Timothy J. Donohue

• Metagenomes and metagenome-assembled genomes from microbial communities in a biological nutrient removal plant operated at Hamptons Road Sanitation District (HRSD) with high and low dissolved oxygen conditions
  May 14, 2026
  Blaise M Enuh, Kevin S Myers, Charles Bott, Stephanie Klaus, Kester McCullough, Lilian McIntosh, Natalie Beach, Michelle Young, Timothy J Donohue, Daniel R Noguera Microbiology resource announcements
• Using Novosphingobium aromaticivorans for Concurrent Production of Intracellular and Extracellular Products from Aromatics Extracted from Poplar Biomass
  March 19, 2026
  Bumkyu Kim, Benjamin W Hall, Dennis V Haak, Jason Coplien, Steven D Karlen, Timothy J Donohue, Daniel R Noguera ACS ES&T engineering
• Genome sequences of nicotine-degrading Pseudomonas and Stutzerimonas strains isolated from nicotine-enriched activated sludge
  February 27, 2026
  N Myers, T Navaratna, B Kim, K S Myers, D R Noguera, T J Donohue, J C A Bardwell Microbiology resource announcements
• Solvent selection for a biomass-to-bioproduct pipeline through integrated reductive catalytic fractionation and microbial funneling
  February 27, 2026
  Sripada, S., Rajbangshi, J., Aboagye, E. A., Garcia, M. A., Donohue, T. J., Noguera, D. R., Van Lehn, R. C., Maravelias, C. T., Karlen, S. D., and C. Sener Green Chemistry
• Metagenomes and metagenome-assembled genomes from a nutrient removal plant at Los Angeles County Sanitation Districts (LACSD) that transitioned from high to low dissolved oxygen
  February 23, 2026
  Blaise M Enuh, Kevin S Myers, Phil Ackman, Thomas Weiland, Natalie Beach, Michelle Young, Timothy J Donohue, Daniel R Noguera Microbiology resource announcements
• Engineered Accumulation of Protocatechuate in Corn Biomass to Enhance Biomanufacturing
  November 28, 2025
  Yang Tian, Bumkyu Kim, Irem Pamukçu, Emine Akyuz Turumtay, Alexis H Tan, Victoria Saini, Ariana Irma Chavez, Anna Tang, Anna Z Su, Edward E K Baidoo, Jorge Rencoret, José C Del Río, Timothy J Donohue, Daniel R Noguera, Aymerick Eudes ACS sustainable chemistry & engineering
• Novosphingobium aromaticivorans LigR coordinates transcription of genes involved in metabolism of multiple types of aromatics
  November 28, 2025
  Laura Rodríguez-Castro, Kevin S Myers, Alexandra M Linz, Erin L Mettert, Walter Camp, Patricia J Kiley, Daniel R Noguera, Timothy J Donohue mSystems
• Integrating catalytic fractionation and microbial funneling to produce 2-pyrone-4,6-dicarboxylic acid and ethanol
  November 4, 2025
  Canan Sener, Emmanuel A. Aboagye, Steven D. Karlen, Jose M. Perez, German E. Umana, Yaoping Zhang, José Serate, Timothy J. Donohue, Daniel R. Noguera, Christos T. Maravelias Green Chemistry
• Biotransformation of Phenolics in Spent Liquor from Aqueous Ammonia Pretreatment
  September 10, 2025
  Shengfei Zhou, Maximiliano García-Mancilla, Jordi Francis Clar, Troy M Runge, Timothy J Donohue, Daniel R Noguera, Steven D Karlen ChemSusChem
• MarK, a Novosphingobium aromaticivorans kinase required for catabolism of multiple aromatic monomers
  August 21, 2025
  Benjamin W Hall, Jeanette C Neri, Craig A Bingman, Avery C Vilbert, Jacob B Eckmann, Kevin S Myers, Bryan S Sibert, Elizabeth R Wright, Brian G Fox, Patricia J Kiley, Daniel R Noguera, Timothy J Donohue The Journal of biological chemistry
• Transcriptomic data sets for Novosphingobium aromaticivorans DSM12444 and a ΔSARO_RS14285 mutant grown in the presence of glucose and either protocatechuic, vanillic, syringic, or 4-coumaric acid
  July 31, 2025
  Laura Rodriguez-Castro, Kevin S Myers, Daniel R Noguera, Timothy J Donohue Microbiology resource announcements
