Daofeng Li

发表

Integrative analysis of 111 reference human epigenomes

Michael Q. Zhang, Nicholas A. Sinnott-Armstrong, Michael T. McManus, 2015, Nature.

Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods

Jeffrey B. Cheng, K. Ligon, M. Marra, 2013, RECOMB.

Title : Estimating Absolute Methylation Levels at Single CpG Resolution from Methylation Enrichment and Restriction Enzyme Sequencing Methods Running title : methylCRF predicts single CpG resolution methylome

Jeffrey B. Cheng, K. Ligon, M. Marra, 2013 .

Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation.

B. Zhang, Daofeng Li, Ting Wang, 2015, Methods.

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm

Richard A. Moore, Jeffrey B. Cheng, K. Ligon, 2013, Genome research.

Transposable elements drive widespread expression of oncogenes in human cancers

Nakul M. Shah, Erica C. Pehrsson, J. Gordon, 2019, Nature Genetics.

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos

Stephen L. Johnson, R. Lowdon, B. Zhang, 2015, Nature Communications.

Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome

J. Payton, J. Costello, B. Zhang, 2016, G3: Genes, Genomes, Genetics.

DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats

Nakul M. Shah, Christopher R. Schmidt, C. Plass, 2017, Nature Genetics.

Exploring long-range genome interactions using the WashU Epigenome Browser

Ting Wang, Daofeng Li, H. A. Lawson, 2013, Nature Methods.

The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions

Ting Wang, Feng Yue, Yun Li, 2017, Genome Biology.

Intermediate DNA methylation is a conserved signature of genome regulation

Ting Wang, Manolis Kellis, Martin Hirst, 2015, Nature Communications.

Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser

Ivan Smirnov, Bo Zhang, Ting Wang, 2015, Nature Biotechnology.

MicroRNAs Induce a Permissive Chromatin Environment that Enables Neuronal Subtype-Specific Reprogramming of Adult Human Fibroblasts.

J. Dougherty, Daofeng Li, Ting Wang, 2017, Cell stem cell.

DeepH&M: Estimating single-CpG hydroxymethylation and methylation levels from enrichment and restriction enzyme sequencing methods

J. Dougherty, Daofeng Li, Ting Wang, 2020, Science Advances.

A map of cis-regulatory elements and 3D genome structures in zebrafish

R. Hardison, Feng Yue, Yanli Wang, 2020, Nature.

WashU Epigenome Browser update 2019

Ting Wang, Daofeng Li, Silas Hsu, 2019, Nucleic Acids Res..

Exploring the coronavirus pandemic with the WashU Virus Genome Browser

Daofeng Li, Ting Wang, Xiaoyu Zhuo, 2020, Nature Genetics.

Exploring the coronavirus epidemic using the new WashU Virus Genome Browser

Daofeng Li, Ting Wang, Xiaoyu Zhuo, 2020, bioRxiv.

Regulatory Network Decoded from Epigenomes of Surface Ectoderm-Derived Cell Types

Jeffrey B. Cheng, M. Marra, P. Farnham, 2014, Nature Communications.

WashU Epigenome Browser update 2022

Daofeng Li, Ting Wang, Jason Xu, 2022, Nucleic Acids Res..

Title : Widespread transposable element-driven oncogene expression in cancers

Nakul M. Shah, Erica C. Pehrsson, J. Gordon, 2018 .

Identification and characterization of MtMTP1, a Zn transporter of CDF family, in the Medicago truncatula.

Daofeng Li, Jiangli Dong, Tao Wang, 2009, Plant physiology and biochemistry : PPB.

DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape

Keith L. Ligon, Martin Hirst, Marco A. Marra, 2013, Nature Genetics.

Single-cell transcriptional regulation and genetic evolution of neuroendocrine prostate cancer

C. Collins, Daofeng Li, Jialiang Huang, 2022, iScience.

Embryonic vitamin D deficiency programs hematopoietic stem cells to induce type 2 diabetes

Daofeng Li, Ting Wang, X. Xing, 2022, bioRxiv.

Integrative analysis of 111 reference human epigenomes Open

David Haussler, Michael Q. Zhang, Gerald T. Quon, 2015, Nat..

The dynseq browser track shows context-specific features at nucleotide resolution

Brian T. Lee, A. Kundaje, B. Raney, 2022, Nature Genetics.

Semi-automated assembly of high-quality diploid human reference genomes

Ira M. Hall, Nathan D. Olson, Mark J. P. Chaisson, 2022, bioRxiv.

Widespread contribution of transposable elements to the innovation of gene regulatory networks

Zhihai Ma, Yong Cheng, M. Snyder, 2014, Genome research.

