KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance

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 · see citing works

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 · see citing works

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895 · see citing works

HTSeq—a Python framework to work with high-throughput sequencing data

Anders, S., Pyl, P. T., & Huber, W. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu638 · Cited by 21,464 · see citing works

Model-based Analysis of ChIP-Seq (MACS)

Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386 · see citing works

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., & Salzberg, S. L. (2013) · Genome Biology · doi:10.1186/gb-2013-14-4-r36 · Cited by 12,668 · see citing works

Comprehensive molecular portraits of human breast tumours

The Cancer Genome Atlas Network (2012) · Nature · doi:10.1038/nature11412 · Cited by 12,129 · see citing works

A framework for variation discovery and genotyping using next-generation DNA sequencing data

DePristo, M. A., Banks, E., Poplin, R. E., Garimella, K. V., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,216 · see citing works

From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline

Van der Auwera, G. A., Carneiro, M. O., Hartl, C., Poplin, R., del Angel, G., Levy‐Moonshine, A., Jordan, T., Shakir, K., Roazen, D., Thibault, J., et al. (2013) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1110s43 · Cited by 6,687 · see citing works

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

Tirosh, I., Izar, B., Prakadan, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., Lian, C., Murphy, G., et al. (2016) · Science · doi:10.1126/science.aad0501 · Cited by 4,944 · see citing works

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 4,838 · see citing works

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 · see citing works

A Chromatin-Mediated Reversible Drug-Tolerant State in Cancer Cell Subpopulations

Sharma, S. V., Lee, D. Y., Li, B., Quinlan, M. P., Takahashi, F., Maheswaran, S., McDermott, U., Azizian, N., Zou, L., Fischbach, M. A., et al. (2010) · Cell · doi:10.1016/j.cell.2010.02.027 · Cited by 2,770 · see citing works

EMT, CSCs, and drug resistance: the mechanistic link and clinical implications

Shibue, T., & Weinberg, R. A. (2017) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2017.44 · Cited by 2,539 · see citing works

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

Bendall, S. C., Simonds, E. F., Qiu, P., Amir, E.-A. D., Krutzik, P. O., Finck, R., Bruggner, R. V., Melamed, R., Trejo, A., Ornatsky, O. I., et al. (2011) · Science · doi:10.1126/science.1198704 · Cited by 2,279 · see citing works

Circular binary segmentation for the analysis of array-based DNA copy number data

Olshen, A. B., Venkatraman, E. S., Lucito, R., & Wigler, M. H. (2004) · Biostatistics · doi:10.1093/biostatistics/kxh008 · Cited by 2,256 · see citing works

Intra-tumour heterogeneity: a looking glass for cancer?

Marusyk, A., Almendro, V., & Polyák, K. (2012) · Nature reviews. Cancer · doi:10.1038/nrc3261 · Cited by 2,003 · see citing works

EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations

McCabe, M. T., Ott, H. M., Ganji, G., Korenchuk, S., Thompson, C., Van Aller, G. S., Liu, Y., Graves, A. P., III, A. D. P., Diaz, E., et al. (2012) · Nature · doi:10.1038/nature11606 · Cited by 1,786 · see citing works

Tumor heterogeneity: Causes and consequences

Marusyk, A., & Polyák, K. (2009) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2009.11.002 · Cited by 1,596 · see citing works

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

McLaren, W. M., Yates, B., Ríos, D., Chen, Y., Flicek, P., & Cunningham, F. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq330 · Cited by 1,586 · see citing works

Evolution and impact of subclonal mutations in chronic lymphocytic leukemia

Landau, D. A., Carter, S. L., Stojanov, P., McKenna, A., Stevenson, K., Lawrence, M. S., Sougnez, C., Stewart, C., Sivachenko, A., Wang, L., et al. (2013) · Cell · doi:10.1016/j.cell.2013.01.019 · Cited by 1,379 · see citing works

Epigenetic plasticity and the hallmarks of cancer

Flavahan, W. A., Gaskell, E., & Bernstein, B. E. (2017) · Science · doi:10.1126/science.aal2380 · Cited by 1,340 · see citing works

FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

Shen, R., & Seshan, V. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw520 · Cited by 1,263 · see citing works

Biological determinants of endocrine resistance in breast cancer

Musgrove, E. A., & Sutherland, R. L. (2009) · Nature reviews. Cancer · doi:10.1038/nrc2713 · Cited by 1,254 · see citing works

MECHANISMS OF ENDOCRINE RESISTANCE IN BREAST CANCER

Osborne, C., & Schiff, R. (2011) · Annual Review of Medicine · doi:10.1146/annurev-med-070909-182917 · Cited by 1,205 · see citing works

