| Wilkinson S, JS Almeida (2014) QMachine: commodity supercomputing in web browsers. BMC Bioinformatics |
24913605 |
| Ping Z, GP Siegal, JS Almeida, SJ Schnitt, D Shen (2014) Mining genome sequencing data to identify the genomic features linked to breast cancer histopathology. J Pathology Informatics 5:3 |
24672738 |
| Robbins DE, Gruneberg A, Deus HF, Tanik MM, Almeida JS (2013) A Self-Updating Roadmap of The Cancer Genome Atlas. Bioinformatics, 15;29(10):1333-40. [doi: 10.1093/bioinformatics/btt141]. |
23595662 |
| Kim YW, Koul D, Kim SH, Lucio-Eterovic AK, Freire PR, Yao J, Wang J, Almeida JS, Aldape K, Yung WK. (2013) "Identification of prognostic gene signatures of glioblastoma: a study based on TCGA data analysis." Neuro-Oncology, 15(7):829-39. [doi: 10.1093/neuonc/not024]. |
23502430 |
| Almeida JS, Iriabho EE, Gorrepati VL, Wilkinson SR, Grüneberg A, Robbins DE, Hackney JR (2012) ImageJS: personalized, participated, pervasive and reproducible image bioinformatics in the web browser. J Pathology Informatics 3:25. [doi: 10.4103/2153-3539.98813]. |
22934238 |
| Almeida JS, A Grüneberg, W Maass, S Vinga (2012) Fractal MapReduce decomposition of sequence alignment. Algorithms for Molecular Biology 7:12 |
22551205 |
| Vinga S, AM Carvalho, AP Francisco, LMS Russo, JS Almeida (2012) Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis. Algorithms for Molecular Biology 7:10 |
22551152 |
| Neely BA, JL Soper, DJ Greig, KP Carlin, EG Favre, FMD Gulland, JS Almeida and MJanech (2012) Serum profiling by MALDI-TOF mass spectrometry as a diagnostic tool for domoic acid toxicosis in California sea lions. Proteome Science 2012, 10:18 |
22429742 |
| Ravenell RL, Kamen DL, Spence JD, Hollis BW, Fleury TJ, Janech MG, Almeida JS, Shaftman SR, Oates JC (2012). Premature Atherosclerosis Is Associated With Hypovitaminosis D and Angiotensin-Converting Enzyme Inhibitor Non-use in Lupus Patients. AM J Med Sciences, 344(4):268-73. |
22222338 |
| Deus HF, MC Correa, R Stanislaus , M Miragaia , W Maass , H de Lencastre, R Fox, JS Almeida (2011) S3QL: A distributed domain specific language for controlled semantic integration of life sciences data. BMC Bioinformatics 2011, 12:285. |
21756325 |
| Correa MC, HF Deus, AT Vasconcelos, Y Hayashi, JA Ajani, SV Patnana, JS Almeida (2010) AGUIA: autonomous graphical user interface assembly for clinical tirals semantic data services. BMC Medical Informatics and Decision Making, (10)35. |
20977768 |
| Chen YA, JS Almeida, AJ Richards, P Müller, RJ. Carroll, B Rohrer (2010) A Nonparametric Approach to Detect Nonlinear Correlation in Gene Expression. Journal of Computational and Graphical Statistics, Vol. 19, No. 3: 552–568. |
20877445 |
| Almeida JS (2010) Computational ecosystems for data-driven medical genomics. Genome Medicine 2010, 2:67. |
20854645 |
| Deus HF, DF Veiga, PR Freire, JN Weinstein, GB Mills, JS Almeida (2010) Exposing The Cancer Genome Atlas as a SPARQL endpoint. Journal Biomedical Informatics. |
20851208 |
| Robinson CJ, Hill EG, Alanis MC, Chang EY, Johnson DD, Almeida JS (2010) Examining the Effect of Maternal Obesity on Outcome of Labor Induction in Patients with Preeclampsia. Hypertens Pregnancy. 2010 Sep 6. |
20818957 |
| 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 (2010) The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative. Proteomics. 2010 Sep;10(17):3073-81. |
20677327 |
| Almeida JS, Deus HF, Maass W. (2010) S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinformatics. 2010 Jul 20;11(1):387. |
20646315 |
