Daofeng Li

Research output

Research output per year 2007 2013 2015 2017 2018 2021 2022 2023 2024 2024

• 59 Article
• 6 Comment/debate
• 5 Letter
• 2 Chapter
• 2 More
  • 1 Editorial
  • 1 Review article

Research output per year

Research output per year

Search results

• 2024

  Author Correction: Conserved and divergent gene regulatory programs of the mammalian neocortex (Nature, (2023), 624, 7991, (390-402), 10.1038/s41586-023-06819-6)

  Zemke, N. R., Armand, E. J., Wang, W., Lee, S., Zhou, J., Li, Y. E., Liu, H., Tian, W., Nery, J. R., Castanon, R. G., Bartlett, A., Osteen, J. K., Li, D., Zhuo, X., Xu, V., Chang, L., Dong, K., Indralingam, H. S., Rink, J. A. & Xie, Y. & 13 others, Miller, M., Krienen, F. M., Zhang, Q., Taskin, N., Ting, J., Feng, G., McCarroll, S. A., Callaway, E. M., Wang, T., Lein, E. S., Behrens, M. M., Ecker, J. R. & Ren, B., Jan 25 2024, In: Nature. 625, 7996, p. E26

  Research output: Contribution to journal › Comment/debate

  Open Access

  • Neocortex 100%
  • Gene Regulatory Programs 100%
  • Divergent Genes 100%
  • Conserved Genes 100%
  • Locus Control Region 100%

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

  Tian, W., Ding, W., Shen, J., Li, D., Wang, T. & Ecker, J. R., Jul 1 2024, In: Bioinformatics. 40, 7, btae404.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • DNA Methylation 100%
  • Cell DNA 100%
  • Cytosine 100%
  • Data Type 100%
  • Parsing 100%

• Deciphering the impact of genomic variation on function

  UM1HG011969, UM1HG011966, Single Cell, QTL/Statgen, Phenotypic Impact and Function, Neuro, Noncoding Variants, MPRA, iPSC, Impact on Diverse Populations, Immune, Imaging, Evolution, Enumerating Variants, Defining and Systematizing Function, CRISPR, Coding Variants, Cellular Programs and Networks, Cardiometabolic & Standards and Pipelines & 61 others, Networks, Mapping, Project Design, Computational Analysis, Modeling, and Prediction, Characterization, Catalog, Code of Conduct Committee (alphabetical by last name), Steering Committee Co-Chairs (alphabetical by last name), IGVF Consortium, NHGRI Program Management (alphabetical by last name), IGVF Affiliate Member Projects (contact PIs, other members (alphabetical by last name)), Data and Administrative Coordinating Center Awards (contact PI, MPIs (alphabetical by last name), other members (alphabetical by last name)), Network Projects (contact PI, MPIs (alphabetical by last name), other members (alphabetical by last name)), Predictive Modeling Awards (contact PI, MPIs (alphabetical by last name), other members (alphabetical by last name)), Mapping Awards (contact PI, MPIs (alphabetical by last name), other members (alphabetical by last name)), Characterization Awards (contact PI, MPIs (alphabetical by last name), other members (alphabetical by last name)), Working Group and Focus Group Co-Chairs (alphabetical by last name), Writing group (ordered by contribution), Yi lab, Xu lab, Seruggia lab, Sanjana lab, Reilly lab, Ray lab, Pollard lab, Pennacchio and Visel lab, Mostafavi lab, Moore lab, Jones lab, Heinig lab, Gupta lab, Grimes lab, Gazal lab, Dey lab, Ciccia lab, Brennand lab, U24HG012070, U24HG012012, U01HG012103, U01HG012079, U01HG012059, U01HG012051, U01HG012047, U01HG012041, U01HG012069, U01HG012064, U01HG012039, U01HG012022, U01HG012009, U01HG011967, U01HG011952, UM1HG012077, UM1HG012076, UM1HG011986, UM1HG012053, UM1HG012010, UM1HG012003, UM1HG011996, UM1HG011989, UM1HG011972 & Samer, E. K., Sep 5 2024, In: Nature. 633, 8028, p. 47-57 11 p.

