Ferhat Ay

Title(s)Associate Adjunct Professor, Pediatrics
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
ORCID ORCID Icon0000-0002-0708-6914 Additional info
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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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing. Bioinformatics. 2023 10 03; 39(10). Sapci AOB, Lu S, Yan S, Ay F, Tastan O, Keles S. PMID: 37740957; PMCID: PMC10564618.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    2. TWEAK functions with TNF and IL-17 on keratinocytes and is a potential target for psoriasis therapy. Sci Immunol. 2021 Nov 19; 6(65):eabi8823. Gupta RK, Gracias DT, Figueroa DS, Miki H, Miller J, Fung K, Ay F, Burkly L, Croft M. PMID: 34797693; PMCID: PMC8756771.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    3. COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types. Nat Commun. 2021 11 19; 12(1):6760. Schmiedel BJ, Rocha J, Gonzalez-Colin C, Bhattacharyya S, Madrigal A, Ottensmeier CH, Ay F, Chandra V, Vijayanand P. PMID: 34799557; PMCID: PMC8604964.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    4. ExTraMapper: exon- and transcript-level mappings for orthologous gene pairs. Bioinformatics. 2021 Oct 25; 37(20):3412-3420. Chakraborty A, Ay F, Davuluri RV. PMID: 34014317; PMCID: PMC8545320.
      View in: PubMed   Mentions: 2     Fields:    
    5. Author Correction: Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network. Genome Biol. 2021 Sep 20; 22(1):272. 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, Chen N, Celik I, Zhu Y, Yan Z, Fu C, Liu S, Jiao B, Wang Z, Zhang H, Gülsoy G, Luo J, Qin B, Gao S, Kapranov P, Esteban MA, Zhang S, Li W, Ay F, Chen R, Hoffman AR, Cui J, Hu JF. PMID: 34544465; PMCID: PMC8451145.
      View in: PubMed   Mentions: 1     Fields:    
    6. Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network. Genome Biol. 2021 08 19; 22(1):233. 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, Chen N, Celik I, Zhu Y, Yan Z, Fu C, Liu S, Jiao B, Wang Z, Zhang H, Gülsoy G, Luo J, Qin B, Gao S, Kapranov P, Esteban MA, Zhang S, Li W, Ay F, Chen R, Hoffman AR, Cui J, Hu JF. PMID: 34412677; PMCID: PMC8375132.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    7. Intratumoral follicular regulatory T cells curtail anti-PD-1 treatment efficacy. Nat Immunol. 2021 08; 22(8):1052-1063. Eschweiler S, Clarke J, Ramírez-Suástegui C, Panwar B, Madrigal A, Chee SJ, Karydis I, Woo E, Alzetani A, Elsheikh S, Hanley CJ, Thomas GJ, Friedmann PS, Sanchez-Elsner T, Ay F, Ottensmeier CH, Vijayanand P. PMID: 34168370; PMCID: PMC8434898.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansAnimalsCells
    8. Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants. Genome Res. 2021 05; 31(5):834-851. Xia J, Venkat A, Bainbridge RE, Reese ML, Le Roch KG, Ay F, Boyle JP. PMID: 33906962; PMCID: PMC8092015.
      View in: PubMed   Mentions: 15     Fields:    Translation:Animals
    9. The tumor suppressor kinase DAPK3 drives tumor-intrinsic immunity through the STING-IFN-β pathway. Nat Immunol. 2021 04; 22(4):485-496. Takahashi M, Lio CJ, Campeau A, Steger M, Ay F, Mann M, Gonzalez DJ, Jain M, Sharma S. PMID: 33767426; PMCID: PMC8300883.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansAnimalsCells
    10. Sox2-Evf2 lncRNA-mediated mechanisms of chromosome topological control in developing forebrain. Development. 2021 03 15; 148(6). Cajigas I, Chakraborty A, Lynam M, Swyter KR, Bastidas M, Collens L, Luo H, Ay F, Kohtz JD. PMID: 33593819; PMCID: PMC7990859.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    11. Multi-cell type gene coexpression network analysis reveals coordinated interferon response and cross-cell type correlations in systemic lupus erythematosus. Genome Res. 2021 04; 31(4):659-676. Panwar B, Schmiedel BJ, Liang S, White B, Rodriguez E, Kalunian K, McKnight AJ, Soloff R, Seumois G, Vijayanand P, Ay F. PMID: 33674349; PMCID: PMC8015858.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    12. Severely ill COVID-19 patients display impaired exhaustion features in SARS-CoV-2-reactive CD8+ T cells. Sci Immunol. 2021 01 21; 6(55). Kusnadi A, Ramírez-Suástegui C, Fajardo V, Chee SJ, Meckiff BJ, Simon H, Pelosi E, Seumois G, Ay F, Vijayanand P, Ottensmeier CH. PMID: 33478949; PMCID: PMC8101257.
