Christopher S. Henry

19 papers Misc 1Journal 17Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
Scalable Agentic Reasoning for Designing Biologics Targeting Intrinsically Disordered Proteins.
CoRR
Matthew Sinclair, Moeen Meigooni, Archit Vasan, Ozan Gökdemir, Xinran Lian, Heng Ma, Yadu N. Babuji, Alexander Brace, Khalid Hossain, Carlo Siebenschuh, Thomas S. Brettin, Kyle Chard, Christopher S. Henry, Venkatram Vishwanath, Rick L. Stevens, Ian T. Foster, Arvind Ramanathan
2023 J jnl
kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase.
Bioinform.
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, Kelly C. Wrighton
2022 J jnl
A roadmap for the functional annotation of protein families: a community perspective.
Database J. Biol. Databases Curation
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, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M. Gyori, Christopher S. Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D. Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria Jesus Martin, Claire D. McWhite, Gaurav D. Moghe, Paul Monaghan, Anne Morgat, Christopher J. Mungall, Darren A. Natale, William C. Nelson, Seán I. O'Donoghue, Christine A. Orengo, Katherine H. O'Toole, Predrag Radivojac, Colbie Reed, Richard J. Roberts, Dmitri Rodionov, Irina A. Rodionova, Jeffrey DePons, Lana Saleh, Gloria M. Sheynkman, Françoise Thibaud-Nissen, Paul D. Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter Weigele, Valerie Wood, Elisha M. Wood-Charlson, Jin Xu
2022 J jnl
ORT: a workflow linking genome-scale metabolic models with reactive transport codes.
Bioinform.
Rebecca L. Rubinstein, Mikayla A. Borton, Haiyan Zhou, Michael Shaffer, David W. Hoyt, James C. Stegen, Christopher S. Henry, Kelly C. Wrighton, Roelof Versteeg
2021 J jnl
ELRUNA: Elimination Rule-based Network Alignment.
ACM J. Exp. Algorithmics
Zirou Qiu, Ruslan Shaydulin, Xiaoyuan Liu, Yuri Alexeev, Christopher S. Henry, Ilya Safro
2021 J jnl
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).
Nucleic Acids Res.
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, Jeffrey A. Kimbrel, Patrik D'haeseleer, Sean R. McCorkle, Jay R. Bolton, Erik Pearson, Shane Canon, Elisha M. Wood-Charlson, Robert W. Cottingham, Adam P. Arkin, Christopher S. Henry
2021 J jnl
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes.
Nucleic Acids Res.
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, Jeffrey A. Kimbrel, Patrik D'haeseleer, Sean R. McCorkle, Jay R. Bolton, Erik Pearson, Shane Canon, Elisha M. Wood-Charlson, Robert W. Cottingham, Adam P. Arkin, Christopher S. Henry
2020 J jnl
Benchmarking Bitcoin Adoption in Canada: Awareness, Ownership and Usage in 2018.
Ledger
Kim P. Huynh, Christopher S. Henry, Gradon Nicholls, Mitchell W. Nicholson
2019 Misc conf
Implementing and Evaluating A Gaussian Mixture Framework for Identifying Gene Function from TnSeq Data.
PSB
Kevin Li, Rachel Chen, William Lindsey, Aaron A. Best, Matthew DeJongh, Christopher S. Henry, Nathan L. Tintle
2019 J jnl
Network Alignment by Propagating Reliable Similarities.
CoRR
Zirou Qiu, Ruslan Shaydulin, Xiaoyuan Liu, Yuri Alexeev, Christopher S. Henry, Ilya Safro
2017 J jnl
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.
Nucleic Acids Res.
Alice R. Wattam, James J. Davis, Rida Assaf, Sébastien Boisvert, Thomas S. Brettin, Christopher Bun, Neal Conrad, Emily M. Dietrich, Terry Disz, Joseph L. Gabbard, Svetlana Gerdes, Christopher S. Henry, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Eric K. Nordberg, Gary J. Olsen, Daniel E. Murphy-Olson, Robert Olson, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, Maulik Shukla, Veronika Vonstein, Andrew S. Warren, Fangfang Xia, Hyun Seung Yoo, Rick L. Stevens
2016 J jnl
Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in
PLoS Comput. Biol.
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
2016 J jnl
The (nested) word problem.
Inf. Process. Lett.
Christopher S. Henry
2015 J jnl
MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics.
J. Cheminformatics
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
2014 J jnl
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models.
Briefings Bioinform.
José P. Faria, Ross A. Overbeek, Fangfang Xia, Miguel Rocha, Isabel Rocha, Christopher S. Henry
2014 J jnl
Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models.
PLoS Comput. Biol.
Matthew N. Benedict, Michael B. Mundy, Christopher S. Henry, Nicholas Chia, Nathan D. Price
2013 J jnl
The (Nested) Word Problem.
CoRR
Christopher S. Henry
2010 — conf
Analysis of the Effect of Reversibility Constraints on the Predictions of Genome-Scale Metabolic Models.
IWPACBB
José P. Faria, Miguel Rocha, Rick L. Stevens, Christopher S. Henry
2005 J jnl
Exploring the diversity of complex metabolic networks.
Bioinform.
Vassily Hatzimanikatis, Chunhui Li, Justin A. Ionita, Christopher S. Henry, Matthew D. Jankowski, Linda J. Broadbelt