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Ferhat Ay

Photo of 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. Loss of TET function in T regulatory cells yields ex-Treg cells biased toward T follicular helper cells, causing autoimmune diseases through autoantibody production. bioRxiv. 2025 Sep 03. Suzuki K, Arteaga-Vazquez LJ, Reveles BV, Hernández-Espinosa L, López-Moyado IF, Onodera A, Samaniego-Castruita D, Ay F, Lara-Custodio A, Hogan PG, Sepulveda H, Rao A. PMID: 40949964; PMCID: PMC12424951.
      View in: PubMed   Mentions:
    2. Distinct interferon response patterns link to increased transposable element expression in leukocytes of systemic lupus erythematosus patients. bioRxiv. 2025 Aug 12. Arteaga-Vazquez LJ, Sepulveda H, Reveles BV, Suzuki K, Kalunian KC, Ay F, Boothby MR, Rao A. PMID: 40501751; PMCID: PMC12157377.
      View in: PubMed   Mentions:
    3. Single-cell transcriptomics of ventral forebrain progenitors identifies Evf2 enhancer lncRNA-enhancer gene guidance through direct RNA binding and RNP recruitment domains. Nat Commun. 2025 Jul 26; 16(1):6902. Li E, Chakraborty A, Kohtz SJ, Cajigas I, Hinojosa-Gonzalez L, Shiau F, Bertossi R, Vassar RJ, Kessler JA, Ay F, Clark BS, Kohtz JD. PMID: 40715144; PMCID: PMC12297475.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    4. Master transcription-factor binding sites constitute the core of early replication control elements. EMBO J. 2025 Aug; 44(16):4499-4524. Turner JL, Hinojosa-Gonzalez L, Sasaki T, Uchino S, Vouzas A, Soto MS, Chakraborty A, Alexander KE, Fitch CA, Brown AN, Ay F, Gilbert DM. PMID: 40676214; PMCID: PMC12361434.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    5. Soffritto: a deep learning model for predicting high-resolution replication timing. Bioinformatics. 2025 Jul 01; 41(Supplement_1):i580-i589. Bolzan D, Ay F. PMID: 40662815; PMCID: PMC12261407.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    6. Loop Catalog: a comprehensive HiChIP database of human and mouse samples. Genome Biol. 2025 Jun 20; 26(1):175. Reyna J, Fetter K, Ignacio R, Marandi CCA, Ma A, Rao N, Jiang Z, Figueroa DS, Bhattacharyya S, Ay F. PMID: 40542429; PMCID: PMC12180236.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    7. Perspective on recent developments and challenges in regulatory and systems genomics. Bioinform Adv. 2025; 5(1):vbaf106. Zeitlinger J, Roy S, Ay F, Mathelier A, Medina-Rivera A, Mahony S, Sinha S, Ernst J. PMID: 40626041; PMCID: PMC12233095.
      View in: PubMed   Mentions: 1  
    8. Putting computational models of immunity to the test-An invited challenge to predict B.pertussis vaccination responses. PLoS Comput Biol. 2025 Mar; 21(3):e1012927. Shinde P, Willemsen L, Anderson M, Aoki M, Basu S, Burel JG, Cheng P, Ghosh Dastidar S, Dunleavy A, Einav T, Forschmiedt J, Fourati S, Garcia J, Gibson W, Greenbaum JA, Guan L, Guan W, Gygi JP, Ha B, Hou J, Hsiao J, Huang Y, Jansen R, Kakoty B, Kang Z, Kobie JJ, Kojima M, Konstorum A, Lee J, Lewis SA, Li A, Lock EF, Mahita J, Mendes M, Meng H, Neher A, Nili S, Olsen LR, Orfield S, Overton JA, Pai N, Parker C, Qian B, Rasmussen M, Reyna J, Richardson E, Safo S, Sorenson J, Srinivasan A, Thrupp N, Tippalagama R, Trevizani R, Ventz S, Wang J, Wu CC, Ay F, Grant B, Kleinstein SH, Peters B. PMID: 40163550; PMCID: PMC11978014.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCellsPHPublic Health
    9. Genomic Language Model for Predicting Enhancers and Their Allele-Specific Activity in the Human Genome. bioRxiv. 2025 Mar 18. Sathian R, Dutta P, Ay F, Davuluri RV. PMID: 40166250; PMCID: PMC11957021.
