Publications by authors named "Daofeng Li"

53Publications

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

Bioinformatics 2020 Sep 17. Epub 2020 Sep 17.

Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis MO, USA.

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http://dx.doi.org/10.1093/bioinformatics/btaa771DOI Listing
September 2020

Author Correction: Exploring the coronavirus pandemic with the WashU Virus Genome Browser.

Nat Genet 2020 Oct;52(10):1132

The Edison Family Center for Genome Sciences & Systems Biology, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.

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http://dx.doi.org/10.1038/s41588-020-00714-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7493292PMC
October 2020

Exploring the coronavirus pandemic with the WashU Virus Genome Browser.

Nat Genet 2020 10;52(10):986-991

The Edison Family Center for Genome Sciences & Systems Biology, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.

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http://dx.doi.org/10.1038/s41588-020-0697-zDOI Listing
October 2020

WashU Epigenome Browser update 2019.

Nucleic Acids Res 2019 07;47(W1):W158-W165

Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.

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http://dx.doi.org/10.1093/nar/gkz348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602459PMC
July 2019

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

Cell Rep 2018 11;25(6):1404-1414.e6

Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247183163
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http://dx.doi.org/10.1016/j.celrep.2018.10.043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6261530PMC
November 2018

A non-randomized procedure for large-scale heterogeneous multiple discrete testing based on randomized tests.

Biometrics 2019 06 9;75(2):638-649. Epub 2019 Mar 9.

Department of Genetics, Washington University in St. Louis, Saint Louis, Missouri.

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http://doi.wiley.com/10.1111/biom.12996
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http://dx.doi.org/10.1111/biom.12996DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6565503PMC
June 2019

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

Genome Biol 2018 10 4;19(1):151. Epub 2018 Oct 4.

Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, 16802, USA.

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http://dx.doi.org/10.1186/s13059-018-1519-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172833PMC
October 2018

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

J Reprod Immunol 2018 08 23;128:2-8. Epub 2018 May 23.

Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA; Genetics, Genomics, & Bioinformatics Program, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jri.2018.05.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6086739PMC
August 2018

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

Methods Mol Biol 2018 ;1708:209-246

The Edison Family Center for Genome Sciences and Systems Biology, Department of Genetics, Washington University, 4515 McKinley Ave., St. Louis, MO, 63108, USA.

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http://dx.doi.org/10.1007/978-1-4939-7481-8_12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007844PMC
July 2018

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

J Exp Med 2017 06 1;214(6):1643-1653. Epub 2017 May 1.

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110

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http://dx.doi.org/10.1084/jem.20160923DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5460995PMC
June 2017

Whole-Genome DNA Methylation Profiling Identifies Epigenetic Signatures of Uterine Carcinosarcoma.

Neoplasia 2017 02 12;19(2):100-111. Epub 2017 Jan 12.

Department of Genetics, Washington University School of Medicine, St. Louis, MO; Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO.

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http://dx.doi.org/10.1016/j.neo.2016.12.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5237802PMC
February 2017

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

G3 (Bethesda) 2016 04 7;6(4):973-86. Epub 2016 Apr 7.

Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108 Department of Computer Science and Engineering, Washington University in St. Louis, Missouri 63130

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http://dx.doi.org/10.1534/g3.115.025437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4825665PMC
April 2016

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

BMC Genomics 2015 Oct 19;16:818. Epub 2015 Oct 19.

State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.

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http://dx.doi.org/10.1186/s12864-015-2019-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615886PMC
October 2015

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

PLoS One 2015 26;10(8):e0136210. Epub 2015 Aug 26.

State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, P.R. China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0136210PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4550256PMC
June 2016

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

EMBO Rep 2015 May 23;16(5):654-69. Epub 2015 Mar 23.

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA Developmental, Regenerative, and Stem Cell Biology Program, Washington University School of Medicine, St. Louis, MO, USA

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http://dx.doi.org/10.15252/embr.201439939DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4428045PMC
May 2015

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

Nat Commun 2015 Feb 20;6:6315. Epub 2015 Feb 20.

1] Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA [2] Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/ncomms7315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4339225PMC
February 2015

Integrative analysis of 111 reference human epigenomes.

Nature 2015 Feb;518(7539):317-30

1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature14248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530010PMC
February 2015

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

Methods 2015 Jan 6;72:29-40. Epub 2014 Nov 6.

Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2014.10.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300244PMC
January 2015

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

Genome Res 2014 Dec 15;24(12):1963-76. Epub 2014 Oct 15.

Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA;

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http://dx.doi.org/10.1101/gr.168872.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248313PMC
December 2014

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

Bioinformatics 2014 Aug 10;30(15):2206-7. Epub 2014 Apr 10.

Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA and Department of Neurosurgery, Brain Tumor Research Center, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94143, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103599PMC
August 2014

Recurrent epimutations activate gene body promoters in primary glioblastoma.

Genome Res 2014 May 7;24(5):761-74. Epub 2014 Apr 7.

Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California 94143, USA;

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http://dx.doi.org/10.1101/gr.164707.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009606PMC
May 2014

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

Genome Res 2013 Sep 26;23(9):1541-53. Epub 2013 Jun 26.

Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1101/gr.152231.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3759729PMC
September 2013

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

BMC Genomics 2012 Feb 6;13:60. Epub 2012 Feb 6.

State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-13-60DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3298476PMC
February 2012

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

BMC Genomics 2009 Nov 11;10:517. Epub 2009 Nov 11.

State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China.

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http://www.springerlink.com/index/k666465726673235.pdf
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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-10-517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779821PMC
November 2009

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

Mol Biol Rep 2010 Oct 4;37(7):3283-9. Epub 2009 Nov 4.

State Key Laboratory for Agro-biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China.

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http://dx.doi.org/10.1007/s11033-009-9913-8DOI Listing
October 2010

PMRD: plant microRNA database.

Nucleic Acids Res 2010 Jan 6;38(Database issue):D806-13. Epub 2009 Oct 6.

State Key Laboratory of Plant Physiology and Biochemistry and State Key Laboratory for Agricultural Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkp818DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808885PMC
January 2010

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

Plant Physiol Biochem 2009 Nov-Dec;47(11-12):1089-94. Epub 2009 Sep 4.

State Key Laboratory for Agro-Biotechnology, College of Biological Science, China Agricultural University, 100193 Beijing, China.

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http://dx.doi.org/10.1016/j.plaphy.2009.08.006DOI Listing
March 2010

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

Mol Plant Microbe Interact 2007 Dec;20(12):1505-11

State Key Laboratory of Agro-Biotechnology, China Aricultural University, Beijing, P.R. China.

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http://dx.doi.org/10.1094/MPMI-20-12-1505DOI Listing
December 2007

HC-Pro protein of Potato virus Y can interact with three Arabidopsis 20S proteasome subunits in planta.

J Virol 2007 Dec 26;81(23):12881-8. Epub 2007 Sep 26.

State Key Laboratory of Agro-biotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100094, PR China.

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http://dx.doi.org/10.1128/JVI.00913-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2169110PMC
December 2007

[River continuum characteristics of Xiangxi River].

Ying Yong Sheng Tai Xue Bao 2004 Jan;15(1):141-4

State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.

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January 2004

[Spatial distribution of water quality in Xiangxi River, China].

Ying Yong Sheng Tai Xue Bao 2003 Nov;14(11):1959-62

State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.

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November 2003