A Temporarily Distinct Subpopulation of Slow-Cycling Melanoma Cells Is Required for Continuous Tumor Growth

Roesch, A., Fukunaga‐Kalabis, M., Schmidt, E. C., Zabierowski, S. E., Brafford, P. A., Vultur, A., Basu, D., Gimotty, P. A., VOGT, T. M., & Herlyn, M. (2010) · Cell · doi:10.1016/j.cell.2010.04.020 · Cited by 1,162 · see citing works

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts

L. Lun, A. T., Bach, K., & Marioni, J. C. (2016) · Genome Biology · doi:10.1186/s13059-016-0947-7 · Cited by 1,108 · see citing works

Genome Regulation by Polycomb and Trithorax: 70 Years and Counting

Schuettengruber, B., Bourbon, H.-M., Di Croce, L., & Cavalli, G. (2017) · Cell · doi:10.1016/j.cell.2017.08.002 · Cited by 1,094 · see citing works

Widespread Genetic Heterogeneity in Multiple Myeloma: Implications for Targeted Therapy

Lohr, J. G., Stojanov, P., Carter, S. L., Cruz-Gordillo, P., Lawrence, M. S., Auclair, D., Sougnez, C., Knoechel, B., Gould, J., Saksena, G., et al. (2014) · Cancer Cell · doi:10.1016/j.ccr.2013.12.015 · Cited by 988 · see citing works

Tumor cells can follow distinct evolutionary paths to become resistant to epidermal growth factor receptor inhibition

Hata, A. N., Niederst, M. J., Archibald, H. L., Gomez-Caraballo, M., Siddiqui, F. M., Mulvey, H. E., Maruvka, Y. E., Ji, F., Bhang, H.-E. C., Krishnamurthy Radhakrishna, V., et al. (2016) · Nature Medicine · doi:10.1038/nm.4040 · Cited by 985 · see citing works

Genetic and transcriptional evolution alters cancer cell line drug response

Ben-David, U., Siranosian, B., Ha, G., Tang, H., Oren, Y., Hinohara, K., Strathdee, C. A., Dempster, J., Lyons, N. J., Burns, R., et al. (2018) · Nature · doi:10.1038/s41586-018-0409-3 · Cited by 931 · see citing works

Epigenetic modulators, modifiers and mediators in cancer aetiology and progression

Feinberg, A. P., Koldobskiy, M. A., & Göndör, A. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.13 · Cited by 878 · see citing works

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

Vaske, C. J., Benz, S. C., Sanborn, J. Z., Earl, D., Szeto, C., Zhu, J., Haussler, D., & Stuart, J. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq182 · Cited by 786 · see citing works

ESR1 mutations—a mechanism for acquired endocrine resistance in breast cancer

Jeselsohn, R. M., Buchwalter, G., Angelis, C. D., Brown, M. A., & Schiff, R. (2015) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2015.117 · Cited by 718 · see citing works

Single-cell barcoding and sequencing using droplet microfluidics

Žilionis, R., Nainys, J., Veres, A., Savova, V., Zemmour, D., Klein, A. M., & Mažutis, L. (2016) · Nature Protocols · doi:10.1038/nprot.2016.154 · Cited by 715 · see citing works

Clonal status of actionable driver events and the timing of mutational processes in cancer evolution

McGranahan, N., Favero, F., de Bruin, E. C., Birkbak, N. J., Szallasi, Z., & Swanton, C. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aaa1408 · Cited by 685 · see citing works

Overcoming Intrinsic Multidrug Resistance in Melanoma by Blocking the Mitochondrial Respiratory Chain of Slow-Cycling JARID1Bhigh Cells

Roesch, A., Vultur, A., Bogeski, I., Wang, H., Zimmermann, K. M., Speicher, D., Körbel, C., Laschke, M. W., Gimotty, P. A., Philipp, S. E., et al. (2013) · Cancer Cell · doi:10.1016/j.ccr.2013.05.003 · Cited by 670 · see citing works

Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations

Brastianos, P. K., Horowitz, P. M., Santagata, S., Jones, R. T., McKenna, A., Getz, G. A., Ligon, K. L., Palescandolo, E., Hummelen, P. V., Ducar, M. D., et al. (2013) · Nature Genetics · doi:10.1038/ng.2526 · Cited by 651 · see citing works

H3K4me3 breadth is linked to cell identity and transcriptional consistency

Benayoun, B. A., Pollina, E. A., Ucar, D., Mahmoudi, S., Karra, K., Wong, E. D., Devarajan, K., Daugherty, A. C., Kundaje, A. B., Mancini, E., et al. (2014) · Cell · doi:10.1016/j.cell.2014.06.027 · Cited by 536 · see citing works