      View in: PubMed   Mentions:
    10. Loop Catalog: a comprehensive HiChIP database of human and mouse samples. bioRxiv. 2025 Mar 06. Reyna J, Fetter K, Ignacio R, Ali Marandi CC, Ma A, Rao N, Jiang Z, Figueroa DS, Bhattacharyya S, Ay F. PMID: 38746164; PMCID: PMC11092438.
      View in: PubMed   Mentions:
    11. Master transcription factor binding sites constitute the core of early replication control elements. bioRxiv. 2025 Feb 13. Turner JL, Hinojosa-Gonzalez L, Sasaki T, Uchino S, Vouzas A, Soto MS, Chakraborty A, Alexander KE, Fitch CA, Brown AN, Ay F, Gilbert DM. PMID: 39990485; PMCID: PMC11844392.
      View in: PubMed   Mentions:
    12. nipalsMCIA: flexible multi-block dimensionality reduction in R via nonlinear iterative partial least squares. Bioinformatics. 2024 Dec 26; 41(1). Mattessich M, Reyna J, Aron E, Ay F, Kilmer M, Kleinstein SH, Konstorum A. PMID: 39799512; PMCID: PMC11783316.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    13. Author Correction: Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft. Sci Rep. 2024 Dec 17; 14(1):30519. 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, Harrell JC. PMID: 39690151; PMCID: PMC11652608.
      View in: PubMed   Mentions:    Fields:    
    14. Eosinophilic esophagitis drives tissue fibroblast regenerative programs toward pathologic dysfunction. J Allergy Clin Immunol. 2025 Apr; 155(4):1333-1345. Jumabay M, Abud EM, Okamoto K, Dutta P, Chiang AWT, Li H, Manresa MC, Zhu YP, Frederick D, Kurten R, Croker B, Lewis NE, Kennedy JL, Dohil R, Croft M, Ay F, Wechsler JB, Aceves SS. PMID: 39617290; PMCID: PMC11980045.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    15. Comparison of CD30L and OX40L Reveals CD30L as a Promising Therapeutic Target in Atopic Dermatitis. Allergy. 2025 Feb; 80(2):500-512. Gupta RK, Figueroa DS, Ay F, Causton B, Abdollahi S, Croft M. PMID: 39589186; PMCID: PMC12330979.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    16. Identifying genetic variants associated with chromatin looping and genome function. Nat Commun. 2024 09 18; 15(1):8174. Bhattacharyya S, Ay F. PMID: 39289357; PMCID: PMC11408621.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    17. Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes. bioRxiv. 2024 Sep 08. Shinde P, Willemsen L, Anderson M, Aoki M, Basu S, Burel JG, Cheng P, Dastidar SG, Dunleavy A, Einav T, Forschmiedt J, Fourati S, Garcia J, Gibson W, Greenbaum JA, Guan L, Guan W, Gygi JP, Ha B, Hou J, Hsiao J, Huang Y, Jansen R, Kakoty B, Kang Z, Kobie JJ, Kojima M, Konstorum A, Lee J, Lewis SA, Li A, Lock EF, Mahita J, Mendes M, Meng H, Neher A, Nili S, Olsen LR, Orfield S, Overton JA, Pai N, Parker C, Qian B, Rasmussen M, Reyna J, Richardson E, Safo S, Sorenson J, Srinivasan A, Thrupp N, Tippalagama R, Trevizani R, Ventz S, Wang J, Wu CC, Ay F, Grant B, Kleinstein SH, Peters B. PMID: 39282381; PMCID: PMC11398469.
