The DOI matches its Crossref record; 40 of the 40 references it cites were found in a registry or an index.
Regulatory networks define phenotypic classes of human stem cell lines
Open accessAbstract
Stem cells are defined as self-renewing cell populations that can differentiate into multiple distinct cell types. However, hundreds of different human cell lines from embryonic, fetal and adult sources have been called stem cells, even though they range from pluripotent cells-typified by embryonic stem cells, which are capable of virtually unlimited proliferation and differentiation-to adult stem cell lines, which can generate a far more limited repertoire of differentiated cell types. The rapid increase in reports of new sources of stem cells and their anticipated value to regenerative medicine has highlighted the need for a general, reproducible method for classification of these cells. We report here the creation and analysis of a database of global gene expression profiles (which we call the 'stem cell matrix') that enables the classification of cultured human stem cells in the context of a wide variety of pluripotent, multipotent and differentiated cell types. Using an unsupervised clustering method to categorize a collection of approximately 150 cell samples, we discovered that pluripotent stem cell lines group together, whereas other cell types, including brain-derived neural stem cell lines, are very diverse. Using further bioinformatic analysis we uncovered a protein-protein network (PluriNet) that is shared by the pluripotent cells (embryonic stem cells, embryonal carcinomas and induced pluripotent cells). Analysis of published data showed that the PluriNet seems to be a common characteristic of pluripotent cells, including mouse embryonic stem and induced pluripotent cells and human oocytes. Our results offer a new strategy for classifying stem cells and support the idea that pluripotency and self-renewal are under tight control by specific molecular networks.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“While gene expression-based models can potentially overcome these limitations (e.g., transcriptional entropy (11–13), pluripotency-associated gene sets (14), and machine learning strategies (15)), their utility across diverse developmental systems and single-cell sequencing technologies is still unclear.”
From Single-cell transcriptional diversity is a hallmark of developmental potential (2020) · cites this paper as [14]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625
Takahashi, K., & Yamanaka, S. (2006) · Cell · doi:10.1016/j.cell.2006.07.024 · Cited by 26,673
Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors
Takahashi, K., Tanabe, K., Ohnuki, M., Narita, M., Ichisaka, T., Tomoda, K., & Yamanaka, S. (2007) · Cell · doi:10.1016/j.cell.2007.11.019 · Cited by 20,221
Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., Coller, H., Loh, M. L., Downing, J. R., Caligiuri, M. A., et al. (1999) · Science · doi:10.1126/science.286.5439.531 · Cited by 11,516
Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells
Yu, J., Vodyanik, M. A., Smuga-Otto, K., Antosiewicz-Bourget, J., Frane, J. L., Tian, S., Nie, J., Jonsdottir, G. A., Ruotti, V., Stewart, R., et al. (2007) · Science · doi:10.1126/science.1151526 · Cited by 10,310
Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells
Boyer, L. A., Lee, T. I., Cole, M. F., Johnstone, S. E., Levine, S. S., Zucker, J. P., Guenther, M. G., Kumar, R. M., Murray, H. L., Jenner, R. G., et al. (2005) · Cell · doi:10.1016/j.cell.2005.08.020 · Cited by 4,505
Generation of germline-competent induced pluripotent stem cells
Okita, K., Ichisaka, T., & Yamanaka, S. (2007) · Nature · doi:10.1038/nature05934 · Cited by 4,408
Integration of biological networks and gene expression data using Cytoscape
