| Year |
Citation |
Score |
| 2024 |
Duan Z, Xu S, Sai Srinivasan S, Hwang A, Lee CY, Yue F, Gerstein M, Luan Y, Girgenti M, Zhang J. scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding. Briefings in Bioinformatics. 25. PMID 38493342 DOI: 10.1093/bib/bbae096 |
0.329 |
|
| 2024 |
Szczepanski A, Tsuboyama N, Lyu H, Wang P, Beytullahoglu O, Zhang T, Singer BD, Yue F, Zhao Z, Wang L. A SWI/SNF-dependent transcriptional regulation mediated by POU2AF2/C11orf53 at enhancer. Nature Communications. 15: 2067. PMID 38453939 DOI: 10.1038/s41467-024-46492-5 |
0.356 |
|
| 2023 |
Wang X, Yue F. HiCLift: A fast and efficient tool for converting chromatin interaction data between genome assemblies. Bioinformatics (Oxford, England). PMID 37335863 DOI: 10.1093/bioinformatics/btad389 |
0.416 |
|
| 2023 |
Xiang G, He X, Giardine BM, Weaver KJ, Taylor DJ, McCoy RC, Jansen C, Keller CA, Wixom AQ, Cockburn A, Miller A, Qi Q, He Y, Li Y, Lichtenberg J, ... ... Yue F, et al. Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Biorxiv : the Preprint Server For Biology. PMID 37066352 DOI: 10.1101/2023.04.02.535219 |
0.338 |
|
| 2023 |
Liu T, Wang J, Yang H, Jin Q, Wang X, Fu Y, Luan Y, Wang Q, Youngblood MW, Lu X, Casadei L, Pollock R, Yue F. Enhancer co-amplification and hijacking promote oncogene expression in liposarcoma. Cancer Research. PMID 36847778 DOI: 10.1158/0008-5472.CAN-22-1858 |
0.43 |
|
| 2023 |
Wang X, Yue F. HiCLift: A fast and efficient tool for converting chromatin interaction data between genome assemblies. Biorxiv : the Preprint Server For Biology. PMID 36712087 DOI: 10.1101/2023.01.17.524475 |
0.416 |
|
| 2022 |
Bi H, Hou Y, Wang J, Xia Z, Wang D, Liu Y, Bao H, Han X, Ren K, Li E, Yue F, Ji P. Chromatin reconstruction during mouse terminal erythropoiesis. Iscience. 25: 105554. PMID 36465116 DOI: 10.1016/j.isci.2022.105554 |
0.375 |
|
| 2022 |
Xu J, Song F, Lyu H, Kobayashi M, Zhang B, Zhao Z, Hou Y, Wang X, Luan Y, Jia B, Stasiak L, Wong JH, Wang Q, Jin Q, Jin Q, ... ... Yue F, et al. Subtype-specific 3D genome alteration in acute myeloid leukaemia. Nature. PMID 36289338 DOI: 10.1038/s41586-022-05365-x |
0.735 |
|
| 2022 |
Wang X, Luan Y, Yue F. EagleC: A deep-learning framework for detecting a full range of structural variations from bulk and single-cell contact maps. Science Advances. 8: eabn9215. PMID 35704579 DOI: 10.1126/sciadv.abn9215 |
0.338 |
|
| 2022 |
Lee HJ, Hou Y, Maeng JH, Shah NM, Chen Y, Lawson HA, Yang H, Yue F, Wang T. Epigenomic analysis reveals prevalent contribution of transposable elements to -regulatory elements, tissue-specific expression, and alternative promoters in zebrafish. Genome Research. PMID 35649578 DOI: 10.1101/gr.276052.121 |
0.343 |
|
| 2022 |
Wei X, Xiang Y, Peters DT, Marius C, Sun T, Shan R, Ou J, Lin X, Yue F, Li W, Southerland KW, Diao Y. HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization. Molecular Cell. PMID 35196517 DOI: 10.1016/j.molcel.2022.01.023 |
0.721 |
|
| 2022 |
