Shibu Yooseph

Publication Activity (10 Years)

Years Active: 1994-2022
Publications (10 Years): 8

Top Topics

Variational Approximation

Top Venues

J. Comput. Biol.

Publications

Shibu Yooseph, Sahar Tavakoli
Variational Approximation-Based Model Selection for Microbial Network Inference. J. Comput. Biol. 29 (7) (2022)
Cuncong Zhong, Youngik Yang, Shibu Yooseph
GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data. BMC Bioinform. (11) (2019)
S. M. Iqbal Morshed, Shibu Yooseph
SOF: An Efficient String Graph Construction Algorithm. BIBM (2019)
Sahar Tavakoli, Shibu Yooseph
Learning a mixture of microbial networks using minorization-maximization. Bioinform. 35 (14) (2019)
Sahar Tavakoli, Shibu Yooseph
Algorithms for inferring multiple microbial networks. BIBM (2019)
Cuncong Zhong, Youngik Yang, Shibu Yooseph
GRASP2: Fast and memory-efficient gene-centric assembly and homolog search. ICCABS (2017)
Cuncong Zhong, Youngik Yang, Shibu Yooseph
GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly. BMC Bioinform. 17 (S-8) (2016)
Cuncong Zhong, Anna Edlund, Youngik Yang, Jeffrey S. McLean, Shibu Yooseph
Metagenome and Metatranscriptome Analyses Using Protein Family Profiles. PLoS Comput. Biol. 12 (7) (2016)
Youngik Yang, Cuncong Zhong, Shibu Yooseph
SFA-SPA: a suffix array based short peptide assembler for metagenomic data. Bioinform. 31 (11) (2015)
Sitao Wu, Weizhong Li, Larry Smarr, Karen Nelson, Shibu Yooseph, Manolito Torralba
Large memory high performance computing enables comparison across human gut microbiome of patients with autoimmune diseases and healthy subjects. XSEDE (2013)
Johannes Goll, Douglas B. Rusch, David M. Tanenbaum, Mathangi Thiagarajan, Kelvin Li, Barbara A. Methé, Shibu Yooseph
METAREP: JCVI metagenomics reports - an open source tool for high-performance comparative metagenomics. Bioinform. 26 (20) (2010)
Robert Denroche, Ramana Madupu, Shibu Yooseph, Granger G. Sutton, Hagit Shatkay
Toward Computer-Assisted Text Curation: Classification Is Easy (Choosing Training Data Can Be Hard...). BioLINK@ISMB/ECCB (2008)
Shibu Yooseph, Weizhong Li, Granger G. Sutton
Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering. BMC Bioinform. 9 (2008)
Vineet Bafna, Dan Gusfield, Sridhar Hannenhalli, Shibu Yooseph
A Note on Efficient Computation of Haplotypes via Perfect Phylogeny. J. Comput. Biol. 11 (5) (2004)
Hagit Shatkay, Jason R. Miller, Clark M. Mobarry, Michael Flanigan, Shibu Yooseph, Granger G. Sutton
ThurGood: Evaluating Assembly-to-Assembly Mapping. J. Comput. Biol. 11 (5) (2004)
Vineet Bafna, Dan Gusfield, Giuseppe Lancia, Shibu Yooseph
Haplotyping as Perfect Phylogeny: A Direct Approach. J. Comput. Biol. 10 (3/4) (2003)
Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail
Combinatorial Problems Arising in SNP and Haplotype Analysis. DMTCS (2003)
Yair Bartal, Martin Farach-Colton, Shibu Yooseph, Lisa Zhang
Fast, Fair and Frugal Bandwidth Allocation in ATM Networks. Algorithmica 33 (3) (2002)
Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail
A Survey of Computational Methods for Determining Haplotypes. Computational Methods for SNPs and Haplotype Inference (2002)
Mengxiang Tang, Michael S. Waterman, Shibu Yooseph
Zinc Finger Gene Clusters and Tandem Gene Duplication. J. Comput. Biol. 9 (2) (2002)
Mengxiang Tang, Michael S. Waterman, Shibu Yooseph
Zinc finger gene clusters and tandem gene duplication. RECOMB (2001)
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
Visualization challenges for a new cyberpharmaceutical computing paradigm. IEEE Symposium on Parallel and Large-Data Visualization and Graphics (2001)
Yair Bartal, Martin Farach-Colton, Shibu Yooseph, Lisa Zhang
Fast, Fair, and Frugal Bandwidth Allocation in ATM Networks. SODA (1999)
Daniel H. Huson, Scott Nettles, Kenneth Rice, Tandy J. Warnow, Shibu Yooseph
Hybrid Tree Reconstruction Methods. ACM J. Exp. Algorithmics 4 (1999)
Maria Luisa Bonet, Cynthia A. Phillips, Tandy J. Warnow, Shibu Yooseph
Constructing Evolutionary Trees in the Presence of Polymorphic Characters. SIAM J. Comput. 29 (1) (1999)
Maria Luisa Bonet, Mike A. Steel, Tandy J. Warnow, Shibu Yooseph
Better Methods for Solving Parsimony and Compatibility. J. Comput. Biol. 5 (3) (1998)
Maria Luisa Bonet, Mike A. Steel, Tandy J. Warnow, Shibu Yooseph
Better methods for solving parsimony and compatibility. RECOMB (1998)
Sanguthevar Rajasekaran, Shibu Yooseph
TAL Recognition in O(M(n»)) Time. J. Comput. Syst. Sci. 56 (1) (1998)
Daniel H. Huson, Scott Nettles, Kenneth Rice, Tandy J. Warnow, Shibu Yooseph
Hybrid Tree Reconstruction Methods. WAE (1998)
Sanguthevar Rajasekaran, Wang Chen, Shibu Yooseph
Unifying Themes for Selection on Any Network. J. Parallel Distributed Comput. 46 (1) (1997)
Maria Luisa Bonet, Cynthia A. Phillips, Tandy J. Warnow, Shibu Yooseph
Inferring evolutionary trees from polymorphic characters, and an analysis of the Indo-European family of languages. Mathematical Hierarchies and Biology (1996)
Maria Luisa Bonet, Cynthia A. Phillips, Tandy J. Warnow, Shibu Yooseph
Constructing Evolutionary Trees in the Presence of Polymorphic Characters. STOC (1996)
Sampath Kannan, Tandy J. Warnow, Shibu Yooseph
Computing the Local Consensus of Trees. SODA (1995)
Sanguthevar Rajasekaran, Wang Chen, Shibu Yooseph
Unifying Themes for Network Selection. ISAAC (1994)