Professor of Informatics and Computing
Adjunct Professor in Biology
Office: Lindley Hall 301D
E-mail: hatang (at) indiana.edu
Lab: Computational Omics Lab (COL)
Go to Bioinformatics programs at IU Bloomington
School of Informatics and Computing
150 S. Woodlawn Avenue
Bloomington, IN 47405-7104
Ph.D. in Biochemistry, Shanghai Institute of Biochemistry, Chinese
Academy of Sciences.
B.S. in Physics, Department of Physics, Nanjing University, China.
- Computational mass spectrometry:
We are interested in developing algorithmic and machine learning approaches to tackle challenging problems in analyzing
mass spectrometric data, in particular for proteomics, glycomics and glycoproteomics.
My group introduced the new concept, the peptide detectability in
MS-based proteomics, and showed it can be predicted from the amino acid sequence of an entire protein.
This concept was widely used in proteomics now by many groups. Based on the concept, my group developed
a Bayesian framework to improve protein identification and protein inference.
Funded by a NSF CAREER Award in 2007 and funding from NIH, my group developed the first set of software tools to assist the
automated analysis of MS data for glycan profiling and the mapping site-specific glycosylations in proteins,
including MultiGlycan, GlycoFragwork and GlycoSeq.
- Privacy preserving techniques for analysis and dissemination of human genome data:
Since 2008, my group has pioneered the application of privacy preserving techniques to sharing and
analyzing genome data. My group studied the information leaks in published genome-wide association
studies (GWAS), and developed a computational approach to assessing the privacy risks in to-be-released
GWAS data. This work received the prestigious PET Award in 2011.
In collaboration with the iDASH center at UCSD, we organized the NIH-funded challange
for applying privacy-preserving techniques to human genome data (see Nature News and Genomeweb for reports
of our efforts). The most recent challenge is ongoing (see here)
I am also an active participant of the privacy/security working group at GA4GH for sharing
human genome data.
- Mobile genetic elements:
My group has developed MGEScan and ISEScan for the identification of mobile genetic elements in eukaryotic
and bacterial genomes, and GRASPERfor the characterization of their insertion polymorphisms in natural populations of eukaryotic and bacterial species.
- Fragment assembly:
My early research focuses on the fragment assembly problem in DNA sequencing.
Working with Drs. Pevzner and Waterman, I developed the Eulerian path approach to genome assembly, which was later
adopted by most assemblers (such as Velvet, SOAPDenovo, ALLPATHS, etc) for assembling next-generation sequencing (NGS) data.
Our work received the Test-of-time Award from the RECOMB conference in 2013 (see here).
project for bioinformatics master students
Topics in Informatics:
Introduction to genomics (for non-biology
Introduction to Bioinformatics
in comparative genomics
Seminar in Bioinformatics
Informatics in life sciences and chemistry
Biological sequence analysis
Advanced algorithms in bioinformatics
Biological sequence analysis
Mathematics foundations in Informatics
NSF Early Career Development (CAREER) Award, 2007.
Indiana University Outstanding Junior Faculty Award, 2009.
Privacy Enhancing Technology (PET) Award, 2011.
RECOMB Test-of-time Award, 2013.
Books and Book Chapters
H. Tang, How does influenza virus jump from animals to humans? pp148-1640, in “Bioinformatics for Biologists”, P. A. Pevzner and R. Shamir (Eds), Cambridge University Press, 2011. Amazon
S. Kim, H. Tang and E. Mardis, ed. Genome sequencing technology and algorithms, Artech House Publishers (2007). Amazon
H. Tang and S. Kim, Bioinformatics: Mining the massive data from high throughput genomics experiments, pp1-24,
in Analysis of Biological Data: A Soft Computing Approach, edited by Sanghamitra Bandyopadhyay, Ujjwal Maulik and Jason T. L. Wang, World Scientific Press (2007).
Y. Ye and H. Tang, Dynamic programming algorithms for sequence and structure comparison, pp9-28,
Bioinformatics Algorithms: Techniques and Applications
, edited by Ion Mandoiu and Alexander Zelikovsky , Wiley Press (2008).
H. Tang, How does influenza virus jump from animals to humans? Bioinformatics for Biologists, edited by P. A. Pevzner and R. Shamir, Cambridge University Press, (2011).
- M. Rho, Y. Wu, H. Tang, T. Doak and Y. Ye (2011), Diverse CRISPRs evolving in human microbiomes, Plos Genetics, in press.
