Systematic conformational search with constraint satisfaction. - Lisa Tucker-Kellogg (2002)

Composing Globally Consistent Pathway Parameter Estimates Through Belief Propagation. - Geoffrey Koh; Lisa Tucker-Kellogg; David Hsu; P. S. Thiagarajan (WABI, 2007)

pFlexAna: detecting conformational changes in remotely related proteins. - Anshul Nigham; Lisa Tucker-Kellogg; Ivana Mihalek; Chandra Verma; David Hsu (Nucleic Acids Res., 2008)

The Steady States and Dynamics of Urokinase-mediated Plasmin Activation. - Lakshmi Venkatraman; Hanry Yu; Sourav S. Bhowmick; C. Forbes Dewey Jr.; Lisa Tucker-Kellogg (Pacific Symposium on Biocomputing, 2010)

Pani: a novel algorithm for fast discovery of putative target nodes in signaling networks. - Huey-Eng Chua; Qing Zhao; Sourav S. Bhowmick; C. Forbes Dewey Jr.; Lisa Tucker-Kellogg; Hanry Yu (BCB, 2011)

STEROID: in silico heuristic target combination identification for disease-related signaling networks. - Huey-Eng Chua; Sourav S. Bhowmick; Lisa Tucker-Kellogg; C. Forbes Dewey Jr. (BCB, 2012)

PANI: an interactive data-driven tool for target prioritization in signaling networks. - Huey-Eng Chua; Sourav S. Bhowmick; Lisa Tucker-Kellogg; Yingqi Wang; C. Forbes Dewey Jr.; Hanry Yu (IHI, 2012)

In silico identification of endo16 regulators in the sea urchin endomesoderm gene regulatory network. - Huey-Eng Chua; Sourav S. Bhowmick; Lisa Tucker-Kellogg; Qing Zhao; C. Forbes Dewey Jr.; Hanry Yu (IHI, 2012)

Systematic parameter estimation in data-rich environments for cell signalling dynamics. - Tri Hieu Nim; Le Luo; Marie-Véronique Clément; Jacob K. White 001; Lisa Tucker-Kellogg (Bioinform., 2013)

Computational modelling of LY303511 and TRAIL-induced apoptosis suggests dynamic regulation of cFLIP. - Yuan Shi; Gregory Mellier; Sinong Huang; Jacob K. White 001; Shazib Pervaiz; Lisa Tucker-Kellogg (Bioinform., 2013)

SPEDRE: a web server for estimating rate parameters for cell signaling dynamics in data-rich environments. - Tri Hieu Nim; Jacob K. White 001; Lisa Tucker-Kellogg (Nucleic Acids Res., 2013)

One feature doesn't fit all: characterizing topological features of targets in signaling networks. - Huey-Eng Chua; Sourav S. Bhowmick; Lisa Tucker-Kellogg (BCB, 2014)

The Self-Limiting Dynamics of TGF-β Signaling In Silico and In Vitro, with Negative Feedback through PPM1A Upregulation. - Junjie Wang; Lisa Tucker-Kellogg; Inn Chuan Ng; Ruirui Jia; P. S. Thiagarajan; Jacob K. White 001; Hanry Yu (PLoS Comput. Biol., 2014)

TENET: topological feature-based target characterization in signalling networks. - Huey-Eng Chua; Sourav S. Bhowmick; Lisa Tucker-Kellogg; C. Forbes Dewey Jr. (Bioinform., 2015)

Non-canonical Activation of Akt in Serum-Stimulated Fibroblasts, Revealed by Comparative Modeling of Pathway Dynamics. - Tri Hieu Nim; Le Luo; Jacob K. White 001; Marie-Véronique Clément; Lisa Tucker-Kellogg (PLoS Comput. Biol., 2015)

TAPESTRY: Network-centric Target Prioritization in Disease-related Signaling Networks. - Huey-Eng Chua; Sourav S. Bhowmick; Jie Zheng 002; Lisa Tucker-Kellogg (BCB, 2016)

TENET: A Machine Learning-Based System for Target Characterization in Signaling Networks. - Huey-Eng Chua; Sourav S. Bhowmick; Lisa Tucker-Kellogg; C. Forbes Dewey Jr. (ICDM Workshops, 2016)

Superpixel-based segmentation of muscle fibers in multi-channel microscopy. - Binh P. Nguyen; Hans Heemskerk; Peter T. C. So; Lisa Tucker-Kellogg (BMC Syst. Biol., 2016)

TINTIN: Exploiting Target Features for Signaling Network Similarity Computation and Ranking. - Huey-Eng Chua; Sourav S. Bhowmick; Lisa Tucker-Kellogg (BCB, 2017)

Computational analysis reveals the coupling between bistability and the sign of a feedback loop in a TGF-β1 activation model. - Huipeng Li; Lakshmi Venkatraman; Balakrishnan Chakrapani Narmada; Jacob K. White 001; Hanry Yu; Lisa Tucker-Kellogg (BMC Syst. Biol., 2017)

De novo Ensemble Modeling Suggests that AP2-Binding to Disordered Regions Can Increase StericVolume of Epsin but Not Eps15. - N. Suhas Jagannathan; Christopher W. V. Hogue; Lisa Tucker-Kellogg (PSB, 2020)

Transcompp: understanding phenotypic plasticity by estimating Markov transition rates for cell state transitions. - N. Suhas Jagannathan; Mario O. Ihsan; Xiao Xuan Kin; Roy E. Welsch; Marie-Véronique Clément; Lisa Tucker-Kellogg (Bioinform., 2020)

Computational modeling suggests binding-induced expansion of Epsin disordered regions upon association with AP2. - N. Suhas Jagannathan; Christopher W. V. Hogue; Lisa Tucker-Kellogg (PLoS Comput. Biol., 2021)

ArcheGEO: towards improving relevance of gene expression omnibus search results. - Huey-Eng Chua; Lisa Tucker-Kellogg; Sourav S. Bhowmick (BCB, 2022)

Quantification of muscle fiber malformations using edge detection to investigate chronic muscle pressure ulcers. - Charlene Zhi Lin Ong; N. Jannah M. Nasir; Roy E. Welsch; Lisa Tucker-Kellogg; Jagath C. Rajapakse (Frontiers Bioinform., 2024)