Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Li, B., & Dewey, C. N. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-323 · Cited by 22,179

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849

Radiotherapy Plus Concomitant and Adjuvant Temozolomide for Glioblastoma

Stupp, R., Mason, W. P., van den Bent, M. J., Weller, M., Fisher, B., Taphoorn, M. J. B., Belanger, K., Brandes, A. A., Marosi, C., Bogdahn, U., et al. (2005) · New England Journal of Medicine · doi:10.1056/nejmoa043330 · Cited by 21,807

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

Gerlinger, M., Rowan, A. J., Horswell, S., Larkin, J., Endesfelder, D., Gronroos, E., Martinez, P., Matthews, N., Stewart, A., Tarpey, P., et al. (2012) · New England Journal of Medicine · doi:10.1056/nejmoa1113205 · Cited by 7,774

Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

Verhaak, R. G. W., Hoadley, K. A., Purdom, E., Wang, V., Qi, Y., Wilkerson, M. D., Miller, C. R., Ding, L., Golub, T., Mesirov, J. P., et al. (2010) · Cancer Cell · doi:10.1016/j.ccr.2009.12.020 · Cited by 7,575

Identification of human brain tumour initiating cells

Singh, S. K., Hawkins, C. E., Clarke, I. D., Squire, J. A., Bayani, J., Hide, T., Henkelman, R. M., Cusimano, M. D., & Dirks, P. B. (2004) · Nature · doi:10.1038/nature03128 · Cited by 7,564

Glioma stem cells promote radioresistance by preferential activation of the DNA damage response

Bao, S., Wu, Q., McLendon, R. E., Hao, Y., Shi, Q., Hjelmeland, A. B., Dewhirst, M. W., Bigner, D. D., & Rich, J. N. (2006) · Nature · doi:10.1038/nature05236 · Cited by 6,517

An Integrated Genomic Analysis of Human Glioblastoma Multiforme

Parsons, D. W., Jones, S., Zhang, X., Lin, J. C.-H., Leary, R. J., Angenendt, P., Mankoo, P., Carter, H., Siu, I.-M., Gallia, G. L., et al. (2008) · Science · doi:10.1126/science.1164382 · Cited by 5,857

The Somatic Genomic Landscape of Glioblastoma

Brennan, C. W., Verhaak, R. G. W., McKenna, A., Campos, B., Noushmehr, H., Salama, S. R., Zheng, S., Chakravarty, D., Sanborn, J. Z., Berman, S. H., et al. (2013) · Cell · doi:10.1016/j.cell.2013.09.034 · Cited by 5,016

A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function

Cahoy, J. D., Emery, B., Kaushal, A., Foo, L. C., Zamanian, J. L., Christopherson, K. S., Xing, Y., Lubischer, J. L., Krieg, P. A., Krupenko, S. A., et al. (2008) · The Journal of Neuroscience · doi:10.1523/jneurosci.4178-07.2008 · Cited by 3,129

Single-cell analysis reveals altered tumor microenvironments of relapse- and remission-associated pediatric acute myeloid leukemia

Mumme, H., Thomas, B. E., Bhasin, S. S., Krishnan, U., Dwivedi, B., Perumalla, P., Sarkar, D., Ulukaya, G. B., Sabnis, H. S., Park, S. I., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-41994-0 · Cited by 91

Breaching barriers in glioblastoma. Part I: Molecular pathways and novel treatment approaches

Miranda, A., Blanco‐Prieto, M. J., Sousa, J., Pais, A. A. C. C., & Vitorino, C. (2017) · International Journal of Pharmaceutics · doi:10.1016/j.ijpharm.2017.07.056 · Cited by 87

Single cell RNA-seq highlights a role for a partial EMT in head and neck cancer

Puram, S. V., Parikh, A. S., & Tirosh, I. (2018) · Molecular & Cellular Oncology · doi:10.1080/23723556.2018.1448244 · Cited by 87

Systems Immunology: Learning the Rules of the Immune System

Villani, A., Sarkizova, S., & Hacohen, N. (2018) · Annual Review of Immunology · doi:10.1146/annurev-immunol-042617-053035 · Cited by 89

Single-cell transcriptome-based multilayer network biomarker for predicting prognosis and therapeutic response of gliomas

Zhang, J., Guan, M., Wang, Q., Zhang, J., Zhou, T., & Sun, X. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz040 · Cited by 85

P53-R273H mutation enhances colorectal cancer stemness through regulating specific lncRNAs

