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)

Predicting reliable regions in protein sequence alignments. - Melissa S. Cline; Richard Hughey; Kevin Karplus (Bioinform., 2002)

Gene structure-based splice variant deconvolution using a microarry platform. - Hui Wang 007; Earl Hubbell; Jing-Shan Hu; Gangwu Mei; Melissa S. Cline; Gang Lu; Tyson Clark; Michael A. Siani-Rose; Manuel Ares; David Kulp; David Haussler (ISMB (Supplement of Bioinformatics), 2003)

GPCR-GRAPA-LIB-a refined library of hidden Markov Models for annotating GPCRs. - Ron Shigeta; Melissa S. Cline; Guoying Liu; Michael A. Siani-Rose (Bioinform., 2003)

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)

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)

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)

Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays. - Charles W. Sugnet; Karpagam Srinivasan; Tyson Clark; Georgeann O'Brien; Melissa S. Cline; Hui Wang 007; Alan Williams; David Kulp; John Blume; David Haussler; Manuel Ares (PLoS Comput. Biol., 2006)

GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. - Olivier Garcia; Cosmin Saveanu; Melissa S. Cline; Micheline Fromont-Racine; Alain Jacquier; Benno Schwikowski; Tero Aittokallio (Bioinform., 2007)

Integrating expression data with domain interaction networks. - Dorothea Emig; Melissa S. Cline; Thomas Lengauer; Mario Albrecht (Bioinform., 2008)

Integrative Visual Analysis of the Effects of Alternative Splicing on Protein Domain Interaction Networks. - Dorothea Emig; Melissa S. Cline; Karsten Klein 001; Anne Kunert; Petra Mutzel; Thomas Lengauer; Mario Albrecht (J. Integr. Bioinform., 2008)

Affy exon tissues: exon levels in normal tissues in human, mouse and rat. - Andrew A. Pohl; Charles W. Sugnet; Tyson Clark; Kayla E. Smith; Pauline A. Fujita; Melissa S. Cline (Bioinform., 2009)

Using bioinformatics to predict the functional impact of SNVs. - Melissa S. Cline; Rachel Karchin (Bioinform., 2011)

The UCSC Genome Browser database: update 2011. - Pauline A. Fujita; Brooke L. Rhead; Ann S. Zweig; Angie S. Hinrichs; Donna Karolchik; Melissa S. Cline; Mary Goldman; Galt P. Barber; Hiram Clawson; António Coelho; Mark Diekhans; Timothy R. Dreszer; et al. (Nucleic Acids Res., 2011)

ENCODE whole-genome data in the UCSC genome browser (2011 update). - Brian J. Raney; Melissa S. Cline; Kate R. Rosenbloom; Timothy R. Dreszer; Katrina Learned; Galt P. Barber; Laurence R. Meyer; Cricket A. Sloan; Venkat S. Malladi; Krishna M. Roskin; Bernard B. Suh; Angie S. Hinrichs; et al. (Nucleic Acids Res., 2011)

The UCSC Genome Browser database: extensions and updates 2011. - Timothy R. Dreszer; Donna Karolchik; Ann S. Zweig; Angie S. Hinrichs; Brian J. Raney; Robert M. Kuhn; Laurence R. Meyer; Matthew C. Wong; Cricket A. Sloan; Kate R. Rosenbloom; Greg Roe; Brooke L. Rhead; et al. (Nucleic Acids Res., 2012)

ENCODE whole-genome data in the UCSC Genome Browser: update 2012. - Kate R. Rosenbloom; Timothy R. Dreszer; Jeffrey C. Long; Venkat S. Malladi; Cricket A. Sloan; Brian J. Raney; Melissa S. Cline; Donna Karolchik; Galt P. Barber; Hiram Clawson; Mark Diekhans; Pauline A. Fujita; et al. (Nucleic Acids Res., 2012)

The UCSC Cancer Genomics Browser: update 2013. - Mary Goldman; Brian Craft; Teresa Swatloski; Kyle Ellrott; Melissa S. Cline; Mark Diekhans; Singer Ma; Chris Wilks; Joshua M. Stuart; David Haussler; Jingchun Zhu (Nucleic Acids Res., 2013)

The UCSC Genome Browser database: extensions and updates 2013. - Laurence R. Meyer; Ann S. Zweig; Angie S. Hinrichs; Donna Karolchik; Robert M. Kuhn; Matthew C. Wong; Cricket A. Sloan; Kate R. Rosenbloom; Greg Roe; Brooke L. Rhead; Brian J. Raney; Andy Pohl; et al. (Nucleic Acids Res., 2013)

The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. - Christopher Wilks; Melissa S. Cline; Erich Weiler; Mark Diekhans; Brian Craft; Christy Martin; Daniel Murphy; Howdy Pierce; John Black; Donavan Nelson; Brian Litzinger; Thomas Hatton; et al. (Database J. Biol. Databases Curation, 2014)

The UCSC Genome Browser database: 2014 update. - Donna Karolchik; Galt P. Barber; Jonathan Casper; Hiram Clawson; Melissa S. Cline; Mark Diekhans; Timothy R. Dreszer; Pauline A. Fujita; Luvina Guruvadoo; Maximilian Haeussler; Rachel A. Harte; Steven G. Heitner; et al. (Nucleic Acids Res., 2014)

RBPmap: a web server for mapping binding sites of RNA-binding proteins. - Inbal Paz; Idit Kosti; Manuel Ares; Melissa S. Cline; Yael Mandel-Gutfreund (Nucleic Acids Res., 2014)

The UCSC Cancer Genomics Browser: update 2015. - Mary Goldman; Brian Craft; Teresa Swatloski; Melissa S. Cline; Olena Morozova; Mark Diekhans; David Haussler; Jingchun Zhu (Nucleic Acids Res., 2015)

Data Sharing and Reproducible Clinical Genetic Testing: Successes and Challenges. - Shan Yang; Melissa S. Cline; Can Zhang; Benedict Paten; Stephen E. Lincoln (PSB, 2017)

The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation of Molecular Variation. - Alex H. Wagner; Lawrence J. Babb; Melissa S. Cline; Helen Schuilenburg; Tristan Nelson; Robert R. Freimuth; Reece Hart (AMIA, 2021)

Modeling the impact of data sharing on variant classification. - James Casaletto; Melissa S. Cline; Brian H. Shirts (J. Am. Medical Informatics Assoc., 2023)