| Year |
Citation |
Score |
| 2024 |
Ma W, Song X, Yuan GC, Wang P. RECCIPE: A new framework assessing localized cell-cell interaction on gene expression in multicellular ST data. Frontiers in Genetics. 15: 1322886. PMID 38327830 DOI: 10.3389/fgene.2024.1322886 |
0.33 |
|
| 2023 |
Choi J, Ehrlich ME, Roussos P, Wang P, Yuan GC, Song X. QuadST: A Powerful and Robust Approach for Identifying Cell-Cell Interaction-Changed Genes on Spatially Resolved Transcriptomics. Biorxiv : the Preprint Server For Biology. PMID 38106025 DOI: 10.1101/2023.12.04.570019 |
0.323 |
|
| 2023 |
Zhu K, Bendl J, Rahman S, Vicari JM, Coleman C, Clarence T, Latouche O, Tsankova NM, Li A, Brennand KJ, Lee D, Yuan GC, Fullard JF, Roussos P. Multi-omic profiling of the developing human cerebral cortex at the single-cell level. Science Advances. 9: eadg3754. PMID 37824614 DOI: 10.1126/sciadv.adg3754 |
0.371 |
|
| 2022 |
Qin G, Park ES, Chen X, Han S, Xiang D, Ren F, Liu G, Chen H, Yuan GC, Li Z. Distinct niche structures and intrinsic programs of fallopian tube and ovarian surface epithelial cells. Iscience. 26: 105861. PMID 36624845 DOI: 10.1016/j.isci.2022.105861 |
0.32 |
|
| 2021 |
Cha HJ, Uyan Ö, Kai Y, Liu T, Zhu Q, Tothova Z, Botten GA, Xu J, Yuan GC, Dekker J, Orkin SH. Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture. Nature Communications. 12: 6241. PMID 34716321 DOI: 10.1038/s41467-021-26574-4 |
0.34 |
|
| 2021 |
Yu F, Sankaran VG, Yuan GC. CUT&RUNTools 2.0: A pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis. Bioinformatics (Oxford, England). PMID 34244724 DOI: 10.1093/bioinformatics/btab507 |
0.336 |
|
| 2021 |
Takei Y, Yun J, Zheng S, Ollikainen N, Pierson N, White J, Shah S, Thomassie J, Suo S, Eng CL, Guttman M, Yuan GC, Cai L. Integrated spatial genomics reveals global architecture of single nuclei. Nature. PMID 33505024 DOI: 10.1038/s41586-020-03126-2 |
0.377 |
|
| 2020 |
Cai W, Huang J, Zhu Q, Li BE, Seruggia D, Zhou P, Nguyen M, Fujiwara Y, Xie H, Yang Z, Hong D, Ren P, Xu J, Pu WT, Yuan GC, et al. Enhancer dependence of cell-type-specific gene expression increases with developmental age. Proceedings of the National Academy of Sciences of the United States of America. PMID 32817427 DOI: 10.1073/Pnas.2008672117 |
0.494 |
|
| 2020 |
Luoma AM, Suo S, Williams HL, Sharova T, Sullivan K, Manos M, Bowling P, Hodi FS, Rahma O, Sullivan RJ, Boland GM, Nowak JA, Dougan SK, Dougan M, Yuan GC, et al. Molecular Pathways of Colon Inflammation Induced by Cancer Immunotherapy. Cell. PMID 32603654 DOI: 10.1016/J.Cell.2020.06.001 |
0.337 |
|
| 2020 |
Dong R, Yuan GC. GiniClust3: a fast and memory-efficient tool for rare cell type identification. Bmc Bioinformatics. 21: 158. PMID 32334526 DOI: 10.1186/S12859-020-3482-1 |
0.334 |
|
| 2020 |
McCarthy N, Manieri E, Storm EE, Saadatpour A, Luoma AM, Kapoor VN, Madha S, Gaynor LT, Cox C, Keerthivasan S, Wucherpfennig K, Yuan GC, de Sauvage FJ, Turley SJ, Shivdasani RA. Distinct Mesenchymal Cell Populations Generate the Essential Intestinal BMP Signaling Gradient. Cell Stem Cell. PMID 32084389 DOI: 10.1016/J.Stem.2020.01.008 |
0.354 |
|
| 2020 |
Chen J, Liang X, Zhang S, Wang S, Garcia SP, Yan P, Yu H, Li Z, Liu L, Zhang F, Wei W, Le H, Zhang Y, Yuan GC, Chen S, et al. Two faces of bivalent domain regulate VEGFA responsiveness and angiogenesis. Cell Death & Disease. 11: 75. PMID 32001672 DOI: 10.1038/S41419-020-2228-3 |
0.409 |
|
| 2019 |
de Andrade LF, Lu Y, Luoma A, Ito Y, Pan D, Pyrdol JW, Yoon CH, Yuan GC, Wucherpfennig KW. Discovery of specialized NK cell populations infiltrating human melanoma metastases. Jci Insight. 4. PMID 31801909 DOI: 10.1172/Jci.Insight.133103 |
0.377 |
|
| 2019 |
Hu X, Xiang D, Xie Y, Tao L, Zhang Y, Jin Y, Pinello L, Wan Y, Yuan GC, Li Z. LSD1 suppresses invasion, migration and metastasis of luminal breast cancer cells via activation of GATA3 and repression of TRIM37 expression. Oncogene. PMID 31409898 DOI: 10.1038/S41388-019-0923-2 |
0.381 |
|