Studying clonal dynamics in response to cancer therapy using high-complexity barcoding

Bhang, H.-E. C., Ruddy, D. A., Krishnamurthy Radhakrishna, V., Caushi, J. X., Zhao, R., Hims, M. M., Singh, A. P., Kao, I., Rakiec, D., Shaw, P., et al. (2015) · Nature Medicine · doi:10.1038/nm.3841 · Cited by 507 · see citing works

The Aging Epigenome

Booth, L. N., & Brunet, A. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.013 · Cited by 499 · see citing works

Non-genetic heterogeneity — a mutation-independent driving force for the somatic evolution of tumours

Brock, A., Chang, H. H., & Huang, S. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2556 · Cited by 481 · see citing works

Single-cell multiomics: multiple measurements from single cells

Macaulay, I. C., Ponting, C. P., & Voet, T. (2017) · Trends in Genetics · doi:10.1016/j.tig.2016.12.003 · Cited by 451 · see citing works

An inhibitor of KDM5 demethylases reduces survival of drug-tolerant cancer cells

Vinogradova, M. V., Gehling, V. S., Gustafson, A. E., Arora, S., Tindell, C., WILSON, C. A., Williamson, K. E., Guler, G. D., Gangurde, P., Manieri, W., et al. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2085 · Cited by 358 · see citing works

Chromatin repressive complexes in stem cells, development, and cancer

Laugesen, A., & Helin, K. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.05.006 · Cited by 352 · see citing works

Aging increases cell-to-cell transcriptional variability upon immune stimulation

Martinez-Jimenez, C. P., Eling, N., Chen, H.-C., Vallejos, C. A., Kolodziejczyk, A. A., Connor, F., Stojic, L., Rayner, T. F., Stubbington, M. J. T., Teichmann, S. A., et al. (2017) · Science · doi:10.1126/science.aah4115 · Cited by 339 · see citing works

GiniClust: detecting rare cell types from single-cell gene expression data with Gini index

Jiang, L., Chen, H., Pinello, L., & Yuan, G. (2016) · Genome biology · doi:10.1186/s13059-016-1010-4 · Cited by 296 · see citing works

JARID1B Is a Luminal Lineage-Driving Oncogene in Breast Cancer

Yamamoto, S., Wu, Z., Russnes, H. G., Takagi, S., Peluffo, G., Vaske, C. J., Zhao, X., Vollan, H. K. M., Maruyama, R., Ekram, M. B., et al. (2014) · Cancer Cell · doi:10.1016/j.ccr.2014.04.024 · Cited by 208 · see citing works

A Gene Expression Signature that Can Predict the Recurrence of Tamoxifen-Treated Primary Breast Cancer

Chanrion, M., Nègre, V., Fontaine, H., et al. (2008) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-07-1833 · Cited by 203 · see citing works

Cancer: Evolution Within a Lifetime

Gerlinger, M., McGranahan, N., Dewhurst, S. M., Burrell, R. A., Tomlinson, I. P. M., & Swanton, C. (2014) · Annual Review of Genetics · doi:10.1146/annurev-genet-120213-092314 · Cited by 202 · see citing works

Structural analysis of human KDM5B guides histone demethylase inhibitor development

Johansson, C., Velupillai, S., Tumber, A., Szykowska, A., Hookway, E. S., Nowak, R. P., Strain-Damerell, C. M., Gileadi, C., Philpott, M., Burgess-Brown, N., et al. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2087 · Cited by 200 · see citing works

Genetic and non-genetic instability in tumor progression: link between the fitness landscape and the epigenetic landscape of cancer cells

Huang, S. (2013) · Cancer and Metastasis Reviews · doi:10.1007/s10555-013-9435-7 · Cited by 183 · see citing works

Potent and Selective KDM5 Inhibitor Stops Cellular Demethylation of H3K4me3 at Transcription Start Sites and Proliferation of MM1S Myeloma Cells

Tumber, A., Nuzzi, A., Hookway, E. S., Hatch, S. B., Velupillai, S., Johansson, C., Kawamura, A., Savitsky, P. A., Yapp, C., Szykowska, A., et al. (2017) · Cell chemical biology · doi:10.1016/j.chembiol.2017.02.006 · Cited by 149 · see citing works

ZMYND8 Reads the Dual Histone Mark H3K4me1-H3K14ac to Antagonize the Expression of Metastasis-Linked Genes

Li, N., Li, Y., Lv, J., Zheng, X., Wen, H., Shen, H., Zhu, G., Chen, T.-Y., Dhar, S. S., Kan, P.-Y., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.06.035 · Cited by 141 · see citing works

Characterization of a Linked Jumonji Domain of the KDM5/JARID1 Family of Histone H3 Lysine 4 Demethylases

