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Items: 1 to 50 of 69

1.

Inference of clonal selection in cancer populations using single-cell sequencing data.

Skums P, Tsyvina V, Zelikovsky A.

Bioinformatics. 2019 Jul 15;35(14):i398-i407. doi: 10.1093/bioinformatics/btz392.

PMID:
31510696
2.

Preface: 14th International Symposium on Bioinformatics Research and Applications (ISBRA 2018).

Cai Z, Skums P, Zelikovsky A.

J Comput Biol. 2019 Aug;26(8):767-768. doi: 10.1089/cmb.2019.29022.zc. No abstract available.

PMID:
31407929
3.

Delineating Surface Epitopes of Lyme Disease Pathogen Targeted by Highly Protective Antibodies of New Zealand White Rabbits.

Rogovskyy AS, Caoili SEC, Ionov Y, Piontkivska H, Skums P, Tsyvina V, Zelikovsky A, Waghela SD.

Infect Immun. 2019 Jul 23;87(8). pii: e00246-19. doi: 10.1128/IAI.00246-19. Print 2019 Aug.

PMID:
31085705
4.

New Zealand White Rabbits Effectively Clear Borrelia burgdorferi B31 despite the Bacterium's Functional vlsE Antigenic Variation System.

Batool M, Hillhouse AE, Ionov Y, Kochan KJ, Mohebbi F, Stoica G, Threadgill DW, Zelikovsky A, Waghela SD, Wiener DJ, Rogovskyy AS.

Infect Immun. 2019 Jun 20;87(7). pii: e00164-19. doi: 10.1128/IAI.00164-19. Print 2019 Jul.

PMID:
30988058
5.

Systematic benchmarking of omics computational tools.

Mangul S, Martin LS, Hill BL, Lam AK, Distler MG, Zelikovsky A, Eskin E, Flint J.

Nat Commun. 2019 Mar 27;10(1):1393. doi: 10.1038/s41467-019-09406-4. Review.

6.

Automated quality control for a molecular surveillance system.

Sims S, Longmire AG, Campo DS, Ramachandran S, Medrzycki M, Ganova-Raeva L, Lin Y, Sue A, Thai H, Zelikovsky A, Khudyakov Y.

BMC Bioinformatics. 2018 Oct 22;19(Suppl 11):358. doi: 10.1186/s12859-018-2329-5.

7.

Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants.

Tsyvina V, Campo DS, Sims S, Zelikovsky A, Khudyakov Y, Skums P.

BMC Bioinformatics. 2018 Oct 22;19(Suppl 11):360. doi: 10.1186/s12859-018-2333-9.

8.

Identification of Surface Epitopes Associated with Protection against Highly Immune-Evasive VlsE-Expressing Lyme Disease Spirochetes.

Batool M, Caoili SEC, Dangott LJ, Gerasimov E, Ionov Y, Piontkivska H, Zelikovsky A, Waghela SD, Rogovskyy AS.

Infect Immun. 2018 Jul 23;86(8). pii: e00182-18. doi: 10.1128/IAI.00182-18. Print 2018 Aug.

9.

Special Issue Preface: 13th International Symposium on BioinformaticsResearch and Applications (ISBRA 2017).

Cai Z, Skums P, Zelikovsky A.

J Comput Biol. 2018 Mar;25(3):251-252. doi: 10.1089/cmb.2018.29012.zc. No abstract available.

PMID:
29641252
10.

Repeat-aware evaluation of scaffolding tools.

Mandric I, Knyazev S, Zelikovsky A.

Bioinformatics. 2018 Aug 1;34(15):2530-2537. doi: 10.1093/bioinformatics/bty131.

11.

QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data.

Skums P, Zelikovsky A, Singh R, Gussler W, Dimitrova Z, Knyazev S, Mandric I, Ramachandran S, Campo D, Jha D, Bunimovich L, Costenbader E, Sexton C, O'Connor S, Xia GL, Khudyakov Y.

Bioinformatics. 2018 Jan 1;34(1):163-170. doi: 10.1093/bioinformatics/btx402.

12.

Inference of genetic relatedness between viral quasispecies from sequencing data.

Glebova O, Knyazev S, Melnyk A, Artyomenko A, Khudyakov Y, Zelikovsky A, Skums P.

BMC Genomics. 2017 Dec 6;18(Suppl 10):918. doi: 10.1186/s12864-017-4274-5.

13.

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.

14.

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
15.

GaussianCpG: a Gaussian model for detection of CpG island in human genome sequences.

Yu N, Guo X, Zelikovsky A, Pan Y.

BMC Genomics. 2017 May 24;18(Suppl 4):392. doi: 10.1186/s12864-017-3731-5.

16.

HapIso: An Accurate Method for the Haplotype- Specific Isoforms Reconstruction From Long Single-Molecule Reads.

Mangul S, Yang TH, Hormozdiari F, Dainis AM, Tseng E, Ashley EA, Zelikovsky A, Eskin E.

IEEE Trans Nanobioscience. 2017 Mar;16(2):108-115. doi: 10.1109/TNB.2017.2675981. Epub 2017 Mar 17.

PMID:
28328508
17.

Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants.

Artyomenko A, Wu NC, Mangul S, Eskin E, Sun R, Zelikovsky A.

J Comput Biol. 2017 Jun;24(6):558-570. doi: 10.1089/cmb.2016.0146. Epub 2016 Nov 30.