      View in: PubMed   Mentions: 114     Fields:    Translation:HumansCells
    13. Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants. Nat Genet. 2021 01; 53(1):110-119. 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. PMID: 33349701; PMCID: PMC8053422.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansCells
    14. COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types. bioRxiv. 2020 Dec 02. Schmiedel BJ, Chandra V, Rocha J, Gonzalez-Colin C, Bhattacharyya S, Madrigal A, Ottensmeier CH, Ay F, Vijayanand P. PMID: 33299987; PMCID: PMC7724655.
      View in: PubMed   Mentions: 2  
    15. Imbalance of Regulatory and Cytotoxic SARS-CoV-2-Reactive CD4+ T Cells in COVID-19. Cell. 2020 11 25; 183(5):1340-1353.e16. Meckiff BJ, Ramírez-Suástegui C, Fajardo V, Chee SJ, Kusnadi A, Simon H, Eschweiler S, Grifoni A, Pelosi E, Weiskopf D, Sette A, Ay F, Seumois G, Ottensmeier CH, Vijayanand P. PMID: 33096020; PMCID: PMC7534589.
      View in: PubMed   Mentions: 279     Fields:    Translation:HumansCells
    16. Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation. Genome Biol. 2020 09 30; 21(1):256. Roayaei Ardakany A, Gezer HT, Lonardi S, Ay F. PMID: 32998764; PMCID: PMC7528378.
      View in: PubMed   Mentions: 52     Fields:    Translation:Cells
    17. Severely ill COVID-19 patients display augmented functional properties in SARS-CoV-2-reactive CD8 + T cells. bioRxiv. 2020 Jul 10. Kusnadi A, Ramírez-Suástegui C, Fajardo V, Chee SJ, Meckiff BJ, Simon H, Pelosi E, Seumois G, Ay F, Vijayanand P, Ottensmeier CH. PMID: 32676602; PMCID: PMC7359524.
      View in: PubMed   Mentions: 2  
    18. Single-Cell Transcriptomic Analysis of SARS-CoV-2 Reactive CD4 + T Cells. SSRN. 2020 Jul 07; 3641939. Meckiff BJ, Ramírez-Suástegui C, Fajardo V, Chee SJ, Kusnadi A, Simon H, Grifoni A, Pelosi E, Weiskopf D, Sette A, Ay F, Seumois G, Ottensmeier CH, Vijayanand P. PMID: 32742242; PMCID: PMC7385998.
      View in: PubMed   Mentions:
    19. Single-cell transcriptomic analysis of SARS-CoV-2 reactive CD4 + T cells. bioRxiv. 2020 Jun 13. Meckiff BJ, Ramírez-Suástegui C, Fajardo V, Chee SJ, Kusnadi A, Simon H, Grifoni A, Pelosi E, Weiskopf D, Sette A, Ay F, Seumois G, Ottensmeier CH, Vijayanand P. PMID: 32587963; PMCID: PMC7310619.
      View in: PubMed   Mentions:
    20. Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2. Nat Protoc. 2020 03; 15(3):991-1012. Kaul A, Bhattacharyya S, Ay F. PMID: 31980751; PMCID: PMC7451401.
      View in: PubMed   Mentions: 65     Fields:    Translation:HumansAnimalsCells
    21. NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains. Nat Commun. 2019 10 24; 10(1):4843. 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. PMID: 31649247; PMCID: PMC6813313.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansCells
    22. Identification of significant chromatin contacts from HiChIP data by FitHiChIP. Nat Commun. 2019 09 17; 10(1):4221. Bhattacharyya S, Chandra V, Vijayanand P, Ay F. PMID: 31530818; PMCID: PMC6748947.
