Shibu Yooseph's home page






Shibu Yooseph, Ph.D.


Professor of Computer Science at the University of Central Florida
Genomics and Bioinformatics Cluster Lead
Secondary Joint Appointment in the Burnett School of Biomedical Sciences

Email: SHIBU dot YOOSEPH at UCF dot EDU





Education

  • Ph.D., Computer and Information Science, University of Pennsylvania, 1997
  • B.Tech., Computer Science and Engineering, Indian Institute of Technology, Banaras Hindu University, 1992

Previous Appointments

  • Human Longevity Inc. (2014-2016)
    • Senior Director of Bioinformatics / Microbiome Lead
  • J. Craig Venter Institute (2003-2016)
    • Professor of Informatics (2014-2016)
    • Director of Informatics, San Diego (2009-2011)
    • Associate Professor of Informatics (2009-2013)
    • Senior Computational Scientist (2003-2008)
  • Celera Genomics (2000-2003)
    • Computer Scientist
  • University of Southern California (1998-2000)
    • Research Associate
  • DIMACS, Rutgers University (1997-1998)
    • Postdoctoral Fellow
  • Lucent Technologies, Bell Labs (1997-1998)
    • Consultant

Research areas


  • Algorithm design and combinatorial optimization
  • Genomics, Computational Biology, and Bioinformatics
    • Metagenomics
    • Sequence Assembly
    • Homology Detection
    • Phylogenetics
    • Biomarker Discovery
    • Clustering and Ordination
    • Functional Genomics
  • Microbiome research
    • Host-microbiome associations and mechanisms in the context of health and disease
    • Microbial diversity in different environments including water, air, and human
    • Analysis and integration of ‘-omics’ data

Publications (>24000 Citations)