      View in: PubMed   Mentions:
    18. nipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Non-linear Iterative Partial Least Squares. bioRxiv. 2024 Jun 10. Mattessich M, Reyna J, Aron E, Ay F, Kilmer M, Kleinstein SH, Konstorum A. PMID: 38915554; PMCID: PMC11195050.
      View in: PubMed   Mentions:
    19. Predicting gene expression state and prioritizing putative enhancers using 5hmC signal. Genome Biol. 2024 06 03; 25(1):142. Gonzalez-Avalos E, Onodera A, Samaniego-Castruita D, Rao A, Ay F. PMID: 38825692; PMCID: PMC11145787.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    20. A multi-omics systems vaccinology resource to develop and test computational models of immunity. Cell Rep Methods. 2024 Mar 25; 4(3):100731. Shinde P, Soldevila F, Reyna J, Aoki M, Rasmussen M, Willemsen L, Kojima M, Ha B, Greenbaum JA, Overton JA, Guzman-Orozco H, Nili S, Orfield S, Gygi JP, da Silva Antunes R, Sette A, Grant B, Olsen LR, Konstorum A, Guan L, Ay F, Kleinstein SH, Peters B. PMID: 38490204; PMCID: PMC10985234.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    21. LIGHT signaling through LTβR and HVEM in keratinocytes promotes psoriasis and atopic dermatitis-like skin inflammation. J Autoimmun. 2024 04; 144:103177. Gupta RK, Figueroa DS, Fung K, Miki H, Miller J, Ay F, Croft M. PMID: 38368767; PMCID: PMC12406946.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    22. Chromatin structure and var2csa - a tango in regulation of var gene expression in the human malaria parasite, Plasmodium falciparum? bioRxiv. 2024 Feb 13. Lenz T, Zhang X, Chakraborty A, Ardakany AR, Prudhomme J, Ay F, Deitsch K, Le Roch KG. PMID: 38405848; PMCID: PMC10888805.
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    23. Integrative Keratinocyte Responses to TWEAK with IL-13 and IL-22 Reveal Pathogenic Transcriptomes Associated with Atopic Dermatitis. J Invest Dermatol. 2024 05; 144(5):1071-1074.e6. Gupta RK, Fung K, Figueroa DS, Ay F, Croft M. PMID: 38072390; PMCID: PMC11034708.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    24. Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS. Cell. 2023 11 22; 186(24):5269-5289.e22. Hu Y, Salgado Figueroa D, Zhang Z, Veselits M, Bhattacharyya S, Kashiwagi M, Clark MR, Morgan BA, Ay F, Georgopoulos K. PMID: 37995656; PMCID: PMC10895928.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    25. Atypical B cells consist of subsets with distinct functional profiles. iScience. 2023 Dec 15; 26(12):108496. Reyes RA, Batugedara G, Dutta P, Reers AB, Garza R, Ssewanyana I, Jagannathan P, Feeney ME, Greenhouse B, Bol S, Ay F, Bunnik EM. PMID: 38098745; PMCID: PMC10720271.
      View in: PubMed   Mentions: 9  
    26. Brd2 is dispensable for genome compartmentalization and replication timing. bioRxiv. 2023 Nov 19. Hinojosa-Gonzalez L, Turner JL, Sasaki T, Ay F, Gilbert DM. PMID: 38249518; PMCID: PMC10798648.
      View in: PubMed   Mentions:
    27. 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: 1     Fields:    Translation:Humans
    28. A systems vaccinology resource to develop and test computational models of immunity. bioRxiv. 2023 Aug 29. Shinde P, Soldevila F, Reyna J, Aoki M, Rasmussen M, Willemsen L, Kojima M, Ha B, Greenbaum JA, Overton JA, Guzman-Orozco H, Nili S, Orfield S, Gygi JP, da Silva Antunes R, Sette A, Grant B, Olsen LR, Konstorum A, Guan L, Ay F, Kleinstein SH, Peters B. PMID: 37693565; PMCID: PMC10491180.
