Shibu Yooseph

According to our database, Shibu Yooseph authored at least 29 papers between 1994 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2022

Variational Approximation-Based Model Selection for Microbial Network Inference.

Shibu Yooseph, Sahar Tavakoli

J. Comput. Biol., 2022

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

Learning a mixture of microbial networks using minorization-maximization.

Sahar Tavakoli, Shibu Yooseph

Bioinform., 2019

Algorithms for inferring multiple microbial networks.

Sahar Tavakoli, Shibu Yooseph

Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

SOF: An Efficient String Graph Construction Algorithm.

S. M. Iqbal Morshed, Shibu Yooseph

Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

2017

GRASP2: Fast and memory-efficient gene-centric assembly and homolog search.

Cuncong Zhong, Youngik Yang, Shibu Yooseph

Proceedings of the 7th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2017

2016

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles.

Cuncong Zhong, Anna Edlund, Youngik Yang, Jeffrey S. McLean, Shibu Yooseph

PLoS Comput. Biol., 2016

GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly.

Cuncong Zhong, Youngik Yang, Shibu Yooseph

BMC Bioinform., 2016

2015

SFA-SPA: a suffix array based short peptide assembler for metagenomic data.

Youngik Yang, Cuncong Zhong, Shibu Yooseph

Bioinform., 2015

2013

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

Proceedings of the Extreme Science and Engineering Discovery Environment: Gateway to Discovery, 2013

2010

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

2008

Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering.

Shibu Yooseph, Weizhong Li, Granger G. Sutton

BMC Bioinform., 2008

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

Proceedings of the Linking Literature, Information, and Knowledge for Biology, 2008

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

A Note on Efficient Computation of Haplotypes via Perfect Phylogeny.

Vineet Bafna, Dan Gusfield, Sridhar Hannenhalli, Shibu Yooseph

J. Comput. Biol., 2004

2003

Haplotyping as Perfect Phylogeny: A Direct Approach.

Vineet Bafna, Dan Gusfield, Giuseppe Lancia, Shibu Yooseph

J. Comput. Biol., 2003

Combinatorial Problems Arising in SNP and Haplotype Analysis.

Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail

Proceedings of the Discrete Mathematics and Theoretical Computer Science, 2003

2002

Zinc Finger Gene Clusters and Tandem Gene Duplication.

Mengxiang Tang, Michael S. Waterman, Shibu Yooseph

J. Comput. Biol., 2002

Fast, Fair and Frugal Bandwidth Allocation in ATM Networks.

Yair Bartal, Martin Farach-Colton, Shibu Yooseph, Lisa Zhang

Algorithmica, 2002

A Survey of Computational Methods for Determining Haplotypes.

Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail

Proceedings of the Computational Methods for SNPs and Haplotype Inference, 2002

2001

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, Shibu Yooseph, Sorin Istrail

Proceedings of the IEEE 2001 Symposium on Parallel and Large-Data Visualization and Graphics, 2001

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

Hybrid Tree Reconstruction Methods.

Daniel H. Huson, Scott Nettles, Kenneth Rice, Tandy J. Warnow, Shibu Yooseph

ACM J. Exp. Algorithmics, 1999

1998

TAL Recognition in O(M(n»)) Time.

Sanguthevar Rajasekaran, Shibu Yooseph

J. Comput. Syst. Sci., 1998

Better Methods for Solving Parsimony and Compatibility.

Maria Luisa Bonet, Mike A. Steel, Tandy J. Warnow, Shibu Yooseph

J. Comput. Biol., 1998

1997

Unifying Themes for Selection on Any Network.

Sanguthevar Rajasekaran, Wang Chen, Shibu Yooseph

J. Parallel Distributed Comput., 1997

1996

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

Proceedings of the Mathematical Hierarchies and Biology, 1996

1995

Computing the Local Consensus of Trees.

Sampath Kannan, Tandy J. Warnow, Shibu Yooseph

Proceedings of the Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, 1995

1994

Unifying Themes for Network Selection.

Sanguthevar Rajasekaran, Wang Chen, Shibu Yooseph

Proceedings of the Algorithms and Computation, 5th International Symposium, 1994