BioPP: a tool for web-publication of biological networks. - Ganesh A. Viswanathan; German Nudelman; Sonali Patil; Stuart C. Sealfon (BMC Bioinform., 2007)

Getting Started in Biological Pathway Construction and Analysis. - Ganesh A. Viswanathan; Jeremy Seto; Sonali Patil; German Nudelman; Stuart C. Sealfon (PLoS Comput. Biol., 2008)

Misty Mountain clustering: application to fast unsupervised flow cytometry gating. - István P. Sugár; Stuart C. Sealfon (BMC Bioinform., 2010)

Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase. - Sonali Patil; Hanna Pincas; Jeremy Seto; German Nudelman; Irina Nudelman; Stuart C. Sealfon (BMC Syst. Biol., 2010)

Plato's Cave Algorithm: Inferring Functional Signaling Networks from Early Gene Expression Shadows. - Yishai Shimoni; Marc Y. Fink; Soon-gang Choi; Stuart C. Sealfon (PLoS Comput. Biol., 2010)

flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding. - Yongchao Ge; Stuart C. Sealfon (Bioinform., 2012)

Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection. - Elena Zaslavsky; German Nudelman; Susanna Marquez; Uri Hershberg; Boris M. Hartmann; Juilee Thakar; Stuart C. Sealfon; Steven H. Kleinstein (BMC Bioinform., 2013)

Noise propagation through extracellular signaling leads to fluctuations in gene expression. - Omar P. Tabbaa; German Nudelman; Stuart C. Sealfon; Fernand Hayot; Ciriyam Jayaprakash (BMC Syst. Biol., 2013)

Hybrid Bayesian-rank integration approach improves the predictive power of genomic dataset aggregation. - Marcus A. Badgeley; Stuart C. Sealfon; Maria D. Chikina (Bioinform., 2015)

CellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations. - Maria D. Chikina; Elena Zaslavsky; Stuart C. Sealfon (Bioinform., 2015)

MOCCASIN: converting MATLAB ODE models to SBML. - Harold F. Gómez; Michael Hucka; Sarah M. Keating; German Nudelman; Dagmar Iber; Stuart C. Sealfon (Bioinform., 2016)

Elucidation of molecular kinetic schemes from macroscopic traces using system identification. - Miguel Fribourg; Diomedes E. Logothetis; Javier González-Maeso; Stuart C. Sealfon; Belén Galocha-Iragüen; Fernando Las-Heras Andrés; Vladimir Brezina (PLoS Comput. Biol., 2017)

Correction: Elucidation of molecular kinetic schemes from macroscopic traces using system identification. - Miguel Fribourg; Diomedes E. Logothetis; Javier González-Maeso; Stuart C. Sealfon; Belén Galocha-Iragüen; Fernando Las-Heras Andrés; Vladimir Brezina (PLoS Comput. Biol., 2018)

Tellurium notebooks - An environment for reproducible dynamical modeling in systems biology. - J. Kyle Medley; Kiri Choi; Matthias König 003; Lucian P. Smith; Stanley Gu; Joseph L. Hellerstein; Stuart C. Sealfon; Herbert M. Sauro (PLoS Comput. Biol., 2018)

Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. - Xi Chen; Yuan Wang 084; Antonio Cappuccio; Wan-Sze Cheng; Frederique Ruf Zamojski; Venugopalan D. Nair; Clare M. Miller; Aliza B. Rubenstein; German Nudelman; Alicja Tadych; Chandra L. Theesfeld; Alexandria Vornholt; et al. (Nat. Comput. Sci., 2023)

Author Correction: Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. - Xi Chen; Yuan Wang 084; Antonio Cappuccio; Wan-Sze Cheng; Frederique Ruf Zamojski; Venugopalan D. Nair; Clare M. Miller; Aliza B. Rubenstein; German Nudelman; Alicja Tadych; Chandra L. Theesfeld; Alexandria Vornholt; et al. (Nat. Comput. Sci., 2023)