Shibu Yooseph

发表

Constructing evolutionary trees in the presence of polymorphic characters

Cynthia A. Phillips, Maria Luisa Bonet, Tandy J. Warnow, 1996, STOC '96.

Toward Computer-Assisted Text Curation: Classification Is Easy (Choosing Training Data Can Be Hard...)

Hagit Shatkay, Shibu Yooseph, Robert Denroche, 2008, BioLINK@ISMB/ECCB.

Zinc Finger Gene Clusters and Tandem Gene Duplication

Shibu Yooseph, Mengxiang Tang, Michael S. Waterman, 2002, J. Comput. Biol..

Hybrid tree reconstruction methods

Daniel H. Huson, Tandy J. Warnow, Shibu Yooseph, 1999, JEAL.

A Note on Efficient Computation of Haplotypes via Perfect Phylogeny

Shibu Yooseph, Vineet Bafna, Dan Gusfield, 2004, J. Comput. Biol..

Fast, Fair and Frugal Bandwidth Allocation in ATM Networks

Lisa Zhang, Shibu Yooseph, Martin Farach-Colton, 1999, SODA '99.

Visualization challenges for a new cyber-pharmaceutical computing paradigm

Russell Schwartz, Daniel H. Huson, Shibu Yooseph, 2001, Proceedings IEEE 2001 Symposium on Parallel and Large-Data Visualization and Graphics (Cat. No.01EX520).

Constructing Evolutionary Trees in the Presence of Polymorphic Characters

Cynthia A. Phillips, Maria Luisa Bonet, Tandy J. Warnow, 1999, SIAM J. Comput..

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles

Shibu Yooseph, Youngik Yang, Cuncong Zhong, 2016, PLoS Comput. Biol..

ThurGood: Evaluating Assembly-to-Assembly Mapping

Hagit Shatkay, Shibu Yooseph, Jason R. Miller, 2004, J. Comput. Biol..

A Case Study for Large-Scale Human Microbiome Analysis Using JCVI’s Metagenomics Reports (METAREP)

Shibu Yooseph, Curtis Huttenhower, Barbara A. Methé, 2012, PloS one.

Unifying Themes for Selection on Any Network

Sanguthevar Rajasekaran, Shibu Yooseph, Wang Chen, 1997, J. Parallel Distributed Comput..

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

Shibu Yooseph, Youngik Yang, Cuncong Zhong, 2015, Bioinform..

Large memory high performance computing enables comparison across human gut microbiome of patients with autoimmune diseases and healthy subjects

Shibu Yooseph, Larry Smarr, Sitao Wu, 2013, XSEDE.

Haplotyping as Perfect Phylogeny: A Direct Approach

Shibu Yooseph, Giuseppe Lancia, Vineet Bafna, 2003, J. Comput. Biol..

Unifying Themes for Network Selection

Sanguthevar Rajasekaran, Shibu Yooseph, Wang Chen, 1994, ISAAC.

Better methods for solving parsimony and compatibility

Maria Luisa Bonet, Tandy J. Warnow, Shibu Yooseph, 1998, RECOMB '98.

Bioinformatics Applications Note Database and Ontologies Metarep: Jcvi Metagenomics Reports—an Open Source Tool for High-performance Comparative Metagenomics

Johannes Goll, Shibu Yooseph, David M. Tanenbaum, 2022 .

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

Shibu Yooseph, Granger G. Sutton, Weizhong Li, 2007, BMC Bioinformatics.

TAL Recognition in O(M(n»)) Time

Sanguthevar Rajasekaran, Shibu Yooseph, S. Yooseph, 1998, J. Comput. Syst. Sci..

Inferring evolutionary trees from polymorphic characters, and an analysis of the Indo-European family of languages

Cynthia A. Phillips, Maria Luisa Bonet, Tandy J. Warnow, 1996, Mathematical Hierarchies and Biology.

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

Shibu Yooseph, Youngik Yang, Cuncong Zhong, 2016, BMC Bioinformatics.

Combinatorial Problems Arising in SNP and Haplotype Analysis

Shibu Yooseph, Sorin Istrail, Vineet Bafna, 2003, DMTCS.

GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data

Shibu Yooseph, Youngik Yang, Cuncong Zhong, 2019, BMC Bioinformatics.

Visualization Challenges for a New Cyberpharmaceutical Computing

Russell Schwartz, Daniel H. Huson, Shibu Yooseph, 2001 .

A Survey of Computational Methods for Determining Haplotypes

Shibu Yooseph, Sorin Istrail, Vineet Bafna, 2002, Computational Methods for SNPs and Haplotype Inference.

Zinc finger gene clusters and tandem gene duplication

Shibu Yooseph, Mengxiang Tang, Michael S. Waterman, 2001, J. Comput. Biol..

Phylogeny construction and consensus methods

Shibu Yooseph, 1998 .

SPA: a short peptide assembler for metagenomic data

Shibu Yooseph, S. Yooseph, Youngik Yang, 2013, Nucleic acids research.

Viral photosynthetic reaction center genes and transcripts in the marine environment

Shibu Yooseph, Yael Mandel-Gutfreund, Michael Shmoish, 2007, The ISME Journal.

Metagenomic Exploration of Viruses throughout the Indian Ocean

Shibu Yooseph, Andrey Tovchigrechko, Lisa Zeigler Allen, 2012, PloS one.

From bacterial to microbial ecosystems (metagenomics).

Shibu Yooseph, S. Yooseph, S. Williamson, 2012, Methods in molecular biology.

GRASP: Guided Reference-based Assembly of Short Peptides

Shibu Yooseph, Cuncong Zhong, S. Yooseph, 2014, Nucleic acids research.

An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome

Shibu Yooseph, Xuesong He, Anna Edlund, 2013, Microbiome.

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

Hamidreza Chitsaz, Shibu Yooseph, Pavel A Pevzner, 2013, Proceedings of the National Academy of Sciences.

Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection

Shibu Yooseph, Ogobara K. Doumbo, Peter D. Crompton, 2015, BMC Genomics.

Genomic and functional adaptation in surface ocean planktonic prokaryotes

Shibu Yooseph, Andrey Tovchigrechko, Kenneth H. Nealson, 2010, Nature.

Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease.

Shibu Yooseph, Victor Seguritan, Rohit Loomba, 2017, Cell metabolism.

Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism

Shibu Yooseph, Pieter C Dorrestein, Xuesong He, 2015, The ISME Journal.

Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Pelin Yilmaz, Folker Meyer, Shibu Yooseph, 2018, Nature Biotechnology.

Haplotyping as Perfect Phylogeny

Shibu Yooseph, Giuseppe Lancia, Vineet Bafna, 2002, RECOMB 2002.

A Metagenomic Framework for the Study of Airborne Microbial Communities

Shibu Yooseph, Mark D. Adams, Daniel Brami, 2013, PloS one.

Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies

Shibu Yooseph, Victor Seguritan, William W. Greenwald, 2017, BMC Genomics.