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Ion Mandoiu PhD
Title Associate Professor
Institution University of Connecticut
Department Computer Science and Engineering
Address Information Technologies Engineering Building, UNIT 2155
371 Fairfield Way
Storrs, CT 06269
Telephone 860-486-3784
Fax 860-486-4817
Email
Publications
1. Hemphill E, Lindsay J, Lee C, Mandoiu II, Nelson CE. Feature selection and classifier performance on diverse bio- logical datasets. BMC Bioinformatics. 2014 Nov 13; 15 Suppl 13:S4.
  View in: PubMed
 
2. Al Seesi S, Tiagueu Y, Zelikovsky A, Mandoiu II. Bootstrap-based differential gene expression analysis for RNA-Seq data with and without replicates. BMC Genomics. 2014 Nov 13; 15 Suppl 8:S2.
  View in: PubMed
 
3. Skums P, Artyomenko A, Glebova O, Ramachandran S, Mandoiu I, Campo DS, Dimitrova Z, Zelikovsky A, Khudyakov Y. Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling. Bioinformatics. 2015 Mar 1; 31(5):682-90.
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4. Duan F, Duitama J, Al Seesi S, Ayres CM, Corcelli SA, Pawashe AP, Blanchard T, McMahon D, Sidney J, Sette A, Baker BM, Mandoiu II, Srivastava PK. Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity. J Exp Med. 2014 Oct 20; 211(11):2231-48.
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5. Lindsay J, Salooti H, Mandoiu I, Zelikovsky A. ILP-based maximum likelihood genome scaffolding. BMC Bioinformatics. 2014; 15 Suppl 9:S9.
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6. Banday AR, Baumgartner M, Al Seesi S, Karunakaran DK, Venkatesh A, Congdon S, Lemoine C, Kilcollins AM, Mandoiu I, Punzo C, Kanadia RN. Replication-dependent histone genes are actively transcribed in differentiating and aging retinal neurons. Cell Cycle. 2014 Aug 15; 13(16):2526-41.
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7. Mandoiu I, Pop M, Rajasekaran S, Spouge JL. This special issue includes a selection of papers presented at the 2nd IEEE International Conference. Introduction. Int J Bioinform Res Appl. 2014; 10(4-5):341-4.
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8. Huang Y, Khan MI, Khan M, Mandoiu I, Mandoiu II. Neuraminidase subtyping of avian influenza viruses with PrimerHunter-designed primers and quadruplicate primer pools. PLoS One. 2013; 8(11):e81842.
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9. Mandoiu II, Wang J, Zelikovsky A. Guest editors' introduction to the special section on bioinformatics research and applications. IEEE/ACM Trans Comput Biol Bioinform. 2013 Nov-Dec; 10(6):1345-6.
  View in: PubMed
 
10. Menikarachchi LC, Hill DW, Hamdalla MA, Mandoiu II, Grant DF. In silico enzymatic synthesis of a 400,000 compound biochemical database for nontargeted metabolomics. J Chem Inf Model. 2013 Sep 23; 53(9):2483-92.
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11. Skums P, Mancuso N, Artyomenko A, Tork B, Mandoiu I, Khudyakov Y, Zelikovsky A. Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows. BMC Bioinformatics. 2013; 14 Suppl 9:S2.
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12. Hamdalla MA, Mandoiu II, Hill DW, Rajasekaran S, Grant DF. BioSM: metabolomics tool for identifying endogenous mammalian biochemical structures in chemical structure space. J Chem Inf Model. 2013 Mar 25; 53(3):601-12.
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13. Chen J, Mandoiu I, Sunderraman R, Wang J, Zelikovsky A. Guest editors' introduction. BMC Bioinformatics. 2012; 13 Suppl 10:S1.
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14. Duan F, Simeone S, Wu R, Grady J, Mandoiu I, Srivastava PK. Area under the curve as a tool to measure kinetics of tumor growth in experimental animals. J Immunol Methods. 2012 Aug 31; 382(1-2):224-8.
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15. Duitama J, Srivastava PK, Mandoiu II. Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data. BMC Genomics. 2012; 13 Suppl 2:S6.
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16. Astrovskaya I, Tork B, Mangul S, Westbrooks K, Mandoiu I, Balfe P, Zelikovsky A. Inferring viral quasispecies spectra from 454 pyrosequencing reads. BMC Bioinformatics. 2011; 12 Suppl 6:S1.
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17. Lee C, Mandoiu II, Nelson CE. Inferring ethnicity from mitochondrial DNA sequence. BMC Proc. 2011; 5 Suppl 2:S11.
  View in: PubMed
 