  Research output: Contribution to journal › Article › peer-review

  • Genomics 100%
  • Genetic Predisposition to Disease 16%
  • Gene Expression 14%
  • Cell Function 14%
  • DNA Sequence 14%
  11 Scopus citations

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

  Jang, H. J., Shah, N. M., Maeng, J. H., Liang, Y., Basri, N. L., Ge, J., Qu, X., Mahlokozera, T., Tzeng, S. C., Williams, R. B., Moore, M. J., Annamalai, D., Chen, J. Y., Lee, H. J., DeSouza, P. A., Li, D., Xing, X., Kim, A. H. & Wang, T., Sep 2024, In: Nature Genetics. 56, 9, p. 1903-1913 11 p.

  Research output: Contribution to journal › Article › peer-review

  • Tumor 100%
  • Transposable Elements 100%
  • Glioblastoma Cells 100%
  • Epigenetic Therapy 100%
  • Transcription 100%
  2 Scopus citations

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

  Guo, J., Zhang, W., Chen, X., Yen, A., Chen, L., Shively, C. A., Li, D., Wang, T., Dougherty, J. D. & Mitra, R. D., Feb 1 2024, In: Bioinformatics. 40, 2, btae070.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Calling Cards 100%
  • Integrated Environment 100%
  • Comparative Analysis 100%
  • Technology Card 100%
  • Scientific Visualization 100%
• 2023

  Capture Methylation-Sensitive Restriction Enzyme Sequencing (Capture MRE-Seq) for Methylation Analysis of Highly Degraded DNA Samples

  Xing, X., Karlow, J. A., Li, D., Jang, H. S., Lee, H. J. & Wang, T., 2023, Methods in Molecular Biology. Humana Press Inc., p. 73-89 17 p. (Methods in Molecular Biology; vol. 2621).

  Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

  • DNA Samples 100%
  • Methylation Analysis 100%
  • Highly Degraded DNA 100%
  • Methylation-sensitive Restriction Enzyme 100%
  • Methylation 100%

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

  Zhuo, X., Hsu, S., Purushotham, D., Kuntala, P. K., Harrison, J. K., Du, A. Y., Chen, S., Li, D. & Wang, T., May 2023, In: Genome research. 33, 5, p. 824-835 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Browser 100%
  • Genomic Features 100%
  • Across Species 100%
  • Epigenome 100%
  • Epigenomic Features 100%
  3 Scopus citations

• Conserved and divergent gene regulatory programs of the mammalian neocortex

  Zemke, N. R., Armand, E. J., Wang, W., Lee, S., Zhou, J., Li, Y. E., Liu, H., Tian, W., Nery, J. R., Castanon, R. G., Bartlett, A., Osteen, J. K., Li, D., Zhuo, X., Xu, V., Chang, L., Dong, K., Indralingam, H. S., Rink, J. A. & Xie, Y. & 13 others, Miller, M., Krienen, F. M., Zhang, Q., Taskin, N., Ting, J., Feng, G., McCarroll, S. A., Callaway, E. M., Wang, T., Lein, E. S., Behrens, M. M., Ecker, J. R. & Ren, B., Dec 14 2023, In: Nature. 624, 7991, p. 390-402 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Neocortex 100%
  • Cis-regulatory Elements 100%
  • Gene Regulatory Programs 100%
  • Divergent Genes 100%
  • Conserved Genes 100%
  25 Scopus citations

• Modbed track: Visualization of modified bases in single-molecule sequencing

  Li, D., Zhuo, X., Harrison, J. K., Liu, S. & Wang, T., Dec 13 2023, In: Cell Genomics. 3, 12, 100455.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Epigenome 100%
  • Single-molecule Sequencing 100%
  • Modified Bases 100%
  • Browser 66%
  • Recent Advances 33%

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

  Shah, N. M., Jang, H. J., Liang, Y., Maeng, J. H., Tzeng, S. C., Wu, A., Basri, N. L., Qu, X., Fan, C., Li, A., Katz, B., Li, D., Xing, X., Evans, B. S. & Wang, T., Apr 2023, In: Nature Genetics. 55, 4, p. 631-639 9 p.

