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Items: 1 to 50 of 53

1.

Mass spectrometry driven exploration reveals nuances of neoepitope-driven tumor rejection.

Ebrahimi-Nik H, Michaux J, Corwin WL, Keller GL, Shcheglova T, Pak H, Coukos G, Baker BM, Mandoiu II, Bassani-Sternberg M, Srivastava PK.

JCI Insight. 2019 Jun 20;5. pii: 129152. doi: 10.1172/jci.insight.129152.

2.

Methylome Dynamics of Bovine Gametes and in vivo Early Embryos.

Duan JE, Jiang ZC, Alqahtani F, Mandoiu I, Dong H, Zheng X, Marjani SL, Chen J, Tian XC.

Front Genet. 2019 May 28;10:512. doi: 10.3389/fgene.2019.00512. eCollection 2019.

3.

CD91 on dendritic cells governs immunosurveillance of nascent, emerging tumors.

Sedlacek AL, Younker TP, Zhou YJ, Borghesi L, Shcheglova T, Mandoiu II, Binder RJ.

JCI Insight. 2019 Apr 4;4(7). pii: 127239. doi: 10.1172/jci.insight.127239. eCollection 2019 Apr 4.

4.

Locality Sensitive Imputation for Single Cell RNA-Seq Data.

Moussa M, Măndoiu II.

J Comput Biol. 2019 Aug;26(8):822-835. doi: 10.1089/cmb.2018.0236. Epub 2019 Feb 19.

PMID:
30785309
5.

Dosage Compensation and Gene Expression of the X Chromosome in Sheep.

Duan JE, Flock K, Jue N, Zhang M, Jones A, Seesi SA, Mandoiu I, Pillai S, Hoffman M, O'Neill R, Zinn S, Govoni K, Reed S, Jiang H, Jiang ZC, Tian XC.

G3 (Bethesda). 2019 Jan 9;9(1):305-314. doi: 10.1534/g3.118.200815.

6.

CircMarker: a fast and accurate algorithm for circular RNA detection.

Li X, Chu C, Pei J, Măndoiu I, Wu Y.

BMC Genomics. 2018 Aug 13;19(Suppl 6):572. doi: 10.1186/s12864-018-4926-0.

7.

Single cell RNA-seq data clustering using TF-IDF based methods.

Moussa M, Măndoiu II.

BMC Genomics. 2018 Aug 13;19(Suppl 6):569. doi: 10.1186/s12864-018-4922-4.

8.

Effects of maternal nutrition on the expression of genomic imprinted genes in ovine fetuses.

Duan JE, Zhang M, Flock K, Seesi SA, Mandoiu I, Jones A, Johnson E, Pillai S, Hoffman M, McFadden K, Jiang H, Reed S, Govoni K, Zinn S, Jiang Z, Tian XC.

Epigenetics. 2018;13(8):793-807. doi: 10.1080/15592294.2018.1503489. Epub 2018 Sep 21.

9.

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.

Ebrahimi-Nik H, Corwin WL, Shcheglova T, Das Mohapatra A, Mandoiu II, Srivastava PK.

Cancer Immunol Immunother. 2018 Sep;67(9):1449-1459. doi: 10.1007/s00262-018-2202-4. Epub 2018 Jul 20.

10.

Draft Genome Sequence of Lactobacillus paracasei DUP 13076, Which Exhibits Potent Antipathogenic Effects against Salmonella enterica Serovars Enteritidis, Typhimurium, and Heidelberg.

Muyyarikkandy MS, Alqahtani FH, Mandoiu I, Amalaradjou MA.

Genome Announc. 2018 Feb 15;6(7). pii: e00065-18. doi: 10.1128/genomeA.00065-18.

11.

Draft Genome Sequence of Lactobacillus rhamnosus NRRL B-442, a Potential Probiotic Strain.

Muyyarikkandy MS, Alqahtani FH, Mandoiu I, Amalaradjou MA.

