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Photo of Michelle O'Malley

Michelle O'Malley

ICB Systems and Synthetic Biology Co-Leader
Professor
Chemical Engineering
UC Santa Barbara
Phone:
+1 805-893-4769
Email:
momalley@engineering.ucsb.edu
Website:
Website
Twitter Link:
@omalleylab

Research Focus Areas

Research Interests

My research develops new technologies to genetically engineer non-model microbes and anaerobic consortia for sustainable chemical production, remediation, and natural product discovery. Our approach combines classical microbiology with cutting-edge tools (genome sequencing, RNA-Seq) to engineer the processes that underlie protein and enzyme production. Current efforts include discovery of novel enzymes from anaerobic gut fungi, metabolic engineering for enhanced anaerobic cooperation, engineering of synthetic enzyme complexes for consolidated bioprocessing, and deciphering the structure-function relationship of membrane proteins.

News

Displaying 21 - 40 of 42

ICB Supported Publications

Harnessing nature’s anaerobes for biotechnology and bioprocessing

Igor A. Podolsky, Susanna Seppälä, Thomas S. Lankiewicz, Jennifer L. Brown, Candice L. Swift, and Michelle O'Malley
Annual Review of Chemical and Biomolecular Engineering,
10.1146/annurev-chembioeng-060718-030340

Linking ‘omics’ to function unlocks the biotech potential of non-model fungi

St. Elmo Wilken, Candice L.Swift, Igor A.Podolsky, Tom S.Lankiewicz, Susanna Seppälä, Michelle O'Malley
Current Opinion in Systems Biology,
10.1016/j.coisb.2019.02.001

Biomass-Degrading Enzymes Are Catabolite Repressed in Anaerobic Gut Fungi

John K. Henske, Sean P. Gilmore, Charles H. Haitjema, Kevin V. Solomon and Michelle O’Malley
AIChE Journal,
10.1002/aic.16395

Catabolic repression in early-diverging anaerobic fungi is partially mediated by natural antisense transcripts

Kevin V. Solomon, John K. Henske, Sean P. Gilmore, Anna Lipzen, Igor Grigoriev, Dawn A. Thompson and Michelle O’Malley
Fungal Genetics & Biology,
10.1016/j.fgb.2018.09.004

In Silico Identification of Microbial Partners to Form Consortia with Anaerobic Fungi

St. Elmo Wilken , Mohan Saxena , Linda R. Petzold and Michelle O’Malley
Processes,
10.3390/pr6010007

Metabolic characterization of anaerobic fungi provides a path forward for bioprocessing of crude lignocellulose

John K. Henske, St. Elmo Wilken, Kevin V. Solomon, Chuck R. Smallwood, Vaithiyalingam Shutthanandan, James E. Evans, Michael K. Theodorou and Michelle O'Malley
Biotechnology and Bioengineering,
10.1002/bit.26515

Substrate-based differential expression analysis reveals control of biomass degrading enzymes in Pycnoporus cinnabarinus

John K. Henske, Stephen D. Springer, Michelle O’Malley and Alison Butler
Biochemical Engineering Journal,
10.1016/j.bej.2017.11.015

Transcriptomic characterization of Caecomyces churrovis: a novel, non-rhizoid-forming lignocellulolytic anaerobic fungus

John K. Henske, Sean P. Gilmore, Doriv Knop, Francis J. Cunningham, Jessica A. Sexton, Chuck R. Smallwood, Vaithiyalingam Shutthanandan, James E. Evans, Michael K. Theodorou and Michelle O’Malley
Biotechnology for Biofuels,
10.1186/s13068-017-0997-4

PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities

Joan E. Edwards, Robert J. Forster, Tony M. Callaghan, Veronika Dollhofer, Sumit S. Dagar, Yanfen Cheng, Jongsoo Chang, Sandra Kittelmann, Katerina Fliegerova, Anil K. Puniya, John K. Henske, Sean P. Gilmore, Michelle O’Malley, Gareth W. Griffith and Hauke Smidt
Frontiers in Microbiology,
10.3389/fmicb.2017.01657

The importance of sourcing enzymes from non-conventional fungi for metabolic engineering and biomass breakdown