  • Torralba M.G., J.S. Franks, A. Gomez, S. Yooseph, K.E. Nelson, and D.J. Grimes, Effect of Macondo Prospect 252 Oil on Microbiota Associated with Pelagic Sargassum in the Northern Gulf of Mexico. Microb Ecol, 2017. 73(1): p. 91-100. REF
  • Zhong, C., Y. Yang, and S. Yooseph, GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly. BMC Bioinformatics, 2016. 17 Suppl 8: p. 283. REF
  • Zhong, C., A. Edlund, Y. Yang, J.S. McLean, and S. Yooseph, Metagenome and Metatranscriptome Analyses Using Protein Family Profiles. PLoS Comput Biol, 2016. 12(7): p. e1004991. REF
  • Rajagopala, S.V., S. Yooseph, D.M. Harkins, K.J. Moncera, K.B. Zabokrtsky, M.G. Torralba, A. Tovchigrechko, S.K. Highlander, R. Pieper, L. Sender, et al., Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis. BMC Genomics, 2016. 17(1): p. 635. REF
  • Rosas-Salazar C., M.H. Shilts, A. Tovchigrechko, S. Schobel, J.D. Chappell, E.K. Larkin, J. Shankar, S. Yooseph, K.E. Nelson, R.A. Halpin, et al., Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection With Human Rhinovirus and Respiratory Syncytial Virus in Infancy. J Infect Dis, 2016. 214(12): p. 1924-1928. REF
  • Kent, A.G., C.L. Dupont, S. Yooseph, and A.C. Martiny, Global biogeography of Prochlorococcus genome diversity in the surface ocean. ISME J, 2016. REF
  • Diez, B., J.A. Nylander, K. Ininbergs, C.L. Dupont, A.E. Allen, S. Yooseph, D.B. Rusch, and B. Bergman, Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution. PLoS One, 2016. 11(5): p. e0155757. REF
  • Celepli N., J. Sundh, M. Ekman, C.L. Dupont, S. Yooseph, B. Bergman, and K. Ininbergs, Meta-omic analyses of Baltic Sea cyanobacteria: diversity, community structure and salt acclimation. Environ Microbiol, 2016. REF
  • Brindefalk, B., M. Ekman, K. Ininbergs, C.L. Dupont, S. Yooseph, J. Pinhassi, and B. Bergman, Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters. Environ Microbiol, 2016 REF
  • Anderson, E.L., W. Li, N. Klitgord, S.K. Highlander, M. Dayrit, V. Seguritan, S. Yooseph, W. Biggs, J.C. Venter, K.E. Nelson, et al., A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome. Sci Rep, 2016. 6: p. 31731. REF
  • Abeles, S.R., M.B. Jones, T.M. Santiago-Rodriguez, M. Ly, N. Klitgord, S. Yooseph, K.E. Nelson, and D.T. Pride, Microbial diversity in individuals and their household contacts following typical antibiotic courses. Microbiome, 2016. 4(1): p. 39. REF
  • Zhong, C., Y. Yang, and S. Yooseph. GRASPx: Efficient Homolog-Search of Short-Peptide Metagenome Database through Simultaneous Alignment and Assembly. in 11th International Symposium on Bioinformatics Research and Applications. 2015. Norfolk, VA.
  • Zhong, C., Y. Yang, and S. Yooseph, GRASP: Guided Reference-based Assembly of Short Peptides. Nucleic Acids Res, 2015. 43(3): p. e18. REF
  • Yooseph, S., E.F. Kirkness, T.M. Tran, D.M. Harkins, M.B. Jones, M.G. Torralba, E. O'Connell, T.B. Nutman, S. Doumbo, O.K. Doumbo, et al., Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection. BMC Genomics, 2015. 16(1): p. 631. REF
  • Yang, Y., C. Zhong, and S. Yooseph, SFA-SPA: a suffix array based short peptide assembler for metagenomic data. Bioinformatics, 2015 REF
  • Llorens-Mares, T., S. Yooseph, J. Goll, J. Hoffman, M. Vila-Costa, C.M. Borrego, C.L. Dupont, and E.O. Casamayor, Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics. ISME J, 2015 REF
  • Jones, M.B., S.K. Highlander, E.L. Anderson, W. Li, M. Dayrit, N. Klitgord, M.M. Fabani, V. Seguritan, J. Green, D.T. Pride, et al., Library preparation methodology can influence genomic and functional predictions in human microbiome research. Proc Natl Acad Sci U S A, 2015. 112(45): p. 14024-9. REF
  • Inskeep, W.P., Z.J. Jay, R.E. Macur, S. Clingenpeel, A. Tenney, D. Lovalvo, J.P. Beam, M.A. Kozubal, W.C. Shanks, L.A. Morgan, et al., Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: geochemical controls on microbial community structure and function. Front Microbiol, 2015. 6: p. 1044. REF
