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Items: 1 to 20 of 52

1.

Signal reachability facilitates characterization of probabilistic signaling networks.

Gabr H, Kahveci T.

BMC Bioinformatics. 2015;16 Suppl 17:S6. doi: 10.1186/1471-2105-16-S17-S6. Epub 2015 Dec 7.

2.

Computing interaction probabilities in signaling networks.

Gabr H, Rivera-Mulia JC, Gilbert DM, Kahveci T.

EURASIP J Bioinform Syst Biol. 2015 Nov 11;2015(1):10. eCollection 2015 Dec.

3.

Indexing a protein-protein interaction network expedites network alignment.

Hasan MM, Kahveci T.

BMC Bioinformatics. 2015 Oct 9;16:326. doi: 10.1186/s12859-015-0756-0.

4.

Reachability Analysis in Probabilistic Biological Networks.

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

IEEE/ACM Trans Comput Biol Bioinform. 2015 Jan-Feb;12(1):53-66. doi: 10.1109/TCBB.2014.2343967.

PMID:
26357078
5.

Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells.

Rivera-Mulia JC, Buckley Q, Sasaki T, Zimmerman J, Didier RA, Nazor K, Loring JF, Lian Z, Weissman S, Robins AJ, Schulz TC, Menendez L, Kulik MJ, Dalton S, Gabr H, Kahveci T, Gilbert DM.

Genome Res. 2015 Aug;25(8):1091-103. doi: 10.1101/gr.187989.114. Epub 2015 Jun 8.

6.

Hierarchical decomposition of dynamically evolving regulatory networks.

Ay A, Gong D, Kahveci T.

BMC Bioinformatics. 2015 May 15;16:161. doi: 10.1186/s12859-015-0529-9.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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
13.

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
14.

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.

15.

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
16.
17.

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
18.

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.

19.

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.

20.

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.

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