2025
99. Increased aluminum exposure induces widespread changes in silicon, carbon, and nitrogen metabolism in Entomoneis vertebralis
R.Ragunathan, H.M. Purdy, S. Seppala, H. Gwak, et al.
97. The anaerobic fungus Neocallimastix californiae shifts metabolism and produces melanin in response to lignin-derived aromatic compounds
T.S. Lankiewicz, B.Amer, E.E.K. Baidoo, P.A. Leggieri & M.A. O’Malley.
98. Untargeted GC-MS Metabolic Profiling of Anaerobic Gut Fungi Reveals Putative Terpenoids and Strain-Specific Metabolites
L.V. Butkovich, C.L. Swift, C.S. Clendinen, HM. Olson, S.O. Purvine, O.B. Vining and M.A. O’Malley.
96. High-quality draft genome sequence of Thermobifida halotolerans DSM 44931
C.B. Ahern, I. Chen, M. Huntemann, N. Ivanova, N. Kyrpides, et al.
95. A large-scale screening campaign of putative carbohydrate-active enzymes reveals a novel xylanase from anaerobic gut fungi
S Jin, IR Farrand, Y Chen, JW Gin, B Zhang, E Kirschke, CJ Petzold, et al.
94. Microbial Enrichments Contribute to Characterization of Desert Tortoise Gut Microbiota
E.M. Blair, N.J. Margalith, M.A. O’Malley.
93. Genomic and Transcriptomic Characterization of Carbohydrate-Active Enzymes in the Anaerobic Fungus Neocallimastix cameroonii var. constans
E.M. Blair, T.A. Navaratna, C.B. Ahern, R. Ragunathan, J.L. Brown, S.J. Mondo, et al.
92. An Argument for Using Anaerobes as Microbial Cell Factories to Advance Synthetic Biology and Biomanufacturing
T.S. Lankiewicz, N.H. Elisabeth, D.L. Valentine, M.A. O'Malley.
91. Separation of Life Stages within Anaerobic Fungi (Neocallimastigomycota) Highlights Differences in Global Transcription and Metabolism
L.V. Butkovich, P.A. Leggieri, S.P. Lillington, T.A. Navaratna, C.L. Swift, et al.
90. Editorial Reflections on BioEnergy: Perspectives from 2024
S. Agarwala, M.A. O’Malley, T. Eng.
89. New Approaches to Secondary Metabolite Discovery from Anaerobic Gut Microbes
L.V. Butkovich, O.B. Vining, M.A. O’Malley.
2024
88. Toward a Circular Bioeconomy: Designing Microbes and Polymers for Biodegradation.
V. Mubayi, C.B. Ahern, M. Calusinska, M.A. O’Malley.
87. Metagenomics Analysis Yields Assembled Genomes from Prokaryotic Anaerobes with Polymer‐Degrading Potential
E.M. Blair, J.L. Brown, D. Li, P.A. Holden, M.A. O'Malley.
86. Anaerobic Fungi Contain Abundant, Diverse, and Transcriptionally Active Long Terminal Repeat Retrotransposons
T.A. Navaratna, N. Alansari, A.R. Eisenberg, M.A. O’Malley.
85. Targeted Hypermutation of Putative Antigen Sensors in Multicellular Bacteria
H. Doré, A.R. Eisenberg, E.N. Junkins, G.E. Leventhal, A. Ganesh, O.X. Cordero, et al.
84. Pontiella agarivorans sp. nov., a Novel Marine Anaerobic Bacterium Capable of Degrading Macroalgal Polysaccharides and Fixing Nitrogen
N. Liu, V. Kivenson, X. Peng, Z. Cui, T.S. Lankiewicz, K.M. Gosselin, et al.
83. Continuous Culture of Anaerobic Fungi Enables Growth and Metabolic Flux Tuning Without Use of Genetic Tools
P.A. Leggieri, E.M. Blair, T.S. Lankiewicz, M.A. O'Malley.
2023
82. Targeted rRNA depletion enables efficient mRNA sequencing in diverse bacterial species and complex co-cultures
K.A. Heom, C. Wangsanuwat, L.V. Butkovich, S.C. Tam, A.R. Rowe, M.A. O’Malley.
