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Items: 1 to 50 of 153

1.

An Unusual Case of Tricuspid Stenosis.

Ferreira S, Barbosa A, Gomes F, Almeida J, Almeida JS, Amorim MJ, Araújo JP.

Eur J Case Rep Intern Med. 2018 Apr 24;5(4):000836. doi: 10.12890/2018_000836. eCollection 2018.

2.

Serverless OpenHealth at data commons scale-traversing the 20 million patient records of New York's SPARCS dataset in real-time.

Almeida JS, Hajagos J, Saltz J, Saltz M.

PeerJ. 2019 Jan 15;7:e6230. doi: 10.7717/peerj.6230. eCollection 2019.

3.

Enabling precision medicine via standard communication of HTS provenance, analysis, and results.

Alterovitz G, Dean D, Goble C, Crusoe MR, Soiland-Reyes S, Bell A, Hayes A, Suresh A, Purkayastha A, King CH, Taylor D, Johanson E, Thompson EE, Donaldson E, Morizono H, Tsang H, Vora JK, Goecks J, Yao J, Almeida JS, Keeney J, Addepalli K, Krampis K, Smith KM, Guo L, Walderhaug M, Schito M, Ezewudo M, Guimera N, Walsh P, Kahsay R, Gottipati S, Rodwell TC, Bloom T, Lai Y, Simonyan V, Mazumder R.

PLoS Biol. 2018 Dec 31;16(12):e3000099. doi: 10.1371/journal.pbio.3000099. eCollection 2018 Dec.

4.

Effect of Age on NK Cell Compartment in Chronic Myeloid Leukemia Patients Treated With Tyrosine Kinase Inhibitors.

Rodrigues-Santos P, López-Sejas N, Almeida JS, Ruzičková L, Couceiro P, Alves V, Campos C, Alonso C, Tarazona R, Freitas-Tavares P, Solana R, Santos-Rosa M.

Front Immunol. 2018 Nov 8;9:2587. doi: 10.3389/fimmu.2018.02587. eCollection 2018.

5.

Molecular Modeling and In Vitro Studies of a Neutral Oxime as a Potential Reactivator for Acetylcholinesterase Inhibited by Paraoxon.

de Paula RL, de Almeida JSFD, Cavalcante SFA, Gonçalves AS, Simas ABC, Franca TCC, Valis M, Kuca K, Nepovimova E, Granjeiro JM.

Molecules. 2018 Nov 12;23(11). pii: E2954. doi: 10.3390/molecules23112954.

6.

Aquatic macrophytes and trophic interactions: a scientometric analyses and research perspectives.

Rocha CMC, Lima D, Cunha MCC, Almeida JS.

Braz J Biol. 2018 Oct 29. pii: S1519-69842018005029102. doi: 10.1590/1519-6984.185505. [Epub ahead of print]

7.

Multivariate optimization of ultrasound-assisted extraction using Doehlert matrix for simultaneous determination of Fe and Ni in vegetable oils by high-resolution continuum source graphite furnace atomic absorption spectrometry.

Almeida JS, Santos GL, Brandão GC, Korn MGA, Teixeira LSG.

Food Chem. 2019 Feb 1;273:130-135. doi: 10.1016/j.foodchem.2018.01.112. Epub 2018 Feb 3.

PMID:
30292358
8.

Molecular Modeling Studies on the Interactions of Aflatoxin B1 and Its Metabolites with Human Acetylcholinesterase. Part II: Interactions with the Catalytic Anionic Site (CAS).

de Almeida JSFD, Dolezal R, Krejcar O, Kuca K, Musilek K, Jun D, França TCC.

Toxins (Basel). 2018 Sep 25;10(10). pii: E389. doi: 10.3390/toxins10100389.

9.

Kinomics toolbox-A web platform for analysis and viewing of kinomic peptide array data.

Dussaq AM, Kennell T Jr, Eustace NJ, Anderson JC, Almeida JS, Willey CD.

PLoS One. 2018 Aug 21;13(8):e0202139. doi: 10.1371/journal.pone.0202139. eCollection 2018.

10.

A New Approach to Diagnose Parkinson's Disease Using a Structural Cooccurrence Matrix for a Similarity Analysis.

de Souza JWM, Alves SSA, Rebouças ES, Almeida JS, Rebouças Filho PP.

Comput Intell Neurosci. 2018 Apr 24;2018:7613282. doi: 10.1155/2018/7613282. eCollection 2018.

11.

Treatment of dental biofilm with a tincture of Bauhinia forficata leaves: an ex-vivo study.

