Calculated based on number of publications stored in Pure and citations from Scopus
Calculated based on number of publications stored in Pure and citations from Scopus
Calculated based on number of publications stored in Pure and citations from Scopus
20072025

Research activity per year

Search results

  • 2020

    Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells

    Hardison, R. C., Zhang, Y., Keller, C. A., Xiang, G., Heuston, E. F., An, L., Lichtenberg, J., Giardine, B. M., Bodine, D., Mahony, S., Li, Q., Yue, F., Weiss, M. J., Blobel, G. A., Taylor, J., Hughes, J., Higgs, D. R. & Göttgens, B., Jan 1 2020, In: IUBMB Life. 72, 1, p. 27-38 12 p.

    Research output: Contribution to journalReview articlepeer-review

    Open Access
    5 Scopus citations
  • 2019

    Ikaros tumor suppressor function includes induction of active enhancers and super-enhancers along with pioneering activity

    Ding, Y., Zhang, B., Payne, J. L., Song, C., Ge, Z., Gowda, C., Iyer, S., Dhanyamraju, P. K., Dorsam, G., Reeves, M. E., Desai, D., Huang, S., Payne, K. J., Yue, F. & Dovat, S., Nov 1 2019, In: Leukemia. 33, 11, p. 2720-2731 12 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    32 Scopus citations
  • Measuring the reproducibility and quality of Hi-C data

    Yardımcı, G. G., Ozadam, H., Sauria, M. E. G., Ursu, O., Yan, K. K., Yang, T., Chakraborty, A., Kaul, A., Lajoie, B. R., Song, F., Zhan, Y., Ay, F., Gerstein, M., Kundaje, A., Li, Q., Taylor, J., Yue, F., Dekker, J. & Noble, W. S., Mar 19 2019, In: Genome biology. 20, 1, 57.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    98 Scopus citations
  • 2018

    CD4 T cells control development and maintenance of brain-resident CD8 T cells during polyomavirus infection

    Mockus, T. E., Shwetank, Lauver, M. D., Ren, H. M., Netherby, C. S., Salameh, T., Kawasawa, Y. I., Yue, F., Broach, J. R. & Lukacher, A. E., Oct 2018, In: PLoS pathogens. 14, 10, e1007365.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    28 Scopus citations
  • Dynamic chromatin accessibility unveils a regulatory landscape in early embryogenesis in human

    Liu, T. & Yue, F., Dec 1 2018, In: Biology of reproduction. 99, 6, p. 1116-1118 3 p.

    Research output: Contribution to journalComment/debatepeer-review

    Open Access
  • Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus

    Zhang, Y., An, L., Xu, J., Zhang, B., Zheng, W. J., Hu, M., Tang, J. & Yue, F., Dec 1 2018, In: Nature communications. 9, 1, 750.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    133 Scopus citations
  • Integrative detection and analysis of structural variation in cancer genomes

    Dixon, J. R., Xu, J., Dileep, V., Zhan, Y., Song, F., Le, V. T., Yardımcı, G. G., Chakraborty, A., Bann, D. V., Wang, Y., Clark, R., Zhang, L., Yang, H., Liu, T., Iyyanki, S., An, L., Pool, C., Sasaki, T., Rivera-Mulia, J. C. & Ozadam, H. & 17 others, Lajoie, B. R., Kaul, R., Buckley, M., Lee, K., Diegel, M., Pezic, D., Ernst, C., Hadjur, S., Odom, D. T., Stamatoyannopoulos, J. A., Broach, J. R., Hardison, R. C., Ay, F., Noble, W. S., Dekker, J., Gilbert, D. M. & Yue, F., Oct 1 2018, In: Nature Genetics. 50, 10, p. 1388-1398 11 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    232 Scopus citations
  • The 3D Genome Browser: A web-based browser for visualizing 3D genome organization and long-range chromatin interactions

    Wang, Y., Song, F., Zhang, B., Zhang, L., Xu, J., Kuang, D., Li, D., Choudhary, M. N. K., Li, Y., Hu, M., Hardison, R., Wang, T. & Yue, F., Oct 4 2018, In: Genome biology. 19, 1, 151.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    329 Scopus citations
  • 2017

    Corrigendum: The 4D nucleome project (Nature (2017) 549 (219-226) DOI: 10.1038/nature23884)

    4D Nucleome Network, Dec 14 2017, In: Nature. 552, 7684, p. 278 1 p.

