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Results: 1 to 20 of 46

1.

Topologically associating domains are stable units of replication-timing regulation.

Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B, Gilbert DM.

Nature. 2014 Nov 20;515(7527):402-5. doi: 10.1038/nature13986.

PMID:
25409831
[PubMed - in process]
2.

A comparative encyclopedia of DNA elements in the mouse genome.

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium.

Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.

PMID:
25409824
[PubMed - in process]
3.

Network-based Prediction of Cancer under Genetic Storm.

Ay A, Gong D, Kahveci T.

Cancer Inform. 2014 Oct 15;13(Suppl 3):15-31. doi: 10.4137/CIN.S14025. eCollection 2014.

PMID:
25368507
[PubMed]
Free PMC Article
4.

Large scale analysis of signal reachability.

Todor A, Gabr H, Dobra A, Kahveci T.

Bioinformatics. 2014 Jun 15;30(12):i96-104. doi: 10.1093/bioinformatics/btu262.

PMID:
24932011
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

A scalable method for discovering significant subnetworks.

Hasan MM, Kavurucu Y, Kahveci T.

BMC Syst Biol. 2013;7 Suppl 4:S3. doi: 10.1186/1752-0509-7-S4-S3. Epub 2013 Oct 23.

PMID:
24565174
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Characterizing the topology of probabilistic biological networks.

Todor A, Dobra A, Kahveci T.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Jul-Aug;10(4):970-83. doi: 10.1109/TCBB.2013.108.

PMID:
24334390
[PubMed - indexed for MEDLINE]
7.

Characterizing Topology of Probabilistic Biological Networks.

Todor A, Dobra A, Kahveci T.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Sep 6. [Epub ahead of print]

PMID:
24018700
[PubMed - as supplied by publisher]
8.

Metabolomic analysis reveals extended metabolic consequences of marginal vitamin B-6 deficiency in healthy human subjects.

Gregory JF 3rd, Park Y, Lamers Y, Bandyopadhyay N, Chi YY, Lee K, Kim S, da Silva V, Hove N, Ranka S, Kahveci T, Muller KE, Stevens RD, Newgard CB, Stacpoole PW, Jones DP.

PLoS One. 2013 Jun 11;8(6):e63544. doi: 10.1371/journal.pone.0063544. Print 2013.

PMID:
23776431
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Probabilistic biological network alignment.

Todor A, Dobra A, Kahveci T.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Jan-Feb;10(1):109-21. doi: 10.1109/TCBB.2012.142.

PMID:
23702548
[PubMed - indexed for MEDLINE]
10.

From uncertain protein interaction networks to signaling pathways through intensive color coding.

Gabr H, Dobra A, Kahveci T.

Pac Symp Biocomput. 2013:111-22.

PMID:
23424117
[PubMed - indexed for MEDLINE]
Free Article
11.

Large-scale signaling network reconstruction.

Hashemikhabir S, Ayaz ES, Kavurucu Y, Can T, Kahveci T.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Nov-Dec;9(6):1696-708. doi: 10.1109/TCBB.2012.128.

PMID:
23221085
[PubMed - indexed for MEDLINE]
12.

Stability analysis of phylogenetic trees.

Sheikh SI, Kahveci T, Ranka S, Gordon Burleigh J.

Bioinformatics. 2013 Jan 15;29(2):166-74. doi: 10.1093/bioinformatics/bts657. Epub 2012 Nov 18.

PMID:
23162082
[PubMed - indexed for MEDLINE]
Free Article
13.

A scalable method for identifying frequent subtrees in sets of large phylogenetic trees.

Ramu A, Kahveci T, Burleigh JG.

BMC Bioinformatics. 2012 Oct 3;13:256. doi: 10.1186/1471-2105-13-256.

PMID:
23033843
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

HIDEN: Hierarchical decomposition of regulatory networks.

Gülsoy G, Bandhyopadhyay N, Kahveci T.

BMC Bioinformatics. 2012 Sep 28;13:250. doi: 10.1186/1471-2105-13-250.

PMID:
23016513
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Topac: alignment of gene regulatory networks using topology-aware coloring.

Gülsoy G, Gandhi B, Kahveci T.

J Bioinform Comput Biol. 2012 Feb;10(1):1240001. doi: 10.1142/S021972001240001X.

PMID:
22809302
[PubMed - indexed for MEDLINE]
16.

Metabolic network alignment in large scale by network compression.

Ay F, Dang M, Kahveci T.

BMC Bioinformatics. 2012 Mar 21;13 Suppl 3:S2. doi: 10.1186/1471-2105-13-S3-S2.

PMID:
22536900
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

CMRF: analyzing differential gene regulation in two group perturbation experiments.

Bandyopadhyay N, Somaiya M, Ranka S, Kahveci T.

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

PMID:
22537297
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks.

Marbach D, Roy S, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M.

Genome Res. 2012 Jul;22(7):1334-49. doi: 10.1101/gr.127191.111. Epub 2012 Mar 28.

PMID:
22456606
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

SSLPred: predicting synthetic sickness lethality.

Bandyopadhyay N, Ranka S, Kahveci T.

Pac Symp Biocomput. 2012:7-18.

PMID:
22174258
[PubMed - indexed for MEDLINE]
Free Article
20.

RINQ: Reference-based Indexing for Network Queries.

Gülsoy G, Kahveci T.

Bioinformatics. 2011 Jul 1;27(13):i149-58. doi: 10.1093/bioinformatics/btr203.

PMID:
21685064
[PubMed - indexed for MEDLINE]
Free PMC Article

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