  • He, X., J.S. McLean, A. Edlund, S. Yooseph, A.P. Hall, S.Y. Liu, P.C. Dorrestein, E. Esquenazi, R.C. Hunter, G. Cheng, et al., Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proc Natl Acad Sci U S A, 2015. 112(1): p. 244-9. REF
  • Edlund, A., Y. Yang, S. Yooseph, A.P. Hall, D.D. Nguyen, P.C. Dorrestein, K.E. Nelson, X. He, R. Lux, W. Shi, et al., Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism. ISME J, 2015 REF
  • Zarrinpar, A., A. Chaix, S. Yooseph, and S. Panda, Diet and feeding pattern affect the diurnal dynamics of the gut microbiome. Cell Metab, 2014. 20(6): p. 1006-17. REF
  • Ma, Y., R. Madupu, U. Karaoz, C.W. Nossa, L. Yang, S. Yooseph, P.S. Yachimski, E.L. Brodie, K.E. Nelson, and Z. Pei, Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets. J Virol, 2014. 88(9): p. 4786-97. REF
  • Larsson, J., N. Celepli, K. Ininbergs, C.L. Dupont, S. Yooseph, B. Bergman, and M. Ekman, Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea. ISME J, 2014. 8(9): p. 1892-903. REF
  • Dupont, C.L., J. Larsson, S. Yooseph, K. Ininbergs, J. Goll, J. Asplund-Samuelsson, J.P. McCrow, N. Celepli, L.Z. Allen, M. Ekman, et al., Functional tradeoffs underpin salinity-driven divergence in microbial community composition. PLoS One, 2014. 9(2): p. e89549. REF
  • Yooseph, S., C. Andrews-Pfannkoch, A. Tenney, J. McQuaid, S. Williamson, M. Thiagarajan, D. Brami, L. Zeigler-Allen, J. Hoffman, J.B. Goll, et al., A metagenomic framework for the study of airborne microbial communities. PLoS One, 2013. 8(12): p. e81862. REF
  • Yang, Y. and S. Yooseph, SPA: a short peptide assembler for metagenomic data. Nucleic acids research, 2013 REF
  • Wu, S., W. Li, L. Smarr, K. Nelson, S. Yooseph, and M. Torralba, Large memory high performance computing enables comparison across human gut microbiome of patients with autoimmune diseases and healthy subjects, in Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery. 2013, ACM: San Diego, California. p. 1-6.
  • Tran, S., B. Nicolau, T. Huang, K. Ka, A. Hsu, K.Q. Nguyen, R. Khosravi, K.E. Nelson, and S. Yooseph, Obesity and Periodontal Disease, in Encyclopedia of Metagenomics, K.E. Nelson, Editor. 2013, SpringerReference: Springer-Verlag Berlin Heidelberg.
  • Nealson, K.H. and S. Yooseph, Microbial diversity of the oceanic surface picoplankton: insights from the Global Ocean Sampling (GOS) program. 2nd ed. Encyclopedia of Biodiversity, ed. S.A. Levin. 2013.
  • McLean, J.S., M.J. Lombardo, J.H. Badger, A. Edlund, M. Novotny, J. Yee-Greenbaum, N. Vyahhi, A.P. Hall, Y. Yang, C.L. Dupont, et al., Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proc Natl Acad Sci U S A, 2013. 110(26): p. E2390-9. REF
  • Edlund, A., Y. Yang, A.P. Hall, L. Guo, R. Lux, X. He, K.E. Nelson, K.H. Nealson, S. Yooseph, W. Shi, et al., An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome. Microbiome, 2013. 1(1): p. 25. REF
  • Brim, H., S. Yooseph, E.G. Zoetendal, E. Lee, M. Torralba, A.O. Laiyemo, B. Shokrani, K. Nelson, and H. Ashktorab, Microbiome Analysis of Stool Samples from African Americans with Colon Polyps. PLoS One, 2013. 8(12): p. e81352.
  • Williamson, S.J. and S. Yooseph, From bacterial to microbial ecosystems (metagenomics). Methods in molecular biology, 2012. 804: p. 35-55. REF
  • Williamson, S.J., L.Z. Allen, H.A. Lorenzi, D.W. Fadrosh, D. Brami, M. Thiagarajan, J.P. McCrow, A. Tovchigrechko, S. Yooseph, and J.C. Venter, Metagenomic Exploration of Viruses throughout the Indian Ocean. PLoS One, 2012. 7(10): p. e42047. REF
  • Ward, D.V., D. Gevers, G. Giannoukos, A.M. Earl, B.A. Methe, E. Sodergren, M. Feldgarden, D.M. Ciulla, D. Tabbaa, C. Arze, et al., Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research. PLoS One, 2012. 7(6). REF
