Publications by Year

134. Shaping the future of early-onset colorectal cancer prevention

134. Tian, Ruiyi; Azadnajafabad, Sina; Waters, Erika A.; Balskus, Emily P.; Belkaid, Yasmine; Bell, Jordana T.; Berry, Sarah E.; Buenrostro, Jason D.; Huttenhower, Curtis; Patel, Anisha; Patti, Gary J.; Segata, Nicola; Sirohi, Bhawna; Spector, Tim D.; Yilmaz, Ömer H.; Chan, Andrew T.; Cao, Yin. Shaping the Future of Early-Onset Colorectal Cancer Prevention. Nat. Rev. Cancer 2026, 26, 830–848. DOI: https://doi.org/10.1038/s41568-026-00965-5.

133. ExpoLib: a framework for an MS/MS exposome library of anthropogenic and natural toxicants and their biotransformation products

133. Hernandes, Vinicius Verri; Aguilar Ramos, Miguel A.; Breinbauer, Rolf; Fruhmann, Philipp; Mikula, Hannes; Ehling-Schulz, Monika; Zechner, Ellen L.; Balskus, Emily P.; Warth, Benedikt. ExpoLib: A Framework for an MS/MS Exposome Library of Anthropogenic and Natural Toxicants and Their Biotransformation Products. Metabolomics 2026, 22. DOI: https://doi.org/10.1007/s11306-026-02481-x.

132. Colibactin produced by a honeybee gut symbiont mediates pathogen defence

132. Song, Yulin; Powell, J. Elijah; Wong, Joel W. H.; Liu, Yunxi; Aguilar Ramos, Miguel A.; De Jong, Tyler; Lariviere, Patrick J.; Maganti, Jayaditya; Balskus, Emily P.; Moran, Nancy A. Colibactin Produced by a Honeybee Gut Symbiont Mediates Pathogen Defence. Nat. Microbiol. 2026, 11, 2408–2422. DOI: https://doi.org/10.1038/s41564-026-02438-9.
Preprint: bioRxiv 2025. DOI: https://doi.org/10.64898/2025.12.27.695564.

131. A genotoxin associated with colorectal cancer linked to gut dysbiosis in children with cystic fibrosis.

131. Barrack, Kaitlyn E.; Surve, Sarvesh V.; de Sousa Bezerra, Ana V.; Murphy, Caitlin E.; Soucy, Shannon M.; Aguilar Ramos, Miguel A.; Valls, Rebecca A.; Ruff, Rebekah D.; Balskus, Emily P.; Sanville, Julie L.; Madan, Juliette C.; O’Toole, George A. A Genotoxin Associated with Colorectal Cancer Linked to Gut Dysbiosis in Children with Cystic Fibrosis. J. Bacteriol. 2026, e00190-26. DOI: https://doi.org/10.1128/jb.00190-26.
Preprint: bioRxiv 2025. DOI: https://doi.org/10.1101/2025.09.04.674286.

130. The Structural Basis of Malodorant Skatole Formation by the Glycyl Radical Enzyme Indoleacetate Decarboxylase

130. Imrich, Christa N.; Backman, Lindsey R. F.; Allworth, Abigail P.; Andorfer, Mary C.; Paris, Jared C.; Greeley, Nina M.; Fu, Beverly; Balskus, Emily P.; Drennan, Catherine L. The Structural Basis of Malodorant Skatole Formation by the Glycyl Radical Enzyme Indoleacetate Decarboxylase. bioRxiv 2026, 2026.05.24.727522. DOI: https://doi.org/10.64898/2026.05.24.727522.

128. A previously unappreciated class of metal-dependent bile salt hydrolases from the human gut microbiome

128. Cui, Zheng; Meng, Christopher J.; Irwin, Stephania M.; Augustijn, Hannah E.; Papageorgiou, Panagiotis Panagopoulos; Nguyen, Anh T. P.; Yu, Ruocheng; Aguilar Ramos, Miguel A.; Kulik, Heather J.; Balskus, Emily P. A Previously Unappreciated Class of Metal-Dependent Bile Salt Hydrolases from the Human Gut Microbiome. bioRxiv 2026, 2026.04.05.716592. DOI: https://doi.org/10.64898/2026.04.05.716592.

