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Yang E Li - Publications

Affiliations: 
Ludwig Institute for Cancer Research, San Diego 
Area:
Bioinformatics, Genomics
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37 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
2024 Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, et al. Author Correction: Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature. PMID 38200319 DOI: 10.1038/s41586-023-07013-4  0.376
2023 Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, et al. Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature. 624: 390-402. PMID 38092918 DOI: 10.1038/s41586-023-06819-6  0.473
2023 Zu S, Li YE, Wang K, Armand EJ, Mamde S, Amaral ML, Wang Y, Chu A, Xie Y, Miller M, Xu J, Wang Z, Zhang K, Jia B, Hou X, et al. Single-cell analysis of chromatin accessibility in the adult mouse brain. Nature. 624: 378-389. PMID 38092917 DOI: 10.1038/s41586-023-06824-9  0.588
2023 Liu H, Zeng Q, Zhou J, Bartlett A, Wang BA, Berube P, Tian W, Kenworthy M, Altshul J, Nery JR, Chen H, Castanon RG, Zu S, Li YE, Lucero J, et al. Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain. Nature. 624: 366-377. PMID 38092913 DOI: 10.1038/s41586-023-06805-y  0.715
2023 Li Y, Zhang J, Cai Z, Gao X, Zhang L, Lu Z, Wang X, Yu P, Li J, Fang F. Disitamab Vedotin (RC48) for HER2-positive advanced breast cancer: a case report and literature review. Frontiers in Oncology. 13: 1286392. PMID 38074635 DOI: 10.3389/fonc.2023.1286392  0.457
2023 Tian W, Zhou J, Bartlett A, Zeng Q, Liu H, Castanon RG, Kenworthy M, Altshul J, Valadon C, Aldridge A, Nery JR, Chen H, Xu J, Johnson ND, Lucero J, ... ... Li YE, et al. Single-cell DNA methylation and 3D genome architecture in the human brain. Science (New York, N.Y.). 382: eadf5357. PMID 37824674 DOI: 10.1126/science.adf5357  0.513
2023 Li YE, Preissl S, Miller M, Johnson ND, Wang Z, Jiao H, Zhu C, Wang Z, Xie Y, Poirion O, Kern C, Pinto-Duarte A, Tian W, Siletti K, Emerson N, et al. A comparative atlas of single-cell chromatin accessibility in the human brain. Science (New York, N.Y.). 382: eadf7044. PMID 37824643 DOI: 10.1126/science.adf7044  0.729
2023 Xie Y, Zhu C, Wang Z, Tastemel M, Chang L, Li YE, Ren B. Droplet-based single-cell joint profiling of histone modifications and transcriptomes. Nature Structural & Molecular Biology. PMID 37563440 DOI: 10.1038/s41594-023-01060-1  0.73
2023 Xie F, Armand EJ, Yao Z, Liu H, Bartlett A, Behrens MM, Li YE, Lucero JD, Luo C, Nery JR, Pinto-Duarte A, Poirion OB, Preissl S, Rivkin AC, Tasic B, et al. Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes. Cell Genomics. 3: 100342. PMID 37492103 DOI: 10.1016/j.xgen.2023.100342  0.491
2023 Hawrylycz M, Martone ME, Ascoli GA, Bjaalie JG, Dong HW, Ghosh SS, Gillis J, Hertzano R, Haynor DR, Hof PR, Kim Y, Lein E, Liu Y, Miller JA, Mitra PP, ... ... Li Y, et al. A guide to the BRAIN Initiative Cell Census Network data ecosystem. Plos Biology. 21: e3002133. PMID 37390046 DOI: 10.1371/journal.pbio.3002133  0.445
2023 Raviram R, Raman A, Preissl S, Ning J, Wu S, Koga T, Zhang K, Brennan CW, Zhu C, Luebeck J, Van Deynze K, Han JY, Hou X, Ye Z, Mischel AK, ... Li YE, et al. Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity. Proceedings of the National Academy of Sciences of the United States of America. 120: e2210991120. PMID 37155843 DOI: 10.1073/pnas.2210991120  0.758
