DNA methylation disruption reshapes the hematopoietic differentiation landscape

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400

STAR: ultrafast universal RNA-seq aligner

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.004 · Cited by 13,382

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

Kuleshov, M. V., Jones, M. R., Rouillard, A. D., Fernandez, N. F., Duan, Q., Wang, Z., Koplev, S., Jenkins, S. L., Jagodnik, K. M., Lachmann, A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw377 · Cited by 10,799

Generalized linear mixed models: a practical guide for ecology and evolution

Bolker, B. M., Brooks, M. E., Clark, C. J., Geange, S. W., Poulsen, J. R., Stevens, M. H. H., & White, J.-S. S. (2009) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2008.10.008 · Cited by 8,910

DNA methylation patterns and epigenetic memory

Bird, A. (2002) · Genes & Development · doi:10.1101/gad.947102 · Cited by 7,124

Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.

Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.002 · Cited by 7,110

Scenic: single-cell regulatory network inference and clustering.

Aibar, S., González-Blas, C. B., Moerman, T., Huynh-Thu, V. A., Imrichova, H., Hulselmans, G., Rambow, F., Marine, J.-C., Geurts, P., Aerts, J., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4463 · Cited by 6,520

Mutational heterogeneity in cancer and the search for new cancer-associated genes

Lawrence, M. S., Stojanov, P., Polak, P., Kryukov, G. V., Cibulskis, K., Sivachenko, A., Carter, S. L., Stewart, C., Mermel, C. H., Roberts, S. A., et al. (2013) · Nature · doi:10.1038/nature12213 · Cited by 5,461

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

Krueger, F., & Andrews, S. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr167 · Cited by 5,324

Age-related clonal hematopoiesis associated with adverse outcomes

Jaiswal, S., Fontanillas, P., Flannick, J., Manning, A., Grauman, P. V., Mar, B. G., Lindsley, R. C., Mermel, C. H., Burtt, N., Chavez, A., et al. (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1408617 · Cited by 4,841

Cytokine-mediated regulation of CXCR4 expression in human neutrophils

Nagase, H., Miyamasu, M., Yamaguchi, M., Imanishi, M., Tsuno, N. H., Matsushima, K., Yamamoto, K., Morita, Y., & Hirai, K. (2002) · Journal of Leukocyte Biology · doi:10.1189/jlb.71.4.711 · Cited by 4,713

GENCODE: The reference human genome annotation for The ENCODE Project

Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., et al. (2012) · Genome Research · doi:10.1101/gr.135350.111 · Cited by 4,585

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

Hafemeister, C., & Satija, R. (2019) · Genome Biology · doi:10.1186/s13059-019-1874-1 · Cited by 4,479

Full-length RNA-seq from single cells using Smart-seq2

Picelli, S., Faridani, O. R., Björklund, Å. K., Winberg, G., Sagasser, S., & Sandberg, R. (2014) · Nature Protocols · doi:10.1038/nprot.2014.006 · Cited by 4,137

Oncometabolite 2-Hydroxyglutarate Is a Competitive Inhibitor of α-Ketoglutarate-Dependent Dioxygenases

Xu, W., Yang, H., Liu, Y., Yang, Y., Wang, P., Kim, S.-H., Ito, S., Yang, C., Wang, P., Xiao, M.-T., et al. (2011) · Cancer Cell · doi:10.1016/j.ccr.2010.12.014 · Cited by 2,875

Clonal hematopoiesis and risk of atherosclerotic cardiovascular disease

Jaiswal, S., Natarajan, P., Silver, A. J., Gibson, C. J., Bick, A. G., Shvartz, E., McConkey, M., Gupta, N., Gabriel, S., Ardissino, D., et al. (2017) · New England Journal of Medicine · doi:10.1056/nejmoa1701719 · Cited by 2,683

The accessible chromatin landscape of the human genome

Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B., et al. (2012) · Nature · doi:10.1038/nature11232 · Cited by 2,679

Maintenance of the Hematopoietic Stem Cell Pool by CXCL12-CXCR4 Chemokine Signaling in Bone Marrow Stromal Cell Niches

