Ferhat Ay, Ph.D. - Publications

2011 University of Florida, Gainesville, Gainesville, FL, United States 
Computer Engineering, Computer Science, Bioinformatics Biology

31 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Rivera-Mulia JC, Kim S, Gabr H, Chakraborty A, Ay F, Kahveci T, Gilbert DM. Replication timing networks reveal a link between transcription regulatory circuits and replication timing control. Genome Research. PMID 31434679 DOI: 10.1101/gr.247049.118  1
2019 Zhang S, Wang Y, Jia L, Wen X, Zhonghua D, Wang C, Hao Y, Yu D, Zhou L, Chen N, Chen J, Chen H, Zhang H, Celik I, Gulsoy G, ... ... Ay F, et al. Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing. Genome Research. PMID 31315906 DOI: 10.1101/gr.244996.118  0.88
2018 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 (San Diego, Calif.). PMID 29382556 DOI: 10.1016/j.ymeth.2018.01.014  0.88
2016 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 Biology. 17: 114. PMID 27233632 DOI: 10.1186/s13059-016-0962-8  1
2015 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 Research. PMID 26546512 DOI: 10.1093/nar/gkv1181  0.96
2015 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 Research. PMID 26338778 DOI: 10.1093/nar/gkv865  0.96
2015 Ay F, Noble WS. Analysis methods for studying the 3D architecture of the genome. Genome Biology. 16: 183. PMID 26328929 DOI: 10.1186/s13059-015-0745-7  1
2015 Gittelman RM, Hun E, Ay F, Madeoy J, Pennacchio L, Noble WS, Hawkins DR, Akey JM. Comprehensive identification and analysis of human accelerated regulatory DNA. Genome Research. PMID 26104583 DOI: 10.1101/gr.192591.115  1
2015 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 Research. PMID 25995270 DOI: 10.1101/gr.183699.114  1
2015 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 Research. 43: 5331-9. PMID 25940625 DOI: 10.1093/nar/gkv424  1
2015 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. 16: 121. PMID 25887659 DOI: 10.1186/s12864-015-1236-7  1
2015 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 Research. 25: 544-57. PMID 25677182 DOI: 10.1101/gr.184341.114  1
2015 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. Nature Methods. 12: 71-8. PMID 25437436 DOI: 10.1038/nmeth.3205  1
2015 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 : News and Reviews in Molecular, Cellular and Developmental Biology. 37: 182-94. PMID 25394267 DOI: 10.1002/bies.201400145  1
2014 Varoquaux N, Ay F, Noble WS, Vert JP. A statistical approach for inferring the 3D structure of the genome. Bioinformatics (Oxford, England). 30: i26-33. PMID 24931992 DOI: 10.1093/bioinformatics/btu268  1
2014 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 Research. 24: 974-88. PMID 24671853 DOI: 10.1101/gr.169417.113  1
2014 Ay F, Bailey TL, Noble WS. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Research. 24: 999-1011. PMID 24501021 DOI: 10.1101/gr.160374.113  1
2013 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 (Austin, Tex.). 4: 487-93. PMID 24448439 DOI: 10.4161/nucl.27364  1
2013 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. 8: e73974. PMID 24019942 DOI: 10.1371/journal.pone.0073974  1
2012 Ay F, Dang M, Kahveci T. Metabolic network alignment in large scale by network compression. Bmc Bioinformatics. 13: S2. PMID 22536900 DOI: 10.1186/1471-2105-13-S3-S2  1
2012 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 Research. 22: 1334-49. PMID 22456606 DOI: 10.1101/gr.127191.111  1
2012 Ay F, Gülsoy G, Kahveci T. Mining Biological Networks for Similar Patterns Intelligent Systems Reference Library. 25: 63-99. DOI: 10.1007/978-3-642-23151-3_5  1
2011 Ay F, Kellis M, Kahveci T. SubMAP: aligning metabolic pathways with subnetwork mappings. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 219-35. PMID 21385030 DOI: 10.1089/cmb.2010.0280  1
2011 Dang M, Ay F, Kahveci T. A novel framework for large scale metabolic network alignments by compression 2011 Acm Conference On Bioinformatics, Computational Biology and Biomedicine, Bcb 2011. 274-283. DOI: 10.1145/2147805.2147835  1
2010 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, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/science.1198374  1
2010 Ay F, Kahveci T. Functional similarities of reaction sets in metabolic pathways 2010 Acm International Conference On Bioinformatics and Computational Biology, Acm-Bcb 2010. 102-111. DOI: 10.1145/1854776.1854795  1
2010 Ay F, Gulsoy G, Kahveci T. Finding steady states of large scale regulatory networks through partitioning 2010 Ieee International Workshop On Genomic Signal Processing and Statistics, Gensips 2010. DOI: 10.1109/GENSIPS.2010.5719669  1
2010 Ay F, Dinh TN, Thai MT, Kahveci T. Finding dynamic modules of biological regulatory networks 10th Ieee International Conference On Bioinformatics and Bioengineering 2010, Bibe 2010. 136-143. DOI: 10.1109/BIBE.2010.31  1
2009 Ay F, Xu F, Kahveci T. Scalable steady state analysis of Boolean biological regulatory networks. Plos One. 4: e7992. PMID 19956604 DOI: 10.1371/journal.pone.0007992  1
2009 Ay F, Kahveci T, DE Crécy-Lagard V. A fast and accurate algorithm for comparative analysis of metabolic pathways. Journal of Bioinformatics and Computational Biology. 7: 389-428. PMID 19507283  1
2008 Ay F, Kahveci T, de Crécy-Lagard V. Consistent alignment of metabolic pathways without abstraction. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 7: 237-48. PMID 19642284  1
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