2023 Liu H, Zeng Q, Zhou J, Bartlett A, Wang BA, Berube P, Tian W, Kenworthy M, Altshul J, Nery JR, Chen H, Castanon RG, Zu S, Li YE, Lucero J, et al. Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain. Biorxiv : the Preprint Server For Biology. PMID 37131654 DOI: 10.1101/2023.04.16.536509  0.714
2023 Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, et al. Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex. Biorxiv : the Preprint Server For Biology. PMID 37066152 DOI: 10.1101/2023.04.08.536119  0.491
2022 D'Aurizio R, Catona O, Pitasi M, Li YE, Ren B, Nicolis SK. Bridging between Mouse and Human Enhancer-Promoter Long-Range Interactions in Neural Stem Cells, to Understand Enhancer Function in Neurodevelopmental Disease. International Journal of Molecular Sciences. 23. PMID 35887306 DOI: 10.3390/ijms23147964  0.472
2022 Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, ... ... Li YE, et al. Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature. PMID 35319013 DOI: 10.1038/s41586-022-04562-y  0.337
2022 Luo J, Chen Y, Yang Y, Zhang K, Liu Y, Zhao H, Dong L, Xu J, Li Y, Wei W. Prognosis Prediction of Uveal Melanoma After Plaque Brachytherapy Based on Ultrasound With Machine Learning. Frontiers in Medicine. 8: 777142. PMID 35127747 DOI: 10.3389/fmed.2021.777142  0.305
2021 Zhang K, Hocker JD, Miller M, Hou X, Chiou J, Poirion OB, Qiu Y, Li YE, Gaulton KJ, Wang A, Preissl S, Ren B. A single-cell atlas of chromatin accessibility in the human genome. Cell. PMID 34774128 DOI: 10.1016/j.cell.2021.10.024  0.539
2021 Li YE, Preissl S, Hou X, Zhang Z, Zhang K, Qiu Y, Poirion OB, Li B, Chiou J, Liu H, Pinto-Duarte A, Kubo N, Yang X, Fang R, Wang X, et al. An atlas of gene regulatory elements in adult mouse cerebrum. Nature. 598: 129-136. PMID 34616068 DOI: 10.1038/s41586-021-03604-1  0.683
2021 Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, ... ... Li YE, et al. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature. 598: 103-110. PMID 34616066 DOI: 10.1038/s41586-021-03500-8  0.468
2021 Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, ... ... Li YE, et al. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature. 598: 111-119. PMID 34616062 DOI: 10.1038/s41586-021-03465-8  0.477
2021 Liu H, Zhou J, Tian W, Luo C, Bartlett A, Aldridge A, Lucero J, Osteen JK, Nery JR, Chen H, Rivkin A, Castanon RG, Clock B, Li YE, Hou X, et al. DNA methylation atlas of the mouse brain at single-cell resolution. Nature. 598: 120-128. PMID 34616061 DOI: 10.1038/s41586-020-03182-8  0.714
2021 Hocker JD, Poirion OB, Zhu F, Buchanan J, Zhang K, Chiou J, Wang TM, Zhang Q, Hou X, Li YE, Zhang Y, Farah EN, Wang A, McCulloch AD, Gaulton KJ, et al. Cardiac cell type-specific gene regulatory programs and disease risk association. Science Advances. 7. PMID 33990324 DOI: 10.1126/sciadv.abf1444  0.481
2021 Fang R, Preissl S, Li Y, Hou X, Lucero J, Wang X, Motamedi A, Shiau AK, Zhou X, Xie F, Mukamel EA, Zhang K, Zhang Y, Behrens MM, Ecker JR, et al. Comprehensive analysis of single cell ATAC-seq data with SnapATAC. Nature Communications. 12: 1337. PMID 33637727 DOI: 10.1038/s41467-021-21583-9  0.549
2021 Zhu C, Zhang Y, Li YE, Lucero J, Behrens MM, Ren B. Joint profiling of histone modifications and transcriptome in single cells from mouse brain. Nature Methods. PMID 33589836 DOI: 10.1038/s41592-021-01060-3  0.735