Cline, M. S., Smoot, M., Cerami, E., Kuchinsky, A., Landys, N., Workman, C., Christmas, R., Avila-Campilo, I., Creech, M., Gross, B., et al. (2007) · Nature Protocols · doi:10.1038/nprot.2007.324 · Cited by 2,507
Reprogramming of human somatic cells to pluripotency with defined factors
Park, I.-H., Zhao, R., West, J. A., Yabuuchi, A., Huo, H., Ince, T. A., Lerou, P. H., Lensch, M. W., & Daley, G. Q. (2008) · Nature · doi:10.1038/nature06534 · Cited by 2,436
Self-citationNew cell lines from mouse epiblast share defining features with human embryonic stem cells
Tesar, P. J., Chenoweth, J. G., Brook, F. A., Davies, T. J., Evans, E. P., Mack, D. L., Gardner, R. L., & McKay, R. D. G. (2007) · Nature · doi:10.1038/nature05972 · Cited by 2,187
Research works printed but not linked: 1
- Efron, B. & Tibshirani, R. On testing the significance of sets of genes. Ann. Appl. Stat. 1, 107–129 (2007) · DOI
Cited by
Sorted by citations
Items 101–200 of 342
Recher, G., Jouralet, J., Brombin, A., Heuzé, A., Dambroise, E., Hermel, J., Salomé‐Desnoulez, S., Savy, T., Herbomel, P., Bourrat, F., et al. (2013) · Development · doi:10.1242/dev.099010 · Cited by 56
Ament, S. A., Blatti, C. A., Alaux, C., Wheeler, M. M., Toth, A. L., Conte, Y. L., Hunt, G. J., Guzmán‐Novoa, E., DeGrandi‐Hoffman, G., Uribe-Rubio, J. L., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1205283109 · Cited by 61
Hasegawa, Y., Taylor, D. M., Ovchinnikov, D. A., Wolvetang, E. J., de Torrenté, L., & Mar, J. C. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005428 · Cited by 57
Abrajano, J. J., Qureshi, I., Gökhan, Ş., Molero, A. E., Zheng, D., Bergman, A., & Mehler, M. F. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906917107 · Cited by 59
Proteome adaptation in cell reprogramming proceeds via distinct transcriptional networks
Benevento, M., Tonge, P. D., Puri, M. C., Hussein, S. M. I., Cloonan, N., Wood, D., Grimmond, S. M., Nagy, A., Muñoz, J., & Heck, A. J. R. (2014) · Nature Communications · doi:10.1038/ncomms6613 · Cited by 56
Farshidfar, F., Rhrissorrakrai, K., Levovitz, C., Peng, C., Knight, J., Bacchiocchi, A., Su, J., Yin, M., Sznol, M., Ariyan, S., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28566-4 · Cited by 59
Boué, S., Paramonov, I., Barrero, M. J., & Belmonte, J. C. I. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012664 · Cited by 55
Zhang, J., & Huang, K. (2014) · Cancer Informatics · doi:10.4137/cin.s14021 · Cited by 60
Bridging the Gap between Genotype and Phenotype via Network Approaches
Kim, Y.-A., & Przytycka, T. M. (2013) · Frontiers in Genetics · doi:10.3389/fgene.2012.00227 · Cited by 55
Trott, J., Hayashi, K., Surani, M. A., Babu, M. M., & Martínez-Arias, A. (2012) · Molecular BioSystems · doi:10.1039/c1mb05398a · Cited by 51
Pluripotency transcription factors and Tet1/2 maintain Brd4-independent stem cell identity
Finley, L. W. S., Vardhana, S. A., Carey, B. W., Alonso‐Curbelo, D., Koche, R. P., Chen, Y., Wen, D., King, B., Radler, M. R., Rafii, S., et al. (2018) · Nature Cell Biology · doi:10.1038/s41556-018-0086-3 · Cited by 51
Continuous Hypoxic Culturing of Human Embryonic Stem Cells Enhances SSEA-3 and MYC Levels
Närvä, E., Pursiheimo, J., Laiho, A., Rahkonen, N., Emani, M., Viitala, M., Laurila, K., Sahla, R., Lund, R., Lähdesmäki, H. J., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0078847 · Cited by 49
Subgraph augmented non-negative tensor factorization (SANTF) for modeling clinical narrative text
Luo, Y., Xin, Y., Hochberg, E. P., Joshi, R., Uzuner, Ö., & Szolovits, P. (2015) · Journal of the American Medical Informatics Association · doi:10.1093/jamia/ocv016 · Cited by 53
RNA: state memory and mediator of cellular phenotype
Kim, J., & Eberwine, J. H. (2010) · Trends in Cell Biology · doi:10.1016/j.tcb.2010.03.003 · Cited by 49
Tafessu, A., O’Hara, R. A., Martire, S., Dube, A. L., Saha, P., Gant, V. U., & Banaszynski, L. A. (2023) · Genome biology · doi:10.1186/s13059-023-02867-3 · Cited by 49
