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Yan Li - Publications

Affiliations: 
Case Western Reserve University, Cleveland Heights, OH, United States 
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31 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
2023 Weng C, Gu A, Zhang S, Lu L, Ke L, Gao P, Liu X, Wang Y, Hu P, Plummer D, MacDonald E, Zhang S, Xi J, Lai S, Leskov K, ... ... Li Y, et al. Single cell multiomic analysis reveals diabetes-associated β-cell heterogeneity driven by HNF1A. Nature Communications. 14: 5400. PMID 37669939 DOI: 10.1038/s41467-023-41228-3  0.68
2023 Chen H, Zhang L, Yue F, Cui C, Li Y, Zhang Q, Liang L, Meng L, Zhang C. Effects of assisted reproductive technology on gene expression in heart and spleen tissues of adult offspring mouse. Frontiers in Endocrinology. 14: 1035161. PMID 37065763 DOI: 10.3389/fendo.2023.1035161  0.432
2022 Zhang S, Plummer D, Lu L, Cui J, Xu W, Wang M, Liu X, Prabhakar N, Shrinet J, Srinivasan D, Fraser P, Li Y, Li J, Jin F. DeepLoop robustly maps chromatin interactions from sparse allele-resolved or single-cell Hi-C data at kilobase resolution. Nature Genetics. 54: 1013-1025. PMID 35817982 DOI: 10.1038/s41588-022-01116-w  0.684
2021 Dong C, Simonett SP, Shin S, Stapleton DS, Schueler KL, Churchill GA, Lu L, Liu X, Jin F, Li Y, Attie AD, Keller MP, Keleş S. INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants. Genome Biology. 22: 241. PMID 34425882 DOI: 10.1186/s13059-021-02450-8  0.688
2020 Weng C, Xi J, Li H, Cui J, Gu A, Lai S, Leskov K, Ke L, Jin F, Li Y. Single-cell lineage analysis reveals extensive multimodal transcriptional control during directed beta-cell differentiation. Nature Metabolism. PMID 33257854 DOI: 10.1038/s42255-020-00314-2  0.714
2020 Karakose E, Wang H, Inabnet W, Thakker RV, Libutti S, Fernandez-Ranvier G, Suh H, Stevenson M, Kinoshita Y, Donovan M, Antipin Y, Li Y, Liu X, Jin F, Wang P, et al. Aberrant methylation underlies insulin gene expression in human insulinoma. Nature Communications. 11: 5210. PMID 33060578 DOI: 10.1038/s41467-020-18839-1  0.684
2020 Van Buren E, Hu M, Weng C, Jin F, Li Y, Wu D, Li Y. TWO-SIGMA: A novel two-component single cell model-based association method for single-cell RNA-seq data. Genetic Epidemiology. PMID 32989764 DOI: 10.1002/gepi.22361  0.674
2020 Hsu J, Huang HT, Lee CT, Choudhuri A, Wilson NK, Abraham BJ, Moignard V, Kucinski I, Yu S, Hyde RK, Tober J, Cai X, Li Y, Guo Y, Yang S, et al. CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation. Proceedings of the National Academy of Sciences of the United States of America. PMID 32883883 DOI: 10.1073/Pnas.2003228117  0.467
2020 Lu L, Liu X, Huang WK, Giusti-Rodríguez P, Cui J, Zhang S, Xu W, Wen Z, Ma S, Rosen JD, Xu Z, Bartels CF, Kawaguchi R, Hu M, Scacheri PC, ... ... Li Y, ... ... Li Y, et al. Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases. Molecular Cell. PMID 32592681 DOI: 10.1016/J.Molcel.2020.06.007  0.707
2020 Demir E, Qin T, Li Y, Zhang Y, Guo X, Ingle T, Yan J, Orza AI, Biris AS, Ghorai S, Zhou T, Chen T. Cytotoxicity and genotoxicity of cadmium oxide nanoparticles evaluated using in vitro assays. Mutation Research. 850: 503149. PMID 32247558 DOI: 10.1016/J.Mrgentox.2020.503149  0.402
2019 Fang Z, Weng C, Li H, Tao R, Mai W, Liu X, Lu L, Lai S, Duan Q, Alvarez C, Arvan P, Wynshaw-Boris A, Li Y, Pei Y, Jin F, ... Li Y, et al. Single-Cell Heterogeneity Analysis and CRISPR Screen Identify Key β-Cell-Specific Disease Genes. Cell Reports. 26: 3132-3144.e7. PMID 30865899 DOI: 10.1016/J.Celrep.2019.02.043  0.722
2018 Elitt MS, Shick HE, Madhavan M, Allan KC, Clayton BLL, Weng C, Miller TE, Factor DC, Barbar L, Nawash BS, Nevin ZS, Lager AM, Li Y, Jin F, Adams DJ, et al. Chemical Screening Identifies Enhancers of Mutant Oligodendrocyte Survival and Unmasks a Distinct Pathological Phase in Pelizaeus-Merzbacher Disease. Stem Cell Reports. PMID 30146490 DOI: 10.1016/J.Stemcr.2018.07.015  0.673
2017 Mack SC, Pajtler KW, Chavez L, Okonechnikov K, Bertrand KC, Wang X, Erkek S, Federation A, Song A, Lee C, Wang X, McDonald L, Morrow JJ, Saiakhova A, Sin-Chan P, ... ... Li Y, et al. Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling. Nature. PMID 29258295 DOI: 10.1038/Nature25169  0.307
