MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences. - Scott Schwartz; Laura Elnitski; Mei Li; Matthew T. Weirauch; Cathy Riemer; Arian Smit; Eric D. Green; Ross C. Hardison; Webb Miller (Nucleic Acids Res., 2003)

Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results. - Laura Elnitski; Belinda Giardine; Prachi Shah; Yi Zhang; Cathy Riemer; Matthew T. Weirauch; Richard Burhans; Webb Miller; Ross C. Hardison (Nucleic Acids Res., 2005)

Clustering of gene locations. - Eli Walters; Naomi S. Altman; Laura Elnitski (Comput. Stat. Data Anal., 2006)

Promoter studies in the human genome: one perspective on an unfinished story. - Mary Qu Yang; Laura Elnitski (BIBE, 2007)

An Overview of Bidirectional Promoters. - Mary Qu Yang; Laura Elnitski (BIBE, 2007)

Orthology and Multiple Class Prediction of Functional Elements in the Human Genome. - Mary Qu Yang; Laura Elnitski (BIOCOMP, 2007)

Rigorous Mapping of Orthologous Bidirectional Promoters in Vertebrates Defines their Evolutionary History. - Mary Qu Yang; James Taylor; Laura Elnitski (IMSCCS, 2007)

Invited Talk: A Computational Study of Bidirectional Promoters in the Human Genome. - Mary Qu Yang; Laura Elnitski (ISBRA, 2007)

Comprehensive Annotation of Bidirectional Promoters Identifies Co-Regulation among Breast and Ovarian Cancer Genes. - Mary Qu Yang; Laura M. Koehly; Laura Elnitski (PLoS Comput. Biol., 2007)

New Frontiers in Computational Genomics: Identification of Novel Functional Elements and Genome-scale Pattern Analysis. - Laura Elnitski; Lonnie R. Welch (Scalable Comput. Pract. Exp., 2007)

Word-Based Characterization of the Bidirectional Promoters from the Human DNA-Repair Pathway. - Jens Lichtenberg; Edwin Jacox; Mary Qu Yang; Laura Elnitski; Lonnie R. Welch (BIOCOMP, 2008)

Comparative analyses of bidirectional promoters in vertebrates. - Mary Qu Yang; James Taylor; Laura Elnitski (BMC Bioinform., 2008)

Regulatory network nodes of check point factors in DNA repair pathways. - Laura Elnitski; Jens Lichtenberg; Lonnie R. Welch (BCB, 2010)

WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures. - Jens Lichtenberg; Kyle Kurz; Xiaoyu Liang; Rami Al-ouran; Lev Neiman; Lee J. Nau; Joshua D. Welch; Edwin Jacox; Thomas Bitterman; Klaus Ecker; Laura Elnitski; Frank Drews; et al. (BMC Bioinform., 2010)

Orthology-driven mapping of bidirectional promoters in human and mouse genomes. - Mary Qu Yang; Laura Elnitski (BMC Bioinform., 2014)

SigSeeker: a peak-calling ensemble approach for constructing epigenetic signatures. - Jens Lichtenberg; Laura Elnitski; David M. Bodine (Bioinform., 2017)

Significant associations between driver gene mutations and DNA methylation alterations across many cancer types. - Yun-Ching Chen; Valer Gotea; Gennady Margolin; Laura Elnitski (PLoS Comput. Biol., 2017)

Discovering Gene Regulatory Elements Using Coverage-Based Heuristics. - Rami Al-ouran; Robert Schmidt; Ashwini Naik; Jeffrey Jones; Frank Drews; David W. Juedes; Laura Elnitski; Lonnie R. Welch (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Aberrant DNA methylation defines isoform usage in cancer, with functional implications. - Yun-Ching Chen; Laura Elnitski (PLoS Comput. Biol., 2019)

Characterization and clustering of kinase isoform expression in metastatic melanoma. - David O. Holland; Valer Gotea; Kevin Fedkenheuer; Sushil K. Jaiswal; Catherine Baugher; Hua Tan; Michael Fedkenheuer; Laura Elnitski (PLoS Comput. Biol., 2022)

iSoMAs: Finding isoform expression and somatic mutation associations in human cancers. - Hua Tan; Valer Gotea; Sushil K. Jaiswal; Nancy E. Seidel; David O. Holland; Kevin Fedkenheuer; Abdel G. Elkahloun; Sara R. Bang-Christensen; Laura Elnitski (PLoS Comput. Biol., 2025)