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Items: 1 to 50 of 51

1.

Integrative detection and analysis of structural variation in cancer genomes.

Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F.

Nat Genet. 2018 Sep 10. doi: 10.1038/s41588-018-0195-8. [Epub ahead of print]

PMID:
30202056
2.

The Evf2 Ultraconserved Enhancer lncRNA Functionally and Spatially Organizes Megabase Distant Genes in the Developing Forebrain.

Cajigas I, Chakraborty A, Swyter KR, Luo H, Bastidas M, Nigro M, Morris ER, Chen S, VanGompel MJW, Leib D, Kohtz SJ, Martina M, Koh S, Ay F, Kohtz JD.

Mol Cell. 2018 Sep 20;71(6):956-972.e9. doi: 10.1016/j.molcel.2018.07.024. Epub 2018 Aug 23.

PMID:
30146317
3.

The role of 3D genome organization in disease: From compartments to single nucleotides.

Chakraborty A, Ay F.

Semin Cell Dev Biol. 2018 Jul 16. pii: S1084-9521(17)30593-1. doi: 10.1016/j.semcdb.2018.07.005. [Epub ahead of print] Review.

PMID:
30017907
4.

Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages.

Bunnik EM, Cook KB, Varoquaux N, Batugedara G, Prudhomme J, Cort A, Shi L, Andolina C, Ross LS, Brady D, Fidock DA, Nosten F, Tewari R, Sinnis P, Ay F, Vert JP, Noble WS, Le Roch KG.

Nat Commun. 2018 May 15;9(1):1910. doi: 10.1038/s41467-018-04295-5.

6.

A distinct correlation between the vibrational and thermal transport properties of group VA monolayer crystals.

Kocabaş T, Çakır D, Gülseren O, Ay F, Kosku Perkgöz N, Sevik C.

Nanoscale. 2018 Apr 26;10(16):7803-7812. doi: 10.1039/c7nr09349g.

PMID:
29664085
7.

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution.

Ma W, Ay F, Lee C, Gulsoy G, Deng X, Cook S, Hesson J, Cavanaugh C, Ware CB, Krumm A, Shendure J, Blau CA, Disteche CM, Noble WS, Duan Z.

Methods. 2018 Jun 1;142:59-73. doi: 10.1016/j.ymeth.2018.01.014. Epub 2018 Jan 31.

PMID:
29382556
8.

Identification of copy number variations and translocations in cancer cells from Hi-C data.

Chakraborty A, Ay F.

Bioinformatics. 2017 Oct 18. doi: 10.1093/bioinformatics/btx664. [Epub ahead of print]

PMID:
29048467
9.

PacBio assembly of a Plasmodium knowlesi genome sequence with Hi-C correction and manual annotation of the SICAvar gene family.

Lapp SA, Geraldo JA, Chien JT, Ay F, Pakala SB, Batugedara G, Humphrey J; MaHPIC consortium, DeBARRY JD, Le Roch KG, Galinski MR, Kissinger JC.

Parasitology. 2018 Jan;145(1):71-84. doi: 10.1017/S0031182017001329. Epub 2017 Jul 19.

10.

Plasmodium knowlesi: a superb in vivo nonhuman primate model of antigenic variation in malaria.

Galinski MR, Lapp SA, Peterson MS, Ay F, Joyner CJ, LE Roch KG, Fonseca LL, Voit EO; MAHPIC CONSORTIUM.

Parasitology. 2018 Jan;145(1):85-100. doi: 10.1017/S0031182017001135. Epub 2017 Jul 17. Review.

11.

EVALUATION OF THE EFFECTS OF THE HYDRO-ETHANOLIC ROOT EXTRACT OF ZANTHOXYLUM ZANTHOXYLOIDES ON HEMATOLOGICAL PARAMETERS AND OXIDATIVE STRESS IN CYCLOPHOSPAMIDE TREATED RATS.

Vo I, O A, K R, Ay F.

Afr J Tradit Complement Altern Med. 2016 Aug 12;13(5):153-159. doi: 10.21010/ajtcam.v13i5.20. eCollection 2016.

12.

Form and function of topologically associating genomic domains in budding yeast.

Eser U, Chandler-Brown D, Ay F, Straight AF, Duan Z, Noble WS, Skotheim JM.

Proc Natl Acad Sci U S A. 2017 Apr 11;114(15):E3061-E3070. doi: 10.1073/pnas.1612256114. Epub 2017 Mar 27. Erratum in: Proc Natl Acad Sci U S A. 2017 Oct 10;114(41):E8801.

13.

17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells.

Schmiedel BJ, Seumois G, Samaniego-Castruita D, Cayford J, Schulten V, Chavez L, Ay F, Sette A, Peters B, Vijayanand P.

