Conservation cores: reducing the energy of mature computations. - Ganesh Venkatesh; Jack Sampson; Nathan Goulding; Saturnino Garcia; Vladyslav Bryksin; Jose Lugo-Martinez; Steven Swanson; Michael Bedford Taylor (ASPLOS, 2010)

Generalized graphlet kernels for probabilistic inference in sparse graphs. - Jose Lugo-Martinez; Predrag Radivojac (Netw. Sci., 2014)

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies. - James F. Denton; Jose Lugo-Martinez; Abraham E. Tucker; Daniel R. Schrider; Wesley C. Warren; Matthew W. Hahn (PLoS Comput. Biol., 2014)

The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease. - Jose Lugo-Martinez; Vikas Pejaver; Kymberleigh A. Pagel; Shantanu Jain; Matthew E. Mort; David N. Cooper; Sean D. Mooney; Predrag Radivojac (PLoS Comput. Biol., 2016)

Classification in biological networks with hypergraphlet kernels. - Jose Lugo-Martinez; Predrag Radivojac (CoRR, 2017)

Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data. - Makoto Yamada; Jiliang Tang; Jose Lugo-Martinez; Ermin Hodzic; Raunak Shrestha; Avishek Saha; Hua Ouyang; Dawei Yin; Hiroshi Mamitsuka; Süleyman Cenk Sahinalp; Predrag Radivojac; Filippo Menczer; et al. (IEEE Trans. Knowl. Data Eng., 2018)

Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes. - Jose Lugo-Martinez; Jörn Dengjel; Ziv Bar-Joseph; Robert F. Murphy (BCB, 2019)

Classification in biological networks with hypergraphlet kernels. - Jose Lugo-Martinez; Daniel Zeiberg; Thomas Gaudelet; Noël Malod-Dognin; Natasa Przulj; Predrag Radivojac (Bioinform., 2021)

Integrating longitudinal clinical and microbiome data to predict growth faltering in preterm infants. - Jose Lugo-Martinez; Siwei Xu; Justine Levesque; Daniel Gallagher; Leslie A. Parker; Josef Neu; Christopher J. Stewart; Janet E. Berrington; Nicholas D. Embleton; Gregory Young; Katherine E. Gregory; Misty Good; et al. (J. Biomed. Informatics, 2022)

A hybrid positive unlabeled learning framework for uncovering scaffolds across human proteome by measuring the propensity to drive phase separation. - Peiran Jiang; Ruoxi Cai; Jose Lugo-Martinez; Yaping Guo (Briefings Bioinform., 2023)

Special Issue Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC) Workshop (2022). - Hyundoo Jeong; Jose Lugo-Martinez; Anna M. Ritz; Yijie Wang; Chi Zhang 021 (J. Comput. Biol., 2023)

Combined Topological Data Analysis and Geometric Deep Learning Reveal Niches by the Quantification of Protein Binding Pockets. - Peiran Jiang; Jose Lugo-Martinez (J. Comput. Biol., 2025)