• Using DNA affinity purification sequencing (DAP-seq) to identify in vitro binding sites of potential Novosphingobium aromaticivorans DSM12444 transcription factors
  July 22, 2025
  Kevin S Myers, Alexandra M Linz, Leo A Baumgart, Yu Zhang, Ian Blaby, Ritesh Mewalal, Vivian Ng, Daniel R Noguera, Timothy J Donohue Microbiology resource announcements
• Metagenome-assembled genomes from microbial communities producing lactic acid from dairy residues
  April 29, 2025
  Faith Koester, Kevin S Myers, Timothy J Donohue, Daniel R Noguera Microbiology resource announcements
• RB-TnSeq barcode abundance data sets for Novosphingobium aromaticivorans grown on the β-5-linked aromatic dimer dehydrodiconiferyl alcohol
  December 12, 2024
  Fletcher Metz, Marco N Allemann, Joshua K Michener, Kevin S Myers, Fachuang Lu, Daniel R Noguera, Timothy J Donohue Microbiology resource announcements
• Quantitating Storage Granule Size, Accumulation, and Localization in Rhodobacter sphaeroides Using Cryo-Electron Tomography and Light Microscopy
  October 31, 2024
  Daniel Parrell, Rachelle A S Lemke, Joseph Olson, Timothy J Donohue, Elizabeth Wright Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada
• Transcriptomic data sets for Novosphingobium aromaticivorans grown with the β-5-linked aromatic dimer dehydrodiconiferyl alcohol and the related G-aromatic monomers vanillin and ferulic acid
  October 4, 2024
  Fletcher Metz, Kevin S Myers, Fachuang Lu, Daniel R Noguera, Timothy J Donohue Microbiology resource announcements
• Tools for genetic engineering and gene expression control in Novosphingobium aromaticivorans and Rhodobacter sphaeroides
  September 26, 2024
  Ashley N Hall, Benjamin W Hall, Kyle J Kinney, Gabby G Olsen, Amy B Banta, Daniel R Noguera, Timothy J Donohue, Jason M Peters Applied and environmental microbiology
• Scientists' call to action: Microbes, planetary health, and the Sustainable Development Goals
  September 20, 2024
  Thomas W Crowther, Rino Rappuoli, Cinzia Corinaldesi, Roberto Danovaro, Timothy J Donohue, Jef Huisman, Lisa Y Stein, James Kenneth Timmis, Kenneth Timmis, Matthew Z Anderson, Lars R Bakken, Matthew Baylis, Michael J Behrenfeld, Philip W Boyd, Ian Brettell, Ricardo Cavicchioli, Camille S Delavaux, Christine M Foreman, Janet K Jansson, Britt Koskella, Kat Milligan-McClellan, Justin A […]
• Insights into Alphaproteobacterial regulators of cell envelope remodeling
  September 4, 2024
  Bryan Lakey, François Alberge, Timothy J Donohue Current opinion in microbiology
• Quantitative Analysis of Rhodobacter sphaeroides Storage Organelles via Cryo-Electron Tomography and Light Microscopy
  August 29, 2024
  Daniel Parrell, Joseph Olson, Rachelle A Lemke, Timothy J Donohue, Elizabeth R Wright Biomolecules
• Auto-MuRCiS: a streamlined software package for analysis of multiplex, randomized CRISPR interference sequencing data
  July 31, 2024
  Kevin S Myers, Michael Place, Audrey P Gasch, Daniel R Noguera, Timothy J Donohue Microbiology resource announcements
• Catabolism of β-5 linked aromatics by Novosphingobium aromaticivorans
  July 16, 2024
  Fletcher Metz, Abigail M Olsen, Fachuang Lu, Kevin S Myers, Marco N Allemann, Joshua K Michener, Daniel R Noguera, Timothy J Donohue mBio
• Achieving high productivity of 2-pyrone-4,6-dicarboxylic acid from aqueous aromatic streams with Novosphingobium aromaticivorans
  June 20, 2024
  Bumkyu Kim, Jose M. Perez, Steven D. Karlen, Jason Coplien, Timothy J. Donohue, Daniel R. Noguera Green Chemistry
• Metagenome-assembled genomes from microbiomes fermenting dairy coproducts
  May 31, 2024