      View in: PubMed   Mentions: 87     Fields:    Translation:AnimalsCells
    23. Replication timing networks reveal a link between transcription regulatory circuits and replication timing control. Genome Res. 2019 09; 29(9):1415-1428. Rivera-Mulia JC, Kim S, Gabr H, Chakraborty A, Ay F, Kahveci T, Gilbert DM. PMID: 31434679; PMCID: PMC6724675.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    24. Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing. Genome Res. 2019 09; 29(9):1521-1532. Zhang S, Wang Y, Jia L, Wen X, Du Z, Wang C, Hao Y, Yu D, Zhou L, Chen N, Chen J, Chen H, Zhang H, Celik I, Gülsoy G, Luo J, Qin B, Cui X, Liu Z, Zhang S, Esteban MA, Ay F, Xu W, Chen R, Li W, Hoffman AR, Hu JF, Cui J. PMID: 31315906; PMCID: PMC6724666.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    25. Selfish: discovery of differential chromatin interactions via a self-similarity measure. Bioinformatics. 2019 07 15; 35(14):i145-i153. Ardakany AR, Ay F, Lonardi S. PMID: 31510653; PMCID: PMC6612869.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    26. Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer. J Exp Med. 2019 09 02; 216(9):2128-2149. Clarke J, Panwar B, Madrigal A, Singh D, Gujar R, Wood O, Chee SJ, Eschweiler S, King EV, Awad AS, Hanley CJ, McCann KJ, Bhattacharyya S, Woo E, Alzetani A, Seumois G, Thomas GJ, Ganesan AP, Friedmann PS, Sanchez-Elsner T, Ay F, Ottensmeier CH, Vijayanand P. PMID: 31227543; PMCID: PMC6719422.
      View in: PubMed   Mentions: 107     Fields:    Translation:HumansCells
    27. Human Eosinophils Express a Distinct Gene Expression Program in Response to IL-3 Compared with Common β-Chain Cytokines IL-5 and GM-CSF. J Immunol. 2019 07 15; 203(2):329-337. Nelson RK, Brickner H, Panwar B, Ramírez-Suástegui C, Herrera-de la Mata S, Liu N, Diaz D, Alexander LEC, Ay F, Vijayanand P, Seumois G, Akuthota P. PMID: 31175163; PMCID: PMC6616007.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    28. TET enzymes augment activation-induced deaminase (AID) expression via 5-hydroxymethylcytosine modifications at the Aicda superenhancer. Sci Immunol. 2019 04 26; 4(34). Lio CJ, Shukla V, Samaniego-Castruita D, González-Avalos E, Chakraborty A, Yue X, Schatz DG, Ay F, Rao A. PMID: 31028100; PMCID: PMC6599614.
      View in: PubMed   Mentions: 43     Fields:    Translation:AnimalsCells
    29. Measuring the reproducibility and quality of Hi-C data. Genome Biol. 2019 03 19; 20(1):57. Yardimci 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, Taylor J, Yue F, Dekker J, Noble WS. PMID: 30890172; PMCID: PMC6423771.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansCells
    30. Reduced expression of phosphatase PTPN2 promotes pathogenic conversion of Tregs in autoimmunity. J Clin Invest. 2019 03 01; 129(3):1193-1210. 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. PMID: 30620725; PMCID: PMC6391091.
      View in: PubMed   Mentions: 27     Fields:    Translation:AnimalsCells
    31. Comparative 3D genome organization in apicomplexan parasites. Proc Natl Acad Sci U S A. 2019 02 19; 116(8):3183-3192. 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. PMID: 30723152; PMCID: PMC6386730.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansAnimalsCells
    32. Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies. Elife. 2019 01 31; 8. Zheng Y, Ay F, Keles S. PMID: 30702424; PMCID: PMC6450682.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    33. Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. Cell. 2019 02 07; 176(4):816-830.e18. 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. PMID: 30595451; PMCID: PMC6546437.
      View in: PubMed   Mentions: 75     Fields:    Translation:AnimalsCells
    34. Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming. Sci Data. 2018 11 20; 5:180255. 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. PMID: 30457566; PMCID: PMC6244186.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    35. Integrative detection and analysis of structural variation in cancer genomes. Nat Genet. 2018 10; 50(10):1388-1398. 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. PMID: 30202056; PMCID: PMC6301019.
      View in: PubMed   Mentions: 147     Fields:    Translation:HumansCells
    36. The Evf2 Ultraconserved Enhancer lncRNA Functionally and Spatially Organizes Megabase Distant Genes in the Developing Forebrain. Mol Cell. 2018 09 20; 71(6):956-972.e9. 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. PMID: 30146317; PMCID: PMC6428050.