Ebrahimkhani, M. R., Young, C. L., Lauffenburger, D. A., Griffith, L. G., & Borenstein, J. T. (2014) · Drug Discovery Today · doi:10.1016/j.drudis.2014.04.017 · Cited by 49
Defining an informativeness metric for clustering gene expression data
Mar, J. C., Wells, C. A., & Quackenbush, J. F. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr074 · Cited by 45
Remo, A., Simeone, I., Pancione, M., Parcesepe, P., Finetti, P., Cerulo, L., Bensmail, H., Birnbaum, D., Laere, S. V., Colantuoni, V., et al. (2015) · Journal of Translational Medicine · doi:10.1186/s12967-015-0492-2 · Cited by 44
Translational Prospects for Human Induced Pluripotent Stem Cells
CSETE, M. E. (2010) · Regenerative Medicine · doi:10.2217/rme.10.39 · Cited by 43
Sinclair, K. A., Yerkovich, S. T., Chen, T., McQualter, J. L., Hopkins, P. M.-A., Wells, C. A., & Chambers, D. C. (2016) · Stem Cells · doi:10.1002/stem.2419 · Cited by 41
attract: A Method for Identifying Core Pathways That Define Cellular Phenotypes
Mar, J. C., Matigian, N., Quackenbush, J. F., & Wells, C. A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025445 · Cited by 40
Stemness, cancer, and cancer stem cells
Wong, D. J., Segal, E., & Chang, H. Y. (2008) · Cell Cycle · doi:10.4161/cc.7.23.7104 · Cited by 39
Lmo2 expression defines tumor cell identity during T‐cell leukemogenesis
García‐Ramírez, I., Bhatia, S., Rodríguez-Hernández, G., González‐Herrero, I., Walter, C., de Tena‐Dávila, S. G., Parvin, S., Haas, O. A., Woessmann, W., Stanulla, M., et al. (2018) · The EMBO Journal · doi:10.15252/embj.201798783 · Cited by 43
Allegro: Analyzing expression and sequence in concert to discover regulatory programs
Halperin, Y., Linhart, C., Ulitsky, I., & Ron Shamir, A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn1064 · Cited by 40
Self-citationImpact of new technologies for cellular screening along the drug value chain
Möller, C., & Slack, M. (2010) · Drug Discovery Today · doi:10.1016/j.drudis.2010.02.010 · Cited by 38
Keeping an eye on retinoblastoma control of human embryonic stem cells
Conklin, J. F., & Sage, J. (2009) · Journal of Cellular Biochemistry · doi:10.1002/jcb.22342 · Cited by 38
Importin 13 Serves as a Potential Marker for Corneal Epithelial Progenitor Cells
Wang, H., Tao, T., Tang, J., Mao, Y., Li, W. S., Peng, J., Tan, G., Zhou, Y., Zhong, J., Tseng, S. C. G., et al. (2009) · Stem Cells · doi:10.1002/stem.174 · Cited by 37
Masaki, T., & Matsumura, K. (2010) · BioMed Research International · doi:10.1155/2010/740403 · Cited by 36
MYBL2, a link between proliferation and differentiation in maturing colon epithelial cells
Papetti, M., & Augenlicht, L. H. (2010) · Journal of Cellular Physiology · doi:10.1002/jcp.22399 · Cited by 36
Bertani, S., Pineau, P., Loli, S., Moura, J., Zimic, M., Deharo, E., & Ruíz, E. (2013) · PLoS ONE · doi:10.1371/journal.pone.0067756 · Cited by 35
Network-Based Identification of Biomarkers Coexpressed with Multiple Pathways
Guo, N. L., & Wan, Y. (2014) · Cancer Informatics · doi:10.4137/cin.s14054 · Cited by 35
Pasumarthy, K. K., Jayavelu, N. D., Kilpinen, L., Andrus, C. R., Battle, S. L., Korhonen, M. O., Lehenkari, P. P., Lund, R., Laitinen, S., & Hawkins, R. D. (2017) · Stem Cell Reports · doi:10.1016/j.stemcr.2017.07.018 · Cited by 36
DNA Methylation and Chromatin: Role(s) of Methyl-CpG-Binding Protein ZBTB38
de Dieuleveult, M., & Miotto, B. (2018) · Epigenetics Insights · doi:10.1177/2516865718811117 · Cited by 34
The SUMO Conjugating Enzyme Ubc9 Is Required for Inducing and Maintaining Stem Cell Pluripotency
Tahmasebi, S., Ghorbani, M., Savage, P., Gocevski, G., & Yang, X. (2013) · Stem Cells · doi:10.1002/stem.1600 · Cited by 33
Epigenetic Modifiers Facilitate Induction and Pluripotency of Porcine iPSCs
Mao, J., Zhang, Q., Deng, W. W., Wang, H., Liu, K., Fu, H., Zhao, Q., Wang, X., & Liu, L. (2016) · Stem Cell Reports · doi:10.1016/j.stemcr.2016.11.013 · Cited by 33
