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Items: 1 to 50 of 78

1.

DeepKinZero: Zero-Shot Learning for Predicting Kinase-Phosphosite Associations Involving Understudied Kinases.

Deznabi I, Arabaci B, Koyutürk M, Tastan O.

Bioinformatics. 2020 Feb 11. pii: btaa013. doi: 10.1093/bioinformatics/btaa013. [Epub ahead of print]

PMID:
32044914
2.

In-vitro investigation of calcitonin associated effects on the trophoblastic cells.

Ozdemir B, Ozkan S, Guzel E, Koyuturk M.

Acta Histochem. 2020 Feb 3:151510. doi: 10.1016/j.acthis.2020.151510. [Epub ahead of print]

PMID:
32024606
3.

Cross-population analysis for functional characterization of type II diabetes variants.

Elmansy D, Koyutürk M.

BMC Bioinformatics. 2019 Jun 20;20(Suppl 12):320. doi: 10.1186/s12859-019-2835-0.

4.

Interplay of transcriptional signaling by progesterone, cyclic AMP, and inflammation in myometrial cells: implications for the control of human parturition.

Stanfield Z, Amini P, Wang J, Yi L, Tan H, Chance MR, Koyutürk M, Mesiano S.

Mol Hum Reprod. 2019 Jul 1;25(7):408-422. doi: 10.1093/molehr/gaz028.

PMID:
31211832
5.

Corrigendum: Myometrial Transcriptional Signatures of Human Parturition.

Stanfield Z, Lai PF, Lei K, Johnson MR, Blanks AM, Romero R, Chance MR, Mesiano S, Koyutürk M.

Front Genet. 2019 May 28;10:515. doi: 10.3389/fgene.2019.00515. eCollection 2019.

6.

Myometrial Transcriptional Signatures of Human Parturition.

Stanfield Z, Lai PF, Lei K, Johnson MR, Blanks AM, Romero R, Chance MR, Mesiano S, Koyutürk M.

Front Genet. 2019 Apr 1;10:185. doi: 10.3389/fgene.2019.00185. eCollection 2019. Erratum in: Front Genet. 2019 May 28;10:515.

7.

Characterizing human genomic coevolution in locus-gene regulatory interactions.

Savel D, Koyutürk M.

BioData Min. 2019 Mar 15;12:8. doi: 10.1186/s13040-019-0195-y. eCollection 2019.

8.

Comparison of different cryopreservation protocols for human umbilical cord tissue as source of mesenchymal stem cells.

Isildar B, Ozkan S, Oncul M, Baslar Z, Kaleli S, Tasyurekli M, Koyuturk M.

Acta Histochem. 2019 Apr;121(3):361-367. doi: 10.1016/j.acthis.2019.02.008. Epub 2019 Mar 2.

PMID:
30837094
9.

CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis.

Ayati M, Wiredja D, Schlatzer D, Maxwell S, Li M, Koyutürk M, Chance MR.

PLoS Comput Biol. 2019 Feb 27;15(2):e1006678. doi: 10.1371/journal.pcbi.1006678. eCollection 2019 Feb.

10.

ELF3 is an antagonist of oncogenic-signalling-induced expression of EMT-TF ZEB1.

Liu D, Skomorovska Y, Song J, Bowler E, Harris R, Ravasz M, Bai S, Ayati M, Tamai K, Koyuturk M, Yuan X, Wang Z, Wang Y, Ewing RM.

Cancer Biol Ther. 2019;20(1):90-100. doi: 10.1080/15384047.2018.1507256. Epub 2018 Aug 27.

11.

Ultrastructural analysis of human umbilical cord derived MSCs at undifferentiated stage and during osteogenic and adipogenic differentiation.

Ozkan S, Isildar B, Oncul M, Baslar Z, Kaleli S, Koyuturk M.

Ultrastruct Pathol. 2018 May-Jun;42(3):199-210. doi: 10.1080/01913123.2018.1453905. Epub 2018 Apr 6.

PMID:
29624114
12.

Phosphoproteomics Profiling of Nonsmall Cell Lung Cancer Cells Treated with a Novel Phosphatase Activator.

Wiredja DD, Ayati M, Mazhar S, Sangodkar J, Maxwell S, Schlatzer D, Narla G, Koyutürk M, Chance MR.

Proteomics. 2017 Nov;17(22). doi: 10.1002/pmic.201700214. Epub 2017 Oct 25. Erratum in: Proteomics. 2018 Dec;18(24):e1870214.

PMID:
28961369
13.

The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics.

Wiredja DD, Koyutürk M, Chance MR.

Bioinformatics. 2017 Nov 1;33(21):3489-3491. doi: 10.1093/bioinformatics/btx415. Epub 2017 Jun 26.

14.

Prioritizing tests of epistasis through hierarchical representation of genomic redundancies.

Cowman T, Koyutürk M.

Nucleic Acids Res. 2017 Aug 21;45(14):e131. doi: 10.1093/nar/gkx505.

15.

CB-1R and GLP-1R gene expressions and oxidative stress in the liver of diabetic rats treated with sitagliptin.

Coskun ZM, Koyuturk M, Karabulut S, Bolkent S.

Pharmacol Rep. 2017 Aug;69(4):822-829. doi: 10.1016/j.pharep.2017.03.013. Epub 2017 Mar 20.

PMID:
28599244
16.

Linearity of network proximity measures: implications for set-based queries and significance testing.

Maxwell S, Chance MR, Koyutürk M.