  • Sedghizadeh, P.P., S. Yooseph, D.W. Fadrosh, L. Zeigler-Allen, M. Thiagarajan, H. Salek, F. Farahnik, and S.J. Williamson, Metagenomic investigation of microbes and viruses in patients with jaw osteonecrosis associated with bisphosphonate therapy. Oral surgery, oral medicine, oral pathology and oral radiology, 2012. 114(6): p. 764-70. REF
  • Paralanov, V., J. Lu, L.B. Duffy, D.M. Crabb, S. Shrivastava, B.A. Methe, J. Inman, S. Yooseph, L. Xiao, G.H. Cassell, et al., Comparative genome analysis of 19 Ureaplasma urealyticum and Ureaplasma parvum strains. BMC microbiology, 2012. 12(1): p. 88. REF
  • Methe, B.A., K.E. Nelson, M. Pop, H.H. Creasy, M.G. Giglio, C. Huttenhower, D. Gevers, J.F. Petrosino, S. Abubucker, J.H. Badger, et al., A framework for human microbiome research. Nature, 2012. 486(7402): p. 215-221. REF
  • Li, K., M. Bihan, S. Yooseph, and B.A. Methe, Analyses of the Microbial Diversity across the Human Microbiome. PLoS One, 2012. 7(6): p. e32118. REF
  • Huttenhower, C., D. Gevers, R. Knight, S. Abubucker, J.H. Badger, A.T. Chinwalla, H.H. Creasy, A.M. Earl, M.G. FitzGerald, R.S. Fulton, et al., Structure, function and diversity of the healthy human microbiome. Nature, 2012. 486(7402): p. 207-214. REF
  • Goll, J., M. Thiagarajan, S. Abubucker, C. Huttenhower, S. Yooseph, and B.A. Methe, A Case Study for Large-Scale Human Microbiome Analysis Using JCVI's Metagenomics Reports (METAREP). PLoS One, 2012. 7(6): p. e29044. REF
  • Wu, D., M. Wu, A. Halpern, D.B. Rusch, S. Yooseph, M. Frazier, J.C. Venter, and J.A. Eisen, Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. PLoS One, 2011. 6(3): p. e18011. REF
  • Eloe, E.A., D.W. Fadrosh, M. Novotny, L. Zeigler Allen, M. Kim, M.J. Lombardo, J. Yee-Greenbaum, S. Yooseph, E.E. Allen, R. Lasken, et al., Going deeper: metagenome of a hadopelagic microbial community. PLoS One, 2011. 6(5): p. e20388. REF
  • Dupont, C.L., D.B. Rusch, S. Yooseph, M.J. Lombardo, R. Alexander Richter, R. Valas, M. Novotny, J. Yee-Greenbaum, J.D. Selengut, D.H. Haft, et al., Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. The ISME journal, 2011 REF
  • Yooseph, S., K.H. Nealson, D.B. Rusch, J.P. McCrow, C.L. Dupont, M. Kim, J. Johnson, R. Montgomery, S. Ferriera, K. Beeson, et al., Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature, 2010. 468(7320): p. 60-6. REF
  • Yang, L., W. Oberdorf, E. Gerz, T. Parsons, P. Shah, S. Bedi, C. Nossa, S. Brown, Y. Chen, M. Liu, et al., Foregut microbiome in development of esophageal adenocarcinoma. Available from Nature Precedings, 2010. REF
  • Xiao, L., J.I. Glass, V. Paralanov, S. Yooseph, G.H. Cassell, L.B. Duffy, and K.B. Waites, Detection and characterization of human Ureaplasma species and serovars by real-time PCR. J Clin Microbiol, 2010. 48(8): p. 2715-23. REF
  • Tian, Y., X. He, M. Torralba, S. Yooseph, K.E. Nelson, R. Lux, J.S. McLean, G. Yu, and W. Shi, Using DGGE profiling to develop a novel culture medium suitable for oral microbial communities. Molecular Oral Microbiology, 2010. 25(5): p. 357-367.
  • Tanenbaum, D., J. Goll, S. Murphy, P. Kumar, N. Zafar, M. Thiagarajan, R. Madupu, T. Davidsen, L. Kagan, S. Kravitz, et al., The JCVI Standard Operating Procedure for Annotating Prokaryotic Metagenomic Shotgun Sequencing Data. Standards in Genomic Sciences, 2010. 2(2).
  • Roske, K., M.F. Foecking, S. Yooseph, J.I. Glass, M.J. Calcutt, and K.S. Wise, A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes. BMC Genomics, 2010. 11: p. 430. REF
  • Li, K., E. Venter, S. Yooseph, T.B. Stockwell, L.D. Eckerle, M.R. Denison, D.J. Spiro, and B.A. Methe, ANDES: Statistical tools for the ANalyses of DEep Sequencing. BMC Res Notes, 2010. 3: p. 199. REF
  • Goll, J., D. Rusch, D.M. Tanenbaum, M. Thiagarajan, K. Li, B.A. Methe, and S. Yooseph, METAREP: JCVI Metagenomics Reports - an open source tool for high-performance comparative metagenomics. Bioinformatics, 2010 REF
