Patterns and Complexity in Biological Systems: A Study of Sequence Structure and Ontology-based Networks. - Kimberly Glass (2010)

Sexually-dimorphic targeting of functionally-related genes in COPD. - Kimberly Glass; John Quackenbush; Edwin K. Silverman; Bartolome Celli; Stephen I. Rennard; Guo-Cheng Yuan; Dawn L. DeMeo (BMC Syst. Biol., 2014)

High performance computing of gene regulatory networks using a message-passing model. - Kimberly Glass; John Quackenbush; Jeremy Kepner (HPEC, 2015)

A network model for angiogenesis in ovarian cancer. - Kimberly Glass; John Quackenbush; Dimitrios Spentzos; Benjamin Haibe-Kains; Guo-Cheng Yuan (BMC Bioinform., 2015)

Finding New Order in Biological Functions from the Network Structure of Gene Annotations. - Kimberly Glass; Michelle Girvan (PLoS Comput. Biol., 2015)

PyPanda: a Python package for gene regulatory network reconstruction. - David G. P. van IJzendoorn; Kimberly Glass; John Quackenbush; Marieke L. Kuijjer (Bioinform., 2016)

Estimating gene regulatory networks with pandaR. - Daniel Schlauch; Joseph N. Paulson; Albert Young; Kimberly Glass; John Quackenbush (Bioinform., 2017)

Biomarker correlation network in colorectal carcinoma by tumor anatomic location. - Reiko Nishihara; Kimberly Glass; Kosuke Mima; Tsuyoshi Hamada; Jonathan A. Nowak; Zhi Rong Qian; Peter Kraft; Edward L. Giovannucci; Charles S. Fuchs; Andrew T. Chan; John Quackenbush; Shuji Ogino; et al. (BMC Bioinform., 2017)

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. - Joseph N. Paulson; Cho-Yi Chen; Camila Miranda Lopes-Ramos; Marieke L. Kuijjer; John Platig; Abhijeet R. Sonawane; Maud Fagny; Kimberly Glass; John Quackenbush (BMC Bioinform., 2017)

Precision VISSTA: Bring-Your-Own-Device (BYOD) mHealth Data for Precision Health. - Arlene E. Chung; Kimberly Glass; Jacob Leisey-Bartsch; Lucas Mentch; Nils Gehlenborg; David Gotz (AMIA, 2019)

Precision VISSTA: Machine Learning Prediction and Inference for Bring-Your-Own-Device (BYOD) mHealth Data. - Tim Coleman; Lucas Mentch; Kimberly Glass; David Gotz; Nils Gehlenborg; Arlene E. Chung (AMIA, 2019)

PUMA: PANDA Using MicroRNA Associations. - Marieke L. Kuijjer; Maud Fagny; Alessandro Marin; John Quackenbush; Kimberly Glass (Bioinform., 2020)

Gene Regulatory Network Inference as Relaxed Graph Matching. - Deborah A. Weighill; Marouen Ben Guebila; Camila Miranda Lopes-Ramos; Kimberly Glass; John Quackenbush; John Platig; Rebekka Burkholz (AAAI, 2021)

GRAND: a database of gene regulatory network models across human conditions. - Marouen Ben Guebila; Camila Miranda Lopes-Ramos; Deborah A. Weighill; Abhijeet Rajendra Sonawane; Rebekka Burkholz; Behrouz Shamsaei; John Platig; Kimberly Glass; Marieke L. Kuijjer; John Quackenbush (Nucleic Acids Res., 2022)

Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data. - Ping-Han Hsieh; Camila Miranda Lopes-Ramos; Manuela Zucknick; Geir Kjetil Sandve; Kimberly Glass; Marieke L. Kuijjer (Bioinform., 2023)

BONOBO: Bayesian Optimized Sample-Specific Networks Obtained by Omics Data. - Enakshi Saha; Viola Fanfani; Panagiotis Mandros; Marouen Ben Guebila; Jonas Fischer; Katherine H. Shutta; Kimberly Glass; Dawn L. DeMeo; Camila Miranda Lopes-Ramos; John Quackenbush (RECOMB, 2024)

Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals. - Michele Gentili; Kimberly Glass; Enrico Maiorino; Brian D. Hobbs; Zhonghui Xu; Peter J. Castaldi; Michael H. Cho; Craig P. Hersh; Dandi Qiao; Jarrett D. Morrow; Vincent J. Carey; John Platig; et al. (PLoS Comput. Biol., 2024)