Systems biology: a way to make complex problems more understandable
Open accessAbstract
Despite major advances in biomedical research, exceptional difficulties remain arising from the complexity of various diseases and their variability. Development of many disorders and their therapeutic responses are associated with disturbances in cell death pathways. Although for >40 years our knowledge about cell death was restricted to apoptosis and pathological necrosis, nowadays based on Recommendations of the Nomenclature Committee of Cell Death, there are >10 different cell death modalities recognized. 1 Cell death was classified according to its morphological appearance, enzymological criteria, functional aspects or immunological characteristics. 2 Intensive work in the field, for example, by the beginning of 2014 >400 000 publications in PubMed are related to this area of research, led to understanding the biochemical features of various modes of cell death and some of molecular mechanisms of their activation/development/execution.
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
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?
Most common approaches in systems biology modelling include kinetic, constraint-based, logic and agent-based modelling.
“The most common approaches in systems biology modelling include kinetic, constraint-based, logic and agent-based modelling 21 .”
From Reproducibility in systems biology modelling (2020) · cites this paper as [21]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Cleavage of BID by Caspase 8 Mediates the Mitochondrial Damage in the Fas Pathway of Apoptosis
Li, H., Zhu, H., Xu, C.-J., & Yuan, J. (1998) · Cell · doi:10.1016/s0092-8674(00)81590-1 · Cited by 4,445 · see citing works
Classification of cell death: recommendations of the Nomenclature Committee on Cell Death 2009
Kroemer, G., Galluzzi, L., Vandenabeele, P., Abrams, J., Alnemri, E. S., Baehrecke, E. H., Blagosklonny, M. V., El-Deiry, W. S., Golstein, P., Green, D. R., et al. (2009) · Cell Death & Differentiation · doi:10.1038/cdd.2008.150 · Cited by 3,399 · see citing works
Self-citationMuzio, M., Chinnaiyan, A. M., Kischkel, F. C., O'Rourke, K., Shevchenko, A., Ni, J., Scaffidi, C., Bretz, J. D., Zhang, M., Gentz, R., et al. (1996) · Cell · doi:10.1016/s0092-8674(00)81266-0 · Cited by 3,046 · see citing works
Tumoricidal activity of tumor necrosis factor-related apoptosis-inducing ligand in vivo.
Walczak, H., Miller, R. E., Ariail, K., Gliniak, B., Griffith, T. S., Kubin, M., Chin, W., Jones, J., Woodward, A., Le, T., et al. (1999) · Nature Medicine · doi:10.1038/5517 · Cited by 2,497 · see citing works
Galluzzi, L., Vitale, I., Abrams, J. M., Alnemri, E. S., Baehrecke, E. H., Blagosklonny, M. V., Dawson, T. M., Dawson, V. L., El-Deiry, W. S., Fulda, S., et al. (2012) · Cell Death & Differentiation · doi:10.1038/cdd.2011.96 · Cited by 2,421 · see citing works
Self-citationBoldin, M. P., Goncharov, T. M., Goltseve, Y. V., & Wallach, D. (1996) · Cell · doi:10.1016/s0092-8674(00)81265-9 · Cited by 2,292 · see citing works
Calpain-mediated cleavage of Atg5 switches autophagy to apoptosis
Yousefi, S., Perozzo, R., Schmid, I., Ziemiecki, A., Schaffner, T. J., Scapozza, L., Brunner, T., & Simon, H. (2006) · Nature Cell Biology · doi:10.1038/ncb1482 · Cited by 1,300 · see citing works
Systems biology of cisplatin resistance: past, present and future
Galluzzi, L., Vitale, I., Michels, J., Brenner, C., Szabadkai, G., Harel-Bellan, A., Castedo, M., & Kroemer, G. (2014) · Cell Death & Disease · doi:10.1038/cddis.2013.428 · Cited by 782 · see citing works
Dickens, L. S., Boyd, R. S., Jukes-Jones, R., Hughes, M. A., Robinson, G. L., Fairall, L., Schwabe, J. W. R., Cain, K., & MacFarlane, M. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.05.004 · Cited by 349 · see citing works
Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis
Bentele, M., Lavrik, I. N., Ulrich, M., Stößer, S., Heermann, D. W., Kalthoff, H., Krammer, P. H., & Eils, R. (2004) · The Journal of Cell Biology · doi:10.1083/jcb.200404158 · Cited by 311 · see citing works
Self-citationWürstle, M. L., Laussmann, M. A., & Rehm, M. (2012) · Experimental Cell Research · doi:10.1016/j.yexcr.2012.02.013 · Cited by 272 · see citing works
Life in the balance – a mechanistic view of the crosstalk between autophagy and apoptosis
Rubinstein, A. D., & Kimchi, A. (2012) · Journal of Cell Science · doi:10.1242/jcs.115865 · Cited by 248 · see citing works
Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement
Calzone, L., Tournier, L., Fourquet, S., Thieffry, D., Zhivotovsky, B., Barillot, E., & Zinovyev, A. Y. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000702 · Cited by 210 · see citing works