    Research output: Contribution to journalComment/debatepeer-review

    Open Access
    4 Scopus citations
  • HiCComp: Multiple-level comparative analysis of Hi-C data by triplet network

    Zhang, Y., Zhang, B., Zheng, W. J., Tang, J. & Yue, F., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C.-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 92-96 5 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

    Yang, T., Zhang, F., Yardımci, G. G., Song, F., Hardison, R. C., Noble, W. S., Yue, F. & Li, Q., Nov 2017, In: Genome research. 27, 11, p. 1939-1949 11 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    280 Scopus citations
  • Identification of a rare LAMB4 variant associated with familial diverticulitis through exome sequencing

    Coble, J. L., Yue, F., Salameh, T. J., Harris, L. R., Deiling, S., Ruggiero, F. M., Eshelman, M. A., Yochum, G. S., Koltun, W. A., Gerhard, G. S. & Broach, J. R., Aug 15 2017, In: Human molecular genetics. 26, 16, p. 3212-3220 9 p., ddx204.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    29 Scopus citations
  • 2016

    FOXA1, GATA3 and PPARIγ Cooperate to drive luminal subtype in bladder cancer: A molecular analysis of established human cell lines

    Warrick, J. I., Walter, V., Yamashita, H., Chung, E., Shuman, L., Amponsa, V. O., Zheng, Z., Chan, W., Whitcomb, T. L., Yue, F., Iyyanki, T., Kawasawa, Y. I., Kaag, M., Guo, W., Raman, J. D., Park, J. S. & Degraff, D. J., Dec 7 2016, In: Scientific reports. 6, 38531.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    103 Scopus citations
  • HiView: An integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants

    Xu, Z., Zhang, G., Duan, Q., Chai, S., Zhang, B., Wu, C., Jin, F., Yue, F., Li, Y. & Hu, M., Mar 11 2016, In: BMC Research Notes. 9, 1, 159.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    10 Scopus citations
  • Jointly characterizing epigenetic dynamics across multiple human cell types

    Zhang, Y., An, L., Yue, F. & Hardison, R. C., Aug 19 2016, In: Nucleic acids research. 44, 14, p. 6721-6731 11 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    57 Scopus citations
  • Transcriptional enhancers: Bridging the genome and phenome

    Ren, B. & Yue, F., 2016, 21st Century Genetics Genes at Work, 2015. Grodzicker, T., Stillman, B. & Stewart, D. (eds.). Cold Spring Harbor Laboratory Press, p. 17-26 10 p. (Cold Spring Harbor Symposia on Quantitative Biology; vol. 80).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Open Access
    22 Scopus citations
  • 2015

    Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates

    Wang, A., Yue, F., Li, Y., Xie, R., Harper, T., Patel, N. A., Muth, K., Palmer, J., Qiu, Y., Wang, J., Lam, D. K., Raum, J. C., Stoffers, D. A., Ren, B. & Sander, M., Apr 2 2015, In: Cell stem cell. 16, 4, p. 386-399 14 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    181 Scopus citations
  • Integrative analysis of haplotype-resolved epigenomes across human tissues

    Leung, D., Jung, I., Rajagopal, N., Schmitt, A., Selvaraj, S., Lee, A. Y., Yen, C. A., Lin, S., Lin, Y., Qiu, Y., Xie, W., Yue, F., Hariharan, M., Ray, P., Kuan, S., Edsall, L., Yang, H., Chi, N. C., Zhang, M. Q. & Ecker, J. R. & 1 others, Ren, B., Feb 19 2015, In: Nature. 518, 7539, p. 350-354 5 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    168 Scopus citations
  • Lymphoid neoplasia: A genome-wide association study of susceptibility to acute lymphoblastic leukemia in adolescents and young adults

    Perez-Andreu, V., Roberts, K. G., Xu, H., Smith, C., Zhang, H., Yang, W., Harvey, R. C., Payne-Turner, D., Devidas, M., Cheng, I. M., Carroll, W. L., Heerema, N. A., Carroll, A. J., Raetz, E. A., Gastier-Foster, J. M., Marcucci, G., Bloomfield, C. D., Mrózek, K., Kohlschmidt, J. & Stock, W. & 21 others, Kornblau, S. M., Konopleva, M., Paietta, E., Rowe, J. M., Luger, S. M., Tallman, M. S., Dean, M., Burchard, E. G., Torgerson, D. G., Yue, F., Wang, Y., Pui, C. H., Jeha, S., Relling, M. V., Evans, W. E., Gerhard, D. S., Loh, M. L., Willman, C. L., Hunger, S. P., Mullighan, C. G. & Yang, J. J., Jan 22 2015, In: Blood. 125, 4, p. 680-686 7 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    95 Scopus citations
  • 2014