126. Phenotypic high-throughput screening identifies modulators of gut microbial choline metabolism

126. Woo, Amelia Y. M.; Sandoval-Espinola, Walter J.; Bollenbach, Maud; Wong, Alison; Sakanaka-Yokoyama, Mariko; Zhang, Qijun; Nieto, Vincent; Rey, Federico E.; Balskus, Emily P. Phenotypic High-Throughput Screening Identifies Modulators of Gut Microbial Choline Metabolism. mBio 2026, e0117225. DOI: https://doi.org/10.1128/mbio.01172-25.
Preprint: bioRxiv 2024. DOI: https://doi.org/10.1101/2024.11.08.621386.

124 - Flavoaffinins, Elusive Cellulose-Binding Natural Products from an Anaerobic Bacterium.

124. Kountz, Duncan J.; Yu, Ruocheng; Lee, Jessie H.; Maloney, Katherine N.; Balskus, Emily P. Flavoaffinins, Elusive Cellulose-Binding Natural Products from an Anaerobic Bacterium. J. Am. Chem. Soc. 2026, 148, 2838–2842. DOI: https://doi.org/10.1021/jacs.5c15360.
Preprint: bioRxiv 2025. DOI: https://doi.org/10.1101/2025.02.08.637243.

123 - The specificity and structure of DNA cross-linking by the gut bacterial genotoxin colibactin

123. Carlson, Erik S.; Haslecker, Raphael; Lecchi, Chiara; Aguilar Ramos, Miguel A.; Vennelakanti, Vyshnavi; Honaker, Linda; Stornetta, Alessia; Millán, Estela S.; Johnson, Bruce A.; Kulik, Heather J.; Balbo, Silvia; Villalta, Peter W.; D’Souza, Victoria M.; Balskus, Emily P. The Specificity and Structure of DNA Cross-Linking by the Gut Bacterial Genotoxin Colibactin. Science 2025, 390, eady3571. DOI: https://doi.org/10.1126/science.ady3571.

122 - The Fanconi anemia pathway repairs colibactin-induced DNA interstrand cross-links

122. Altshuller, Maria; He, Xu; MacKrell, Elliot J.; Wernke, Kevin M.; Airan, Yougant; Wong, Joel W. H.; Sellés-Baiget, Selene; Wang, Ting-Yu; Chou, Tsui-Fen; Duxin, Julien P.; Balskus, Emily P.; Herzon, Seth B.; Semlow, Daniel R. The Fanconi Anemia Pathway Repairs Colibactin-Induced DNA Interstrand Cross-Links. Nat. Commun. 2025, 16, 10563. DOI: https://doi.org/10.1038/s41467-025-65606-1.

121 - Systematic identification and characterization of regulators of aryl hydrocarbon receptor signaling

121. Verma, Manasvi; Desai, Kushaal; Ding, Yufang; Wang, Xingren; Bae, Minwoo; Rakoff-Nahoum, Seth; Balskus, Emily P.; Fischbach, Michael A.; Jost, Marco. Systematic Identification and Characterization of Regulators of Aryl Hydrocarbon Receptor Signaling. bioRxiv 2025, 2025.09.15.676391. DOI: https://doi.org/10.1101/2025.09.15.676391.

120 - Characterizing and engineering post-translational modifications with high-throughput cell-free expression

120. Wong, Derek A.; Shaver, Zachary M.; Cabezas, Maria D.; Daniel-Ivad, Martin; Warfel, Katherine F.; Prasanna, Deepali V.; Sobol, Sarah E.; Fernandez, Regina; Tobias, Fernando; Filip, Szymon K.; Hulbert, Sophia W.; Faull, Peter; Nicol, Robert; DeLisa, Matthew P.; Balskus, Emily P.; Karim, Ashty S.; Jewett, Michael C. Characterizing and Engineering Post-Translational Modifications with High-Throughput Cell-Free Expression. Nat. Commun. 2025, 16, 7215. DOI: https://doi.org/10.1038/s41467-025-60526-6.
Preprint: bioRxiv 2024. DOI: https://doi.org/10.1101/2024.03.25.586624.

119 - Bacterial peptide deformylase inhibitors induce prophages in competitors

119. Chen, Julie; Pfeifer, Katarina; Steensen, Kerrin; Crooke, Anne Marie; Wolfram, Michael; Bobonis, Jacob; Lopatina, Anna; Bartlau, Nina; Hussain, Fatima A.; Balskus, Emily P.; Polz, Martin F.; Blainey, Paul C. Bacterial Peptide Deformylase Inhibitors Induce Prophages in Competitors. bioRxiv 2025, 2025.06.06.656871. DOI: https://doi.org/10.1101/2025.06.06.656871.