- Y. Zhao, H. Tang and Y. Ye (2011) RAPSearch2: a fast and memory-efficient protein similarity search tool for next generation sequencing data. Bioinformatics, in press. Pubmed
- S. Lee, M. Kwon, H. Lee, Y. Paik, H. Tang, J. K. Lee and T. Park (2011) Enhanced peptide quantification using spectral count clustering and cluster abundance, BMC Bioinformatics, 12:423. Pubmed
- X. Lai, L. Wang, H. Tang and F. A. Witzmann (2011) A Novel Alignment Method and Multiple Filters for Exclusion of Unqualified Peptides To Enhance Label-Free Quantification Using Peptide Intensity in LC-MS/MS, Journal of Proteome Research, 10:4799-4812. Pubmed
- Y. Ye, J. Choi and H. Tang (2011) RAPSearch: a fast protein similarity search tool for short reads, BMC Bioinformatics. 12:159. Pubmed
- A. Mayampurath, C. Yu and H. Tang (2011), Bioinformatic approach to glycomics and glycoproteomics, Current Proteomics, 8(4):309-324. online
- Y. Chen, B. Peng, X. Wang and H. Tang (2012), Large-Scale Privacy-Preserving Mapping of Human Genomic Sequences on Hybrid Clouds, Proceeding of the 19th Network & Distributed System Security Symposium (NDSS'12), accepted.
- X. Zhou, B. Peng, Y. F. Li, Y. Chen, H. Tang and X. Wang (2011) To release or not to release: evaluating information leaks in aggregate human-genome Data, Proceedings of the 16th European conference on Research in computer security (ESORICS'11), Lecture Notes in Computer Science, 6879:607-627. LNCS
- Daphnia Genome Consortium (2011), The expansive genome of Daphnia pulex with environment-dependent gene regulation, Science, (6017):555-561. Science online , Science comment
- L. Cherbas, A. Willingham, D. Zhang, L. Yang, Y. Zou, B. D. Eads, J. W. Carlson, J. M. Landolin, P. Kapranov, J. Dumais, A. Samsonova, J.-H. Choi, J. Roberts, C. A. Davis, H. Tang, M. J. van Baren, S. Ghosh, A. Dobin, K. Bell, W. Lin, L. Langton, M. O. Duff, A. E. Tenney, C. Zaleski, M. R. Brent, R. A. Hoskins, T. C. Kaufman, J. Andrews, B. R. Graveley, N. Perrimon, S. E. Celniker, T. R. Gingeras and P. Cherbas (2011) The transcriptional diversity of 25 Drosophila cell lines, Genome Research, 21:301-314. Pubmed
- N. Shah, H. Tang, T. G. Doak and Y. Ye (2011), Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics. Pac Symp Biocomput. 2011:165-176. Fulltext from PSB online proceeding.
- S. Li, R. J. Arnold, H. Tang and P. Radivojac (2010) On the accuracy and limits of peptide fragmentation spectrum prediction. Analytical Chemistry, in press. Pubmed.
- M. Rho, H. Tang and Y. Ye (2010) FragGeneScan: predicting genes in short and error-prone reads. Nucl. Acids Res., 38(20):e191. Pubmed, Free fulltext at NAR online.
- C. Zhong, H. Tang, and S. Zhang (2010), RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment. Nucl. Acids Res., 38(18): e176. Pubmed, Free fulltext at NAR online.
- Y. F. Li, R. J. Arnold, H. Tang and P. Radivojac (2010), The importance of peptide detectability for protein identification, quantification, and experiment design in MS/MS proteomics. J. Proteome Research. 9(12): 6288-6297. Pubmed.
- B. C. Bohrer, Y. F. Li, J. P. Reilly, D. E. Clemmer, R. D. DiMarchi, P. Radivojac, H. Tang and R. J. Arnold (2010), Combinatorial Libraries of Synthetic Peptides as a Model for Shotgun Proteomics. Anal. Chem. 82 (15): 6559-6568. Pubmed.
- M. Rho, S. Schaack, X. Gao, S. Kim, M. Lynch and H. Tang (2010), LTR retroelements in the genome of Daphnia pulex, BMC Genomics, 11:425. Pubmed.
- Y. Wu, Y. Mechref, I. Klouckova, A. Mayampurath, M. V. Novotny and H. Tang (2010), Mapping Site-specific Protein N-Glycosylations through Liquid Chromatography/Mass Spectrometry and Targeted Tandem Mass Spectrometry, Rapid Communication of Mass Spectrometry, 24(7):965-72. Pubmed.
- D. Hajkova, Y. Imanishi, V. Palamalai, K. C. S. Rao, C. Yuan, Q. Sheng, H. Tang, R. Zeng, R. M. Darrow, D. T Organisciak and M. Miyagi (2010), Proteomic changes in the photoreceptor outer segment upon intense light exposure, J. Proteome Res., 9(2):1173-1181. Pubmed.