| Bland AM, MG Janech, JS Almeida, JM Arthur (2010) Sources of variability among replicate samples separated by two-dimensional gel electrophoresis. Journal of biomolecular techniques : JBT 2010;21(1):3-8. |
20357976 |
| Varghese SA, Powell TB, Janech MG, Budisavljevic MN, Stanislaus RC, Almeida JS, Arthur JM (2010) Identification of Diagnostic Urinary Biomarkers for Acute Kidney Injury. J Investig Med. 2010 Mar 10. |
20224435 |
| Macey BM, Jenny MJ, Williams HR, Thibodeaux LK, Beal M, Almeida JS, Cunningham C, Mancia A, Warr GW, Burge EJ, Holland AF, Gross PS, Hikima S, Burnett KG, Burnett L, Chapman RW (2009) Modelling interactions of acid-base balance and respiratory status in the toxicity of metal mixtures in the American oyster Crassostrea virginica. Comp Biochem Physiol A Mol Integr Physiol. |
19958840 |
| Diogo F T Veiga, Helena F Deus, Caner Akdemir, Ana T R Vasconcelos and Jonas S Almeida (2009) DASMiner: discovering and integrating data from DAS sources. BMC Syst Biol. 2009 Nov 17;3:109. |
19919683 |
| Karpievitch YV, Hill EG, Leclerc AP, Dabney AR, Almeida JS. (2009) An introspective comparison of random forest-based classifiers for the analysis of cluster-correlated data by way of RF++. PLoS One. 2009 Sep 18;4(9):e7087 |
19763254 |
| Fernandes F, Freitas AT, Almeida JS, Vinga S. (2009) Entropic Profiler - Detection of conservation in genomes using Information Theory. BMC Res Notes. 2009 May 5;2(1):72. |
19416538 |
| Vilela M, Vinga S, Grivet Mattoso Maia MA, Voit EO, Almeida JS. (2009) Identification of neutral biochemical network models from time series data. BMC Syst Biol. 2009 May 5;3(1):47. |
19416537 |
| Almeida JS, Vinga S. (2009) Biological sequences as pictures: a generic two dimensional solution for iterated maps. BMC Bioinformatics. 2009 Mar 31;10:100 |
19335894 |
| Freire P, M Vilela, HF Deus, YW Kim, D Koul, H Colman, KD Aldape, O Bogler, WKA Yung, K Coombes, GB Mills, AT Vasconcelos, JS Almeida (2008) Exploratory Analysis of the Copy Number Alterations in Glioblastoma Multiforme. PLoS ONE 3(12): e4076doi:10.1371/journal.pone.0004076. |
19115005 |
| Stanislaus R, M Carey, HF Deus, K Coombes, BT Hennessy, GB Mills, JS Almeida (2008) RPPAML/RIMS: A meta data format and an information management system for Reverse Phase Protein Arrays. BMC Bioinformatics 9(1):555. |
19102773 |
| Deus FH, R Stanislaus1, DF Veiga, C Behrens, II Wistuba, JD Minna, HR Garner, SG Swisher, JA Roth, AM Correa, B Broom, K Coombes, A Chang, LH Vogel, JS Almeida (2008) A Semantic Web management model for integrative biomedical informatics. PLoS ONE. Aug 13;3(8):e2946. |
18698353 |
| Robinson CJ, Swift S, Johnson DD, Almeida JS (2008) Prediction of pelvic organ prolapse using an artificial neural network. American Journal of Obstetrics and Gynecology Jun 2. |
18533119 |
| Hennessy BT, M Murph, M Nanjundan, M Carey, N Auersperg, JS Almeida, Coombes KR, Liu J, Lu Y, Gray JW, Mills GB. Ovarian cancer: linking genomics to new target discovery and molecular markers--the way ahead. (2008) Adv Exp Med Biol. 617:23-40. |
18497028 |
| Vilela M, I-Chun Chou , S Vinga , ATR Vasconcelos , EO Voit, JS Almeida (2008) Parameter optimization in S-system models. BMC Systems Biology 2:35. |
18416837 |
| Arthur JM, Janech MG, Varghese SA, Almeida JS, Powell TB (2008) Diagnostic and prognostic biomarkers in acute renal failure. Contrib Nephrol 160:53-64. |
18179696 |
| Stanislaus R, JM Arthur, B Rajagopalan, R Moerschell, B McGlothlen, JS Almeida (2008). An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis, BMC Bioinformatics. Jan 7;9:4. |
18179696 |