| 2019 |
Debruyne DN, Dries R, Sengupta S, Seruggia D, Gao Y, Sharma B, Huang H, Moreau L, McLane M, Day DS, Marco E, Chen T, Gray NS, Wong KK, Orkin SH, ... Yuan GC, et al. BORIS promotes chromatin regulatory interactions in treatment-resistant cancer cells. Nature. PMID 31391581 DOI: 10.1038/S41586-019-1472-0 |
0.458 |
|
| 2019 |
Tracy S, Yuan GC, Dries R. RESCUE: imputing dropout events in single-cell RNA-sequencing data. Bmc Bioinformatics. 20: 388. PMID 31299886 DOI: 10.1186/S12859-019-2977-0 |
0.306 |
|
| 2019 |
Sethi I, Cai Z, Roberts TM, Yuan GC. Molecular profiling establishes genetic features predictive of the efficacy of the p110β inhibitor KIN-193. Cancer Research. PMID 31292159 DOI: 10.1158/0008-5472.Can-19-0588 |
0.315 |
|
| 2019 |
Tsoucas D, Dong R, Chen H, Zhu Q, Guo G, Yuan GC. Accurate estimation of cell-type composition from gene expression data. Nature Communications. 10: 2975. PMID 31278265 DOI: 10.1038/S41467-019-10802-Z |
0.392 |
|
| 2019 |
Joyce CE, Saadatpour A, Ruiz-Gutierrez M, Bolukbasi OV, Jiang L, Thomas DD, Young S, Hofmann I, Sieff C, Myers KC, Whangbo J, Libermann TA, Nusbaum C, Yuan GC, Shimamura A, et al. TGFβ signaling underlies hematopoietic dysfunction and bone marrow failure in Shwachman-Diamond Syndrome. The Journal of Clinical Investigation. 130. PMID 31211692 DOI: 10.1172/Jci125375 |
0.352 |
|
| 2019 |
Chen H, Albergante L, Hsu JY, Lareau CA, Lo Bosco G, Guan J, Zhou S, Gorban AN, Bauer DE, Aryee MJ, Langenau DM, Zinovyev A, Buenrostro JD, Yuan GC, Pinello L. Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nature Communications. 10: 1903. PMID 31015418 DOI: 10.1038/S41467-019-09670-4 |
0.384 |
|
| 2019 |
Krajewska M, Dries R, Grassetti AV, Dust S, Gao Y, Huang H, Sharma B, Day DS, Kwiatkowski N, Pomaville M, Dodd O, Chipumuro E, Zhang T, Greenleaf AL, Yuan GC, et al. CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation. Nature Communications. 10: 1757. PMID 30988284 DOI: 10.1038/S41467-019-09703-Y |
0.383 |
|
| 2019 |
Eng CL, Lawson M, Zhu Q, Dries R, Koulena N, Takei Y, Yun J, Cronin C, Karp C, Yuan GC, Cai L. Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. Nature. PMID 30911168 DOI: 10.1038/S41586-019-1049-Y |
0.364 |
|
| 2019 |
Wang S, Chen J, Garcia SP, Liang X, Zhang F, Yan P, Yu H, Wei W, Li Z, Wang J, Le H, Han Z, Luo X, Day DS, Stevens SM, ... ... Yuan GC, et al. A dynamic and integrated epigenetic program at distal regions orchestrates transcriptional responses to VEGFA. Genome Research. PMID 30670628 DOI: 10.1101/Gr.239053.118 |
0.321 |
|
| 2019 |
Cartwright ANR, Jiang P, Saadatpour A, Yuan G, Liu SX, Wucherpfennig KW. Abstract A176: Overcoming CD8 T-cell suppression in the tumor microenvironment Cancer Immunology Research. 7. DOI: 10.1158/2326-6074.Cricimteatiaacr18-A176 |
0.307 |
|
| 2019 |
Pan D, Kobayashi A, Jiang P, Yuan G, Liu XS, Doench J, Qiu X, Rao P, Long H, Brown MA, Wucherpfennig KW, Andrade LFd, Tay RE, Luoma AM, Tsoucas D, et al. Abstract A146: Systematic discovery of immune regulatory mechanisms in tumor cells Cancer Immunology Research. 7. DOI: 10.1158/2326-6074.Cricimteatiaacr18-A146 |
0.388 |
|
| 2018 |
Barros-Silva JD, Linn DE, Steiner I, Guo G, Ali A, Pakula H, Ashton G, Peset I, Brown M, Clarke NW, Bronson RT, Yuan GC, Orkin SH, Li Z, Baena E. Single-Cell Analysis Identifies LY6D as a Marker Linking Castration-Resistant Prostate Luminal Cells to Prostate Progenitors and Cancer. Cell Reports. 25: 3504-3518.e6. PMID 30566873 DOI: 10.1016/J.Celrep.2018.11.069 |
0.382 |
|
| 2018 |
Suo S, Zhu Q, Saadatpour A, Fei L, Guo G, Yuan GC. Revealing the Critical Regulators of Cell Identity in the Mouse Cell Atlas. Cell Reports. 25: 1436-1445.e3. PMID 30404000 DOI: 10.1016/J.Celrep.2018.10.045 |
0.408 |
|
| 2018 |
Zhu Q, Shah S, Dries R, Cai L, Yuan GC. Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. Nature Biotechnology. PMID 30371680 DOI: 10.1038/Nbt.4260 |
0.406 |
|
| 2018 |
Guo Y, Jardin BD, Zhou P, Sethi I, Akerberg BN, Toepfer CN, Ai Y, Li Y, Ma Q, Guatimosim S, Hu Y, Varuzhanyan G, VanDusen NJ, Zhang D, Chan DC, ... Yuan GC, et al. Hierarchical and stage-specific regulation of murine cardiomyocyte maturation by serum response factor. Nature Communications. 9: 3837. PMID 30242271 DOI: 10.1038/S41467-018-06347-2 |
0.33 |
|
| 2018 |
Glass K, Thibault D, Guo F, Mitchel JA, Pham B, Qiu W, Li Y, Jiang Z, Castaldi PJ, Silverman EK, Raby B, Park JA, Yuan GC, Zhou X. Integrative epigenomic analysis in differentiated human primary bronchial epithelial cells exposed to cigarette smoke. Scientific Reports. 8: 12750. PMID 30143676 DOI: 10.1038/S41598-018-30781-3 |
0.396 |
|
| 2018 |
Tsoucas D, Yuan GC. GiniClust2: a cluster-aware, weighted ensemble clustering method for cell-type detection. Genome Biology. 19: 58. PMID 29747686 DOI: 10.1186/S13059-018-1431-3 |
0.318 |
|
| 2018 |
Ferrari de Andrade L, Tay RE, Pan D, Luoma AM, Ito Y, Badrinath S, Tsoucas D, Franz B, May KF, Harvey CJ, Kobold S, Pyrdol JW, Yoon C, Yuan GC, Hodi FS, et al. Antibody-mediated inhibition of MICA and MICB shedding promotes NK cell-driven tumor immunity. Science (New York, N.Y.). 359: 1537-1542. PMID 29599246 DOI: 10.1126/Science.Aao0505 |
0.316 |
|
| 2018 |
Jiang L, Tsoucas D, Yuan GC. Assessing Inequality in Transcriptomic Data. Cell Systems. 6: 149-150. PMID 29494801 DOI: 10.1016/J.Cels.2018.02.007 |
0.373 |
|
| 2018 |
Han X, Wang R, Zhou Y, Fei L, Sun H, Lai S, Saadatpour A, Zhou Z, Chen H, Ye F, Huang D, Xu Y, Huang W, Jiang M, Jiang X, ... ... Yuan GC, et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell. 172: 1091-1107.e17. PMID 29474909 DOI: 10.1016/J.Cell.2018.02.001 |
0.399 |
|
| 2018 |
Pinello L, Farouni R, Yuan GC. Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements. Bioinformatics (Oxford, England). PMID 29360936 DOI: 10.1093/Bioinformatics/Bty031 |
0.465 |
|
| 2018 |
Pan D, Kobayashi A, Jiang P, Ferrari de Andrade L, Tay RE, Luoma A, Tsoucas D, Qiu X, Lim K, Rao P, Long HW, Yuan GC, Doench J, Brown M, Liu S, et al. A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. Science (New York, N.Y.). PMID 29301958 DOI: 10.1126/Science.Aao1710 |
0.387 |
|
| 2017 |
Huang D, Guo G, Yuan P, Ralston A, Sun L, Huss M, Mistri T, Pinello L, Ng HH, Yuan G, Ji J, Rossant J, Robson P, Han X. The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during the first developmental cell lineage segregation. Scientific Reports. 7: 17156. PMID 29214996 DOI: 10.1038/S41598-017-16009-W |
0.477 |
|
| 2017 |
Jadhav U, Saxena M, O'Neill NK, Saadatpour A, Yuan GC, Herbert Z, Murata K, Shivdasani RA. Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells. Cell Stem Cell. PMID 28648363 DOI: 10.1016/J.Stem.2017.05.001 |
0.419 |
|
| 2017 |
Yuan GC, Cai L, Elowitz M, Enver T, Fan G, Guo G, Irizarry R, Kharchenko P, Kim J, Orkin S, Quackenbush J, Saadatpour A, Schroeder T, Shivdasani R, Tirosh I. Challenges and emerging directions in single-cell analysis. Genome Biology. 18: 84. PMID 28482897 DOI: 10.1186/S13059-017-1218-Y |
0.418 |
|
| 2017 |
Min L, Zhang C, Qu L, Huang J, Jiang L, Liu J, Pinello L, Yuan GC, Shou C. Gene regulatory pattern analysis reveals essential role of core transcriptional factors' activation in triple-negative breast cancer. Oncotarget. 8: 21938-21953. PMID 28423538 DOI: 10.18632/Oncotarget.15749 |
0.313 |
|
| 2017 |
Adeegbe D, Liu Y, Lizotte PH, Kamihara Y, Aref AR, Almonte C, Dries R, Li Y, Liu S, Wang X, Warner-Hatten T, Castrillon J, Yuan GC, Poudel-Neupane N, Zhang H, et al. Synergistic Immunostimulatory Effects and Therapeutic Benefit of Combined Histone Deacetylase and Bromodomain Inhibition in Non-small Cell Lung Cancer. Cancer Discovery. PMID 28408401 DOI: 10.1158/2159-8290.Cd-16-1020 |
0.355 |
|
| 2017 |
Marco E, Meuleman W, Huang J, Glass K, Pinello L, Wang J, Kellis M, Yuan GC. Multi-scale chromatin state annotation using a hierarchical hidden Markov model. Nature Communications. 8: 15011. PMID 28387224 DOI: 10.1038/Ncomms15011 |
0.31 |
|
| 2017 |
Guo Y, VanDusen NJ, Zhang L, Gu W, Sethi I, Guatimosim S, Ma Q, Jardin BD, Ai Y, Zhang D, Chen B, Guo A, Yuan GC, Song LS, Pu WT. Analysis of Cardiac Myocyte Maturation Using CASAAV, A Platform for Rapid Dissection of Cardiac Myocyte Gene Function In Vivo. Circulation Research. PMID 28356340 DOI: 10.1161/Circresaha.116.310283 |
0.319 |
|
| 2017 |
Tu S, Yuan GC, Shao Z. The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features. Scientific Reports. 7: 41669. PMID 28139710 DOI: 10.1038/Srep41669 |
0.315 |
|
| 2017 |
Han X, Yu H, Huang D, Xu Y, Saadatpour A, Li X, Wang L, Yu J, Pinello L, Lai S, Jiang M, Tian X, Zhang F, Cen Y, Fujiwara Y, ... ... Yuan GC, et al. A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations. Cell Research. PMID 28128194 DOI: 10.1038/Cr.2017.17 |
0.449 |
|
| 2017 |
Tsoucas D, Yuan GC. Recent progress in single-cell cancer genomics. Current Opinion in Genetics & Development. 42: 22-32. PMID 28126650 DOI: 10.1016/J.Gde.2017.01.002 |
0.358 |
|
| 2017 |
Blinka S, Reimer MH, Pulakanti K, Pinello L, Yuan GC, Rao S. Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing. Methods in Molecular Biology (Clifton, N.J.). 1468: 91-109. PMID 27662872 DOI: 10.1007/978-1-4939-4035-6_8 |
0.374 |
|
| 2017 |
Dorantes-Acosta E, Huang H, Garcia SP, Stieglitz E, Loh M, Yuan G, Cantor AB. Abstract 26: RUNX1 as a transcriptional target of activated Shp2 (PTPN11) in juvenile myelomonocytic leukemia Clinical Cancer Research. 23: 26-26. DOI: 10.1158/1557-3265.Hemmal17-26 |
0.406 |
|
| 2017 |
Hu X, Xiang D, Tao L, Xie Y, Jin Y, Guo Y, Pinello L, Yuan G, Li Z. Abstract 2563: LSD1 maintains differentiation and survival of mammary luminal cells and suppresses invasion of luminal breast cancer cells via GATA3 Cancer Research. 77: 2563-2563. DOI: 10.1158/1538-7445.Am2017-2563 |
0.38 |
|
| 2017 |
Cantor A, Dorantes-Costa E, Huang H, Garcia S, Stieglitz E, Loh M, Yuan G. Dysregulation of the transcription factor runx1 in juvenile myelomonocytic leukemia Experimental Hematology. 53. DOI: 10.1016/J.Exphem.2017.06.077 |
0.313 |
|
| 2016 |
Beyaz S, Kim JH, Pinello L, Xifaras ME, Hu Y, Huang J, Kerenyi MA, Das PP, Barnitz RA, Herault A, Dogum R, Haining WN, Yilmaz ÖH, Passegue E, Yuan GC, et al. The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells. Nature Immunology. PMID 27992400 DOI: 10.1038/Ni.3644 |
0.405 |
|
| 2016 |
Lizotte PH, Ivanova EV, Awad MM, Jones RE, Keogh L, Liu H, Dries R, Almonte C, Herter-Sprie GS, Santos A, Feeney NB, Paweletz CP, Kulkarni MM, Bass AJ, Rustgi AK, ... Yuan GC, et al. Multiparametric profiling of non-small-cell lung cancers reveals distinct immunophenotypes. Jci Insight. 1: e89014. PMID 27699239 DOI: 10.1172/Jci.Insight.89014 |
0.325 |
|
| 2016 |
Kim TH, Saadatpour A, Guo G, Saxena M, Cavazza A, Desai N, Jadhav U, Jiang L, Rivera MN, Orkin SH, Yuan GC, Shivdasani RA. Single-Cell Transcript Profiles Reveal Multilineage Priming in Early Progenitors Derived from Lgr5(+) Intestinal Stem Cells. Cell Reports. PMID 27524622 DOI: 10.1016/J.Celrep.2016.07.056 |
0.448 |
|
| 2016 |
Jiang L, Chen H, Pinello L, Yuan GC. GiniClust: detecting rare cell types from single-cell gene expression data with Gini index. Genome Biology. 17: 144. PMID 27368803 DOI: 10.1186/S13059-016-1010-4 |
0.431 |
|
| 2016 |
Jadhav U, Nalapareddy K, Saxena M, O'Neill NK, Pinello L, Yuan GC, Orkin SH, Shivdasani RA. Acquired Tissue-Specific Promoter Bivalency Is a Basis for PRC2 Necessity in Adult Cells. Cell. PMID 27212235 DOI: 10.1016/J.Cell.2016.04.031 |
0.419 |
|
| 2016 |
Giecold G, Marco E, Garcia SP, Trippa L, Yuan GC. Robust lineage reconstruction from high-dimensional single-cell data. Nucleic Acids Research. PMID 27207878 DOI: 10.1093/Nar/Gkw452 |
0.4 |
|
| 2016 |
Stelloh C, Reimer MH, Pulakanti K, Blinka S, Peterson J, Pinello L, Jia S, Roumiantsev S, Hessner MJ, Milanovich S, Yuan GC, Rao S. The cohesin-associated protein Wapal is required for proper Polycomb-mediated gene silencing. Epigenetics & Chromatin. 9: 14. PMID 27087855 DOI: 10.1186/S13072-016-0063-7 |
0.437 |
|
| 2016 |
Beyaz S, Mana MD, Roper J, Kedrin D, Saadatpour A, Hong SJ, Bauer-Rowe KE, Xifaras ME, Akkad A, Arias E, Pinello L, Katz Y, Shinagare S, Abu-Remaileh M, Mihaylova MM, ... ... Yuan GC, et al. High-fat diet enhances stemness and tumorigenicity of intestinal progenitors. Nature. 531: 53-8. PMID 26935695 DOI: 10.1038/Nature17173 |
0.332 |
|
| 2016 |
Guo G, Pinello L, Han X, Lai S, Shen L, Lin TW, Zou K, Yuan GC, Orkin SH. Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell Analysis. Cell Reports. PMID 26804902 DOI: 10.1016/J.Celrep.2015.12.089 |
0.427 |
|
| 2016 |
Huang J, Liu X, Li D, Shao Z, Cao H, Zhang Y, Trompouki E, Bowman TV, Zon LI, Yuan GC, Orkin SH, Xu J. Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis. Developmental Cell. 36: 9-23. PMID 26766440 DOI: 10.1016/J.Devcel.2015.12.014 |
0.314 |
|
| 2016 |
Joyce C, Saadatpour A, Jiang L, Ruiz-Gutierrez M, Bolukbasi OV, Hofmann I, Sieff CA, Nusbaum C, Shimamura A, Yuan G, Novina CD. Single Cell Transcriptional Profiling Reveals Activation of TNF-Alpha Signaling in Hematopoietic Stem and Progenitor Cells from Shwachman-Diamond Syndrome Patients Blood. 128: 335-335. DOI: 10.1182/Blood.V128.22.335.335 |
0.346 |
|
| 2016 |
Linn DE, Barros-Silva J, Guo G, Brown M, Ashton G, Clarke NW, Yuan G, Orkin SH, Baena E, Li Z. Abstract LB-275: Single cell analysis identified LY6D as a novel marker of castration-resistant multipotent luminal progenitors Cancer Research. 76. DOI: 10.1158/1538-7445.Am2016-Lb-275 |
0.367 |
|
| 2015 |
Wu JN, Pinello L, Yissachar E, Wischhusen JW, Yuan GC, Roberts CW. Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia. Epigenetics & Chromatin. 8: 53. PMID 26633995 DOI: 10.1186/S13072-015-0046-0 |
0.396 |
|
| 2015 |
Saadatpour A, Lai S, Guo G, Yuan GC. Single-Cell Analysis in Cancer Genomics. Trends in Genetics : Tig. 31: 576-86. PMID 26450340 DOI: 10.1016/J.Tig.2015.07.003 |
0.365 |
|
| 2015 |
Huang J, Marco E, Pinello L, Yuan GC. Predicting chromatin organization using histone marks. Genome Biology. 16: 162. PMID 26272203 DOI: 10.1186/S13059-015-0740-Z |
0.378 |
|
| 2015 |
Hu T, Yeh JE, Pinello L, Jacob J, Chakravarthy S, Yuan GC, Chopra R, Frank DA. Impact of the N-terminal domain of STAT3 in STAT3-dependent transcriptional activity. Molecular and Cellular Biology. PMID 26169829 DOI: 10.1128/Mcb.00060-15 |
0.412 |
|
| 2015 |
Glass K, Quackenbush J, Spentzos D, Haibe-Kains B, Yuan GC. A network model for angiogenesis in ovarian cancer. Bmc Bioinformatics. 16: 115. PMID 25888305 DOI: 10.1186/S12859-015-0551-Y |
0.342 |
|
| 2015 |
Xu J, Shao Z, Li D, Xie H, Kim W, Huang J, Taylor JE, Pinello L, Glass K, Jaffe JD, Yuan GC, Orkin SH. Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions. Molecular Cell. 57: 304-16. PMID 25578878 DOI: 10.1016/J.Molcel.2014.12.009 |
0.321 |
|
| 2015 |
Bauer DE, Canver MC, Smith EC, Sher F, Pinello L, Sanjana NE, Shalem O, Chen DD, Schupp PG, Vinjamur DS, Garcia SP, Luc S, Kurita R, Nakamura Y, Fujiwara Y, ... ... Yuan G, et al. Crispr-Cas9 Saturating Mutagenesis Reveals an Achilles Heel in the BCL11A Erythroid Enhancer for Fetal Hemoglobin Induction (by Genome Editing) Blood. 126: 638-638. DOI: 10.1182/Blood.V126.23.638.638 |
0.406 |
|
| 2015 |
Chipumuro E, Marco E, Christensen CL, Kwiatkowski N, Zhang T, Hatheway CM, Abraham BJ, Sharma B, Yeung C, Altabef A, Perez-Atayde A, Wong K, Yuan G, Gray NS, Young RA, et al. Abstract PR05: Targeting of CDK7 inhibits super-enhancer-associated oncogenic programs in MYCN-amplified tumor cells Molecular Cancer Research. 13. DOI: 10.1158/1557-3125.Myc15-Pr05 |
0.392 |
|
| 2014 |
Saadatpour A, Guo G, Orkin SH, Yuan GC. Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis. Genome Biology. 15: 525. PMID 25517911 DOI: 10.1186/S13059-014-0525-9 |
0.328 |
|
| 2014 |
Marco E, Karp RL, Guo G, Robson P, Hart AH, Trippa L, Yuan GC. Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape. Proceedings of the National Academy of Sciences of the United States of America. 111: E5643-50. PMID 25512504 DOI: 10.1073/Pnas.1408993111 |
0.455 |
|
| 2014 |
Chipumuro E, Marco E, Christensen CL, Kwiatkowski N, Zhang T, Hatheway CM, Abraham BJ, Sharma B, Yeung C, Altabef A, Perez-Atayde A, Wong KK, Yuan GC, Gray NS, Young RA, et al. CDK7 inhibition suppresses super-enhancer-linked oncogenic transcription in MYCN-driven cancer. Cell. 159: 1126-39. PMID 25416950 DOI: 10.1016/J.Cell.2014.10.024 |
0.418 |
|
| 2014 |
Riddell J, Gazit R, Garrison BS, Guo G, Saadatpour A, Mandal PK, Ebina W, Volchkov P, Yuan GC, Orkin SH, Rossi DJ. Reprogramming committed murine blood cells to induced hematopoietic stem cells with defined factors. Cell. 157: 549-64. PMID 24766805 DOI: 10.1016/J.Cell.2014.04.006 |
0.391 |
|
| 2014 |
Pinello L, Xu J, Orkin SH, Yuan GC. Analysis of chromatin-state plasticity identifies cell-type-specific regulators of H3K27me3 patterns. Proceedings of the National Academy of Sciences of the United States of America. 111: E344-53. PMID 24395799 DOI: 10.1073/Pnas.1322570111 |
0.372 |
|
| 2014 |
Das PP, Shao Z, Beyaz S, Apostolou E, Pinello L, De Los Angeles A, O'Brien K, Atsma JM, Fujiwara Y, Nguyen M, Ljuboja D, Guo G, Woo A, Yuan GC, Onder T, et al. Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity. Molecular Cell. 53: 32-48. PMID 24361252 DOI: 10.1016/J.Molcel.2013.11.011 |
0.313 |
|
| 2014 |
Pinello L, Lo Bosco G, Yuan GC. Applications of alignment-free methods in epigenomics. Briefings in Bioinformatics. 15: 419-30. PMID 24197932 DOI: 10.1093/Bib/Bbt078 |
0.39 |
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| 2014 |
Xu J, Shao Z, Li D, Xie H, Kim W, Huang J, Pinello L, Glass K, Yuan G, Orkin SH. Developmental Control of Polycomb Subunit Composition Mediates a Switch to Non-Canonical Functions during Hematopoiesis Blood. 124: 241-241. DOI: 10.1182/Blood.V124.21.241.241 |
0.477 |
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| 2014 |
Chipumuro E, Marco E, Zhang T, Christensen C, Kwiatkowski N, Sharma B, Hatheway C, Altabef A, Abraham BJ, Wong K, Yuan G, Young RA, Gray NS, George RE. Abstract LB-125: Selective inhibition of CDK7 targets MYCN-driven transcriptional amplification in neuroblastoma Cancer Research. 74. DOI: 10.1158/1538-7445.Am2014-Lb-125 |
0.407 |
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| 2013 |
Nag A, Savova V, Fung HL, Miron A, Yuan GC, Zhang K, Gimelbrant AA. Chromatin signature of widespread monoallelic expression. Elife. 2: e01256. PMID 24381246 DOI: 10.7554/eLife.01256 |
0.369 |
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| 2013 |
Ku WL, Girvan M, Yuan GC, Sorrentino F, Ott E. Modeling the dynamics of bivalent histone modifications. Plos One. 8: e77944. PMID 24223747 DOI: 10.1371/Journal.Pone.0077944 |
0.463 |
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| 2013 |
Guo G, Luc S, Marco E, Lin TW, Peng C, Kerenyi MA, Beyaz S, Kim W, Xu J, Das PP, Neff T, Zou K, Yuan GC, Orkin SH. Mapping cellular hierarchy by single-cell analysis of the cell surface repertoire. Cell Stem Cell. 13: 492-505. PMID 24035353 DOI: 10.1016/J.Stem.2013.07.017 |
0.326 |
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| 2013 |
Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. Plos One. 8: e64832. PMID 23741402 DOI: 10.1371/Journal.Pone.0064832 |
0.322 |
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| 2013 |
Walker SR, Nelson EA, Yeh JE, Pinello L, Yuan GC, Frank DA. STAT5 outcompetes STAT3 to regulate the expression of the oncogenic transcriptional modulator BCL6. Molecular and Cellular Biology. 33: 2879-90. PMID 23716595 DOI: 10.1128/Mcb.01620-12 |
0.416 |
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| 2013 |
Larson JL, Huttenhower C, Quackenbush J, Yuan GC. A tiered hidden Markov model characterizes multi-scale chromatin states. Genomics. 102: 1-7. PMID 23570996 DOI: 10.1016/J.Ygeno.2013.03.009 |
0.713 |
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| 2013 |
Bauer DE, Kamran SC, Lessard S, Xu J, Fujiwara Y, Lin C, Shao Z, Canver MC, Smith EC, Pinello L, Sabo PJ, Vierstra J, Voit RA, Yuan G, Porteus MH, et al. Fine-Mapping and Genome Editing Reveal An Essential Erythroid Enhancer At The HbF-Associated BCL11A Locus Blood. 122: 437-437. DOI: 10.1182/Blood.V122.21.437.437 |
0.428 |
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| 2013 |
Wu J, Pinello L, Yissachar E, Yuan G, Roberts C. Abstract PR10: Modulation of chromatin structure and transcription by the SWI/SNF complex in acute lymphoblastic leukemia Cancer Research. 73. DOI: 10.1158/1538-7445.Cec13-Pr10 |
0.422 |
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| 2013 |
Baena E, Shao Z, Linn D, Glass K, Hamblen M, Fujiwara Y, Kim J, Nguyen M, Zhang X, Godinho F, Bronson RT, Mucci L, Loda M, Yuan G, Li Z, et al. Abstract 5393: ETV1 directs androgen metabolism and confers aggressive prostate cancer in engineered mice and patients. Cancer Research. 73: 5393-5393. DOI: 10.1158/1538-7445.Am2013-5393 |
0.324 |
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| 2012 |
Shao Z, Zhang Y, Yuan GC, Orkin SH, Waxman DJ. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Genome Biology. 13: R16. PMID 22424423 DOI: 10.1186/Gb-2012-13-3-R16 |
0.442 |
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| 2012 |
Larson JL, Yuan GC. Chromatin states accurately classify cell differentiation stages. Plos One. 7: e31414. PMID 22363642 DOI: 10.1371/Journal.Pone.0031414 |
0.76 |
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| 2012 |
Yuan GC. Linking genome to epigenome. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 4: 297-309. PMID 22344857 DOI: 10.1002/Wsbm.1165 |
0.413 |
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| 2012 |
Xu J, Shao Z, Glass K, Bauer DE, Pinello L, Van Handel B, Hou S, Stamatoyannopoulos JA, Mikkola HKA, Yuan G, Orkin SH. Genomic Determinants of Human Fetal and Adult Erythroid Gene Expression Blood. 120: 1227-1227. DOI: 10.1182/Blood.V120.21.1227.1227 |
0.45 |
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| 2012 |
Walker SR, Cerchietti LC, Nicolais MC, Yuan G, Melnick A, Frank DA. Abstract 971: Identification of BCL6 targeted therapies for breast cancer through gene expression networks Cancer Research. 72: 971-971. DOI: 10.1158/1538-7445.Am2012-971 |
0.359 |
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| 2012 |
Baena E, Shao Z, Linn D, Hamblen M, Glass K, Saumyadipta P, Fujiwara Y, Godinho F, Kim J, Al-Shhrour F, Nguyen M, Yuan G, Bronson RT, Loda M, Orkin SH, et al. Abstract 2965: ERG and ETV1 regulate a common transcriptional network in prostate cells but in an opposite fashion Cancer Research. 72: 2965-2965. DOI: 10.1158/1538-7445.Am2012-2965 |
0.329 |
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| 2011 |
Van Rechem C, Black JC, Abbas T, Allen A, Rinehart CA, Yuan GC, Dutta A, Whetstine JR. The SKP1-Cul1-F-box and leucine-rich repeat protein 4 (SCF-FbxL4) ubiquitin ligase regulates lysine demethylase 4A (KDM4A)/Jumonji domain-containing 2A (JMJD2A) protein. The Journal of Biological Chemistry. 286: 30462-70. PMID 21757720 DOI: 10.1074/Jbc.M111.273508 |
0.344 |
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| 2011 |
Yuan GC. Prediction of epigenetic target sites by using genomic DNA sequence Handbook of Research On Computational and Systems Biology: Interdisciplinary Applications. 187-201. DOI: 10.4018/978-1-60960-491-2.ch008 |
0.324 |
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| 2010 |
Larson JL, Yuan GC. Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model. Bmc Bioinformatics. 11: 557. PMID 21073706 DOI: 10.1186/1471-2105-11-557 |
0.74 |
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| 2010 |
Rao S, Zhen S, Roumiantsev S, McDonald LT, Yuan GC, Orkin SH. Differential roles of Sall4 isoforms in embryonic stem cell pluripotency. Molecular and Cellular Biology. 30: 5364-80. PMID 20837710 DOI: 10.1128/Mcb.00419-10 |
0.436 |
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| 2010 |
Fang R, Barbera AJ, Xu Y, Rutenberg M, Leonor T, Bi Q, Lan F, Mei P, Yuan GC, Lian C, Peng J, Cheng D, Sui G, Kaiser UB, Shi Y, et al. Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating intragenic H3K4me2 methylation. Molecular Cell. 39: 222-33. PMID 20670891 DOI: 10.1016/J.Molcel.2010.07.008 |
0.436 |
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| 2010 |
Chastanet A, Vitkup D, Yuan GC, Norman TM, Liu JS, Losick RM. Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis. Proceedings of the National Academy of Sciences of the United States of America. 107: 8486-91. PMID 20404177 DOI: 10.1073/Pnas.1002499107 |
0.335 |
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| 2010 |
Liu Y, Shao Z, Yuan GC. Prediction of Polycomb target genes in mouse embryonic stem cells. Genomics. 96: 17-26. PMID 20353814 DOI: 10.1016/J.Ygeno.2010.03.012 |
0.416 |
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| 2010 |
Lantermann AB, Straub T, Strålfors A, Yuan GC, Ekwall K, Korber P. Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae. Nature Structural & Molecular Biology. 17: 251-7. PMID 20118936 DOI: 10.1038/Nsmb.1741 |
0.369 |
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| 2010 |
Larson J, Yuan G. A hidden Markov model for detecting multi-gene chromatin domains Bmc Bioinformatics. 11. DOI: 10.1186/1471-2105-11-S10-O5 |
0.711 |
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| 2009 |
Shen X, Kim W, Fujiwara Y, Simon MD, Liu Y, Mysliwiec MR, Yuan GC, Lee Y, Orkin SH. Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells. Cell. 139: 1303-14. PMID 20064376 DOI: 10.1016/J.Cell.2009.12.003 |
0.412 |
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| 2009 |
Wippo CJ, Krstulovic BS, Ertel F, Musladin S, Blaschke D, Stürzl S, Yuan GC, Hörz W, Korber P, Barbaric S. Differential cofactor requirements for histone eviction from two nucleosomes at the yeast PHO84 promoter are determined by intrinsic nucleosome stability. Molecular and Cellular Biology. 29: 2960-81. PMID 19307305 DOI: 10.1128/Mcb.01054-08 |
0.362 |
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| 2009 |
Yuan GC. Targeted recruitment of histone modifications in humans predicted by genomic sequences. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 341-55. PMID 19193151 DOI: 10.1089/Cmb.2008.18Tt |
0.379 |
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| 2009 |
Di Gesù V, Lo Bosco G, Pinello L, Yuan GC, Corona DF. A multi-layer method to study genome-scale positions of nucleosomes. Genomics. 93: 140-5. PMID 18951969 DOI: 10.1016/J.Ygeno.2008.09.012 |
0.367 |
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| 2008 |
Shen X, Liu Y, Hsu YJ, Fujiwara Y, Kim J, Mao X, Yuan GC, Orkin SH. EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Molecular Cell. 32: 491-502. PMID 19026780 DOI: 10.1016/J.Molcel.2008.10.016 |
0.342 |
|
| 2008 |
Yuan GC, Liu JS. Genomic sequence is highly predictive of local nucleosome depletion. Plos Computational Biology. 4: e13. PMID 18225943 DOI: 10.1371/Journal.Pcbi.0040013 |
0.355 |
|
| 2007 |
Dennis JH, Fan HY, Reynolds SM, Yuan G, Meldrim JC, Richter DJ, Peterson DG, Rando OJ, Noble WS, Kingston RE. Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Research. 17: 928-39. PMID 17568008 DOI: 10.1101/Gr.5636607 |
0.387 |
|
| 2006 |
Yuan GC, Ma P, Zhong W, Liu JS. Statistical assessment of the global regulatory role of histone acetylation in Saccharomyces cerevisiae. Genome Biology. 7: R70. PMID 16884527 DOI: 10.1186/Gb-2006-7-8-R70 |
0.418 |
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| 2005 |
Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ. Genome-scale identification of nucleosome positions in S. cerevisiae. Science (New York, N.Y.). 309: 626-30. PMID 15961632 DOI: 10.1126/Science.1112178 |
0.404 |
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