      View in: PubMed   Mentions:
    29. Social and moral psychology of COVID-19 across 69 countries. Sci Data. 2023 05 11; 10(1):272. Azevedo F, Pavlovic T, Rêgo GG, Ay FC, Gjoneska B, Etienne TW, Ross RM, Schönegger P, Riaño-Moreno JC, Cichocka A, Capraro V, Cian L, Longoni C, Chan HF, Van Bavel JJ, Sjåstad H, Nezlek JB, Alfano M, Gelfand MJ, Birtel MD, Cislak A, Lockwood PL, Abts K, Agadullina E, Aruta JJB, Besharati SN, Bor A, Choma BL, Crabtree CD, Cunningham WA, De K, Ejaz W, Elbaek CT, Findor A, Flichtentrei D, Franc R, Gruber J, Gualda E, Horiuchi Y, Huynh TLD, Ibanez A, Imran MA, Israelashvili J, Jasko K, Kantorowicz J, Kantorowicz-Reznichenko E, Krouwel A, Laakasuo M, Lamm C, Leygue C, Lin MJ, Mansoor MS, Marie A, Mayiwar L, Mazepus H, McHugh C, Minda JP, Mitkidis P, Olsson A, Otterbring T, Packer DJ, Perry A, Petersen MB, Puthillam A, Rothmund T, Santamaría-García H, Schmid PC, Stoyanov D, Tewari S, Todosijevic B, Tsakiris M, Tung HH, Umbres RG, Vanags E, Vlasceanu M, Vonasch A, Yucel M, Zhang Y, Abad M, Adler E, Akrawi N, Mdarhri HA, Amara H, Amodio DM, Antazo BG, Apps M, Ba MH, Barbosa S, Bastian B, Berg A, Bernal-Zárate MP, Bernstein M, Bialek M, Bilancini E, Bogatyreva N, Boncinelli L, Booth JE, Borau S, Buchel O, Cameron CD, Carvalho CF, Celadin T, Cerami C, Chalise HN, Cheng X, Cockcroft K, Conway J, Córdoba-Delgado MA, Crespi C, Crouzevialle M, Cutler J, Cypryanska M, Dabrowska J, Daniels MA, Davis VH, Dayley PN, Delouvée S, Denkovski O, Dezecache G, Dhaliwal NA, Diato AB, Di Paolo R, Drosinou M, Dulleck U, Ekmanis J, Ertan AS, Farhana HH, Farkhari F, Farmer H, Fenwick A, Fidanovski K, Flew T, Fraser S, Frempong RB, Fugelsang JA, Gale J, Garcia-Navarro EB, Garladinne P, Ghajjou O, Gkinopoulos T, Gray K, Griffin SM, Gronfeldt B, Gümren M, Gurung RL, Halperin E, Harris E, Herzon V, Hruška M, Huang G, Hudecek MFC, Isler O, Jangard S, Jorgensen FJ, Kachanoff F, Kahn J, Dangol AK, Keudel O, Koppel L, Koverola M, Kubin E, Kunnari A, Kutiyski Y, Laguna OM, Leota J, Lermer E, Levy J, Levy N, Li C, Long EU, Maglic M, McCashin D, Metcalf AL, Mikloušic I, El Mimouni S, Miura A, Molina-Paredes J, Monroy-Fonseca C, Morales-Marente E, Moreau D, Muda R, Myer A, Nash K, Nesh-Nash T, Nitschke JP, Nurse MS, Ohtsubo Y, de Mello VO, O'Madagain C, Onderco M, Palacios-Galvez MS, Palomöki J, Pan Y, Papp Z, Pärnamets P, Paruzel-Czachura M, Pavlovic Z, Payán-Gómez C, Perander S, Pitman MM, Prasad R, Pyrkosz-Pacyna J, Rathje S, Raza A, Rhee K, Robertson CE, Rodríguez-Pascual I, Saikkonen T, Salvador-Ginez O, Santi GC, Santiago-Tovar N, Savage D, Scheffer JA, Schultner DT, Schutte EM, Scott A, Sharma M, Sharma P, Skali A, Stadelmann D, Stafford CA, Stanojevic D, Stefaniak A, Sternisko A, Stoica A, Stoyanova KK, Strickland B, Sundvall J, Thomas JP, Tinghög G, Torgler B, Traast IJ, Tucciarelli R, Tyrala M, Ungson ND, Uysal MS, Van Lange PAM, van Prooijen JW, van Rooy D, Västfjäll D, Verkoeijen P, Vieira JB, von Sikorski C, Walker AC, Watermeyer J, Wetter E, Whillans A, White K, Habib R, Willardt R, Wohl MJA, Wójcik AD, Wu K, Yamada Y, Yilmaz O, Yogeeswaran K, Ziemer CT, Zwaan RA, Boggio PS, Sampaio WM. PMID: 37169799; PMCID: PMC10173241.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansPHPublic Health
    30. Publisher Correction: Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft. Sci Rep. 2023 May 09; 13(1):7522. 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, Harrell JC. PMID: 37160896; PMCID: PMC10170154.