Self-citationSchleich, K., Warnken, U., Fricker, N., Öztürk, S., Richter, P., Kammerer, K., Schnölzer, M., Krammer, P. H., & Lavrik, I. N. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.05.006 · Cited by 198 · see citing works
Self-citationKaminskyy, V. O., Piskunova, T. S., Zborovskaya, I. B., Tchevkina, E. M., & Zhivotovsky, B. (2012) · Autophagy · doi:10.4161/auto.20123 · Cited by 165 · see citing works
Self-citationATG5 is induced by DNA-damaging agents and promotes mitotic catastrophe independent of autophagy
Maskey, D., Yousefi, S., Schmid, I., Zlobec, I., Perren, A. A., Friis, R. R., & Simon, H. (2013) · Nature Communications · doi:10.1038/ncomms3130 · Cited by 151 · see citing works
Dynamics of outer mitochondrial membrane permeabilization during apoptosis
Rehm, M., Huber, H. J., Hellwig, C. T., Anguissola, S., Düßmann, H., & Prehn, J. H. M. (2009) · Cell Death and Differentiation · doi:10.1038/cdd.2008.187 · Cited by 141 · see citing works
Systems biology of death receptor networks: live and let die
Lavrik, I. N. (2014) · Cell Death and Disease · doi:10.1038/cddis.2014.160 · Cited by 89 · see citing works
Self-citationApoptosis CED-4 is a stranger no more
Hengartner, M. P. (1997) · Nature · doi:10.1038/41873 · Cited by 88 · see citing works
Osteopontin deficiency aggravates hepatic injury induced by ischemia–reperfusion in mice
Patouraux, S., Rousseau, D., Rubio, A., Bonnafous, S., Lavallard, V., Lauron, J., Saint-Paul, M. C., Bailly‐Maitre, B., Tran, A., Crénesse, D., et al. (2014) · Cell Death and Disease · doi:10.1038/cddis.2014.174 · Cited by 48 · see citing works
Cell-to-cell variability in cell death: can systems biology help us make sense of it all?
Xia, X., Owen, M., Lee, R., & Gaudet, S. (2014) · Cell Death and Disease · doi:10.1038/cddis.2014.199 · Cited by 39 · see citing works
Würstle, M. L., Zink, E., Prehn, J. H. M., & Rehm, M. (2014) · Cell Death and Disease · doi:10.1038/cddis.2014.36 · Cited by 33 · see citing works
Systems biology approaches to develop innovative strategies for lung cancer therapy
Viktorsson, K., Lewensohn, R., & Zhivotovsky, B. (2014) · Cell Death and Disease · doi:10.1038/cddis.2014.28 · Cited by 27 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Reproducibility in systems biology modelling
Tiwari, K., Kananathan, S., Roberts, M. G., Meyer, J. P., Sharif Shohan, M. U., Xavier, A., Maire, M., Zyoud, A., Men, J., Ng, S., et al. (2021) · Molecular Systems Biology · doi:10.15252/msb.20209982 · Cited by 131 · see citing works
Regulation of extrinsic apoptotic signaling by c-FLIP: towards targeting cancer networks
Ivanisenko, N. V., Seyrek, K., Hillert-Richter, L. K., König, C., Espe, J., Bose, K., & Lavrik, I. N. (2021) · Trends in cancer · doi:10.1016/j.trecan.2021.12.002 · Cited by 72 · see citing works
Self-citationSystems Biology: A Multi-Omics Integration Approach to Metabolism and the Microbiome
Son, J. W., Shoaie, S., & Lee, S. (2020) · Endocrinology and Metabolism · doi:10.3803/enm.2020.303 · Cited by 25 · see citing works
Systems biology: perspectives on multiscale modeling in research on endocrine-related cancers
Clarke, R. C., Tyson, J. J., Tan, M. T., Baumann, W. T., Lu, J., Xuan, J., & Wang, Y. (2019) · Endocrine Related Cancer · doi:10.1530/erc-18-0309 · Cited by 19 · see citing works
Nampoothiri, S. S., Fayaz, S. M., & Rajanikant, G. K. (2018) · Molecular Neurobiology · doi:10.1007/s12035-018-0963-6 · Cited by 17 · see citing works
Reproducibility in systems biology modelling
Tiwari, K., Kananathan, S., Roberts, M. G., Meyer, J. P., Sharif Shohan, M. U., Xavier, A., Maire, M., Zyoud, A., Men, J., Ng, S., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.07.239855 · Cited by 131 · see citing works
- Authors
- Lavrik, I. N., & Zhivotovsky, B.
- Affiliations
- Lomonosov Moscow State University (RU)
- Corresponding author
- Zhivotovsky, B
- Venue
- Cell Death & Disease
- Published
- 2014-05-29
- Volume
- 5
- Issue
- 5
- Pages
- e1256-e1256
- ISSN
- 2041-4889 (ISSN-L)
- PMC
- PMC4047879
- OpenAlex
- W2019813017
- Cited by
- 5
- References
- 23
- Citations by year
- 2021: 2 · 2020: 1 · 2019: 1 · 2018: 1
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Cell Death and Disease (publishedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- Russian Foundation for Fundamental Investigations
- Bundesministerium für Bildung und Forschung (RFFI 14-04-00699, 0316170G)
- Vetenskapsrådet
- Barncancerfonden
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Cell death mechanisms and regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- systems biology, cell death, apoptosis, disease complexity
- MeSH terms
- Models, Biological, Systems Biology
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