Zhao, Y., Li, Y., Sheng, J., Wu, F., Li, K., Huang, R. S., Wang, X., Jiao, T., Guan, X., Lu, Y., et al. (2019) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-019-1375-9 · Cited by 85

Single-cell analysis of childhood leukemia reveals a link between developmental states and ribosomal protein expression as a source of intra-individual heterogeneity

Caron, M., St-Onge, P., Sontag, T., Wang, Y. C., Richer, C., Ragoussis, J., Sinnett, D., & Bourque, G. (2020) · Scientific Reports · doi:10.1038/s41598-020-64929-x · Cited by 83

Metabolic detection and systems analyses of pancreatic ductal adenocarcinoma through machine learning, lipidomics, and multi-omics

Wang, G., Yao, H., Gong, Y., Lu, Z., Pang, R., Li, Y., Yuan, Y., Song, H., Liu, J., Jin, Y., et al. (2021) · Science Advances · doi:10.1126/sciadv.abh2724 · Cited by 86

PDIA3P1 promotes Temozolomide resistance in glioblastoma by inhibiting C/EBPβ degradation to facilitate proneural-to-mesenchymal transition

Gao, Z., Xu, J., Yang, F., Qi, Y., Wang, S., Zhao, S., Guo, X., Xue, H., Deng, L., Zhao, R., et al. (2022) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-022-02431-0 · Cited by 86

Evolutionary history of transformation from chronic lymphocytic leukemia to Richter syndrome

Parry, E. M., Leshchiner, I., Guièze, R., Johnson, C., Tausch, E., Parikh, S. A., Lemvigh, C. K., Broséus, J., Hergalant, S., Messer, C., et al. (2023) · Nature Medicine · doi:10.1038/s41591-022-02113-6 · Cited by 87

Using droplet digital PCR to analyzeMYCNandALKcopy number in plasma from patients with neuroblastoma

Lodrini, M., Sprüssel, A., Astrahantseff, K., Tiburtius, D., Konschak, R., Lode, H. N., Fischer, M., Keilholz, U., Eggert, A., & Deubzer, H. E. (2017) · Oncotarget · doi:10.18632/oncotarget.19076 · Cited by 87

PDGF Family Expression in Glioblastoma Multiforme: Data Compilation from Ivy Glioblastoma Atlas Project Database

Cantanhede, I. G., & de Oliveira, J. R. M. (2017) · Scientific Reports · doi:10.1038/s41598-017-15045-w · Cited by 84

The microcosmos of intratumor heterogeneity: the space-time of cancer evolution

Janiszewska, M. (2019) · Oncogene · doi:10.1038/s41388-019-1127-5 · Cited by 90

Transcription and Beyond: Delineating FOXG1 Function in Cortical Development and Disorders

Hou, P., hAilín, D. Ó., Vogel, T., & Hanashima, C. (2020) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2020.00035 · Cited by 82

HDAC Inhibitors: Dissecting Mechanisms of Action to Counter Tumor Heterogeneity

Karagiannis, D., & Rampias, T. N. (2021) · Cancers · doi:10.3390/cancers13143575 · Cited by 88

Enhance explainability of manifold learning

Han, H., Li, W., Wang, J., Qin, G., & Qin, X. (2022) · Neurocomputing · doi:10.1016/j.neucom.2022.05.119 · Cited by 83

Hypoxia within the glioblastoma tumor microenvironment: a master saboteur of novel treatments

Feldman, L. A. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1384249 · Cited by 97

Single-cell RNA sequencing identifies distinct mouse medial ganglionic eminence cell types

Chen, Y.-J. J., Friedman, B. A., Ha, C., Durinck, S., Liu, J., Rubenstein, J. L. R., Seshagiri, S., & Modrusan, Z. D. (2017) · Scientific Reports · doi:10.1038/srep45656 · Cited by 80

Deep Learning AI Applications in the Imaging of Glioma

Zlochower, A. B., Chow, D. S., Chang, P. D., Khatri, D., Boockvar, J. A., & Filippi, C. G. (2020) · Topics in Magnetic Resonance Imaging · doi:10.1097/rmr.0000000000000237 · Cited by 83

Super-enhancer RNA m6A promotes local chromatin accessibility and oncogene transcription in pancreatic ductal adenocarcinoma

Li, R., Zhao, H., Huang, X., Zhang, J., Bai, R., Zhuang, L., Wen, S., Wu, S., Zhou, Q., Li, M., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01568-8 · Cited by 84