Nat Commun. 2016 Nov 16;7:13426. doi: 10.1038/ncomms13426.

14.

Neocentromeres Provide Chromosome Segregation Accuracy and Centromere Clustering to Multiple Loci along a Candida albicans Chromosome.

Burrack LS, Hutton HF, Matter KJ, Clancey SA, Liachko I, Plemmons AE, Saha A, Power EA, Turman B, Thevandavakkam MA, Ay F, Dunham MJ, Berman J.

PLoS Genet. 2016 Sep 23;12(9):e1006317. doi: 10.1371/journal.pgen.1006317. eCollection 2016 Sep.

15.

Vibrational and mechanical properties of single layer MXene structures: a first-principles investigation.

Yorulmaz U, Özden A, Perkgöz NK, Ay F, Sevik C.

Nanotechnology. 2016 Aug 19;27(33):335702. doi: 10.1088/0957-4484/27/33/335702. Epub 2016 Jul 5.

PMID:
27377143
16.

A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions.

Fotuhi Siahpirani A, Ay F, Roy S.

Genome Biol. 2016 May 27;17(1):114. doi: 10.1186/s13059-016-0962-8.

17.

Health Beliefs of Midwifery Students at Istanbul University about Breast Cancer and Breast Self-Examination Acknowledgements.

Gençtürk N, Demirezen E, Ay F.

J Cancer Educ. 2017 Dec;32(4):784-789. doi: 10.1007/s13187-016-1014-5.

PMID:
26988098
18.

A predictive modeling approach for cell line-specific long-range regulatory interactions.

Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R.

Nucleic Acids Res. 2016 Feb 29;44(4):1977-8. doi: 10.1093/nar/gkv1181. Epub 2015 Nov 5. No abstract available.

19.

A predictive modeling approach for cell line-specific long-range regulatory interactions.

Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R.

Nucleic Acids Res. 2015 Oct 15;43(18):8694-712. doi: 10.1093/nar/gkv865. Epub 2015 Sep 3. Erratum in: Nucleic Acids Res. 2016 Feb 29;44(4):1977-8.

20.

Analysis methods for studying the 3D architecture of the genome.

Ay F, Noble WS.

Genome Biol. 2015 Sep 2;16:183. doi: 10.1186/s13059-015-0745-7. Review.

21.

Bipartite structure of the inactive mouse X chromosome.

Deng X, Ma W, Ramani V, Hill A, Yang F, Ay F, Berletch JB, Blau CA, Shendure J, Duan Z, Noble WS, Disteche CM.

Genome Biol. 2015 Aug 7;16:152. doi: 10.1186/s13059-015-0728-8.

22.

Comprehensive identification and analysis of human accelerated regulatory DNA.

Gittelman RM, Hun E, Ay F, Madeoy J, Pennacchio L, Noble WS, Hawkins RD, Akey JM.

Genome Res. 2015 Sep;25(9):1245-55. doi: 10.1101/gr.192591.115. Epub 2015 Jun 23.

23.

Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program.

Dileep V, Ay F, Sima J, Vera DL, Noble WS, Gilbert DM.

Genome Res. 2015 Aug;25(8):1104-13. doi: 10.1101/gr.183699.114. Epub 2015 May 20.

24.

Accurate identification of centromere locations in yeast genomes using Hi-C.

Varoquaux N, Liachko I, Ay F, Burton JN, Shendure J, Dunham MJ, Vert JP, Noble WS.

Nucleic Acids Res. 2015 Jun 23;43(11):5331-9. doi: 10.1093/nar/gkv424. Epub 2015 May 4.

25.

Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C.

Ay F, Vu TH, Zeitz MJ, Varoquaux N, Carette JE, Vert JP, Hoffman AR, Noble WS.

BMC Genomics. 2015 Feb 25;16:121. doi: 10.1186/s12864-015-1236-7.

26.

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression.

Libbrecht MW, Ay F, Hoffman MM, Gilbert DM, Bilmes JA, Noble WS.

Genome Res. 2015 Apr;25(4):544-57. doi: 10.1101/gr.184341.114. Epub 2015 Feb 12.

27.

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes.

Ma W, Ay F, Lee C, Gulsoy G, Deng X, Cook S, Hesson J, Cavanaugh C, Ware CB, Krumm A, Shendure J, Blau CA, Disteche CM, Noble WS, Duan Z.

Nat Methods. 2015 Jan;12(1):71-8. doi: 10.1038/nmeth.3205. Epub 2014 Dec 1.

28.

Erbium-doped spiral amplifiers with 20 dB of net gain on silicon.

Vázquez-Córdova SA, Dijkstra M, Bernhardi EH, Ay F, Wörhoff K, Herek JL, García-Blanco SM, Pollnau M.

Opt Express. 2014 Oct 20;22(21):25993-6004. doi: 10.1364/OE.22.025993.