    A comparative encyclopedia of DNA elements in the mouse genome

    Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., Sandstrom, R., Ma, Z., Davis, C., Pope, B. D., Shen, Y., Pervouchine, D. D., Djebali, S., Thurman, R. E., Kaul, R., Rynes, E., Kirilusha, A., Marinov, G. K., Williams, B. A. & Trout, D. & 117 others, Amrhein, H., Fisher-Aylor, K., Antoshechkin, I., DeSalvo, G., See, L. H., Fastuca, M., Drenkow, J., Zaleski, C., Dobin, A., Prieto, P., Lagarde, J., Bussotti, G., Tanzer, A., Denas, O., Li, K., Bender, M. A., Zhang, M., Byron, R., Groudine, M. T., McCleary, D., Pham, L., Ye, Z., Kuan, S., Edsall, L., Wu, Y. C., Rasmussen, M. D., Bansal, M. S., Kellis, M., Keller, C. A., Morrissey, C. S., Mishra, T., Jain, D., Dogan, N., Harris, R. S., Cayting, P., Kawli, T., Boyle, A. P., Euskirchen, G., Kundaje, A., Lin, S., Lin, Y., Jansen, C., Malladi, V. S., Cline, M. S., Erickson, D. T., Kirkup, V. M., Learned, K., Sloan, C. A., Rosenbloom, K. R., De Sousa, B. L., Beal, K., Pignatelli, M., Flicek, P., Lian, J., Kahveci, T., Lee, D., Kent, W. J., Santos, M. R., Herrero, J., Notredame, C., Johnson, A., Vong, S., Lee, K., Bates, D., Neri, F., Diegel, M., Canfield, T., Sabo, P. J., Wilken, M. S., Reh, T. A., Giste, E., Shafer, A., Kutyavin, T., Haugen, E., Dunn, D., Reynolds, A. P., Neph, S., Humbert, R., Hansen, R. S., De Bruijn, M., Selleri, L., Rudensky, A., Josefowicz, S., Samstein, R., Eichler, E. E., Orkin, S. H., Levasseur, D., Papayannopoulou, T., Chang, K. H., Skoultchi, A., Gosh, S., Disteche, C., Treuting, P., Wang, Y., Weiss, M. J., Blobel, G. A., Cao, X., Zhong, S., Wang, T., Good, P. J., Lowdon, R. F., Adams, L. B., Zhou, X. Q., Pazin, M. J., Feingold, E. A., Wold, B., Taylor, J., Mortazavi, A., Weissman, S. M., Stamatoyannopoulos, J. A., Snyder, M. P., Guigo, R., Gingeras, T. R., Gilbert, D. M., Hardison, R. C., Beer, M. A. & Ren, B., Nov 20 2014, In: Nature. 515, 7527, p. 355-364 10 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    1248 Scopus citations
  • Topologically associating domains are stable units of replication-timing regulation

    Pope, B. D., Ryba, T., Dileep, V., Yue, F., Wu, W., Denas, O., Vera, D. L., Wang, Y., Hansen, R. S., Canfield, T. K., Thurman, R. E., Cheng, Y., Gülsoy, G., Dennis, J. H., Snyder, M. P., Stamatoyannopoulos, J. A., Taylor, J., Hardison, R. C., Kahveci, T. & Ren, B. & 1 others, Gilbert, D. M., Nov 20 2014, In: Nature. 515, 7527, p. 402-405 4 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    633 Scopus citations
  • 2013

    Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

    Hon, G. C., Rajagopal, N., Shen, Y., McCleary, D. F., Yue, F., Dang, M. D. & Ren, B., Oct 2013, In: Nature Genetics. 45, 10, p. 1198-1206 9 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    369 Scopus citations
  • Inherited GATA3 variants are associated with Ph-like childhood acute lymphoblastic leukemia and risk of relapse

    Perez-Andreu, V., Roberts, K. G., Harvey, R. C., Yang, W., Cheng, C., Pei, D., Xu, H., Gastier-Foster, J., Shuyu, E., Lim, J. Y. S., Chen, I. M., Fan, Y., Devidas, M., Borowitz, M. J., Smith, C., Neale, G., Burchard, E. G., Torgerson, D. G., Klussmann, F. A. & Villagran, C. R. N. & 18 others, Winick, N. J., Camitta, B. M., Raetz, E., Wood, B., Yue, F., Carroll, W. L., Larsen, E., Bowman, W. P., Loh, M. L., Dean, M., Bhojwani, D., Pui, C. H., Evans, W. E., Relling, M. V., Hunger, S. P., Willman, C. L., Mullighan, C. G. & Yang, J. J., Dec 2013, In: Nature Genetics. 45, 12, p. 1494-1498 5 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    248 Scopus citations
  • 2012

