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Ferhat Ay, Ph.D. - Publications

Affiliations: 
2011 University of Florida, Gainesville, Gainesville, FL, United States 
Area:
Computer Engineering, Computer Science, Bioinformatics Biology
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63 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
2024 Lenz T, Zhang X, Chakraborty A, Ardakany AR, Prudhomme J, Ay F, Deitsch K, Le Roch KG. Chromatin structure and - a tango in regulation of gene expression in the human malaria parasite, ? Biorxiv : the Preprint Server For Biology. PMID 38405848 DOI: 10.1101/2024.02.13.580059  0.341
2023 Hu Y, Salgado Figueroa D, Zhang Z, Veselits M, Bhattacharyya S, Kashiwagi M, Clark MR, Morgan BA, Ay F, Georgopoulos K. Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS. Cell. 186: 5269-5289.e22. PMID 37995656 DOI: 10.1016/j.cell.2023.10.023  0.402
2023 Dozmorov MG, Marshall MA, Rashid NS, Grible JM, Valentine A, Olex AL, Murthy K, Chakraborty A, Reyna J, Figueroa DS, Hinojosa-Gonzalez L, Da-Inn Lee E, Baur BA, Roy S, Ay F, et al. Publisher Correction: Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft. Scientific Reports. 13: 7522. PMID 37160896 DOI: 10.1038/s41598-023-33284-y  0.53
2023 Dozmorov MG, Marshall MA, Rashid NS, Grible JM, Valentine A, Olex AL, Murthy K, Chakraborty A, Reyna J, Figueroa DS, Hinojosa-Gonzalez L, Da-Inn Lee E, Baur BA, Roy S, Ay F, et al. Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft. Scientific Reports. 13: 5420. PMID 37012431 DOI: 10.1038/s41598-023-32568-7  0.605
2022 Wang Y, Jia L, Wang C, Du Z, Zhang S, Zhou L, Wen X, Li H, Chen H, Nie Y, Li D, Liu S, Figueroa DS, Ay F, Xu W, et al. Pluripotency exit is guided by the Peln1-mediated disruption of intrachromosomal architecture. The Journal of Cell Biology. 221. PMID 35171230 DOI: 10.1083/jcb.202009134  0.324
2021 Du Z, Wen X, Wang Y, Jia L, Zhang S, Liu Y, Zhou L, Li H, Yang W, Wang C, Chen J, Hao Y, Salgado Figueroa D, Chen H, Li D, ... ... Ay F, et al. Author Correction: Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network. Genome Biology. 22: 272. PMID 34544465 DOI: 10.1186/s13059-021-02487-9  0.77
2021 Du Z, Wen X, Wang Y, Jia L, Zhang S, Liu Y, Zhou L, Li H, Yang W, Wang C, Chen J, Hao Y, Chen H, Li D, Chen N, ... ... Ay F, et al. Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network. Genome Biology. 22: 233. PMID 34412677 DOI: 10.1186/s13059-021-02444-6  0.787
2021 Chakraborty A, Ay F, Davuluri RV. ExTraMapper: Exon- and Transcript-level mappings for orthologous gene pairs. Bioinformatics (Oxford, England). PMID 34014317 DOI: 10.1093/bioinformatics/btab393  0.344
2021 Cajigas I, Chakraborty A, Lynam M, Swyter KR, Bastidas M, Collens L, Luo H, Ay F, Kohtz JD. Sox2- lncRNA mechanisms of chromosome topological control in developing forebrain. Development (Cambridge, England). PMID 33593819 DOI: 10.1242/dev.197202  0.385
2020 Chandra V, Bhattacharyya S, Schmiedel BJ, Madrigal A, Gonzalez-Colin C, Fotsing S, Crinklaw A, Seumois G, Mohammadi P, Kronenberg M, Peters B, Ay F, Vijayanand P. Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants. Nature Genetics. PMID 33349701 DOI: 10.1038/s41588-020-00745-3  0.324
2020 Kaul A, Bhattacharyya S, Ay F. Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2. Nature Protocols. PMID 31980751 DOI: 10.1038/S41596-019-0273-0  0.395
2019 Lhoumaud P, Badri S, Rodriguez-Hernaez J, Sakellaropoulos T, Sethia G, Kloetgen A, Cornwell M, Bhattacharyya S, Ay F, Bonneau R, Tsirigos A, Skok JA. NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains. Nature Communications. 10: 4843. PMID 31649247 DOI: 10.1038/S41467-019-12811-4  0.453
2019 Bhattacharyya S, Chandra V, Vijayanand P, Ay F. Identification of significant chromatin contacts from HiChIP data by FitHiChIP. Nature Communications. 10: 4221. PMID 31530818 DOI: 10.1038/S41467-019-11950-Y  0.433
2019 Ardakany AR, Ay F, Lonardi S. Selfish: discovery of differential chromatin interactions via a self-similarity measure. Bioinformatics (Oxford, England). 35: i145-i153. PMID 31510653 DOI: 10.1093/Bioinformatics/Btz362  0.466
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  0.712
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  0.804
2019 Lio CJ, Shukla V, Samaniego-Castruita D, González-Avalos E, Chakraborty A, Yue X, Schatz DG, Ay F, Rao A. TET enzymes augment activation-induced deaminase (AID) expression via 5-hydroxymethylcytosine modifications at the superenhancer. Science Immunology. 4. PMID 31028100 DOI: 10.1126/Sciimmunol.Aau7523  0.382
2019 Yardımcı GG, Ozadam H, Sauria MEG, Ursu O, Yan KK, Yang T, Chakraborty A, Kaul A, Lajoie BR, Song F, Zhan Y, Ay F, Gerstein M, Kundaje A, Li Q, et al. Measuring the reproducibility and quality of Hi-C data. Genome Biology. 20: 57. PMID 30890172 DOI: 10.1186/S13059-019-1658-7  0.372
2019 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, ... ... Ay F, et al. Comparative 3D genome organization in apicomplexan parasites. Proceedings of the National Academy of Sciences of the United States of America. PMID 30723152 DOI: 10.1073/Pnas.1810815116  0.421