18.

Antibody Response to Lyme Disease Spirochetes in the Context of VlsE-Mediated Immune Evasion.

Rogovskyy AS, Gillis DC, Ionov Y, Gerasimov E, Zelikovsky A.

Infect Immun. 2016 Dec 29;85(1). pii: e00890-16. doi: 10.1128/IAI.00890-16. Print 2017 Jan.

19.

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.

20.

Searching High-Order SNP Combinations for Complex Diseases Based on Energy Distribution Difference.

Ding X, Wang J, Zelikovsky A, Guo X, Xie M, Pan Y.

IEEE/ACM Trans Comput Biol Bioinform. 2015 May-Jun;12(3):695-704. doi: 10.1109/TCBB.2014.2363459.

PMID:
26357280
21.

ScaffMatch: scaffolding algorithm based on maximum weight matching.

Mandric I, Zelikovsky A.

Bioinformatics. 2015 Aug 15;31(16):2632-8. doi: 10.1093/bioinformatics/btv211. Epub 2015 Apr 17.

PMID:
25890305
22.

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.

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.

Transcriptome assembly and quantification from Ion Torrent RNA-Seq data.

Mangul S, Caciula A, Al Seesi S, Brinza D, Mӑndoiu I, Zelikovsky A.

BMC Genomics. 2014;15 Suppl 5:S7. doi: 10.1186/1471-2164-15-S5-S7. Epub 2014 Jul 14.

26.

Accurate viral population assembly from ultra-deep sequencing data.

Mangul S, Wu NC, Mancuso N, Zelikovsky A, Sun R, Eskin E.

Bioinformatics. 2014 Jun 15;30(12):i329-37. doi: 10.1093/bioinformatics/btu295.

27.

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
28.

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.

29.

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
30.

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
31.

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

Chen J, Zelikovsky A.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jul-Aug;9(4):1002-3. No abstract available.

PMID:
22950129
32.

Efficient error correction for next-generation sequencing of viral amplicons.

Skums P, Dimitrova Z, Campo DS, Vaughan G, Rossi L, Forbi JC, Yokosawa J, Zelikovsky A, Khudyakov Y.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S6. doi: 10.1186/1471-2105-13-S10-S6.

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.

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.

35.

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

Borodovsky M, Przytycka TM, Rajasekaran S, Zelikovsky A.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul-Aug;8(4):865-6. No abstract available.

PMID:
21812137
36.

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.

37.

MetNetAligner: a web service tool for metabolic network alignments.

Cheng Q, Harrison R, Zelikovsky A.

Bioinformatics. 2009 Aug 1;25(15):1989-90. doi: 10.1093/bioinformatics/btp287. Epub 2009 May 4.

PMID:
19414533
38.

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
39.

Association testing by haplotype-sharing methods applicable to whole-genome analysis.

Nolte IM, de Vries AR, Spijker GT, Jansen RC, Brinza D, Zelikovsky A, Te Meerman GJ.

BMC Proc. 2007;1 Suppl 1:S129. Epub 2007 Dec 18.

40.

2SNP: scalable phasing method for trios and unrelated individuals.

Brinza D, Zelikovsky A.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Apr-Jun;5(2):313-8. doi: 10.1109/TCBB.2007.1068.

PMID:
18451440
41.

Design and validation of methods searching for risk factors in genotype case-control studies.

Brinza D, Zelikovsky A.

J Comput Biol. 2008 Jan-Feb;15(1):81-90. doi: 10.1089/cmb.2007.0081.

PMID:
18199025
42.

Linear reduction method for predictive and informative tag SNP selection.

He J, Westbrooks K, Zelikovsky A.

Int J Bioinform Res Appl. 2005;1(3):249-60.

PMID:
18048134
43.

Family trio phasing and missing data recovery.

Brinza D, He J, Mao W, Zelikovsky A.

Int J Bioinform Res Appl. 2005;1(2):221-9.

PMID:
18048132
44.

Combinatorial search methods for multi-SNP disease association.

Brinza D, He J, Zelikovsky A.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:5802-5.

PMID:
17946721
45.

Multiple linear regression for index SNP selection on unphased genotypes.

He J, Zelikovsky A.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:5759-62.

PMID:
17946329
46.

A novel method for signal transduction network inference from indirect experimental evidence.

Albert R, DasGupta B, Dondi R, Kachalo S, Sontag E, Zelikovsky A, Westbrooks K.

J Comput Biol. 2007 Sep;14(7):927-49.

PMID:
17803371
47.

Informative SNP selection methods based on SNP prediction.

He J, Zelikovsky A.

IEEE Trans Nanobioscience. 2007 Mar;6(1):60-7.

PMID:
17393851
48.

A combinatorial method for predicting genetic susceptibility to complex diseases.

Mao W, He J, Brinza D, Zelikovsky A.

Conf Proc IEEE Eng Med Biol Soc. 2005;1:224-7.

PMID:
17282153
49.

Consolidating software tools for DNA microarray design and manufacturing.

Atlas M, Hundewale N, Perelygina L, Zelikovsky A.

Conf Proc IEEE Eng Med Biol Soc. 2004;1:172-5.

PMID:
17271633
50.

Linear reduction methods for tag SNP selection.

He J, Zelikovsky A.

Conf Proc IEEE Eng Med Biol Soc. 2004;4:2840-3.

PMID:
17270869

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