Sugiyama, T., Kohara, H., Noda, M., & Nagasawa, T. (2006) · Immunity · doi:10.1016/j.immuni.2006.10.016 · Cited by 2,419

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

Akalin, A., Kormáksson, M., Li, S., Garrett-Bakelman, F. E., Figueroa, M. E., Melnick, A. M., & Mason, C. E. (2012) · Genome biology · doi:10.1186/gb-2012-13-10-r87 · Cited by 2,269

The Common Feature of Leukemia-Associated IDH1 and IDH2 Mutations Is a Neomorphic Enzyme Activity Converting α-Ketoglutarate to 2-Hydroxyglutarate

Ward, P. S., Patel, J., Wise, D. R., Abdel-Wahab, O., Bennett, B. D., Coller, H. A., Cross, J. R., Fantin, V. R., Hedvat, C. V., Perl, A. E., et al. (2010) · Cancer Cell · doi:10.1016/j.ccr.2010.01.020 · Cited by 2,020

DNMT3A Mutations in Acute Myeloid Leukemia

Ley, T. J., Ding, L., Walter, M. J., McLellan, M. D., Lamprecht, T., Larson, D. E., Kandoth, C., Payton, J. E., Baty, J., Welch, J., et al. (2010) · New England Journal of Medicine · doi:10.1056/nejmoa1005143 · Cited by 1,983

Clonal hematopoiesis of indeterminate potential and its distinction from myelodysplastic syndromes

Steensma, D. P., Bejar, R., Jaiswal, S., Lindsley, R. C., Sekeres, M. A., Hasserjian, R. P., & Ebert, B. L. (2015) · Blood · doi:10.1182/blood-2015-03-631747 · Cited by 1,971

Mutation in TET2 in Myeloid Cancers

Delhommeau, F., Dupont, S., Valle, V. D., James, C., Trannoy, S., Massé, A., Kosmider, O., Le Couedic, J.-P., Robert, F., Alberdi, A., et al. (2009) · New England Journal of Medicine · doi:10.1056/nejmoa0810069 · Cited by 1,776

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

Schep, A. N., Wu, B., Buenrostro, J. D., & Greenleaf, W. J. (2017) · Nature Methods · doi:10.1038/nmeth.4401 · Cited by 1,680

Inducible Gene Targeting in Mice

Kühn, R., Schwenk, F., Aguet, M., & Rajewsky, K. (1995) · Science · doi:10.1126/science.7660125 · Cited by 1,641

Mapping the Mouse Cell Atlas by Microwell-Seq

Han, X., Wang, R., Zhou, Y., Fei, L., Sun, H., Lai, S., Saadatpour, A., Zhou, Z., Chen, H., Ye, F., et al. (2018) · Cell · doi:10.1016/j.cell.2018.02.001 · Cited by 1,597

Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation

Moran-Crusio, K., Reavie, L., Shih, A., Abdel-Wahab, O., Ndiaye-Lobry, D., Lobry, C., Figueroa, M. E., Vasanthakumar, A., Patel, J., Zhao, X., et al. (2011) · Cancer Cell · doi:10.1016/j.ccr.2011.06.001 · Cited by 1,339

Impact of cytosine methylation on DNA binding specificities of human transcription factors

Yin, Y., Morgunova, E., Jolma, A., Kaasinen, E., Sahu, B., Khund-Sayeed, S., Das, P. K., Kivioja, T., Dave, K., Zhong, F., et al. (2017) · Science · doi:10.1126/science.aaj2239 · Cited by 1,257

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

Paul, F., Arkin, Y., Giladi, A., Jaitin, D. A., Kenigsberg, E., Keren-Shaul, H., Winter, D., Lara-Astiaso, D., Gury, M., Weiner, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.013 · Cited by 1,082

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

Chang, H. H., Hemberg, M., Barahona, M., Ingber, D. E., & Huang, S. (2008) · Nature · doi:10.1038/nature06965 · Cited by 1,067

