Solving the Lagrangian Dual when the Number of Constraints is Fixed. - Richa Agarwala; David Fernández-Baca (FSTTCS, 1992)

A Polynomial-Time Algorithm for the Perfect Phylogeny Problem when the Number of Character States is Fixed. - Richa Agarwala; David Fernández-Baca (SIAM J. Comput., 1994)

Algorithms for weighted multidimensional search and perfect phylogeny. - Richa Agarwala (1994)

Weighted Search in the Plane. - Richa Agarwala; David Fernández-Baca (Inf. Process. Lett., 1995)

Fast Algorithms for Inferring Evolutionary Trees. - Richa Agarwala; David Fernández-Baca; Giora Slutzki (J. Comput. Biol., 1995)

On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics). - Richa Agarwala; Vineet Bafna; Martin Farach; Babu O. Narayanan; Mike Paterson; Mikkel Thorup (SODA, 1996)

Simple Algorithms for Perfect Phylogeny and Triangulating Colored Graphs. - Richa Agarwala; David Fernández-Baca (Int. J. Found. Comput. Sci., 1996)

Weighted Multidimensional Search and Its Application to Convex Optimization. - Richa Agarwala; David Fernández-Baca (SIAM J. Comput., 1996)

Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. - Richa Agarwala; Serafim Batzoglou; Vlado Dancík; Scott E. Decatur; Martin Farach; Sridhar Hannenhalli; Steven Skiena (SODA, 1997)

Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. - Richa Agarwala; Serafim Batzoglou; Vlado Dancík; Scott E. Decatur; Sridhar Hannenhalli; Martin Farach; S. Muthukrishnan 001; Steven Skiena (J. Comput. Biol., 1997)

On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics). - Richa Agarwala; Vineet Bafna; Martin Farach; Mike Paterson; Mikkel Thorup (SIAM J. Comput., 1999)

Inverse inbreeding coefficient problems with an application to linkage analysis of recessive diseases in inbred populations. - Richa Agarwala; Leslie G. Biesecker; Alejandro A. Schäffer (Discret. Appl. Math., 2000)

WindowMasker: window-based masker for sequenced genomes. - Aleksandr Morgulis; E. Michael Gertz; Alejandro A. Schäffer; Richa Agarwala (Bioinform., 2006)

A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences. - Aleksandr Morgulis; E. Michael Gertz; Alejandro A. Schäffer; Richa Agarwala (J. Comput. Biol., 2006)

COBALT: constraint-based alignment tool for multiple protein sequences. - Jason S. Papadopoulos; Richa Agarwala (Bioinform., 2007)

rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control. - Alejandro A. Schäffer; Edward Stallknecht Rice; William J. Cook; Richa Agarwala (Bioinform., 2007)

Improved BLAST searches using longer words for protein seeding. - Sergey A. Shiryev; Jason S. Papadopoulos; Alejandro A. Schäffer; Richa Agarwala (Bioinform., 2007)

Database indexing for production MegaBLAST searches. - Aleksandr Morgulis; George Coulouris; Yan Raytselis; Thomas L. Madden; Richa Agarwala; Alejandro A. Schäffer (Bioinform., 2008)

The National Center for Biotechnology Information's Protein Clusters Database. - William Klimke; Richa Agarwala; Azat Badretdin; Slava Chetvernin; Stacy Ciufo; Boris Fedorov; Boris Kiryutin; Kathleen O'Neill; Wolfgang Resch; Sergei Resenchuk; Susan Schafer; Igor Tolstoy; et al. (Nucleic Acids Res., 2009)

High-throughput sequencing of the DBA/2J mouse genome. - Xusheng Wang; Richa Agarwala; John A. Capra; Zugen Chen; Deanna M. Church; Daniel C. Ciobanu; Zhengsheng Li; Lu Lu 004; Khyobeni Mozhui; Megan K. Mulligan; Stanley F. Nelson; Katherine S. Pollard; et al. (BMC Bioinform., 2010)

Database resources of the National Center for Biotechnology Information. - Eric W. Sayers; Richa Agarwala; Evan Bolton; J. Rodney Brister; Kathi Canese; Karen Clark; Ryan Connor; Nicolas Fiorini; Kathryn Funk; Timothy Hefferon; J. Bradley Holmes; Sunghwan Kim 002; et al. (Nucleic Acids Res., 2019)

SAUTE: sequence assembly using target enrichment. - Alexandre Souvorov; Richa Agarwala (BMC Bioinform., 2021)