Ferreira-Filho JCC, Marre ATO, Almeida JSS, Lobo LA, Farah A, Valença AMG, Fonseca-Gonçalves A.

Nat Prod Res. 2018 May 21:1-4. doi: 10.1080/14786419.2018.1477146. [Epub ahead of print]

PMID:
29781298
12.

Molecular modeling studies on the interactions of aflatoxin B1 and its metabolites with the peripheral anionic site of human acetylcholinesterase.

de Almeida JSFD, Cavalcante SFA, Dolezal R, Kuca K, Musilek K, Jun D, França TCC.

J Biomol Struct Dyn. 2018 Nov 2:1-8. doi: 10.1080/07391102.2018.1475259. [Epub ahead of print]

PMID:
29749305
13.

Rational Design of a New Class of Toll-Like Receptor 4 (TLR4) Tryptamine Related Agonists by Means of the Structure- and Ligand-Based Virtual Screening for Vaccine Adjuvant Discovery.

Honegr J, Dolezal R, Malinak D, Benkova M, Soukup O, Almeida JSFD, Franca TCC, Kuca K, Prymula R.

Molecules. 2018 Jan 4;23(1). pii: E102. doi: 10.3390/molecules23010102.

14.

A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images.

Saltz J, Sharma A, Iyer G, Bremer E, Wang F, Jasniewski A, DiPrima T, Almeida JS, Gao Y, Zhao T, Saltz M, Kurc T.

Cancer Res. 2017 Nov 1;77(21):e79-e82. doi: 10.1158/0008-5472.CAN-17-0316.

15.

Inactivation of MarR gene homologs increases susceptibility to antimicrobials in Bacteroides fragilis.

Silva CMG, Silva DNDS, Costa SBD, Almeida JSS, Boente RF, Teixeira FL, Domingues RMCP, Lobo LA.

Braz J Microbiol. 2018 Jan - Mar;49(1):200-206. doi: 10.1016/j.bjm.2017.05.005. Epub 2017 Aug 9.

16.

Dipeptidyl peptidase-4 levels are increased and partially related to body fat distribution in patients with familial partial lipodystrophy type 2.

Valerio CM, de Almeida JS, Moreira RO, Aguiar LBS, Siciliano PO, Carvalho DP, Godoy-Matos AF.

Diabetol Metab Syndr. 2017 Apr 24;9:26. doi: 10.1186/s13098-017-0226-0. eCollection 2017.

17.

Safe "cloudification" of large images through picker APIs.

Bremer E, Kurc T, Gao Y, Saltz J, Almeida JS.

AMIA Annu Symp Proc. 2017 Feb 10;2016:342-351. eCollection 2016.

18.

Differential Gene Expression in Ductal Carcinoma In Situ of the Breast Based on ERBB2 Status.

Agosto-Arroyo E, Isayeva T, Wei S, Almeida JS, Harada S.

Cancer Control. 2017 Jan;24(1):102-110.

PMID:
28178722
19.

Isomorphic semantic mapping of variant call format (VCF2RDF).

Penha ED, Iriabho E, Dussaq A, de Oliveira DM, Almeida JS.

Bioinformatics. 2017 Feb 15;33(4):547-548. doi: 10.1093/bioinformatics/btw652.

20.

Mechanistic Parameterization of the Kinomic Signal in Peptide Arrays.

Dussaq A, Anderson JC, Willey CD, Almeida JS.

J Proteomics Bioinform. 2016 May;9(5):151-157. Epub 2016 May 24.

21.

Comparison of Two Types of Insoles on Musculoskeletal Symptoms and Plantar Pressure Distribution in a Work Environment: A Randomized Clinical Trial.

Almeida JS, Vanderlei FM, Pastre EC, Martins RA, Padovani CR, Filho GC.

Clin Med Res. 2016 Jun;14(2):67-74. doi: 10.3121/cmr.2016.1301. Epub 2016 May 26.

22.

Docking and molecular dynamics studies of peripheral site ligand-oximes as reactivators of sarin-inhibited human acetylcholinesterase.

de Almeida JS, Cuya Guizado TR, Guimarães AP, Ramalho TC, Gonçalves AS, de Koning MC, França TC.

J Biomol Struct Dyn. 2016 Dec;34(12):2632-2642. Epub 2016 May 9.

PMID:
26612005
23.

Computational Pathology: A Path Ahead.

Louis DN, Feldman M, Carter AB, Dighe AS, Pfeifer JD, Bry L, Almeida JS, Saltz J, Braun J, Tomaszewski JE, Gilbertson JR, Sinard JH, Gerber GK, Galli SJ, Golden JA, Becich MJ.

