Nicholas Chia

29 papers A* 1B 1Journal 23Unranked 4
YearRankTypeTitle / Venue / Authors
2026 J jnl
Benchmarking community drug response prediction models: datasets, models, tools, and metrics for cross-dataset generalization analysis.
Briefings Bioinform.
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
2025 J jnl
A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions.
BMC Bioinform.
Rohan Gnanaolivu, Gavin R. Oliver, W. Garrett Jenkinson, Emily Blake, Wenan Chen, Nicholas Chia, Eric W. Klee, Chen Wang
2025 — conf
AdaParse: An Adaptive Parallel PDF Parsing and Resource Scaling Engine.
MLSys
Carlo Siebenschuh, Kyle Hippe, Ozan Gökdemir, Alexander Brace, Arham Mushtaq Khan, Khalid Hossain, Yadu N. Babuji, Nicholas Chia, Venkatram Vishwanath, Arvind Ramanathan, Rick L. Stevens, Ian T. Foster, Robert Underwood
2025 J jnl
AdaParse: An Adaptive Parallel PDF Parsing and Resource Scaling Engine.
CoRR
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
2025 J jnl
Benchmarking community drug response prediction models: datasets, models, tools, and metrics for cross-dataset generalization analysis.
CoRR
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
2025 — conf
Exploring Distributed Vector Databases Performance on HPC Platforms: A Study with Qdrant.
SC Workshops
Seth Ockerman, Amal Gueroudji, Song Young Oh, Robert Underwood, Nicholas Chia, Kyle Chard, Robert B. Ross, Shivaram Venkataraman
2025 J jnl
Exploring Distributed Vector Databases Performance on HPC Platforms: A Study with Qdrant.
CoRR
Seth Ockerman, Amal Gueroudji, Song Young Oh, Robert Underwood, Nicholas Chia, Kyle Chard, Robert B. Ross, Shivaram Venkataraman
2025 — conf
HiPerRAG: High-Performance Retrieval Augmented Generation for Scientific Insights.
PASC
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
2025 J jnl
HiPerRAG: High-Performance Retrieval Augmented Generation for Scientific Insights.
CoRR
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
2024 J jnl
Assessing Reusability of Deep Learning-Based Monotherapy Drug Response Prediction Models Trained with Omics Data.
CoRR
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
2024 J jnl
Variational and Explanatory Neural Networks for Encoding Cancer Profiles and Predicting Drug Responses.
CoRR
Tianshu Feng, Rohan Gnanaolivu, Abolfazl Safikhani, Yuanhang Liu, Jun Jiang, Nicholas Chia, Alexander Partin, Priyanka Vasanthakumari, Yitan Zhu, Chen Wang
2021 J jnl
Invariant Risk Minimisation for Cross-Organism Inference: Substituting Mouse Data for Human Data in Human Risk Factor Discovery.
CoRR
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
2021 J jnl
On Invariance Penalties for Risk Minimization.
CoRR
Kia Khezeli, Arno Blaas, Frank Soboczenski, Nicholas Chia, John Kalantari
2021 — conf
Prototyping CRISP: A Causal Relation and Inference Search Platform applied to Colorectal Cancer Data.
LifeTech
Samuel Budd, Arno Blaas, Adrienne Hoarfrost, Kia Khezeli, Krittika D'Silva, Frank Soboczenski, Graham Mackintosh, Nicholas Chia, John Kalantari
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
Detecting evolutionary patterns of cancers using consensus trees.
Bioinform.
Sarah A. Christensen, Juho Kim, Nicholas Chia, Oluwasanmi Koyejo, Mohammed El-Kebir
2020 J jnl
Minimizing the number of optimizations for efficient community dynamic flux balance analysis.
PLoS Comput. Biol.
James D. Brunner, Nicholas Chia
2020 J jnl
PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors.
PLoS Comput. Biol.
Leah L. Weber, Nuraini Aguse, Nicholas Chia, Mohammed El-Kebir
2020 A* conf
The Unreasonable Effectiveness of Inverse Reinforcement Learning in Advancing Cancer Research.
AAAI
John Kalantari, Heidi Nelson, Nicholas Chia
2018 J jnl
HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data.
BMC Bioinform.
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
2017 J jnl
Mackinac: a bridge between ModelSEED and COBRApy to generate and analyze genome-scale metabolic models.
Bioinform.
Michael B. Mundy, Helena Mendes-Soares, Nicholas Chia
2016 J jnl
MMinte: an application for predicting metabolic interactions among the microbial species in a community.
BMC Bioinform.
Helena Mendes-Soares, Michael B. Mundy, Luis Mendes Soares, Nicholas Chia
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
Compression-based distance (CBD): a simple, rapid, and accurate method for microbiota composition comparison.
BMC Bioinform.
Fang Yang, Nicholas Chia, Bryan A. White, Lawrence B. Schook
2011 J jnl
A performance enhanced PSI-BLAST based on hybrid alignment.
Bioinform.
Yuheng Li, Nicholas Chia, Mario Lauria, Ralf Bundschuh
2011 J jnl
Towards an Evolutionary Model of Animal-Associated Microbiomes.
Entropy
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
2006 J jnl
A Practical Approach to Significance Assessment in Alignment with Gaps.
J. Comput. Biol.
Nicholas Chia, Ralf Bundschuh
2005 B conf
A Practical Approach to Significance Assessment in Alignment with Gaps.
RECOMB
Nicholas Chia, Ralf Bundschuh