GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041

Integrated analysis of multimodal single-cell data

Hao, Y., Hao, S., Andersen-Nissen, E., Mauck, W. M., Zheng, S., Butler, A., Lee, M. J., Wilk, A. J., Darby, C., Zagar, M., et al. (2020) · doi:10.1101/2020.10.12.335331 · Cited by 15,508

Tissue-based map of the human proteome

Uhlén, M., Fagerberg, L., Hallström, B. M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, Å., Kampf, C., Sjöstedt, E., Asplund, A., et al. (2015) · Science · doi:10.1126/science.1260419 · Cited by 15,286

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

Ye, J., Coulouris, G., Zaretskaya, I., Cutcutache, I., Rozen, S., & Madden, T. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-134 · Cited by 6,507

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

The Cancer Genome Atlas Research Network (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1301689 · Cited by 5,078

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

Cibulskis, K., Lawrence, M. S., Carter, S. L., Sivachenko, A., Jaffe, D. B., Sougnez, C. L., Gabriel, S., Meyerson, M. M., Lander, E. S., & Getz, G. A. (2013) · Nature Biotechnology · doi:10.1038/nbt.2514 · Cited by 5,013

COSMIC: the Catalogue Of Somatic Mutations In Cancer

Tate, J. G., Bamford, S., Jubb, H. C., Sondka, Z., Beare, D. M., Bindal, N., Boutselakis, H., Cole, C. G., Creatore, C., Dawson, E., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1015 · Cited by 4,867

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

Genomic classification and prognosis in acute myeloid leukemia

Papaemmanuil, E., Gerstung, M., Bullinger, L., Gaidzik, V. I., Paschka, P., Roberts, N. D., Potter, N. E., Heuser, M., Thol, F., Bolli, N., et al. (2016) · New England Journal of Medicine · doi:10.1056/nejmoa1516192 · Cited by 4,350

Fast gene set enrichment analysisPreprint

Korotkevich, G., Sukhov, V., Budin, N., Shpak, B., Artyomov, M. N., & Sergushichev, A. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/060012 · Cited by 3,742

Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence

Genovese, G., Kähler, A. K., Handsaker, R. E., Lindberg, J., Rose, S. A., Bakhoum, S. F., Chambert, K., Mick, E., Neale, B. M., Fromer, M., et al. (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1409405 · Cited by 3,531

Pan-cancer analysis of whole genomes

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S.-M., Aikata, H., et al. (2020) · Nature · doi:10.1038/s41586-020-1969-6 · Cited by 3,064

Clonal heterogeneity and tumor evolution: past, present, and the future

McGranahan, N., & Swanton, C. (2017) · Cell · doi:10.1016/j.cell.2017.01.018 · Cited by 2,840

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

Corces, M. R., Trevino, A. E., Hamilton, E. G., Greenside, P. G., Sinnott-Armstrong, N. A., Vesuna, S., Satpathy, A. T., Rubin, A. J., Montine, K. S., Wu, B., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4396 · Cited by 2,496

Single-cell chromatin accessibility reveals principles of regulatory variation

Buenrostro, J. D., Wu, B., Litzenburger, U. M., Ruff, D., Gonzales, M. L., Snyder, M. P., Chang, H. Y., & Greenleaf, W. J. (2015) · Nature · doi:10.1038/nature14590 · Cited by 2,308

Age-related mutations associated with clonal hematopoietic expansion and malignancies

Xie, M., Lu, C., Wang, J., McLellan, M. D., Johnson, K. J., Wendl, M. C., McMichael, J. F., Schmidt, H. K., Yellapantula, V., Miller, C. A., et al. (2014) · Nature Medicine · doi:10.1038/nm.3733 · Cited by 1,874

Chromatin accessibility and the regulatory epigenome

Klemm, S. L., Shipony, Z., & Greenleaf, W. J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-018-0089-8 · Cited by 1,793

Single-cell chromatin state analysis with Signac

Stuart, T., Srivastava, A., Madad, S., Lareau, C. A., & Satija, R. (2021) · Nature Methods · doi:10.1038/s41592-021-01282-5 · Cited by 1,769

A single–cell type transcriptomics map of human tissues

Karlsson, M., Zhang, C., Méar, L., Zhong, W., Digre, A., Katona, B., Sjöstedt, E., Butler, L., Odeberg, J., Dusart, P., et al. (2021) · Science Advances · doi:10.1126/sciadv.abh2169 · Cited by 1,768