Yang H, Zhang H, Luan Y, Liu T, Yang W, Roberts KG, Qian MX, Zhang B, Yang W, Perez-Andreu V, Xu J, Iyyanki S, Kuang D, Stasiak LA, Reshmi SC, ... ... Yue F, et al. Noncoding genetic variation in GATA3 increases acute lymphoblastic leukemia risk through local and global changes in chromatin conformation. Nature Genetics. 54: 170-179. PMID 35115686 DOI: 10.1038/s41588-021-00993-x |
0.36 |
|
| 2022 |
Song F, Xu J, Dixon J, Yue F. Analysis of Hi-C Data for Discovery of Structural Variations in Cancer. Methods in Molecular Biology (Clifton, N.J.). 2301: 143-161. PMID 34415534 DOI: 10.1007/978-1-0716-1390-0_7 |
0.68 |
|
| 2021 |
Zhang H, Song L, Wang X, Cheng H, Wang C, Meyer CA, Liu T, Tang M, Aluru S, Yue F, Liu XS, Li H. Fast alignment and preprocessing of chromatin profiles with Chromap. Nature Communications. 12: 6566. PMID 34772935 DOI: 10.1038/s41467-021-26865-w |
0.376 |
|
| 2021 |
Zhao Z, Szczepanski AP, Tsuboyama N, Abdala-Valencia H, Goo YA, Singer BD, Bartom ET, Yue F, Wang L. PAX9 determines epigenetic state transition and cell fate in cancer. Cancer Research. PMID 34341073 DOI: 10.1158/0008-5472.CAN-21-1114 |
0.339 |
|
| 2021 |
Wang X, Xu J, Zhang B, Hou Y, Song F, Lyu H, Yue F. Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes. Nature Methods. 18: 661-668. PMID 34092790 DOI: 10.1038/s41592-021-01164-w |
0.421 |
|
| 2021 |
Wang J, Huang TY, Hou Y, Bartom E, Lu X, Shilatifard A, Yue F, Saratsis A. Epigenomic landscape and 3D genome structure in pediatric high-grade glioma. Science Advances. 7. PMID 34078608 DOI: 10.1126/sciadv.abg4126 |
0.393 |
|
| 2021 |
Iyyanki T, Zhang B, Wang Q, Hou Y, Jin Q, Xu J, Yang H, Liu T, Wang X, Song F, Luan Y, Yamashita H, Chien R, Lyu H, Zhang L, ... ... Yue F, et al. Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer. Genome Biology. 22: 105. PMID 33858483 DOI: 10.1186/s13059-021-02325-y |
0.471 |
|
| 2020 |
Yang H, Luan Y, Liu T, Lee HJ, Fang L, Wang Y, Wang X, Zhang B, Jin Q, Ang KC, Xing X, Wang J, Xu J, Song F, Sriranga I, ... ... Yue F, et al. A map of cis-regulatory elements and 3D genome structures in zebrafish. Nature. PMID 33239788 DOI: 10.1038/s41586-020-2962-9 |
0.496 |
|
| 2020 |
Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky L, ... ... Yue F, et al. An integrative ENCODE resource for cancer genomics. Nature Communications. 11: 3696. PMID 32728046 DOI: 10.1038/S41467-020-14743-W |
0.495 |
|
| 2020 |
Salameh TJ, Wang X, Song F, Zhang B, Wright SM, Khunsriraksakul C, Ruan Y, Yue F. A supervised learning framework for chromatin loop detection in genome-wide contact maps. Nature Communications. 11: 3428. PMID 32647330 DOI: 10.1038/s41467-020-17239-9 |
0.398 |
|
| 2020 |
Xiang G, Keller CA, Heuston EF, Giardine BM, An L, Wixom AQ, Miller A, Cockburn A, Sauria MEG, Weaver K, Lichtenberg J, Göttgens B, Li Q, Bodine D, Mahony S, ... ... Yue F, et al. An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis. Genome Research. PMID 32132109 DOI: 10.1101/Gr.255760.119 |
0.449 |
|
| 2019 |
Hardison RC, Zhang Y, Keller CA, Xiang G, Heuston EF, An L, Lichtenberg J, Giardine BM, Bodine D, Mahony S, Li Q, Yue F, Weiss MJ, Blobel GA, Taylor J, et al. Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells. Iubmb Life. PMID 31769130 DOI: 10.1002/Iub.2195 |
0.464 |
|
| 2019 |
