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- Habil Zare, Parisa Shooshtari, Arvind Gupta, Ryan R. Brinkman
- BMC Bioinformatics
- 2009

Recent biological discoveries have shown that clustering large datasets is essential for better understanding biology in many areas. Spectral clustering in particular has proven to be a powerful tool amenable for many applications. However, it cannot be directly applied to large datasets due to time and memory limitations. To address this issue, we have… (More)

- Arvind Gupta, Naomi Nishimura
- Algorithmica
- 1998

As trees are used in a wide variety of application areas, the comparison of trees arises in many guises. Here we consider two generalizations of classical tree pattern matching, which consists of determining if one tree is isomorphic to a subgraph of another. For the embedding problems of subgraph isomorphism and topological embedding, we present algorithms… (More)

- Arvind Gupta, Naomi Nishimura
- Theor. Comput. Sci.
- 1996

- Arvind Gupta, Pavol Hell, Mehdi Karimi, Arash Rafiey
- LATIN
- 2008

For digraphs G and H, a homomorphism of G to H is a mapping f : V (G)→V (H) such that uv ∈ A(G) implies f(u)f(v) ∈ A(H). If moreover each vertex u ∈ V (G) is associated with costs ci(u), i ∈ V (H), then the cost of a homomorphism f is ∑ u∈V (G) cf(u)(u). For each fixed digraph H, the minimum cost homomorphism problem for H, denoted MinHOM(H), is the… (More)

- Javad Safaei, Ján Manuch, Arvind Gupta, Ladislav Stacho, Steven Pelech
- Proteome Science
- 2011

Complex intracellular signaling networks monitor diverse environmental inputs to evoke appropriate and coordinated effector responses. Defective signal transduction underlies many pathologies, including cancer, diabetes, autoimmunity and about 400 other human diseases. Therefore, there is high impetus to define the composition and architecture of cellular… (More)

- Ján Manuch, Murray Patterson, Arvind Gupta
- ISBRA
- 2011

- Julia M. Schulze, Thomas Hentrich, +4 authors Michael S. Kobor
- Genes & development
- 2011

Monoubiquitination of H2BK123 (H2BK123ub), catalyzed by Rad6/Bre1, is a transient histone modification with roles in transcription and is essential for establishing H3K4 and H3K79 trimethylations (H3K4me3 and H3K79me3). Here, we investigated the chromatin network around H2BK123ub by examining its localization and co-occurrence with its dependent marks as… (More)

- Arvind Gupta, Ján Manuch, Ladislav Stacho
- Journal of Computational Biology
- 2005

The inverse protein folding problem is that of designing an amino acid sequence which has a particular native protein fold. This problem arises in drug design where a particular structure is necessary to ensure proper protein-protein interactions. In this paper, we show that in the 2D HP model of Dill it is possible to solve this problem for a broad class… (More)

- Arvind Gupta, Naomi Nishimura
- SWAT
- 1994

We present sequential and parallel algorithms for various embedding problems on bounded degree partial k trees and k connected partial k trees these include subgraph isomorphism and topological embedding known to be NP complete for general partial k trees As well as contributing to our understanding of the types of graphs for which these problems are… (More)

- Murray Patterson, Yongmei Liu, Eugenia Ternovska, Arvind Gupta
- IJCAI
- 2007

Mitchell and Ternovska [49, 50] propose a constraint programming framework for search problems that is based on classical logic extended with inductive definitions. They formulate a search problem as the problem of model expansion (MX). In this framework, the problem is encoded in a logic, an instance of the problem is represented by a finite structure, and… (More)