Single cell deciphering of progression trajectories of the tumor ecosystem in head and neck cancer

Liu, Z. L., Meng, X., Bao, R., Shen, M. Y., Sun, J. J., Chen, W. D., Liu, F., & He, Y. (2024) · Nature Communications · doi:10.1038/s41467-024-46912-6 · Cited by 87

The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1

Romero, R., Chu, T., González-Robles, T. J., Smith, P., Xie, Y., Kaur, H., Yoder, S., Zhao, H., Mao, C., Kang, W., et al. (2024) · Nature Cancer · doi:10.1038/s43018-024-00838-6 · Cited by 95

Tumor‐targeted nanotherapeutics: overcoming treatment barriers for glioblastoma

Wadajkar, A. S., Dancy, J. G., Hersh, D. S., Anastasiadis, P., Tran, N. L., Woodworth, G. F., Winkles, J. A., & Kim, A. J. (2016) · Wiley Interdisciplinary Reviews Nanomedicine and Nanobiotechnology · doi:10.1002/wnan.1439 · Cited by 85

Applications of DNA-Based Liquid Biopsy for Central Nervous System Neoplasms

Wang, J., & Bettegowda, C. (2016) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2016.08.007 · Cited by 87

Hypoxia drives transient site-specific copy gain and drug-resistant gene expressionPreprint

Black, J. C., Atabakhsh, E., Kim, J., Biette, K. M., Rechem, C. V., Ladd, B., Burrowes, P. D., Donado, C. A., Mattoo, H., Kleinstiver, B. P., et al. (2015) · Genes & Development · doi:10.1101/gad.259796.115 · Cited by 87

Glioma Stem Cells but Not Bulk Glioma Cells Upregulate IL-6 Secretion in Microglia/Brain Macrophages via Toll-like Receptor 4 Signaling

Dzaye, O., Hu, F., Derkow, K., Haage, V. C., Euskirchen, P., Harms, C., Lehnardt, S., Synowitz, M., Wolf, S. A., & Kettenmann, H. (2016) · Journal of Neuropathology and Experimental Neurology · doi:10.1093/jnen/nlw016 · Cited by 68

Cancer cell reprogramming: a promising therapy converting malignancy to benignity

Gong, L., Yan, Q., Zhang, Y., Fang, X., Liu, B., & Guan, X. (2019) · 癌症：英文版 · doi:10.1186/s40880-019-0393-5 · Cited by 83

Glioblastoma cell populations with distinct oncogenic programs release podoplanin as procoagulant extracellular vesicles

Tawil, N., Bassawon, R., Meehan, B., Nehme, A., Montermini, L., Gayden, T., Jay, N. D., Spinelli, C., Chennakrishnaiah, S., Choi, D., et al. (2021) · Blood Advances · doi:10.1182/bloodadvances.2020002998 · Cited by 82

Glioblastoma Microenvironment and Cellular Interactions

Crivii, C.-B., Boșca, A. B., Melincovici, C. S., Constantin, A.-M., Mărginean, M., Dronca, E., Suflețel, R., Gonciar, D., Bungărdean, M., & Șovrea, A. (2022) · Cancers · doi:10.3390/cancers14041092 · Cited by 81

Molecular subtypes of ALS are associated with differences in patient prognosis

Eshima, J., O’Connor, S. A., Marschall, E., Bowser, R. P., Plaisier, C. L., & Smith, B. S. (2023) · Nature Communications · doi:10.1038/s41467-022-35494-w · Cited by 81

Using single‐cell multiple omics approaches to resolve tumor heterogeneity

Ortega, M. A., Poirion, O., Zhu, X., Huang, S., Wolfgruber, T. K., Sebra, R., & Garmire, L. X. (2017) · Clinical and Translational Medicine · doi:10.1186/s40169-017-0177-y · Cited by 81

Regulation of human glioma cell migration, tumor growth, and stemness gene expression using a Lck targeted inhibitor

Zepecki, J. P., Snyder, K. M., Moreno, M. M., Fajardo, E. J., Fiser, A., Ness, J. K., Sarkar, A., Toms, S. A., & Tapinos, N. (2018) · Oncogene · doi:10.1038/s41388-018-0546-z · Cited by 81

Organoid Models of Glioblastoma and Their Role in Drug Discovery

Rybin, M. J., Ivan, M. E., Ayad, N. G., & Zeier, Z. R. (2021) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2021.605255 · Cited by 83