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

FoxOs Are Critical Mediators of Hematopoietic Stem Cell Resistance to Physiologic Oxidative Stress

Tothova, Z., Kollipara, R., Huntly, B. J., Lee, B. H., Castrillon, D. H., Cullen, D. E., McDowell, E. P., Lazo-Kallanian, S., Williams, I. R., Sears, C., et al. (2007) · Cell · doi:10.1016/j.cell.2007.01.003 · Cited by 1,562

Somatic mutation in cancer and normal cells

Martincorena, I., & Campbell, P. J. (2015) · Science · doi:10.1126/science.aab4082 · Cited by 1,396

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

Granja, J. M., Corces, M. R., Pierce, S. E., Bagdatli, S. T., Choudhry, H., Chang, H. Y., & Greenleaf, W. J. (2021) · Nature Genetics · doi:10.1038/s41588-021-00790-6 · Cited by 1,392

Effector and memory CD8+ T cell fate coupled by T-bet and eomesodermin

Intlekofer, A. M., Takemoto, N., Wherry, E. J., Longworth, S. A., Northrup, J. T., Palanivel, V., Mullen, A. C., Gasink, C. R., Kaech, S. M., Miller, J. D., et al. (2005) · Nature Immunology · doi:10.1038/ni1268 · Cited by 1,293

Resistance Mechanisms for the Bruton's Tyrosine Kinase Inhibitor Ibrutinib

Woyach, J. A., Furman, R. R., Liu, T.-M., Ozer, H. G., Zapatka, M., Ruppert, A. S., Xue, L., Li, D. H.-H., Steggerda, S. M., Versele, M., et al. (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1400029 · Cited by 1,275

The chromatin accessibility landscape of primary human cancers

Corces, M. R., Granja, J. M., Shams, S., Louie, B. H., Seoane, J. A., Zhou, W., Silva, T. C., Groeneveld, C., Wong, C. K., Cho, S. W., et al. (2018) · Science · doi:10.1126/science.aav1898 · Cited by 1,230

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

Corces, M. R., Buenrostro, J. D., Wu, B., Greenside, P. G., Chan, S. M., Koenig, J. L., Snyder, M. P., Pritchard, J. K., Kundaje, A., Greenleaf, W. J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3646 · Cited by 1,151

A rapid and robust method for single cell chromatin accessibility profiling

Chen, X., Miragaia, R. J., Natarajan, K. N., & Teichmann, S. A. (2018) · Nature Communications · doi:10.1038/s41467-018-07771-0 · Cited by 1,147

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

Ma, S., Zhang, B., LaFave, L. M., Earl, A. S., Chiang, Z., Hu, Y., Ding, J., Brack, A., Kartha, V. K., Tay, T., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.056 · Cited by 1,146

Haploinsufficiency of CBFA2 causes familial thrombocytopenia with propensity to develop acute myelogenous leukaemia

Song, W.-J., Sullivan, M. G., Legare, R. D., Hutchings, S., Tan, X., Kufrin, D., Ratajczak, J., Resende, I. C., Haworth, C., Hock, R., et al. (1999) · Nature Genetics · doi:10.1038/13793 · Cited by 1,100

gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler

Kolberg, L., Raudvere, U., Kuzmin, I., Vilo, J., & Peterson, H. (2020) · F1000Research · doi:10.12688/f1000research.24956.2 · Cited by 1,098

Nucleosome positioning and gene regulation: advances through genomics

Jiang, C., & Pugh, B. F. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2522 · Cited by 1,092

Stem cell gene expression programs influence clinical outcome in human leukemia

Eppert, K., Takenaka, K., Lechman, E. R., Waldron, L., Nilsson, B., van Galen, P., Metzeler, K. H., Poeppl, A., Ling, V., Beyene, J., et al. (2011) · Nature Medicine · doi:10.1038/nm.2415 · Cited by 1,041

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

Lai, Z., Markovets, A. A., Ahdesmaki, M. J., Chapman, B., Hofmann, O., McEwen, R. K., Johnson, J., Dougherty, B. A., Barrett, J. C., & Dry, J. R. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw227 · Cited by 984