- M. Rho and H. Tang (2009), MGEScan-nonLTR: computational identification and classification of Non-LTR retrotransposons in eukaryotic genomes. Nucleic Acid Res, 37(21):e143. Free fulltext at NAR online
- R. Wang, F. Y. Li, X. Wang, H. Tang and X. Zhou (2009), Learning your identity and disease from research papers: information leaks in genome wide association study. Proceeding of 16th ACM conference on Computer and Communication Security (CCS'09). CCS online
- R. Wang, X. Wang, Z. Li, H. Tang, M. Reiter and Z. Dong (2009), Privacy-preserving genomic computation through program specialization. Proceeding of 16th ACM conference on Computer and Communication Security (CCS'09). CCS online
- Y. F. Li, R. J. Arnold, Y. Li, P. Radivojac, Q. Sheng and H. Tang (2009), A Bayesian approach to protein inference problem in shotgun proteomics. J. Comp. Biol., 16(8): 1183-1193. Pubmed
- Y. Ye and H. Tang (2009), An ORFome assembly approach to metagenomics sequences analysis. J. Bioinf. Comp. Biol., 7(3):455-71. Pubmed
- M. Rho, M. Zhou, X. Gao, S. Kim, H. Tang, M. Lynch (2009), Independent Mammalian Genome Contractions Following the KT Boundary. Gen. Biol. Evol. 1:2-12. Free Fulltext at GBE online
- B. Mann, M. Madera, Q. Sheng, H. Tang, Y. Mechref, M. V. Novotny (2008), ProteinQuant Suite: a bundle of automated software tools for label-free quantitative proteomics, Rapid Comm. Mass Spec., 22:3823-3834. Pubmed
- Q. Sheng, Y. Mechref, Y. Li, M. V. Novotny, H. Tang (2008), A computational approach to characterizing bond linkage of glycan isomers using MALDI-TOF-TOF mass spectrometry, Rapid Comm. Mass Spec. 22:3561-3569. Pubmed
- C. Shen, Q. Sheng, J. Dai, Y. Li, R. Zeng, H. Tang (2008), On the estimation of false positives in peptide identifications using decoy search strategy, Proteomics, 9(1):194-204. Pubmed
- C. Yuan, Q. Sheng, H. Tang, Y. Li, R. Zeng, R. J. Solaro (2008), Quantitative comparison of Sarcomeric phosphoproteomes of neonatal and adult rat hearts, Am. J Physiol. Heart Circ. Physiol., 295(2):H647-56. Pubmed
- Y. Ye, H. Tang (2008), An ORFome assembly approach to metagenomics sequences analysis. Proceedings of the 7th Annual International Conference on Computational Systems Biology (CSB'08), 3-13. CSB online
- Y. F. Li, R. J. Arnold, Y. Li, P. Radivojac, Q. Sheng, H. Tang (2008), A Bayesian approach to protein inference problem in shotgun proteomics. Proceedings of the 12th Annual International Conference on Computational Molecular Biology (RECOMB08), LNBI 4955, 167-180. LNBI online
- S. Saha, S. H. Harrison, C. Shen, H. Tang, P. Radivojac, R. J. Arnold, X. Zhang, J. Y. Chen (2008), HIP2: An online database of human plasma proteins from healthy individuals. BMC Med Genomics. 1:12. Pubmed
- J. H. Choi, S. Kim, H. Tang, J. Andrew, D. G. Gilbert, J. K. Colbourne (2008), A machine-learning approach to combined evidence validation of genome assemblies, Bioinformatics, 24(6):744-50. Pubmed
- P. Alves, R. J. Arnold, D. E. Clemmer, Y. Li, J. P. Reilly, Q. Sheng, H. Tang, Z. Xun, R. Zeng, and P. Radivojac (2008), Fast and accurate identification of semi-tryptic peptides in shotgun proteomics, Bioinformatics, 24: 102-109. Pubmed
- Z. Jiang, H. Tang, M. Ventura, M. F. Cardone, T. Marques-Bonet, X. She, P. A. Pevzner, E. E. Eichler (2007), Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat Genet. 39:1361-1368. Pubmed, Commentary on Nature Genetics.
- 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. 23:2619-2621. 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, 4532:96-107, LNCS online.
- 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 (2006), Checking for base-calling errors in repeats. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 4(1):54-64, 2007, Pubmed
- H. Tang, R. J. Arnold, P. Alves, Z. Xun, D. E. Clemmer, M. V. Novotny, J. P. Reilly and P. Radivojac (2006), A computational approach toward label-free protein quantification using predicted peptide detectability.
Bioinformatics, 22(14):e481-488, ISMB 2006. Pubmed.
- V. Bafna, H. Tang and Shaojie Zhang (2006), Consensus Folding of Unaligned RNA Sequences Revisited. J. Comp. Biol. 13(2):283-295, 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.
- N. Bandeira, H. Tang, V. Bafna and P. A. Pevzner, Shotgun protein
sequencing by tandem mass assembly. Analytical Chemistry, 2004,
- P. A. Pevzner, H. Tang and G. P. Tesler, De novo repeat classification and
fragment assembly. Genome Res. 2004 Sep; 14(9): 1786-96.
- M. Chaisson M, P. A. Pevzner and H. Tang, Fragment assembly with
short reads. Bioinformatics. 2004 Sep 1; 20(13): 2067-74.
- 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).
- P. A. Pevzner and H. Tang, Fragment assembly
with double-barreled data. Bioinformatics. 2001 Jun;17 Suppl 1:S225-33
(Special ISMB 2001 issue).
- 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
- Q. Tu, H. Tang and D. Ding, MedBlast: searching articles related to a biological sequence.
- 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.
- S. Kruglyak and H. Tang (2001) A New
Estimator of Significance of Correlation in Time Series Data, J. Comp.
- S. Kruglyak and H. Tang (2000) Regulation of
Adjecent Yeast Genes. Trends in Genetics, 16:109-111.