  Research output: Contribution to journal › Article › peer-review

  • Transposable Elements 100%
  • Tumor Antigen 100%
  • Pan-cancer Analysis 100%
  • Malignant Neoplasm 100%
  • Transposon 100%
  58 Scopus citations

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

  Jung, B. C., You, D., Lee, I., Li, D., Schill, R. L., Ma, K., Pi, A., Song, Z., Mu, W. C., Wang, T., MacDougald, O. A., Banks, A. S. & Kang, S., Oct 31 2023, In: Cell Reports. 42, 10, 113196.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • White Adipose Tissue 100%
  • Diet-induced 100%
  • TET3 100%
  • Adipose Development 100%
  • Precursor 100%
  2 Scopus citations
• 2022

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

  Li, D., Harrison, J. K., Purushotham, D. & Wang, T., Aug 2022, In: Nature Methods. 19, 8, p. 909-910 2 p.

  Research output: Contribution to journal › Letter › peer-review

  Open Access
  12 Scopus citations

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

  Human Pangenome Reference Consortium, Cody, S., Fulton, R. S., Fulton, L. L., Li, D., Lindsay, T., Regier, A., Stitziel, N. O., Wang, T. & Hall, I., Nov 17 2022, In: Nature. 611, 7936, p. 519-531 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Semi-automated 100%
  • Genome Assembly 100%
  • Reference Genome 100%
  • Pan-genome 100%
  • Automated Assembly 100%
  90 Scopus citations

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

  Wang, Z., Wang, T., Hong, D., Dong, B., Wang, Y., Huang, H., Zhang, W., Lian, B., Ji, B., Shi, H., Qu, M., Gao, X., Li, D., Collins, C., Wei, G., Xu, C., Lee, H. J., Huang, J. & Li, J., Jul 15 2022, In: iScience. 25, 7, 104576.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Genetic Evolution 100%
  • Transcriptional Regulation 100%
  • Neuroendocrine Prostate Cancer 100%
  • Tumor Cell 100%
  • Transcription Factors 100%
  29 Scopus citations

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

  Nair, S., Barrett, A., Li, D., Raney, B. J., Lee, B. T., Kerpedjiev, P., Ramalingam, V., Pampari, A., Lekschas, F., Wang, T., Haeussler, M. & Kundaje, A., Nov 2022, In: Nature Genetics. 54, 11, p. 1581-1583 3 p.

  Research output: Contribution to journal › Comment/debate

  Open Access
  3 Scopus citations

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

  Human Pangenome Reference Consortium, Apr 1 2022, In: Nature. 604, 7906, p. 437-446 10 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Genetic Diversity 100%
  • Pan-genome 100%
  • Global Resources 100%
  • Genomics 100%
  • Reference Genome 50%
  217 Scopus citations

• WashU Epigenome Browser update 2022

  Li, D., Purushotham, D., Harrison, J. K., Hsu, S., Zhuo, X., Fan, C., Liu, S., Xu, V., Chen, S., Xu, J., Ouyang, S., Wu, A. S. & Wang, T., Jul 5 2022, In: Nucleic acids research. 50, W1, p. W774-W781

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Browser 100%
  • Epigenome 100%
  • Time Series Data 100%
  • Genomics 100%
  • Annotation 50%
  74 Scopus citations

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

  Peng, V., Xing, X., Bando, J. K., Trsan, T., Di Luccia, B., Collins, P. L., Li, D., Wang, W. L., Lee, H. J., Oltz, E. M., Wang, T. & Colonna, M., Apr 2022, In: Nature immunology. 23, 4, p. 619-631 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Innate Lymphoid Cells 100%
  • Genomic Profiling 100%
  • DNA Hydroxymethylation 100%
  • Regulatory Programs 100%
  • DNA Methylation 100%
  16 Scopus citations
• 2021

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

  Liu, S., Li, D., Lyu, C., Gontarz, P. M., Miao, B., Madden, P. A. F., Wang, T. & Zhang, B., Aug 2021, In: Genomics, Proteomics and Bioinformatics. 19, 4, p. 641-651 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Integrative Analysis 100%
  • High-throughput Sequencing Data 100%
  • Assay for Transposase-Accessible Chromatin 100%
  • ATAC-seq 100%
  • Sequencing Data Analysis 100%
  21 Scopus citations

• Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish

  Jang, H. S., Chen, Y., Ge, J., Wilkening, A. N., Hou, Y., Lee, H. J., Choi, Y. R., Lowdon, R. F., Xing, X., Li, D., Kaufman, C. K., Johnson, S. L. & Wang, T., Dec 2021, In: Genome biology. 22, 1, 282.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Zebrafish 100%
  • Cell Fate 100%
  • Melanophore 100%
  • Epigenetic Dynamics 100%
  • Iridophore 100%
  13 Scopus citations

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

  Zhuo, X., Du, A. Y., Pehrsson, E. C., Li, D. & Wang, T., 2021, In: Genome research. 31, 2, p. 279-290 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Structural Variation 100%
  • Epigenomics 100%
  • Chimpanzee 100%
  • Indel 100%
  • Induced Pluripotent Stem Cells (iPSCs) 50%
  8 Scopus citations

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

  Zhang, B., Kim, M. Y., Elliot, G. N., Zhou, Y., Zhao, G., Li, D., Lowdon, R. F., Gormley, M., Kapidzic, M., Robinson, J. F., McMaster, M. T., Hong, C., Mazor, T., Hamilton, E., Sears, R. L., Pehrsson, E. C., Marra, M. A., Jones, S. J. M., Bilenky, M. & Hirst, M. & 3 others, Wang, T., Costello, J. F. & Fisher, S. J., May 3 2021, In: Developmental cell. 56, 9, p. 1238-1252.e5

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Cytotrophoblast 100%
  • Epigenome 100%
  • Placental Dysfunction 100%
  • Dynamics 100%
  • Pregnancy 100%
  37 Scopus citations

• The qBED track: A novel genome browser visualization for point processes

  Moudgil, A., Li, D., Hsu, S., Purushotham, D., Wang, T. & Mitra, R. D., Apr 15 2021, In: Bioinformatics. 37, 8, p. 1168-1170 3 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Genome Browser 100%
  • Calling Cards 100%
  • Point Process 100%
  • Genomics 100%
  • Annotation 100%
  3 Scopus citations
• 2020

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

  Yang, H., Luan, Y., Liu, T., Lee, H. J., Fang, L., Wang, Y., Wang, X., Zhang, B., Jin, Q., Ang, K. C., Xing, X., Wang, J., Xu, J., Song, F., Sriranga, I., Khunsriraksakul, C., Salameh, T., Li, D., Choudhary, M. N. K. & Topczewski, J. & 6 others, Wang, K., Gerhard, G. S., Hardison, R. C., Wang, T., Cheng, K. C. & Yue, F., Dec 10 2020, In: Nature. 588, 7837, p. 337-343 7 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Zebrafish 100%
  • Cis-regulatory Elements 100%
  • 3D Genome Organization 100%
  • Regulatory Sequence 100%
  • Zebra Fish 100%
  81 Scopus citations

• Author Correction: Exploring the coronavirus pandemic with the WashU Virus Genome Browser (Nature Genetics, (2020), 52, 10, (986-991), 10.1038/s41588-020-0697-z)

  Flynn, J. A., Purushotham, D., Choudhary, M. N. K., Zhuo, X., Fan, C., Matt, G., Li, D. & Wang, T., Oct 1 2020, In: Nature Genetics. 52, 10, p. 1132 1 p.

  Research output: Contribution to journal › Comment/debate

  Open Access

  • Virus Genome 100%
  • Genome Browser 100%
  • Coronavirus Pandemic 100%
  • Genetics 100%
  • Coronavirinae 100%

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

  He, Y., Jang, H. S., Xing, X., Li, D., Vasek, M. J., Dougherty, J. D. & Wang, T., Jul 2020, In: Science Advances. 6, 27, eaba0521.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Sequence Method 100%
  • Restriction Enzyme 100%
  • Methylation Status 100%
  • 5-hydroxymethylcytosine (5hmC) 100%
  • Hydroxymethylation 100%
  6 Scopus citations

• Exploring the coronavirus pandemic with the WashU Virus Genome Browser

  Flynn, J. A., Purushotham, D., Choudhary, M. N. K., Zhuo, X., Fan, C., Matt, G., Li, D. & Wang, T., Oct 1 2020, In: Nature Genetics. 52, 10, p. 986-991 6 p.