Human haematopoietic stem cell lineage commitment is a continuous process

Velten, L., Haas, S. F., Raffel, S., Blaszkiewicz, S., Islam, S., Hennig, B. P., Hirche, C., Lutz, C., Buss, E. C., Nowak, D., et al. (2017) · Nature Cell Biology · doi:10.1038/ncb3493 · Cited by 925

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

Kulakovskiy, I. V., Vorontsov, I. E., Yevshin, I., Sharipov, R., Fedorova, A. D., Rumynskiy, E. I., Medvedeva, Y. A., Magana-Mora, A., Bajić, V. B., Papatsenko, D., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1106 · Cited by 902

Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy

Martin, J. P. D., Chang, C., Boschetti, G., Ungaro, R. C., Giri, M., Grout, J. A., Gettler, K., Chuang, L.-S. F., Nayar, S., Greenstein, A. J., et al. (2019) · Cell · doi:10.1016/j.cell.2019.08.008 · Cited by 890

Prediction of acute myeloid leukaemia risk in healthy individuals

Abelson, S., Collord, G., Ng, S. W. K., Weissbrod, O., Mendelson Cohen, N., Niemeyer, E., Barda, N., Zuzarte, P. C., Heisler, L., Sundaravadanam, Y., et al. (2018) · Nature · doi:10.1038/s41586-018-0317-6 · Cited by 850

Recurrent somatic TET2 mutations in normal elderly individuals with clonal hematopoiesis

Busque, L., Patel, J. P., Figueroa, M. E., Vasanthakumar, A., Provost, S., Hamilou, Z., Mollica, L., Li, J., Viale, A., Heguy, A., et al. (2012) · Nature Genetics · doi:10.1038/ng.2413 · Cited by 830

c-Myc controls the balance between hematopoietic stem cell self-renewal and differentiation

Wilson, A., Murphy, M. J., Oskarsson, T., Kaloulis, K., Bettess, M. D., Oser, G. M., Pasche, A.-C., Knabenhans, C., MacDonald, H. R., & Trumpp, A. (2004) · Genes & Development · doi:10.1101/gad.313104 · Cited by 823

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

Macaulay, I. C., Haerty, W., Kumar, P., Li, Y. I., Hu, T. X., Teng, M. J., Goolam, M., Saurat, N., Coupland, P., Shirley, L. M., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3370 · Cited by 750

Cancer-associated metabolite 2-hydroxyglutarate accumulates in acute myelogenous leukemia with isocitrate dehydrogenase 1 and 2 mutations

Gross, S., Cairns, R. A., Minden, M. D., Driggers, E. M., Bittinger, M. A., Jang, H. G., Sasaki, M., Jin, S., Schenkein, D. P., Su, S. M., et al. (2010) · Journal of Experimental Medicine · doi:10.1084/jem.20092506 · Cited by 736

The genetics of myelodysplastic syndrome: from clonal haematopoiesis to secondary leukaemia

Sperling, A. S., Gibson, C. J., & Ebert, B. L. (2016) · Nature reviews. Cancer · doi:10.1038/nrc.2016.112 · Cited by 706

The role of mutations in epigenetic regulators in myeloid malignancies

Shih, A. H., Abdel-Wahab, O. I., Patel, J. P., & Levine, R. L. (2012) · Nature reviews. Cancer · doi:10.1038/nrc3343 · Cited by 696

Comprehensive methylome map of lineage commitment from haematopoietic progenitors

Ji, H., Ehrlich, L. I. R., Seita, J., Murakami, P. N., Doi, A., Lindau, P., Lee, H.-J., Aryee, M. J., Irizarry, R. A., Kim, K., et al. (2010) · Nature · doi:10.1038/nature09367 · Cited by 636

Methylation-Sensitive Sequence-Specific DNA Binding by the c-Myc Basic Region

Prendergast, G. C., & Ziff, E. B. (1991) · Science · doi:10.1126/science.1987636 · Cited by 578

Replacement of lost Lgr5-positive stem cells through plasticity of their enterocyte-lineage daughters