  • Denroche, R., R. Madupu, S. Yooseph, G. Sutton, and H. Shatkay, Toward computer-assisted text curation: classification is easy (choosing training data can be hard...), in Proceedings of the 2009 workshop of the BioLink Special Interest Group, international conference on Linking Literature, Information, and Knowledge for Biology. 2010, Springer-Verlag: Stockholm. p. 33-42.
  • Maroti, G., Y. Tong, S. Yooseph, H. Baden-Tillson, H.O. Smith, K.L. Kovacs, M. Frazier, J.C. Venter, and Q. Xu, Discovery of [NiFe] hydrogenase genes in metagenomic DNA: cloning and heterologous expression in Thiocapsa roseopersicina. Appl Environ Microbiol, 2009. 75(18): p. 5821-30. REF
  • Yooseph, S., W. Li, and G. Sutton, Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering. BMC Bioinformatics, 2008. 9: p. 182. REF
  • Williamson, S.J., D.B. Rusch, S. Yooseph, A.L. Halpern, K.B. Heidelberg, J.I. Glass, C. Andrews-Pfannkoch, D. Fadrosh, C.S. Miller, G. Sutton, et al., The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples. PLoS ONE, 2008. 3(1): p. e1456. REF
  • Yooseph, S., G. Sutton, D.B. Rusch, A.L. Halpern, S.J. Williamson, K. Remington, J.A. Eisen, K.B. Heidelberg, G. Manning, W. Li, et al., The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol, 2007. 5(3): p. e16. REF
  • Sharon, I., S. Tzahor, S. Williamson, M. Shmoish, D. Man-Aharonovich, D.B. Rusch, S. Yooseph, G. Zeidner, S.S. Golden, S.R. Mackey, et al., Viral photosynthetic reaction center genes and transcripts in the marine environment. Isme J, 2007. 1(6): p. 492-501. REF
  • Rusch, D.B., A.L. Halpern, G. Sutton, K.B. Heidelberg, S. Williamson, S. Yooseph, D. Wu, J.A. Eisen, J.M. Hoffman, K. Remington, et al., The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol, 2007. 5(3): p. e77. REF
  • Kannan, N., J. Wu, G.S. Anand, S. Yooseph, A.F. Neuwald, J.C. Venter, and S.S. Taylor, Evolution of allostery in the cyclic nucleotide binding module. Genome Biol, 2007. 8(12): p. R264. REF
  • Glass, J.I., N. Assad-Garcia, N. Alperovich, S. Yooseph, M.R. Lewis, M. Maruf, C.A. Hutchison, 3rd, H.O. Smith, and J.C. Venter, Essential genes of a minimal bacterium. Proc Natl Acad Sci U S A, 2006. 103(2): p. 425-30. REF
  • Shatkay, H., J. Miller, C. Mobarry, M. Flanigan, S. Yooseph, and G. Sutton, ThurGood: evaluating assembly-to-assembly mapping. J Comput Biol, 2004. 11(5): p. 800-11. REF
  • Istrail, S., G.G. Sutton, L. Florea, A.L. Halpern, C.M. Mobarry, R. Lippert, B. Walenz, H. Shatkay, I. Dew, J.R. Miller, et al., Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A, 2004. 101(7): p. 1916-21. REF
  • Halldorsson, B.V., V. Bafna, N. Edwards, R. Lippert, S. Yooseph, and S. Istrail, A survey of computational methods for determining haplotypes. Computational Methods for Snps and Haplotype Inference, 2004. 2983: p. 26-47.
  • Bafna, V., D. Gusfield, S. Hannenhalli, and S. Yooseph, A note on efficient computation of haplotypes via perfect phylogeny. J Comput Biol, 2004. 11(5): p. 858-66. REF
  • Halldorsson, B.V., V. Bafna, N. Edwards, R. Lippert, S. Yooseph, and S. Istrail, Combinatorial problems arising in SNP and haplotype analysis. Discrete Mathematics and Theoretical Computer Science, Proceedings, 2003. 2731: p. 26-47.
  • Bafna, V., D. Gusfield, G. Lancia, and S. Yooseph, Haplotyping as perfect phylogeny: a direct approach. J Comput Biol, 2003. 10(3-4): p. 323-40. REF
  • Tang, M., M. Waterman, and S. Yooseph, Zinc finger gene clusters and tandem gene duplication. J Comput Biol, 2002. 9(2): p. 429-46. REF
  • Mural, R.J., M.D. Adams, E.W. Myers, H.O. Smith, G.L. Miklos, R. Wides, A. Halpern, P.W. Li, G.G. Sutton, J. Nadeau, et al., A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science, 2002. 296(5573): p. 1661-71. REF