2019 Zheng Y, Ay F, Keles S. Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies. Elife. 8. PMID 30702424 DOI: 10.7554/Elife.38070  0.371
2019 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, ... ... Ay F, et al. Reduced expression of phosphatase PTPN2 promotes pathogenic conversion of Tregs in autoimmunity. The Journal of Clinical Investigation. PMID 30620725 DOI: 10.1172/Jci123267  0.312
2019 Okonechnikov K, Hübner J, Chapman O, Chakraborty A, Bump R, Chandran S, Kraft K, Acuna Hidalgo R, Mundlos S, Coufal N, Levy M, Crawford J, Ay F, Mesirov J, Pajtler K, et al. GENE-15. TARGETING OF EPENDYMOMA AS INFORMED BY ONCOGENIC 3D GENOME ORGANIZATION Neuro-Oncology. 21: vi100-vi100. DOI: 10.1093/Neuonc/Noz175.417  0.41
2018 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, et al. Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming. Scientific Data. 5: 180255. PMID 31745204 DOI: 10.1038/sdata.2018.255  0.307
2018 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, ... ... Ay F, et al. Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. Cell. PMID 30595451 DOI: 10.1016/J.Cell.2018.11.036  0.392
2018 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, et al. Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming. Scientific Data. 5: 180255. PMID 30457566 DOI: 10.1038/Sdata.2018.255  0.419
2018 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, ... ... Ay F, et al. Integrative detection and analysis of structural variation in cancer genomes. Nature Genetics. PMID 30202056 DOI: 10.1038/S41588-018-0195-8  0.408
2018 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. Molecular Cell. PMID 30146317 DOI: 10.1016/J.Molcel.2018.07.024  0.45
2018 Chakraborty A, Ay F. The role of 3D genome organization in disease: From compartments to single nucleotides. Seminars in Cell & Developmental Biology. PMID 30017907 DOI: 10.1016/J.Semcdb.2018.07.005  0.371
2018 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, et al. Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages. Nature Communications. 9: 1910. PMID 29765020 DOI: 10.1038/S41467-018-04295-5  0.421
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  0.78
2017 Chakraborty A, Ay F. Identification of copy number variations and translocations in cancer cells from Hi-C data. Bioinformatics (Oxford, England). PMID 29048467 DOI: 10.1093/Bioinformatics/Btx664  0.428
2017 Lapp SA, Geraldo JA, Chien JT, Ay F, Pakala SB, Batugedara G, Humphrey J, DeBARRY JD, Le Roch KG, Galinski MR, Kissinger JC. PacBio assembly of a Plasmodium knowlesi genome sequence with Hi-C correction and manual annotation of the SICAvar gene family. Parasitology. 1-14. PMID 28720171 DOI: 10.1017/S0031182017001329  0.368
2017 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 28348222 DOI: 10.1073/Pnas.1612256114  0.495
2016 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 Genetics. 12: e1006317. PMID 27662467 DOI: 10.1371/Journal.Pgen.1006317  0.364
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  0.633
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  0.572
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  0.69
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  0.401
2015 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 Biology. 16: 152. PMID 26248554 DOI: 10.1186/S13059-015-0728-8  0.375
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  0.426
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  0.351
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  0.416
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  0.457
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  0.422
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  0.789
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  0.393
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  0.399
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  0.465
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  0.453
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  0.391
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  0.352
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  0.632
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  0.755
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  0.613
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  0.68
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  0.594
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  0.672
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  0.544
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  0.596
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  0.644
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  0.631
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 DOI: 10.1142/S0219720009004163  0.59
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  0.545
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