Unifying Themes for Network Selection. - Sanguthevar Rajasekaran; Wang Chen; Shibu Yooseph (ISAAC, 1994)

Computing the Local Consensus of Trees. - Sampath Kannan; Tandy J. Warnow; Shibu Yooseph (SODA, 1995)

Inferring evolutionary trees from polymorphic characters, and an analysis of the Indo-European family of languages. - Maria Luisa Bonet; Cynthia A. Phillips; Tandy J. Warnow; Shibu Yooseph (Mathematical Hierarchies and Biology, 1996)

Unifying Themes for Selection on Any Network. - Sanguthevar Rajasekaran; Wang Chen; Shibu Yooseph (J. Parallel Distributed Comput., 1997)

Better Methods for Solving Parsimony and Compatibility. - Maria Luisa Bonet; Mike A. Steel; Tandy J. Warnow; Shibu Yooseph (J. Comput. Biol., 1998)

TAL Recognition in O(M(n»)) Time. - Sanguthevar Rajasekaran; Shibu Yooseph (J. Comput. Syst. Sci., 1998)

Hybrid Tree Reconstruction Methods. - Daniel H. Huson; Scott Nettles; Kenneth Rice; Tandy J. Warnow; Shibu Yooseph (ACM J. Exp. Algorithmics, 1999)

Constructing Evolutionary Trees in the Presence of Polymorphic Characters. - Maria Luisa Bonet; Cynthia A. Phillips; Tandy J. Warnow; Shibu Yooseph (SIAM J. Comput., 1999)

Visualization challenges for a new cyberpharmaceutical computing paradigm. - Russell J. Turner; Kabir Chaturvedi; Nathan Edwards; Daniel P. Fasulo; Aaron L. Halpern; Daniel H. Huson; Oliver Kohlbacher; Jason R. Miller; Knut Reinert; Karin A. Remington; Russell Schwartz; Brian Walenz; et al. (IEEE Symposium on Parallel and Large-Data Visualization and Graphics, 2001)

A Survey of Computational Methods for Determining Haplotypes. - Bjarni V. Halldórsson; Vineet Bafna; Nathan Edwards; Ross Lippert; Shibu Yooseph; Sorin Istrail (Computational Methods for SNPs and Haplotype Inference, 2002)

Fast, Fair and Frugal Bandwidth Allocation in ATM Networks. - Yair Bartal; Martin Farach-Colton; Shibu Yooseph; Lisa Zhang (Algorithmica, 2002)

Zinc Finger Gene Clusters and Tandem Gene Duplication. - Mengxiang Tang; Michael S. Waterman; Shibu Yooseph (J. Comput. Biol., 2002)

Combinatorial Problems Arising in SNP and Haplotype Analysis. - Bjarni V. Halldórsson; Vineet Bafna; Nathan Edwards; Ross Lippert; Shibu Yooseph; Sorin Istrail (DMTCS, 2003)

Haplotyping as Perfect Phylogeny: A Direct Approach. - Vineet Bafna; Dan Gusfield; Giuseppe Lancia; Shibu Yooseph (J. Comput. Biol., 2003)

A Note on Efficient Computation of Haplotypes via Perfect Phylogeny. - Vineet Bafna; Dan Gusfield; Sridhar Hannenhalli; Shibu Yooseph (J. Comput. Biol., 2004)

ThurGood: Evaluating Assembly-to-Assembly Mapping. - Hagit Shatkay; Jason R. Miller; Clark M. Mobarry; Michael Flanigan; Shibu Yooseph; Granger G. Sutton (J. Comput. Biol., 2004)

Toward Computer-Assisted Text Curation: Classification Is Easy (Choosing Training Data Can Be Hard...). - Robert Denroche; Ramana Madupu; Shibu Yooseph; Granger G. Sutton; Hagit Shatkay (BioLINK@ISMB/ECCB, 2008)

Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering. - Shibu Yooseph; Weizhong Li 002; Granger G. Sutton (BMC Bioinform., 2008)

METAREP: JCVI metagenomics reports - an open source tool for high-performance comparative metagenomics. - Johannes Goll; Douglas B. Rusch; David M. Tanenbaum; Mathangi Thiagarajan; Kelvin Li; Barbara A. Methé; Shibu Yooseph (Bioinform., 2010)

Large memory high performance computing enables comparison across human gut microbiome of patients with autoimmune diseases and healthy subjects. - Sitao Wu; Weizhong Li; Larry Smarr; Karen Nelson; Shibu Yooseph; Manolito Torralba (XSEDE, 2013)

SFA-SPA: a suffix array based short peptide assembler for metagenomic data. - Youngik Yang; Cuncong Zhong; Shibu Yooseph (Bioinform., 2015)

GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly. - Cuncong Zhong; Youngik Yang; Shibu Yooseph (BMC Bioinform., 2016)

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles. - Cuncong Zhong; Anna Edlund; Youngik Yang; Jeffrey S. McLean; Shibu Yooseph (PLoS Comput. Biol., 2016)

GRASP2: Fast and memory-efficient gene-centric assembly and homolog search. - Cuncong Zhong; Youngik Yang; Shibu Yooseph (ICCABS, 2017)

SOF: An Efficient String Graph Construction Algorithm. - S. M. Iqbal Morshed; Shibu Yooseph (BIBM, 2019)

Algorithms for inferring multiple microbial networks. - Sahar Tavakoli; Shibu Yooseph (BIBM, 2019)

Learning a mixture of microbial networks using minorization-maximization. - Sahar Tavakoli; Shibu Yooseph (Bioinform., 2019)

GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data. - Cuncong Zhong; Youngik Yang; Shibu Yooseph (BMC Bioinform., 2019)

Variational Approximation-Based Model Selection for Microbial Network Inference. - Shibu Yooseph; Sahar Tavakoli (J. Comput. Biol., 2022)