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Yaping Liu, Ph.D. - Publications

Affiliations: 
2004-2008 Nanjing University, Nanjing Shi, Jiangsu Sheng, China 
 2009-2014 University of Southern California, Los Angeles, CA, United States 
 2019-2023 Cincinnati Children's Hospital Medical Center, University of Cincinnati 
 2023- Department of Biochemistry and Molecular Genetics Northwestern University Feinberg School of Medicine, Chicago, IL, United States 
Area:
Epigenomics, Computational Biology
Website:
https://epifluidlab.github.io/
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28 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 Li JW, Bandaru R, Liu Y. FinaleToolkit: Accelerating Cell-Free DNA Fragmentation Analysis with a High-Speed Computational Toolkit. Biorxiv : the Preprint Server For Biology. PMID 38854007 DOI: 10.1101/2024.05.29.596414  0.318
2024 Liu Y, Reed SC, Lo C, Choudhury AD, Parsons HA, Stover DG, Ha G, Gydush G, Rhoades J, Rotem D, Freeman S, Katz DW, Bandaru R, Zheng H, Fu H, et al. FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. Nature Communications. 15: 2790. PMID 38555308 DOI: 10.1038/s41467-024-47196-6  0.596
2024 Tian H, Luan P, Liu Y, Li G. Tet-mediated DNA methylation dynamics affect chromosome organization. Nucleic Acids Research. PMID 38300758 DOI: 10.1093/nar/gkae054  0.469
2024 Liu Y, Reed SC, Lo C, Choudhury AD, Parsons HA, Stover DG, Ha G, Gydush G, Rhoades J, Rotem D, Freeman S, Katz D, Bandaru R, Zheng H, Fu H, et al. FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. Biorxiv : the Preprint Server For Biology. PMID 38260558 DOI: 10.1101/2024.01.02.573710  0.647
2023 Fu H, Zheng H, Chen X, Weirauch MT, Muglia LJ, Wang L, Liu Y. NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule. Genome Biology. 24: 50. PMID 36927507 DOI: 10.1186/s13059-023-02889-x  0.4
2021 Liu Y. At the dawn: cell-free DNA fragmentomics and gene regulation. British Journal of Cancer. PMID 34815523 DOI: 10.1038/s41416-021-01635-z  0.455
2020 Zheng H, Zhu MS, Liu Y. FinaleDB: a browser and database of cell-free DNA fragmentation patterns. Bioinformatics (Oxford, England). PMID 33258919 DOI: 10.1093/bioinformatics/btaa999  0.495
2019 Wan N, Weinberg D, Liu TY, Niehaus K, Ariazi EA, Delubac D, Kannan A, White B, Bailey M, Bertin M, Boley N, Bowen D, Cregg J, Drake AM, Ennis R, ... ... Liu Y, et al. Machine learning enables detection of early-stage colorectal cancer by whole-genome sequencing of plasma cell-free DNA. Bmc Cancer. 19: 832. PMID 31443703 DOI: 10.1186/S12885-019-6003-8  0.445
2019 Li G, Liu Y, Zhang Y, Kubo N, Yu M, Fang R, Kellis M, Ren B. Joint profiling of DNA methylation and chromatin architecture in single cells. Nature Methods. PMID 31384045 DOI: 10.1038/S41592-019-0502-Z  0.729
2019 Liu Y, Liu T, Weinberg D, Torre CJDL, Tan CL, Schmitt AD, Selvaraj S, Tran V, Laurent LC, Bidard F, Haque IS. Abstract 5177: Spatial co-fragmentation pattern of cell-free DNA recapitulates in vivo chromatin organization and identifies tissue-of-origin Cancer Research. DOI: 10.1158/1538-7445.Sabcs18-5177  0.493
2019 Wan N, Weinberg D, Liu T, Niehaus K, Delubac D, Kannan A, White B, Ariazi EA, Bailey M, Bertin M, Boley N, Bowen D, Cregg J, Drake A, Ennis R, ... ... Liu Y, et al. Su1658 – Machine Learning Enables Detection of Early-Stage Colorectal Cancer by Whole-Genome Sequencing of Plasma Cell-Free Dna Gastroenterology. 156. DOI: 10.1016/S0016-5085(19)38396-9  0.361
2017 Luo H, Xi Y, Li W, Li J, Li Y, Dong S, Peng L, Liu Y, Yu W. Cell identity bookmarking through heterogeneous chromatin landscape maintenance during the cell cycle. Human Molecular Genetics. 26: 4231-4243. PMID 29088426 DOI: 10.1093/Hmg/Ddx312  0.524
2017 Liu Y, Sarkar A, Kheradpour P, Ernst J, Kellis M. Evidence of reduced recombination rate in human regulatory domains. Genome Biology. 18: 193. PMID 29058599 DOI: 10.1186/S13059-017-1308-X  0.773
