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Items: 1 to 50 of 69

1.

ANCA: Alignment-based Network Construction Algorithm.

Chow K, Sarkar A, Elhesha R, Cinaglia P, Ay A, Kahveci T.

IEEE/ACM Trans Comput Biol Bioinform. 2019 Jun 18. doi: 10.1109/TCBB.2019.2923620. [Epub ahead of print]

PMID:
31226082
2.

Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC).

Yoon BJ, Qian X, Kahveci T, Pal R.

BMC Bioinformatics. 2019 Jun 20;20(Suppl 12):316. doi: 10.1186/s12859-019-2830-5. No abstract available.

3.

Characterizing building blocks of resource constrained biological networks.

Ren Y, Ay A, Dobra A, Kahveci T.

BMC Bioinformatics. 2019 Jun 20;20(Suppl 12):318. doi: 10.1186/s12859-019-2838-x.

4.

Identification of co-evolving temporal networks.

Elhesha R, Sarkar A, Boucher C, Kahveci T.

BMC Genomics. 2019 Jun 13;20(Suppl 6):434. doi: 10.1186/s12864-019-5719-9.

5.

An efficient algorithm for identifying mutated subnetworks associated with survival in cancer.

Sarkar A, Atay Y, Erickson AL, Arisi I, Saltini C, Kahveci T.

IEEE/ACM Trans Comput Biol Bioinform. 2019 Apr 15. doi: 10.1109/TCBB.2019.2911069. [Epub ahead of print]

PMID:
30990435
6.

Aligning Optical Maps to De Bruijn Graphs.

Mukherjee K, Alipanahi B, Kahveci T, Salmela L, Boucher C.

Bioinformatics. 2019 Jan 30. doi: 10.1093/bioinformatics/btz069. [Epub ahead of print]

PMID:
30698651
7.

Shortest path counting in probabilistic biological networks.

Ren Y, Ay A, Kahveci T.

BMC Bioinformatics. 2018 Dec 4;19(1):465. doi: 10.1186/s12859-018-2480-z.

8.

Stability Analysis of Biological Networks' Diffusion State.

Altuntas V, Gok M, Kahveci T.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Nov 19. doi: 10.1109/TCBB.2018.2881887. [Epub ahead of print]

PMID:
30452376
9.

Identification of jointly correlated gene sets.

Ren Y, Ay A, Gerke TA, Kahveci T.

J Bioinform Comput Biol. 2018 Oct;16(5):1840019. doi: 10.1142/S021972001840019X.

PMID:
30419787
10.

Construction of Signaling Pathways with RNAi Data and Multiple Reference Networks.

Alim MA, Ay A, Hasan MM, Thai MT, Kahveci T.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Jul-Aug;15(4):1079-1091. doi: 10.1109/TCBB.2017.2710129.

PMID:
30102599
11.

A new algorithm for counting independent motifs in probabilistic networks.

Sarkar A, Ren Y, Elhesha R, Kahveci T.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Apr 2. doi: 10.1109/TCBB.2018.2821666. [Epub ahead of print]

PMID:
29994098
12.

ProMotE: an efficient algorithm for counting independent motifs in uncertain network topologies.

Ren Y, Sarkar A, Kahveci T.

BMC Bioinformatics. 2018 Jun 26;19(1):242. doi: 10.1186/s12859-018-2236-9.

13.

Counting motifs in dynamic networks.

Mukherjee K, Hasan MM, Boucher C, Kahveci T.

BMC Syst Biol. 2018 Apr 11;12(Suppl 1):6. doi: 10.1186/s12918-018-0533-6.

14.

Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC).

Yoon BJ, Qian X, Kahveci T, Pal R.

BMC Bioinformatics. 2018 Mar 21;19(Suppl 3):69. doi: 10.1186/s12859-018-2058-9. No abstract available.

15.

Selected research articles from the 2016 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC).

Yoon BJ, Qian X, Kahveci T.

BMC Bioinformatics. 2017 Mar 22;18(Suppl 4):159. doi: 10.1186/s12859-017-1521-3. No abstract available.

16.

Identification of large disjoint motifs in biological networks.

Elhesha R, Kahveci T.

BMC Bioinformatics. 2016 Oct 6;17(1):408.

17.

Integrating Domain Specific Knowledge and Network Analysis to Predict Drug Sensitivity of Cancer Cell Lines.

Kim S, Sundaresan V, Zhou L, Kahveci T.

PLoS One. 2016 Sep 8;11(9):e0162173. doi: 10.1371/journal.pone.0162173. eCollection 2016.

18.

Identifying the topology of signaling networks from partial RNAi data.

Ren Y, Wang Q, Hasan MM, Ay A, Kahveci T.

BMC Syst Biol. 2016 Aug 1;10 Suppl 2:53. doi: 10.1186/s12918-016-0301-4.

19.

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.

20.

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.

21.

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.

22.

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
23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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
31.

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.

32.

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
33.
34.

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
35.

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
36.

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.

37.

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.

38.

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
39.

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.

40.

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.

41.

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.

42.

SSLPred: predicting synthetic sickness lethality.

Bandyopadhyay N, Ranka S, Kahveci T.

Pac Symp Biocomput. 2012:7-18.

43.

RINQ: Reference-based Indexing for Network Queries.

Gülsoy G, Kahveci T.

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

44.

TRIAL: a tool for finding distant structural similarities.

Venkateswaran JG, Song B, Kahveci T, Jermaine C.

IEEE/ACM Trans Comput Biol Bioinform. 2011 May-Jun;8(3):819-31. doi: 10.1109/TCBB.2009.28.

PMID:
21393655
45.

SubMAP: aligning metabolic pathways with subnetwork mappings.

Ay F, Kellis M, Kahveci T.

J Comput Biol. 2011 Mar;18(3):219-35. doi: 10.1089/cmb.2010.0280.

46.

A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification.

El Yacoubi B, Hatin I, Deutsch C, Kahveci T, Rousset JP, Iwata-Reuyl D, Murzin AG, de Crécy-Lagard V.

EMBO J. 2011 Mar 2;30(5):882-93. doi: 10.1038/emboj.2010.363. Epub 2011 Feb 1.

47.

Manipulating the steady state of metabolic pathways.

Song B, Büyüktahtakin IE, Ranka S, Kahveci T.

IEEE/ACM Trans Comput Biol Bioinform. 2011 May-Jun;8(3):732-47. doi: 10.1109/TCBB.2010.41.

PMID:
20479507
48.

GBA manager: an online tool for querying low-complexity regions in proteins.

Bandyopadhyay N, Kahveci T.

J Comput Biol. 2010 Jan;17(1):73-7. doi: 10.1089/cmb.2009.0006.

PMID:
20078398
49.

Scalable steady state analysis of Boolean biological regulatory networks.

Ay F, Xu F, Kahveci T.

PLoS One. 2009 Dec 1;4(12):e7992. doi: 10.1371/journal.pone.0007992.

50.

Inferring progression models for CGH data.

Liu J, Bandyopadhyay N, Ranka S, Baudis M, Kahveci T.

Bioinformatics. 2009 Sep 1;25(17):2208-15. doi: 10.1093/bioinformatics/btp365. Epub 2009 Jun 15.

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