 2013 Aug 5. Erratum in: J Exp Med. 2013 Oct 21;210(11):2493.

47.

Antiapoptotic Mcl-1 is critical for the survival and niche-filling capacity of Foxp3⁺ regulatory T cells.

Pierson W, Cauwe B, Policheni A, Schlenner SM, Franckaert D, Berges J, Humblet-Baron S, Schönefeldt S, Herold MJ, Hildeman D, Strasser A, Bouillet P, Lu LF, Matthys P, Freitas AA, Luther RJ, Weaver CT, Dooley J, Gray DH, Liston A.

Nat Immunol. 2013 Sep;14(9):959-65. doi: 10.1038/ni.2649. Epub 2013 Jul 14.

48.

Improved analysis of excited state proton transfer kinetics by the combination of standard and convolution methods.

Freitas AA, Maçanita AA, Quina FH.

Photochem Photobiol Sci. 2013 May;12(5):902-10. doi: 10.1039/c3pp25445c.

PMID:
23471212
49.

Automatic design of decision-tree algorithms with evolutionary algorithms.

Barros RC, Basgalupp MP, de Carvalho AC, Freitas AA.

Evol Comput. 2013 Winter;21(4):659-84. doi: 10.1162/EVCO_a_00101. Epub 2013 Aug 8.

PMID:
23339552
50.

Coping with unbalanced class data sets in oral absorption models.

Newby D, Freitas AA, Ghafourian T.

J Chem Inf Model. 2013 Feb 25;53(2):461-74. doi: 10.1021/ci300348u. Epub 2013 Jan 24.

PMID:
23293925

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