2017 Liu Y, Reed S, Choudhury AD, Parsons HA, Stover DG, Ha G, Gydush G, Rhoades J, Rotem D, Freeman S, Adalsteinsson V, Kellis M. Abstract 5689: Identify tissue-of-origin in cancer cfDNA by whole genome sequencing Cancer Research. 77: 5689-5689. DOI: 10.1158/1538-7445.Am2017-5689  0.647
2016 Smith JG, Felix JF, Morrison AC, Kalogeropoulos A, Trompet S, Wilk JB, Gidlöf O, Wang X, Morley M, Mendelson M, Joehanes R, Ligthart S, Shan X, Bis JC, Wang YA, ... ... Liu Y, et al. Discovery of Genetic Variation on Chromosome 5q22 Associated with Mortality in Heart Failure. Plos Genetics. 12: e1006034. PMID 27149122 DOI: 10.1371/Journal.Pgen.1006034  0.634
2015 Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, Cooper LA, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, ... ... Liu Y, ... ... Liu Y, et al. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. The New England Journal of Medicine. 372: 2481-98. PMID 26061751 DOI: 10.1056/Nejmoa1402121  0.726
2015 Lay FD, Liu Y, Kelly TK, Witt H, Farnham PJ, Jones PA, Berman BP. The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Research. 25: 467-77. PMID 25747664 DOI: 10.1101/Gr.183368.114  0.742
2015 Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, ... ... Liu Y, et al. Integrative analysis of 111 reference human epigenomes. Nature. 518: 317-30. PMID 25693563 DOI: 10.1038/Nature14248  0.501
2014 Arking DE, Pulit SL, Crotti L, van der Harst P, Munroe PB, Koopmann TT, Sotoodehnia N, Rossin EJ, Morley M, Wang X, Johnson AD, Lundby A, Gudbjartsson DF, Noseworthy PA, Eijgelsheim M, ... ... Liu Y, et al. Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization. Nature Genetics. 46: 826-36. PMID 24952745 DOI: 10.1038/Ng.3014  0.611
2014 Lay FD, Liu Y, Kelly TK, Witt H, Blattler A, Farnham PJ, Berman BP, Jones PA. Abstract 4780: The effects of the global loss of DNA methylation on the functional organization of the epigenome Cancer Research. 74: 4780-4780. DOI: 10.1158/1538-7445.Am2014-4780  0.6
2013 Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, et al. Extensive variation in chromatin states across humans. Science (New York, N.Y.). 342: 750-2. PMID 24136358 DOI: 10.1126/Science.1242510  0.573
2013 Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, et al. Integrated genomic characterization of endometrial carcinoma. Nature. 497: 67-73. PMID 23636398 DOI: 10.1038/Nature12113  0.509
2012 Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Research. 22: 2497-506. PMID 22960375 DOI: 10.1101/Gr.143008.112  0.751
2012 Liu Y, Siegmund KD, Laird PW, Berman BP. Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biology. 13: R61. PMID 22784381 DOI: 10.1186/Gb-2012-13-7-R61  0.718
2012 Wiggs JL, Yaspan BL, Hauser MA, Kang JH, Allingham RR, Olson LM, Abdrabou W, Fan BJ, Wang DY, Brodeur W, Budenz DL, Caprioli J, Crenshaw A, Crooks K, Delbono E, ... ... Liu Y, et al. Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma. Plos Genetics. 8: e1002654. PMID 22570617 DOI: 10.1371/Journal.Pgen.1002654  0.629
2012 Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, Noushmehr H, Lange CP, van Dijk CM, Tollenaar RA, Van Den Berg D, Laird PW. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nature Genetics. 44: 40-6. PMID 22120008 DOI: 10.1038/Ng.969  0.798
2012 Berman BP, Weisenberger DJ, Hinoue T, Noushmehr H, Liu Y, Aman JF, Hinoue T, Shen H, Malik S, Mahurkar S, Triche T, Ramjan Z, Nicolet CM, Van Den Berg D, Cope L, et al. Exploring the cancer methylome Bmc Proceedings. 6. DOI: 10.1186/1753-6561-6-S6-O24  0.803
2012 Nebozhyn M, Cristescu R, Liu Y, Feldman I, Lezhnin S, Zhang T, Zawel L, Fawell S, Dai H, Li J, Loboda A. Abstract 4931: Biomarker discovery in a large panel of cell lines shows different sample size requirement for prediction of response across a set of compounds Cancer Research. 72: 4931-4931. DOI: 10.1158/1538-7445.Am2012-4931  0.303
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