      View in: PubMed   Mentions: 1     Fields:    
    31. 3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. Nat Commun. 2023 04 21; 14(1):2300. Okonechnikov K, Camgöz A, Chapman O, Wani S, Park DE, Hübner JM, Chakraborty A, Pagadala M, Bump R, Chandran S, Kraft K, Acuna-Hidalgo R, Reid D, Sikkink K, Mauermann M, Juarez EF, Jenseit A, Robinson JT, Pajtler KW, Milde T, Jäger N, Fiesel P, Morgan L, Sridhar S, Coufal NG, Levy M, Malicki D, Hobbs C, Kingsmore S, Nahas S, Snuderl M, Crawford J, Wechsler-Reya RJ, Davidson TB, Cotter J, Michaiel G, Fleischhack G, Mundlos S, Schmitt A, Carter H, Michealraj KA, Kumar SA, Taylor MD, Rich J, Buchholz F, Mesirov JP, Pfister SM, Ay F, Dixon JR, Kool M, Chavez L. PMID: 37085539; PMCID: PMC10121654.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    32. Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft. Sci Rep. 2023 04 03; 13(1):5420. 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, Harrell JC. PMID: 37012431; PMCID: PMC10070455.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    33. Lymphotoxin beta receptor signaling directly controls airway smooth muscle deregulation and asthmatic lung dysfunction. J Allergy Clin Immunol. 2023 04; 151(4):976-990.e5. Miki H, Kiosses WB, Manresa MC, Gupta RK, Sethi GS, Herro R, Da Silva Antunes R, Dutta P, Miller M, Fung K, Chawla A, Dobaczewska K, Ay F, Broide DH, Tumanov AV, Croft M. PMID: 36473503; PMCID: PMC10081945.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    34. dcHiC detects differential compartments across multiple Hi-C datasets. Nat Commun. 2022 11 11; 13(1):6827. Chakraborty A, Wang JG, Ay F. PMID: 36369226; PMCID: PMC9652325.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansAnimalsCells
    35. A double-negative thymocyte-specific enhancer augments Notch1 signaling to direct early T cell progenitor expansion, lineage restriction and β-selection. Nat Immunol. 2022 11; 23(11):1628-1643. Kashiwagi M, Figueroa DS, Ay F, Morgan BA, Georgopoulos K. PMID: 36316479; PMCID: PMC10187983.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    36. Intermittent PI3Kδ inhibition sustains anti-tumour immunity and curbs irAEs. Nature. 2022 05; 605(7911):741-746. Eschweiler S, Ramírez-Suástegui C, Li Y, King E, Chudley L, Thomas J, Wood O, von Witzleben A, Jeffrey D, McCann K, Simon H, Mondal M, Wang A, Dicker M, Lopez-Guadamillas E, Chou TF, Dobbs NA, Essame L, Acton G, Kelly F, Halbert G, Sacco JJ, Schache AG, Shaw R, McCaul JA, Paterson C, Davies JH, Brennan PA, Singh RP, Loadman PM, Wilson W, Hackshaw A, Seumois G, Okkenhaug K, Thomas GJ, Jones TM, Ay F, Friberg G, Kronenberg M, Vanhaesebroeck B, Vijayanand P, Ottensmeier CH. PMID: 35508656; PMCID: PMC9132770.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansAnimalsCellsCTClinical Trials
    37. Author Correction: National identity predicts public health support during a global pandemic. Nat Commun. 2022 Apr 06; 13(1):1949. Van Bavel JJ, Cichocka A, Capraro V, Sjåstad H, Nezlek JB, Pavlovic T, Alfano M, Gelfand MJ, Azevedo F, Birtel MD, Cislak A, Lockwood PL, Ross RM, Abts K, Agadullina E, Aruta JJB, Besharati SN, Bor A, Choma BL, Crabtree CD, Cunningham WA, De K, Ejaz W, Elbaek CT, Findor A, Flichtentrei D, Franc R, Gjoneska B, Gruber J, Gualda E, Horiuchi Y, Huynh TLD, Ibanez A, Imran MA, Israelashvili J, Jasko K, Kantorowicz J, Kantorowicz-Reznichenko E, Krouwel A, Laakasuo M, Lamm C, Leygue C, Lin MJ, Mansoor MS, Marie A, Mayiwar L, Mazepus H, McHugh C, Minda JP, Mitkidis P, Olsson A, Otterbring T, Packer DJ, Perry A, Petersen MB, Puthillam A, Riaño-Moreno JC, Rothmund T, Santamaría-García H, Schmid PC, Stoyanov D, Tewari S, Todosijevic B, Tsakiris M, Tung