Genome Announc. 2018 Feb 15;6(7). pii: e00046-18. doi: 10.1128/genomeA.00046-18.

12.

Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire.

Gerasimov E, Zelikovsky A, Măndoiu I, Ionov Y.

BMC Bioinformatics. 2017 Jun 7;18(Suppl 8):244. doi: 10.1186/s12859-017-1661-5.

13.

Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data.

Mandric I, Temate-Tiagueu Y, Shcheglova T, Al Seesi S, Zelikovsky A, Mandoiu II.

Bioinformatics. 2017 Oct 15;33(20):3302-3304. doi: 10.1093/bioinformatics/btx365.

PMID:
28605502
14.

Tumor Control Index as a new tool to assess tumor growth in experimental animals.

Corwin WL, Ebrahimi-Nik H, Floyd SM, Tavousi P, Mandoiu II, Srivastava PK.

J Immunol Methods. 2017 Jun;445:71-76. doi: 10.1016/j.jim.2017.03.013. Epub 2017 Mar 20.

15.

Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development.

Karunakaran DK, Al Seesi S, Banday AR, Baumgartner M, Olthof A, Lemoine C, Măndoiu II, Kanadia RN.

BMC Genomics. 2016 Aug 31;17 Suppl 5:495. doi: 10.1186/s12864-016-2822-z.

16.

Inferring metabolic pathway activity levels from RNA-Seq data.

Temate-Tiagueu Y, Seesi SA, Mathew M, Mandric I, Rodriguez A, Bean K, Cheng Q, Glebova O, Măndoiu I, Lopanik NB, Zelikovsky A.

BMC Genomics. 2016 Aug 31;17 Suppl 5:542. doi: 10.1186/s12864-016-2823-y.

17.

This special issue includes a selection of papers presented at the 2nd IEEE International Conference. Introduction.

Mandoiu I, Pop M, Rajasekaran S, Spouge JL.

Int J Bioinform Res Appl. 2014;10(4-5):341-4. No abstract available.

PMID:
25715438
18.

Metabolic pathway predictions for metabolomics: a molecular structure matching approach.

Hamdalla MA, Rajasekaran S, Grant DF, Măndoiu II.

J Chem Inf Model. 2015 Mar 23;55(3):709-18. doi: 10.1021/ci500517v. Epub 2015 Feb 24.

PMID:
25668446
19.

Minor splicing snRNAs are enriched in the developing mouse CNS and are crucial for survival of differentiating retinal neurons.

Baumgartner M, Lemoine C, Al Seesi S, Karunakaran DK, Sturrock N, Banday AR, Kilcollins AM, Mandoiu I, Kanadia RN.

Dev Neurobiol. 2015 Sep;75(9):895-907. doi: 10.1002/dneu.22257. Epub 2014 Dec 19.

20.

Replication-dependent histone genes are actively transcribed in differentiating and aging retinal neurons.

Banday AR, Baumgartner M, Al Seesi S, Karunakaran DK, Venkatesh A, Congdon S, Lemoine C, Kilcollins AM, Mandoiu I, Punzo C, Kanadia RN.

Cell Cycle. 2014;13(16):2526-41. doi: 10.4161/15384101.2015.941757.

21.

Bootstrap-based differential gene expression analysis for RNA-Seq data with and without replicates.

Al Seesi S, Tiagueu YT, Zelikovsky A, Măndoiu II.

BMC Genomics. 2014;15 Suppl 8:S2. doi: 10.1186/1471-2164-15-S8-S2. Epub 2014 Nov 13.

22.

Feature selection and classifier performance on diverse bio- logical datasets.

Hemphill E, Lindsay J, Lee C, Măndoiu II, Nelson CE.

BMC Bioinformatics. 2014;15 Suppl 13:S4. doi: 10.1186/1471-2105-15-S13-S4. Epub 2014 Nov 13.

23.

Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling.

