Michelle A. O’Malley

发表

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

Sean P. Gilmore, J. Edwards, H. Smidt, 2017, Front. Microbiol..

Common principles and best practices for engineering microbiomes

Ophelia S. Venturelli, Brian F. Pfleger, William R. Harcombe, 2019, Nature Reviews Microbiology.

Widespread adenine N6-methylation of active genes in fungi

Robert J. Schmitz, Adam J. Bewick, A. Visel, 2017, Nature Genetics.

Extracting data from the muck: deriving biological insight from complex microbial communities and non-model organisms with next generation sequencing.

Kevin V. Solomon, D. Thompson, Michelle A. O’Malley, 2014, Current opinion in biotechnology.

Adenosine A2a receptors form distinct oligomers in protein detergent complexes

Michelle A. O’Malley, Songi Han, M. Rieth, 2016, FEBS letters.

Heterologous GPCR Expression: A Bottleneck to Obtaining Crystal Structures

A. Robinson, Michelle A. O’Malley, Emily C. McCusker, 2008, Biotechnology progress.

Oligomerization of the Human Adenosine A2A Receptor is Driven by the Intrinsically Disordered C-terminus

Michelle A. O’Malley, Blake Mertz, Songi Han, 2020, bioRxiv.

Non-destructive quantification of anaerobic gut fungi and methanogens in co-culture reveals increased fungal growth rate and changes in metabolic flux relative to mono-culture

Michelle A. O’Malley, M. Valentine, P. Leggieri, 2021, Microbial Cell Factories.

Efficient and cost-effective bacterial mRNA sequencing from low input samples through ribosomal RNA depletion

Siddharth S. Dey, Michelle A. O’Malley, Chatarin Wangsanuwat, 2020, BMC Genomics.

Efficient and cost-effective bacterial mRNA sequencing from low input samples through ribosomal RNA depletion

Siddharth S. Dey, Michelle A. O’Malley, Chatarin Wangsanuwat, 2020, BMC genomics.

An Arduino based automatic pressure evaluation system to quantify growth of non‐model anaerobes in culture

M. Theodorou, Michelle A. O’Malley, M. Reilly, 2020 .

Nature's recyclers: anaerobic microbial communities drive crude biomass deconstruction.

Michelle A. O’Malley, P. Leggieri, Kellie A Heom, 2020, Current opinion in biotechnology.

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

Michelle A. O’Malley, Susanna Seppälä, Candice L Swift, 2019, Current Opinion in Systems Biology.

Driving biomass breakdown through engineered cellulosomes

Sean P. Gilmore, J. Henske, Michelle A. O’Malley, 2015, Bioengineered.

Ecology and molecular targets of hypermutation in the global microbiome

S. Hallam, S. Saleska, R. Cavicchioli, 2020, Nature Communications.

Microbial communities and their enzymes facilitate degradation of recalcitrant polymers in anaerobic digestion.

Michelle A. O’Malley, E. Blair, K. Dickson, 2021, Current opinion in microbiology.

Methods for Genomic Characterization and Maintenance of Anaerobic Fungi.

M. Theodorou, Michelle A. O’Malley, Candice L Swift, 2018, Methods in molecular biology.

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

L. Petzold, Michelle A. O’Malley, S. Wilken, 2018 .

Top-down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation.

Sean P. Gilmore, D. Valentine, M. Theodorou, 2019, ACS synthetic biology.

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

James E. Evans, Sean P. Gilmore, M. Theodorou, 2017, Biotechnology for Biofuels.

Genomic analysis of methanogenic archaea reveals a shift towards energy conservation

Lauren M. Huyett, Kevin V. Solomon, Sean P. Gilmore, 2017, BMC Genomics.

Thousands of small, novel genes predicted in global phage genomes.

Vincent J. Denef, Eoin L. Brodie, William F. Whitman, 2022, Cell reports.

Enzyme Discovery in Anaerobic Fungi (Neocallimastigomycetes) Enables Lignocellulosic Biorefinery Innovation

Michelle A. O’Malley, Stephen P Lillington, Thomas S. Lankiewicz, 2022, Microbiology and molecular biology reviews : MMBR.

UNIVERSITY OF CALIFORNIA Santa Barbara Population of Tau Embedded in Parallel β-Sheets Depends on Heparin Stoichiometry A Thesis submitted in partial satisfaction of the requirements for the degree Master of Science in Chemical Engineering by

Michelle A. O’Malley, Z. Oberholtzer, Songi Han, 2016 .

Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes.

Ophelia S. Venturelli, Bryce M. Connors, Michelle A. O’Malley, 2021, Annual review of biomedical engineering.

Expansion of the global RNA virome reveals diverse clades of bacteriophages

Vincent J. Denef, Natalia N. Ivanova, David A. C. Beck, 2022, Cell.

