A Practical Approach to Significance Assessment in Alignment with Gaps. - Nicholas Chia; Ralf Bundschuh (J. Comput. Biol., 2006)

A performance enhanced PSI-BLAST based on hybrid alignment. - Yuheng Li; Nicholas Chia; Mario Lauria; Ralf Bundschuh (Bioinform., 2011)

Towards an Evolutionary Model of Animal-Associated Microbiomes. - Carl J. Yeoman; Nicholas Chia; Suleyman Yildirim; Margret E. Berg Miller; Angela Kent; Rebecca Stumpf; Steven R. Leigh; Karen E. Nelson; Bryan A. White; Brenda A. Wilson (Entropy, 2011)

Compression-based distance (CBD): a simple, rapid, and accurate method for microbiota composition comparison. - Fang Yang; Nicholas Chia; Bryan A. White; Lawrence B. Schook (BMC Bioinform., 2013)

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)

MMinte: an application for predicting metabolic interactions among the microbial species in a community. - Helena Mendes-Soares; Michael B. Mundy; Luis Mendes Soares; Nicholas Chia (BMC Bioinform., 2016)

Mackinac: a bridge between ModelSEED and COBRApy to generate and analyze genome-scale metabolic models. - Michael B. Mundy; Helena Mendes-Soares; Nicholas Chia (Bioinform., 2017)

HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data. - Saurabh Baheti; Xiaojia Tang; Daniel R. O'Brien; Nicholas Chia; Lewis R. Roberts; Heidi Nelson; Judy C. Boughey; Liewei Wang; Matthew P. Goetz; Jean-Pierre A. Kocher; Krishna R. Kalari (BMC Bioinform., 2018)

The Unreasonable Effectiveness of Inverse Reinforcement Learning in Advancing Cancer Research. - John Kalantari; Heidi Nelson; Nicholas Chia (AAAI, 2020)

Detecting evolutionary patterns of cancers using consensus trees. - Sarah A. Christensen; Juho Kim; Nicholas Chia; Oluwasanmi Koyejo; Mohammed El-Kebir (Bioinform., 2020)

Minimizing the number of optimizations for efficient community dynamic flux balance analysis. - James D. Brunner; Nicholas Chia (PLoS Comput. Biol., 2020)

PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors. - Leah L. Weber; Nuraini Aguse; Nicholas Chia; Mohammed El-Kebir (PLoS Comput. Biol., 2020)

Prototyping CRISP: A Causal Relation and Inference Search Platform applied to Colorectal Cancer Data. - Samuel Budd; Arno Blaas; Adrienne Hoarfrost; Kia Khezeli; Krittika D'Silva; Frank Soboczenski; Graham Mackintosh; Nicholas Chia; John Kalantari (LifeTech, 2021)

On Invariance Penalties for Risk Minimization. - Kia Khezeli; Arno Blaas; Frank Soboczenski; Nicholas Chia; John Kalantari (CoRR, 2021)

Invariant Risk Minimisation for Cross-Organism Inference: Substituting Mouse Data for Human Data in Human Risk Factor Discovery. - Odhran O'Donoghue; Paul Duckworth; Giuseppe Ughi; Linus Scheibenreif; Kia Khezeli; Adrienne Hoarfrost; Samuel Budd; Patrick Foley; Nicholas Chia; John Kalantari; Graham Mackintosh; Frank Soboczenski; et al. (CoRR, 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)

Variational and Explanatory Neural Networks for Encoding Cancer Profiles and Predicting Drug Responses. - Tianshu Feng; Rohan Gnanaolivu; Abolfazl Safikhani; Yuanhang Liu; Jun Jiang; Nicholas Chia; Alexander Partin; Priyanka Vasanthakumari; Yitan Zhu; Chen Wang (CoRR, 2024)

Assessing Reusability of Deep Learning-Based Monotherapy Drug Response Prediction Models Trained with Omics Data. - Jamie C. Overbeek; Alexander Partin; Thomas S. Brettin; Nicholas Chia; Oleksandr Narykov; Priyanka Vasanthakumari; Andreas Wilke; Yitan Zhu; Austin Clyde; Sara Jones; Rohan Gnanaolivu; Yuanhang Liu; et al. (CoRR, 2024)

HiPerRAG: High-Performance Retrieval Augmented Generation for Scientific Insights. - Ozan Gökdemir; Carlo Siebenschuh; Alexander Brace; Azton Wells; Brian Hsu; Kyle Hippe; Priyanka Setty; Aswathy Ajith; J. Gregory Pauloski; Varuni Sastry; Sam Foreman; Huihuo Zheng; et al. (PASC, 2025)

Benchmarking community drug response prediction models: datasets, models, tools, and metrics for cross-dataset generalization analysis. - Alexander Partin; Priyanka Vasanthakumari; Oleksandr Narykov; Andreas Wilke; Natasha Koussa; Sara E. Jones; Yitan Zhu; Jamie C. Overbeek; Rajeev Jain; Gayara Demini Fernando; Cesar Sanchez-Villalobos; Cristina Garcia-Cardona; et al. (CoRR, 2025)

AdaParse: An Adaptive Parallel PDF Parsing and Resource Scaling Engine. - Carlo Siebenschuh; Kyle Hippe; Ozan Gökdemir; Alexander Brace; Arham Khan; Khalid Hossain; Yadu N. Babuji; Nicholas Chia; Venkatram Vishwanath; Rick Stevens; Arvind Ramanathan; Ian T. Foster; et al. (CoRR, 2025)

HiPerRAG: High-Performance Retrieval Augmented Generation for Scientific Insights. - Ozan Gökdemir; Carlo Siebenschuh; Alexander Brace; Azton Wells; Brian Hsu; Kyle Hippe; Priyanka Vasanthakumari; Aswathy Ajith; J. Gregory Pauloski; Varuni Katti Sastry; Sam Foreman; Huihuo Zheng; et al. (CoRR, 2025)

A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions. - Rohan Gnanaolivu; Gavin R. Oliver; W. Garrett Jenkinson; Emily Blake; Wenan Chen; Nicholas Chia; Eric W. Klee; Chen Wang (BMC Bioinform., 2025)