Ding Y, Zhang B, Payne JL, Song C, Ge Z, Gowda C, Iyer S, Dhanyamraju PK, Dorsam G, Reeves ME, Desai D, Huang S, Payne KJ, Yue F, Dovat S. Ikaros tumor suppressor function includes induction of active enhancers and super-enhancers along with pioneering activity. Leukemia. PMID 31073152 DOI: 10.1038/S41375-019-0474-0 |
0.345 |
|
| 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, ... ... Yue F, et al. Measuring the reproducibility and quality of Hi-C data. Genome Biology. 20: 57. PMID 30890172 DOI: 10.1186/S13059-019-1658-7 |
0.388 |
|
| 2019 |
Gowda C, Song C, Steffens S, Ding Y, Zhang B, Yue F, Iyer S, Dhanyamraju Pk, Payne J, Reed M, Payne KJ, Dovat S. CK2 Inhibitor CX4945 Shows Strong In Vivo Anti Leukemia Effect in AML Via Augmented Ikaros-Mediated Regulation of Global Epigenetic Landscape Blood. 134: 2522-2522. DOI: 10.1182/Blood-2019-131200 |
0.402 |
|
| 2019 |
Broach JR, Xu J, Schleicher E, Pool C, Hennessy M, Sheldon K, Annageldiyev C, Sharma A, Chang Y, Hastie A, Miller B, Goldenberg D, Claxton D, Moldovan G, Yue F. Abstract 1708: An integrated framework for genome analysis reveals numerous previously unrecognizable structural variants in leukemia patients’ samples Cancer Research. DOI: 10.1158/1538-7445.Sabcs18-1708 |
0.422 |
|
| 2018 |
Hu X, Xu H, Shang Y, Guo L, Song L, Zhang H, Yue F, Jiang H, Zheng B. First genome sequence of a bla-carrying Citrobacter koseri isolate collected from a patient with diarrhea. Journal of Global Antimicrobial Resistance. PMID 30291901 DOI: 10.1016/j.jgar.2018.09.016 |
0.32 |
|
| 2018 |
Wang Y, Song F, Zhang B, Zhang L, Xu J, Kuang D, Li D, Choudhary MNK, Li Y, Hu M, Hardison R, Wang T, Yue F. The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. Genome Biology. 19: 151. PMID 30286773 DOI: 10.1186/S13059-018-1519-9 |
0.545 |
|
| 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, ... ... Yue F, et al. Integrative detection and analysis of structural variation in cancer genomes. Nature Genetics. PMID 30202056 DOI: 10.1038/S41588-018-0195-8 |
0.742 |
|
| 2018 |
Hu X, Shang Y, Guo J, Zhang H, Liang Y, Sun J, Yue F. Draft Genome Sequence of Staphylococcus microti DSM 22147, Isolated from the Common Vole. Genome Announcements. 6. PMID 29773631 DOI: 10.1128/genomeA.00420-18 |
0.356 |
|
| 2018 |
Zhang Y, An L, Xu J, Zhang B, Zheng WJ, Hu M, Tang J, Yue F. Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus. Nature Communications. 9: 750. PMID 29467363 DOI: 10.1038/S41467-018-03113-2 |
0.582 |
|
| 2018 |
Dovat S, Ding Y, Zhang B, Payne J, Payne K, Yue F. Epigenetic Regulation of Gene Expression and Tumor Suppression in T-Cell Acute Lymphoblastic Leukemia by Ikaros Experimental Hematology. 64. DOI: 10.1016/J.Exphem.2018.06.216 |
0.309 |
|
| 2017 |
Zhai L, Xie J, Lin Y, Cheng K, Wang L, Yue F, Guo J, Liu J, Yao S. Genome sequencing and heterologous expression of antiporters reveal alkaline response mechanisms of Halomonas alkalicola. Extremophiles : Life Under Extreme Conditions. PMID 29270851 DOI: 10.1007/s00792-017-0991-6 |
0.301 |
|
| 2017 |
Yang T, Zhang F, Yardimci GG, Song F, Hardison RC, Noble WS, Yue F, Li Q. HiCRep: assessing the reproducibility of Hi-C data using a stratum- adjusted correlation coefficient. Genome Research. PMID 28855260 DOI: 10.1101/Gr.220640.117 |
