GeneBox: Interactive Visualization of Microarray Data Sets. - Nameeta Y. Shah; Vladimir Filkov; Bernd Hamann; Kenneth I. Joy (METMBS, 2003)

Inferring Cis-region Hierarchies from Patterns in Time-Course Gene Expression Data - Vladimir Filkov; Nameeta Y. Shah (Regulatory Genomics, 2004)

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. - Nameeta Y. Shah; Olivier Couronne; Len A. Pennacchio; Michael Brudno; Serafim Batzoglou; E. Wes Bethel; Edward M. Rubin; Bernd Hamann; Inna Dubchak (Bioinform., 2004)

SNP-VISTA: An interactive SNP visualization tool. - Nameeta Y. Shah; Michael V. Teplitsky; Simon Minovitsky; Len A. Pennacchio; Philip Hugenholtz; Bernd Hamann; Inna Dubchak (BMC Bioinform., 2005)

PointCloudXplore: Visual Analysis of 3D Gene Expression Data Using Physical Views and Parallel Coordinates. - Oliver Rübel; Gunther H. Weber; Soile V. E. Keränen; Charless C. Fowlkes; Cris L. Luengo Hendriks; Lisa Simirenko; Nameeta Y. Shah; Michael B. Eisen; Mark D. Biggin; Hans Hagen; Damir Sudar; Jitendra Malik; et al. (EuroVis, 2006)

PointCloudXplore: A Visualization Tool for 3D Gene Expression Data. - Oliver Rübel; Gunther H. Weber; Soile V. E. Keränen; Charless C. Fowlkes; Cris L. Luengo Hendriks; Lisa Simirenko; Nameeta Y. Shah; Michael B. Eisen; Mark D. Biggin; Hans Hagen; Damir Sudar; Jitendra Malik; et al. (VLUDS, 2006)

A Simple Model of the Modular Structure of Transcriptional Regulation in Yeast. - Vladimir Filkov; Nameeta Y. Shah (J. Comput. Biol., 2008)

Volume Visualization of Multiple Alignment of Large Genomic DNA. - Nameeta Y. Shah; Scott E. Dillard; Gunther H. Weber; Bernd Hamann (Mathematical Foundations of Scientific Visualization, Computer Graphics, and Massive Data Exploration, 2009)