Nicholas Chia

According to our database, Nicholas Chia authored at least 18 papers between 2006 and 2024.

Collaborative distances:

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

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

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