Susanna Seppäläa, St. Elmo Wilken, Doriv Knopa, Kevin V. Solomo and Michelle O’Malley
Metabolic Engineering,

Genomic analysis of methanogenic archaea reveals a shift towards energy conservation

Sean P. Gilmore, John K. Henske, Jessica A. Sexton, Kevin V. Solomon, Susanna Seppälä, Justin I Yoo, Lauren M. Huyett, Abe Pressman, James Z. Cogan, Veronika Kivenson, Xuefeng Peng, YerPeng Tan, David L. Valentine and Michelle O’Malley
BMC Genomics,
10.1186/s12864-017-4036-4

A parts list for fungal cellulosomes revealed by comparative genomics

Haitjema, C.H., Gilmore, S.P., Henske, J.K., Solomon, K.V., deGroot, R., Kuo, A., Mondo, S J., Salamov, A.A., LaButti, K., Zhao, Z., Chiniquy, J., Barry,K., Brewer, H.M., Purvine, S.O., Wright, A.T., Hainaut, M., Boxma, B., van Alen, T., Hackstein, J.H.P., Henrissat, B., Baker, S.E., Grigoriev, I.V. and Michelle O’Malley, M.A.
Nature Microbiology,
10.1038/nmicrobiol.2017.87

Widespread adenine n6-methylation of active genes in fungi

Mondo, S.J.,Dannebaum, R.O., Kuo, R., LaButti, K., Haridas, S., Kuo, A., Salamov, A., Ahrendt, S.R., Lipzen, A., Sullivan, W., Andreopolous, W., Clum, A., Lindquist, E.,. Daum, C., Ramamoorthy, G., Gryganskyi, A., Dulley, D., Magnuson, J., James, T.Y., Michelle O’Malley, M.A., Stajich, J.E., Spatafora, J.W., Visel, A. and Grigoriev, I.V.
Nature Genetics,
10.1038/ng.3859

Engineering live cell surfaces with functional polymers via cytocompatible controlled radical polymerization

Niu, J., Lunn, D.J., Pusuluri, A., Yoo, J.I., O'Malley, M.A., Mitragotri, S., Soh, H.T. and Hawker, C.J.
Nature Chemistry,
10.1038/NCHEM.2713

Mapping the membrane proteome of anaerobic fungi identifies a wealth of carbohydrate binding proteins and transporters

Seppala, S., Solomon, K.V., Gilmore, S.P., Henske, J.K. and O’Malley, M.A.
Microbial Cell Factories,
10.1186/s12934-016-0611-7

Microbial communities for bioprocessing: lessons learned from nature

Peng, X., Gilmore, S.P. and O’Malley, M.A.
Current Opinion in Chemical Engineering,
10.1016/j.coche.2016.09.003

Fungal diversity notes 253-366: taxonomic and phylogenetic contributions to fungal taxa

Li, G.J., et al. (+134 additional authors including Solomon, K.V., Henske, J.K., Haitjema, C.H., Gilmore, S.P., Theodorou, M.K. and O’Malley, M.A.
Fungal Diversity,
10.1007/s13225-016-0366-9

Early-branching gut fungi possess a large comprehensive array of biomass-degrading enzymes

Solomon, K.V., Haitjema, C. H., Henske, J. K., Gilmore, S. P., Borges-Rivera, D., Lipzen, A., Brewer, H. M., Purvien, S. O., Wright, A. T., Theodorou, M. K., Grigoriev, I. V., Regev, A., Thompson, D. A. and O’Malley, M. A.
Science,
10.1126/science.aad1431

Early-branching gut fungi possess a large comprehensive array of biomass-degrading enzymes

Solomon K. V., Haitjema, C. H., Henske, J. K., Gilmore, S. P., Borges-Rivera, D., Lipzen, A., Brewer, H. M., Purvien, S. O., Wright, A. T., Theodorou, M. K., Grigoriev, I. V., Regev, A., Thompson, D. A. and O’Malley, M. A.
Science,
10.1126/science.aad1431

Driving biomass breakdown through engineered cellulosomes

S. P. Gilmore, J. K. Henske, and Michelle O’Malley
Bioengineered,
10.1080/21655979.2015.1060379
Emblems