81. Expression and Characterization of Spore Coat CotH Kinases from the Cellulosomes of Anaerobic Fungi (Neocallimastigomycetes)
S.P. Lillington, M. Hamilton, J.F. Cheng, Y. Yoshikuni, M.A. O'Malley.
80. Structure and Enzymatic Characterization of CelD Endoglucanase from the Anaerobic Fungus Piromyces finnis
A. Dementiev, S.P. Lillington, S. Jin, Y. Kim, R. Jedrzejczak, K. Michalska, et al.
79. Identification and Expression of Small Multidrug Resistance Transporters in Early‐Branching Anaerobic Fungi
S. Seppälä, T. Gierke, E.E. Schauer, J.L. Brown, M.A. O'Malley.
78. High-Quality RNA Extraction and the Regulation of Genes Encoding Cellulosomes Are Correlated with Growth Stage in Anaerobic Fungi
J.L. Brown, T. Gierke, L.V. Butkovich, C.L. Swift, V. Singan, C. Daum, K. Barry, et al.
77. Lignin Deconstruction by Anaerobic Fungi
T.S. Lankiewicz, H. Choudhary, Y. Gao, B. Amer, S.P. Lillington, P.A. Leggieri, et al.
76. Lipid Membrane Mimetics and Oligomerization Tune Functional Properties of Proteorhodopsin
C.T. Han, K.D.Q. Nguyen, M.W. Berkow, S. Hussain, A. Kiani, M. Kinnebrew, et al.
2022
75. Co Cultivation of Anaerobic Fungi with Clostridium acetobutylicum Bolsters Butyrate and Butanol Production from Cellulose and Lignocellulose
J.L. Brown, M.A. Perisin, C.L. Swift, M. Benyamin, S. Liu, V. Singan, Y. Zhang, et al.
74. Expansion of the Global RNA Virome Reveals Diverse Clades of Bacteriophages
U. Neri, Y.I. Wolf, S. Roux, A.P. Camargo, B. Lee, D. Kazlauskas, I.M. Chen, et al.
73. Biofilm Disruption Enhances Growth Rate and Carbohydrate-Active Enzyme Production in Anaerobic Fungi
P.A. Leggieri, M.T. Valentine, M.A. O'Malley.
72. Characterization and rank assignment criteria for the Anaerobic Fungi (Neocallimastigomycota)
M.S. Elshahed, R.A. Hanafy, Y. Cheng, S.S. Dagar, J.E. Edwards, V. Flad, et al.
71. Enzyme Discovery in Anaerobic Fungi (Neocallimastigomycetes) Enables Lignocellulosic Biorefinery Innovation
T.S. Lankiewicz, S.P. Lillington, M.A. O’Malley.
70. Thousands of Small, Novel Genes Predicted in Global Phage Genomes
B.J. Fremin, A.S. Bhatt, N.C. Kyrpides, A. Sengupta, A. Sczyrba, A.M. da Silva, et al.
69. Identification of Novel Membrane Proteins for Improved Lignocellulose Conversion
I.A. Podolsky, E.E. Schauer, S. Seppälä, M.A. O’Malley.
68. GPCR-FEX: A Fluoride-Based Selection System for Rapid GPCR Screening and Engineering
J.I. Yoo, T.A. Navaratna, P. Kolence, M.A. O’Malley.
2021
67. 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
J.L. Brown, C.L. Swift, S.J. Mondo, S. Seppälä, A. Salamov, V. Singan, et al.
66. Microbial communities and their enzymes facilitate degradation of recalcitrant polymers in anaerobic digestion
E.M. Blair, K.L. Dickson, M.A. O’Malley.
65. 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
P.A. Leggieri, C. Kerdman-Andrade, T.S. Lankiewicz, M.T. Valentine, et al.
64. Co-cultivation of anaerobic fungi with rumen bacteria establishes an antagonistic relationship
C.L. Swift, K.B. Louie, B.P. Bowen, C.A. Hooker, K.V. Solomon, V. Singan, et al.
63. A genomic catalog of stress response genes in anaerobic fungi for applications in bioproduction
C.L. Swift, N.G. Malinov, S.J. Mondo, A. Salamov, I.V. Grigoriev, M.A. O'Malley.
62. Homo-oligomerization of the human adenosine A2A receptor is driven by the intrinsically disordered C-terminus
K.D. Nguyen, M. Vigers, E. Sefah, S. Seppälä, J. Hoover, B. Mertz, et al.