Glioblastoma genetic drivers dictate the function of tumor-associated macrophages/microglia and responses to CSF1R inhibition

Rao, R., Han, R., Ogurek, S., Xue, C., Wu, L. M. N., Zhang, L., Zhang, L., HU, J. L., Phoenix, T. N., Waggoner, S. N., et al. (2021) · Neuro-Oncology · doi:10.1093/neuonc/noab228 · Cited by 83

Heterogeneity of Cancer Stem Cells: Rationale for Targeting the Stem Cell Niche

Boesch, M., Sopper, S., Zeimet, A. G., Reimer, D., Gastl, G. A., Ludewig, B., & Wolf, D. G. F. (2016) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2016.10.003 · Cited by 81

PyMINEr Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq

Tyler, S. R., Rotti, P. G., Sun, X., Yi, Y., Xie, W., Winter, M. C., Flamme‐Wiese, M. J., Tucker, B. A., Mullins, R. F., Norris, A. W., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.01.063 · Cited by 77

Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity

Chen, X., Litzenburger, U. M., Wei, Y., Schep, A. N., LaGory, E. L., Choudhry, H., Giaccia, A. J., Greenleaf, W. J., & Chang, H. Y. (2018) · Nature Communications · doi:10.1038/s41467-018-07115-y · Cited by 80

Single-cell sequencing and its applications in head and neck cancer

Qi, Z., Barrett, T. F., Parikh, A. S., Tirosh, I., & Puram, S. V. (2019) · Oral Oncology · doi:10.1016/j.oraloncology.2019.104441 · Cited by 82

Immunology in the Era of Single-Cell Technologies

Efremova, M., Vento‐Tormo, R., Park, J.-E., Teichmann, S. A., & James, K. R. (2020) · Annual Review of Immunology · doi:10.1146/annurev-immunol-090419-020340 · Cited by 80

The CNS and the Brain Tumor Microenvironment: Implications for Glioblastoma Immunotherapy

Desland, F. A., & Hormigo, A. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21197358 · Cited by 82

The evolution of the cancer stem cell state in glioblastoma: emerging insights into the next generation of functional interactions

Mitchell, K., Troike, K. M., Silver, D. J., & Lathia, J. D. (2020) · Neuro-Oncology · doi:10.1093/neuonc/noaa259 · Cited by 84

Single-cell RNA-seq dissects the intratumoral heterogeneity of triple-negative breast cancer based on gene regulatory networks

Zhou, S., Huang, Y., Liu, H., Zhou, X., Yuan, M., Hou, F., Wang, L., & Jiang, W. (2020) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2020.12.018 · Cited by 78

Multimodal single-cell analysis of cutaneous T-cell lymphoma reveals distinct subclonal tissue-dependent signatures

Herrera, A. M., Cheng, A., Mimitou, E. P., Seffens, A., George, D. D., Bar‐Natan, M., Heguy, A., Ruggles, K. V., Scher, J. U., Hymes, K. B., et al. (2021) · Blood · doi:10.1182/blood.2020009346 · Cited by 81

Bridging live-cell imaging and next-generation cancer treatment

Alieva, M., Wezenaar, A. K. L., Wehrens, E. J., & Rios, A. C. (2023) · Nature reviews. Cancer · doi:10.1038/s41568-023-00610-5 · Cited by 84

High-throughput, label-free, single-cell photoacoustic microscopy of intratumoral metabolic heterogeneity

Hai, P., Imai, T., Xu, S., Zhang, R., Aft, R., Zou, J., & Wang, L. V. (2019) · Nature Biomedical Engineering · doi:10.1038/s41551-019-0376-5 · Cited by 80

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists

Zhu, X., Wolfgruber, T., Tasato, A., Arisdakessian, C. G., Garmire, D. G., & Garmire, L. X. (2017) · Genome Medicine · doi:10.1186/s13073-017-0492-3 · Cited by 80

Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells

Reitman, Z. J., Paolella, B. R., Bergthold, G., Pelton, K., Becker, S., Jones, R. E., Sinai, C. E., Malkin, H., Huang, Y., Grimmett, L., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11493-2 · Cited by 78

Detrimental activation of AhR pathway in cancer: an overview of therapeutic strategies

Leclerc, D., Pires, A. S., Guillemin, G. J., & Gilot, D. (2021) · Current Opinion in Immunology · doi:10.1016/j.coi.2020.12.003 · Cited by 82

Diversity and intratumoral heterogeneity in human gallbladder cancer progression revealed by single‐cell RNA sequencing

