Ferhat Ay

Title(s)Assistant Adjunct Professor, Pediatrics
SchoolHealth Sciences
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Bunnik EM, Venkat A, Shao J, McGovern KE, Batugedara G, Worth D, Prudhomme J, Lapp SA, Andolina C, Ross LS, Lawres L, Brady D, Sinnis P, Nosten F, Fidock DA, Wilson EH, Tewari R, Galinski MR, Ben Mamoun C, Ay F, Le Roch KG. Comparative 3D genome organization in apicomplexan parasites. Proc Natl Acad Sci U S A. 2019 Feb 05. PMID: 30723152.
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    2. Zheng Y, Ay F, Keles S. Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies. Elife. 2019 Jan 31; 8. PMID: 30702424.
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    3. Svensson MN, Doody KM, Schmiedel BJ, Bhattacharyya S, Panwar B, Wiede F, Yang S, Santelli E, Wu DJ, Sacchetti C, Gujar R, Seumois G, Kiosses WB, Aubry I, Kim G, Mydel P, Sakaguchi S, Kronenberg M, Tiganis T, Tremblay ML, Ay F, Vijayanand P, Bottini N. Reduced expression of phosphatase PTPN2 promotes pathogenic conversion of Tregs in autoimmunity. J Clin Invest. 2019 Jan 08. PMID: 30620725.
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    4. Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner JL, Paulsen MT, Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM. Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. Cell. 2018 Dec 21. PMID: 30595451.
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    5. Du Z, Jia L, Wang Y, Wang C, Wen X, Chen J, Zhu Y, Yu D, Zhou L, Chen N, Zhang S, Celik I, Ay F, Gao S, Zhang S, Li W, Hoffman AR, Cui J, Hu JF. Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming. Sci Data. 2018 11 20; 5:180255. PMID: 30457566.
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    6. Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardimci 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. Integrative detection and analysis of structural variation in cancer genomes. Nat Genet. 2018 Oct; 50(10):1388-1398. PMID: 30202056.
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    7. 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. The Evf2 Ultraconserved Enhancer lncRNA Functionally and Spatially Organizes Megabase Distant Genes in the Developing Forebrain. Mol Cell. 2018 Sep 20; 71(6):956-972.e9. PMID: 30146317.
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    8. Chakraborty A, Ay F. The role of 3D genome organization in disease: From compartments to single nucleotides. Semin Cell Dev Biol. 2018 Jul 16. PMID: 30017907.
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    9. 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. Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages. Nat Commun. 2018 05 15; 9(1):1910. PMID: 29765020.
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    10. 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. Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution. Methods. 2018 06 01; 142:59-73. PMID: 29382556.
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    11. Chakraborty A, Ay F. Identification of copy number variations and translocations in cancer cells from Hi-C data. Bioinformatics. 2017 Oct 18. PMID: 29048467.
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    12. Eser U, Chandler-Brown D, Ay F, Straight AF, Duan Z, Noble WS, Skotheim JM. Form and function of topologically associating genomic domains in budding yeast. Proc Natl Acad Sci U S A. 2017 04 11; 114(15):E3061-E3070. PMID: 28348222.
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    13. Schmiedel BJ, Seumois G, Samaniego-Castruita D, Cayford J, Schulten V, Chavez L, Ay F, Sette A, Peters B, Vijayanand P. 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells. Nat Commun. 2016 11 16; 7:13426. PMID: 27848966.
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    14. 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. Neocentromeres Provide Chromosome Segregation Accuracy and Centromere Clustering to Multiple Loci along a Candida albicans Chromosome. PLoS Genet. 2016 Sep; 12(9):e1006317. PMID: 27662467.
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    15. Fotuhi Siahpirani A, Ay F, Roy S. A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions. Genome Biol. 2016 05 27; 17(1):114. PMID: 27233632; PMCID: PMC4882777.
    16. Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R. A predictive modeling approach for cell line-specific long-range regulatory interactions. Nucleic Acids Res. 2016 Feb 29; 44(4):1977-8. PMID: 26546512; PMCID: PMC4770215.
    17. Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R. A predictive modeling approach for cell line-specific long-range regulatory interactions. Nucleic Acids Res. 2015 Oct 15; 43(18):8694-712. PMID: 26338778; PMCID: PMC4605315.
    18. Ay F, Noble WS. Analysis methods for studying the 3D architecture of the genome. Genome Biol. 2015 Sep 02; 16:183. PMID: 26328929; PMCID: PMC4556012.
    19. Deng X, Ma W, Ramani V, Hill A, Yang F, Ay F, Berletch JB, Blau CA, Shendure J, Duan Z, Noble WS, Disteche CM. Bipartite structure of the inactive mouse X chromosome. Genome Biol. 2015 Aug 07; 16:152. PMID: 26248554; PMCID: PMC4539712.
