| Year |
Citation |
Score |
| 2024 |
Reyna J, Fetter K, Ignacio R, Ali Marandi CC, Rao N, Jiang Z, Figueroa DS, Bhattacharyya S, Ay F. Loop Catalog: a comprehensive HiChIP database of human and mouse samples. Biorxiv : the Preprint Server For Biology. PMID 38746164 DOI: 10.1101/2024.04.26.591349 |
0.361 |
|
| 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 |
0.34 |
|
| 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 |
0.401 |
|
| 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 |
0.529 |
|
| 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 |
0.604 |
|
| 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 |
0.769 |
|
| 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 |
0.786 |
|
| 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 |
0.343 |
|
| 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 |
0.711 |
|
| 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 |
0.42 |
|
| 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 |
0.409 |
|
| 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 |
0.779 |
|
| 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 |
0.494 |
|
| 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 |
0.571 |
|
| 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 |
0.689 |
|
| 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 |
0.4 |
|
| 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 |
0.415 |
|
| 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 |
0.421 |
|
| 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 |
0.392 |
|
| 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 |
0.464 |
|
| 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 |
0.631 |
|
| 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 |
0.757 |
|
| 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 |
0.612 |
|
| 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 |
0.678 |
|
| 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 |
0.673 |
|
| 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 |
0.543 |
|
| 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 |
0.595 |
|
| 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 |
0.643 |
|
| 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 |
0.63 |
|
| 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 |
0.589 |
|
| 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 |
0.544 |
|
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