18. Nicolae M, Mangul S, Mandoiu II, Zelikovsky A. Estimation of alternative splicing isoform frequencies from RNA-Seq data. Algorithms Mol Biol. 2011; 6(1):9.
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19. Duitama J, Kennedy J, Dinakar S, Hernández Y, Wu Y, Mandoiu II. Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads. BMC Bioinformatics. 2011; 12 Suppl 1:S53.
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20. Mancuso N, Tork B, Skums P, Ganova-Raeva L, Mandoiu I, Zelikovsky A. Reconstructing viral quasispecies from NGS amplicon reads. In Silico Biol. 2011-2012; 11(5-6):237-49.
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21. Mangul S, Caciula A, Glebova O, Mandoiu I, Zelikovsky A. Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations. In Silico Biol. 2011-2012; 11(5-6):251-61.
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22. Mandoiu I, Narasimhan G, Pan Y, Zhang Y. Guest Editors' introduction to the special section on bioinformatics research and applications. IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec; 7(4):577-8.
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23. Jun J, Mandoiu II, Nelson CE. Identification of mammalian orthologs using local synteny. BMC Genomics. 2009; 10:630.
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24. Jun J, Ryvkin P, Hemphill E, Mandoiu I, Nelson C. The birth of new genes by RNA- and DNA-mediated duplication during mammalian evolution. J Comput Biol. 2009 Oct; 16(10):1429-44.
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25. Duitama J, Kumar DM, Hemphill E, Khan M, Mandoiu II, Nelson CE. PrimerHunter: a primer design tool for PCR-based virus subtype identification. Nucleic Acids Res. 2009 May; 37(8):2483-92.
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26. Kennedy J, Mandoiu I, Pasaniuc B. Genotype error detection using Hidden Markov Models of haplotype diversity. J Comput Biol. 2008 Nov; 15(9):1155-71.
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27. Mandoiu II, Pan Y, Zelikovsky A. Guest editors' introduction to the special section on bioinformatics research and applications. IEEE/ACM Trans Comput Biol Bioinform. 2008 Jul-Sep; 5(3):321-2.
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28. Gusev A, Mandoiu II, Pasaniuc B. Highly scalable genotype phasing by entropy minimization. IEEE/ACM Trans Comput Biol Bioinform. 2008 Apr-Jun; 5(2):252-61.
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29. Mandoiu II, Prajescu C. High-throughput SNP genotyping by SBE/SBH. IEEE Trans Nanobioscience. 2007 Mar; 6(1):28-35.
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30. Mandoiu II, Trinca D. Exact and approximation algorithms for DNA tag set design. J Comput Biol. 2006 Apr; 13(3):732-44.
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31. Pasaniuc B, Mandoiu I. Highly scalable genotype phasing by entropy minimization. Conf Proc IEEE Eng Med Biol Soc. 2006; 1:3482-6.
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32. DasGupta B, Konwar KM, Mandoiu II, Shvartsman AA. DNA-BAR: distinguisher selection for DNA barcoding. Bioinformatics. 2005 Aug 15; 21(16):3424-6.
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33. Dasgupta B, Konwar KM, Mandoiu II, Shvartsman AA. Highly scalable algorithms for robust string barcoding. Int J Bioinform Res Appl. 2005; 1(2):145-61.
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34. Kahng AB, Mandoiu II, Pevzner PA, Reda S, Zelikovsky AZ. Scalable heuristics for design of DNA probe arrays. J Comput Biol. 2004; 11(2-3):429-47.
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Keyword
Last Name
Institution
    
 
 
 
Keywords   
Algorithms
Computational Biology
Polymorphism, Single Nucleotide
Sequence Analysis, DNA
Genotype
See all (108) keywords
Co-Authors  
Al Seesi, Sahar
Grady, James
Grant, David
Rajasekaran, Sanguthevar
Srivastava, Pramod
See all (7) people
Physical Neighbors  
Huang, Chun-Hsi
Khan, Mohammad
Al Seesi, Sahar
Rajasekaran, Sanguthevar
Wu, Yufeng
 
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