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

Satpathy, A. T., Granja, J. M., Yost, K. E., Qi, Y., Meschi, F., McDermott, G. P., Olsen, B. N., Mumbach, M. R., Pierce, S. E., Corces, M. R., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0206-z · Cited by 980

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

Novershtern, N., Subramanian, A., Lawton, L. N., Mak, R. H., Haining, W. N., McConkey, M. E., Habib, N., Yosef, N., Chang, C. Y., Shay, T., et al. (2011) · Cell · doi:10.1016/j.cell.2011.01.004 · Cited by 942

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

Cao, J., Cusanovich, D. A., Ramani, V., Aghamirzaie, D., Pliner, H. A., Hill, A. J., Daza, R. M., McFaline-Figueroa, J. L., Packer, J. S., Christiansen, L., et al. (2018) · Science · doi:10.1126/science.aau0730 · Cited by 938

Progenitor and Terminal Subsets of CD8 + T Cells Cooperate to Contain Chronic Viral Infection

Paley, M., Kroy, D. C., Odorizzi, P. M., Johnnidis, J. B., Dolfi, D. V., Barnett, B. E., Bikoff, E. K., Robertson, E. J., Lauer, G. M., Reiner, S. L., et al. (2012) · Science · doi:10.1126/science.1229620 · Cited by 935

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

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

Yang, H., & Wang, K. (2015) · Nature Protocols · doi:10.1038/nprot.2015.105 · Cited by 873

Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia

Jan, M., Snyder, T. M., Corces-Zimmerman, M. R., Vyas, P., Weissman, I. L., Quake, S. R., & Majeti, R. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3004315 · Cited by 721

Preleukemic mutations in human acute myeloid leukemia affect epigenetic regulators and persist in remission

Corces-Zimmerman, M. R., Hong, W.-J., Weissman, I. L., Medeiros, B. C., & Majeti, R. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1324297111 · Cited by 705

Coexistence of LMPP-like and GMP-like Leukemia Stem Cells in Acute Myeloid Leukemia

Goardon, N., Marchi, E., Atzberger, A., Quek, L. S., Schuh, A., Soneji, S., Woll, P. S., Mead, A. J., Alford, K. A., Rout, R., et al. (2011) · Cancer Cell · doi:10.1016/j.ccr.2010.12.012 · Cited by 682

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

Sperling, A. S., Gibson, C. J., & Ebert, B. L. (2017) · Nature Reviews Cancer · doi:10.1038/nrc.2016.112 · Cited by 678

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

Buenrostro, J. D., Corces, M. R., Lareau, C. A., Wu, B., Schep, A. N., Aryee, M. J., Majeti, R., Chang, H. Y., & Greenleaf, W. J. (2018) · Cell · doi:10.1016/j.cell.2018.03.074 · Cited by 670

Tracing the origins of relapse in acute myeloid leukaemia to stem cells

Shlush, L. I., Mitchell, A., Heisler, L. E., Abelson, S., Ng, S., Trotman-Grant, A. C., Medeiros, J. J. F., Rao‐Bhatia, A., Jaciw-Zurakowsky, I., Marke, R., et al. (2017) · Nature · doi:10.1038/nature22993 · Cited by 616

Transcription factors in myeloid development: balancing differentiation with transformation

Rosenbauer, F., & Tenen, D. G. (2007) · Nature Reviews Immunology · doi:10.1038/nri2024 · Cited by 606

Decoding human fetal liver haematopoiesis

Popescu, D.-M., Botting, R. A., Stephenson, E., Green, K., Webb, S., Jardine, L., Calderbank, E. F., Polanski, K., Goh, I., Efremova, M., et al. (2019) · Nature · doi:10.1038/s41586-019-1652-y · Cited by 606

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

Mimitou, E. P., Lareau, C. A., Chen, K. Y., Zorzetto-Fernandes, A. L., Hao, Y., Takeshima, Y., Luo, W., Huang, T.-S., Yeung, B. Z., Papalexi, E., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00927-2 · Cited by 529

Single-cell mutation analysis of clonal evolution in myeloid malignancies

Miles, L. A., Bowman, R. L., Merlinsky, T. R., Csete, I. S., Ooi, A. T., Durruthy-Durruthy, R., Bowman, M., Famulare, C., Patel, M. A., Mendez, P., et al. (2020) · Nature · doi:10.1038/s41586-020-2864-x · Cited by 512

