Design of Artificial Tubular Protein Structures in 3D Hexagonal Prism Lattice Under HP Model. - Arvind Gupta; Mehdi Karimi 001; Alireza Hadj Khodabakhshi; Ján Manuch; Arash Rafiey (BIOCOMP, 2007)

Minimum Cost Homomorphisms to Locally Semicomplete and Quasi-Transitive Digraphs - Arvind Gupta; Gregory Z. Gutin; Mehdi Karimi 001; Eun Jung Kim 002; Arash Rafiey (CoRR, 2007)

Minimum Cost Homomorphism Dichotomy for Locally In-Semicomplete Digraphs. - Arvind Gupta; Mehdi Karimi 001; Eun Jung Kim 002; Arash Rafiey (COCOA, 2008)

Minimum Cost Homomorphisms to Reflexive Digraphs. - Arvind Gupta; Pavol Hell; Mehdi Karimi 001; Arash Rafiey (LATIN, 2008)

Minimum Cost Homomorphism to Oriented Cycles with Some Loops. - Mehdi Karimi 001; Arvind Gupta (CATS, 2009)

Minimum cost homomorphisms to locally semicomplete digraphs and quasi-transitive digraphs. - Arvind Gupta; Gregory Z. Gutin; Mehdi Karimi 001; Eun Jung Kim 002; Arash Rafiey (Australas. J Comb., 2010)

Haplotype Inferring via Galled-Tree Networks Is NP-Complete. - Arvind Gupta; Mohammad M. Karimi; Ján Manuch; Ladislav Stacho; Xiaohong Zhao (J. Comput. Biol., 2010)

An Interactive Analysis and Exploration Tool for Epigenomic Data. - Hamid Younesy; Cydney B. Nielsen; Torsten Möller; Olivia Alder; Rebecca Cullum; Matthew C. Lorincz; Mohammad M. Karimi; Steven J. M. Jones (Comput. Graph. Forum, 2013)

ALEA: a toolbox for allele-specific epigenomics analysis. - Hamid Younesy; Torsten Möller; Alireza Heravi Moussavi; Jeffrey B. Cheng; Joseph F. Costello; Matthew C. Lorincz; Mohammad M. Karimi; Steven J. M. Jones (Bioinform., 2014)

VisRseq: R-based visual framework for analysis of sequencing data. - Hamid Younesy; Torsten Möller; Matthew C. Lorincz; Mohammad M. Karimi; Steven J. M. Jones (BMC Bioinform., 2015)

ChAsE: chromatin analysis and exploration tool. - Hamid Younesy; Cydney B. Nielsen; Matthew C. Lorincz; Steven J. M. Jones; Mohammad M. Karimi; Torsten Möller (Bioinform., 2016)

LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq. - Artem Babaian; I. Richard Thompson; Jake Lever; Liane Gagnier; Mohammad M. Karimi; Dixie L. Mager (Bioinform., 2019)

iNucs: inter-nucleosome interactions. - Mehrdad Oveisi; Manu Shukla; Nogayhan Seymen; Masae Ohno; Yuichi Taniguchi; Sunil Nahata; Remco Loos; Ghulam J. Mufti; Robin C. Allshire; Stefan Dimitrov; Mohammad M. Karimi (Bioinform., 2021)

ModEx: a general purpose computer model exploration system. - Hamid Younesy; Joseph Pober; Torsten Möller; Mohammad M. Karimi (Frontiers Bioinform., 2023)