  Kevin A Walters, Kevin S Myers, Timothy J Donohue, Daniel R Noguera Microbiology resource announcements
• Engineering Novosphingobium aromaticivorans to produce cis,cis-muconic acid from biomass aromatics
  December 20, 2023
  Avery C Vilbert, Wayne S Kontur, Derek Gille, Daniel R Noguera, Timothy J Donohue Applied and environmental microbiology
• A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes
  December 14, 2023
  Nicole A Ellis, Kevin S Myers, Jessica Tung, Anne Davidson Ward, Kathryn Johnston, Katherine E Bonnington, Timothy J Donohue, Matthias P Machner eLife
• Production of carotenoids from aromatics and pretreated lignocellulosic biomass by Novosphingobium aromaticivorans
  November 28, 2023
  Benjamin W Hall, Wayne S Kontur, Jeanette C Neri, Derek M Gille, Daniel R Noguera, Timothy J Donohue Applied and environmental microbiology
• An account of American Academy of Microbiology reforms and pandemic operations
  October 26, 2023
  Arturo Casadevall, Peggy A Cotter, Lynn Enquist, Timothy J Donohue, Stefano Bertuzzi, Nguyen K Nguyen mBio
• Tools for Genetic Engineering and Gene Expression Control in Novosphingobium aromaticivorans and Rhodobacter sphaeroides
  September 4, 2023
  Ashley N Hall, Benjamin W Hall, Kyle J Kinney, Gabby G Olsen, Amy B Banta, Daniel R Noguera, Timothy J Donohue, Jason M Peters bioRxiv : the preprint server for biology
• A previously uncharacterized divisome-associated lipoprotein, DalA, is needed for normal cell division in Rhodobacterales
  June 30, 2023
  François Alberge, Bryan D Lakey, Ryan E Schaub, Alice C Dohnalkova, Kimberley C Lemmer, Joseph P Dillard, Daniel R Noguera, Timothy J Donohue mBio
• A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate
  June 16, 2023
  Kevin A Walters, Geethaanjali Mohan, Kevin S Myers, Abel T Ingle, Timothy J Donohue, Daniel R Noguera Frontiers in bioengineering and biotechnology
• The role of CenKR in the coordination of Rhodobacter sphaeroides cell elongation and division
  June 7, 2023
  Bryan D Lakey, François Alberge, Daniel Parrell, Elizabeth R Wright, Daniel R Noguera, Timothy J Donohue mBio
• Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization
  June 1, 2023
  Kevin S Myers, Abel T Ingle, Kevin A Walters, Nathaniel W Fortney, Matthew J Scarborough, Timothy J Donohue, Daniel R Noguera Frontiers in bioengineering and biotechnology
• A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes
  March 22, 2023
  Nicole A Ellis, Kevin S Myers, Jessica Tung, Anne Davidson Ward, Kathryn Johnston, Katherine E Bonnington, Timothy J Donohue, Matthias P Machner bioRxiv : the preprint server for biology
• A broad specificity β-propeller enzyme from Rhodopseudomonas palustris that hydrolyzes many lactones including γ-valerolactone
  December 12, 2022
  Benjamin W Hall, Craig A Bingman, Brian G Fox, Daniel R Noguera, Timothy J Donohue The Journal of biological chemistry
• Metagenome-Assembled Genomes from a Microbiome Grown in Dairy Manure Hydrolysate
  July 27, 2022
  Abel T Ingle, Nathaniel W Fortney, Kevin S Myers, Kevin A Walters, Matthew J Scarborough, Timothy J Donohue, Daniel R Noguera Microbiology resource announcements
• Metagenomes and Metagenome-Assembled Genomes from Microbiomes Metabolizing Thin Stillage from an Ethanol Biorefinery
  July 21, 2022
  Nathaniel W Fortney, Kevin S Myers, Abel T Ingle, Kevin A Walters, Matthew J Scarborough, Timothy J Donohue, Daniel R Noguera Microbiology resource announcements
• Metagenomes and Metagenome-Assembled Genomes from Microbial Communities Fermenting Ultrafiltered Milk Permeate
  June 30, 2022