      View in: PubMed   Mentions: 35     Fields:    Translation:AnimalsCells
    37. The role of 3D genome organization in disease: From compartments to single nucleotides. Semin Cell Dev Biol. 2019 06; 90:104-113. Chakraborty A, Ay F. PMID: 30017907; PMCID: PMC6335187.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    38. Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages. Nat Commun. 2018 05 15; 9(1):1910. 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. PMID: 29765020; PMCID: PMC5954139.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansAnimalsCells
    39. Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution. Methods. 2018 06 01; 142:59-73. 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. PMID: 29382556; PMCID: PMC5993575.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    40. Identification of copy number variations and translocations in cancer cells from Hi-C data. Bioinformatics. 2018 Jan 15; 34(2):338-345. Chakraborty A, Ay F. PMID: 29048467; PMCID: PMC8210825.
      View in: PubMed   Mentions: 42     Fields:    
    41. PacBio assembly of a Plasmodium knowlesi genome sequence with Hi-C correction and manual annotation of the SICAvar gene family. Parasitology. 2018 01; 145(1):71-84. 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. PMID: 28720171; PMCID: PMC5798397.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    42. Plasmodium knowlesi: a superb in vivo nonhuman primate model of antigenic variation in malaria. Parasitology. 2018 01; 145(1):85-100. Galinski MR, Lapp SA, Peterson MS, Ay F, Joyner CJ, LE Roch KG, Fonseca LL, Voit EO, MAHPIC CONSORTIUM. PMID: 28712361; PMCID: PMC5798396.
      View in: PubMed   Mentions: 20     Fields:    Translation:Animals
    43. 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. Eser U, Chandler-Brown D, Ay F, Straight AF, Duan Z, Noble WS, Skotheim JM. PMID: 28348222; PMCID: PMC5393236.
      View in: PubMed   Mentions: 36     Fields:    Translation:AnimalsCells
    44. 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells. Nat Commun. 2016 11 16; 7:13426. Schmiedel BJ, Seumois G, Samaniego-Castruita D, Cayford J, Schulten V, Chavez L, Ay F, Sette A, Peters B, Vijayanand P. PMID: 27848966; PMCID: PMC5116091.
      View in: PubMed   Mentions: 65     Fields:    Translation:HumansCells
    45. Neocentromeres Provide Chromosome Segregation Accuracy and Centromere Clustering to Multiple Loci along a Candida albicans Chromosome. PLoS Genet. 2016 Sep; 12(9):e1006317. 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. PMID: 27662467; PMCID: PMC5035033.
      View in: PubMed   Mentions: 17     Fields:    
    46. 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. Fotuhi Siahpirani A, Ay F, Roy S. PMID: 27233632; PMCID: PMC4882777.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    47. A predictive modeling approach for cell line-specific long-range regulatory interactions. Nucleic Acids Res. 2016 Feb 29; 44(4):1977-8. Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R. PMID: 26546512; PMCID: PMC4770215.
      View in: PubMed   Mentions: 6     Fields:    
    48. A predictive modeling approach for cell line-specific long-range regulatory interactions. Nucleic Acids Res. 2015 Oct 15; 43(18):8694-712. Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R. PMID: 26338778; PMCID: PMC4605315.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansCells
    49. Analysis methods for studying the 3D architecture of the genome. Genome Biol. 2015 Sep 02; 16:183. Ay F, Noble WS. PMID: 26328929; PMCID: PMC4556012.
      View in: PubMed   Mentions: 77     Fields:    Translation:HumansAnimalsCells
    50. Bipartite structure of the inactive mouse X chromosome. Genome Biol. 2015 Aug 07; 16:152. Deng X, Ma W, Ramani V, Hill A, Yang F, Ay F, Berletch JB, Blau CA, Shendure J, Duan Z, Noble WS, Disteche CM. PMID: 26248554; PMCID: PMC4539712.
      View in: PubMed   Mentions: 125     Fields:    Translation:HumansAnimalsCells
    51. Comprehensive identification and analysis of human accelerated regulatory DNA. Genome Res. 2015 Sep; 25(9):1245-55. Gittelman RM, Hun E, Ay F, Madeoy J, Pennacchio L, Noble WS, Hawkins RD, Akey JM. PMID: 26104583; PMCID: PMC4561485.
      View in: PubMed   Mentions: 54     Fields:    Translation:HumansAnimalsCells
    52. 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. Dileep V, Ay F, Sima J, Vera DL, Noble WS, Gilbert DM. PMID: 25995270; PMCID: PMC4509995.