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

L. H. Hagen, Anil K. Shukla, S. Tringe, 2020, The ISME Journal.

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

Kevin V. Solomon, Sean P. Gilmore, D. Thompson, 2016, Science.

The Anaerobic Fungi: Challenges and Opportunities for Industrial Lignocellulosic Biofuel Production

M. Theodorou, J. Chong, Michelle A. O’Malley, 2021, Microorganisms.

17 The Biotechnological Potential of Anaerobic Gut Fungi

Kevin V. Solomon, M. Theodorou, G. Griffith, 2020 .

Biomass‐degrading enzymes are catabolite repressed in anaerobic gut fungi

Kevin V. Solomon, Sean P. Gilmore, J. Henske, 2018, AIChE Journal.

Anaerobic gut fungi: Advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production

Kevin V. Solomon, M. Theodorou, J. Henske, 2014, Biotechnology and bioengineering.

Evaluating expression and catalytic activity of anaerobic fungal fibrolytic enzymes native topiromyces sp E2 inSaccharomyces cerevisiae

C. Kaiser, M. Theodorou, Michelle A. O’Malley, 2012 .

Characterization and rank assignment criteria for the anaerobic fungi (Neocallimastigomycota).

Kevin V. Solomon, J. Edwards, M. Lebuhn, 2022, International journal of systematic and evolutionary microbiology.

Cellulosome Localization Patterns Vary across Life Stages of Anaerobic Fungi

James E. Evans, Sean P. Gilmore, W. Chrisler, 2021, mBio.

Anaerobic gut fungi are an untapped reservoir of natural products

Kevin V. Solomon, A. Salamov, S. Purvine, 2021, Proceedings of the National Academy of Sciences.

Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus

Jonathan M. Monk, Christopher E. Lawson, B. Palsson, 2021, mSystems.

Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes

Sean P. Gilmore, A. Salamov, D. Valentine, 2021, Nature Microbiology.

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

Kevin V. Solomon, Sean P. Gilmore, J. Henske, 2016, Microbial Cell Factories.

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

Kevin V. Solomon, Jia Jia Chen, Samantha C. Karunarathna, 2016, Fungal Diversity.

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

Kevin V. Solomon, Michelle A. O’Malley, Susanna Seppälä, 2017, Metabolic engineering.

Designing chimeric enzymes inspired by fungal cellulosomes

Sean P. Gilmore, Michelle A. O’Malley, Charles H. Haitjema, 2020, Synthetic and systems biotechnology.

Toward rational design of protein detergent complexes: determinants of mixed micelles that are critical for the in vitro stabilization of a G-protein coupled receptor.

N. Wagner, A. Robinson, Michelle A. O’Malley, 2011, Biophysical journal.

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

David J. Lunn, S. Mitragotri, C. Hawker, 2017, Nature Chemistry.

Bridging non-overlapping reads illuminates high-order epistasis between distal protein sites in a GPCR

P. Daugherty, Michelle A. O’Malley, Justin I. Yoo, 2020, Nature Communications.

Genomic and proteomic biases inform metabolic engineering strategies for anaerobic fungi

A. Salamov, I. Grigoriev, J. Henske, 2019, Metabolic engineering communications.

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

Kevin V. Solomon, Sean P. Gilmore, D. Thompson, 2018, Fungal genetics and biology : FG & B.

A genomic catalog of Earth’s microbiomes

Vincent J. Denef, Natalia N. Ivanova, Paramvir S. Dehal, 2020, Nature Biotechnology.

Bridging non-overlapping reads illuminates high-order epistasis between distal protein sites in a GPCR

P. Daugherty, Michelle A. O’Malley, Justin I. Yoo, 2020, Nature Communications.

Emerging technologies for protease engineering: New tools to clear out disease.

P. Daugherty, Michelle A. O’Malley, J. Guerrero, 2017, Biotechnology and bioengineering.

A Genomic Catalog of Stress Response Genes in Anaerobic Fungi for Applications in Bioproduction

A. Salamov, I. Grigoriev, Michelle A. O’Malley, 2021, Frontiers in Fungal Biology.

Progress toward heterologous expression of active G‐protein‐coupled receptors in Saccharomyces cerevisiae: Linking cellular stress response with translocation and trafficking

A. Robinson, C. Young, Michelle A. O’Malley, 2009, Protein science : a publication of the Protein Society.

Homo-oligomerization of the human adenosine A2A receptor is driven by the intrinsically disordered C-terminus

Michelle A. O’Malley, Blake Mertz, Songi Han, 2021, eLife.

The morphology and composition of cholesterol-rich micellar nanostructures determine transmembrane protein (GPCR) activity.

N. Wagner, A. Robinson, Michelle A. O’Malley, 2011, Biophysical journal.

Analysis of adenosine A₂a receptor stability: effects of ligands and disulfide bonds.