  Kevin A Walters, Kevin S Myers, Hui Wang, Nathaniel W Fortney, Abel T Ingle, Matthew J Scarborough, Timothy J Donohue, Daniel R Noguera Microbiology resource announcements
• The essential Rhodobacter sphaeroides CenKR two-component system regulates cell division and envelope biosynthesis
  June 29, 2022
  Bryan D Lakey, Kevin S Myers, François Alberge, Erin L Mettert, Patricia J Kiley, Daniel R Noguera, Timothy J Donohue PLoS genetics
• Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms
  June 24, 2022
  Caryn S Wadler, John F Wolters, Nathaniel W Fortney, Kurt O Throckmorton, Yaoping Zhang, Caroline R Miller, Rachel M Schneider, Evelyn Wendt-Pienkowski, Cameron R Currie, Timothy J Donohue, Daniel R Noguera, Chris Todd Hittinger, Michael G Thomas Biotechnology for biofuels and bioproducts
• Metagenomes from 25 Low-Abundance Microbes in a Partial Nitritation Anammox Microbiome
  May 16, 2022
  Natalie K Beach, Kevin S Myers, Timothy J Donohue, Daniel R Noguera Microbiology resource announcements
• iNovo479: Metabolic Modeling Provides a Roadmap to Optimize Bioproduct Yield from Deconstructed Lignin Aromatics by Novosphingobium aromaticivorans
  April 21, 2022
  Alexandra M Linz, Yanjun Ma, Samuel Scholz, Daniel R Noguera, Timothy J Donohue Metabolites
• Correction for Beach et al., "Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome"
  April 13, 2022
  Natalie K Beach, Kevin S Myers, Brian R Owen, Matt Seib, Timothy J Donohue, Daniel R Noguera mSystems
• Metagenome-Assembled Genomes from a Microbiome Converting Xylose to Medium-Chain Carboxylic Acids
  March 28, 2022
  Matthew J Scarborough, Kevin S Myers, Nathaniel W Fortney, Abel T Ingle, Timothy J Donohue, Daniel R Noguera Microbiology resource announcements
• Editorial overview: Microbial activities powering society
  March 17, 2022
  Timothy J Donohue Current opinion in microbiology
• Integrating lignin depolymerization with microbial funneling processes using agronomically relevant feedstocks
  March 10, 2022
  Jose M. Perez, Canan Sener, Shamik Misra, German E. Umana, Jason Coplien, Dennis Haak, Yanding Li, Christos T. Maravelias, Steven D. Karlen, John Ralph, Timothy J. Donohue, Daniel R. Noguera Green Chemistry
• Using Genome Scale Mutant Libraries to Identify Essential Genes
  October 28, 2021
  Kevin S Myers, Piyush Behari Lal, Daniel R Noguera, Timothy J Donohue Methods in molecular biology (Clifton, N.J.)
• Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome
  October 12, 2021
  Natalie K Beach, Kevin S Myers, Brian R Owen, Matt Seib, Timothy J Donohue, Daniel R Noguera mSystems
• Aromatic Dimer Dehydrogenases from Novosphingobium aromaticivorans Reduce Monoaromatic Diketones
  October 6, 2021
  Alexandra M Linz, Yanjun Ma, Jose M Perez, Kevin S Myers, Wayne S Kontur, Daniel R Noguera, Timothy J Donohue Applied and environmental microbiology
• Mixed Acid Fermentation of Carbohydrate-Rich Dairy Manure Hydrolysate
  August 20, 2021
  Abel T Ingle, Nathaniel W Fortney, Kevin A Walters, Timothy J Donohue, Daniel R Noguera Frontiers in bioengineering and biotechnology
• Diverse Profile of Fermentation Byproducts From Thin Stillage
  August 2, 2021
  Nathaniel W Fortney, Nathaniel J Hanson, Paula R F Rosa, Timothy J Donohue, Daniel R Noguera Frontiers in bioengineering and biotechnology
• Promoter Architecture Differences among Alphaproteobacteria and Other Bacterial Taxa
  July 13, 2021
  Kevin S Myers, Daniel R Noguera, Timothy J Donohue mSystems
• Stratifying Deterioration Risk by Acuity at Admission Offers Triage Insights for Coronavirus Disease 2019 Patients
  May 3, 2021
  Joseph Beals, Jaime J Barnes, Daniel J Durand, Joan M Rimar, Thomas J Donohue, S Mahfuz Hoq, Kathy W Belk, Alpesh N Amin, Michael J Rothman Critical care explorations