Chen, P., Wang, Y., Li, J., Bo, X., Wang, J., Nan, L., Wang, C., Ba, Q., Liu, H., & Wang, H. (2021) · Clinical and Translational Medicine · doi:10.1002/ctm2.462 · Cited by 79

Conjugation of glucosylated polymer chains to checkpoint blockade antibodies augments their efficacy and specificity for glioblastoma

Yang, T., Mochida, Y., Liu, X., Zhou, H., Xie, J., Anraku, Y., Kinoh, H., Cabral, H., & Kataoka, K. (2021) · Nature Biomedical Engineering · doi:10.1038/s41551-021-00803-z · Cited by 80

Applications of Radiomics and Radiogenomics in High-Grade Gliomas in the Era of Precision Medicine

Kazerooni, A. F., Bagley, S. J., Akbari, H., Saxena, S., Bagheri, S., Guo, J. F., Chawla, S., Nabavizadeh, A., Mohan, S., Bakas, S., et al. (2021) · Cancers · doi:10.3390/cancers13235921 · Cited by 79

Bifunctional cancer cell–based vaccine concomitantly drives direct tumor killing and antitumor immunity

Chen, K., Reinshagen, C., van Schaik, T., Rossignoli, F., Borges, P., Mendonca, N. C., Abdi, R., Simon, B. G., Reardon, D. A., Wakimoto, H., et al. (2023) · Science Translational Medicine · doi:10.1126/scitranslmed.abo4778 · Cited by 81

Targeting PTPRZ inhibits stem cell-like properties and tumorigenicity in glioblastoma cells

Fujikawa, A., Sugawara, H., Tanaka, T., Matsumoto, M., Kuboyama, K., Suzuki, R., Tanga, N., Ogata, A., Masumura, M., & Noda, M. (2017) · Scientific Reports · doi:10.1038/s41598-017-05931-8 · Cited by 75

Histone deacetylase inhibitors exert anti-tumor effects on human adherent and stem-like glioma cells

Was, H., Krol, S. K., Rotili, D., Mai, A., Wojtas, B., Kaminska, B., & Maleszewska, M. (2019) · Clinical Epigenetics · doi:10.1186/s13148-018-0598-5 · Cited by 78

Precision cancer therapy is impacted by oncogene-dependent epigenome remodeling

Liu, F., Mischel, P. S., & Cavenee, W. K. (2017) · npj Precision Oncology · doi:10.1038/s41698-017-0005-2 · Cited by 78

Using single nucleotide variations in single-cell RNA-seq to identify subpopulations and genotype-phenotype linkage

Poirion, O., Zhu, X., Ching, T. H., & Garmire, L. X. (2018) · Nature Communications · doi:10.1038/s41467-018-07170-5 · Cited by 79

Reconstructing the molecular life history of gliomas

Barthel, F. P., Wesseling, P., & Verhaak, R. G. W. (2018) · Acta Neuropathologica · doi:10.1007/s00401-018-1842-y · Cited by 86

Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemiaPreprint

Wang, L., Fan, J., Francis, J. M., Georghiou, G. P., Hergert, S., Li, S., Gambe, R. G., Zhou, C. W., Yang, C., Xiao, S., et al. (2017) · Genome Research · doi:10.1101/gr.217331.116 · Cited by 77

Targeting cancer metabolism by simultaneously disrupting parallel nutrient access pathways

Kim, S. M., Roy, S. G., Chen, B., Nguyen, T. M., McMonigle, R. J., McCracken, A. N., Zhang, Y., Kofuji, S., Hou, J., Selwan, E., et al. (2016) · Journal of Clinical Investigation · doi:10.1172/jci87148 · Cited by 77

Glioblastoma’s Next Top Model: Novel Culture Systems for Brain Cancer Radiotherapy Research

Caragher, S. P., Chalmers, A. J., & Gomez-Roman, N. (2019) · Cancers · doi:10.3390/cancers11010044 · Cited by 80

Extracellular Vesicle-Mediated Bilateral Communication between Glioblastoma and Astrocytes

Nieland, L., Morsett, L. M., Broekman, M. L. D., Breakefield, X. O., & Abels, E. R. (2020) · Trends in Neurosciences · doi:10.1016/j.tins.2020.10.014 · Cited by 77

Single‐cell transcriptomes reveal heterogeneity of high‐grade serous ovarian carcinoma