PMID:
25401633
29.
30.

A statistical approach for inferring the 3D structure of the genome.

Varoquaux N, Ay F, Noble WS, Vert JP.

Bioinformatics. 2014 Jun 15;30(12):i26-33. doi: 10.1093/bioinformatics/btu268.

31.

Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression.

Ay F, Bunnik EM, Varoquaux N, Bol SM, Prudhomme J, Vert JP, Noble WS, Le Roch KG.

Genome Res. 2014 Jun;24(6):974-88. doi: 10.1101/gr.169417.113. Epub 2014 Mar 26.

32.

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts.

Ay F, Bailey TL, Noble WS.

Genome Res. 2014 Jun;24(6):999-1011. doi: 10.1101/gr.160374.113. Epub 2014 Feb 5.

33.

Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome.

Zeitz MJ, Lerner PP, Ay F, Van Nostrand E, Heidmann JD, Noble WS, Hoffman AR.

Nucleus. 2013 Nov-Dec;4(6):487-93. doi: 10.4161/nucl.27364. Epub 2013 Dec 5.

34.

Barriers that prevent implementation of research findings in nursing: education-research hospitals case.

Ay F, Gençtürk N, Turan Miral M.

Int J Nurs Pract. 2014 Dec;20(6):646-54. doi: 10.1111/ijn.12226. Epub 2013 Nov 21.

PMID:
24256131
35.

Genomic interaction profiles in breast cancer reveal altered chromatin architecture.

Zeitz MJ, Ay F, Heidmann JD, Lerner PL, Noble WS, Steelman BN, Hoffman AR.

PLoS One. 2013 Sep 3;8(9):e73974. doi: 10.1371/journal.pone.0073974. eCollection 2013.

36.

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.

37.

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.

38.

Cloning, purification and characterization of a thermostable carboxylesterase from Anoxybacillus sp. PDF1.

Ay F, Karaoglu H, Inan K, Canakci S, Belduz AO.

Protein Expr Purif. 2011 Nov;80(1):74-9. doi: 10.1016/j.pep.2011.06.019. Epub 2011 Jul 14.

PMID:
21782026
39.

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.

40.

Monolithic integration of erbium-doped amplifiers with silicon-on-insulator waveguides.

Agazzi L, Bradley JD, Dijkstra M, Ay F, Roelkens G, Baets R, Wörhoff K, Pollnau M.

Opt Express. 2010 Dec 20;18(26):27703-11. doi: 10.1364/OE.18.027703.

PMID:
21197045
41.

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M.

Science. 2010 Dec 24;330(6012):1787-97. doi: 10.1126/science.1198374. Epub 2010 Dec 22.

42.

Integrated Al2O3:Er3+ ring lasers on silicon with wide wavelength selectivity.

Bradley JD, Stoffer R, Agazzi L, Ay F, Wörhoff K, Pollnau M.

Opt Lett. 2010 Jan 1;35(1):73-5. doi: 10.1364/OL.35.000073.

PMID:
20664677
43.

Advanced oxidation of amoxicillin by Fenton's reagent treatment.

Ay F, Kargi F.

J Hazard Mater. 2010 Jul 15;179(1-3):622-7. doi: 10.1016/j.jhazmat.2010.03.048. Epub 2010 Mar 17.

PMID:
20363555
44.

[Approaches taken by nurses in treating postoperative pain].

Ay F, Alpar SE.

Agri. 2010 Jan;22(1):21-9. Turkish.

45.

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.

46.

A fast and accurate algorithm for comparative analysis of metabolic pathways.

Ay F, Kahveci T, DE Crécy-Lagard V.

J Bioinform Comput Biol. 2009 Jun;7(3):389-428.

PMID:
19507283
47.

A statistical experiment design approach for advanced oxidation of Direct Red azo-dye by photo-Fenton treatment.

Ay F, Catalkaya EC, Kargi F.

J Hazard Mater. 2009 Feb 15;162(1):230-6. doi: 10.1016/j.jhazmat.2008.05.027. Epub 2008 May 13.

PMID:
18555599
48.

Consistent alignment of metabolic pathways without abstraction.

Ay F, Kahveci T, de Crécy-Lagard V.

Comput Syst Bioinformatics Conf. 2008;7:237-48.

49.

Postnatal transitions in myosin heavy chain isoforms of the rabbit superficial masseter and digastric muscle.

Korfage JA, van Wessel T, Langenbach GE, Ay F, van Eijden TM.

J Anat. 2006 Jun;208(6):743-51.

50.

High-refractive-index measurement with an elastomeric grating coupler.

Kocabas A, Ay F, Dâna A, Kiyat I, Aydinli A.

Opt Lett. 2005 Dec 1;30(23):3150-2.

PMID:
16342705

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