A. Robinson, Michelle A. O’Malley, T. Lazarova, 2010, Biochemistry.

High-level expression in Saccharomyces cerevisiae enables isolation and spectroscopic characterization of functional human adenosine A2a receptor.

A. Robinson, Michelle A. O’Malley, T. Lazarova, 2007, Journal of structural biology.

Lignin deconstruction by anaerobic fungi

Mojgan Amirebrahimi, B. Simmons, S. Singer, 2023, Nature Microbiology.

Biofilm disruption enhances growth rate and carbohydrate-active enzyme production in anaerobic fungi.

Michelle A. O’Malley, M. Valentine, P. Leggieri, 2022, Bioresource technology.

Co‑cultivation of anaerobic fungi with Clostridium acetobutylicum bolsters butyrate and butanol production from cellulose and lignocellulose

Matthew A. Perisin, Marcus S. Benyamin, I. Grigoriev, 2022, Journal of industrial microbiology & biotechnology.

Cocultivation of Anaerobic Fungi with Rumen Bacteria Establishes an Antagonistic Relationship

Kevin V. Solomon, K. Barry, T. Northen, 2021, mBio.

Intracellular FRET-based Screen for Redesigning the Specificity of Secreted Proteases.

P. Daugherty, Michelle A. O’Malley, J. Guerrero, 2016, ACS chemical biology.

Co-cultivation of the anaerobic fungus Anaeromyces robustus with Methanobacterium bryantii enhances transcription of carbohydrate active enzymes

Michelle A. O’Malley, Susanna Seppälä, Jennifer L. Brown, 2019, Journal of Industrial Microbiology & Biotechnology.

Lipo-chitooligosaccharides as regulatory signals of fungal growth and development

M. Sussman, Virginie Puech-Pagès, G. Bécard, 2020, Nature Communications.

Structure and function of G protein-coupled receptor oligomers: implications for drug discovery

Michelle A. O’Malley, Nicole S. Schonenbach, Sunyia Hussain, 2014 .

Microbial communities for bioprocessing: lessons learned from nature

Xuefeng “Nick” Peng, Sean P. Gilmore, Michelle A. O'Malley, 2016 .

Identification of novel membrane proteins for improved lignocellulose conversion.

Michelle A. O’Malley, Susanna Seppälä, Igor A Podolsky, 2021, Current opinion in biotechnology.

A SWEET surprise: Anaerobic fungal sugar transporters and chimeras enhance sugar uptake in yeast.

Yong‐Su Jin, Michelle A. O’Malley, Susanna Seppälä, 2021, Metabolic engineering.

Mitochondrial targeting increases specific activity of a heterologous valine assimilation pathway in Saccharomyces cerevisiae

Kevin V. Solomon, Michelle A. O’Malley, Elisa M. Ovadia, 2016, Metabolic engineering communications.

A parts list for fungal cellulosomes revealed by comparative genomics

Kevin V. Solomon, Sean P. Gilmore, A. Salamov, 2017, Nature Microbiology.

Heterologous transporters from anaerobic fungi bolster fluoride tolerance in Saccharomyces cerevisiae

Michelle A. O’Malley, Susanna Seppälä, Justin I. Yoo, 2019, Metabolic engineering communications.

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

James E. Evans, Kevin V. Solomon, M. Theodorou, 2018, Biotechnology and bioengineering.

Efficient and cost-effective bacterial mRNA sequencing from low input samples through ribosomal RNA depletion

Siddharth S. Dey, Michelle A. O’Malley, Chatarin Wangsanuwat, 2020, BMC Genomics.

Pontiella agarivorans sp. nov., a novel marine anaerobic bacterium capable of degrading macroalgal polysaccharides and fixing nitrogen

D. Valentine, Michelle A. O’Malley, Chance J. English, 2023, bioRxiv.

Tuning Vector Stability and Integration Frequency Elevates Functional GPCR Production and Homogeneity in Saccharomyces cerevisiae.

Michelle A. O’Malley, Justin I. Yoo, 2018, ACS synthetic biology.

GPCR-FEX: A Fluoride-Based Selection System for Rapid GPCR Screening and Engineering.

Michelle A. O’Malley, Justin I. Yoo, Tejas A Navaratna, 2022, ACS synthetic biology.

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

A. Butler, J. Henske, Michelle A. O’Malley, 2018 .

Harnessing Nature's Anaerobes for Biotechnology and Bioprocessing.

Michelle A. O’Malley, Susanna Seppälä, Igor A Podolsky, 2019, Annual Review of Chemical and Biomolecular Engineering.

Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa

Hernawati, Kevin V. Solomon, Jia Jia Chen, 2016, Fungal Diversity.

Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates

A. Salamov, B. Henrissat, Elodie Drula, 2021, Biotechnology for Biofuels.

Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules

A. Salamov, B. Henrissat, K. Barry, 2021, bioRxiv.