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Results: 1 to 20 of 57


QMachine: commodity supercomputing in web browsers.

Wilkinson SR, Almeida JS.

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


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;5:3. doi: 10.4103/2153-3539.126147. eCollection 2014.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


S3QL: a distributed domain specific language for controlled semantic integration of life sciences data.

Deus HF, Correa MC, Stanislaus R, Miragaia M, Maass W, de Lencastre H, Fox R, Almeida JS.

BMC Bioinformatics. 2011 Jul 14;12:285. doi: 10.1186/1471-2105-12-285.


AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services.

Correa MC, Deus HF, Vasconcelos AT, Hayashi Y, Ajani JA, Patnana SV, Almeida JS.

BMC Med Inform Decis Mak. 2010 Oct 26;10:65. doi: 10.1186/1472-6947-10-65.


A nonparametric approach to detect nonlinear correlation in gene expression.

Chen YA, Almeida JS, Richards AJ, Müller P, Carroll RJ, Rohrer B.

J Comput Graph Stat. 2010 Sep 1;19(3):552-568.


Computational ecosystems for data-driven medical genomics.

Almeida JS.

Genome Med. 2010 Sep 20;2(9):67. doi: 10.1186/gm188.


Exposing the cancer genome atlas as a SPARQL endpoint.

Deus HF, Veiga DF, Freire PR, Weinstein JN, Mills GB, Almeida JS.

J Biomed Inform. 2010 Dec;43(6):998-1008. doi: 10.1016/j.jbi.2010.09.004.


Examining the effect of maternal obesity on outcome of labor induction in patients with preeclampsia.

Robinson CJ, Hill EG, Alanis MC, Chang EY, Johnson DD, Almeida JS.

Hypertens Pregnancy. 2010;29(4):446-56. doi: 10.3109/10641950903452386.


The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative.

Gibson F, Hoogland C, Martinez-Bartolomé S, Medina-Aunon JA, Albar JP, Babnigg G, Wipat A, Hermjakob H, Almeida JS, Stanislaus R, Paton NW, Jones AR.

Proteomics. 2010 Sep;10(17):3073-81. doi: 10.1002/pmic.201000120.


S3DB core: a framework for RDF generation and management in bioinformatics infrastructures.

Almeida JS, Deus HF, Maass W.

BMC Bioinformatics. 2010 Jul 20;11:387. doi: 10.1186/1471-2105-11-387.

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