DBI-1564936

Book Chapters:

O. Glebova and Y. Temate-Tiagueu and A. Caciula and S. Al Seesi and A. Artyomenko and S. Mangul and J. Lindsay and I.I. Mandoiu and A. Zelikovsky, Transcriptome Quantification and Differential Expression from NGS Data, In I.I. Mandoiu and A. Zelikovsky, Computational Methods for Next Generation Sequencing Data Analysis, John Wiley & Sons, pp. 301-327, 2016, publisher url, bibtex

I. Mandric and J. Lindsay and I.I. Mandoiu and A. Zelikovsky, Scaffolding Algorithms, In I.I. Mandoiu and A. Zelikovsky, Computational Methods for Next Generation Sequencing Data Analysis, John Wiley & Sons, pp. 105-131, 2016, publisher url, bibtex

Journal Articles:

F. Rondel and R. Hosseini and B. Sahoo and S. Knyazev and I. Mandric and F. Stewart and I.I. Mandoiu and B. Pasaniuc and Y.Porozov and A. Zelikovsky, Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data, Journal of Computational Biology 28, pp. 842-855, 2021, publisher url, bibtex

M. Moussa and I.I. Mandoiu, SC1: A Tool for Interactive Web-Based Single Cell RNA-Seq Data Analysis, Journal of Computational Biology 28, pp. 820-841, 2021, publisher url, bibtex

L.L. Boshans and H. Soh and W.M. Wood and M. William and T.M. Nolan and I.I. Mandoiu and Y. Yanagawa and A.V. Tzingounis and A. Nishiyama, Akiko, Direct reprogramming of oligodendrocyte precursor cells into GABAergic inhibitory neurons by a single homeodomain transcription factor Dlx2, Scientific Reports 11, 3552, 2021, publisher url, bibtex

E. Sherafat and J. Force and I.I Mandoiu, Semi-Supervised Learning for Somatic Variant Calling and Peptide Identification in Personalized Cancer Immunotherapy, BMC Bioinformatics 21, 498, 2020, pdf preprint, publisher url, bibtex

F. Alqahtani and I.I. Mandoiu, Statistical Mitogenome Assembly with RepeaTs, Journal of Computational Biology 27, pp. 1407-1421, 2020, publisher url, bibtex

F. Alqahtani and D. Duckett and S. Pirro and I.I. Mandoiu, Complete mitochondrial genome of the water vole, Microtus richardsoni(Cricetidae, Rodentia), Mitochondrial DNA Part B 5:3, pp. 2498-2499, 2020, publisher url, bibtex

D. Lähnemann, J. Köster, E. Szczurek, ..., I.I. Mandoiu, et al., Eleven grand challenges in single-cell data science, Genome Biology 21(31), 2020, publisher url, bibtex

M. Moussa and I.I. Mandoiu, Locality Sensitive Imputation for Single-Cell RNA-Seq Data, Journal of Computational Biology 26, pp. 822-835, 2019, publisher url, bibtex

L.L. Boshans and D.C. Factor and V. Singh and J. Liu and C. Zhao and I.I. Mandoiu and Q.R. Lu and P. Casaccia and P.J. Tesar and A. Nishiyama, The chromatin environment around interneuron genes in oligodendrocyte precursor cells and their potential for interneuron reprogramming, Frontiers in Neuroscience 13:829, 2019, publisher url, bibtex

H. Ebrahimi-Nik and J. Michaux and W.L. Corwin and G.L.J. Keller and T. Shcheglova and H.S. Pak and G. Coukos and B.M. Baker and I.I. Mandoiu and M. Bassani-Sternberg and P.K. Srivastava, Mass spectrometry driven exploration reveals nuances of neoepitope-driven tumor rejection, JCI Insight 4, 2019, publisher url, bibtex

J. Duan and Z. Jiang and F. Alqahtani and I.I. Mandoiu and D. Hong and X. Zheng and S.L. Marjani and J. Chen and X. Tian, Methylome dynamics of bovine gametes and in vivo early embryos, Frontiers in Genetics 10:512, 2019, publisher url, bibtex

A.L. Sedlacek and T.P. Younker and Y. Zhou and L. Borghesi and T. Shcheglova and I.I. Mandoiu and R.J. Binder, CD91 on dendritic cells governs immunosurveillance of nascent, emerging tumors, JCI Insight 4(7):e127239, 2019, publisher url, bibtex

J. Duan and K. Flock and N. Jue and M. Zhang and A. Jones and S. Al Seesi and I.I. Mandoiu and S. Pillai and M. Hoffman and R. O'Neill and S. Zinn and K. Govoni and S. Reed and H. Jiang and Z. Jiang and X. Tian, Dosage Compensation and Gene Expression of the X Chromosome in Sheep, G3: Genes, Genomes, Genetics 9, pp. 305-314, 2019, publisher url, bibtex

J. Duan and M. Zhang and K. Flock and S. Al Seesi and I.I. Mandoiu and A. Jones and E. Johnson and S. Pillai and M. Hoffman and K. McFadden and H. Jiang and S. Reed and K. Govoni and S. Zinn and Z. Jiang and X. Tian, Effects of Maternal Nutrition on the Expression of Genomic Imprinted Genes in Ovine Fetuses, Epigenetics 13, pp. 793-807, 2018, publisher url, bibtex