0.361 |
|
| 2017 |
Coble JL, Sheldon K, Yue F, Salameh T, Harris L, Deiling S, Ruggiero F, Eshelman M, Yochum GS, Koltun WA, Gerhard GS, Broach JR. Identification of a rare LAMB4 variant associated with familial diverticulitis through exome sequencing. Human Molecular Genetics. PMID 28595269 DOI: 10.1093/Hmg/Ddx204 |
0.356 |
|
| 2017 |
Zhang H, Yang H, Liu T, Qian M, Yang W, Roberts KG, Perez-Andreu V, Xu H, Gastier-Foster JM, Smith C, Pui C, Evans WE, Relling MV, Hunger SP, Mullighan CG, ... ... Yue F, et al. Characterization of Causal Variants at the GATA3 Loci Associated with Susceptibility to Ph-like Acute Lymphoblastic Leukemia Blood. 130: 475-475. DOI: 10.1182/Blood.V130.Suppl_1.475.475 |
0.415 |
|
| 2017 |
Pool C, Xu J, Bann D, Goldenberg D, Sharma A, Claxton D, Yue F, Broach J. Abstract 994: Diagnosing leukemia structural variations via a novel genome mapping approach Cancer Research. 77: 994-994. DOI: 10.1158/1538-7445.Am2017-994 |
0.409 |
|
| 2016 |
Warrick JI, Walter V, Yamashita H, Chung E, Shuman L, Amponsa VO, Zheng Z, Chan W, Whitcomb TL, Yue F, Iyyanki T, Kawasawa YI, Kaag M, Guo W, Raman JD, et al. FOXA1, GATA3 and PPARɣ Cooperate to Drive Luminal Subtype in Bladder Cancer: A Molecular Analysis of Established Human Cell Lines. Scientific Reports. 6: 38531. PMID 27924948 DOI: 10.1038/Srep38531 |
0.341 |
|
| 2016 |
Zhang Y, An L, Yue F, Hardison RC. Jointly characterizing epigenetic dynamics across multiple human cell types. Nucleic Acids Research. PMID 27095202 DOI: 10.1093/Nar/Gkw278 |
0.43 |
|
| 2016 |
Xu Z, Zhang G, Duan Q, Chai S, Zhang B, Wu C, Jin F, Yue F, Li Y, Hu M. HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. Bmc Research Notes. 9: 159. PMID 26969411 DOI: 10.1186/S13104-016-1947-0 |
0.733 |
|
| 2015 |
Ren B, Yue F. Transcriptional Enhancers: Bridging the Genome and Phenome. Cold Spring Harbor Symposia On Quantitative Biology. PMID 26582789 DOI: 10.1101/Sqb.2015.80.027219 |
0.635 |
|
| 2015 |
Wang A, Yue F, Li Y, Xie R, Harper T, Patel NA, Muth K, Palmer J, Qiu Y, Wang J, Lam DK, Raum JC, Stoffers DA, Ren B, Sander M. Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates. Cell Stem Cell. 16: 386-99. PMID 25842977 DOI: 10.1016/J.Stem.2015.02.013 |
0.544 |
|
| 2015 |
Leung D, Jung I, Rajagopal N, Schmitt A, Selvaraj S, Lee AY, Yen CA, Lin S, Lin Y, Qiu Y, Xie W, Yue F, Hariharan M, Ray P, Kuan S, et al. Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature. 518: 350-4. PMID 25693566 DOI: 10.1038/Nature14217 |
0.639 |
|
| 2015 |
Perez-Andreu V, Roberts KG, Xu H, Smith C, Zhang H, Yang W, Harvey RC, Payne-Turner D, Devidas M, Cheng IM, Carroll WL, Heerema NA, Carroll AJ, Raetz EA, Gastier-Foster JM, ... ... Yue F, et al. A genome-wide association study of susceptibility to acute lymphoblastic leukemia in adolescents and young adults. Blood. 125: 680-6. PMID 25468567 DOI: 10.1182/Blood-2014-09-595744 |
0.323 |
|
| 2015 |
Yue F, Shen Y, Ye Z, Ren B. Abstract 2211: A comparative analysis of the cis-regulatory landscape between human and mouse Cancer Research. 75: 2211-2211. DOI: 10.1158/1538-7445.Am2015-2211 |