Balasubramaniyan, V., Vaillant, B. D., Wang, S., Gumin, J., Butalid, M. E., Sai, K., Mukheef, F., Kim, S. H., Boddeke, H. W. G. M., Lang, F. F., et al. (2015) · Oncotarget · doi:10.18632/oncotarget.5219 · Cited by 32
Collins, J. J. P., Lithopoulos, M. A., dos Santos, C. C., Issa, N. G., Möbius, M. A., Ito, C. Y., Zhong, S., Vadivel, A., & Thébaud, B. (2018) · Stem Cells and Development · doi:10.1089/scd.2017.0145 · Cited by 32
A large scale screen for neural stem cell markers in Xenopus retina
Parain, K., Mazurier, N., Bronchain, O. J., Borday, C., Cabochette, P., Chesneau, A., Colozza, G., Yakoubi, W. E., Hamdache, J., Locker, M., et al. (2011) · Developmental Neurobiology · doi:10.1002/dneu.20973 · Cited by 32
The multi-omic landscape of transcription factor inactivation in cancer
Teschendorff, A. E., Zheng, S., Feber, A., Yang, Z., Beck, S., & Widschwendter, M. (2016) · Genome Medicine · doi:10.1186/s13073-016-0342-8 · Cited by 30
Ghosh, A., & Som, A. (2020) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2020.107239 · Cited by 30
Madsen, R. R., Erickson, E. C., Rueda, O. M., Robin, X., Caldas, C., Toker, A., Semple, R. K., & Vanhaesebroeck, B. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009876 · Cited by 33
Traditional Human Embryonic Stem Cell Culture
Schwartz, P. H., Brick, D. J., Nethercott, H. E., & Stover, A. E. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-201-4_8 · Cited by 31
Self-citationRetinoblastoma-binding proteins 4 and 9 are important for human pluripotent stem cell maintenance
O’Connor, M. D., Wederell, E. D., Robertson, G., Delaney, A. D., Morozova, O., Poon, S. S. S., Yap, D., Fee, J., Zhao, Y., McDonald, H., et al. (2011) · Experimental Hematology · doi:10.1016/j.exphem.2011.05.008 · Cited by 31
Plaisted, W. C., Zavala, A., Hingco, E. E., Tran, H. T. T., Coleman, R., Lane, T. E., Loring, J. F., & Walsh, C. M. (2016) · PLoS ONE · doi:10.1371/journal.pone.0157620 · Cited by 33
Self-citationA highly efficient multi-core algorithm for clustering extremely large datasets
Kraus, J. M., & Kestler, H. A. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-169 · Cited by 30
Assessment of human pluripotent stem cells with PluriTest
Müller, F.-J. (2014) · StemBook · doi:10.3824/stembook.1.84.1 · Cited by 28
Self-citationBanking on cord blood stem cells
Sullivan, M. J. (2008) · Nature reviews. Cancer · doi:10.1038/nrc2418-c3 · Cited by 29
Twisselmann, N., Pagel, J., Künstner, A., Weckmann, M., Hartz, A., Glaser, K., Hilgendorff, A., Göpel, W., Busch, H. S., Herting, E., et al. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.762789 · Cited by 28
MicroRNAs in vascular tissue engineering and post-ischemic neovascularization
Caputo, M., Saif, J., Rajakaruna, C., Brooks, M. J., Angelini, G. D., & Emanueli, C. (2015) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2015.05.003 · Cited by 31
Important precautions when deriving patient-specific neural elements from pluripotent cells
Parsons, X. H., Teng, Y. D., & Snyder, E. Y. (2009) · Cytotherapy · doi:10.3109/14653240903180092 · Cited by 29
Gene Editing Correction of a Urea Cycle Defect in Organoid Stem Cell Derived Hepatocyte-like Cells
Zabulica, M., Jakobsson, T., Ravaioli, F., Vosough, M., Gramignoli, R., Ellis, E. C. S., Rooyackers, O., & Strom, S. C. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22031217 · Cited by 29
Guo, N. L., & Wan, Y. (2012) · Artificial Intelligence in Medicine · doi:10.1016/j.artmed.2012.01.001 · Cited by 28
Wang, H., Zhang, K., Liu, Y., Fu, Y., Gao, S., Gong, P., Wang, H., Zhou, Z., Zeng, M., Wu, Z., et al. (2017) · BMC Biology · doi:10.1186/s12915-017-0453-8 · Cited by 26
Peng, B., Zhu, D., Ander, B. P., Zhang, X., Xue, F., Sharp, F. R., & Yang, X. (2013) · PLoS ONE · doi:10.1371/journal.pone.0067672 · Cited by 28
