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Results: 1 to 20 of 47

1.

DB2: a probabilistic approach for accurate detection of tandem duplication breakpoints using paired-end reads.

Yava G, Koyutürk M, Gould MP, McMahon S, Laframboise T.

BMC Genomics. 2014 Mar 5;15(1):175. [Epub ahead of print]

PMID:
24597945
[PubMed - as supplied by publisher]
Free Article
2.

Network signatures of survival in glioblastoma multiforme.

Patel VN, Gokulrangan G, Chowdhury SA, Chen Y, Sloan AE, Koyutürk M, Barnholtz-Sloan J, Chance MR.

PLoS Comput Biol. 2013;9(9):e1003237. doi: 10.1371/journal.pcbi.1003237. Epub 2013 Sep 19.

PMID:
24068912
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Gene, pathway and network frameworks to identify epistatic interactions of single nucleotide polymorphisms derived from GWAS data.

Liu Y, Maxwell S, Feng T, Zhu X, Elston RC, Koyutürk M, Chance MR.

BMC Syst Biol. 2012;6 Suppl 3:S15. doi: 10.1186/1752-0509-6-S3-S15. Epub 2012 Dec 17.

PMID:
23281810
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Identifying stage-specific protein subnetworks for colorectal cancer.

Erten S, Chowdhury SA, Guan X, Nibbe RK, Barnholtz-Sloan JS, Chance MR, Koyutürk M.

BMC Proc. 2012 Nov 13;6 Suppl 7:S1. doi: 10.1186/1753-6561-6-S7-S1. Epub 2012 Nov 13.

PMID:
23173715
[PubMed]
Free PMC Article
5.

Network-based approaches for extending the Wnt signalling pathway and identifying context-specific sub-networks.

Saha S, Roman T, Galante A, Koyutürk M, Ewing RM.

Int J Comput Biol Drug Des. 2012;5(3-4):185-205. doi: 10.1504/IJCBDD.2012.049203. Epub 2012 Sep 24.

PMID:
23013649
[PubMed - indexed for MEDLINE]
6.

Accurate estimation of short read mapping quality for next-generation genome sequencing.

Ruffalo M, Koyutürk M, Ray S, LaFramboise T.

Bioinformatics. 2012 Sep 15;28(18):i349-i355. doi: 10.1093/bioinformatics/bts408.

PMID:
22962451
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Estradiol induces JNK-dependent apoptosis in glioblastoma cells.

Altiok N, Ersoz M, Koyuturk M.

Oncol Lett. 2011 Nov;2(6):1281-1285. Epub 2011 Aug 17.

PMID:
22848302
[PubMed]
Free PMC Article
8.

Integrative analysis of common neurodegenerative diseases using gene association, interaction networks and mRNA expression data.

Liu Y, Koyutürk M, Maxwell S, Zhao Z, Chance MR.

AMIA Jt Summits Transl Sci Proc. 2012;2012:62-71. Epub 2012 Mar 19.

PMID:
22779053
[PubMed]
Free PMC Article
9.

Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases.

Liu Y, Koyutürk M, Barnholtz-Sloan JS, Chance MR.

BMC Syst Biol. 2012 Jun 13;6:65. doi: 10.1186/1752-0509-6-65.

PMID:
22694839
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Network biology methods integrating biological data for translational science.

Bebek G, Koyutürk M, Price ND, Chance MR.

Brief Bioinform. 2012 Jul;13(4):446-59. doi: 10.1093/bib/bbr075. Epub 2012 Mar 5. Review.

PMID:
22390873
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks.

Erten S, Bebek G, Koyutürk M.

J Comput Biol. 2011 Nov;18(11):1561-74. doi: 10.1089/cmb.2011.0154. Epub 2011 Oct 28.

PMID:
22035267
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Comparative analysis of algorithms for next-generation sequencing read alignment.

Ruffalo M, LaFramboise T, Koyutürk M.

Bioinformatics. 2011 Oct 15;27(20):2790-6. doi: 10.1093/bioinformatics/btr477. Epub 2011 Aug 19.

PMID:
21856737
[PubMed - indexed for MEDLINE]
Free Article
13.

DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization.

Erten S, Bebek G, Ewing RM, Koyutürk M.

BioData Min. 2011 Jun 24;4:19. doi: 10.1186/1756-0381-4-19.

PMID:
21699738
[PubMed]
Free PMC Article
14.

Subnetwork state functions define dysregulated subnetworks in cancer.

Chowdhury SA, Nibbe RK, Chance MR, Koyutürk M.

J Comput Biol. 2011 Mar;18(3):263-81. doi: 10.1089/cmb.2010.0269.

PMID:
21385033
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Systems biology analyses of gene expression and genome wide association study data in obstructive sleep apnea.

Liu Y, Patel S, Nibbe R, Maxwell S, Chowdhury SA, Koyuturk M, Zhu X, Larkin EK, Buxbaum SG, Punjabi NM, Gharib SA, Redline S, Chance MR.

Pac Symp Biocomput. 2011:14-25.

PMID:
21121029
[PubMed - indexed for MEDLINE]
Free Article
16.

Protein-protein interaction networks and subnetworks in the biology of disease.

Nibbe RK, Chowdhury SA, Koyutürk M, Ewing R, Chance MR.

Wiley Interdiscip Rev Syst Biol Med. 2011 May-Jun;3(3):357-67. doi: 10.1002/wsbm.121. Epub 2010 Sep 23. Review.

PMID:
20865778
[PubMed - indexed for MEDLINE]
17.

Algorithmic and analytical methods in network biology.

Koyutürk M.

Wiley Interdiscip Rev Syst Biol Med. 2010 May-Jun;2(3):277-92. doi: 10.1002/wsbm.61. Review.

PMID:
20836029
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Functional characterization and topological modularity of molecular interaction networks.

Pandey J, Koyutürk M, Grama A.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S35. doi: 10.1186/1471-2105-11-S1-S35.

PMID:
20122208
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

An integrative -omics approach to identify functional sub-networks in human colorectal cancer.

Nibbe RK, Koyutürk M, Chance MR.

PLoS Comput Biol. 2010 Jan 15;6(1):e1000639. doi: 10.1371/journal.pcbi.1000639.

PMID:
20090827
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

COKGEN: a software for the identification of rare copy number variation from SNP microarrays.

Yavaş G, Koyutürk M, Ozsoyoğlu M, Gould MP, Laframboise T.

Pac Symp Biocomput. 2010:371-82.

PMID:
19908389
[PubMed - indexed for MEDLINE]
Free Article

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