HH, Umbre? RG, Vanags E, Vlasceanu M, Vonasch A, Yucel M, Zhang Y, Abad M, Adler E, Akrawi N, Mdarhri HA, Amara H, Amodio DM, Antazo BG, Apps M, Ay FC, Ba MH, Barbosa S, Bastian B, Berg A, Bernal-Zárate MP, Bernstein M, Bialek M, Bilancini E, Bogatyreva N, Boncinelli L, Booth JE, Borau S, Buchel O, Cameron CD, Carvalho CF, Celadin T, Cerami C, Chalise HN, Cheng X, Cian L, Cockcroft K, Conway J, Córdoba-Delgado MA, Crespi C, Crouzevialle M, Cutler J, Cypryanska M, Dabrowska J, Daniels MA, Davis VH, Dayley PN, Delouvee S, Denkovski O, Dezecache G, Dhaliwal NA, Diato AB, Di Paolo R, Drosinou M, Dulleck U, Ekmanis J, Ertan AS, Etienne TW, Farhana HH, Farkhari F, Farmer H, Fenwick A, Fidanovski K, Flew T, Fraser S, Frempong RB, Fugelsang JA, Gale J, Garcia-Navarro EB, Garladinne P, Ghajjou O, Gkinopoulos T, Gray K, Griffin SM, Gronfeldt B, Gümren M, Gurung RL, Halperin E, Harris E, Herzon V, Hruška M, Huang G, Hudecek MFC, Isler O, Jangard S, Jørgensen FJ, Kachanoff F, Kahn J, Dangol AK, Keudel O, Koppel L, Koverola M, Kubin E, Kunnari A, Kutiyski Y, Laguna O, Leota J, Lermer E, Levy J, Levy N, Li C, Long EU, Longoni C, Maglic M, McCashin D, Metcalf AL, Mikloušic I, El Mimouni S, Miura A, Molina-Paredes J, Monroy-Fonseca C, Morales-Marente E, Moreau D, Muda R, Myer A, Nash K, Nesh-Nash T, Nitschke JP, Nurse MS, Ohtsubo Y, Oldemburgo de Mello V, O'Madagain C, Onderco M, Palacios-Galvez MS, Palomäki J, Pan Y, Papp Z, Pärnamets P, Paruzel-Czachura M, Pavlovic Z, Payán-Gómez C, Perander S, Pitman MM, Prasad R, Pyrkosz-Pacyna J, Rathje S, Raza A, Rêgo GG, Rhee K, Robertson CE, Rodríguez-Pascual I, Saikkonen T, Salvador-Ginez O, Sampaio WM, Santi GC, Santiago-Tovar N, Savage D, Scheffer JA, Schönegger P, Schultner DT, Schutte EM, Scott A, Sharma M, Sharma P, Skali A, Stadelmann D, Stafford CA, Stanojevic D, Stefaniak A, Sternisko A, Stoica A, Stoyanova KK, Strickland B, Sundvall J, Thomas JP, Tinghög G, Torgler B, Traast IJ, Tucciarelli R, Tyrala M, Ungson ND, Uysal MS, Van Lange PAM, van Prooijen JW, van Rooy D, Västfjäll D, Verkoeijen P, Vieira JB, von Sikorski C, Walker AC, Watermeyer J, Wetter E, Whillans A, Willardt R, Wohl MJA, Wójcik AD, Wu K, Yamada Y, Yilmaz O, Yogeeswaran K, Ziemer CT, Zwaan RA, Boggio PS. PMID: 35388016; PMCID: PMC8986871.
      View in: PubMed   Mentions:    Fields:    
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    39. Pluripotency exit is guided by the Peln1-mediated disruption of intrachromosomal architecture. J Cell Biol. 2022 04 04; 221(4). 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, Zhang S, Li W, Cui J, Hoffman AR, Guo H, Hu JF. PMID: 35171230; PMCID: PMC8855478.
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    44. 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.
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    49. 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.
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    50. 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.
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    52. 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.
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    65. 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.
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    66. 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.
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    69. 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.
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    70. 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.
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    71. 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.