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

Granja, J. M., Klemm, S., McGinnis, L. M., Kathiria, A. S., Mezger, A., Corces, M. R., Parks, B., Gars, E., Liedtke, M., Zheng, G. X. Y., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0332-7 · Cited by 498

Clonal Hematopoiesis and Evolution to Hematopoietic Malignancies

Bowman, R. L., Busque, L., & Levine, R. L. (2018) · Cell stem cell · doi:10.1016/j.stem.2018.01.011 · Cited by 448

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility

Lareau, C. A., Duarte, F. M., Chew, J. G., Kartha, V. K., Burkett, Z. D., Kohlway, A. S., Pokholok, D., Aryee, M. J., Steemers, F. J., Lebofsky, R., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0147-6 · Cited by 444

JunB Deficiency Leads to a Myeloproliferative Disorder Arising from Hematopoietic Stem Cells

Passegue, E. A., Wagner, E. F., & Weissman, I. L. (2004) · Cell · doi:10.1016/j.cell.2004.10.010 · Cited by 443

Association of a Leukemic Stem Cell Gene Expression Signature With Clinical Outcomes in Acute Myeloid Leukemia

Gentles, A. J. (2010) · JAMA · doi:10.1001/jama.2010.1862 · Cited by 413

TNF-α Coordinates Hematopoietic Stem Cell Survival and Myeloid Regeneration

Yamashita, M., & Passegué, E. (2019) · Cell Stem Cell · doi:10.1016/j.stem.2019.05.019 · Cited by 387

Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics

Morita, K., Wang, F., Jahn, K., Hu, T., Tanaka, T., Sasaki, Y., Kuipers, J., Loghavi, S., Wang, S. A., Yan, Y., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19119-8 · Cited by 383

Redundant Regulation of T Cell Differentiation and TCRα Gene Expression by the Transcription Factors LEF-1 and TCF-1

Okamura, R. M., Sigvardsson, M., Galcerán, J., Verbeek, S. J., Clevers, H. C., & Grosschedl, R. (1998) · Immunity · doi:10.1016/s1074-7613(00)80454-9 · Cited by 340

The role of HOX genes in normal hematopoiesis and acute leukemia

Alharbi, R. A., Pettengell, R., Pandha, H. S., & Morgan, R. (2013) · Leukemia · doi:10.1038/leu.2012.356 · Cited by 335

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

Prospective separation of normal and leukemic stem cells based on differential expression of TIM3, a human acute myeloid leukemia stem cell marker

Jan, M., Chao, M. P., Cha, A. C., Alizadeh, A. A., Gentles, A. J., Weissman, I. L., & Majeti, R. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1100551108 · Cited by 323

Transcriptional diversity during lineage commitment of human blood progenitors

Chen, L., Kostadima, M. A., Martens, J. H. A., Canu, G., Garcia, S. P., Turro, E., Downes, K., Macaulay, I. C., Bielczyk-Maczyńska, E., Coe, S., et al. (2014) · Science · doi:10.1126/science.1251033 · Cited by 315

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling

Lareau, C. A., Ludwig, L. S., Muus, C., Gohil, S. H., Zhao, T., Chiang, Z., Pelka, K., Verboon, J. M., Luo, W., Christian, E., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0645-6 · Cited by 315

Tel/Etv6 is an essential and selective regulator of adult hematopoietic stem cell survivalPreprint

Hock, H. R., Meade, E., Medeiros, S., Schindler, J. W., Valk, P. J. M., Fujiwara, Y., & Orkin, S. H. (2004) · Genes & Development · doi:10.1101/gad.1239604 · Cited by 310

Tree inference for single-cell data

Jahn, K., Kuipers, J., & Beerenwinkel, N. (2016) · Genome biology · doi:10.1186/s13059-016-0936-x · Cited by 310

Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing

Rodriguez-Meira, A., Buck, G., Clark, S.-A., Povinelli, B. J., Alcolea, V., Louka, E., McGowan, S., Hamblin, A., Sousos, N., Barkas, N., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.01.009 · Cited by 305

Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells

Karamitros, D., Stoilova, B., Aboukhalil, Z., Hamey, F., Reinisch, A., Samitsch, M., Quek, L. S., Otto, G., Repapi, E., Doondeea, J. B., et al. (2017) · Nature Immunology · doi:10.1038/s41590-017-0001-2 · Cited by 280

RUNX1 Mutations Are Associated With Poor Outcome in Younger and Older Patients With Cytogenetically Normal Acute Myeloid Leukemia and With Distinct Gene and MicroRNA Expression Signatures

Mendler, J. H., Maharry, K. S., Radmacher, M. D., Mrózek, K., Becker, H., Metzeler, K. H., Schwind, S., Whitman, S. P., Khalife, J., Kohlschmidt, J., et al. (2012) · Journal of Clinical Oncology · doi:10.1200/jco.2011.40.6652 · Cited by 277

Meis1 is an essential and rate-limiting regulator of MLL leukemia stem cell potentialPreprint

Wong, P., 岩崎, 正., Somervaille, T. C. P., So, C. W. E., & Cleary, M. L. (2007) · Genes & Development · doi:10.1101/gad.1602107 · Cited by 274

Ultra-sensitive Sequencing Identifies High Prevalence of Clonal Hematopoiesis-Associated Mutations throughout Adult Life

Acuna-Hidalgo, R., Sengul, H., Steehouwer, M., van de Vorst, M., Vermeulen, S. H., Kiemeney, L. A. L. M., Veltman, J. A., Gilissen, C., & Hoischen, A. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.05.013 · Cited by 264

Mosaicism in health and disease — clones picking up speed

Forsberg, L. A., Gisselsson, D., & Dumanski, J. P. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.145 · Cited by 263

Pbx1 Regulates Self-Renewal of Long-Term Hematopoietic Stem Cells by Maintaining Their Quiescence

Ficara, F., Murphy, M., Lin, M., & Cleary, M. L. (2008) · Cell stem cell · doi:10.1016/j.stem.2008.03.004 · Cited by 244

DNA methylation disruption reshapes the hematopoietic differentiation landscape

Izzo, F., Lee, S. C., Poran, A., Chaligne, R., Gaiti, F., Gross, B., Murali, R. R., Deochand, S. D., Ang, C., Jones, P. W., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0595-4 · Cited by 236

High meningioma 1 (MN1) expression as a predictor for poor outcome in acute myeloid leukemia with normal cytogenetics

Heuser, M., Beutel, G., Krauter, J., Döhner, K., Neuhoff, N. V., Schlegelberger, B., & Ganser, A. (2006) · Blood · doi:10.1182/blood-2006-04-014845 · Cited by 232

Bcl11a is essential for lymphoid development and negatively regulates p53

Yu, Y., Wang, J., Khaled, W. T., Burke, S., Li, P., Chen, X., Yang, W., Jenkins, N. A., Copeland, N. G., Zhang, S., et al. (2012) · The Journal of Experimental Medicine · doi:10.1084/jem.20121846 · Cited by 231

Clonal heterogeneity of acute myeloid leukemia treated with the IDH2 inhibitor enasidenib

Quek, L., David, M. D., Kennedy, A., Metzner, M., Amatangelo, M., Shih, A., Stoilova, B., Quivoron, C., Heiblig, M., Willekens, C., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0115-6 · Cited by 200

Essential role of Jun family transcription factors in PU.1 knockdown–induced leukemic stem cells

Steidl, U., Rosenbauer, F., Verhaak, R. G. W., Gu, X., Ebralidze, A., Otu, H. H., Klippel, S., Steidl, C., Bruns, I., Costa, D. B., et al. (2006) · Nature Genetics · doi:10.1038/ng1898 · Cited by 184

c-Jun Is a JNK-independent Coactivator of the PU.1 Transcription Factor

Behre, G., Whitmarsh, A. J., Coghlan, M. P., Hoang, T., Carpenter, C. L., Zhang, D.-E., Davis, R. J., & Tenen, D. G. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.8.4939 · Cited by 180

Non-canonical PRC1.1 Targets Active Genes Independent of H3K27me3 and Is Essential for Leukemogenesis

van den Boom, V., Maat, H., Geugien, M., López, A. R., Sotoca, A. M., Jaques, J., Brouwers-Vos, A. Z., Fusetti, F., Groen, R. W. J., Yuan, H., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.12.034 · Cited by 167

The leukemia-associated AML1 (Runx1)--CBF beta complex functions as a DNA-induced molecular clamp.

