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Publications

DSC_0304Google Scholar – Pubmed

Nazrul Islam, Yonghyun Kim, Julia M. Ross and Mark R. Marten, “Proteomic analysis of Staphylococcus aureus biofilm cells grown under physiologically relevant fluid shear stress conditions.”Proteome Science, 12:21, (2014).

Ramsubramaniam, Nikhil; Tao, Feng; Li, Shuwei; Marten, Mark R., “Cost effective isobaric tagging for quantitative phosphoproteomics using DiART reagents.” Molecular BioSystems, 9:2981-2987, (2013).

Ramsubramaniam, Nikhil; Tao, Feng; Li, Shuwei; Marten, Mark R., “Novel and cost effective 6-plex isobaric tagging reagent, DiART is effective for identification and relative quantification of complex protein mixtures using PQD fragmentation.” In press,J. Mass Spectrometry, 48:1032-1041, (2013).

Klionsky DJ, et al.  “Guidelines for the use and interpretation of assays for monitoring autophagy.”  Autophagy. 2012; 8(4):445-544.

Y. Kim, N. Islam, B.J. Moss, M.P. Nandakumar, M.R. Marten, “Autophagy induced by rapamycin and carbon-starvation have distinct proteome profiles in Aspergillus nidulans,” Biotechnology Bioengineering, 108:2705-2715, (2011).

J.K. Pollack, S.D. Harris, and M.R. Marten, “Autophagy in Filamentous Fungi,” Fungal Genetics and Biology, 46:1–8, (2009).

J.R. Garcia, H.J. Cha, G.G. Rao, M.R. Marten, W.E. Bentley, “Microbial nar-GFP cell sensors reveal oxygen limitations in highly agitated and aerated laboratory-scale fermentors,”  Microbial Cell Factories,8:6 (2009).

J.K. Pollack, S.D. Harris, and M.R. Marten, “Autophagy in Filamentous Fungi,” Fungal Genetics and Biology, 46:1–8 (2009).

M.P. Zustiak, J.K. Pollack, M.R. Marten and M.J. Betenbaugh, “Feast or famine: autophagy control and engineering in eukaryotic cell culture,” Current Opinion in Biotechnology, 19:518–526, 2008.

J.K. Pollack, Z.J. Li, and M.R. Marten, “Fungal mycelia show lag time before re-growth on endogenous carbon,” Bioengineering and Biotechnology, in print (2008).

Y. Kim, M.P. Nandakumar, M.R. Marten, “The current state of proteome profiling in the filamentous fungal genus Aspergillus.  Briefings in Functional Genomics and Proteomics, in print (2007).

Y. Kim, M.P. Nandakumar, M.R. Marten, “Proteomics of filamentous fungi,” Trends in Biotechnology, 25:395-400, (2007).

Y. Kim, M.P. Nandakumar, M.R. Marten, “Proteome map of Aspergillus nidulans during osmoadaptation,”Fungal Genetics & Biology,  44:886-895, (2007).

Nandakumar, M.P., Cheung, A.  & Marten, M.R. “Proteomic analysis of extracellular proteins from E. coliW3110,” Journal of Proteome Research, 5:1155-1161, (2006).

Potra, F.A., Liu, X., Seillier-Moiseiwitsch, F., Roy, A., Hang, Y., Marten, M.R., Raman, B. & Whisnant, C., Protein Image Alignment via Piecewise Affine, Journal of Computational Biology, 13: 614–630 (2006).

Vallejos, J.R., Kostov, Y., Marten, M.R., and Rao, G., Confocal optical system: a novel noninvasive sensor to study mixing. Biotechnology Progress, 21:1531-1536 (2005).

Vallejos, J.R., Kostov, Y., Ram, A., French, J.A., Marten, M.R., and Rao, G., Optical Analysis of Liquid Mixing in a Microbioreactor. Biotechnol. Bioeng., 93:906-911 (2005).

Raman, B.; Nandakumar, M.P.; Muthuvijayan, V.; Marten, M.R. Proteome Analysis to Assess Physiological Changes in Escherichia Coli Grown under Glucose-Limited Fed-Batch Conditions. Biotechnol Bioeng, 92: 384-92 (2005).

Nandakumar R, Nandakumar M.P., Marten M.R. and Ross, J.M, “Proteome analysis of cell wall associated proteins from Staphylococcus aureus: lysis and sample preparation protocols,” J. Proteome Research, 21(1):292-9, (2005).