  • Bartal, Y., M. Farach-Colton, S. Yooseph, and L. Zhang, Fast, fair and frugal bandwidth allocation in ATM networks. Algorithmica, 2002. 33(3): p. 272-286.
  • Venter, J.C., M.D. Adams, E.W. Myers, P.W. Li, R.J. Mural, G.G. Sutton, H.O. Smith, M. Yandell, C.A. Evans, R.A. Holt, et al., The sequence of the human genome. Science, 2001. 291(5507): p. 1304-51. REF
  • Turner, R.J., K. Chaturvedi, N.J. Edwards, D. Fasulo, A.L. Halpern, D.H. Huson, O. Kohlbacher, J.R. Miller, K. Reinert, K.A. Remington, et al. Visualization challenges for a new cyberpharmaceutical computing paradigm. in IEEE symposium on parallel and large-data visualization and graphics. 2001. San Diego, California.
  • Tang, M., M. Waterman, and S. Yooseph, Zinc finger gene clusters and tandem gene duplication, in Proceedings of the fifth annual international conference on Computational biology. 2001, ACM: Montreal, Quebec, Canada. p. 297-304.
  • Huson, D., S. Nettles, K. Rice, T. Warnow, and S. Yooseph, Hybrid Tree Reconstruction Methods. ACM Journal of Experimental Algorithmics, 1999. 4.
  • Heyer, L.J., S. Kruglyak, and S. Yooseph, Exploring expression data: identification and analysis of coexpressed genes. Genome Res, 1999. 9(11): p. 1106-15. REF
  • Bonet, M., C. Phillips, T. Warnow, and S. Yooseph, Constructing evolutionary trees in the presence of polymorphic characters. Siam Journal on Computing, 1999. 29(1): p. 103-131.
  • Bartal, Y., M. Farach-Colton, S. Yooseph, and L. Zhang, Fast, fair, and frugal bandwidth allocation in ATM networks, in Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms. 1999, Society for Industrial and Applied Mathematics: Baltimore, Maryland, USA. p. 92-101.
  • Rajasekaran, S. and S. Yooseph, TAL recognition in O(M(n^2)) time. Journal of Computer and System Sciences, 1998. 56(1): p. 83-89.
  • Kannan, S., T. Warnow, and S. Yooseph, Computing the local consensus of trees. Siam Journal on Computing, 1998. 27(6): p. 1695-1724.
  • Huson, D., S. Nettles, L. Parida, T. Warnow, and S. Yooseph. The Disk-Covering Method for Tree Reconstruction. in Algorithms and Experiments (ALEX). 1998. Trento, Italy.
  • Bonet, M., M. Steel, T. Warnow, and S. Yooseph, Better methods for solving parsimony and compatibility. J Comput Biol, 1998. 5(3): p. 391-407. REF
  • Rajasekaran, S., W. Chen, and S. Yooseph, Unifying themes for selection on any network. Journal of Parallel and Distributed Computing, 1997. 46(1): p. 105-111.
  • Bonet, M., C. Phillips, T. Warnow, and S. Yooseph, Inferring Evolutionary Trees from Polymorphic Characters, and an Analysis of the Indo-European Family of Languages. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 1997. 37.
  • Bonet, M., C. Phillips, T.J. Warnow, and S. Yooseph, Constructing evolutionary trees in the presence of polymorphic characters, in Proceedings of the twenty-eighth annual ACM symposium on Theory of computing. 1996, ACM: Philadelphia, Pennsylvania, USA. p. 220-229.
  • Rajasekaran, S. and S. Yooseph, TAL recognition in O(M(n^2)) time, in Proceedings of the 33rd annual meeting on Association for Computational Linguistics. 1995, Association for Computational Linguistics: Cambridge, Massachusetts. p. 166-173.
  • Kannan, S., T. Warnow, and S. Yooseph, Computing the local consensus of trees, in Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms. 1995, Society for Industrial and Applied Mathematics: San Francisco, California, USA. p. 68-77.
  • Rajasekaran, S., W. Chen, and S. Yooseph, Unifying Themes for Network Selection, in Proceedings of the 5th International Symposium on Algorithms and Computation. 1994, Springer-Verlag. p. 92-100.


College of Engineering and Computer Science
Harris Engineering – Suite 239A
P.O. Box 162362
University of Central Florida
Orlando, FL 32816

Email: SHIBU dot YOOSEPH at UCF dot EDU
Telephone: 407-823-5307