• Delila-PY, a Pipeline for Utilizing the Delila Suite of Software to Identify Potential DNA Binding Motifs
  April 16, 2021
  Kevin S Myers, Michael Place, Jacek Kominek, Daniel R Noguera, Timothy J Donohue Microbiology resource announcements
• Kinetic modeling of anaerobic degradation of plant-derived aromatic mixtures by Rhodopseudomonas palustris
  March 6, 2021
  Yanjun Ma, Timothy J Donohue, Daniel R Noguera Biodegradation
• Redundancy in aromatic O-demethylation and ring opening reactions in Novosphingobium aromaticivorans and their impact in the metabolism of plant derived phenolics
  February 13, 2021
  Jose M Perez, Wayne S Kontur, Carson Gehl, Derek M Gille, Yanjun Ma, Alyssa V Niles, German Umana, Timothy J Donohue, Daniel R Noguera Applied and environmental microbiology
• A High-Throughput Method for Identifying Novel Genes That Influence Metabolic Pathways Reveals New Iron and Heme Regulation in Pseudomonas aeruginosa
  February 3, 2021
  David G Glanville, Caroline Mullineaux-Sanders, Christopher J Corcoran, Brian T Burger, Saheed Imam, Timothy J Donohue, Andrew T Ulijasz mSystems
• Rewiring the specificity of extracytoplasmic function sigma factors
  December 15, 2020
  Horia Todor, Hendrik Osadnik, Elizabeth A Campbell, Kevin S Myers, Hao Li, Timothy J Donohue, Carol A Gross Proceedings of the National Academy of Sciences of the United States of America
• A majority of Rhodobacter sphaeroides promoters lack a crucial RNA polymerase recognition feature, enabling coordinated transcription activation
  November 10, 2020
  Kemardo K Henry, Wilma Ross, Kevin S Myers, Kimberly C Lemmer, Jessica M Vera, Robert Landick, Timothy J Donohue, Richard L Gourse Proceedings of the National Academy of Sciences of the United States of America
• Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models
  September 30, 2020
  Matthew J Scarborough, Joshua J Hamilton, Elizabeth A Erb, Timothy J Donohue, Daniel R Noguera mSystems
• Genome-Wide Identification of Transcription Start Sites in Two Alphaproteobacteria, Rhodobacter sphaeroides 2.4.1 and Novosphingobium aromaticivorans DSM 12444
  September 5, 2020
  Kevin S Myers, Jessica M Vera, Kimberly C Lemmer, Alexandra M Linz, Robert Landick, Daniel R Noguera, Timothy J Donohue Microbiology resource announcements
• COnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus Database
  June 20, 2020
  Kevin S Myers, Michael Place, Daniel R Noguera, Timothy J Donohue Microbiology resource announcements
• A bacterial biosynthetic pathway for methylated furan fatty acids
  May 22, 2020
  Rachelle A S Lemke, Stephanie M Olson, Kaitlin Morse, Steven D Karlen, Alan Higbee, Emily T Beebe, John Ralph, Joshua J Coon, Brian G Fox, Timothy J Donohue The Journal of biological chemistry
• The NtrYX Two-Component System Regulates the Bacterial Cell Envelope
  May 21, 2020
  Kimberly C Lemmer, François Alberge, Kevin S Myers, Alice C Dohnalkova, Ryan E Schaub, Jonathan D Lenz, Saheed Imam, Joseph P Dillard, Daniel R Noguera, Timothy J Donohue mBio
• Anaerobic Degradation of Syringic Acid by an Adapted Strain of Rhodopseudomonas palustris
  November 17, 2019
  J Zachary Oshlag, Yanjun Ma, Kaitlin Morse, Brian T Burger, Rachelle A Lemke, Steven D Karlen, Kevin S Myers, Timothy J Donohue, Daniel R Noguera Applied and environmental microbiology
• Medium-Chain Fatty Acid Synthesis by "Candidatus Weimeria bifida" gen. nov., sp. nov., and "Candidatus Pseudoramibacter fermentans" sp. nov
  November 10, 2019
  Matthew J Scarborough, Kevin S Myers, Timothy J Donohue, Daniel R Noguera Applied and environmental microbiology