Horton, J. R., Engstrom, A., Zoeller, E. L., Liu, X., Shanks, J. R., Zhang, X., Johns, M. A., Vertino, P. M., Fu, H., & Cheng, X. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.698449 · Cited by 131 · see citing works

The Evolving Role of the Estrogen Receptor Mutations in Endocrine Therapy-Resistant Breast Cancer

Jeselsohn, R. M., Angelis, C. D., Brown, M. A., & Schiff, R. (2017) · Current Oncology Reports · doi:10.1007/s11912-017-0591-8 · Cited by 115 · see citing works

Cell population heterogeneity and evolution towards drug resistance in cancer: Biological and mathematical assessment, theoretical treatment optimisation

Chisholm, R. H., Lorenzi, T., & Clairambault, J. (2016) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2016.06.009 · Cited by 96 · see citing works

Building the Connectivity Map of epigenetics: Chromatin profiling by quantitative targeted mass spectrometry

Creech, A. L., Taylor, J. E., Maier, V., Wu, X., Feeney, C. M., Udeshi, N. D., Peach, S. E., Boehm, J. S., Lee, J. T., Carr, S. A., et al. (2014) · Methods · doi:10.1016/j.ymeth.2014.10.033 · Cited by 62 · see citing works

Lead optimization of a pyrazolo[1,5-a]pyrimidin-7(4H)-one scaffold to identify potent, selective and orally bioavailable KDM5 inhibitors suitable for in vivo biological studies

Liang, J., Zhang, B., Labadie, S. S., Ortwine, D. F., Vinogradova, M. V., Kiefer, J. R., Gehling, V. S., Harmange, J.-C., Cummings, R. T., Lai, T., et al. (2016) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2016.06.078 · Cited by 50 · see citing works

Gene expression profiling of human breast tissue samples using SAGE-SeqPreprint

Wu, Z. J., Meyer, C. A., Choudhury, S. A., Shipitsin, M. V., Maruyama, R., Bessarabova, M., Nikolskaya, T., Sukumar, S. V., Schwartzman, A., Liu, J. S., et al. (2010) · Genome Research · doi:10.1101/gr.108217.110 · Cited by 41 · see citing works

SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution

McDonald, T. O., & Michor, F. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx146 · Cited by 7 · see citing works

Overcoming Endocrine Resistance in Breast Cancer

Hanker, A. B., Sudhan, D. R., & Arteaga, C. L. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.03.009 · Cited by 927 · see citing works

Tumor hypoxia: From basic knowledge to therapeutic implications

Liao, C., Liu, X., Zhang, C., & Zhang, Q. (2023) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2022.12.011 · Cited by 223 · see citing works

Emerging Insights into Targeted Therapy-Tolerant Persister Cells in Cancer

Cabanos, H. F., & Hata, A. N. (2021) · Cancers · doi:10.3390/cancers13112666 · Cited by 189 · see citing works

Drug resistance in colorectal cancer: An epigenetic overview

Luo, M., Yang, X., Chen, H.-N., Nice, E. C., & Huang, C. (2021) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2021.188623 · Cited by 94 · see citing works

Drug tolerance and persistence in bacteria, fungi and cancer cells: Role of non-genetic heterogeneity

El Meouche, I., Jain, P., Jolly, M. K., & Capp, J.-P. (2024) · Translational Oncology · doi:10.1016/j.tranon.2024.102069 · Cited by 22 · see citing works

KDM5B protein expressed in viable and fertile ΔARID mice exhibit no demethylase activity

Jamshidi, S., Catchpole, S., Chen, J., et al. (2021) · International Journal of Oncology · doi:10.3892/ijo.2021.5276 · Cited by 10 · see citing works

Biological roles of LSD1 beyond its demethylase activity

Gu, F., Lin, Y., Wang, Z., Wu, X., Ye, Z., Wang, Y., & Lan, H. (2020) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-020-03489-9 · Cited by 121 · see citing works

When Is a Demethylase Not a Demethylase?

Ray, L. B. (2011) · Science Signaling · doi:10.1126/scisignal.4193ec275

Inhibition of demethylases by GSK-J1/J4

Heinemann, B., Nielsen, J. M., Hudlebusch, H. R., Lees, M. J., Larsen, D. V., Boesen, T. P., Labelle, M., Gerlach, L., Birk, P., & Helin, K. (2014) · Nature · doi:10.1038/nature13688 · Cited by 230 · see citing works

Histone Demethylase LSD2 Acts as an E3 Ubiquitin Ligase and Inhibits Cancer Cell Growth through Promoting Proteasomal Degradation of OGT

Yang, Y., Yin, X., Yang, H., & Xu, Y. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.01.038 · Cited by 92 · see citing works