    20. Gittelman RM, Hun E, Ay F, Madeoy J, Pennacchio L, Noble WS, Hawkins RD, Akey JM. Comprehensive identification and analysis of human accelerated regulatory DNA. Genome Res. 2015 Sep; 25(9):1245-55. PMID: 26104583; PMCID: PMC4561485.
    21. Dileep V, Ay F, Sima J, Vera DL, Noble WS, Gilbert DM. Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program. Genome Res. 2015 Aug; 25(8):1104-13. PMID: 25995270; PMCID: PMC4509995.
    22. Varoquaux N, Liachko I, Ay F, Burton JN, Shendure J, Dunham MJ, Vert JP, Noble WS. Accurate identification of centromere locations in yeast genomes using Hi-C. Nucleic Acids Res. 2015 Jun 23; 43(11):5331-9. PMID: 25940625; PMCID: PMC4477656.
    23. Ay F, Vu TH, Zeitz MJ, Varoquaux N, Carette JE, Vert JP, Hoffman AR, Noble WS. Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C. BMC Genomics. 2015 Feb 25; 16:121. PMID: 25887659; PMCID: PMC4369351.
    24. Libbrecht MW, Ay F, Hoffman MM, Gilbert DM, Bilmes JA, Noble WS. Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression. Genome Res. 2015 Apr; 25(4):544-57. PMID: 25677182; PMCID: PMC4381526.
    25. 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. Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes. Nat Methods. 2015 Jan; 12(1):71-8. PMID: 25437436; PMCID: PMC4281301.
    26. Ay F, Bunnik EM, Varoquaux N, Vert JP, Noble WS, Le Roch KG. Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum: gene regulation via histone modifications, nucleosome positioning and nuclear architecture in P. falciparum. Bioessays. 2015 Feb; 37(2):182-94. PMID: 25394267; PMCID: PMC4385791.
    27. Varoquaux N, Ay F, Noble WS, Vert JP. A statistical approach for inferring the 3D structure of the genome. Bioinformatics. 2014 Jun 15; 30(12):i26-33. PMID: 24931992; PMCID: PMC4229903.
    28. Ay F, Bunnik EM, Varoquaux N, Bol SM, Prudhomme J, Vert JP, Noble WS, Le Roch KG. Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression. Genome Res. 2014 Jun; 24(6):974-88. PMID: 24671853; PMCID: PMC4032861.
    29. Ay F, Bailey TL, Noble WS. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res. 2014 Jun; 24(6):999-1011. PMID: 24501021; PMCID: PMC4032863.
    30. Zeitz MJ, Lerner PP, Ay F, Van Nostrand E, Heidmann JD, Noble WS, Hoffman AR. Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome. Nucleus. 2013 Nov-Dec; 4(6):487-93. PMID: 24448439; PMCID: PMC3925693.
    31. Zeitz MJ, Ay F, Heidmann JD, Lerner PL, Noble WS, Steelman BN, Hoffman AR. Genomic interaction profiles in breast cancer reveal altered chromatin architecture. PLoS One. 2013; 8(9):e73974. PMID: 24019942; PMCID: PMC3760796.
    32. Marbach D, Roy S, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M. Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks. Genome Res. 2012 Jul; 22(7):1334-49. PMID: 22456606; PMCID: PMC3396374.
    33. Ay F, Dang M, Kahveci T. Metabolic network alignment in large scale by network compression. BMC Bioinformatics. 2012 Mar 21; 13 Suppl 3:S2. PMID: 22536900; PMCID: PMC3402922.
    34. Ay F, Kellis M, Kahveci T. SubMAP: aligning metabolic pathways with subnetwork mappings. J Comput Biol. 2011 Mar; 18(3):219-35. PMID: 21385030; PMCID: PMC3123932.
    35. 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. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24; 330(6012):1787-97. PMID: 21177974.
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    36. Ay F, Xu F, Kahveci T. Scalable steady state analysis of Boolean biological regulatory networks. PLoS One. 2009 Dec 01; 4(12):e7992. PMID: 19956604.
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    37. Ay F, Kahveci T, DE Crécy-Lagard V. A fast and accurate algorithm for comparative analysis of metabolic pathways. J Bioinform Comput Biol. 2009 Jun; 7(3):389-428. PMID: 19507283.
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    38. Ay F, Kahveci T, de Crécy-Lagard V. Consistent alignment of metabolic pathways without abstraction. Comput Syst Bioinformatics Conf. 2008; 7:237-48. PMID: 19642284.
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