Perinatal deiodinase 2 expression in hepatocytes defines epigenetic susceptibility to liver steatosis and obesity

Daofeng Li, Ting Wang, A. Bianco, 2015, Proceedings of the National Academy of Sciences.

Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser

Daofeng Li, Ting Wang, Xiaoyu Zhuo, 2022, bioRxiv.

The HC-pro protein of potato virus Y interacts with NtMinD of tobacco.

Daofeng Li, C. Deng, Jiangli Dong, 2007, Molecular plant-microbe interactions : MPMI.

HC-Pro Protein of Potato Virus Y Can Interact with Three Arabidopsis 20S Proteasome Subunits In Planta

Daofeng Li, C. Deng, Jiangli Dong, 2007, Journal of Virology.

Potato virus Y HC-Pro Reduces the ATPase Activity of NtMinD, Which Results in Enlarged Chloroplasts in HC-Pro Transgenic Tobacco

Daofeng Li, Jiangli Dong, Tao Wang, 2015, PloS one.

Monoacylglycerol lipase (MGLL) polymorphism rs604300 interacts with childhood adversity to predict cannabis dependence symptoms and amygdala habituation: Evidence from an endocannabinoid system-level analysis.

Ting Wang, Daofeng Li, Nicholas G Martin, 2015, Journal of abnormal psychology.

Transcriptional profiling of Medicago truncatula under salt stress identified a novel CBF transcription factor MtCBF4 that plays an important role in abiotic stress responses

Zhen Su, Daofeng Li, Jiangli Dong, 2011, BMC Plant Biology.

De novo transcriptome analysis of Medicago falcata reveals novel insights about the mechanisms underlying abiotic stress-responsive pathway

Zhenglin Du, Songnian Hu, Zhen Su, 2015, BMC Genomics.

Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish

Stephen L. Johnson, C. Kaufman, R. Lowdon, 2021, Genome biology.

Soluble inflammatory mediators induce transcriptional re-organization that is independent of dna methylation changes in cultured human chorionic villous trophoblasts

Daofeng Li, Ting Wang, K. Jiang, 2018, Journal of reproductive immunology.

DNA unmethylome profiling by covalent capture of CpG sites

Sun-Chong Wang, Daofeng Li, Ting Wang, 2013, Nature Communications.

Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser

Daofeng Li, Ting Wang, Deepak Purushotham, 2022, Nature Methods.

The NIEHS TaRGET II Consortium and environmental epigenomics

David L. Aylor, Erica C. Pehrsson, S. Rajagopalan, 2018, Nature Biotechnology.

PMRD: plant microRNA database

Tao Wang, Xin Zhou, Zhen Su, 2009, Nucleic Acids Res..

Whole-genome profiling of DNA methylation and hydroxymethylation identifies distinct regulatory programs among innate lymphocytes

Daofeng Li, Ting Wang, M. Colonna, 2022, Nature Immunology.

Whole-genome profiling of DNA methylation and hydroxymethylation identifies distinct regulatory programs among innate lymphocytes

Daofeng Li, Ting Wang, M. Colonna, 2022, Nature immunology.

Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seq.

Ting Wang, Daofeng Li, Xiaoyun Xing, 2018, Methods in molecular biology.

Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation

R. Lowdon, Daofeng Li, Ting Wang, 2017, BMC Genomics.

DNA methyltransferase 3b regulates articular cartilage homeostasis by altering metabolism.

John M. Ashton, Jason R. Myers, Daofeng Li, 2017, JCI insight.

Induction of hematopoietic and endothelial cell program orchestrated by ETS transcription factor ER71/ETV2

Daofeng Li, Ting Wang, D. Watson, 2015, EMBO reports.

The Human Epigenome Browser at Washington University

David Haussler, Jingchun Zhu, Ivan Smirnov, 2011, Nature Methods.

The Human Pangenome Project: a global resource to map genomic diversity

Joshua F. McMichael, Hanlee P. Ji, Adam M. Novak, 2022, Nature.

The qBED track: a novel genome browser visualization for point processes

Ting Wang, Daofeng Li, Silas Hsu, 2020, bioRxiv.

The dynseq genome browser track enables visualization of context-specific, dynamic DNA sequence features at single nucleotide resolution

Brian T. Lee, A. Kundaje, B. Raney, 2022, bioRxiv.

Transposable elements drive widespread expression of oncogenes in human cancers

Nakul M. Shah, Erica C. Pehrsson, J. Gordon, 2019, Nature Genetics.

A map of cis-regulatory elements and 3D genome structures in zebrafish

R. Hardison, Daofeng Li, Ting Wang, 2020, Nature.

Whole-Genome DNA Methylation Profiling Identifies Epigenetic Signatures of Uterine Carcinosarcoma12

D. Mutch, Daofeng Li, Ting Wang, 2017, Neoplasia.

Recurrent epimutations activate gene body promoters in primary glioblastoma

Jun S. Song, A. Olshen, I. Smirnov, 2014, Genome research.