2017 Li Y, Yan J, Ding W, Chen Y, Pack LM, Chen T. Genotoxicity and gene expression analyses of liver and lung tissues of mice treated with titanium dioxide nanoparticles. Mutagenesis. 32: 33-46. PMID 28011748 DOI: 10.1093/mutage/gew065  0.443
2016 Li Y, Doak SH, Yan J, Chen DH, Zhou M, Mittelstaedt RA, Chen Y, Li C, Chen T. Factors affecting the in vitro micronucleus assay for evaluation of nanomaterials. Mutagenesis. PMID 27567283 DOI: 10.1093/mutage/gew040  0.442
2016 Guo X, Li Y, Yan J, Ingle T, Jones MY, Mei N, Boudreau MD, Cunningham CK, Abbas M, Paredes A, Zhou T, Moore MM, Howard PC, Chen T. Size- and coating-dependent cytotoxicity and genotoxicity of silver nanoparticles evaluated using in vitro standard assays. Nanotoxicology. 1-48. PMID 27441588 DOI: 10.1080/17435390.2016.1214764  0.438
2016 Li Y, Qin T, Ingle T, Yan J, He W, Yin JJ, Chen T. Differential genotoxicity mechanisms of silver nanoparticles and silver ions. Archives of Toxicology. PMID 27180073 DOI: 10.1007/S00204-016-1730-Y  0.416
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  0.665
2014 Li Y, Rivera CM, Ishii H, Jin F, Selvaraj S, Lee AY, Dixon JR, Ren B. CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells. Plos One. 9: e114485. PMID 25486255 DOI: 10.1371/Journal.Pone.0114485  0.768
2014 Chen T, Yan J, Li Y. Genotoxicity of titanium dioxide nanoparticles. Journal of Food and Drug Analysis. 22: 95-104. PMID 24673907 DOI: 10.1016/j.jfda.2014.01.008  0.448
2014 Li Y, Bhalli JA, Ding W, Yan J, Pearce MG, Sadiq R, Cunningham CK, Jones MY, Monroe WA, Howard PC, Zhou T, Chen T. Cytotoxicity and genotoxicity assessment of silver nanoparticles in mouse. Nanotoxicology. 8: 36-45. PMID 24266757 DOI: 10.3109/17435390.2013.855827  0.418
2013 Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature. 503: 290-4. PMID 24141950 DOI: 10.1038/Nature12644  0.774
2013 Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, ... ... Li Y, et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell. 153: 1134-48. PMID 23664764 DOI: 10.1016/J.Cell.2013.04.022  0.666
2013 Meng F, Yan J, Li Y, Fu PP, Fossom LH, Sood RK, Mans DJ, Chu PI, Moore MM, Chen T. Genotoxicity of 2-bromo-3'-chloropropiophenone. Toxicology and Applied Pharmacology. 270: 158-63. PMID 23628427 DOI: 10.1016/j.taap.2013.04.012  0.407
2013 Rajagopal N, Xie W, Li Y, Wagner U, Wang W, Stamatoyannopoulos J, Ernst J, Kellis M, Ren B. RFECS: a random-forest based algorithm for enhancer identification from chromatin state. Plos Computational Biology. 9: e1002968. PMID 23526891 DOI: 10.1371/Journal.Pcbi.1002968  0.613
2012 Woodruff RS, Li Y, Yan J, Bishop M, Jones MY, Watanabe F, Biris AS, Rice P, Zhou T, Chen T. Genotoxicity evaluation of titanium dioxide nanoparticles using the Ames test and Comet assay. Journal of Applied Toxicology : Jat. 32: 934-43. PMID 22744910 DOI: 10.1002/Jat.2781  0.423
2012 Sadiq R, Bhalli JA, Yan J, Woodruff RS, Pearce MG, Li Y, Mustafa T, Watanabe F, Pack LM, Biris AS, Khan QM, Chen T. Genotoxicity of TiO(2) anatase nanoparticles in B6C3F1 male mice evaluated using Pig-a and flow cytometric micronucleus assays. Mutation Research. 745: 65-72. PMID 22712079 DOI: 10.1016/J.Mrgentox.2012.02.002  0.41
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  0.757
2011 Jin F, Li Y, Ren B, Natarajan R. Enhancers: multi-dimensional signal integrators. Transcription. 2: 226-30. PMID 22231119 DOI: 10.4161/trns.2.5.17712  0.735
2011 Jin F, Li Y, Ren B, Natarajan R. PU.1 and C/EBP(alpha) synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers. Proceedings of the National Academy of Sciences of the United States of America. 108: 5290-5. PMID 21402921 DOI: 10.1073/Pnas.1017214108  0.743
2008 Li Y, Reddy MA, Miao F, Shanmugam N, Yee JK, Hawkins D, Ren B, Natarajan R. Role of the histone H3 lysine 4 methyltransferase, SET7/9, in the regulation of NF-kappaB-dependent inflammatory genes. Relevance to diabetes and inflammation. The Journal of Biological Chemistry. 283: 26771-81. PMID 18650421 DOI: 10.1074/Jbc.M802800200  0.485
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