Nicholas Chia

According to our database, Nicholas Chia authored at least 24 papers between 2006 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

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., December, 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, Heng Ma, Bharat Kale, Nicholas Chia, Thomas Gibbs, Michael E. Papka, Thomas S. Brettin, Francis J. Alexander, Anima Anandkumar, Ian T. Foster, Rick Stevens, Venkatram Vishwanath, Arvind Ramanathan

CoRR, May, 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, Robert Underwood

CoRR, May, 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, Jamaludin Mohd-Yusof, Nicholas Chia, Justin M. Wozniak, Souparno Ghosh, Ranadip Pal, Thomas S. Brettin, M. Ryan Weil, Rick L. Stevens

CoRR, March, 2025

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, Heng Ma, Bharat Kale, Nicholas Chia, Thomas Gibbs, Michael E. Papka, Thomas S. Brettin, Francis J. Alexander, Anima Anandkumar, Ian T. Foster, Rick Stevens, Venkatram Vishwanath, Arvind Ramanathan

Proceedings of the Platform for Advanced Scientific Computing Conference, 2025

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, Jun Jiang, Chen Wang, Carter Knutson, Andrew D. McNaughton, Neeraj Kumar, Gayara Demini Fernando, Souparno Ghosh, Cesar Sanchez-Villalobos, Ruibo Zhang, Ranadip Pal, M. Ryan Weil, Rick L. Stevens

CoRR, 2024

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

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, 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

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.

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

Nucleic Acids Res., 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, Lauren M. Sanders

CoRR, 2021

On Invariance Penalties for Risk Minimization.

Kia Khezeli, Arno Blaas, Frank Soboczenski, Nicholas Chia, John Kalantari

CoRR, 2021

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

Proceedings of the 3rd IEEE Global Conference on Life Sciences and Technologies, 2021

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

Minimizing the number of optimizations for efficient community dynamic flux balance analysis.

James D. Brunner, Nicholas Chia

PLoS Comput. Biol., 2020

Detecting evolutionary patterns of cancers using consensus trees.

Sarah A. Christensen, Juho Kim, Nicholas Chia, Oluwasanmi Koyejo, Mohammed El-Kebir

Bioinform., 2020

The Unreasonable Effectiveness of Inverse Reinforcement Learning in Advancing Cancer Research.

John Kalantari, Heidi Nelson, Nicholas Chia

Proceedings of the Thirty-Fourth AAAI Conference on Artificial Intelligence, 2020

2018

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

2017

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

2016

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

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

PLoS Comput. Biol., 2014

2013

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

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

A performance enhanced PSI-BLAST based on hybrid alignment.

Yuheng Li, Nicholas Chia, Mario Lauria, Ralf Bundschuh

Bioinform., 2011

2006

A Practical Approach to Significance Assessment in Alignment with Gaps.

Nicholas Chia, Ralf Bundschuh

J. Comput. Biol., 2006