Maternal high-fat diet associated with altered gene expression, DNA methylation, and obesity risk in mouse offspring

J. Cheverud, Daofeng Li, Ting Wang, 2018, PloS one.

Epigenomic differences in the human and chimpanzee genomes are associated with structural variation

Erica C. Pehrsson, Daofeng Li, Ting Wang, 2020, Genome research.

Feasibility of constructing multi-dimensional genomic maps of juvenile idiopathic arthritis

Daofeng Li, M. Buck, K. Jiang, 2018, bioRxiv.

methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser

Ting Wang, Xin Zhou, Rebecca F. Lowdon, 2014, Bioinform..

Cloning and characterization of a functional flavanone-3ß-hydroxylase gene from Medicago truncatula

Daofeng Li, S. Martens, Jiangli Dong, 2010, Molecular Biology Reports.

An expression database for roots of the model legume Medicago truncatula under salt stress

Zhen Su, Daofeng Li, Jiangli Dong, 2009, BMC Genomics.

Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease.

Steven J. M. Jones, Erica C. Pehrsson, Joshua F. Robinson, 2021, Developmental cell.

Characterization of a Mouse Model of Börjeson-Forssman-Lehmann Syndrome Graphical Abstract Highlights

J. Constantino, J. Dougherty, Daofeng Li, 2019 .

ETV2/ER71 regulates hematopoietic regeneration by promoting hematopoietic stem cell proliferation

Daofeng Li, Ting Wang, Kyunghee Choi, 2017, The Journal of experimental medicine.

The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions

R. Hardison, Feng Yue, Ming Hu, 2018, Genome Biology.

Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters

Tao Wang, Zhen Su, Daofeng Li, 2012, BMC Genomics.

AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis

P. Madden, Daofeng Li, Ting Wang, 2021, Genom. Proteom. Bioinform..

Improving ATAC-seq Data Analysis with AIAP, a Quality Control and Integrative Analysis Package

Ting Wang, Bo Zhang, Shaopeng Liu, 2019, bioRxiv.

Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements

Nakul M. Shah, Ju Heon Maeng, B. Evans, 2023, Nature Genetics.

A high-fat diet alters genome-wide DNA methylation and gene expression in SM/J mice

J. Cheverud, Daofeng Li, Ting Wang, 2018, BMC Genomics.

Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex

Fenna M. Krienen, E. Callaway, G. Feng, 2023, bioRxiv.

A high-fat diet alters genome-wide DNA methylation and gene expression in SM/J mice

J. Cheverud, Daofeng Li, Ting Wang, 2018, BMC Genomics.

Characterization of a Mouse Model of Börjeson-Forssman-Lehmann Syndrome

J. Constantino, J. Dougherty, Daofeng Li, 2018, Cell reports.

Widespread contribution of transposable elements to the innovation of gene regulatory networks

Zhihai Ma, Yong Cheng, M. Snyder, 2014, Genome Research.

Semi-automated assembly of high-quality diploid human reference genomes

Ira M. Hall, Nathan D. Olson, Mark J. P. Chaisson, 2022, Nature.

De novo transcriptome analysis of Medicago falcata reveals novel insights about the mechanisms underlying abiotic stress-responsive pathway

Zhenglin Du, Songnian Hu, Zhen Su, 2015, BMC Genomics.

L. Bierut, A. Hariri, G. Montgomery, 2015, Journal of abnormal psychology.

Towards a comprehensive regulatory map of Mammalian Genomes

Daofeng Li, O. Avraham, T. M. Gonçalves, 2023, Research square.

TET3 plays a critical role in white adipose development and diet-induced remodeling

O. MacDougald, Daofeng Li, Sona Kang, 2023, Cell reports.

Effects of Inner Dynamic Excitation of Driving Gear on Locomotive Driving Motor

Daofeng Li, JianXin Liu, Yifan Yan, 2011 .

Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data

R. Mitra, Daofeng Li, Allen Yen, 2024, Bioinform..

Conserved and divergent gene regulatory programs of the mammalian neocortex

Fenna M. Krienen, E. Callaway, S. Mccarroll, 2023, Nature.

BAllC and BAllCools: efficient formatting and operating for single-cell DNA methylation data

Daofeng Li, J. Ecker, Ting Wang, 2023, bioRxiv.

Epigenetic therapy potentiates transposable element transcription to create tumor-enriched antigens in glioblastoma cells.

Nakul M. Shah, Ju Heon Maeng, Daofeng Li, 2024, Nature genetics.