Bravo, J., Li, Z., Speck, N. A., & Warren, A. J. (2001) · Nature Structural Biology · doi:10.1038/86264 · Cited by 158

PBX3 is an important cofactor of HOXA9 in leukemogenesis

Li, Z., Zhang, Z., Li, Y., Arnovitz, S., Chen, P., Huang, H., Jiang, X., Hong, G.-M., Kunjamma, R. B., Ren, H., et al. (2012) · Blood · doi:10.1182/blood-2012-07-442004 · Cited by 154

Identification of leukemic and pre-leukemic stem cells by clonal tracking from single-cell transcriptomics

Velten, L., Story, B. A., Hernández-Malmierca, P., Raffel, S., Leonce, D. R., Milbank, J. H., Paulsen, M. S., Demir, A., Szu‐Tu, C., Frömel, R., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21650-1 · Cited by 146

High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer

Pierce, S. E., Granja, J. M., & Greenleaf, W. J. (2021) · Nature Communications · doi:10.1038/s41467-021-23213-w · Cited by 146

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

NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells

Chen, A. F., Parks, B., Kathiria, A. S., Ober-Reynolds, B., Goronzy, J. J., & Greenleaf, W. J. (2022) · Nature Methods · doi:10.1038/s41592-022-01461-y · Cited by 139

Deletion of the NF-κB subunit p65/RelA in the hematopoietic compartment leads to defects in hematopoietic stem cell function

Stein, S. J., & Baldwin, A. S. (2013) · Blood · doi:10.1182/blood-2013-02-486142 · Cited by 125

ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells

Xu, W. Q., Yang, W., Zhang, Y., Chen, Y., Hong, N., Zhang, Q., Wang, X. J., Hu, Y., Song, K., Jin, W., et al. (2022) · Nature Methods · doi:10.1038/s41592-022-01601-4 · Cited by 121

Wilms tumor 1 mutations in the pathogenesis of acute myeloid leukemia

Rampal, R. K., & Figueroa, M. E. (2016) · Haematologica · doi:10.3324/haematol.2015.141796 · Cited by 120

Interplay of transcription factors in T-cell differentiation and function: the role of Runx

Wong, W. F., Kohu, K., Chiba, T., Sato, T., & Satake, M. (2010) · Immunology · doi:10.1111/j.1365-2567.2010.03381.x · Cited by 118

Dual requirement for the ETS transcription factors Fli-1 and Erg in hematopoietic stem cells and the megakaryocyte lineage

Kruse, E., Loughran, S. J., Baldwin, T. M., Josefsson, E. C., Ellis, S. L., Watson, D. K., Nurden, P., Metcalf, D., Hilton, D. J., Alexander, W. S., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906556106 · Cited by 117

A Non-canonical BCOR-PRC1.1 Complex Represses Differentiation Programs in Human ESCs

Wang, Z., Gearhart, M. D., Lee, Y.-W., Kumar, I., Ramazanov, B. R., Zhang, Y., Hernandez, C. C., Lü, A., Neuenkirchen, N., Deng, J., et al. (2018) · Cell stem cell · doi:10.1016/j.stem.2017.12.002 · Cited by 110

RUNX1 mutations in cytogenetically normal acute myeloid leukemia are associated with a poor prognosis and up-regulation of lymphoid genes

Greif, P. A., Konstandin, N. P., Metzeler, K. H., et al. (2012) · Haematologica · doi:10.3324/haematol.2012.064667 · Cited by 106

NF-Y is necessary for hematopoietic stem cell proliferation and survival

Bungartz, G., Land, H., Scadden, D. T., & Emerson, S. G. (2011) · Blood · doi:10.1182/blood-2011-06-359406 · Cited by 105

Identification of two distinct pathways of human myelopoiesis

Drissen, R., Thongjuea, S., Theilgaard‐Mönch, K., & Nerlov, C. (2019) · Science Immunology · doi:10.1126/sciimmunol.aau7148 · Cited by 104

The orphan nuclear receptor Nurr1 restricts the proliferation of haematopoietic stem cells

Sirin, O., Lukov, G. L., Mao, R., Conneely, O. M., & Goodell, M. A. (2010) · Nature Cell Biology · doi:10.1038/ncb2125 · Cited by 101