Skums P, Artyomenko A, Glebova O, Ramachandran S, Mandoiu I, Campo DS, Dimitrova Z, Zelikovsky A, Khudyakov Y.

Bioinformatics. 2015 Mar 1;31(5):682-90. doi: 10.1093/bioinformatics/btu726. Epub 2014 Oct 29.

PMID:
25359889
24.

ILP-based maximum likelihood genome scaffolding.

Lindsay J, Salooti H, Măndoiu I, Zelikovsky A.

BMC Bioinformatics. 2014;15 Suppl 9:S9. doi: 10.1186/1471-2105-15-S9-S9. Epub 2014 Sep 10.

25.

Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity.

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.

J Exp Med. 2014 Oct 20;211(11):2231-48. doi: 10.1084/jem.20141308. Epub 2014 Sep 22.

26.

Guest editors' introduction to the special section on bioinformatics research and applications.

Mandoiu II, Wang J, Zelikovsky A.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Nov-Dec;10(6):1345-6. No abstract available.

PMID:
24567956
27.

Neuraminidase subtyping of avian influenza viruses with PrimerHunter-designed primers and quadruplicate primer pools.

Huang Y, Khan MI, Măndoiu I.

PLoS One. 2013 Nov 29;8(11):e81842. doi: 10.1371/journal.pone.0081842. eCollection 2013. Erratum in: PLoS One. 2013;8(12). doi:10.1371/annotation/0c03da4e-c4f6-4992-8c5b-bdabdd3bb08f. Khan, Mazhar [corrected to Khan, Mazhar I]; Măndoiu, Ion I [corrected to Măndŏiu, Ion].

28.

In silico enzymatic synthesis of a 400,000 compound biochemical database for nontargeted metabolomics.

Menikarachchi LC, Hill DW, Hamdalla MA, Mandoiu II, Grant DF.

J Chem Inf Model. 2013 Sep 23;53(9):2483-92. doi: 10.1021/ci400368v. Epub 2013 Sep 12.

29.

Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows.

Skums P, Mancuso N, Artyomenko A, Tork B, Mandoiu I, Khudyakov Y, Zelikovsky A.

BMC Bioinformatics. 2013;14 Suppl 9:S2. doi: 10.1186/1471-2105-14-S9-S2. Epub 2013 Jun 28.

30.

BioSM: metabolomics tool for identifying endogenous mammalian biochemical structures in chemical structure space.

Hamdalla MA, Mandoiu II, Hill DW, Rajasekaran S, Grant DF.

J Chem Inf Model. 2013 Mar 25;53(3):601-12. doi: 10.1021/ci300512q. Epub 2013 Feb 27.

31.

Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations.

Mangul S, Caciula A, Glebova O, Mandoiu I, Zelikovsky A.

In Silico Biol. 2011-2012;11(5-6):251-61. doi: 10.3233/ISB-2012-0459.

PMID:
23202426
32.

Reconstructing viral quasispecies from NGS amplicon reads.

Mancuso N, Tork B, Skums P, Ganova-Raeva L, Măndoiu I, Zelikovsky A.

In Silico Biol. 2011-2012;11(5-6):237-49. doi: 10.3233/ISB-2012-0458.

PMID:
23202425
33.

Guest editors' introduction.

Chen J, Măndoiu I, Sunderraman R, Wang J, Zelikovsky A.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S1. doi: 10.1186/1471-2105-13-S10-S1. No abstract available.

34.

Area under the curve as a tool to measure kinetics of tumor growth in experimental animals.

Duan F, Simeone S, Wu R, Grady J, Mandoiu I, Srivastava PK.

J Immunol Methods. 2012 Aug 31;382(1-2):224-8. doi: 10.1016/j.jim.2012.06.005. Epub 2012 Jun 12.

PMID:
22698786
35.

Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data.

Duitama J, Srivastava PK, Măndoiu II.

BMC Genomics. 2012 Apr 12;13 Suppl 2:S6. doi: 10.1186/1471-2164-13-S2-S6.

