Shibu Yooseph

36 papers A* 3B 3Journal 18Unranked 11
YearRankTypeTitle / Venue / Authors
2026 — ed.
Computational Advances in Bio and Medical Sciences - 13th International Conference, ICCABS 2025, Atlanta, GA, USA, January 12-14, 2025, Revised Selected Papers
ICCABS
Mohammed Alser, Mukul S. Bansal, Yury Khudyakov, Serghei Mangul, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Shibu Yooseph, Alexander Zelikovsky
2025 — conf
Model Selection for Sparse Microbial Network Inference Using Variational Approximation.
ICCABS
Shibu Yooseph
2022 J jnl
Variational Approximation-Based Model Selection for Microbial Network Inference.
J. Comput. Biol.
Shibu Yooseph, Sahar Tavakoli
2019 — conf
Algorithms for inferring multiple microbial networks.
BIBM
Sahar Tavakoli, Shibu Yooseph
2019 J jnl
GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data.
BMC Bioinform.
Cuncong Zhong, Youngik Yang, Shibu Yooseph
2019 J jnl
Learning a mixture of microbial networks using minorization-maximization.
Bioinform.
Sahar Tavakoli, Shibu Yooseph
2019 — conf
SOF: An Efficient String Graph Construction Algorithm.
BIBM
S. M. Iqbal Morshed, Shibu Yooseph
2017 — conf
GRASP2: Fast and memory-efficient gene-centric assembly and homolog search.
ICCABS
Cuncong Zhong, Youngik Yang, Shibu Yooseph
2016 J jnl
GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly.
BMC Bioinform.
Cuncong Zhong, Youngik Yang, Shibu Yooseph
2016 J jnl
Metagenome and Metatranscriptome Analyses Using Protein Family Profiles.
PLoS Comput. Biol.
Cuncong Zhong, Anna Edlund, Youngik Yang, Jeffrey S. McLean, Shibu Yooseph
2015 J jnl
SFA-SPA: a suffix array based short peptide assembler for metagenomic data.
Bioinform.
Youngik Yang, Cuncong Zhong, Shibu Yooseph
2013 — conf
Large memory high performance computing enables comparison across human gut microbiome of patients with autoimmune diseases and healthy subjects.
XSEDE
Sitao Wu, Weizhong Li, Larry Smarr, Karen Nelson, Shibu Yooseph, Manolito Torralba
2010 J jnl
METAREP: JCVI metagenomics reports - an open source tool for high-performance comparative metagenomics.
Bioinform.
Johannes Goll, Douglas B. Rusch, David M. Tanenbaum, Mathangi Thiagarajan, Kelvin Li, Barbara A. Methé, Shibu Yooseph
2008 J jnl
Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering.
BMC Bioinform.
Shibu Yooseph, Weizhong Li, Granger G. Sutton
2008 — conf
Toward Computer-Assisted Text Curation: Classification Is Easy (Choosing Training Data Can Be Hard...).
BioLINK@ISMB/ECCB
Robert Denroche, Ramana Madupu, Shibu Yooseph, Granger G. Sutton, Hagit Shatkay
2004 J jnl
A Note on Efficient Computation of Haplotypes via Perfect Phylogeny.
J. Comput. Biol.
Vineet Bafna, Dan Gusfield, Sridhar Hannenhalli, Shibu Yooseph
2004 J jnl
ThurGood: Evaluating Assembly-to-Assembly Mapping.
J. Comput. Biol.
Hagit Shatkay, Jason R. Miller, Clark M. Mobarry, Michael Flanigan, Shibu Yooseph, Granger G. Sutton
2003 — conf
Combinatorial Problems Arising in SNP and Haplotype Analysis.
DMTCS
Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail
2003 J jnl
Haplotyping as Perfect Phylogeny: A Direct Approach.
J. Comput. Biol.
Vineet Bafna, Dan Gusfield, Giuseppe Lancia, Shibu Yooseph
2002 — conf
A Survey of Computational Methods for Determining Haplotypes.
Computational Methods for SNPs and Haplotype Inference
Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail
2002 J jnl
Fast, Fair and Frugal Bandwidth Allocation in ATM Networks.
Algorithmica
Yair Bartal, Martin Farach-Colton, Shibu Yooseph, Lisa Zhang
2002 J jnl
Zinc Finger Gene Clusters and Tandem Gene Duplication.
J. Comput. Biol.
Mengxiang Tang, Michael S. Waterman, Shibu Yooseph
2001 — conf
Visualization challenges for a new cyberpharmaceutical computing paradigm.
IEEE Symposium on Parallel and Large-Data Visualization and Graphics
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
2001 B conf
Zinc finger gene clusters and tandem gene duplication.
RECOMB
Mengxiang Tang, Michael S. Waterman, Shibu Yooseph
1999 J jnl
Constructing Evolutionary Trees in the Presence of Polymorphic Characters.
SIAM J. Comput.
Maria Luisa Bonet, Cynthia A. Phillips, Tandy J. Warnow, Shibu Yooseph
1999 A* conf
Fast, Fair, and Frugal Bandwidth Allocation in ATM Networks.
SODA
Yair Bartal, Martin Farach-Colton, Shibu Yooseph, Lisa Zhang
1999 J jnl
Hybrid Tree Reconstruction Methods.
ACM J. Exp. Algorithmics
Daniel H. Huson, Scott Nettles, Kenneth Rice, Tandy J. Warnow, Shibu Yooseph
1998 J jnl
Better Methods for Solving Parsimony and Compatibility.
J. Comput. Biol.
Maria Luisa Bonet, Mike A. Steel, Tandy J. Warnow, Shibu Yooseph
1998 B conf
Better methods for solving parsimony and compatibility.
RECOMB
Maria Luisa Bonet, Mike A. Steel, Tandy J. Warnow, Shibu Yooseph
1998 — conf
Hybrid Tree Reconstruction Methods.
WAE
Daniel H. Huson, Scott Nettles, Kenneth Rice, Tandy J. Warnow, Shibu Yooseph
1998 J jnl
TAL Recognition in O(M(n»)) Time.
J. Comput. Syst. Sci.
Sanguthevar Rajasekaran, Shibu Yooseph
1997 J jnl
Unifying Themes for Selection on Any Network.
J. Parallel Distributed Comput.
Sanguthevar Rajasekaran, Wang Chen, Shibu Yooseph
1996 A* conf
Constructing Evolutionary Trees in the Presence of Polymorphic Characters.
STOC
Maria Luisa Bonet, Cynthia A. Phillips, Tandy J. Warnow, Shibu Yooseph
1996 — conf
Inferring evolutionary trees from polymorphic characters, and an analysis of the Indo-European family of languages.
Mathematical Hierarchies and Biology
Maria Luisa Bonet, Cynthia A. Phillips, Tandy J. Warnow, Shibu Yooseph
1995 A* conf
Computing the Local Consensus of Trees.
SODA
Sampath Kannan, Tandy J. Warnow, Shibu Yooseph
1994 B conf
Unifying Themes for Network Selection.
ISAAC
Sanguthevar Rajasekaran, Wang Chen, Shibu Yooseph