High-content single-cell combinatorial indexing

Mulqueen, R. M., Pokholok, D., O’Connell, B. L., Thornton, C. A., Zhang, F., O’Roak, B. J., Link, J. M., Yardımcı, G. G., Sears, R. C., Steemers, F. J., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00962-z · Cited by 99

ERG promotes the maintenance of hematopoietic stem cells by restricting their differentiation

Knudsen, K. J., Rehn, M., Hasemann, M. S., Rapin, N., Bagger, F. O., Ohlsson, E., Willer, A., Frank, A.-K., Søndergaard, E., Jendholm, J., et al. (2015) · Genes & Development · doi:10.1101/gad.268409.115 · Cited by 98

JMJD1C is required for the survival of acute myeloid leukemia by functioning as a coactivator for key transcription factorsPreprint

Chen, M., Zhu, N., Liu, X., Laurent, B., Tang, Z., Eng, R., Shi, Y., Armstrong, S. A., & Roeder, R. G. (2015) · Genes & Development · doi:10.1101/gad.267278.115 · Cited by 97

Mapping genomic and epigenomic evolution in cancer ecosystems

Ushijima, T., Clark, S. J., & Tan, P. B. O. (2021) · Science · doi:10.1126/science.abh1645 · Cited by 91

BCOR regulates myeloid cell proliferation and differentiation

Cao, Q., Gearhart, M. D., Gery, S., Shojaee, S., Yang, H. H., Sun, H., Lin, D.-C., Bai, J.-W., Mead, M. D., Zhao, Z., et al. (2016) · Leukemia · doi:10.1038/leu.2016.2 · Cited by 88

getITD for FLT3-ITD-based MRD monitoring in AML

Blätte, T. J., Schmalbrock, L. K., Skambraks, S., Lux, S., Cocciardi, S., Dolnik, A., Döhner, H., Döhner, K., & Bullinger, L. (2019) · Leukemia · doi:10.1038/s41375-019-0483-z · Cited by 88

MEF2C Phosphorylation Is Required for Chemotherapy Resistance in Acute Myeloid Leukemia

Brown, F. C., Still, E., Koche, R. P., Yim, C. Y., Takao, S., Cifani, P., Reed, C., Gunasekera, S., Ficarro, S. B., Romanienko, P. J., et al. (2018) · Cancer Discovery · doi:10.1158/2159-8290.cd-17-1271 · Cited by 85

Homing and invasiveness of MLL/ENL leukemic cells is regulated by MEF2C

Schwieger, M., Schüler, A., Forster, M., Engelmann, A., Arnold, M., Delwel, R., Valk, P. J. M., Löhler, J., Slany, R. K., Olson, E. N., et al. (2009) · Blood · doi:10.1182/blood-2008-05-158196 · Cited by 73

Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis

Kelly, M. J., So, J., Rogers, A. J., Gregory, G. P., Li, J., Zethoven, M., Gearhart, M. D., Bardwell, V. J., Johnstone, R. W., Vervoort, S. J., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09250-6 · Cited by 70

A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility

Xu, W., Wen, Y., Liang, Y., Xu, Q., Wang, X., Jin, W., & Chen, X. (2021) · Nature Protocols · doi:10.1038/s41596-021-00583-5 · Cited by 67

SOCS2 Controls Proliferation and Stemness of Hematopoietic Cells under Stress Conditions and Its Deregulation Marks Unfavorable Acute Leukemias

Vitali, C., Bassani, C., Chiodoni, C., Fellini, E., Guarnotta, C., Miotti, S., Sangaletti, S., Fuligni, F., Cecco, L. D., Piccaluga, P. P., et al. (2015) · Cancer Research · doi:10.1158/0008-5472.can-14-3625 · Cited by 67

PBX3 and MEIS1 cooperate in hematopoietic cells to drive acute myeloid leukemias characterized by a core transcriptome of the MLL-rearranged disease

Li, Z.-J., Chen, P., Su, R., Hu, C., Li, Y.-Y., Elkahloun, A., Zuo, Z., Gurbuxani, S., Arnovitz, S., Weng, H., et al. (2016) · Cancer Research · doi:10.1158/0008-5472.can-15-1566 · Cited by 67