  Research output: Contribution to journal › Comment/debate

  Open Access
  8 Scopus citations
• 2019

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

  Dai, X., Lin, N., Li, D. & Wang, T., 2019, In: Biometrics. 75, 2, p. 638-649 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Random Testing 100%
  • Randomized Procedure 100%
  • Multiple Testing Procedure 100%
  • Multiple Testing 100%
  • Randomized Test 100%
  1 Scopus citations

• Author Correction: Transposable elements drive widespread expression of oncogenes in human cancers (Nature Genetics, (2019), 51, 4, (611-617), 10.1038/s41588-019-0373-3)

  Jang, H. S., Shah, N. M., Du, A. Y., Dailey, Z. Z., Pehrsson, E. C., Godoy, P. M., Zhang, D., Li, D., Xing, X., Kim, S., O’Donnell, D., Gordon, J. I. & Wang, T., May 1 2019, In: Nature Genetics. 51, 5, p. 920 1 p.

  Research output: Contribution to journal › Comment/debate

  Open Access

  • Oncogene 100%
  • Human Cancer 100%
  • Transposable Elements 100%
  • American Cancer Society 100%
  • Erica 100%
  3 Scopus citations

• Transposable elements drive widespread expression of oncogenes in human cancers

  Jang, H. S., Shah, N. M., Du, A. Y., Dailey, Z. Z., Pehrsson, E. C., Godoy, P. M., Zhang, D., Li, D., Xing, X., Kim, S., O’Donnell, D., Gordon, J. I. & Wang, T., Apr 1 2019, In: Nature Genetics. 51, 4, p. 611-617 7 p.

  Research output: Contribution to journal › Letter › peer-review

  Open Access

  • Oncogene 100%
  • Human Cancer 100%
  • Transposable Elements 100%
  • Transposable Element 100%
  • Tumor 25%
  231 Scopus citations

• WashU Epigenome Browser update 2019

  Li, D., Hsu, S., Purushotham, D., Sears, R. L. & Wang, T., Jul 1 2019, In: Nucleic acids research. 47, W1, p. W158-W165

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Browser 100%
  • Epigenomics 100%
  • Epigenome 100%
  • User Interface 100%
  • Data Hub 66%
  187 Scopus citations
• 2018

  A high-fat diet alters genome-wide DNA methylation and gene expression in SM/J mice 06 Biological Sciences 0604 Genetics

  Keleher, M. R., Zaidi, R., Hicks, L., Shah, S., Xing, X., Li, D., Wang, T. & Cheverud, J. M., Dec 7 2018, In: BMC genomics. 19, 1, 888.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Gene Expression 100%
  • High-fat Diet 100%
  • DNA Gene 100%
  • Biological Sciences 100%
  • Genome-wide DNA Methylation 100%
  33 Scopus citations

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

  Cheng, C., Deng, P. Y., Ikeuchi, Y., Yuede, C., Li, D., Rensing, N., Huang, J., Baldridge, D., Maloney, S. E., Dougherty, J. D., Constantino, J., Jahani-Asl, A., Wong, M., Wozniak, D. F., Wang, T., Klyachko, V. A. & Bonni, A., Nov 6 2018, In: Cell Reports. 25, 6, p. 1404-1414.e6

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Mouse Model 100%
  • PHF6 100%
  • Forssman 100%
  • Knock-in Mouse Model 33%
  • Patient-specific 22%
  19 Scopus citations

• Comprehensive whole DNA methylome analysis by integrating MeDIP-seq and MRE-seq

  Xing, X., Zhang, B., Li, D. & Wang, T., 2018, Methods in Molecular Biology. Humana Press Inc., p. 209-246 38 p. (Methods in Molecular Biology; vol. 1708).

  Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

  Open Access

  • DNA Methylome 100%
  • MeDIP-seq 100%
  • MRE-seq 100%
  • Methylome Analysis 100%
  • DNA Methylation 100%
  29 Scopus citations

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

  Keleher, M. R., Zaidi, R., Shah, S., Oakley, M. E., Pavlatos, C., Idrissi, S. E., Xing, X., Li, D., Wang, T. & Cheverud, J. M., Feb 2018, In: PloS one. 13, 2, e0192606.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • High-fat Diet 100%
  • Altered Gene Expression 100%
  • Maternal Diet 100%
  • Obesity Risk 100%
  • DNA Methylation (DNAm) 100%
  96 Scopus citations

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

  Jiang, K., Wong, L., Chen, Y., Xing, X., Li, D., Wang, T. & Jarvis, J. N., Aug 2018, In: Journal of Reproductive Immunology. 128, p. 2-8 7 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Inflammatory Mediators 100%
  • DNA Methylation (DNAm) 100%
  • Methylation Changes 100%
  • Extravillous Trophoblast 100%
  • Chorionic Villous 100%
  3 Scopus citations

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

  Wang, Y., Song, F., Zhang, B., Zhang, L., Xu, J., Kuang, D., Li, D., Choudhary, M. N. K., Li, Y., Hu, M., Hardison, R., Wang, T. & Yue, F., Oct 4 2018, In: Genome biology. 19, 1, 151.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Web-based 100%
  • Browser 100%
  • Genome Browser 100%
  • Long-range Chromatin Interaction 100%
  • Chromatin Interactions 100%
  332 Scopus citations

• The NIEHS TaRGET II Consortium and environmental epigenomics

  TaRGET II Consortium, Mar 6 2018, In: Nature Biotechnology. 36, 3, p. 225-227 3 p.

  Research output: Contribution to journal › Letter › peer-review

  Open Access
  69 Scopus citations
• 2017

  Corrigendum: The 4D nucleome project (Nature (2017) 549 (219-226) DOI: 10.1038/nature23884)

  4D Nucleome Network, Dec 14 2017, In: Nature. 552, 7684, p. 278 1 p.

  Research output: Contribution to journal › Comment/debate

  Open Access

  • National Institutes of Health 100%
  • Project Nature 100%
  • 4D nucleome 100%
  • 2,5-Dimethoxy-4-iodoamphetamine 100%
  • Health Commons 50%
  4 Scopus citations

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

  Shen, J., Wang, C., Li, D., Xu, T., Myers, J., Ashton, J. M., Wang, T., Zuscik, M. J., McAlinden, A. & O'Keefe, R. J., Jun 15 2017, In: JCI Insight. 2, 12, e93612.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Metabolism 100%
  • Articular Cartilage 100%
  • Cartilage Homeostasis 100%
  • DNA Methyltransferase 3B (DNMT3B) 100%
  • Homeostasis 100%
  59 Scopus citations

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

  Brocks, D., Schmidt, C. R., Daskalakis, M., Jang, H. S., Shah, N. M., Li, D., Li, J., Zhang, B., Hou, Y., Laudato, S., Lipka, D. B., Schott, J., Bierhoff, H., Assenov, Y., Helf, M., Ressnerova, A., Islam, M. S., Lindroth, A. M., Haas, S. & Essers, M. & 14 others, Imbusch, C. D., Brors, B., Oehme, I., Witt, O., Lübbert, M., Mallm, J. P., Rippe, K., Will, R., Weichenhan, D., Stoecklin, G., Gerhäuser, C., Oakes, C. C., Wang, T. & Plass, C., Jul 1 2017, In: Nature Genetics. 49, 7, p. 1052-1060 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Histone Deacetylase Inhibitor (HDACi) 100%
  • Transcription Start Site 100%
  • Long Terminal Repeat 100%
  • DNA Methyltransferase Inhibitor 100%
  • Cryptic Transcription 100%
  229 Scopus citations

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

  Xu, C. X., Lee, T. J., Sakurai, N., Krchma, K., Liu, F., Li, D., Wang, T. & Choi, K., Jun 1 2017, In: Journal of Experimental Medicine. 214, 6, p. 1643-1653 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Hematopoietic Stem Cells 100%
  • ETV2 100%
  • Hematopoietic Regeneration 100%
  • ER71 100%
  • Stem Cell Proliferation 100%
  18 Scopus citations