36.

The use of graph matching algorithms to identify biochemical substructures in synthetic chemical compounds: Application to metabolomics.

Hamdalla M, Grant D, Mandoiu I, Hill D, Rajasekaran S, Ammar R.

IEEE Int Conf Comput Adv Bio Med Sci. 2012 Feb;2012. doi: 10.1109/ICCABS.2012.6182637.

37.

Inferring viral quasispecies spectra from 454 pyrosequencing reads.

Astrovskaya I, Tork B, Mangul S, Westbrooks K, Măndoiu I, Balfe P, Zelikovsky A.

BMC Bioinformatics. 2011;12 Suppl 6:S1. doi: 10.1186/1471-2105-12-S6-S1. Epub 2011 Jul 28.

38.

Inferring ethnicity from mitochondrial DNA sequence.

Lee C, Măndoiu II, Nelson CE.

BMC Proc. 2011 May 28;5 Suppl 2:S11. doi: 10.1186/1753-6561-5-S2-S11.

39.

Estimation of alternative splicing isoform frequencies from RNA-Seq data.

Nicolae M, Mangul S, Măndoiu II, Zelikovsky A.

Algorithms Mol Biol. 2011 Apr 19;6(1):9. doi: 10.1186/1748-7188-6-9.

40.

Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads.

Duitama J, Kennedy J, Dinakar S, Hernández Y, Wu Y, Măndoiu II.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S53. doi: 10.1186/1471-2105-12-S1-S53.

41.

Guest Editors' introduction to the special section on bioinformatics research and applications.

Mandoiu I, Narasimhan G, Pan Y, Zhang Y.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec;7(4):577-8. No abstract available.

PMID:
21058452
42.

Identification of mammalian orthologs using local synteny.

Jun J, Mandoiu II, Nelson CE.

BMC Genomics. 2009 Dec 23;10:630. doi: 10.1186/1471-2164-10-630.

43.

The birth of new genes by RNA- and DNA-mediated duplication during mammalian evolution.

Jun J, Ryvkin P, Hemphill E, Mandoiu I, Nelson C.

J Comput Biol. 2009 Oct;16(10):1429-44. doi: 10.1089/cmb.2009.0073.

PMID:
19803737
44.

PrimerHunter: a primer design tool for PCR-based virus subtype identification.

Duitama J, Kumar DM, Hemphill E, Khan M, Mandoiu II, Nelson CE.

Nucleic Acids Res. 2009 May;37(8):2483-92. doi: 10.1093/nar/gkp073. Epub 2009 Mar 5.

45.

Genotype error detection using Hidden Markov Models of haplotype diversity.

Kennedy J, Măndoiu I, Paşaniuc B.

J Comput Biol. 2008 Nov;15(9):1155-71. doi: 10.1089/cmb.2007.0133.

PMID:
18973433
46.

Guest editors' introduction to the special section on bioinformatics research and applications.

Mandoiu II, Pan Y, Zelikovsky A.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Jul-Sep;5(3):321-2. No abstract available.

PMID:
18683323
47.

Highly scalable genotype phasing by entropy minimization.

Gusev A, Măndoiu II, Paşaniuc B.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Apr-Jun;5(2):252-61. doi: 10.1109/TCBB.2007.70223.

PMID:
18451434
48.

Highly scalable algorithms for robust string barcoding.

Dasgupta B, Konwar KM, Mandoiu II, Shvartsman AA.

Int J Bioinform Res Appl. 2005;1(2):145-61.

PMID:
18048126
49.

Highly scalable genotype phasing by entropy minimization.

Pasaniuc B, Mandoiu I.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:3482-6.

PMID:
17946566
50.

High-throughput SNP genotyping by SBE/SBH.

Măndoiu II, Prăjescu C.

IEEE Trans Nanobioscience. 2007 Mar;6(1):28-35.

PMID:
17393847

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