Bioinformatics. 2017 May 1;33(9):1354-1361. doi: 10.1093/bioinformatics/btw733.

17.

Mining Electronic Health Records Data: Domestic Violence and Adverse Health Effects.

Karakurt G, Patel V, Whiting K, Koyutürk M.

J Fam Violence. 2017 Jan;32(1):79-87. doi: 10.1007/s10896-016-9872-5. Epub 2016 Sep 23.

18.

Corrigendum: Drug Response Prediction as a Link Prediction Problem.

Stanfield Z, Coşkun M, Koyutürk M.

Sci Rep. 2017 Mar 23;7:44961. doi: 10.1038/srep44961. No abstract available.

19.

Visually Meaningful Histopathological Features for Automatic Grading of Prostate Cancer.

Niazi MKK, Keluo Yao, Zynger DL, Clinton SK, Chen J, Koyuturk M, LaFramboise T, Gurcan M.

IEEE J Biomed Health Inform. 2017 Jul;21(4):1027-1038. doi: 10.1109/JBHI.2016.2565515. Epub 2016 May 10. Erratum in: IEEE J Biomed Health Inform. 2017 Sep;21(5):1473-1474.

PMID:
28113734
20.

Drug Response Prediction as a Link Prediction Problem.

Stanfield Z, Coşkun M, Koyutürk M.

Sci Rep. 2017 Jan 9;7:40321. doi: 10.1038/srep40321. Erratum in: Sci Rep. 2017 Mar 23;7:44961.

21.

Querying of Disparate Association and Interaction Data in Biomedical Applications.

Qiao S, Koyuturk M, Ozsoyoglu MZ.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Jul-Aug;15(4):1052-1065. Epub 2016 Dec 8.

PMID:
27959818
22.

NETWORK MAP OF ADVERSE HEALTH EFFECTS AMONG VICTIMS OF INTIMATE PARTNER VIOLENCE.

Whiting K, Liu LY, Koyutürk M, Karakurt G.

Pac Symp Biocomput. 2017;22:324-335. doi: 10.1142/9789813207813_0031.

23.

PoCos: Population Covering Locus Sets for Risk Assessment in Complex Diseases.

Ayati M, Koyutürk M.

PLoS Comput Biol. 2016 Nov 11;12(11):e1005195. doi: 10.1371/journal.pcbi.1005195. eCollection 2016 Nov.

24.

Disease gene prioritization by integrating tissue-specific molecular networks using a robust multi-network model.

Ni J, Koyuturk M, Tong H, Haines J, Xu R, Zhang X.

BMC Bioinformatics. 2016 Nov 10;17(1):453.

25.

Pluribus-Exploring the Limits of Error Correction Using a Suffix Tree.

Savel D, LaFramboise T, Grama A, Koyuturk M.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Nov-Dec;14(6):1378-1388. doi: 10.1109/TCBB.2016.2586060. Epub 2016 Jun 29.

26.

Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer.

Ruffalo M, Koyutürk M, Sharan R.

PLoS Comput Biol. 2015 Dec 18;11(12):e1004595. doi: 10.1371/journal.pcbi.1004595. eCollection 2015 Dec.

27.

Whole-exome sequencing enhances prognostic classification of myeloid malignancies.

Ruffalo M, Husseinzadeh H, Makishima H, Przychodzen B, Ashkar M, Koyutürk M, Maciejewski JP, LaFramboise T.

J Biomed Inform. 2015 Dec;58:104-113. doi: 10.1016/j.jbi.2015.10.003. Epub 2015 Oct 8.

28.

MOBAS: identification of disease-associated protein subnetworks using modularity-based scoring.

Ayati M, Erten S, Chance MR, Koyutürk M.

EURASIP J Bioinform Syst Biol. 2015 Jun 30;2015:7. doi: 10.1186/s13637-015-0025-6. eCollection 2015 Dec.

29.

The role of ghrelin on apoptosis, cell proliferation and oxidant-antioxidant system in the liver of neonatal diabetic rats.

Koyuturk M, Sacan O, Karabulut S, Turk N, Bolkent S, Yanardag R, Bolkent S.

Cell Biol Int. 2015 Jul;39(7):834-41. doi: 10.1002/cbin.10464. Epub 2015 Apr 28.

PMID:
25789445
30.

Discovery of common sequences absent in the human reference genome using pooled samples from next generation sequencing.

Liu Y, Koyutürk M, Maxwell S, Xiang M, Veigl M, Cooper RS, Tayo BO, Li L, LaFramboise T, Wang Z, Zhu X, Chance MR.

BMC Genomics. 2014 Aug 16;15:685. doi: 10.1186/1471-2164-15-685.

31.

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

Yavaş G, Koyutürk M, Gould MP, McMahon S, LaFramboise T.

BMC Genomics. 2014 Mar 5;15:175. doi: 10.1186/1471-2164-15-175.

32.

Comprehensive evaluation of composite gene features in cancer outcome prediction.

Hou D, Koyutürk M.

Cancer Inform. 2015 Feb 24;13(Suppl 3):93-104. doi: 10.4137/CIN.S14028. eCollection 2014.

33.

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.

34.

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.

35.

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.

36.

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
37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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
44.

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.

45.

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.

46.

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.

47.

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
48.

Algorithmic and analytical methods in network biology.

Koyutürk M.

Wiley Interdiscip Rev Syst Biol Med. 2010 May-Jun;2(3):277-292. doi: 10.1002/wsbm.61. Review.

49.

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.

50.

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.

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