Hao, Q., Li, J., Zhang, Q., Xu, F., Xie, B., Lu, H., Wu, X., & Zhou, X. Y. (2021) · Clinical and Translational Medicine · doi:10.1002/ctm2.500 · Cited by 76

Th17 Cells Secrete TWEAK to Trigger Epithelial–Mesenchymal Transition and Promote Colorectal Cancer Liver Metastasis

Liu, X., Wang, X. M., Yang, Q., Luo, L., Liu, Z., Ren, X., Lei, K., Li, S., Xie, Z., Zheng, G., et al. (2024) · Cancer Research · doi:10.1158/0008-5472.can-23-2123 · Cited by 80

Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer

Chiaro, P. D., Nacci, L., Arco, F., Brandini, S., Polletti, S., Palamidessi, A., Donati, B., Soriani, C., Gualdrini, F., Frigè, G., et al. (2024) · Cancer Cell · doi:10.1016/j.ccell.2024.02.017 · Cited by 80

High-throughput identification of repurposable neuroactive drugs with potent anti-glioblastoma activity

Lee, S., Weiß, T., Bühler, M., Mena, J., Lottenbach, Z., Wegmann, R., Sun, M., Bihl, M., Augustynek, B., Baumann, S. P., et al. (2024) · Nature Medicine · doi:10.1038/s41591-024-03224-y · Cited by 92

Unraveling the 3D genome: genomics tools for multiscale exploration

Risca, V. I., & Greenleaf, W. J. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.03.010 · Cited by 77

Variation is function: Are single cell differences functionally important?

Dueck, H., Eberwine, J. H., & Kim, J. (2015) · BioEssays · doi:10.1002/bies.201500124 · Cited by 84

Probabilistic Harmonization and Annotation of Single-cell Transcriptomics Data with Deep Generative ModelsPreprint

Xu, C. A., Lopez, R., Mehlman, E., Regier, J., Jordan, M. I., & Yosef, N. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/532895 · Cited by 80

Exploiting single-cell expression to characterize co-expression replicability

Crow, M., Paul, A., Ballouz, S., Huang, Z. J., & Gillis, J. (2016) · Genome Biology · doi:10.1186/s13059-016-0964-6 · Cited by 76

Imaging-genomics reveals driving pathways of MRI derived volumetric tumor phenotype features in Glioblastoma

Großmann, P., Gutman, D. A., Dunn, W. D., Holder, C. A., & Aerts, H. J. W. L. (2016) · BMC Cancer · doi:10.1186/s12885-016-2659-5 · Cited by 77

Current Trends of Microfluidic Single-Cell Technologies

Shinde, P., Mohan, L., Kumar, A. S., Dey, K., Maddi, A., Patananan, A. N., Tseng, F., Chang, H., Nagai, M., & Santra, T. S. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19103143 · Cited by 79

McImpute: Matrix Completion Based Imputation for Single Cell RNA-seq Data

Mongia, A., Sengupta, D., & Majumdar, A. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00009 · Cited by 77

Machine Learning for the Prediction of Molecular Markers in Glioma on Magnetic Resonance Imaging: A Systematic Review and Meta-Analysis

Jian, A., Jang, K., Manuguerra, M., Liu, S., MAGNUSSEN, J. S., & Ieva, A. D. (2021) · Neurosurgery · doi:10.1093/neuros/nyab103 · Cited by 79

Molecular profiling of human non-small cell lung cancer by single-cell RNA-seq

Li, Q., Wang, R., Yang, Z., Li, W., Yang, J., Wang, Z., Bai, H., Cui, Y., Tian, Y., Wu, Z., et al. (2022) · Genome Medicine · doi:10.1186/s13073-022-01089-9 · Cited by 82

Single-cell transcriptomic analyses provide insights into the cellular origins and drivers of brain metastasis from lung adenocarcinoma

Wang, Z., Wang, Y., Chang, M., Wang, Y., Liu, P., Wu, J., Wang, G., Tang, X., Hui, X., Liu, P., et al. (2023) · Neuro-Oncology · doi:10.1093/neuonc/noad017 · Cited by 87

Machine learning reveals diverse cell death patterns in lung adenocarcinoma prognosis and therapy

Wang, S., Wang, R., Hu, D., Zhang, C.-X., Cao, P., & Huang, J. (2024) · npj Precision Oncology · doi:10.1038/s41698-024-00538-5 · Cited by 79