Noncanonical NF-κB Signaling Regulates Hematopoietic Stem Cell Self-Renewal and Microenvironment Interactions

Zhao, C., Xiu, Y., Ashton, J., Xing, L., Morita, Y., Jordan, C. T., & Boyce, B. F. (2012) · Stem Cells · doi:10.1002/stem.1050 · Cited by 65

LanceOtron: a deep learning peak caller for genome sequencing experiments

Hentges, L. D., Sergeant, M. J., Cole, C. B., Downes, D. J., Hughes, J. R., & Taylor, S. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac525 · Cited by 57

Polycomb Group Protein YY1 Is an Essential Regulator of Hematopoietic Stem Cell Quiescence

Lu, Z., Hong, C. C., Kong, G., Assumpção, A. L. F. V., Ong, I. M., Bresnick, E. H., Zhang, J., & Pan, X. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.01.026 · Cited by 56

SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness

Nguyen, C. H., Glüxam, T., Schlerka, A., Bauer, K., Grandits, A. M., Hackl, H., Dovey, O. M., Zöchbauer‐Müller, S., Cooper, J. L., Vassiliou, G. S., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-45579-0 · Cited by 54

PBX3 is essential for leukemia stem cell maintenance in MLL‐rearranged leukemia

Guo, H.-D., Chu, Y., Wang, L., Chen, X., Chen, Y., Cheng, H., Zhang, L., Zhou, Y., Yang, F.-C., Cheng, T., et al. (2017) · International Journal of Cancer · doi:10.1002/ijc.30739 · Cited by 47

TARGET-Seq: A Protocol for High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing

Rodríguez-Meira, A., O’Sullivan, J., Rahman, H., & Mead, A. J. (2020) · STAR Protocols · doi:10.1016/j.xpro.2020.100125 · Cited by 44

Fos modulates myeloid cell survival and differentiation and partially abrogates the c-Myc block in terminal myeloid differentiation

Shafarenko, M., Amanullah, A., Gregory, B., Liebermann, D. A., & Hoffman‐Liebermann, B. (2004) · Blood · doi:10.1182/blood-2002-09-2704 · Cited by 28

Transcription factor MEF2D is required for the maintenance of MLL-rearranged acute myeloid leukemia

Zhao, L., Zhang, P., Galbo, P. M., Zhou, X., Aryal, S., Qiu, S., Zhang, H., Zhou, Y., Li, C., Zheng, D., et al. (2021) · Blood Advances · doi:10.1182/bloodadvances.2021004469 · Cited by 24

Candidate tumor suppressor B-cell translocation gene 3 impedes neoplastic progression by suppression of AKT

Cheng, Y.-C., Chen, P., Chiang, H.-Y., Suen, C.-S., Hwang, M., Lin, T.-Y., Yang, H.-C., Lin, W.-C., Lai, P.-L., & Shieh, S.-Y. (2015) · Cell Death and Disease · doi:10.1038/cddis.2014.550 · Cited by 19

P2X1 enhances leukemogenesis through PBX3-BCAT1 pathways

He, X., Xu, Y., Huang, D., Yu, Z., Yu, J., Xie, L., Liu, L., Yu, Y., Chen, C., Wan, J., et al. (2022) · Leukemia · doi:10.1038/s41375-022-01759-y · Cited by 16

Smart3-ATAC: a highly sensitive method for joint accessibility and full-length transcriptome analysis in single cellsPreprint

Cheng, H., Pui, H., Lentini, A., Kolbeinsdóttir, S., Andrews, N., Pei, Y., Reinius, B., Deng, Q., & Enge, M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.02.470912 · Cited by 11

In-silico probing of AML related RUNX1 cancer-associated missense mutations: Predicted relationships to DNA binding and drug interactions

Ullah, H., Zhang, B., Sharma, N. K., McCrea, P. D., & Srivastava, Y. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.981020 · Cited by 3

Selective advantage of mutant stem cells in human clonal hematopoiesis is associated with attenuated response to inflammation and aging

Jakobsen, N. A., Turkalj, S., Zeng, A. G. X., Stoilova, B., Metzner, M., Rahmig, S., Nagree, M. S., Shah, S., Moore, R., Usukhbayar, B., et al. (2024) · Cell Stem Cell · doi:10.1016/j.stem.2024.05.010 · Cited by 130