Publications

Refereed Journal Articles and Book Chapters

  • S. Mangul, A. P. Ori, K. A. Staats, L. M. O. Loohuis, G. Jospin, J. A. Eisen, E. Eskin1, R. A. Ophoff, ”Increased diversity in blood microbiome across schizophrenia patients”, (in preparation)
  • S. Mangul, N. Strauli, R. Hernandez, R. Ophoff, M. Seibold, E. Eskin, N. Zaitlen, ”Dumpster Diving: Finding the source of every last read”, (in preparation)
  • S. Mangul, N. Wu, N. Mancuso, A. Zelikovsky, R. Sun and E. Eskin, “Accurate HIV population assembly from ultra-deep sequencing data”, 17th Annual International Conference on Research in Computational Molecular Biology (Bioinformatics, ISMB 2014) (accepted, acceptance rate 19%)
  • E. Kang, L. J. Martin, S. Mangul, , E. Eskin, Discovering SNPs Regulating Human GeneExpression Using Allele Specic Expression from RNA-Seq data (submitted)
  • S. Mangul, S. Al Seesi, A. Caciula, D. Brinza, I. Mandoiu and A. Zelikovsky, “TranscriptomeAssembly and Quantication from Ion Torrent RNA-Seq Data(in press)”, BMC Genomics, 2014
  • I. Astrovskaya, N. Mancuso, B. Tork, S. Mangul, A. Artyomenko, P. Skums, L. Ganova-Raeva, I. Măndoiu, and A. Zelikovsky “Inferring Viral Quasispecies Spectra from Shotgun and Amplicon 454 Pyrosequencing Reads”(to appear), book chapter, Genome Analysis: Current Procedures and Applications, 2013
  • S. Al Seesi, S. Mangul, A. Caciula, I. Mandoiu and A. Zelikovsky “Transcriptome Reconstruction and Quantification from RNA-Seq Data” (to appear), book chapter, Genome Analysis: Current Procedures and Applications, 2013
  • S. Mangul, A. Caciula, O. Glebova, I. Mandoiu and A. Zelikovsky, “Improved Transcriptome Quantification and Reconstruction from RNA-Seq Reads using Partial Annotations”, In Silico Biology 11, pp. 251-261, 2012
  • S. Mangul, A. Caciula, O. Glebova, I. Mandoiu and A. Zelikovsky, “RNA-Seq based transcriptome quantification and reconstruction guided by proteincoding gene annotation”(to appear), book chapter, Algorithmic and AI Methods for Protein Bioinformatics, 2012
  • M. Nicolae, S. Mangul, I. Mandoiu and A. Zelikovsky, “Estimation of alternative splicing isoform frequencies from RNA-Seq data”, Algorithms for Molecular Biology, 2011
  • I. Astrovskaya, B. Tork, S. Mangul, K. Westbrooks, I. Mandoiu, P. Balfe and A. Zelikovsky, “Inferring Viral Spectrum from 454 Pyrosequencing Reads”, BMC Bioinformatics, 2011

Refereed Conference/Workshop Articles

  • A. Caciula, O. Glebova, A. Artyomenko, S. Mangul, J. Lindsay, I. Mandoiu and A. Zelikovsky, “Simulated Regression Algorithm for Transcriptome Quantication from RNA-Seq Data” (to appear), Proc. 10th International Symposium on Bioinformatics Research and Applications (ISBRA 2014)
  • S. Mangul, S. Al Seesi, A. Caciula, D. Brinza, I. Mandoiu and A. Zelikovsky, “Transcriptome Assembly and Quantification from Ion Torrent RNA-Seq Data”, Proc. 3rd Workshop on Computational Advances for Next Generation Sequencing (CANGS 2013)
  • A. Caciula, A. Zelikovsky, S. Mangul, J. Lindsay and I. Mandoiu, “Monte-Carlo Regression Algorithm for Isoform Frequency Estimation from RNA-Seq Data”,Proc. 3rd Workshop on Computational Advances for Next Generation Sequencing (CANGS 2013)
  • A. Caciula, S. Mangul, I. Mandoiu and A. Zelikovsky, “Transcriptome Reconstruction from Single RNA-Seq Reads Using Expectation Maximization Algorithm with Expected Deviation Minimization Enhancement”, 9th International Symposium on Bioinformatics Research and Applications (ISBRA 2013)
  • S. Mangul, A. Caciula, S. Al Seesi, D. Brinza, A. Banday, R. Kanadia, I. Mandoiu and A. Zelikovsky, ”Flexible Approach for Novel Transcript Reconstruction from RNA-Seq Data using Maximum Likelihood Integer Programming”, Proc. 5th International Conference on Bioinformatics and Computational Biology (BICoB 2013)
  • S. Mangul, A. Caciula, S. Al Seesi, D. Brinza, A. Banday, R. Kanadia, I. Mandoiu and A. Zelikovsky, ”An Integer Programming Approach to Novel Transcript Reconstruction from Paired-End RNA-Seq Reads”, Proc. 3rd ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB 2012)
  • S. Mangul, A. Caciula, I. Mandoiu and A. Zelikovsky, “Novel Transcript Reconstruction from Paired-End RNA-Seq Reads Using Fragment Length Distribution”, Proc. 2nd Workshop on Computational Advances for Next Generation Sequencing (CANGS 2012)
  • S. Mangul, A. Caciula, I. Mandoiu and A. Zelikovsky, “RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes”, Proc. 1st Workshop on Computational Advances in Molecular Epidemiology (CAME 2011), pp. 118-123, 2011, pdf
  • S. Mangul, I. Astrovskaya, M. Nicolae, B. Tork, I. Mandoiu and A. Zelikovsky, “Maximum Likelihood Estimation of Incomplete Genomic Spectrum from HTS Data”, Proc. 11th Workshop on Algorithms in Bioinformatics (WABI 2011)
  • M. Nicolae, S. Mangul, I. Mandoiu and A. Zelikovsky, “Estimation of Alternative Splicing isoform Frequencies from RNA-Seq Data”, Proc. 10th Workshop on Algorithms in Bioinformatics (WABI 2010), Lecture Notes in Bioinformatics 6293, pp. 202-214
  • Z. Comarova, S. Mangul, “Simulation of Emission Dispersion as the Method of Air Quality Management”, Proc. Workshop Simulation and Assessment of Chemical Processes in a Multiphase Environment (2008), NATO Science for Peace and Security Series, pp. 403-408, pdf
  • I. Mangul, L. Fedotova, S. Mangul, “The Specisity of Climate Change in the Dnister River Basin” , Proc. International Conference Integrated Management of Natural Resources in the Transboundary Dniester River Basin (2004)

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