Antitumor DNA vaccination against the Sox2 transcription factor
Poláková, I., Dušková, M., & Šmahel, M. (2014) · International Journal of Oncology · doi:10.3892/ijo.2014.2402 · Cited by 27
Li, L., Yu, H., Wang, X., Zeng, J., Li, D., Lu, J., Wang, C., Wang, J., Wei, J., Jiang, M., et al. (2013) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/1756-9966-32-28 · Cited by 27
Regulatory Considerations for the Development of Autologous Induced Pluripotent Stem Cell Therapies
Carpenter, M. K., & Couture, L. A. (2010) · Regenerative Medicine · doi:10.2217/rme.10.55 · Cited by 27
Toward Stem Cell Systems Biology: From Molecules to Networks and LandscapesPreprint
MacArthur, B. D., Ma’ayan, A., & Lemischka, I. R. (2008) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2008.73.061 · Cited by 27
Höfner, T., Eisen, C., Klein, C., Rigo‐Watermeier, T., Goeppinger, S. M., Jauch, A. S., Schoell, B., Vogel, V., Noll, E. M., Weichert, W., et al. (2015) · Stem Cell Reports · doi:10.1016/j.stemcr.2015.01.015 · Cited by 26
Concise Review: New Frontiers in MicroRNA-Based Tissue Regeneration
Frith, J. E., Porrello, E. R., & Cooper-White, J. J. (2014) · Stem Cells Translational Medicine · doi:10.5966/sctm.2014-0032 · Cited by 26
Master Regulators Connectivity Map: A Transcription Factors-Centered Approach to Drug Repositioning
Bastiani, M. A. D., Pfaffenseller, B., & Klamt, F. (2018) · Frontiers in Pharmacology · doi:10.3389/fphar.2018.00697 · Cited by 28
Markowetz, F. M., Mulder, K. W., Airoldi, E. M., Lemischka, I. R., & Troyanskaya, O. G. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1001034 · Cited by 26
Jalili, M., Gebhardt, T., Olaf Wolkenhauer, A., & Salehzadeh‐Yazdi, A. (2018) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2018.02.010 · Cited by 25
Kolle, G., Shepherd, J. L., Gardiner, B., Kassahn, K. S., Cloonan, N., Wood, D., Nourbakhsh, E., Taylor, D. F., Wani, S., Chy, H. S., et al. (2011) · Genome Research · doi:10.1101/gr.119321.110 · Cited by 25
Hassan, J., Saeed, S. M., Deka, L., Uddin, M. J., & Das, D. B. (2024) · Pharmaceutics · doi:10.3390/pharmaceutics16020260 · Cited by 28
Association of Gankyrin and Stemness Factor Expression in Human Colorectal Cancer
Mine, H., Sakurai, T., Kashida, H., Matsui, S., Nishida, N., Nagai, T., Hagiwara, S., Watanabe, T., & Kudo, M. (2013) · Digestive Diseases and Sciences · doi:10.1007/s10620-013-2627-8 · Cited by 24
Chung, H. C. Y., Lin, R. C. Y., Logan, G. J., Alexander, I. E., Sachdev, P. S., & Sidhu, K. (2011) · Stem Cells and Development · doi:10.1089/scd.2010.0440 · Cited by 24
Clark, B. J., Lelos, M. J., & Loring, J. F. (2024) · Stem Cells · doi:10.1093/stmcls/sxae042 · Cited by 26
Self-citationToward a complete in silico , multi‐layered embryonic stem cell regulatory network
Xu, H., Schaniel, C., Lemischka, I. R., & Ma’ayan, A. (2010) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.93 · Cited by 25
The 3R principle: advancing clinical application of human pluripotent stem cells
O’Connor, M. D. (2013) · Stem Cell Research & Therapy · doi:10.1186/scrt169 · Cited by 24
Hosseinpour, B., Hajihoseini, V., Kashfi, R., Ebrahimie, E., & Hemmatzadeh, F. (2012) · PLoS ONE · doi:10.1371/journal.pone.0049931 · Cited by 22
Chiriac, A. E., Nelson, T. J., Faustino, R. S., Behfar, A., & Terzic, A. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009943 · Cited by 21
Generation and genetic modification of induced pluripotent stem cells
Schambach, A., Cantz, T., Baum, C., & Cathomen, T. (2010) · Expert Opinion on Biological Therapy · doi:10.1517/14712598.2010.496775 · Cited by 22
Kumar, G., Breen, E. J., & Ranganathan, S. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-12 · Cited by 22
Stage prediction of embryonic stem cell differentiation from genome-wide expression data
Žagar, L., Mulas, F., Garagna, S., Zuccotti, M., Bellazzi, R., & Zupan, B. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr422 · Cited by 21