Zhao, L., Schaefer, D., and Marten, M.R., Assessment of Elasticity and Topography of Aspergillus nidulans Spores via Atomic Force Microscopy. Applied and Environmental Microbiology, 71:955 (2005).

Zhao, L., Schaefer, D., Xu, H., Modi, S.J., LaCourse, W.R., and Marten, M.R., Elastic properties of the cell wall of Aspergillus nidulans studied with atomic force microscopy (AFM). Biotechnol. Prog., 21:292 (2005).

Muthuvijayan, V. and Marten, M.R., In silico reconstruction of nutrient-sensing signal transduction pathways in Aspergillus nidulans. In Silico Biol., 4:0050 (2004).

fermentor photo (original)Bhargava, S., Wenger, K.S., Rane K., Rising V. and Marten M.R., “Effect of cycle time on fungal morphology, broth rheology and recombinant enzyme productivity during pulsed addition of limiting carbon source,” Biotechnology and Bioengineering, 89:524-529 (2005).

Roy A., Seillier-Moiseiwitsch F., Lee K.R., Hang Y., Marten M.R., Raman B., “Analyzing Two-Dimensional Gel Images.” Chance, 16:13-18 (2003).

Davidson KM, Sushil S, Eggleton CD, Marten MR, “Using computational fluid dynamics software to estimate circulation time distributions in bioreactors,” Biotechnol. Prog. 19:1480-6. (2003).

Nandakumar MP, Shen J, Raman B, Marten MR., “Solubilization of trichloroacetic acid (TCA) precipitated microbial proteins via naOH for two-dimensional electrophoresis,” J Proteome Res. 2:89-93, (2003).

S. Bhargava, K.S. Wenger, and M.R. Marten, “Pulsed feeding during fed-batch Aspergillus oryzaefermentation leads to improved oxygen mass transfer,” Biotechnol. Prog. 19:1091-1094 (2003 ).

S. Bhargava, K.S. Wenger, and M.R. Marten, “Pulsed addition of limiting carbon during Aspergillus oryzae fermentation leads to improved productivity of a recombinant enzyme,” Biotechnology and Bioengineering, 82:111-7 (2003).

S. Bhargava, M.P. Nandakumar, A. Roy, K.S. Wenger, and M.R. Marten, “Pulsed feeding during fed-batch fungal fermentation leads to reduced viscosity without detrimentally affecting protein expression,”Biotechnology and Bioengineering, 81:341-7 (2003).

M.P. Nandakumar and M.R. Marten, “Comparison of lysis methods and preparation protocols for one- and two-dimensional electrophoresis of Aspergillus oryzae intracellular proteins,” Electrophoresis 23:2216-2222 (2002).

B. Raman, A. Cheung, and M.R. Marten, “Quantitative comparison and evaluation of two commercially available, two dimensional electrophoresis image analysis software packages, Z3 and Melanie,”Electrophoresis 23:2194-2202 (2002).

Z.J. Li, V. Shukla, K.W. Wenger, A.P. Fordyce, A.G. Pedersen, and M.R. Marten “Effects of increased impeller power in a production-scale Aspergillus oryzae fermentation,” Biotechnol.  Prog., 18:437-444 (2002).

Z.J. Li, S. Bhargava, and M.R. Marten “Measurements of fragmentation rate constant imply that the tensile strength of fungal hyphae can change significantly during growth,” Biotechnol. Lett., 24:1-7 (2002).

Z.J. Li, V. Shukla, K.W. Wenger, A.P. Fordyce, A.G. Pedersen, and M.R. Marten “Estimation of hyphal tensile strength in production-scale Aspergillus oryzae fungal fermentations,” Biotechnol.  Bioeng.,77:601-613, (2002).

T. Shanklin, K. Roper,  P.K. Yegneswaran, and M.R. Marten “Selection of Bioprocess Simulation Software”, Biotechnol. Bioeng., 72: 483-489, (2001).

Z.J. Li, V. Shukla, K.W. Wenger, A.P. Fordyce, A.G. Pedersen, and M.R. Marten “Fungal Morphology and Fragmentation behavior in a Fed-Batch Aspergillus oryzae Fermentation at the Production Scale,”Biotechnol.  Bioeng., 70:300-312, (2000).

M.R. Marten, K.S. Wenger, and S.A. Khan, “Rheology, Mixing Time, and Regime Analysis for a Production-Scale Aspergillus oryzae Fermentation,” Bioreactor and Bioprocess Fluid Dynamics, A.W. Nienow (ed.),  BHRGroup, Cranfield, UK (1997).