    A map of the cis-regulatory sequences in the mouse genome

    Shen, Y., Yue, F., Mc Cleary, D. F., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Ren, B. & Lobanenkov, V. V., Aug 2 2012, In: Nature. 488, 7409, p. 116-120 5 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    1073 Scopus citations
  • Ancestral and conserved cis-regulatory architectures in developmental control genes

    Rebeiz, M., Castro, B., Liu, F., Yue, F. & Posakony, J. W., Feb 15 2012, In: Developmental Biology. 362, 2, p. 282-294 13 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    14 Scopus citations
  • An encyclopedia of mouse DNA elements (Mouse ENCODE)

    Stamatoyannopoulos, J. A., Snyder, M., Hardison, R., Ren, B., Gingeras, T., Gilbert, D. M., Groudine, M., Bender, M., Kaul, R., Canfield, T., Giste, E., Johnson, A., Zhang, M., Balasundaram, G., Byron, R., Roach, V., Sabo, P. J., Sandstrom, R., Stehling, A. S. & Thurman, R. E. & 66 others, Weissman, S. M., Cayting, P., Hariharan, M., Lian, J., Cheng, Y., Landt, S. G., Ma, Z., Wold, B. J., Dekker, J., Crawford, G. E., Keller, C. A., Wu, W., Morrissey, C., Kumar, S. A., Mishra, T., Jain, D., Byrska-Bishop, M., Blankenberg, D., Lajoiel, B. R., Jain, G., Sanyal, A., Chen, K. B., Denas, O., Taylor, J., Blobel, G. A., Weiss, M. J., Pimkin, M., Deng, W., Marinov, G. K., Williams, B. A., Fisher-Aylor, K. I., Desalvo, G., Kiralusha, A., Trout, D., Amrhein, H., Mortazavi, A., Edsall, L., McCleary, D., Kuan, S., Shen, Y., Yue, F., Ye, Z., Davis, C. A., Zaleski, C., Jha, S., Xue, C., Dobin, A., Lin, W., Fastuca, M., Wang, H., Guigo, R., Djebali, S., Lagarde, J., Ryba, T., Sasaki, T., Malladi, V. S., Cline, M. S., Kirkup, V. M., Learned, K., Rosenbloom, K. R., Kent, W. J., Feingold, E. A., Good, P. J., Pazin, M., Lowdon, R. F. & Adams, L. B., Aug 13 2012, In: Genome biology. 13, 8, 418.

    Research output: Contribution to journalLetterpeer-review

    Open Access
    357 Scopus citations
  • Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome

    Xie, W., Barr, C. L., Kim, A., Yue, F., Lee, A. Y., Eubanks, J., Dempster, E. L. & Ren, B., Feb 17 2012, In: Cell. 148, 4, p. 816-831 16 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    434 Scopus citations
  • Topological domains in mammalian genomes identified by analysis of chromatin interactions

    Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S. & Ren, B., May 17 2012, In: Nature. 485, 7398, p. 376-380 5 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    4763 Scopus citations
  • 2009

    A space-efficient algorithm for three sequence alignment and ancestor inference

    Yue, F. & Tang, J., 2009, In: International Journal of Data Mining and Bioinformatics. 3, 2, p. 192-204 13 p.

    Research output: Contribution to journalArticlepeer-review

    4 Scopus citations
  • Simultaneous phylogeny reconstruction and multiple sequence alignment

    Yue, F., Shi, J. & Tang, J., Jan 30 2009, In: BMC bioinformatics. 10, SUPPL. 1, S11.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    16 Scopus citations
  • 2008

    A new approach for tree alignment based on local re-optimization

    Yue, F. & Tang, J., Sep 17 2008, BioMedical Engineering and Informatics: New Development and the Future - Proceedings of the 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008. p. 34-38 5 p. 4548631. (BioMedical Engineering and Informatics: New Development and the Future - Proceedings of the 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008; vol. 1).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    3 Scopus citations
  • Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat

    Yue, F., Cui, L., dePamphilis, C. W., Moret, B. M. E. & Tang, J., Mar 20 2008, In: BMC Genomics. 9, SUPPL. 1, S25.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    36 Scopus citations
  • Phylogenetic reconstruction from transpositions

    Yue, F., Zhang, M. & Tang, J., Sep 16 2008, In: BMC Genomics. 9, SUPPL. 2, S15.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    9 Scopus citations
  • 2007

    A divide-and-conquer implementation of three sequence alignment and ancestor inference

    Yue, F. & Tang, J., 2007, Proceedings - 2007 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2007. p. 143-150 8 p. 4413048. (Proceedings - 2007 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2007).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    9 Scopus citations
  • A heuristic for phylogenetic reconstruction using transposition

    Yue, F., Zhang, M. & Tang, J., 2007, Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE. p. 802-808 7 p. 4375652. (Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations