cached image

Beisi Xu, Ph.D - Publications

2011-2014 City of Hope Medical Center, Duarte, CA, United States 
 2014- Center for Applied Bioinformatics St Jude Children's Research Hospital, New York, NY, United States 

50 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Montefiori LE, Bendig S, Gu Z, Chen X, Polonen P, Ma X, Murison A, Zeng A, Garcia-Prat L, Dickerson K, Iacobucci I, Abdelhamed S, Hiltenbrand R, Mead PE, Mehr CM, ... Xu B, et al. Enhancer hijacking drives oncogenic BCL11B expression in lineage ambiguous stem cell leukemia. Cancer Discovery. PMID 34103329 DOI: 10.1158/2159-8290.CD-21-0145  0.4
2021 Zong X, Hao X, Xu B, Crawford JC, Wright S, Li J, Zhang Y, Bai L, He M, Jiang M, Fan Y, Connelly JP, Pruett-Miller SM, Berns H, Janke L, et al. Foxp3 enhancers synergize to maximize regulatory T cell suppressive capacity. The Journal of Experimental Medicine. 218. PMID 34086055 DOI: 10.1084/jem.20202415  0.52
2021 Djekidel MN, Rosikiewicz W, Peng JC, Kanneganti TD, Hui Y, Jin H, Hedges D, Schreiner P, Fan Y, Wu G, Xu B. CovidExpress: an interactive portal for intuitive investigation on SARS-CoV-2 related transcriptomes. Biorxiv : the Preprint Server For Biology. PMID 34075382 DOI: 10.1101/2021.05.14.444026  0.4
2021 Dikiy S, Li J, Bai L, Jiang M, Janke L, Zong X, Hao X, Hoyos B, Wang ZM, Xu B, Fan Y, Rudensky AY, Feng Y. A distal Foxp3 enhancer enables interleukin-2 dependent thymic Treg cell lineage commitment for robust immune tolerance. Immunity. PMID 33838102 DOI: 10.1016/j.immuni.2021.03.020  0.36
2021 Rai M, Coleman Z, Curley M, Nityanandam A, Platt A, Robles-Murguia M, Jiao J, Finkelstein D, Wang YD, Xu B, Fan Y, Demontis F. Proteasome stress in skeletal muscle mounts a long-range protective response that delays retinal and brain aging. Cell Metabolism. PMID 33773104 DOI: 10.1016/j.cmet.2021.03.005  0.32
2021 Williams J, Xu B, Putnam D, Thrasher A, Li C, Yang J, Chen X. MethylationToActivity: a deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors. Genome Biology. 22: 24. PMID 33461601 DOI: 10.1186/s13059-020-02220-y  0.52
2020 Xu P, Scott DC, Xu B, Yao Y, Feng R, Cheng L, Mayberry K, Bi W, Palmer LE, King MT, Wang H, Li Y, Fan Y, Alpi AF, Li C, et al. FBXO11-Mediated Proteolysis of BAHD1 Relieves PRC2-dependent Transcriptional Repression in Erythropoiesis. Blood. PMID 33156908 DOI: 10.1182/blood.2020007809  0.52
2020 Wang Q, Liu X, Chen C, Chen J, Xu B, Chen L, Zhou J, Huang Y, Chen W, Teng R, Zhao W, Jin L, Shen J, Shen J, Yen Y, et al. A predictive signature for oxaliplatin and 5-fluorouracil based chemotherapy in locally advanced gastric cancer. Translational Oncology. 14: 100901. PMID 33091827 DOI: 10.1016/j.tranon.2020.100901  0.64
2020 Zhang H, Zhang Y, Zhou X, Wright S, Hyle J, Zhao L, An J, Zhao X, Shao Y, Xu B, Lee HM, Chen T, Zhou Y, Chen X, Lu R, et al. Functional interrogation of regulome in MLLr leukemia via reporter-based CRISPR/Cas9 screen. Elife. 9. PMID 33001025 DOI: 10.7554/eLife.57858  0.52
2020 Xu B, Mulvey B, Salie M, Yang X, Matsui Y, Nityanandam A, Fan Y, Peng JC. UTX/KDM6A suppresses AP-1 and a gliogenesis program during neural differentiation of human pluripotent stem cells. Epigenetics & Chromatin. 13: 38. PMID 32977832 DOI: 10.1186/s13072-020-00359-3  0.4
2020 Evans MK, Matsui Y, Xu B, Willis C, Loome J, Milburn L, Fan Y, Pagala V, Peng JC. Ybx1 fine-tunes PRC2 activities to control embryonic brain development. Nature Communications. 11: 4060. PMID 32792512 DOI: 10.1038/S41467-020-17878-Y  0.4
2020 Li J, Wang YN, Xu BS, Liu YP, Zhou M, Long T, Li H, Dong H, Nie Y, Chen PR, Wang ED, Liu RJ. Intellectual disability-associated gene ftsj1 is responsible for 2'-O-methylation of specific tRNAs. Embo Reports. e50095. PMID 32558197 DOI: 10.15252/Embr.202050095  0.64
2020 Zeineldin M, Federico S, Chen X, Fan Y, Xu B, Stewart E, Zhou X, Jeon J, Griffiths L, Nguyen R, Norrie J, Easton J, Mulder H, Yergeau D, Liu Y, et al. MYCN amplification and ATRX mutations are incompatible in neuroblastoma. Nature Communications. 11: 913. PMID 32060267 DOI: 10.1038/S41467-020-14682-6  0.52
2020 Wijaya J, Vo BT, Liu J, Xu B, Wu G, Wang Y, Peng J, Zhang J, Janke LJ, Orr BA, Yu J, Roussel MF, Schuetz JD. An ABC transporter drives medulloblastoma pathogenesis by regulating Sonic Hedgehog signaling. Cancer Research. PMID 31948942 DOI: 10.1158/0008-5472.Can-19-2054  0.76
2020 Williams J, Xu B, Putnam D, Chen X. Abstract 6576: DNA methylation reveals alternative promoter usage in genes critical to pediatric tumors Cancer Research. 80: 6576-6576. DOI: 10.1158/1538-7445.Am2020-6576  0.32
2019 Robles-Murguia M, Rao D, Finkelstein D, Xu B, Fan Y, Demontis F. Muscle-derived Dpp regulates feeding initiation via endocrine modulation of brain dopamine biosynthesis. Genes & Development. PMID 31831628 DOI: 10.1101/Gad.329110.119  0.32
2019 Wei J, Long L, Zheng W, Dhungana Y, Lim SA, Guy C, Wang Y, Wang YD, Qian C, Xu B, Kc A, Saravia J, Huang H, Yu J, Doench JG, et al. Targeting REGNASE-1 programs long-lived effector T cells for cancer therapy. Nature. PMID 31827283 DOI: 10.1038/S41586-019-1821-Z  0.76
2019 Norrie JL, Lupo MS, Xu B, Al Diri I, Valentine M, Putnam D, Griffiths L, Zhang J, Johnson D, Easton J, Shao Y, Honnell V, Frase S, Miller S, Stewart V, et al. Nucleome Dynamics during Retinal Development. Neuron. PMID 31493975 DOI: 10.1016/J.Neuron.2019.08.002  0.52
2019 Tian L, Shao Y, Nance S, Dang J, Xu B, Ma X, Li Y, Ju B, Dong L, Newman S, Zhou X, Schreiner P, Tseng E, Hon T, Ashby M, et al. Long-read sequencing unveils IGH-DUX4 translocation into the silenced IGH allele in B-cell acute lymphoblastic leukemia. Nature Communications. 10: 2789. PMID 31243274 DOI: 10.1038/S41467-019-10637-8  0.52
2019 Hyle J, Zhang Y, Wright S, Xu B, Shao Y, Easton J, Tian L, Feng R, Xu P, Li C. Acute depletion of CTCF directly affects MYC regulation through loss of enhancer-promoter looping. Nucleic Acids Research. PMID 31127282 DOI: 10.1093/Nar/Gkz462  0.52
2019 Silveira AB, Kasper LH, Fan Y, Jin H, Wu G, Shaw TI, Zhu X, Larson JD, Easton J, Shao Y, Yergeau DA, Rosencrance C, Boggs K, Rusch MC, Ding L, ... ... Xu B, et al. Correction to: H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo. Acta Neuropathologica. PMID 30976974 DOI: 10.1007/S00401-019-02006-Y  0.52
2019 Silveira AB, Kasper LH, Fan Y, Jin H, Wu G, Shaw TI, Zhu X, Larson JD, Easton J, Shao Y, Yergeau DA, Rosencrance C, Boggs K, Rusch MC, Ding L, ... ... Xu B, et al. H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo. Acta Neuropathologica. PMID 30770999 DOI: 10.1007/S00401-019-01975-4  0.52
2019 Yang X, Xu B, Mulvey B, Evans M, Jordan S, Wang YD, Pagala V, Peng J, Fan Y, Patel A, Peng JC. Differentiation of human pluripotent stem cells into neurons or cortical organoids requires transcriptional co-regulation by UTX and 53BP1. Nature Neuroscience. PMID 30718900 DOI: 10.1038/S41593-018-0328-5  0.4
2018 Larson JD, Kasper LH, Paugh BS, Jin H, Wu G, Kwon CH, Fan Y, Shaw TI, Silveira AB, Qu C, Xu R, Zhu X, Zhang J, Russell HR, Peters JL, ... ... Xu B, et al. Histone H3.3 K27M Accelerates Spontaneous Brainstem Glioma and Drives Restricted Changes in Bivalent Gene Expression. Cancer Cell. PMID 30595505 DOI: 10.1016/J.Ccell.2018.11.015  0.52
2018 Karmaus PWF, Chen X, Lim SA, Herrada AA, Nguyen TM, Xu B, Dhungana Y, Rankin S, Chen W, Rosencrance C, Yang K, Fan Y, Cheng Y, Easton J, Neale G, et al. Metabolic heterogeneity underlies reciprocal fates of T17 cell stemness and plasticity. Nature. PMID 30568299 DOI: 10.1038/S41586-018-0806-7  0.52
2018 Lavado A, Park JY, Paré J, Finkelstein D, Pan H, Xu B, Fan Y, Kumar RP, Neale G, Kwak YD, McKinnon PJ, Johnson RL, Cao X. The Hippo Pathway Prevents YAP/TAZ-Driven Hypertranscription and Controls Neural Progenitor Number. Developmental Cell. 47: 576-591.e8. PMID 30523785 DOI: 10.1016/J.Devcel.2018.09.021  0.32
2018 Alexander TB, Gu Z, Iacobucci I, Dickerson K, Choi JK, Xu B, Payne-Turner D, Yoshihara H, Loh ML, Horan J, Buldini B, Basso G, Elitzur S, de Haas V, Zwaan CM, et al. The genetic basis and cell of origin of mixed phenotype acute leukaemia. Nature. PMID 30209392 DOI: 10.1038/S41586-018-0436-0  0.48
2018 Stewart E, McEvoy J, Wang H, Chen X, Honnell V, Ocarz M, Gordon B, Dapper J, Blankenship K, Yang Y, Li Y, Shaw TI, Cho JH, Wang X, Xu B, et al. Identification of Therapeutic Targets in Rhabdomyosarcoma through Integrated Genomic, Epigenomic, and Proteomic Analyses. Cancer Cell. PMID 30146332 DOI: 10.1016/J.Ccell.2018.07.012  0.88
2018 Vo BT, Kwon JA, Li C, Finkelstein D, Xu B, Orr BA, Sherr CJ, Roussel MF. Mouse medulloblastoma driven by CRISPR activation of cellular Myc. Scientific Reports. 8: 8733. PMID 29880921 DOI: 10.1038/S41598-018-24956-1  0.52
2018 Wang L, Hiler D, Xu B, AlDiri I, Chen X, Zhou X, Griffiths L, Valentine M, Shirinifard A, Sablauer A, Thiagarajan S, Barabas ME, Zhang J, Johnson D, Frase S, et al. Retinal Cell Type DNA Methylation and Histone Modifications Predict Reprogramming Efficiency and Retinogenesis in 3D Organoid Cultures. Cell Reports. 22: 2601-2614. PMID 29514090 DOI: 10.1016/J.Celrep.2018.01.075  0.48
2018 Zeineldin M, Federico S, Chen X, Xu B, Stewart E, Naranjo A, Hogarty MD, Dyer MA. Abstract IA18: MYCN amplification and ATRX mutations are incompatible in neuroblastoma Cancer Research. 78. DOI: 10.1158/1538-7445.Pedca17-Ia18  0.32
2018 Tian L, Xu B, Shao Y, Ma X, Li Y, Newman S, Zhou X, Ashby M, Hon T, Clark T, Tseng E, Easton J, Zhang J. Abstract 1485: Allelic specificity of immunoglobulin heavy chain (IGH) translocation in B-cell acute lymphoblastic leukemia (B-ALL) unveiled by long-read sequencing Cancer Research. 78: 1485-1485. DOI: 10.1158/1538-7445.Am2018-1485  0.52
2017 Zimmerman MW, Liu Y, He S, Durbin AD, Abraham BJ, Easton J, Shao Y, Xu B, Zhu S, Zhang X, Li Z, Weichert-Leahey N, Young RA, Zhang J, Look AT. c-MYC drives a subset of high-risk pediatric neuroblastomas and is activated through mechanisms including enhancer hijacking and focal enhancer amplification. Cancer Discovery. PMID 29284669 DOI: 10.1158/2159-8290.Cd-17-0993  0.52
2017 Stewart E, Federico SM, Chen X, Shelat AA, Bradley C, Gordon B, Karlstrom A, Twarog NR, Clay MR, Bahrami A, Freeman BB, Xu B, Zhou X, Wu J, Honnell V, et al. Orthotopic patient-derived xenografts of paediatric solid tumours. Nature. PMID 28854174 DOI: 10.1038/Nature23647  0.52
2017 Aldiri I, Xu B, Wang L, Chen X, Hiler D, Griffiths L, Valentine M, Shirinifard A, Thiagarajan S, Sablauer A, Barabas ME, Zhang J, Johnson D, Frase S, Zhou X, et al. The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis. Neuron. 94: 550-568.e10. PMID 28472656 DOI: 10.1016/J.Neuron.2017.04.022  0.52
2017 Larson JD, Kasper LH, Wu G, Fan Y, Finkelstein D, Jin H, Paugh BS, Silveira AB, Xu B, Zhu X, Zhang J, Russell HR, McKinnon PJ, Ellison DW, Zhang J, et al. Abstract 3006: Oncogenic activity of H3.3 K27M in a spontaneous DIPG mouse model Cancer Research. 77: 3006-3006. DOI: 10.1158/1538-7445.Am2017-3006  0.52
2016 Zhang J, McCastlain K, Yoshihara H, Xu B, Chang Y, Churchman ML, Wu G, Li Y, Wei L, Iacobucci I, Liu Y, Qu C, Wen J, Edmonson M, Payne-Turner D, et al. Deregulation of DUX4 and ERG in acute lymphoblastic leukemia. Nature Genetics. PMID 27776115 DOI: 10.1038/Ng.3691  0.44
2016 Jones BG, Penkert RR, Xu B, Fan Y, Neale G, Gearhart PJ, Hurwitz JL. Binding of estrogen receptors to switch sites and regulatory elements in the immunoglobulin heavy chain locus of activated B cells suggests a direct influence of estrogen on antibody expression. Molecular Immunology. 77: 97-102. PMID 27494228 DOI: 10.1016/J.Molimm.2016.07.015  0.44
2016 Hurwitz JL, Penkert RR, Xu B, Fan Y, Partridge JF, Maul RW, Gearhart PJ. Hotspots for Vitamin-Steroid-Thyroid Hormone Response Elements Within Switch Regions of Immunoglobulin Heavy Chain Loci Predict a Direct Influence of Vitamins and Hormones on B Cell Class Switch Recombination. Viral Immunology. PMID 26741514 DOI: 10.1089/Vim.2015.0104  0.44