H. Ebrahimi-Nik and W.L. Corwin and T. Shcheglova and A. Das Mohapatra and I.I. Mandoiu and P.K. Srivastava, CD11c+ MHCIIlo GM-CSF-bone marrow-derived dendritic cells act as antigen donor cells and as antigen presenting cells in neoepitope-elicited tumor immunity against a mouse fibrosarcoma, Cancer Immunology, Immunotherapy 67, pp. 1449–1459, 2018, publisher url, bibtex

M. Moussa and I.I. Mandoiu, Single cell RNA-seq data clustering using TF-IDF based methods, BMC Genomics 19(Suppl 6):569, 2018, publisher url, bibtex

M.S. Muyyarikkandy and F. Alqahtani and I.I. Mandoiu and M.A. Amalaradjou, Draft Genome Sequence of Lactobacillus paracasei DUP 13076, Which Exhibits Potent Antipathogenic Effects against Salmonella enterica Serovars Enteritidis, Typhimurium, and Heidelberg, Genome Announcements 6, pp. e00065-18, 2018, publisher url, bibtex

M.S. Muyyarikkandy and F. Alqahtani and I.I. Mandoiu and M.A. Amalaradjou, Draft Genome Sequence of Lactobacillus rhamnosus NRRL B-442, a Potential Probiotic Strain, Genome Announcements 6, pp. e00046-18, 2018, publisher url, bibtex

I. Mandric and Y.T. Tiagueu and T. Shcheglova and S. Al Seesi and A. Zelikovsky and I.I. Mandoiu, Fast Bootstrapping-Based Estimation of Confidence Intervals of Expression Levels and Differential Expression from RNA-Seq Data, Bioinformatics 33, pp. 3302-3304, 2017, pdf preprint, publisher url, bibtex

Y. Temate-Tiagueu and S. Al Seesi and M. Mathew and I. Mandric and A. Rodriguez and K. Bean and Q. Cheng and O. Glebova and I.I. Mandoiu and N.B. Lopanik and A. Zelikovsky, Inferring metabolic pathway activity levels from RNA-Seq data, BMC Genomics 17(Suppl 5):542, pp. 493-503, 2016, publisher url, bibtex

Conference Articles:

M. Moussa and I.I. Mandoiu, Computational Cell Cycle Analysis of Single Cell RNA-Seq Data, Proc. 10th International Conference on Computational Advances in Bio and Medical Sciences, pp. 71-87, 2021, publisher url, bibtex

M. Moussa and I.I. Mandoiu, SC1: A Tool for Interactive Web-Based Single Cell RNA-Seq Data Analysis, Proc. 16th International Symposium on Bioinformatics Research and Applications, pp. 389–397, 2020, pdf preprint, publisher url, bibtex

F. Rondel and R. Hosseini and B. Sahoo and S. Knyazev and I. Mandric and F. Stewart and I.I. Mandoiu and B. Pasaniuc and A. Zelikovsky, Estimating enzyme participation in metabolic pathways for microbial communities from RNA-seq data, Proc. 16th International Symposium on Bioinformatics Research and Applications, pp. 335-343, 2020, pdf preprint, publisher url, bibtex

F. Alqahtani and I.I. Mandoiu, Mitochondrial Haplogroup Assignment for High-Throughput Sequencing Data from Single Individual and Mixed DNA Samples, Proc. 16th International Symposium on Bioinformatics Research and Applications, pp. 1-12, 2020, pdf preprint, publisher url, bibtex

F. Alqahtani and I.I. Mandoiu, SMART2: Multi-Library Statistical Mitogenome Assembly with Repeats, Proc. 9th International Conference on Computational Advances in Bio and Medical Sciences, pp. 184-198, 2020, pdf preprint, publisher url, ppt, bibtex

M. Moussa and I.I. Mandoiu, Locality Sensitive Imputation for Single-Cell RNA-Seq Data, Proc. 14th International Symposium on Bioinformatics Research and Applications, pp. 347-360, 2018, pdf preprint, publisher url, ppt, bibtex

I. Mandric and S. Knyazev and C. Padilla and F. Stewart and I.I. Mandoiu and A. Zelikovsky, Metabolic analysis of metatranscriptomic data from planktonic communities, Proc. 13th International Symposium on Bioinformatics Research and Applications, pp. 396-402, 2017, publisher url, ppt, bibtex

Technical Reports:

M. Moussa and I.I. Mandoiu, SC1: A Tool for Interactive Web-Based Single Cell RNA-Seq Data Analysis, Cold Spring Harbor Laboratory bioRxiv preprint, , 2021, url, bibtex

M. Moussa and I.I. Mandoiu, Computational cell cycle analysis of single cell RNA-Seq data, Cold Spring Harbor Laboratory bioRxiv preprint, , 2020, url, bibtex

F. Alqahtani and I.I. Mandoiu, SMART: Statistical Mitogenome Assembly with Repeats, Cold Spring Harbor Laboratory bioRxiv preprint, , 2019, url, bibtex

Laehnemann D, et al., 12 Grand challenges in single-cell data science, PeerJ Preprints, , 2019, url, bibtex

M. Moussa and I.I. Mandoiu, Locality Sensitive Imputation for Single-Cell RNA-Seq Data, Cold Spring Harbor Laboratory bioRxiv preprint, , 2018, url, bibtex

Ph.D. Theses:

F. Alqahtani, Algorithms for Mitochondrial Genome Assembly and Haplogroup Assignment from Low-Coverage Whole-Genome Sequencing Data, University of Connecticut, Storrs, CT, January, 2020, url, ppt, bibtex

M. Moussa, Computational Methods for the Analysis of Single-Cell RNA-Seq Data, University of Connecticut, Storrs, CT, April, 2019, url, ppt, bibtex