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Faculty Detail    
Campus Address WP P220 Zip 7331
Phone  205-975-3286
Other websites Biosketch
Google Scholar
Research Gate

Faculty Appointment(s)
Appointment Type Department Division Rank
Primary  Pathology   Pathology Informatics Professor Adjunct

Graduate Biomedical Sciences Affiliations
Biochemistry and Structural Biology 
Molecular and Cellular Pathology Program 

Biographical Sketch 
See "Other websites" above

Society Memberships
Organization Name Position Held Org Link
American Medical Informatics Association 
BMC Medical Genomics  Section Editor 
International Society for Computational Biology 

Research/Clinical Interest
Computational Infrastructure for Integrative Bioinformatics
My research is focused on the computational infrastructure for integrative bioinformatics. Specifically, it seeks to articulate the computational statistics aspects of data analysis with the data representation and management of its acquisition. This domain of enquiry seeks to understand and advance the emergence of unified computational environments that make optimal use of the scalability of cloud computing and the generality of semantic web representations. The practical application of this research is to enable the personalization of medicine by providing its computational vehicle.

Selected Publications 
Publication PUBMEDID
Saleem M, SS Padmanabhuni, AN Ngomo, A Iqbal, JS Almeida, S Decker, HF Deus (2014) TopFed: TCGA Tailored Federated Query Processing and Linking to LOD. J Biomedical Semantics [in press]   
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 
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 

Informatics, computational statistics