• Discovery of the extracytoplasmic function σ factors
  May 23, 2019
  Michael A Lonetto, Timothy J Donohue, Carol A Gross, Mark J Buttner Molecular microbiology
• Shedding light on a Group IV (ECF11) alternative σ factor
  May 22, 2019
  Timothy J Donohue Molecular microbiology
• Funneling aromatic products of chemically depolymerized lignin into 2-pyrone-4-6-dicarboxylic acid with Novosphingobium aromaticivorans
  February 27, 2019
  Jose M. Perez, Wayne S. Kontur, Manar Alherech, Jason Coplien, Steven D. Karlen, Shannon S. Stahl, Timothy J. Donohue and Daniel R. Noguera Green Chemistry
• A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β(R)-aryl ether bond reveals the diversity of bacterial β-etherases
  December 14, 2018
  Wayne S Kontur, Charles N Olmsted, Larissa M Yusko, Alyssa V Niles, Kevin A Walters, Emily T Beebe, Kirk A Vander Meulen, Steven D Karlen, Daniel L Gall, Daniel R Noguera, Timothy J Donohue The Journal of biological chemistry
• Metatranscriptomic and Thermodynamic Insights into Medium-Chain Fatty Acid Production Using an Anaerobic Microbiome
  December 4, 2018
  Matthew J Scarborough, Christopher E Lawson, Joshua J Hamilton, Timothy J Donohue, Daniel R Noguera mSystems
• Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production
  July 24, 2018
  Matthew J Scarborough, Griffin Lynch, Mitch Dickson, Mick McGee, Timothy J Donohue, Daniel R Noguera Biotechnology for biofuels
• Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin
  February 17, 2018
  Wayne S Kontur, Craig A Bingman, Charles N Olmsted, Douglas R Wassarman, Arne Ulbrich, Daniel L Gall, Robert W Smith, Larissa M Yusko, Brian G Fox, Daniel R Noguera, Joshua J Coon, Timothy J Donohue The Journal of biological chemistry
• In Vitro Enzymatic Depolymerization of Lignin with Release of Syringyl, Guaiacyl, and Tricin Units
  November 29, 2017
  Daniel L Gall, Wayne S Kontur, Wu Lan, Hoon Kim, Yanding Li, John Ralph, Timothy J Donohue, Daniel R Noguera Applied and environmental microbiology
• Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides
  July 27, 2017
  Brian T Burger, Saheed Imam, Matthew J Scarborough, Daniel R Noguera, Timothy J Donohue mSystems
• Mutations That Alter the Bacterial Cell Envelope Increase Lipid Production
  May 25, 2017
  Kimberly C Lemmer, Weiping Zhang, Samantha J Langer, Alice C Dohnalkova, Dehong Hu, Rachelle A Lemke, Jeff S Piotrowski, Galya Orr, Daniel R Noguera, Timothy J Donohue mBio
• Biochemical transformation of lignin for deriving valued commodities from lignocellulose
  March 28, 2017
  Daniel L Gall, John Ralph, Timothy J Donohue, Daniel R Noguera Current opinion in biotechnology
• Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges
  May 15, 2016
  Martin J Blaser, Zoe G Cardon, Mildred K Cho, Jeffrey L Dangl, Timothy J Donohue, Jessica L Green, Rob Knight, Mary E Maxon, Trent R Northen, Katherine S Pollard, Eoin L Brodie mBio
• Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6
  March 5, 2016
  Jose Henrique Pereira, Richard A Heins, Daniel L Gall, Ryan P McAndrew, Kai Deng, Keefe C Holland, Timothy J Donohue, Daniel R Noguera, Blake A Simmons, Kenneth L Sale, John Ralph, Paul D Adams The Journal of biological chemistry
• Different Functions of Phylogenetically Distinct Bacterial Complex I Isozymes
  February 3, 2016
  Melanie A Spero, Joshua R Brickner, Jordan T Mollet, Tippapha Pisithkul, Daniel Amador-Noguez, Timothy J Donohue Journal of bacteriology
• Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin
  December 6, 2015
