Epitope Prediction Algorithms for Peptide based Vaccine Design. - Liliana Florea; Bjarni V. Halldórsson; Oliver Kohlbacher; Russell Schwartz; Stephen Hoffman; Sorin Istrail (CSB, 2003)

EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae. - Liliana Florea; Michael McClelland; Cathy Riemer; Scott Schwartz; Webb Miller (Nucleic Acids Res., 2003)

Finding Anchors for Genomic Sequence Comparison. - Ross A. Lippert; Xiaoyue Zhao; Liliana Florea; Clark M. Mobarry; Sorin Istrail (J. Comput. Biol., 2005)

Bioinformatics of alternative splicing and its regulation. - Liliana Florea (Briefings Bioinform., 2006)

Designing Sensitive and Specific Spaced Seeds for Cross-Species mRNA-to-Genome Alignment. - Leming Zhou; Liliana Florea (J. Comput. Biol., 2007)

Effective cluster-based seed design for cross-species sequence comparisons. - Leming Zhou; Ingrid Mihai; Liliana Florea (Bioinform., 2008)

Universal seeds for cDNA-to-genome comparison. - Leming Zhou; Jonathan Stanton; Liliana Florea (BMC Bioinform., 2008)

Spaced Seeds for Cross-species CDNA-to-genome Sequence Alignment. - Liliana Florea; Ingrid Mihai; Leming Zhou (Commun. Inf. Syst., 2010)

Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing. - Brian Walenz; Liliana Florea (Bioinform., 2011)

CLASS: constrained transcript assembly of RNA-seq reads. - Li Song; Liliana Florea (BMC Bioinform., 2013)

Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues. - Liliana Florea; Li Song; Steven L. Salzberg (F1000Research, 2013)

Genome-Guided Transcriptome Assembly in the Age of Next-Generation Sequencing. - Liliana Florea; Steven L. Salzberg (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

JULiP: An efficient model for accurate intron selection from multiple RNA-seq samples. - Guangyu Yang; Liliana Florea (ICCABS, 2016)

Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer. - Bahman Afsari; Theresa Guo; Michael Considine; Liliana Florea; Luciane T. Kagohara; Genevieve L. Stein-O'Brien; Dylan Kelley; Emily Flam; Kristina D. Zambo; Patrick K. Ha; Donald Geman; Michael F. Ochs; et al. (Bioinform., 2018)

Jutils: a visualization toolkit for differential alternative splicing events. - Guangyu Yang; Leslie Cope; Zitong He; Liliana Florea (Bioinform., 2021)