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Computational Omics Lab (COL)
School of Informatics, Indiana University, Bloomington
School of Informatics, Indiana University
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   Selected publications

  

  • H. Tang (2007) Genome assembly, rearrangement and repeats, Chem Rev., 107(8):3391-3406. Pubmed.
  • S. H. Bae, H. Tang, J. Wu, J. Xie and S. Kim (2007), dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis. Pubmed.
  • M. Rho, J. H. Choi, S. Kim, M. Lynch and H. Tang (2007), De novo identification of LTR retrotransposons in eukaryotic genomes. BMC Genomics, 8:90. Pubmed.
  • A. Sundquist, M. Ronaghi, H. Tang, P. A. Pevzner and S. Batzoglou (2007), Whole-genome sequencing and assembly with high-throughput, short-read technologies. PLoS ONE, 2:e484. Pubmed.
  • Y. Wu, Y. Mechref, I. Klouckova, M. V. Novotny and H. Tang (2007), A computational approach for the identification of site-specific protein glycosylations through ion-trap mass spectrometry, The Third RECOMB Satellite meeting on Proteomics, Lecture Notes in Bioinformatics, 4532:97-108.
  • P. Alves, R. J. Arnold, M. V. Novotny, P. Radivojac, J. P. Reilly and H. Tang (2007), Advancement in protein inference from shotgun proteomics using peptide detectability. Pacific Symposium on Biocomputing, 12:409-420. Fulltext from PSB online proceeding.
  • R. Patwardhan, H. Tang, S. Kim and M. Dalkilic (2006), An approximate de Bruijn graph approach to multiple local alignment and motif discovery in protein sequences, The First International Workshop in data mining and bioinformatics, Lecture Notes in Bioinformatics, 4316:158-169.
  • D. Zhi, B. Raphael, A. Price, H. Tang, and P. Pevzner (2006), Identifying repeat domains in large genomes, Genome Biology, 7(1):R7, Pubmed.
  • D. Zhi, R. Keich, P. Pevzner, S. Heber and H. Tang (2007), Checking for base-calling errors in repeats. IEEE/ACM Transactions on Computational Biology and Bioinformatics 4(1):54-64. Pubmed
  • V. Bafna, H. Tang and Shaojie Zhang (2006), Consensus Folding of Unaligned RNA Sequences Revisited. J. Comp. Biol. 13(2):283-95, Pubmed.
  • R. J. Arnold, N. Jayasankar, D. Aggarwal, H. Tang and P. Radivojac (2006), A machine learning approach to predicting peptide fragmentation spectra. Proceeding of Pacific Symposium on Biocomputing, 11:219-230, Fulltext from PSB online proceeding.
  • H. Tang, Y. Mechref and M. Novotny (2005), Automatic Interpretation of MS/MS Spectra of Oligosaccharides. Bioinformatics, 21 Suppl 1:i431-i439, ISMB 2005, Pubmed
  • V. Bafna, H. Tang and Shaojie Zhang (2005), Consensus Folding of Unaligned RNA Sequences Revisited. Proceedings of the Ninth Annual International Conference on Computational Molecular Biology (RECOMB'05), 172-187, May 2005, Boston, USA, ACM.
  • B. Raphael, D. Zhi, H. Tang and P. A. Pevzner, A novel method for multiple alignment of sequences with repeats and shuffled elements. Genome Res. 2004, 14: 2336-2346. Pubmed
  • N. Bandeira, H. Tang, V. Bafna and P. A. Pevzner, Shotgun protein sequencing by tandem mass assembly. Analytical Chemistry, 2004, 76:7221-33. Pubmed
  • P. A. Pevzner, H. Tang and G. P. Tesler, De novo repeat classification and fragment assembly. Genome Res. 2004 Sep; 14(9): 1786-96. Pubmed
  • M. Chaisson M, P. A. Pevzner and H. Tang, Fragment assembly with short reads. Bioinformatics. 2004 Sep 1; 20(13): 2067-74. Pubmed
  • P. A. Pevzner, H. Tang and G. P. Tesler, De novo repeat classification and fragment assembly. Proceedings of the Eighth Annual International Conference on Computational Molecular Biology (RECOMB'04), April 2004, San Diego, USA, ACM Press. 2004 Sep; 14(9): 1786-96.
  • S. Heber, M. Alekseyev M, S. H. Sze, H. Tang and P. A. Pevzner, Splicing graphs and EST assembly problem. Bioinformatics. 2002; 18 Suppl 1 :S181-8 (ISMB 2002 issue). Pubmed
  • P. A. Pevzner and H. Tang, Fragment assembly with double-barreled data. Bioinformatics. 2001 Jun;17 Suppl 1:S225-33 (Special ISMB 2001 issue). Pubmed
  • P. A. Pevzner, H. Tang and M. S. Waterman (2001) A New Approach to Fragment Assembly in DNA Sequencing. Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB'01), April 2001, Montreal, Canada, ACM Press.
  • Q. Tu, H. Tang and D. Ding, MedBlast: searching articles related to a biological sequence. Bioinformatics. 2004,20:75-77. Pubmed
  • P. A. Pevzner, H. Tang and M. S. Waterman (2001), An Eulerian path approach to DNA fragment assembly. Proc. Natl. Acad. Sci. USA, 98:9748-9753. Pubmed
  • S. Kruglyak and H. Tang (2001) A New Estimator of Significance of Correlation in Time Series Data, J. Comp. Biol. 2001,8:463-470. Pubmed
  • S. Kruglyak and H. Tang (2000) Regulation of Adjecent Yeast Genes. Trends in Genetics, 16:109-111. Pubmed
 

 

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