MUSC > Proteomics Center
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Publications

First Year

  • Almeida JS, Voit EO. (2003) Neural-network-based parameter estimation in S-system models of biological networks. Genome Inform Ser Workshop Genome Inform. 2003;14:114-23.
  • Ro KW, Liu J, Busman M, Knapp DR. (2004) Capillary high-performance liquid chromatography-electrospray ionization mass spectrometry using monolithic columns and carbon fiber electrospray ionization emitters. J Chromatogr A. 2004 Aug 20;1047(1):49-57.
  • Liu J, Ro KW, Busman M, Knapp DR. (2004) Electrospray ionization with a pointed carbon fiber emitter. Anal Chem. 2004 Jul 1;76(13):3599-606..
  • Stanislaus R, Jiang LH, Swartz M, Arthur J, Almeida JS. (2004) An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results. BMC Bioinformatics. 2004 Jan 29;5:9.
  • Vinga S, Gouveia-Oliveira R, Almeida JS. (2004) Comparative evaluation of word composition distances for the recognition of SCOP relationships. Bioinformatics. 2004 Jan 22;20(2):206-15.
  • Voit EO, Almeida J. (2004) Decoupling dynamical systems for pathway identification from metabolic profiles. Bioinformatics. 2004 Jul 22;20(11):1670-81.

Second Year

  • Almeida JS, Stalislaus R, Krug E, Arthur JM. (2005) Normalization and analysis of residual variation in 2D Gel Electrophoresis for quantitative differential proteomics. Proteomics. 5(5):1242-9.
  • Lefler DM, Pafford DG, Black N, Raymond JR, and Arthur JM. (2004) Identification of proteins in slow continuous ultrafiltrate by reverse phase chromatography and proteomics. J. Proteome Res. 3(6):1254-60.
  • Liu, Z. and Schey K. (2005) Optimization of a MALDI TOF-TOF Mass Spectrometer for Intact Protein Analysis, J Am Soc Mass Spectrom. 16(4):482-90.
  • Pinto FR, Cowart LA, Hannun YA, Rohrer B, Almeida JS. (2005) Local correlation of expression profiles with gene annotations – proof of concept for a general conciliatory method. Bioinformatics. 21(7):1037-45
  • Rohrer B, Pinto FR, Hulse KE, Lohr HR, Zhang L, Almeida JS. (2004) Multidestructive pathways triggered in photoreceptor cell death of the rd mouse as determined through gene expression profiling. J Biol Chem. 2004 Oct 1;279(40):41903-10.
  • Schwacke JH, Voit EO. (2004) Improved methods for the mathematically controlled comparison of biochemical systems. Theor Biol Med Model. 2004 Jun 4;1(1):1.
  • Veflingstad SR, Almeida J, Voit EO. (2004) Priming nonlinear searches for pathway identification. Theor Biol Med Model. 2004 Sep 14;1(1):8.
  • Vinga S, Almeida JS. (2004) Renyi continuous entropy of DNA sequences. J Theor Biol. 2004 Dec 7;231(3):377-88.
  • Voit, E.O., S. Marino, and R. Lall: (2004) Challenges for the identification of biological systems from in vivo time series data. In Silico Biology, 5, 0010

Third Year

  • Garcia, SP. and Almeida, JS. (2005) Multivariate phase space reconstruction by nearest neighbor embedding with different time delays, Phys Rev E Stat Nonlin Soft Matter Phys. 72(2 Pt 2):027205
  • Garcia, SP. and Almeida, JS.(2005) Nearest neighbor embedding with different time delays. Phys Rev E Stat Nonlin Soft Matter Phys. 71(3 Pt 2B):037204. (also selected for reprinting in Vol 9, Issue 7 of Biological Physics Research)
  • Lall R. and Voit EO. (2005) Parameter Estimation in Modulated, Unbranched Reaction Chains within Biochemical Systems. J. Comput. Biol. Chem. 29(5):309-18.
  • Lindsey ML, Goshorn DK, Comte-Walters S, Hendrick JW, Hapke E, Zile MR, Schey KL. (2005) A Multidimensional Proteomic Approach to Identify Hypertrophy-Associated Proteins. Proteomics, in press.
  • Mitas M, Almeida JS, Mikhitarian K, Gillanders WE, Lewin DN, Spyropoulos DD, Hoover L, Graham A, Glenn T, King P, Cole DJ, Hawes R, Reed CE, Hoffman BJ. (2005) Accurate discrimination of Barrett’s esophagus and esophageal adenocarcinoma using a quantitative three-tiered algorithm and multi-marker real-time RT-PCR. Clin Cancer Res. 11(6):2205-14.
  • Moellering DR, Ulasova E, Landar AL, Vestri HS, Wallace P, Darley-Usmar V, Garvey WT. (2005) Proteomic Analysis of Skeletal Muscle Mitochondria in Type 2 Diabetes Reveals Altered Concentrations and Oxidation of Respiratory Chain Proteins. Diabetes 54 (Suppl. 2):A58.
  • Oates JC, Varghese S, Bland AM, Taylor TP, Self SE, Stanislaus R, Almeida JS and Arthur JM. (2005) Prediction of urinary protein markers in lupus nephritis. Kidney Int. In Press.
  • Stanislaus R, Chen C, Franklin J, Arthur J, Almeida JS. (2005) AGML central: web based gel proteomic infrastructure. Bioinformatics, 21(9):1754-7..
  • Wang X, Gorlitsky R, and Almeida JS. (2005) From XML to RDF: How Semantic Web Technologies Will Change the Design of ‘Omic’ Standards. Nature Biotechnology, 23(9):1099-1103.
  • Wu X, Moellering D, Vestri H, Wei H, Maianu L, Rosinski J, Rhees B, So V, Allison D, Martin M, Garvey WT. (2005) Dysregulation of Mitochondria-Related Genes and Transcription Factors Involved in Mitochondrial Biogenesis in Skeletal Muscle from Insulin Resistant Humans. Diabetes, 54 (Suppl. 2):A273.