Visualization Techniques for Genomic Data. - Ann E. Loraine; Gregg A. Helt (CSB, 2002)

Protein-Based Analysis of Alternative Splicing in the Human Genome. - Ann E. Loraine; Gregg A. Helt; Melissa S. Cline; Michael A. Siani-Rose (CSB, 2002)

Structure-Based Comparison of Four Eukaryotic Genomes. - Melissa S. Cline; Guoying Liu; Ann E. Loraine; Ron Shigeta; Jill Cheng; Gangwu Mei; David Kulp; Michael A. Siani-Rose (Pacific Symposium on Biocomputing, 2002)

NetAffx: affymetrix probeset annotations. - Guoying Liu; Ann E. Loraine; Ron Shigeta; Melissa S. Cline; Jill Cheng; Stephen A. Chervitz; David Kulp; Michael A. Siani-Rose (SAC, 2002)

Visualizing the genome: techniques for presenting human genome data and annotations. - Ann E. Loraine; Gregg A. Helt (BMC Bioinform., 2002)

Exploring Alternative Transcript Structure in the Humangenome Using Blocks and Interpro. - Ann E. Loraine; Gregg A. Helt; Melissa S. Cline; Michael A. Siani-Rose (J. Bioinform. Comput. Biol., 2003)

NetAffx: Affymetrix probesets and annotations. - Guoying Liu; Ann E. Loraine; Ron Shigeta; Melissa S. Cline; Jill Cheng; Venu Valmeekam; Shaw Sun; David Kulp; Michael A. Siani-Rose (Nucleic Acids Res., 2003)

Gene Length and Alternative Transcription in Fruit Fly. - Boris Budagyan; Ann E. Loraine (CSB, 2004)

The Effects of Alternative Splicing on Transmembrane Proteins in the Mouse Genome. - Melissa S. Cline; Ron Shigeta; Raymond Wheeler; Michael A. Siani-Rose; David Kulp; Ann E. Loraine (Pacific Symposium on Biocomputing, 2004)

Gene-Ontology-based analysis of gene expression changes in early development of Ceratopteris spores. - Ann E. Loraine; Mari L. Salmi; Stephen C. Stout; Stanley J. Roux (CSB Workshops, 2005)

Bioinformatics, Genomics, and Proteomics: Getting the Big Picture (Biotechnology in the 21st Century): Ann Finney Batiza. - Ann E. Loraine (Briefings Bioinform., 2008)

Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient. - Jianchao Yao; Chunqi Chang; Mari L. Salmi; Yeung Sam Hung; Ann E. Loraine; Stanley J. Roux (BMC Bioinform., 2008)

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. - John W. Nicol; Gregg A. Helt; Steven G. Blanchard Jr.; Archana Raja; Ann E. Loraine (Bioinform., 2009)

Genoviz Software Development Kit: Java tool kit for building genomics visualization applications. - Gregg A. Helt; John W. Nicol; Ed Erwin; Eric Blossom; Steven G. Blanchard Jr.; Stephen A. Chervitz; Cyrus L. Harmon; Ann E. Loraine (BMC Bioinform., 2009)

Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems. - Ruolin Liu; Ann E. Loraine; Julie A. Dickerson (BMC Bioinform., 2014)

Integrated genome browser: visual analytics platform for genomics. - Nowlan H. Freese; David C. Norris; Ann E. Loraine (Bioinform., 2016)

ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins. - Tarun Mall; John Eckstein; David C. Norris; Hiral Vora; Nowlan H. Freese; Ann E. Loraine (Bioinform., 2016)

Integrated Genome Browser App Store. - Sameer Shanbhag; Riddhi Patil; Noor Zahara; Chirag Shetty; Rachel Weidenhammer; Sneha Watharkar; Pranav Tambvekar; Philip P. Badzuh; Chester Dias; Narendra Vankayala; Prutha Kulkarni; Charan Vallapureddy; et al. (Bioinform., 2022)

BioViz Connect: Web Application Linking CyVerse Cloud Resources to Genomic Visualization in the Integrated Genome Browser. - Karthik Raveendran; Nowlan H. Freese; Chaitanya Kintali; Srishti Tiwari; Pawan Bole; Chester Dias; Ann E. Loraine (Frontiers Bioinform., 2022)