61. A SWEET surprise: anaerobic fungal sugar transporters and chimeras enhance sugar uptake in yeast
I.A. Podolsky, S. Seppälä, H. Xu, Y.S. Jin, M.A. O'Malley.
60. Integrating systems and synthetic biology to understand and engineer microbiomes
P.A. Leggieri, Y. Liu, M. Hayes, B. Connors, S. Seppälä, M.A. O'Malley, et al.
59. Cellulosome localization patterns vary across life stages of anaerobic fungi
S.P. Lillington, W. Chrisler, C.H. Haitjema, S.P. Gilmore, C.R. Smallwood, et al.
58. Ecology and molecular targets of hypermutation in the global microbiome
S. Roux, B.G. Paul, S.C. Bagby, S. Nayfach, M.A. Allen, G. Attwood, et al.
57. Anaerobic gut fungi are an untapped reservoir of natural products
C.L. Swift, K.B. Louie, B.P. Bowen, H.M. Olson, S.O. Purvine, A. Salamov, et al.
56. The anaerobic fungi: challenges and opportunities for industrial lignocellulosic biofuel production
L.M.G. Saye, T.A. Navaratna, J.P.J. Chong, M.A. O’Malley, M.K. Theodorou, et al.
55. Experimentally validated reconstruction and analysis of a genome-scale metabolic model of an anaerobic Neocallimastigomycota fungus
S.E. Wilken, J.M. Monk, P.A. Leggieri, C.E. Lawson, T.S. Lankiewicz, S. Seppälä, et al.
54. Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes
X. Peng, S.E. Wilken, T.S. Lankiewicz, S.P. Gilmore, J.L. Brown, J.K. Henske, et al.
2020
53. A genomic catalog of Earth’s microbiomes
S. Nayfach, S. Roux, R. Seshadri, D. Udwary, N. Varghese, F. Schulz, D. Wu, et al.
52. The biotechnological potential of anaerobic gut fungi
V. Dollhofer, D. Young, S. Seppälä, C. Hooker, N. Youssef, M. Nagler, et al.
51. Engineered fluoride sensitivity enables biocontainment and selection of genetically modified yeasts
J.I. Yoo, S. Seppälä, M.A. OʼMalley.
50. Efficient and cost-effective bacterial mRNA sequencing from low input samples through ribosomal RNA depletion
C. Wangsanuwat, K. Heom, E. Liu, M.A. O’Malley.
49. Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber
L.H. Hagen, C.G. Brooke, C.A. Shaw, A.D. Norbeck, H. Piao, M.Ø. Arntzen, et al.
48. Lipo-chitooligosaccharides as regulatory signals of fungal growth and development
T.A. Rush, V. Puech-Pagès, A. Bascaules, P. Jargeat, F. Maillet, A. Haouy, et al.
47. An Arduino-based automatic pressure evaluation system to quantify growth of non‐model anaerobes in culture
S.E. Wilken, P.A. Leggieri, C. Kerdman‐Andrade, M. Reilly, M.K. Theodorou, et al.
46. Genomic and proteomic biases inform metabolic engineering strategies for anaerobic fungi
S. Seppälä, T.S. Lankiewicz, M. Saxena, J.K. Henske, A.A. Salamov, et al.
45. Nature’s recyclers: anaerobic microbial communities drive crude biomass deconstruction
S.P. Lillington, P.A. Leggieri, K.A. Heom, M.A. O’Malley.
44. Designing chimeric enzymes inspired by fungal cellulosomes
S.P. Gilmore, S.P. Lillington, C.H. Haitjema, R. de Groot, M.A. O'Malley.
43. Bridging non-overlapping reads illuminates high-order epistasis between distal protein sites in a GPCR
J.I. Yoo, P.S. Daugherty, M.A. O’Malley.
2019
42. Heterologous transporters from anaerobic fungi bolster fluoride tolerance in Saccharomyces cerevisiae
S. Seppälä, J.I. Yoo, D. Yur, M.A. O'Malley.
41. Co-cultivation of the anaerobic fungus Anaeromyces robustus with Methanobacterium bryantii enhances transcription of carbohydrate active enzymes
C.L. Swift, J.L. Brown, S. Seppälä, M.A. O’Malley.
