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* Undergraduate Authors
Kelsey Gray, Harley Edwards, Alexander G. Doan, Walker Huso, JungHun Lee, Wanwei Pan*, Nelanne Bolima*, Meredith E. Morse*, Sarah Yoda*, Isha Gautam, Steven D. Harris, Marc Zupan, Tuo Wang, Tagide deCarvalho, Mark R. Marten, “Aspergillus nidulans cell wall integrity kinase, MpkA, impacts cellular phenotypes that alter mycelial-material mechanical properties,” bioRxiv, 2024.
(bioRxiv https://doi.org/10.1101/2024.09.28.615565)
Alexander G Doan, Jessica E Schafer*, Casey M Douglas*, Matthew S Quintanilla*, Meredith E Morse*, Harley Edwards, Walker Huso, Kelsey J Gray, JungHun Lee, Joshua K Dayie*, Steven D. Harris, Mark R. Marten, “Protein Kinases MpkA and SepH Transduce Crosstalk Between CWI and SIN Pathways to Activate Protective Hyphal Septation Under Echinocandin Cell Wall Stress,” bioRxiv, 2024.
(bioRxiv https://doi.org/10.1101/2024.07.23.604799)
Harley Edwards, Joseph Zavorskas, Walker Husos, Alexander G. Doan, Caton Silbiger*, Steven Harris, Ranjan Srivastava, Mark R. Marten, Using flux theory in dynamic omics data sets to identify differentially changing signals using DPoP. BMC Bioinformatics 25, 312 (2024).
(https://doi.org/10.1186/s12859-024-05938-9)
Zavorskas, Joseph; Edwards, Harley; Marten, Mark; Harris, Steven; Srivastava, Ranjan, “Incremental Inverse Design of Desired Soybean Phenotypes,” ACS Omega, in press, 2024
Ryland N. Spence, Walker Huso, Harley Edwards, Alexander Doan, Samantha Reese, Steven Harris, Ranjan Srivastava, Mark R. Marten, “Aspergillus nidulans septa are indispensable for surviving cell wall stress,” Microbiology Spectrum, 10:e02063-21, 2022.
(https://doi.org/10.1128/spectrum.02063-21)
Samantha Reese, Cynthia Chelius, Wayne Riekhof, Mark R Marten, Steven D Harris, “Micafungin-Induced Cell Wall Damage Stimulates Morphological Changes Consistent with Microcycle Conidiation in Aspergillus nidulans,” Journal of Fungi, 7:525, 2021.
(https://doi.org/10.3390/jof7070525)
Trevor Glaros, Elizabeth S. Dhummakupt, Gabrielle M. Rizzo, Ethan McBride, Daniel O. Carmany, Linnzi K.M. Wright, Jeffry S. Forster, Julie A. Renner, Ruth W Moretz, Russel Dorsey, Mark R. Marten, Walker Huso, Alexander Doan, Carrie D. Dorsey, Christopher Phillips, Bernard Benton, Phillip M. Mach, “Discovery of treatment for nerve agents targeting a new metabolic pathway,” Archives of Toxicology, 94:3249–3264, 2020.
(https://doi.org/10.1007/s00204-020-02820-4)
Cynthia Chelius, Walker Huso, Samantha Reese, Alex Doan*, Ste
phen Lincoln, Kelsi Lawson*, Bao Tran, Raj Purohit*, Trevor Glaros, Ranjan Srivastava, Steven Harris, Mark R. Marten, “Dynamic phosphoproteomic and transcriptomic analysis of the CWIS pathway in Aspergillus nidulans.” Molecular and Cellular Proteomics, 2020, mcp.RA119.001769.
(https://doi.org/10.1074/mcp.RA119.001769)
Eliciane Cevolani Mattos, Lilian Pereira Silva, Clara Valero, Patrícia Alves de Castro, Thaila Fernanda dos Reis, Liliane F. C. Ribeiro, Mark R. Marten, Rafael Silva-Rocha, Cauã Westmann, Carlos Henrique Tomich de Paula da Silva, Carlton Anthony Taft, Narjes A l-Furaiji, Michael Bromley, Uffe H. Mortensen, J. Philipp Benz, Neil Andrew Brown, Gustavo H. Goldman, “The Aspergillus fumigatus Phosphoproteome Reveals Roles of High-Osmolarity Glycerol Mitogen-Activated Protein Kinases in Promoting Cell Wall Damage and Caspofungin Tolerance,” mBio, Feb 2020, 11(1):e02962-19
(http://doi.org/10.1128/mBio.02962-19).
Liliane F. C. Ribeiro, Cynthia Chelius, Karthik R. Boppidi, Nisha S. Naik*, Simin Hossain, Jessica J.J.L.A. Ramsey*, Jyothi Kumar, Lucas F. Ribeiro, Marc Ostermeier, Bao Tran, Young Ah Goo, Leandro J. de Assis, Gustavo H. Goldman, Stephen Lincoln, Ranjan Srivastava, Steven D. Harris, Mark R. Marten, “Comprehensive Analysis of Aspergillus nidulans PKA Phosphorylome Identifies a Novel Mode of CreA Regulation,” mBio, 10(3):e02825-18, 2019.
(http://doi.org/10.1128/mBio.02825-18).
Chelius CL, Ribeiro LFC, Huso W, Kumar J, Lincoln S, Tran B, Goo YA, Srivastava R, Harris SD, Marten MR., “Phosphoproteomic and transcriptomic analyses reveal multiple functions for Aspergillus nidulans MpkA independent of cell wall stress.” Fungal Genetics and Biology, 125, 1-12, 2019
(http://doi.org/10.1016/j.fgb.2019.01.003).
Karthik R. Boppidi, Liliane FC Ribeiro, Sirasa Iambamrung*, Sidney M. Nelson*, Yan Wang, Michelle Momany, Elizabeth A. Richardson, Stephen Lincoln, Ranjan Srivastava, Steven D. Harris, Mark R. Marten, “Altered secretion patterns and cell wall organization caused by loss of PodB function in the filamentous fungus Aspergillus nidulans.” Scientific Reports, 8(1), 11433, 2018
(http://doi.org/10.1038/s41598-018-29615-z).
Daniela Quintanilla, Cynthia Chelius, Sirasa Iambamrung*, Sidney Nelson*, Donnel Thomas*, Krist V. Gernaey, Mark R. Marten, “A fast and simple method to estimate relative, hyphal tensile-strength of filamentous fungi used to assess the effect of autophagy.” Biotechnology & Bioengineering, 115(3): 597-605, 2018
(http://dx.doi.org/10.1002/bit.26490).
Liliane FC Ribeiro, Cynthia L Chelius, Steven D Harris and Mark R. Marten, “Insights Regarding Fungal Phosphoproteomic Analysis.” Fungal Genetics and Biology, 104:38-44, 2017.
(http://dx.doi.org/10.1016/j.fgb.2017.03.003)
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).
(https://doi.org/10.1186/1477-5956-12-21)
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).
(https://doi.org/10.1039/c3mb70358d)
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).
(https://doi.org/10.1002/jms.3249)
Klionsky DJ, et al. “Guidelines for the use and interpretation of assays for monitoring autophagy.” Autophagy. 2012
; 8(4):445-544.
(https://doi.org/10.4161/auto.19496)
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).
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).