0.683 |
|
| 2014 |
Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, et al. Topologically associating domains are stable units of replication-timing regulation. Nature. 515: 402-5. PMID 25409831 DOI: 10.1038/Nature13986 |
0.539 |
|
| 2014 |
Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515: 355-64. PMID 25409824 DOI: 10.1038/Nature13992 |
0.742 |
|
| 2013 |
Perez-Andreu V, Roberts KG, Harvey RC, Yang W, Cheng C, Pei D, Xu H, Gastier-Foster J, E S, Lim JY, Chen IM, Fan Y, Devidas M, Borowitz MJ, Smith C, ... ... Yue F, et al. Inherited GATA3 variants are associated with Ph-like childhood acute lymphoblastic leukemia and risk of relapse. Nature Genetics. 45: 1494-8. PMID 24141364 DOI: 10.1038/Ng.2803 |
0.318 |
|
| 2013 |
Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, Ren B. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nature Genetics. 45: 1198-206. PMID 23995138 DOI: 10.1038/Ng.2746 |
0.733 |
|
| 2013 |
Perez-Andreu V, Roberts KG, Harvey RC, Yang W, Cheng C, Pei D, Xu H, Gastier-Fostier J, E S, Lim JY, Chen IL, Fan Y, Devidas M, Borowitz MJ, Smith C, ... ... Yue F, et al. Inherited GATA3 genetic Variants Are Associated With Childhood BCR-ABL1-Like Acute Lymphoblastic Leukemia and Increased Risk Of Relapse Blood. 122: 617-617. DOI: 10.1182/Blood.V122.21.617.617 |
0.321 |
|
| 2012 |
Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, ... ... Yue F, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology. 13: 418. PMID 22889292 DOI: 10.1186/Gb-2012-13-8-418 |
0.697 |
|
| 2012 |
Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B. A map of the cis-regulatory sequences in the mouse genome. Nature. 488: 116-20. PMID 22763441 DOI: 10.1038/Nature11243 |
0.787 |
|
| 2012 |
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 485: 376-80. PMID 22495300 DOI: 10.1038/Nature11082 |
0.771 |
|
| 2012 |
Xie W, Barr CL, Kim A, Yue F, Lee AY, Eubanks J, Dempster EL, Ren B. Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell. 148: 816-31. PMID 22341451 DOI: 10.1016/J.Cell.2011.12.035 |
0.648 |
|
| 2012 |
Rebeiz M, Castro B, Liu F, Yue F, Posakony JW. Ancestral and conserved cis-regulatory architectures in developmental control genes. Developmental Biology. 362: 282-94. PMID 22185795 DOI: 10.1016/J.Ydbio.2011.12.011 |
0.358 |
|
| 2009 |
Yue F, Tang J. A space-efficient algorithm for three sequence alignment and ancestor inference. International Journal of Data Mining and Bioinformatics. 3: 192-204. PMID 19517989 DOI: 10.1504/IJDMB.2009.024851 |
0.459 |
|
| 2009 |
Yue F, Shi J, Tang J. Simultaneous phylogeny reconstruction and multiple sequence alignment. Bmc Bioinformatics. 10: S11. PMID 19208110 DOI: 10.1186/1471-2105-10-S1-S11 |
0.583 |
|
| 2008 |
Yue F, Zhang M, Tang J. Phylogenetic reconstruction from transpositions. Bmc Genomics. 9: S15. PMID 18831780 DOI: 10.1186/1471-2164-9-S2-S15 |
0.635 |
|
| 2008 |
Yue F, Cui L, dePamphilis CW, Moret BM, Tang J. Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat. Bmc Genomics. 9: S25. PMID 18366615 DOI: 10.1186/1471-2164-9-S1-S25 |
0.641 |
|
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