Tumour cells coerce host tissue to cancer spread
Malanchi, I. (2013) · BoneKEy Reports · doi:10.1038/bonekey.2013.105 · Cited by 20
Mybl2, downregulated during colon epithelial cell maturation, is suppressed by miR-365
Papetti, M., & Augenlicht, L. H. (2011) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00066.2011 · Cited by 21
Learning Biomarkers of Pluripotent Stem Cells in Mouse
Scheubert, L., Schmidt, R., Repsilber, D., Luštrek, M., & Fuellen, G. (2011) · DNA Research · doi:10.1093/dnares/dsr016 · Cited by 21
Hills, R., Mossman, J. A., Bratt‐Leal, A. M., Tran, H., Williams, R. M., Stouffer, D. G., Sokolova, I. V., Sanna, P. P., Loring, J. F., & Lelos, M. J. (2023) · Stem Cells and Development · doi:10.1089/scd.2023.0043 · Cited by 23
Self-citationThe genome-wide molecular signature of transcription factors in leukemia
Prange, K. H. M., Singh, A. A., & Martens, J. H. A. (2014) · Experimental Hematology · doi:10.1016/j.exphem.2014.04.012 · Cited by 19
Epigenetic Signatures In Stem Cells And Cancer Stem Cells
Hernández‐Vargas, H., Sinčić, N., Ouzounova, M., & Herceg, Z. (2009) · Epigenomics · doi:10.2217/epi.09.19 · Cited by 20
The niche under siege: novel targets for metastasis therapy
Santamaria‐Martínez, A., & Huelsken, J. (2013) · Journal of Internal Medicine · doi:10.1111/joim.12024 · Cited by 20
Popp, J. M., Rhodes, K., Jangi, R., Li, M., Barr, K., Tayeb, K., Battle, A. J., & Gilad, Y. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100701 · Cited by 22
Expanding the mouse embryonic stem cell proteome: Combining three proteomic approaches
Gundry, R. L., Tchernyshyov, I., Sheng, S., Tarasova, Y. S., Raginski, K., Boheler, K. R., & Eyk, J. E. V. (2010) · PROTEOMICS · doi:10.1002/pmic.201000039 · Cited by 19
Combinatorial epigenetic patterns as quantitative predictors of chromatin biology
Cieslik, M. P., & Bekiranov, S. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-76 · Cited by 19
Recent developments in StemBase: a tool to study gene expression in human and murine stem cells
Sandie, R., Palidwor, G., Huska, M. R., Porter, C. J., Krzyzanowski, P. M., Muro, E. M., Perez‐Iratxeta, C., & Andrade-Navarro, M. A. (2009) · BMC Research Notes · doi:10.1186/1756-0500-2-39 · Cited by 18
A pathway analysis method for genome‐wide association studies
Shahbaba, B., Shachaf, C. M., & Yu, Z. (2012) · Statistics in Medicine · doi:10.1002/sim.4477 · Cited by 18
Multilayer regulation of CD4 T cell subset differentiation in the era of single cell genomics
Sungnak, W., Wang, C., & Kuchroo, V. K. (2019) · Advances in immunology · doi:10.1016/bs.ai.2018.12.001 · Cited by 19
Cell‐cycle dependence of transcriptome gene modules: comparison of regression lines
Vinogradov, A. E., & Anatskaya, O. V. (2020) · FEBS Journal · doi:10.1111/febs.15257 · Cited by 18
Putting stem cells to the test
Dolgin, E. (2010) · Nature Medicine · doi:10.1038/nm1210-1354 · Cited by 18
Seo, M. K., & Cairns, J. (2021) · BMC Cancer · doi:10.1186/s12885-021-08725-4 · Cited by 17
Autologous transplantation of thecal stem cells restores ovarian function in nonhuman primates
Chen, H., Xia, K., Huang, W., Li, H., Wang, C., Ma, Y., Chen, J., Luo, P., Zheng, S., Wang, J., et al. (2021) · Cell Discovery · doi:10.1038/s41421-021-00291-0 · Cited by 17
Williams, R. M., Schuldt, B., & Müller, F. (2011) · BioEssays · doi:10.1002/bies.201100073 · Cited by 17
Self-citationLenz, M., Schuldt, B. M., Müller, F.-J., & Schuppert, A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077627 · Cited by 17
Self-citationIntegrating hypertension phenotype and genotype with hybrid non-negative matrix factorization
Luo, Y., Mao, C., Yang, Y., Wang, F., Ahmad, F. S., Arnett, D. K., Irvin, M. R., & Shah, S. J. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz049 · Cited by 17
Redox Homeostasis and Regulation in Pluripotent Stem Cells: Uniqueness or Versatility?