40. Common principles and best practices for engineering microbiomes
C.E. Lawson, W.R. Harcombe, R. Hatzenpichler, S.R. Lindemann, F.E. Löffler, et al.
39. Top-down enrichment guides in formation of synthetic microbial consortia for biomass degradation
S.P. Gilmore, T.S. Lankiewicz, S.E. Wilken, J.L. Brown, J.A. Sexton, J.K. Henske, et al.
38. Harnessing nature's anaerobes for biotechnology and bioprocessing
I.A. Podolsky, S. Seppälä, T.S. Lankiewicz, J.L. Brown, C.L. Swift, M.A. O'Malley.
37. Linking ‘omics’ to function unlocks the biotech potential of non-model fungi
C.L. Swift, I.A. Podolsky, T.S. Lankiewicz, S. Seppälä, M.A. O'Malley.
2018
36. Catabolic repression in early-diverging anaerobic fungi is partially mediated by natural antisense transcripts
K.V. Solomon, J.K. Henske, S.P. Gilmore, A. Lipzen, I.V. Grigoriev, et al.
35. Biomass‐degrading enzymes are catabolite repressed in anaerobic gut fungi
J.K. Henske, S.P. Gilmore, C.H. Haitjema, K.V. Solomon, M.A. O'Malley.
34. Methods for genomic characterization & maintenance of anaerobic fungi
X. Peng, C.L. Swift, M.K. Theodorou, M.A. O’Malley.
33. Tuning vector stability and integration frequency elevates functional GPCR production and homogeneity in Saccharomyces cerevisiae
J.I. Yoo, M.A. O’Malley.
32. Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes
K.V. Solomon, C.H. Haitjema, J.K. Henske, S.P. Gilmore, D. Borges-Rivera, et al.
31. Substrate-based differential expression analysis reveals control of biomass degrading enzymes in Pycnoporus cinnabarinus
J.K. Henske, S.D. Springer, M.A. O'Malley, A. Butler.
30. In silico identification of microbial partners to form consortia with anaerobic fungi
S.E. Wilken, M. Saxena, L.R. Petzold, M.A. O’Malley.
2017
29. Transcriptomic characterization of Caecomyces churrovis: a novel, non-rhizoid forming lignocellulolytic anaerobic fungus
J.K. Henske, S.P. Gilmore, D. Knop, F.J. Cunningham, J.Sexton, et al.
28. Metabolic characterization of anaerobic fungi provides a path forward for bioprocessing of crude lignocellulose
J.K. Henske, S.E. Wilken, K.V. Solomon, C.R. Smallwood, V. Shutthanandan, et al.
27. The importance of sourcing enzymes from non-conventional fungi for metabolic engineering and biomass breakdown
S. Seppälä, D. Knop, K.V. Solomon, M.A. O’Malley.
26. PCR and omics-based techniques to study the diversity, ecology, and biology of anaerobic fungi: insights, challenges, and opportunities
J.E. Edwards, R.J. Forster, T.M. Callaghan, V. Dollhofer, S.S. Dagar, Y. Cheng, et al.
25. Genomic analysis of methanogenic archaea reveals a shift towards energy conservation
S.P. Gilmore, J.K. Henske, J.A. Sexton, K.V. Solomon, S. Seppälä, J.I. Yoo, et al.
24. A parts list for fungal cellulosomes revealed by comparative genomics
C.H. Haitjema, S.P. Gilmore, J.K. Henske, K.V. Solomon, R. De Groot, A. Kuo, et al.
23. Widespread adenine N6-methylation of active genes in fungi
S.J. Mondo, R.O. Dannebaum, R.C. Kuo, K.B. Louie, A.J. Bewick, K. LaButti, et al.
22. Engineering live cell surfaces with functional polymers via cytocompatible controlled radical polymerization
J. Niu, D.J. Lunn, A. Pusuluri, J.I. Yoo, M.A. O'Malley, S. Mitragotri, H.T. Soh, et al.
2016
21. Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters
S. Seppälä, K.V. Solomon, S.P. Gilmore, J.K. Henske, M.A. O'Malley.
20. Microbial communities for bioprocessing: lessons learned from nature
X.Peng, S.P. Gilmore, M.A. O’Malley.