| Sá-Leão R, Nunes S, Brito-Avô A, Alves CR, Carriço JA, Saldanha J, Almeida JS, Santos-Sanches I, de Lencastre H. (2008) High rates of transmission of and colonization by Streptococcus pneumoniae and Haemophilus influenzae within a day care center revealed in a longitudinal study. J Clin Microbiol. Jan;46(1):225-34. |
18003797 |
| Vinga S, Almeida JS. (2007) Local Renyi entropic profiles of DNA sequences. BMC Bioinformatics. 2007 Oct 16;8(1):393. |
17939871 |
| Vilela M, Borges CC, Vinga S, Vanconcelos AT, Santos H, Voit EO, Almeida JS. (2007) Automated smoother for the numerical decoupling of dynamics models. BMC Bioinformatics 8(1):305. |
17711581 |
| Jenny MJ, Chapman RW, Mancia A, Chen YA, McKillen DJ, Trent H, Lang P, Escoubas JM, Bachere E, Boulo V, Liu ZJ, Gross PS, Cunningham C, Cupit PM, Tanguy A, Guo X, Moraga D, Boutet I, Huvet A, De Guise S, Almeida JS, Warr GW (2007) A cDNA Microarray for Crassostrea virginica and C. gigas. Mar Biotechnol (NY). 2007 Aug 1. |
17668266 |
| Bohn A, Zippel B, Almeida JS, Xavier JB (2007) Stochastic modeling for characterisation of biofilm development with discrete detachment events (sloughing). Water Sci Technol. 2007;55(8-9):257-64. |
17546994 |
| Varghese SA, Powell TB, Budisavljevic MN, Oates JC, Raymond JR, Almeida JS, Arthur JM (2007) Urine Biomarkers Predict the Cause of Glomerular Disease. J Am Soc Nephrol. J Am Soc Nephrol. 18(3):913-22. |
17301191 |
| Wolf G, JS Almeida, JG Crespo, MA Reis (2007) An improved method for two-dimensional fluorescence monitoring of complex bioreactors. J Biotechnol. 128(4):801-12. |
17291616 |
| Pinto FR, Carrico JA, Ramirez M, Almeida JS. (2007) Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement. BMC Bioinformatics 8(1):44. |
17286861 |
| Robalino J, Almeida JS, McKillen D, Colglazier J, Trent Iii HF, Chen YA, Peck ME, Browdy CL, Chapman RW, Warr GW, Gross PS (2007) Physiol Genomics. 14;29(1):44-56. |
17148689 |
| Karpievitch YV, Hill EG, Smolka AJ, Morris JS, Coombes KR, Baggerly KA, Almeida JS. (2007) PrepMS: TOF MS data graphical preprocessing tool. Bioinformatics. 15;23(2):264-5. |
17121773 |
| Mancia A, Lundqvist ML, Romano TA, Peden-Adams MM, Fair PA, Kindy MS, Ellis BC, Gattoni-Celli S, McKillen DJ, Trent HF, Ann Chen Y, Almeida JS, Gross PS, Chapman RW, Warr GW. (2007) A dolphin peripheral blood leukocyte cDNA microarray for studies of immune function and stress reactions. Dev Comp Immunol. 31(5):520-9. |
17084893 |
| Almeida, J.S., S.Vinga (2006) Computing distribution of scale independent motifs in biological sequences. Algorithms for Molecular Biology. 1:18. |
17049089 |
| Geli P, P Rolghamre, JS Almeida, K Ekdahl (2006) Modeling Pneumococcal Resistance to Penicillin in Southern Sweden Using Artificial Neural Networks. Microbial Drug Resistance 12(3):149-157. |
17002540 |
| Voit EO, Almeida JS, Marino S, Lall R, Goel G, Neves AR, Santos H (2006) Regulation of glycolysis in Lactococcus lactis: an unfinished systems biological case study. Syst Biol (Stevenage) Jul;153(4):286-98. |
16986630 |
| Almeida JS, C Chen, R Gorlitsky, R Stanislaus, M Aires-de-Sousa, P Eleutério, JA Carriço, A Maretzek, A Bohn, A Chang, F Zhang, R Mitra, GB Mills, X Wang, HF Deus (2006) Data integration gets 'Sloppy'. Nature Biotechnology 24(9):1070-1071. |
16964209 |
| Bland, A.M., L.R. D'Eugenio, M.A. Dugan, M.G. Janech, J.S. Almeida, M. Zileand J.M. Arthur. Comparison of Variability Associated with Sample Preparation in Two-Dimensional Gel Electrophoresis of Cardiac Tissue. J.Biomol. Tech. In Press: 2006. |
16870710 |
| Carrico JA, Silva-Costa C, Melo-Cristino J, Pinto FR, de Lencastre H, Almeida JS, Ramirez M. (2006) Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes. J Clin Microbiol. 44(7):2524-32. |
16825375 |
|