Ivanova, J. S., & Lyublinskaya, O. G. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222010946 · Cited by 17
Zietlow, R., Precious, S. V., Kelly, C. M., Dunnett, S. B., & Rosser, A. (2012) · Experimental Neurology · doi:10.1016/j.expneurol.2012.03.010 · Cited by 17
Comparative computational analysis of pluripotency in human and mouse stem cells
Ernst, M., Dawud, R. A., Kurtz, A., Schotta, G., Taher, L., & Fuellen, G. (2015) · Scientific Reports · doi:10.1038/srep07927 · Cited by 16
Therapeutic Targeting of Non-oncogene Dependencies in High-risk Neuroblastoma
Huang, C.-T., Hsieh, C.-H., Lee, W.-C., Liu, Y., Yang, T., Hsu, W., Oyang, Y.-J., Huang, H., & Juan, H. (2019) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-4117 · Cited by 17
The association between bromodomain proteins and cancer stemness in different solid tumor types
Czerwińska, P., Jaworska, A. M., Wlodarczyk, N. A., Cisek, M., Karwacka, M., Lipowicz, J. M., Ostapowicz, J., Rosochowicz, M. A., & Mackiewicz, A. A. (2022) · International Journal of Cancer · doi:10.1002/ijc.33937 · Cited by 15
Metadata
- Authors
- Müller, F.-J., Laurent, L. C., Kostka, D., Ulitsky, I., Williams, R., Lu, C., Park, I.-H., Rao, M. S., Shamir, R., Schwartz, P. H., Schmidt, N. O., & Loring, J. F.
- Affiliations
- Scripps Research Institute (US)
- Max Planck Society (DE)
- Tel Aviv University (IL)
- Sanford Burnham Prebys Medical Discovery Institute (US)
- Boston Children's Hospital (US)
- Buck Institute for Research on Aging (US)
- Children's Hospital of Orange County (US)
- University Medical Center Hamburg-Eppendorf (DE)
- Corresponding author
- Müller, Franz-Josef
- Loring, Jeanne F.
- ORCID
- Venue
- Nature
- Published
- 2008-08-24
- Volume
- 455
- Issue
- 7211
- Pages
- 401-405
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2637443
- OpenAlex
- W2014426141
- Cited by
- 343
- References
- 40
- Citations by year
- 2026: 3 · 2025: 5 · 2024: 13 · 2023: 8 · 2022: 5 · 2021: 16 · 2020: 12 · 2019: 7 · 2018: 12 · 2017: 11 · 2016: 18 · 2015: 16 · 2014: 28 · 2013: 36 · 2012: 30
- FWCI
- 16.85
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- National Institute of General Medical Sciences (P20GM075059)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (K12 5K12HD000849-20, K12HD000849)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- pluripotency, protein-protein interaction network, gene expression profiling, embryonic stem cells, induced pluripotent stem cells, embryonal carcinoma, neural stem cells, self-renewal
- MeSH terms
- Algorithms, Animals, Artificial Intelligence, Cell Differentiation, Cell Line, Humans, Oocytes, Phenotype, Protein Binding, Stem Cells, Databases, Factual, Computational Biology, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Multipotent Stem Cells, Pluripotent Stem Cells, Mice, Embryonic Stem Cells
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