Genetic and Functional Diversity of Propagating Cells in Glioblastoma

Piccirillo, S. G. M., Colman, S., Potter, N. E., van Delft, F. W., Lillis, S., Carnicer, M.-J., Kearney, L., Watts, C., & Greaves, M. F. (2014) · Stem Cell Reports · doi:10.1016/j.stemcr.2014.11.003 · Cited by 77

Cancer Metabolism: A Modeling Perspective

Ghaffari, P., Mardinoğlu, A., & Nielsen, J. (2015) · Frontiers in Physiology · doi:10.3389/fphys.2015.00382 · Cited by 76

Emerging circulating biomarkers in glioblastoma: promises and challenges

Touat, M., Durán-Peña, A., Alentorn, A., Lacroix, L., Massard, C., & Idbaïh, A. (2015) · Expert Review of Molecular Diagnostics · doi:10.1586/14737159.2015.1087315 · Cited by 77

Molecular subtypes and differentiation programmes of glioma stem cells as determinants of extracellular vesicle profiles and endothelial cell‐stimulating activities

Spinelli, C., Montermini, L., Meehan, B., Brisson, A. R., Tan, S., Choi, D., Nakano, I., & Rak, J. W. (2018) · Journal of Extracellular Vesicles · doi:10.1080/20013078.2018.1490144 · Cited by 76

KHS101 disrupts energy metabolism in human glioblastoma cells and reduces tumor growth in mice

Polson, E. S., Kuchler, V., Abbosh, C., Ross, E. M., Mathew, R. K., Beard, H. A., da Silva, B., Holding, A. N., Ballereau, S. J., Chuntharpursat‐Bon, E., et al. (2018) · Science Translational Medicine · doi:10.1126/scitranslmed.aar2718 · Cited by 72

Current State and Future Prospects of Immunotherapy for Glioma

Kamran, N., Alghamri, M. S., Núñez, F. J., Shah, D., Asad, A. S., Candolfi, M., Altshuler, D. B., Lowenstein, P. R., & Castro, M. G. (2018) · Immunotherapy · doi:10.2217/imt-2017-0122 · Cited by 77

Emerging approaches to study cell-cell interactions in tumor microenvironment

Nishida‐Aoki, N., & Gujral, T. S. (2019) · Oncotarget · doi:10.18632/oncotarget.26585 · Cited by 76

Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects

Kinaret, P., Serra, A., Federico, A., Kohonen, P. J., Nymark, P. E. H., Liampa, I., Ha, M. K., Choi, J., Jagiełło, K., Sanabria, N. M., et al. (2020) · Nanomaterials · doi:10.3390/nano10040750 · Cited by 79

New hints towards a precision medicine strategy for IDH wild-type glioblastoma

White, K., Connor, K., Clerkin, J., Murphy, B. M., Salvucci, M., O’Farrell, A. C., Rehm, M., O’Brien, D., Prehn, J. H. M., Niclou, S. P., et al. (2020) · Annals of Oncology · doi:10.1016/j.annonc.2020.08.2336 · Cited by 75

WNT Signaling as a Therapeutic Target for Glioblastoma

Latour, M., Her, N.-G., Kesari, S., & Nurmemmedov, E. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22168428 · Cited by 75

Deep learning tackles single-cell analysis—a survey of deep learning for scRNA-seq analysis

Flores, M. A., Liu, Z., Zhang, T., Hasib, M. M., Chiu, Y., Ye, Z., Paniagua, K., Jo, S., Zhang, J., Gao, S., et al. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab531 · Cited by 73

Single-Cell Transcriptomics Revealed Subtype-Specific Tumor Immune Microenvironments in Human Glioblastomas

Xiao, Y., Wang, Z., Zhao, M., Deng, Y., Yang, M., Su, G., Yang, K., Qian, C., Hu, X., Liu, Y., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.914236 · Cited by 74

Spatial multi-omics revealed the impact of tumor ecosystem heterogeneity on immunotherapy efficacy in patients with advanced non-small cell lung cancer treated with bispecific antibody

Song, X., Xiong, A., Wu, F., Li, X., Wang, J., Jiang, T., Chen, P., Zhang, X., Zhao, Z., Liu, H., et al. (2023) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2022-006234 · Cited by 78

Spatial metabolomics reveals glycogen as an actionable target for pulmonary fibrosis

Conroy, L. R., Clarke, H. A., Allison, D. B., Valença, S. S., Sun, Q., Hawkinson, T. R., Young, L. E. A., Ferreira, J. E., Hammonds, A. V., Dunne, J., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-38437-1 · Cited by 79