Tetteh, P. W., Basak, O., Farin, H. F., Wiebrands, K., Kretzschmar, K., Begthel, H., van den Born, M., Korving, J., de Sauvage, F., van Es, J. H., et al. (2016) · Cell stem cell · doi:10.1016/j.stem.2016.01.001 · Cited by 575

Competition between DNA methylation and transcription factors determines binding of NRF1

Domcke, S., Bardet, A. F., Adrian Ginno, P., Hartl, D., Burger, L., & Schübeler, D. (2015) · Nature · doi:10.1038/nature16462 · Cited by 508

TET2 and DNMT3A Mutations in Human T-Cell Lymphoma

Couronné, L., Bastard, C., & Bernard, O. (2012) · New England Journal of Medicine · doi:10.1056/nejmc1111708 · Cited by 494

Single-cell analysis of mixed-lineage states leading to a binary cell fate choice

Olsson, A., Venkatasubramanian, M., Chaudhri, V. K., Aronow, B. J., Salomonis, N., Singh, H., & Grimes, H. L. (2016) · Nature · doi:10.1038/nature19348 · Cited by 476

Granulocyte-Monocyte Progenitors and Monocyte-Dendritic Cell Progenitors Independently Produce Functionally Distinct Monocytes

Yáñez, A., Coetzee, S. G., Olsson, A., Muench, D. E., Berman, B. P., Hazelett, D. J., Salomonis, N., Grimes, H. L., & Goodridge, H. S. (2017) · Immunity · doi:10.1016/j.immuni.2017.10.021 · Cited by 470

Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations

Wilson, N. K., Kent, D. G., Buettner, F., Shehata, M., Macaulay, I. C., Calero-Nieto, F. J., Sánchez Castillo, M., Oedekoven, C. A., Diamanti, E., Schulte, R., et al. (2015) · Cell Stem Cell · doi:10.1016/j.stem.2015.04.004 · Cited by 466

Dynamics of epigenetic regulation at the single-cell level

Bintu, L., Yong, J., Antebi, Y. E., McCue, K., Kazuki, Y., Uno, N., Oshimura, M., & Elowitz, M. B. (2016) · Science · doi:10.1126/science.aab2956 · Cited by 436

DNA Methylation Dynamics during In Vivo Differentiation of Blood and Skin Stem Cells

Bock, C., Beerman, I., Lien, W., Smith, Z. D., Gu, H., Boyle, P., Gnirke, A., Fuchs, E. V., Rossi, D. J., & Meissner, A. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.06.019 · Cited by 389

The cis-Regulatory Atlas of the Mouse Immune System

Yoshida, H., Lareau, C. A., Ramírez, R. N., Rose, S. A., Maier, B. B., Wroblewska, A., Desland, F. A., Chudnovskiy, A., Mortha, A., Dominguez, C. X., et al. (2019) · Cell · doi:10.1016/j.cell.2018.12.036 · Cited by 385

Single-cell characterization of haematopoietic progenitors and their trajectories in homeostasis and perturbed haematopoiesis

Giladi, A., Paul, F., Herzog, Y., Lubling, Y., Weiner, A., Yofe, I., Jaitin, D., Cabezas-Wallscheid, N., Dress, R., Ginhoux, F., et al. (2018) · Nature Cell Biology · doi:10.1038/s41556-018-0121-4 · Cited by 366

Somatic mutations and cell identity linked by Genotyping of Transcriptomes

Nam, A. S., Kim, K.-T., Chaligne, R., Izzo, F., Ang, C., Taylor, J., Myers, R. M., Abu-Zeinah, G., Brand, R., Omans, N. D., et al. (2019) · Nature · doi:10.1038/s41586-019-1367-0 · Cited by 333

Heterogeneity of Embryonic and Adult Stem Cells

Graf, T., & Stadtfeld, M. (2008) · Cell stem cell · doi:10.1016/j.stem.2008.10.007 · Cited by 310

Genomic Characterization of Murine Monocytes Reveals C/EBPβ Transcription Factor Dependence of Ly6C − Cells