  Kate E Helmich, Jose Henrique Pereira, Daniel L Gall, Richard A Heins, Ryan P McAndrew, Craig Bingman, Kai Deng, Keefe C Holland, Daniel R Noguera, Blake A Simmons, Kenneth L Sale, John Ralph, Timothy J Donohue, Paul D Adams, George N Phillips The Journal of biological chemistry
• MICROBIOME. A unified initiative to harness Earth's microbiomes
  October 30, 2015
  A P Alivisatos, M J Blaser, E L Brodie, M Chun, J L Dangl, T J Donohue, P C Dorrestein, J A Gilbert, J L Green, J K Jansson, R Knight, M E Maxon, M J McFall-Ngai, J F Miller, K S Pollard, E G Ruby, S A Taha, Unified Microbiome Initiative Consortium Science (New […]
• A Cardiolipin-Deficient Mutant of Rhodobacter sphaeroides Has an Altered Cell Shape and Is Impaired in Biofilm Formation
  August 19, 2015
  Ti-Yu Lin, Thiago M A Santos, Wayne S Kontur, Timothy J Donohue, Douglas B Weibel Journal of bacteriology
• Metabolism of Multiple Aromatic Compounds in Corn Stover Hydrolysate by Rhodopseudomonas palustris
  June 30, 2015
  Samantha Austin, Wayne S Kontur, Arne Ulbrich, J Zachary Oshlag, Weiping Zhang, Alan Higbee, Yaoping Zhang, Joshua J Coon, David B Hodge, Timothy J Donohue, Daniel R Noguera Environmental science & technology
• Phylogenomic analysis and predicted physiological role of the proton-translocating NADH:quinone oxidoreductase (complex I) across bacteria
  April 16, 2015
  Melanie A Spero, Frank O Aylward, Cameron R Currie, Timothy J Donohue mBio
• Oxygen-dependent regulation of bacterial lipid production
  March 4, 2015
  Kimberly C Lemmer, Alice C Dohnalkova, Daniel R Noguera, Timothy J Donohue Journal of bacteriology
• An integrated approach to reconstructing genome-scale transcriptional regulatory networks
  February 28, 2015
  Saheed Imam, Daniel R Noguera, Timothy J Donohue PLoS computational biology
• CceR and AkgR regulate central carbon and energy metabolism in alphaproteobacteria
  February 5, 2015
  Saheed Imam, Daniel R Noguera, Timothy J Donohue mBio
• Global analysis of photosynthesis transcriptional regulatory networks
  December 16, 2014
  Saheed Imam, Daniel R Noguera, Timothy J Donohue PLoS genetics
• Quantifying the effects of light intensity on bioproduction and maintenance energy during photosynthetic growth of Rhodobacter sphaeroides
  November 28, 2014
  Saheed Imam, Colin M Fitzgerald, Emily M Cook, Timothy J Donohue, Daniel R Noguera Photosynthesis research
• A group of sequence-related sphingomonad enzymes catalyzes cleavage of β-aryl ether linkages in lignin β-guaiacyl and β-syringyl ether dimers
  September 19, 2014
  Daniel L Gall, John Ralph, Timothy J Donohue, Daniel R Noguera Environmental science & technology
• Development of a GC/Quadrupole-Orbitrap mass spectrometer, part I: design and characterization
  September 11, 2014
  Amelia C Peterson, Jan-Peter Hauschild, Scott T Quarmby, Dirk Krumwiede, Oliver Lange, Rachelle A S Lemke, Florian Grosse-Coosmann, Stevan Horning, Timothy J Donohue, Michael S Westphall, Joshua J Coon, Jens Griep-Raming Analytical chemistry
• Synthesis and scavenging role of furan fatty acids
  August 6, 2014
  Rachelle A S Lemke, Amelia C Peterson, Eva C Ziegelhoffer, Michael S Westphall, Henrik Tjellström, Joshua J Coon, Timothy J Donohue Proceedings of the National Academy of Sciences of the United States of America
• Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains
  August 6, 2014
  Nikos C Kyrpides, Philip Hugenholtz, Jonathan A Eisen, Tanja Woyke, Markus Göker, Charles T Parker, Rudolf Amann, Brian J Beck, Patrick S G Chain, Jongsik Chun, Rita R Colwell, Antoine Danchin, Peter Dawyndt, Tom Dedeurwaerdere, Edward F DeLong, John C Detter, Paul De Vos, Timothy J Donohue, Xiu-Zhu Dong, Dusko S Ehrlich, Claire Fraser, Richard […]