Arch Pathol Lab Med. 2016 Jan;140(1):41-50. doi: 10.5858/arpa.2015-0093-SA. Epub 2015 Jun 22.

24.

Proteomic Analysis of Plasma from California Sea Lions (Zalophus californianus) Reveals Apolipoprotein E as a Candidate Biomarker of Chronic Domoic Acid Toxicosis.

Neely BA, Ferrante JA, Chaves JM, Soper JL, Almeida JS, Arthur JM, Gulland FM, Janech MG.

PLoS One. 2015 Apr 28;10(4):e0123295. doi: 10.1371/journal.pone.0123295. eCollection 2014.

25.

Coming into focus: computational pathology as the new big data microscope.

Roth KA, Almeida JS.

Am J Pathol. 2015 Mar;185(3):600-1. doi: 10.1016/j.ajpath.2015.01.002.

PMID:
25701882
26.

Development of novel software to generate anthropometric norms at perinatal autopsy.

Cain MD, Siebert JR, Iriabho E, Gruneberg A, Almeida JS, Faye-Petersen OM.

Pediatr Dev Pathol. 2015 May-Jun;18(3):203-9. doi: 10.2350/14-11-1578-OA.1. Epub 2015 Jan 29.

PMID:
25634794
27.

A unique sex chromosome system in the knifefish Gymnotus bahianus with inferences about chromosomal evolution of Gymnotidae.

Almeida JS, Migues VH, Diniz D, Affonso PR.

J Hered. 2015 Mar-Apr;106(2):177-83. doi: 10.1093/jhered/esu087. Epub 2015 Jan 16.

PMID:
25596613
28.

OpenHealth Platform for Interactive Contextualization of Population Health Open Data.

Almeida JS, Hajagos J, Crnosija I, Kurc T, Saltz M, Saltz J.

AMIA Annu Symp Proc. 2015 Nov 5;2015:297-305. eCollection 2015.

29.

Sequential steps of chromosomal differentiation in Atlantic surgeonfishes: evolutionary inferences.

Affonso PR, Fernandes MA, Almeida JS, Molina WF.

ScientificWorldJournal. 2014;2014:825703. doi: 10.1155/2014/825703. Epub 2014 Aug 12.

30.

QMachine: commodity supercomputing in web browsers.

Wilkinson SR, Almeida JS.

BMC Bioinformatics. 2014 Jun 9;15:176. doi: 10.1186/1471-2105-15-176.

31.

A novel green approach for the preparation of cellulose nanowhiskers from white coir.

Nascimento DM, Almeida JS, Dias AF, Figueirêdo MC, Morais JP, Feitosa JP, de F Rosa M.

Carbohydr Polym. 2014 Sep 22;110:456-63. doi: 10.1016/j.carbpol.2014.04.053. Epub 2014 Apr 24.

PMID:
24906779
32.

Mining genome sequencing data to identify the genomic features linked to breast cancer histopathology.

Ping Z, Siegal GP, Almeida JS, Schnitt SJ, Shen D.

J Pathol Inform. 2014 Jan 31;5(1):3. doi: 10.4103/2153-3539.126147. eCollection 2014.

33.

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.

Cole C, Krampis K, Karagiannis K, Almeida JS, Faison WJ, Motwani M, Wan Q, Golikov A, Pan Y, Simonyan V, Mazumder R.

BMC Bioinformatics. 2014 Jan 27;15:28. doi: 10.1186/1471-2105-15-28.

34.

TopFed: TCGA tailored federated query processing and linking to LOD.

Saleem M, Padmanabhuni SS, Ngomo AC, Iqbal A, Almeida JS, Decker S, Deus HF.

J Biomed Semantics. 2014 Dec 3;5:47. doi: 10.1186/2041-1480-5-47. eCollection 2014.

35.

The use of 185 MBq and 740 MBq of 153-samarium hydroxyapatite for knee synovectomy in haemophilia.

Calegaro JU, Machado J, Furtado RG, de Almeida JS, de Vasconcelos AV, de Barboza MF, de Paula AP.

Haemophilia. 2014 May;20(3):421-5. doi: 10.1111/hae.12319. Epub 2013 Dec 16.

36.

Sequence analysis by iterated maps, a review.

Almeida JS.

Brief Bioinform. 2014 May;15(3):369-75. doi: 10.1093/bib/bbt072. Epub 2013 Oct 25. Review.

37.

Chromosomal variation in the tropical armoured catfish Callichthys callichthys (Siluriformes, Callichthyidae): implications for conservation and taxonomy in a species complex from a Brazilian hotspot.