2021 Yan J, Qiu Y, Ribeiro Dos Santos AM, Yin Y, Li YE, Vinckier N, Nariai N, Benaglio P, Raman A, Li X, Fan S, Chiou J, Chen F, Frazer KA, Gaulton KJ, et al. Systematic analysis of binding of transcription factors to noncoding variants. Nature. PMID 33505025 DOI: 10.1038/s41586-021-03211-0  0.579
2020 Wang Z, Li Y, Hou B, Pronobis MI, Wang M, Wang Y, Cheng G, Weng W, Wang Y, Tang Y, Xu X, Pan R, Lin F, Wang N, Chen Z, ... ... Li Y, et al. An array of 60,000 antibodies for proteome-scale antibody generation and target discovery. Science Advances. 6: eaax2271. PMID 32195335 DOI: 10.1126/Sciadv.Aax2271  0.405
2019 Teng S, Li YE, Yang M, Qi R, Huang Y, Wang Q, Zhang Y, Chen S, Li S, Lin K, Cao Y, Ji Q, Gu Q, Cheng Y, Chang Z, et al. Tissue-specific transcription reprogramming promotes liver metastasis of colorectal cancer. Cell Research. PMID 31811277 DOI: 10.1038/S41422-019-0259-Z  0.522
2019 Gorkin DU, Qiu Y, Hu M, Fletez-Brant K, Liu T, Schmitt AD, Noor A, Chiou J, Gaulton KJ, Sebat J, Li Y, Hansen KD, Ren B. Common DNA sequence variation influences 3-dimensional conformation of the human genome. Genome Biology. 20: 255. PMID 31779666 DOI: 10.1186/S13059-019-1855-4  0.407
2019 Juric I, Yu M, Abnousi A, Raviram R, Fang R, Zhao Y, Zhang Y, Qiu Y, Yang Y, Li Y, Ren B, Hu M. MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. Plos Computational Biology. 15: e1006982. PMID 30986246 DOI: 10.1371/Journal.Pcbi.1006982  0.706
2017 Li YE, Xiao M, Shi B, Yang YT, Wang D, Wang F, Marcia M, Lu ZJ. Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites. Genome Biology. 18: 169. PMID 28886744 DOI: 10.1186/S13059-017-1298-8  0.488
2017 Yang Y, Chen L, Gu J, Zhang H, Yuan J, Lian Q, Lv G, Wang S, Wu Y, Yang YT, Wang D, Liu Y, Tang J, Luo G, Li Y, et al. Recurrently deregulated lncRNAs in hepatocellular carcinoma. Nature Communications. 8: 14421. PMID 28194035 DOI: 10.1038/Ncomms14421  0.484
2016 Schmitt AD, Hu M, Jung I, Xu Z, Qiu Y, Tan CL, Li Y, Lin S, Lin Y, Barr CL, Ren B. A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. Cell Reports. 17: 2042-2059. PMID 27851967 DOI: 10.1016/J.Celrep.2016.10.061  0.458
2016 Wu Y, Qu R, Huang Y, Shi B, Liu M, Li Y, Lu ZJ. RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data. Nucleic Acids Research. PMID 27137891 DOI: 10.1093/nar/gkw362  0.485
2015 Wu J, Feng F, Lian X, Teng X, Wei H, Yu H, Xie W, Yan M, Fan P, Li Y, Ma X, Liu H, Yu S, Wang G, Zhou F, et al. Genome-wide Association Study (GWAS) of mesocotyl elongation based on re-sequencing approach in rice. Bmc Plant Biology. 15: 218. PMID 26362270 DOI: 10.1186/S12870-015-0608-0  0.326
2015 Yang YC, Di C, Hu B, Zhou M, Liu Y, Song N, Li Y, Umetsu J, Lu ZJ. CLIPdb: a CLIP-seq database for protein-RNA interactions. Bmc Genomics. 16: 51. PMID 25652745 DOI: 10.1186/s12864-015-1273-2  0.508
2015 Hu L, Di C, Kai M, Yang YC, Li Y, Qiu Y, Hu X, Yip KY, Zhang MQ, Lu ZJ. A common set of distinct features that characterize noncoding RNAs across multiple species. Nucleic Acids Research. 43: 104-14. PMID 25505163 DOI: 10.1093/Nar/Gku1316  0.51
2014 Xu H, Liu J, Li Y, Yin Y, Zhu C, Lu H. Autofocus using adaptive prediction approximation combined search for the fluorescence microscope in second-generation DNA sequencing system. Applied Optics. 53: 4509-18. PMID 25090072 DOI: 10.1364/AO.53.004509  0.627
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