      View in: PubMed   Mentions: 79     Fields:    Translation:AnimalsCells
    53. Accurate identification of centromere locations in yeast genomes using Hi-C. Nucleic Acids Res. 2015 Jun 23; 43(11):5331-9. Varoquaux N, Liachko I, Ay F, Burton JN, Shendure J, Dunham MJ, Vert JP, Noble WS. PMID: 25940625; PMCID: PMC4477656.
      View in: PubMed   Mentions: 35     Fields:    Translation:AnimalsCells
    54. Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C. BMC Genomics. 2015 Feb 25; 16:121. Ay F, Vu TH, Zeitz MJ, Varoquaux N, Carette JE, Vert JP, Hoffman AR, Noble WS. PMID: 25887659; PMCID: PMC4369351.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansCells
    55. 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. Libbrecht MW, Ay F, Hoffman MM, Gilbert DM, Bilmes JA, Noble WS. PMID: 25677182; PMCID: PMC4381526.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansCells
    56. Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes. Nat Methods. 2015 Jan; 12(1):71-8. 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. PMID: 25437436; PMCID: PMC4281301.
      View in: PubMed   Mentions: 120     Fields:    Translation:HumansCells
    57. 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. Ay F, Bunnik EM, Varoquaux N, Vert JP, Noble WS, Le Roch KG. PMID: 25394267; PMCID: PMC4385791.
      View in: PubMed   Mentions: 26     Fields:    Translation:AnimalsCells
    58. A statistical approach for inferring the 3D structure of the genome. Bioinformatics. 2014 Jun 15; 30(12):i26-33. Varoquaux N, Ay F, Noble WS, Vert JP. PMID: 24931992; PMCID: PMC4229903.
      View in: PubMed   Mentions: 123     Fields:    Translation:AnimalsCells
    59. 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. Ay F, Bunnik EM, Varoquaux N, Bol SM, Prudhomme J, Vert JP, Noble WS, Le Roch KG. PMID: 24671853; PMCID: PMC4032861.
      View in: PubMed   Mentions: 123     Fields:    Translation:AnimalsCells
    60. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res. 2014 Jun; 24(6):999-1011. Ay F, Bailey TL, Noble WS. PMID: 24501021; PMCID: PMC4032863.
      View in: PubMed   Mentions: 240     Fields:    Translation:HumansAnimalsCells
    61. Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome. Nucleus. 2013 Nov-Dec; 4(6):487-93. Zeitz MJ, Lerner PP, Ay F, Van Nostrand E, Heidmann JD, Noble WS, Hoffman AR. PMID: 24448439; PMCID: PMC3925693.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    62. Genomic interaction profiles in breast cancer reveal altered chromatin architecture. PLoS One. 2013; 8(9):e73974. Zeitz MJ, Ay F, Heidmann JD, Lerner PL, Noble WS, Steelman BN, Hoffman AR. PMID: 24019942; PMCID: PMC3760796.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    63. Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks. Genome Res. 2012 Jul; 22(7):1334-49. Marbach D, Roy S, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M. PMID: 22456606; PMCID: PMC3396374.
      View in: PubMed   Mentions: 59     Fields:    Translation:AnimalsCells
    64. Metabolic network alignment in large scale by network compression. BMC Bioinformatics. 2012 Mar 21; 13 Suppl 3:S2. Ay F, Dang M, Kahveci T. PMID: 22536900; PMCID: PMC3402922.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimals
    65. SubMAP: aligning metabolic pathways with subnetwork mappings. J Comput Biol. 2011 Mar; 18(3):219-35. Ay F, Kellis M, Kahveci T. PMID: 21385030; PMCID: PMC3123932.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansAnimals
    66. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24; 330(6012):1787-97. 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. PMID: 21177974; PMCID: PMC3192495.
      View in: PubMed   Mentions: 705     Fields:    Translation:AnimalsCells
    67. Scalable steady state analysis of Boolean biological regulatory networks. PLoS One. 2009 Dec 01; 4(12):e7992. Ay F, Xu F, Kahveci T. PMID: 19956604; PMCID: PMC2779454.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimals
    68. A fast and accurate algorithm for comparative analysis of metabolic pathways. J Bioinform Comput Biol. 2009 Jun; 7(3):389-428. Ay F, Kahveci T, DE Crécy-Lagard V. PMID: 19507283.
      View in: PubMed   Mentions: 6     Fields:    
    69. Consistent alignment of metabolic pathways without abstraction. Comput Syst Bioinformatics Conf. 2008; 7:237-48. Ay F, Kahveci T, de Crécy-Lagard V. PMID: 19642284.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
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