Mildner, A., Schönheit, J., Giladi, A., David, E., Lara‐Astiaso, D., Lorenzo-Vivas, E., Paul, F., Chappell‐Maor, L., Priller, J., Leutz, A., et al. (2017) · Immunity · doi:10.1016/j.immuni.2017.04.018 · Cited by 298

Use Model-Based Analysis of ChIP-Seq (MACS) to Analyze Short Reads Generated by Sequencing Protein–DNA Interactions in Embryonic Stem Cells

Liu, T. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0512-6_4 · Cited by 284

Loss of Cxcl12/Sdf-1 in adult mice decreases the quiescent state of hematopoietic stem/progenitor cells and alters the pattern of hematopoietic regeneration after myelosuppression

Tzeng, Y.-S., Li, H., Kang, Y.-L., Chen, W., Cheng, W., & Lai, D. (2010) · Blood · doi:10.1182/blood-2010-01-266833 · Cited by 279

Metabolic maintenance of cell asymmetry following division in activated T lymphocytes

Verbist, K., Guy, C. S., Milasta, S., Liedmann, S., Kamiński, M. M., Wang, R., & Green, D. R. (2016) · Nature · doi:10.1038/nature17442 · Cited by 273

Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia

Gaiti, F., Chaligne, R., Gu, H., Brand, R. M., Kothen-Hill, S., Schulman, R. C., Grigorev, K., Risso, D., Kim, K.-T., Pastore, A., et al. (2019) · Nature · doi:10.1038/s41586-019-1198-z · Cited by 262

Mutations in epigenetic modifiers in the pathogenesis and therapy of acute myeloid leukemia

Abdel-Wahab, O. I., & Levine, R. L. (2013) · Blood · doi:10.1182/blood-2013-01-451781 · Cited by 261

DNMT3A and TET2 compete and cooperate to repress lineage-specific transcription factors in hematopoietic stem cells

Zhang, X., Su, J., Jeong, M., Ko, M., Huang, Y., Park, H. J., Guzman, A., Lei, Y., Huang, Y.-H., Rao, A., et al. (2016) · Nature Genetics · doi:10.1038/ng.3610 · Cited by 258

Distinct myeloid progenitor–differentiation pathways identified through single-cell RNA sequencing

Drissen, R., Buza-Vidas, N., Woll, P. S., Thongjuea, S., Gambardella, A. R., Giustacchini, A., Mancini, E., Zriwil, A., Lutteropp, M., Grover, A., et al. (2016) · Nature Immunology · doi:10.1038/ni.3412 · Cited by 241

Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells

Yu, V. W. C., Yusuf, R. Z., Oki, T., Wu, J. W., Sáez, B., Wang, X., Cook, C., Baryawno, N., Ziller, M. J., Lee, E., et al. (2017) · Cell · doi:10.1016/j.cell.2017.02.010 · Cited by 239

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regressionPreprint

Hafemeister, C., & Satija, R. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/576827 · Cited by 238

Dnmt3a loss predisposes murine hematopoietic stem cells to malignant transformation

Mayle, A., Yang, L., Rodriguez, B., Zhou, T., Chang, E., Curry, C. V., Challen, G. A., Li, W., Wheeler, D., Rebel, V. I., et al. (2015) · Blood · doi:10.1182/blood-2014-08-594648 · Cited by 235

Ablation of de novo DNA methyltransferase Dnmt3a in the nervous system leads to neuromuscular defects and shortened lifespan

Nguyen, S., Meletis, K., Fu, D., Jhaveri, S., & Jaenisch, R. (2007) · Developmental Dynamics · doi:10.1002/dvdy.21176 · Cited by 203

DNMT3A Loss Drives Enhancer Hypomethylation in FLT3-ITD-Associated Leukemias

Yang, L., Rodriguez, B. A. T., Mayle, A., Park, H. J., Lin, X., Luo, M., Jeong, M., Curry, C. V., Kim, S.-B., Ruau, D., et al. (2016) · Cancer Cell · doi:10.1016/j.ccell.2016.05.003 · Cited by 165

DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer

Stone, A. M., Zotenko, E., Locke, W. J., Korbie, D. J., Millar, E. K. A., Pidsley, R., Stirzaker, C., Graham, P., Trau, M., Musgrove, E. A., et al. (2015) · Nature Communications · doi:10.1038/ncomms8758 · Cited by 136

Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes

Kribelbauer, J. F., Laptenko, O., Chen, S., Martini, G. D., Freed-Pastor, W. A., Prives, C. L., Mann, R. S., & Bussemaker, H. J. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.05.069 · Cited by 130

Tet2 loss leads to hypermutagenicity in haematopoietic stem/progenitor cells

Pan, F., Wingo, T. S., Zhao, Z., Gao, R., Makishima, H., Qu, G., Lin, L., Yu, M., Ortega, J. R., Wang, J., et al. (2017) · Nature Communications · doi:10.1038/ncomms15102 · Cited by 117

Combination Targeted Therapy to Disrupt Aberrant Oncogenic Signaling and Reverse Epigenetic Dysfunction in IDH2 - and TET2 -Mutant Acute Myeloid Leukemia

Shih, A. H., Meydan, C., SHANK, K. R., Garrett-Bakelman, F. E., Ward, P. S., Intlekofer, A. M., Nazir, A., Stein, E. M., Knapp, K. M., Glass, J. L., et al. (2017) · Cancer Discovery · doi:10.1158/2159-8290.cd-16-1049 · Cited by 113

Tissue-specific DNA demethylation is required for proper B-cell differentiation and function

Orlanski, S., Labi, V., Reizel, Y., Spiro, A., Lichtenstein, M., Levin-Klein, R., Koralov, S. B., Skversky‐Blocq, Y., Rajewsky, K., Cedar, H., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1604365113 · Cited by 103

Targeting the CXCL12/CXCR4 axis in acute myeloid leukemia: from bench to bedside

Cho, B., Kim, H., & Konopleva, M. Y. (2017) · The Korean Journal of Internal Medicine · doi:10.3904/kjim.2016.244 · Cited by 97

Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes

Pujato, M. A., Kieken, F., Skiles, A. A., Tapinos, N., & Fiser, A. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1228 · Cited by 93

DNMT3A Loss Drives Enhancer Hypomethylation in FLT3-ITD-Associated Leukemias

Yang, L., Rodriguez, B. A. T., Mayle, A., Park, H. J., Lin, X., Luo, M., Jeong, M., Curry, C. V., Kim, S.-B., Ruau, D., et al. (2016) · Cancer Cell · doi:10.1016/j.ccell.2016.07.015 · Cited by 82

Clonal Hematopoiesis and Blood-Cancer Risk

Genovese, G., Jaiswal, S., Ebert, B. L., & McCarroll, S. A. (2015) · New England Journal of Medicine · doi:10.1056/nejmc1500684 · Cited by 70

Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns

Emperle, M., Adam, S., Kunert, S., Dukatz, M., Baude, A., Plass, C., Rathert, P., Bashtrykov, P., & Jeltsch, A. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz911 · Cited by 69

Dnmt3a regulates T-cell development and suppresses T-ALL transformation

Kramer, A. C., Kothari, A., Wilson, W. C., Celik, H., Nikitas, J., Mallaney, C., Ostrander, E. L., Eultgen, E., Martens, A., Valentine, M. C., et al. (2017) · Leukemia · doi:10.1038/leu.2017.89 · Cited by 53

scMCA: A Tool to Define Mouse Cell Types Based on Single-Cell Digital Expression

Sun, H., Zhou, Y., Fei, L., Chen, H., & Guo, G. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9057-3_6 · Cited by 46

EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation

Lhoumaud, P., Sethia, G., Izzo, F., Sakellaropoulos, T., Snetkova, V., Vidal, S. E., Badri, S., Cornwell, M., Giammartino, D. C. D., Kim, K., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1853-6 · Cited by 41

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

Viner, C., Ishak, C. A., Johnson, J., Walker, N. J., Shi, H., Sjöberg-Herrera, M. K., Shen, S. Y., Lardo, S. M., Adams, D. J., Ferguson-Smith, A. C., et al. (2024) · Genome Biology · doi:10.1186/s13059-023-03070-0 · Cited by 30