19. Adenosine A2a receptors form distinct oligomers in protein detergent complexes
N.S. Sconenbach, M.D. Rieth, S. Han, M.A. O’Malley.
18. Emerging technologies for protease engineering: New tools to clear out disease
J.L. Guerrero, P.S. Daugherty, M.A. O'Malley.
17. Fungal diversity notes 253-366: taxonomic and phylogenetic contributions to fungal taxa
K. V. Solomon, J. K. Henske, C. H. Haitjema, S. P. Gilmore, M. K. Theodorou, M. A. O’Malley.
16. Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi
K.V. Solomon, J.K. Henske, M.K. Theodorou, M.A. O'Malley.
15. Mitochondrial targeting increases specific activity of a heterologous valine assimilation pathway in Saccharomyces cerevisiae
K.V. Solomon, E. Ovadia, F. Yu, W. Mizunashi, M.A. O'Malley.
14. Intracellular FRET-based screen for redesigning the specificity of secreted proteases
J.L. Guerrero, M.A. O'Malley, P.S. Daugherty.
2015
13. Driving biomass breakdown through engineered cellulosomes
S.P. Gilmore, J.K. Henske, M.A. O'Malley.
2014
12. Structure and function of G protein-coupled receptor oligomers: implications for drug
M.A. O'Malley, N. Schonenbach, S. Hussain.
11. Extracting data from the muck: deriving biological insight from complex microbial communities and non-model organisms with next generation sequencing
K.V. Solomon, C.H. Haitjema, D.A. Thompson, M.A. O'Malley.
10. Anaerobic gut fungi: advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production
C.H. Haitjema, K.V. Solomon, J.K. Henske, M.K. Theodorou, M.A. O'Malley.
2011
9. Evaluating expression and catalytic activity of anaerobic fungal fibrolytic enzymes native to Piromyces sp. E2 in Saccharomyces cerevisiae
M.A. O'Malley, M.K. Theodorou, C.A. Kaiser.
8. Neuromethods, Vol. 60: Methods for the Discovery and Characterization of G Protein‐Coupled Receptors
M.A. O'Malley.
7. 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
M.A. O'Malley, M.E. Helgeson, N.J. Wagner, A.S. Robinson.
6. The morphology and composition of cholesterol-rich micellar nanostructures determine transmembrane protein (GPCR) activity
M.A. O'Malley, M.E. Helgeson, N.J. Wagner, A.S. Robinson.
2010
5. Analysis of Adenosine A2a Receptor Stability: Effects of Ligands and Disulfide Bonds
M.A. O'Malley, A.N. Naranjo, T. Lazarova, A.S. Robinson.
2009
4. Progress toward heterologous expression of active G‐protein‐coupled receptors in Saccharomyces cerevisiae: Linking cellular stress response with translocation
M.A. O'Malley, J.D. Mancini, C.L. Young, E.C. McCusker, D. Raden, et al.
2008
3. Heterologous GPCR expression: a bottleneck to obtaining crystal structures
E.C. McCusker, S.E. Bane, M.A. O'Malley, A.S. Robinson.
2. Optimization of the Human Adenosine A2a Receptor Yields in Saccharomyces cerevisiae
A. Wedekind, M.A. O'Malley, R.T. Niebauer, A.S. Robinson.
2007
1. High-level expression in Saccharomyces cerevisiae enables isolation and spectroscopic characterization of functional human adenosine A2a receptor
M.A. O'Malley, T. Lazarova, Z.T. Britton, A.S. Robinson.
Patents
- M.A. O'Malley, I.A. Podolsky, S. Seppala.
US Patent 12,098,171: Hybrid sugar transporters with altered sugar transport activity and uses thereof. - M.A. O'Malley, K. Solomon, C. Haitjema.
US Patent 12,037,371: Proteins from anaerobic fungi and uses thereof. - M.A. O'Malley, K. Solomon, C. Haitjema.
US Patent 11,021,524: Proteins from anaerobic fungi and uses thereof. - MA. O'Malley, K. Solomon, C. Haitjema.
US Patent 10,717,768: Proteins from anaerobic fungi and uses thereof. - M.A. O'Malley, K. Solomon, W. Mizunashi, F. Yu.M
US Patent 10,676,766: Biological production of methyl methacrylate.