The TWEAK receptor Fn14 is a potential cell surface portal for targeted delivery of glioblastoma therapeutics

Perez, J. G., Tran, N. L., Rosenblum, M. G., Schneider, C. S., Connolly, N. P., Kim, A. J., Woodworth, G. F., & Winkles, J. A. (2015) · Oncogene · doi:10.1038/onc.2015.310 · Cited by 77

Pharmacological Targeting of the Histone Chaperone Complex FACT Preferentially Eliminates Glioblastoma Stem Cells and Prolongs Survival in Preclinical Models

Dermawan, J. K. T., Hitomi, M., Silver, D. J., Wu, Q., Sandlesh, P., Sloan, A. E., Purmal, A. A., Gurova, K. V., Rich, J. N., Lathia, J. D., et al. (2016) · Cancer Research · doi:10.1158/0008-5472.can-15-2162 · Cited by 77

Colorectal Cancer Subtypes: Developmental Origin and Microenvironmental Regulation

Fessler, E., & Medema, J. P. (2016) · Trends in cancer · doi:10.1016/j.trecan.2016.07.008 · Cited by 81

Single Cell Profiling Using Ionic Liquid Matrix-Enhanced Secondary Ion Mass Spectrometry for Neuronal Cell Type Differentiation

Do, T. D., Comi, T. J., Dunham, S. J. B., Rubakhin, S. S., & Sweedler, J. V. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.6b04819 · Cited by 79

Intertumoral heterogeneity in patient-specific drug sensitivities in treatment-naïve glioblastoma

Skaga, E., Kulesskiy, E., Fayzullin, A., Sandberg, C. J., Potdar, S., Kyttälä, A., Langmoen, I. A., Laakso, A., Gaál‐Paavola, E., Perola, M., et al. (2019) · BMC Cancer · doi:10.1186/s12885-019-5861-4 · Cited by 75

Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development

Chen, J., Schlitzer, A., Chakarov, S., Ginhoux, F., & Poidinger, M. (2016) · Nature Communications · doi:10.1038/ncomms11988 · Cited by 72

Clinical and molecular relevance of mutant-allele tumor heterogeneity in breast cancer

Ma, D., Jiang, Y., Liu, X., Liu, Y., & Shao, Z. (2017) · Breast Cancer Research and Treatment · doi:10.1007/s10549-017-4113-z · Cited by 74

Imaging Genetic Heterogeneity in Glioblastoma and Other Glial Tumors: Review of Current Methods and Future Directions

Chow, D. S., Chang, P. D., Weinberg, B. D., Bota, D. A., Grinband, J., & Filippi, C. G. (2017) · American Journal of Roentgenology · doi:10.2214/ajr.17.18754 · Cited by 73

Pre-Clinical Drug Testing in 2D and 3D Human In Vitro Models of Glioblastoma Incorporating Non-Neoplastic Astrocytes: Tunneling Nano Tubules and Mitochondrial Transfer Modulates Cell Behavior and Therapeutic Response

Civita, P., Leite, D. M., & Pilkington, G. J. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20236017 · Cited by 74

Single-cell RNA-seq clustering: datasets, models, and algorithms

Peng, L., Tian, X., Tian, G., Xu, J., Huang, X., Weng, Y., Yang, J., & Zhou, L. (2020) · RNA Biology · doi:10.1080/15476286.2020.1728961 · Cited by 77

Intratumoural heterogeneity in primary glioblastoma

(2014) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2014.114

Unravelling glioblastoma heterogeneity by single-cell RNA sequencing

Yang, C., & Cheng, E. (2024) · International Conference on Biological Engineering and Medical Science (ICBioMed) · doi:10.1117/12.3013140 · Cited by 1

Deciphering brain tumor heterogeneity, one cell at a time

Qazi, M. A., Bakhshinyan, D., & Singh, S. K. (2019) · Nature Medicine · doi:10.1038/s41591-019-0605-1 · Cited by 16

Unravelling glioblastoma heterogeneity by means of single-cell RNA sequencing

Martínez, A. H., Madurga, R., Garcia‐Romero, N., & Ayuso‐Sacido, Á. (2021) · Cancer Letters · doi:10.1016/j.canlet.2021.12.008 · Cited by 95

Dissecting human gliomas by single-cell RNA sequencing

Tirosh, I., & Suvà, M. L. (2017) · Neuro-Oncology · doi:10.1093/neuonc/nox126 · Cited by 72