Enhanced Anti-Leukemic Effects through Induction of Immunomodulating Microenvironment by Blocking CXCR4 and PD-L1 in an AML Mouse Model

Hwang, H.-S., Han, A., Lee, J. Y., Park, G. S., Min, W.-S., & Kim, H. (2018) · Immunological Investigations · doi:10.1080/08820139.2018.1497057 · Cited by 21

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

Viner, C., Ishak, C. A., Johnson, J., Walker, N. J., Shi, H., Sjöberg-Herrera, M. K., Shen, S. Y., Lardo, S. M., Adams, D. J., Ferguson-Smith, A. C., et al. (2016) · doi:10.1101/043794 · Cited by 18

Tet2-mutated myeloid progenitors possess aberrant in vitro self-renewal capacity

Kunimoto, H., Fukuchi, Y., Sakurai, M., Takubo, K., Okamoto, S., & Nakajima, H. (2014) · Blood · doi:10.1182/blood-2014-01-552471 · Cited by 15

DNMT3Amutations and prognostic significance in childhood acute lymphoblastic leukemia

Li, W., Gao, C., Cui, L., Liu, S., Zhao, X., Zhang, R., Wu, M., Zheng, H., Deng, G., Li, Z., et al. (2014) · Leukemia & lymphoma/Leukemia and lymphoma · doi:10.3109/10428194.2014.947607 · Cited by 12

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Nam, A. S., Chaligné, R., & Landau, D. A. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0265-5 · Cited by 399

Genetic and non-genetic clonal diversity in cancer evolution

Black, J. R., & McGranahan, N. (2021) · Nature reviews. Cancer · doi:10.1038/s41568-021-00336-2 · Cited by 298

Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states

Chaligné, R., Gaiti, F., Silverbush, D., Schiffman, J. S., Weisman, H. R., Kluegel, L., Gritsch, S., Deochand, S. D., Castro, L. N. G., Richman, A. R., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00927-7 · Cited by 247

Active turnover of DNA methylation during cell fate decisions

Parry, A., Rulands, S., & Reik, W. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-00287-8 · Cited by 214

Hallmarks of the aging T‐cell system

Zhang, H., Weyand, C. M., & Goronzy, J. J. (2021) · FEBS Journal · doi:10.1111/febs.15770 · Cited by 181

Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation

Nam, A. S., Dusaj, N., Izzo, F., Murali, R., Myers, R. M., Mouhieddine, T. H., Sotelo, J., Benbarche, S., Waarts, M., Gaiti, F., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01179-9 · Cited by 140

Single-Cell Analysis of Human Clonal Hematopoiesis Identifies Distinct Impact of DNMT3A and TET2 mutations on Hematopoietic Differentiation

Jakobsen, N. A., Turkalj, S., Stoilova, B., Metzner, M., Moore, R., Usukhbayar, B., Salazar, M. A., Kennedy, A., Newman, S., Kendrick, B. J. L., et al. (2022) · Blood · doi:10.1182/blood-2022-166474 · Cited by 3

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Izzo, F., Poran, A., Lee, S. C.-W., Chaligné, R., Gaiti, F., Kothen-Hill, S., Schulman, R. C., Ki, M., Kenigsberg, E., Abdel-Wahab, O. I., et al. (2017) · Blood · doi:10.1182/blood.v130.suppl_1.559.559

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Hogart, A., Lichtenberg, J., Ajay, S. S., Anderson, S., NIH Intramural Sequencing Center, Margulies, E. H., & Bodine, D. M. (2012) · Genome Research · doi:10.1101/gr.132878.111 · Cited by 101

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Nam, A. S., Dusaj, N. N., Izzo, F., Murali, R., Mouhieddine, T. H., Myers, R. M., Sotelo, J., Benbarche, S., Gaiti, F., Tahri, S., et al. (2020) · Blood · doi:10.1182/blood-2020-142574 · Cited by 1