Almeida JS, Affonso PR, Diniz D, Carneiro PL, Dias AL.

Zebrafish. 2013 Dec;10(4):451-8. doi: 10.1089/zeb.2013.0885. Epub 2013 Oct 1.

PMID:
24083504
38.

Machine learning to predict extubation outcome in premature infants.

Mueller M, Wagner CC, Stanislaus R, Almeida JS.

Proc Int Jt Conf Neural Netw. 2013 Aug;2013:1-6.

39.

Myeloid-derived suppressor cells and associated events in urethane-induced lung cancer.

Teixeira D, Almeida JS, Visniauskas B, Gomes GN, Hirata AE, Bueno V.

Clinics (Sao Paulo). 2013 Jun;68(6):858-64. doi: 10.6061/clinics/2013(06)22.

40.

A self-updating road map of The Cancer Genome Atlas.

Robbins DE, Grüneberg A, Deus HF, Tanik MM, Almeida JS.

Bioinformatics. 2013 May 15;29(10):1333-40. doi: 10.1093/bioinformatics/btt141. Epub 2013 Apr 17.

41.

Identification of prognostic gene signatures of glioblastoma: a study based on TCGA data analysis.

Kim YW, Koul D, Kim SH, Lucio-Eterovic AK, Freire PR, Yao J, Wang J, Almeida JS, Aldape K, Yung WK.

Neuro Oncol. 2013 Jul;15(7):829-39. doi: 10.1093/neuonc/not024. Epub 2013 Mar 15.

42.

Can Machine Learning Methods Predict Extubation Outcome in Premature Infants as well as Clinicians?

Mueller M, Almeida JS, Stanislaus R, Wagner CL.

J Neonatal Biol. 2013;2. pii: 1000118.

43.

Remarkable karyotypic homogeneity in a widespread tropical fish species: Hoplosternum littorale (Siluriformes, Callichthyidae).

Almeida JS, Affonso PR, Dias AL.

J Fish Biol. 2012 Sep;81(4):1415-21. doi: 10.1111/j.1095-8649.2012.03387.x. Epub 2012 Aug 3.

PMID:
22957879
44.

ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser.

Almeida JS, Iriabho EE, Gorrepati VL, Wilkinson SR, Grüneberg A, Robbins DE, Hackney JR.

J Pathol Inform. 2012;3:25. doi: 10.4103/2153-3539.98813. Epub 2012 Jul 20.

45.

Ingestive behavior of pastured crossbred dairy cows offered different supplement types.

Mendes AM, Silva DK, Ferreira Mde A, Veras AS, Ferreira GD, Vigoderis RB, Arcanjo HG, Silva JM Jr, de Almeida JS, Fotius AC, Farias Gde A.

Trop Anim Health Prod. 2013 Jan;45(1):231-7. doi: 10.1007/s11250-012-0195-0. Epub 2012 Jun 8.

PMID:
22678494
46.

Fractal MapReduce decomposition of sequence alignment.

Almeida JS, Grüneberg A, Maass W, Vinga S.

Algorithms Mol Biol. 2012 May 2;7(1):12. doi: 10.1186/1748-7188-7-12.

47.

Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis.

Vinga S, Carvalho AM, Francisco AP, Russo LM, Almeida JS.

Algorithms Mol Biol. 2012 May 2;7(1):10. doi: 10.1186/1748-7188-7-10.

48.

Serum profiling by MALDI-TOF mass spectrometry as a diagnostic tool for domoic acid toxicosis in California sea lions.

Neely BA, Soper JL, Greig DJ, Carlin KP, Favre EG, Gulland FM, Almeida JS, Janech MG.

Proteome Sci. 2012 Mar 19;10(1):18. doi: 10.1186/1477-5956-10-18.

49.

Premature atherosclerosis is associated with hypovitaminosis D and angiotensin-converting enzyme inhibitor non-use in lupus patients.

Ravenell RL, Kamen DL, Spence JD, Hollis BW, Fleury TJ, Janech MG, Almeida JS, Shaftman SR, Oates JC.

Am J Med Sci. 2012 Oct;344(4):268-73.

50.

Hydrogels containing rutin intended for cutaneous administration: efficacy in wound healing in rats.

Almeida JS, Benvegnú DM, Boufleur N, Reckziegel P, Barcelos RC, Coradini K, de Carvalho LM, Bürger ME, Beck RC.

Drug Dev Ind Pharm. 2012 Jul;38(7):792-9. doi: 10.3109/03639045.2011.628676. Epub 2011 Nov 8.

PMID:
22066462

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