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

  Abernathy, D. G., Kim, W. K., McCoy, M. J., Lake, A. M., Ouwenga, R., Lee, S. W., Xing, X., Li, D., Lee, H. J., Heuckeroth, R. O., Dougherty, J. D., Wang, T. & Yoo, A. S., Sep 7 2017, In: Cell Stem Cell. 21, 3, p. 332-348.e9

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Neuronal Subtypes 100%
  • Human Fibroblasts 100%
  • MicroRNA 100%
  • Subtype-specific 100%
  • Chromatin Landscape 100%
  108 Scopus citations

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

  Zhou, J., Sears, R. L., Xing, X., Zhang, B., Li, D., Rockweiler, N. B., Jang, H. S., Choudhary, M. N. K., Lee, H. J., Lowdon, R. F., Arand, J., Tabers, B., Gu, C. C., Cicero, T. J. & Wang, T., Sep 12 2017, In: BMC genomics. 18, 1, 724.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Sequence Conservation 100%
  • Primary Sequence 100%
  • Tissue-specific Methylation 100%
  • DNA Methylation 100%
  • Epigenetics 80%
  71 Scopus citations

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

  Li, J., Xing, X., Li, D., Zhang, B., Mutch, D. G., Hagemann, I. S. & Wang, T., 2017, In: Neoplasia (United States). 19, 2, p. 100-111 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Uterine Carcinosarcoma 100%
  • Epigenetic Signature 100%
  • DNA Methylation Profiling 100%
  • Whole-genome DNA Methylation 100%
  • Carcinosarcoma 100%
  29 Scopus citations
• 2016

  Mapping of variable DNA methylation across multiple cell types defines a dynamic regulatory landscape of the human genome

  Gu, J., Stevens, M., Xing, X., Li, D., Zhang, B., Payton, J. E., Oltz, E. M., Jarvis, J. N., Jiang, K., Cicero, T., Costello, J. F. & Wang, T., 2016, In: G3: Genes, Genomes, Genetics. 6, 4, p. 973-986 14 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Multiple Cell Types 100%
  • Human Genome 100%
  • DNA Methylation (DNAm) 100%
  • Differentially Methylated Regions 100%
  • Regulatory Landscape 100%
  35 Scopus citations
• 2015

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

  Li, D., Zhang, B., Xing, X. & Wang, T., 2015, In: Methods. 72, C, p. 29-40 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Co-immunoprecipitation (co-IP) 100%
  • Methylation 100%
  • CpG Methylation 100%
  • MRE-seq 100%
  • Immunoprecipitation 100%
  89 Scopus citations

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

  Miao, Z., Xu, W., Li, D., Hu, X., Liu, J., Zhang, R., Tong, Z., Dong, J., Su, Z., Zhang, L., Sun, M., Li, W., Du, Z., Hu, S. & Wang, T., Oct 19 2015, In: BMC genomics. 16, 1, p. 1-18 18 p., 818.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Transcriptome Analysis 100%
  • Abiotic Stress 100%
  • Stress-responsive 100%
  • Medicago Falcata 100%
  • De-novo Transcriptome 100%
  56 Scopus citations

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

  Lee, H. J., Lowdon, R. F., Maricque, B., Zhang, B., Stevens, M., Li, D., Johnson, S. L. & Wang, T., Feb 20 2015, In: Nature communications. 6, 6315.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Early Embryo 100%
  • Zebrafish 100%
  • Developmental Stages 100%
  • DNA Methylome 100%
  • Developmental Enhancers 100%
  70 Scopus citations

• Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser

  Zhou, X., Li, D., Zhang, B., Lowdon, R. F., Rockweiler, N. B., Sears, R. L., Madden, P. A. F., Smirnov, I., Costello, J. F. & Wang, T., Apr 1 2015, In: Nature Biotechnology. 33, 4, p. 345-346 2 p.

  Research output: Contribution to journal › Editorial

  Open Access
  68 Scopus citations