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    72. 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.
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    75. 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.
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    76. 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: 20     Fields:    Translation:HumansCells
    77. 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: 68     Fields:    Translation:HumansAnimalsCells
    78. 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: 11     Fields:    Translation:Cells
    79. 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: 53     Fields:    
    80. 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: 27     Fields:    Translation:AnimalsCells
    81. 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: 22     Fields:    Translation:Animals
    82. 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: 46     Fields:    Translation:AnimalsCells
    83. 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: 81     Fields:    Translation:HumansCells
    84. 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: 20     Fields:    
    85. 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: 13     Fields:    Translation:HumansAnimalsCells
    86. 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: 7     Fields:    
    87. 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: 65     Fields:    Translation:HumansCells
    88. 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: 84     Fields:    Translation:HumansAnimalsCells
    89. 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: 149     Fields:    Translation:HumansAnimalsCells
    90. 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: 61     Fields:    Translation:HumansAnimalsCells
    91. 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: 86     Fields:    Translation:AnimalsCells
    92. 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: 43     Fields:    Translation:AnimalsCells
    93. 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: 32     Fields:    Translation:HumansCells
    94. 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: 49     Fields:    Translation:HumansCells
    95. 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: 131     Fields:    Translation:HumansCells
    96. 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: 29     Fields:    Translation:AnimalsCells
    97. 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: 141     Fields:    Translation:AnimalsCells
    98. 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: 134     Fields:    Translation:AnimalsCells
    99. 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: 286     Fields:    Translation:HumansAnimalsCells
    100. 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: 11     Fields:    Translation:HumansCells
    101. 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: 28     Fields:    Translation:HumansCells
    102. 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: 68     Fields:    Translation:AnimalsCells
    103. 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: 6     Fields:    Translation:HumansAnimals
    104. 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: 33     Fields:    Translation:HumansAnimals
    105. 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: 762     Fields:    Translation:AnimalsCells
    106. 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: 12     Fields:    Translation:HumansAnimals
    107. 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:    
    108. 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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