• A Rhodobacter sphaeroides protein mechanistically similar to Escherichia coli DksA regulates photosynthetic growth
  May 1, 2014
  Christopher W Lennon, Kimberly C Lemmer, Jessica L Irons, Max I Sellman, Timothy J Donohue, Richard L Gourse, Wilma Ross mBio
• Prospective chest pain evaluation in the emergency department with use of high-sensitivity C-reactive protein (PROCEED-CRP study)
  April 30, 2014
  Costin N Ionescu, Michael P Chrissoheris, Hannah B Slim, Martin Slade, Joyce Oen-Hsiao, Thomas J Donohue, Amenuve Bekui, Andre E Ghantous Connecticut medicine
• Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 β-aryl etherase pathway
  February 11, 2014
  Daniel L Gall, Hoon Kim, Fachuang Lu, Timothy J Donohue, Daniel R Noguera, John Ralph The Journal of biological chemistry
• The puf operon region of Rhodobacter sphaeroides
  January 16, 2014
  T J Donohue, P J Kiley, S Kaplan Photosynthesis research
• Global insights into energetic and metabolic networks in Rhodobacter sphaeroides
  September 17, 2013
  Saheed Imam, Daniel R Noguera, Timothy J Donohue BMC systems biology
• Psychosocial and cardiac outcomes of yoga for ICD patients: a randomized clinical control trial
  August 29, 2013
  Stefanie C F Toise, Samuel F Sears, Mark H Schoenfeld, Mark L Blitzer, Mark A Marieb, John H Drury, Martin D Slade, Thomas J Donohue Pacing and clinical electrophysiology : PACE

Our laboratory analyzes networks that microbes use to grow or produce bioproducts from renewable resources. To dissect this fundamentally important problem, we dissect genomic, metabolic and regulatory pathways of bacteria that convert renewable resources, such as non-edible lignocellulosic plant biomass, into products that are currently derived from fossil fuels. By mining genome sequence databases, coupling genomic (microarrays & RNAseq, proteomics, metabolomics), computational, molecular and synthetic biology techniques, we define how carbon and energy in nutrients is partitioned into cell growth or formation of bioproducts. The metabolic pathways, signal transduction networks, transcription factors, and signals that control these processes are identified, modelled or re-engineered using mutants, in vitro systems and in silico models. Our long range goals are to understand energy-conserving pathways of societal importance, and to combine computational and experimental systems to design microbial machines with increased capacity to utilize renewable resources, or enable a green production of fuels and chemicals.

• 2018, Promega Biotechnology Research Award, given by the American Academy of Microbiology
• 2016, UW Foundation Chairman Fetzer-Bascom Professor
• 2013, The American Society for Microbiology (ASM) President
• 2009, American Association for the Advancement of Science (AAAS) Fellow
• 2000, American Academy of Microbiology Fellow
• 1993, CALS Pound Research Award

Start and Promotion Dates

• Assistant Professor: 1986
• Associate Professor: 1991
• Full Professor: 1996

Education

B.S., Life Sciences, Polytechnic Institute of Brooklyn
M.S., Microbiology, Pennsylvania State University
Ph.D., Microbiology, Pennsylvania State University
Postdoctoral Research: Microbiology, University of Illinois at Urbana-Champaign

• Blaise Manga Enuh – Postdoc
• Grace Enzien – Grad Student
• Curt Gnatzig – Technician
• Daniel Idowu – Grad Student
• Caiti Kay Lahue – Grad Student
• Rachelle Lemke – Senior Research Specialist
• Fletcher Metz – Grad Student
• Kevin Myers – Assistant Scientist
• Laura Rodriguez-Castro – Postdoc
• Emili Toppari – Grad Student
• Avery Vilbert – Assistant Scientist