2015 Aldiri I, Ajioka I, Xu B, Zhang J, Chen X, Benavente C, Finkelstein D, Johnson D, Akiyama J, Pennacchio LA, Dyer MA. Brg1 coordinates multiple processes during retinogenesis and is a tumor suppressor in retinoblastoma. Development (Cambridge, England). 142: 4092-106. PMID 26628093 DOI: 10.1242/Dev.124800  0.44
2015 Hunt LC, Xu B, Finkelstein D, Fan Y, Carroll PA, Cheng PF, Eisenman RN, Demontis F. The glucose-sensing transcription factor MLX promotes myogenesis via myokine signaling. Genes & Development. PMID 26584623 DOI: 10.1101/Gad.267419.115  0.44
2015 Hiler D, Chen X, Hazen J, Kupriyanov S, Carroll PA, Qu C, Xu B, Johnson D, Griffiths L, Frase S, Rodriguez AR, Martin G, Zhang J, Jeon J, Fan Y, et al. Quantification of Retinogenesis in 3D Cultures Reveals Epigenetic Memory and Higher Efficiency in iPSCs Derived from Rod Photoreceptors. Cell Stem Cell. 17: 101-115. PMID 26140606 DOI: 10.1016/J.Stem.2015.05.015  0.44
2015 Li Z, Dai H, Martos SN, Xu B, Gao Y, Li T, Zhu G, Schones DE, Wang Z. Distinct roles of DNMT1-dependent and DNMT1-independent methylation patterns in the genome of mouse embryonic stem cells. Genome Biology. 16: 115. PMID 26032981 DOI: 10.1186/S13059-015-0685-2  0.44
2014 Jose CC, Xu B, Jagannathan L, Trac C, Mallela RK, Hattori T, Lai D, Koide S, Schones DE, Cuddapah S. Epigenetic dysregulation by nickel through repressive chromatin domain disruption. Proceedings of the National Academy of Sciences of the United States of America. 111: 14631-6. PMID 25246589 DOI: 10.1073/Pnas.1406923111  0.48
2013 Xu B, Schones DE, Wang Y, Liang H, Li G. A structural-based strategy for recognition of transcription factor binding sites. Plos One. 8: e52460. PMID 23320072 DOI: 10.1371/Journal.Pone.0052460  0.92
2011 Xu B, Shen H, Zhu X, Li G. Fast and accurate computation schemes for evaluating vibrational entropy of proteins. Journal of Computational Chemistry. 32: 3188-93. PMID 21953554 DOI: 10.1002/Jcc.21900  0.76
2011 Liu RJ, Tan M, Du DH, Xu BS, Eriani G, Wang ED. Peripheral insertion modulates the editing activity of the isolated CP1 domain of leucyl-tRNA synthetase. The Biochemical Journal. 440: 217-27. PMID 21819379 DOI: 10.1042/Bj20111177  0.64
2011 Chen J, Wang J, Xu B, Zhu W, Li G. Insight into mechanism of small molecule inhibitors of the MDM2-p53 interaction: molecular dynamics simulation and free energy analysis. Journal of Molecular Graphics & Modelling. 30: 46-53. PMID 21764342 DOI: 10.1016/J.Jmgm.2011.06.003  0.76
2009 Xu B, Yang Y, Liang H, Zhou Y. An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles. Proteins. 76: 718-30. PMID 19274740 DOI: 10.1002/Prot.22384  0.92
2004 Xu B, Huang L, Liang H. Thermodynamic behaviors of polyampholytes at low temperatures. The Journal of Chemical Physics. 121: 7494-500. PMID 15473824 DOI: 10.1063/1.1792191  0.92
Show low-probability matches.