ANOSVA: a statistical method for detecting splice variation from expression data. - Melissa S. Cline; John Blume; Simon Cawley; Tyson Clark; Jing-Shan Hu; Gang Lu; Nathan Salomonis; Hui Wang 007; Alan Williams (ISMB (Supplement of Bioinformatics), 2005)

GenMAPP 2: new features and resources for pathway analysis. - Nathan Salomonis; Kristina Hanspers; Alexander C. Zambon; Karen Vranizan; Steven C. Lawlor; Kam D. Dahlquist; Scott Doniger; Joshua M. Stuart; Bruce R. Conklin; Alexander R. Pico (BMC Bioinform., 2007)

Alternative Splicing in the Differentiation of Human Embryonic Stem Cells into Cardiac Precursors. - Nathan Salomonis; Brandon Nelson; Karen Vranizan; Alexander R. Pico; Kristina Hanspers; Allan Kuchinsky; Linda Ta; Mark Mercola; Bruce R. Conklin (PLoS Comput. Biol., 2009)

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. - Dorothea Emig; Nathan Salomonis; Jan Baumbach; Thomas Lengauer; Bruce R. Conklin; Mario Albrecht (Nucleic Acids Res., 2010)

MAAMD: A Workflow to Standardize Meta-Analyses of Affymetrix Microarray Data. - Zhuohui Gan; Jianwu Wang 001; Nathan Salomonis; Ilkay Altintas; Andrew D. McCulloch; Alexander C. Zambon (HISB, 2012)

AltAnalyze - An Optimized Platform for RNA-Seq Splicing and Domain-Level Analyses. - Nathan Salomonis (HISB, 2012)

LineageProfiler: Automated Classification and Visualization of Cell Type Identity for Mammalian Transcriptomes. - Nathan Salomonis (HISB, 2012)

GO-Elite: a flexible solution for pathway and ontology over-representation. - Alexander C. Zambon; Stan Gaj; Isaac Ho; Kristina Hanspers; Karen Vranizan; Chris T. A. Evelo; Bruce R. Conklin; Alexander R. Pico; Nathan Salomonis (Bioinform., 2012)

Mosaic: making biological sense of complex networks. - Chao Zhang 032; Kristina Hanspers; Allan Kuchinsky; Nathan Salomonis; Dong Xu 002; Alexander R. Pico (Bioinform., 2012)

Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data. - Inna Dubchak; Matthew Munoz; Alexander Poliakov; Nathan Salomonis; Simon Minovitsky; Rolf Bodmer; Alexander C. Zambon (Bioinform., 2013)

MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data. - Zhuohui Gan; Jianwu Wang 001; Nathan Salomonis; Jennifer C. Stowe; Gabriel G. Haddad; Andrew D. McCulloch; Ilkay Altintas; Alexander C. Zambon (BMC Bioinform., 2014)

Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson's Leukocytes Identified by RNA Sequencing. - Lilach Soreq; Alessandro Guffanti; Nathan Salomonis; Alon Simchovitz; Zvi Israel; Hagai Bergman; Hermona Soreq (PLoS Comput. Biol., 2014)

Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. - Andre Olsson; Meenakshi Venkatasubramanian; Viren K. Chaudhri; Bruce J. Aronow; Nathan Salomonis; Harinder Singh; H. Leighton Grimes (Nat., 2016)

Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF. - Meenakshi Venkatasubramanian; Kashish Chetal; Daniel J. Schnell; Gowtham Atluri; Nathan Salomonis (Bioinform., 2020)

DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity. - Guangyuan Li; Balaji Iyer; V. B. Surya Prasath; Yizhao Ni; Nathan Salomonis (Briefings Bioinform., 2021)

Pseudocell Tracer - A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination. - Derek Reiman; Godhev Kumar Manakkat Vijay; Heping Xu; Andrew Sonin; Dianyu Chen; Nathan Salomonis; Harinder Singh; Aly A. Khan (PLoS Comput. Biol., 2021)

CellDrift: inferring perturbation responses in temporally sampled single-cell data. - Kang Jin; Daniel J. Schnell; Guangyuan Li; Nathan Salomonis; V. B. Surya Prasath; Rhonda Szczesniak; Bruce J. Aronow (Briefings Bioinform., 2022)

pyInfinityFlow: optimized imputation and analysis of high-dimensional flow cytometry data for millions of cells. - Kyle Ferchen; Nathan Salomonis; H. Leighton Grimes (Bioinform., 2023)