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Ion Mandoiu PhD

TitleAssociate Professor
InstitutionUniversity of Connecticut
DepartmentComputer Science and Engineering
AddressUNIT 2155
Information Technologies Engineering Building
371 Fairfield Way
Phone860-486-3784
Fax860-486-4817
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    Collapse Bibliographic 
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Hamdalla MA, Rajasekaran S, Grant DF, Mandoiu II. Metabolic pathway predictions for metabolomics: a molecular structure matching approach. J Chem Inf Model. 2015 Mar 23; 55(3):709-18. PMID: 25668446.
      View in: PubMed
    2. Baumgartner M, Lemoine C, Al Seesi S, Karunakaran DK, Sturrock N, Banday AR, Kilcollins AM, Mandoiu I, Kanadia RN. Minor splicing snRNAs are enriched in the developing mouse CNS and are crucial for survival of differentiating retinal neurons. Dev Neurobiol. 2015 Sep; 75(9):895-907. PMID: 25492806.
      View in: PubMed
    3. Al Seesi S, Tiagueu YT, Zelikovsky A, Mandoiu II. Bootstrap-based differential gene expression analysis for RNA-Seq data with and without replicates. BMC Genomics. 2014; 15 Suppl 8:S2. PMID: 25435284; PMCID: PMC4248812.
    4. Hemphill E, Lindsay J, Lee C, Mandoiu II, Nelson CE. Feature selection and classifier performance on diverse bio- logical datasets. BMC Bioinformatics. 2014; 15 Suppl 13:S4. PMID: 25434802; PMCID: PMC4248652.
    5. 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. PMID: 25359889.
      View in: PubMed
    6. 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. PMID: 25245761; PMCID: PMC4203949.
    7. Lindsay J, Salooti H, Mandoiu I, Zelikovsky A. ILP-based maximum likelihood genome scaffolding. BMC Bioinformatics. 2014; 15 Suppl 9:S9. PMID: 25253180; PMCID: PMC4168704.
    8. 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; 13(16):2526-41. PMID: 25486194; PMCID: PMC4614993.
    9. 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. PMID: 25715438.
      View in: PubMed
    10. 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. PMID: 24312367; PMCID: PMC3843705.
    11. 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. PMID: 24567956.
      View in: PubMed
    12. 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. PMID: 23991755; PMCID: PMC3819714.
    13. 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. PMID: 23902469; PMCID: PMC3698000.
    14. 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. PMID: 23330685; PMCID: PMC3866231.
    15. Chen J, Mandoiu I, Sunderraman R, Wang J, Zelikovsky A. Guest editors' introduction. BMC Bioinformatics. 2012; 13 Suppl 10:S1. PMID: 22759414; PMCID: PMC3382435.
    16. 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. PMID: 22698786.
      View in: PubMed
    17. 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. PMID: 22537301; PMCID: PMC3394419.
    18. 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. PMID: 21989211; PMCID: PMC3194189.
    19. Lee C, Mandoiu II, Nelson CE. Inferring ethnicity from mitochondrial DNA sequence. BMC Proc. 2011; 5 Suppl 2:S11. PMID: 21554759; PMCID: PMC3090759.
    20. 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. PMID: 21504602; PMCID: PMC3107792.
    21. Duitama J, Kennedy J, Dinakar S, Hern√°ndez Y, Wu Y, Mandoiu II. Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads. BMC Bioinformatics. 2011; 12 Suppl 1:S53. PMID: 21342586; PMCID: PMC3044311.
    22. 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. PMID: 23202426.
      View in: PubMed
    23. 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. PMID: 23202425.
      View in: PubMed
    24. 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. PMID: 21058452.
      View in: PubMed
    25. Jun J, Mandoiu II, Nelson CE. Identification of mammalian orthologs using local synteny. BMC Genomics. 2009; 10:630. PMID: 20030836; PMCID: PMC2807883.
    26. 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. PMID: 19803737.
      View in: PubMed
    27. 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. PMID: 19264805; PMCID: PMC2677861.
    28. 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. PMID: 18973433.
      View in: PubMed
    29. 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. PMID: 18683323.
      View in: PubMed
    30. 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. PMID: 18451434.
      View in: PubMed
    31. Mandoiu II, Prajescu C. High-throughput SNP genotyping by SBE/SBH. IEEE Trans Nanobioscience. 2007 Mar; 6(1):28-35. PMID: 17393847.
      View in: PubMed
    32. Mandoiu II, Trinca D. Exact and approximation algorithms for DNA tag set design. J Comput Biol. 2006 Apr; 13(3):732-44. PMID: 16706722.
      View in: PubMed
    33. Pasaniuc B, Mandoiu I. Highly scalable genotype phasing by entropy minimization. Conf Proc IEEE Eng Med Biol Soc. 2006; 1:3482-6. PMID: 17946566.
      View in: PubMed
    34. DasGupta B, Konwar KM, Mandoiu II, Shvartsman AA. DNA-BAR: distinguisher selection for DNA barcoding. Bioinformatics. 2005 Aug 15; 21(16):3424-6. PMID: 15961439.
      View in: PubMed
    35. 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. PMID: 18048126.
      View in: PubMed
    36. 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. PMID: 15285900.
      View in: PubMed
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