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Items: 18

1.

Multiplexed identification, quantification and genotyping of infectious agents using a semiconductor biochip.

Hassibi A, Manickam A, Singh R, Bolouki S, Sinha R, Jirage KB, McDermott MW, Hassibi B, Vikalo H, Mazarei G, Pei L, Bousse L, Miller M, Heshami M, Savage MP, Taylor MT, Gamini N, Wood N, Mantina P, Grogan P, Kuimelis P, Savalia P, Conradson S, Li Y, Meyer RB, Ku E, Ebert J, Pinsky BA, Dolganov G, Van T, Johnson KA, Naraghi-Arani P, Kuimelis RG, Schoolnik G.

Nat Biotechnol. 2018 Sep;36(8):738-745. doi: 10.1038/nbt.4179. Epub 2018 Jul 16.

PMID:
30010676
2.

Viral quasispecies reconstruction via tensor factorization with successive read removal.

Ahn S, Ke Z, Vikalo H.

Bioinformatics. 2018 Jul 1;34(13):i23-i31. doi: 10.1093/bioinformatics/bty291.

3.

Sparse Tensor Decomposition for Haplotype Assembly of Diploids and Polyploids.

Hashemi A, Zhu B, Vikalo H.

BMC Genomics. 2018 Mar 21;19(Suppl 4):191. doi: 10.1186/s12864-018-4551-y.

4.

aBayesQR: A Bayesian Method for Reconstruction of Viral Populations Characterized by Low Diversity.

Ahn S, Vikalo H.

J Comput Biol. 2018 Jul;25(7):637-648. doi: 10.1089/cmb.2017.0249. Epub 2018 Feb 26.

PMID:
29480740
5.

QSdpR: Viral quasispecies reconstruction via correlation clustering.

Barik S, Das S, Vikalo H.

Genomics. 2018 Nov;110(6):375-381. doi: 10.1016/j.ygeno.2017.12.007. Epub 2017 Dec 19.

PMID:
29268961
6.

End-to-End Optimization of High-Throughput DNA Sequencing.

O'Reilly E, Baccelli F, De Veciana G, Vikalo H.

J Comput Biol. 2016 Oct;23(10):789-800. doi: 10.1089/cmb.2015.0185. Epub 2016 Jul 7.

PMID:
27387090
7.

Decoding Genetic Variations: Communications-Inspired Haplotype Assembly.

Puljiz Z, Vikalo H.

IEEE/ACM Trans Comput Biol Bioinform. 2016 May-Jun;13(3):518-30. doi: 10.1109/TCBB.2015.2462367.

PMID:
27295635
8.

Semi-Supervised Affinity Propagation with Soft Instance-Level Constraints.

Arzeno NM, Vikalo H.

IEEE Trans Pattern Anal Mach Intell. 2015 May;37(5):1041-52. doi: 10.1109/TPAMI.2014.2359454.

PMID:
26353327
9.

Joint haplotype assembly and genotype calling via sequential Monte Carlo algorithm.

Ahn S, Vikalo H.

BMC Bioinformatics. 2015 Jul 16;16:223. doi: 10.1186/s12859-015-0651-8.

10.

Designing optimal mortality risk prediction scores that preserve clinical knowledge.

Arzeno NM, Lawson KA, Duzinski SV, Vikalo H.

J Biomed Inform. 2015 Aug;56:145-56. doi: 10.1016/j.jbi.2015.05.021. Epub 2015 Jun 6.

11.

SDhaP: haplotype assembly for diploids and polyploids via semi-definite programming.

Das S, Vikalo H.

BMC Genomics. 2015 Apr 3;16:260. doi: 10.1186/s12864-015-1408-5.

12.

Bayesian active learning for drug combinations.

Park M, Nassar M, Vikalo H.

IEEE Trans Biomed Eng. 2013 Nov;60(11):3248-55. doi: 10.1109/TBME.2013.2272322. Epub 2013 Jul 4.

PMID:
23846437
13.

Base calling for high-throughput short-read sequencing: dynamic programming solutions.

Das S, Vikalo H.

BMC Bioinformatics. 2013 Apr 15;14:129. doi: 10.1186/1471-2105-14-129.

14.

ParticleCall: a particle filter for base calling in next-generation sequencing systems.

Shen X, Vikalo H.

BMC Bioinformatics. 2012 Jul 9;13:160. doi: 10.1186/1471-2105-13-160.

15.

OnlineCall: fast online parameter estimation and base calling for illumina's next-generation sequencing.

Das S, Vikalo H.

Bioinformatics. 2012 Jul 1;28(13):1677-83. doi: 10.1093/bioinformatics/bts256. Epub 2012 May 7.

16.

A dual Kalman filter for parameter-state estimation in real-time DNA microarrays.

Shamaiah M, Vikalo H.

Conf Proc IEEE Eng Med Biol Soc. 2011;2011:7614-7. doi: 10.1109/IEMBS.2011.6091876.

PMID:
22256101
17.

FRET-based real-time DNA microarrays.

Hassibi A, Vikalo H, Riechmann JL, Hassibi B.

Methods Mol Biol. 2012;815:147-59. doi: 10.1007/978-1-61779-424-7_12.

PMID:
22130990
18.

Real-time DNA microarray analysis.

Hassibi A, Vikalo H, Riechmann JL, Hassibi B.

Nucleic Acids Res. 2009 Nov;37(20):e132. doi: 10.1093/nar/gkp675. Epub 2009 Aug 31.

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