Exploring the diversity of complex metabolic networks. - Vassily Hatzimanikatis; Chunhui Li; Justin A. Ionita; Christopher S. Henry; Matthew D. Jankowski; Linda J. Broadbelt (Bioinform., 2005)

Analysis of the Effect of Reversibility Constraints on the Predictions of Genome-Scale Metabolic Models. - José P. Faria; Miguel Rocha 001; Rick L. Stevens; Christopher S. Henry (IWPACBB, 2010)

Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models. - José P. Faria; Ross A. Overbeek; Fangfang Xia; Miguel Rocha 001; Isabel Rocha; Christopher S. Henry (Briefings Bioinform., 2014)

Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models. - Matthew N. Benedict; Michael B. Mundy; Christopher S. Henry; Nicholas Chia; Nathan D. Price 001 (PLoS Comput. Biol., 2014)

MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics. - James G. Jeffryes; Ricardo L. Colastani; Mona Elbadawi-Sidhu; Tobias Kind; Thomas D. Niehaus; Linda J. Broadbelt; Andrew D. Hanson; Oliver Fiehn; Keith E. J. Tyo; Christopher S. Henry (J. Cheminformatics, 2015)

The (nested) word problem. - Christopher S. Henry (Inf. Process. Lett., 2016)

Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli. - Matthew A. Oberhardt; Raphy Zarecki; Leah Reshef; Fangfang Xia; Miquel Duran-Frigola; Rachel Schreiber; Christopher S. Henry; Nir Ben-Tal; Daniel J. Dwyer; Uri Gophna; Eytan Ruppin (PLoS Comput. Biol., 2016)

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. - Alice R. Wattam; James J. Davis 002; Rida Assaf; Sébastien Boisvert; Thomas S. Brettin; Christopher Bun; Neal Conrad; Emily M. Dietrich; Terry Disz; Joseph L. Gabbard; Svetlana Gerdes; Christopher S. Henry; et al. (Nucleic Acids Res., 2017)

Implementing and Evaluating A Gaussian Mixture Framework for Identifying Gene Function from TnSeq Data. - Kevin Li; Rachel Chen; William Lindsey; Aaron A. Best; Matthew DeJongh; Christopher S. Henry; Nathan L. Tintle (PSB, 2019)

Network Alignment by Propagating Reliable Similarities. - Zirou Qiu; Ruslan Shaydulin; Xiaoyuan Liu 001; Yuri Alexeev; Christopher S. Henry; Ilya Safro (CoRR, 2019)

Benchmarking Bitcoin Adoption in Canada: Awareness, Ownership and Usage in 2018. - Kim P. Huynh; Christopher S. Henry; Gradon Nicholls; Mitchell W. Nicholson (Ledger, 2020)

ELRUNA: Elimination Rule-based Network Alignment. - Zirou Qiu; Ruslan Shaydulin; Xiaoyuan Liu 001; Yuri Alexeev; Christopher S. Henry; Ilya Safro (ACM J. Exp. Algorithmics, 2021)

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. - Samuel M. D. Seaver; Filipe Liu; Qizhi Zhang; James G. Jeffryes; José P. Faria; Janaka N. Edirisinghe; Michael B. Mundy; Nicholas Chia; Elad Noor; Moritz Emanuel Beber; Aaron A. Best; Matthew DeJongh; et al. (Nucleic Acids Res., 2021)

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes (Corrigendum). - Samuel M. D. Seaver; Filipe Liu; Qizhi Zhang; James G. Jeffryes; José P. Faria; Janaka N. Edirisinghe; Michael B. Mundy; Nicholas Chia; Elad Noor; Moritz Emanuel Beber; Aaron A. Best; Matthew DeJongh; et al. (Nucleic Acids Res., 2021)

A roadmap for the functional annotation of protein families: a community perspective. - Valérie de Crécy-Lagard; Rocio Amorin de Hegedus; Cecilia N. Arighi; Jill Babor; Alex Bateman; Ian Blaby; Crysten Blaby-Haas; Alan J. Bridge; Stephen K. Burley; Stacey Cleveland; Lucy J. Colwell; Ana Conesa; et al. (Database J. Biol. Databases Curation, 2022)

ORT: a workflow linking genome-scale metabolic models with reactive transport codes. - Rebecca L. Rubinstein; Mikayla A. Borton; Haiyan Zhou; Michael Shaffer; David W. Hoyt; James C. Stegen; Christopher S. Henry; Kelly C. Wrighton; Roelof Versteeg (Bioinform., 2022)

kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase. - Michael Shaffer; Mikayla A. Borton; Ben Bolduc; José P. Faria; Rory M. Flynn; Parsa Ghadermazi; Janaka N. Edirisinghe; Elisha M. Wood-Charlson; Christopher S. Miller; Siu Hung Joshua Chan; Matthew B. Sullivan; Christopher S. Henry; et al. (Bioinform., 2023)

TranSyT, an innovative framework for identifying transport systems. - Emanuel Cunha; Davide Lagoa; José P. Faria; Filipe Liu; Christopher S. Henry; Oscar Dias (Bioinform., 2023)