{"entity": "journal", "iuid": "33c28079a260477299f110a7a2bea98a", "timestamp": "2026-09-26T23:02:42.515Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/J%20Theor%20Biol.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/J%20Theor%20Biol"}}, "title": "J Theor Biol", "issn": "1095-8541", "issn-l": null, "publications_count": 2, "publications": [{"entity": "publication", "iuid": "1abeab3d646d48d696b0993c37e96213", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1abeab3d646d48d696b0993c37e96213.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1abeab3d646d48d696b0993c37e96213"}}, "title": "The molecular mechanisms associated with PIN7, a protein-protein interaction network of seven pleiotropic proteins.", "authors": [{"family": "Nah\u00e1lkov\u00e1", "given": "Jarmila", "initials": "J"}], "type": "journal article", "published": "2020-02-21", "journal": {"title": "J Theor Biol", "issn": "1095-8541", "volume": "487", "pages": "110124", "issn-l": null}, "abstract": "PIN7 is a protein-protein interaction network of seven pleiotropic proteins (TPPII, CDK2, MYBBP1A, p53, SIRT6, SIRT7, and CD147) with proposed multiple functions in the aging and age-related diseases including cancer and neurodegeneration. Since the animal and cellular models with downregulated or knockout TPPII, p53, SIRT6, SIRT7, and MYBBP1A expression levels demonstrate similar age-related phenotype features, the interaction network was subjected to further investigation. For the identification of the main molecular mechanisms enabling the functions of the interaction network, PIN7 was subjected to the pathway enrichment, protein function prediction, and the protein node prioritization analysis using Cytoscape software and its applications GeneMania, ClusterOne, and Cyto-hubba. The study identified the p53 signaling pathway as the most dominant mediator of PIN7 effect. The top-ranked protein nodes of PIN7 extended by GeneMania application belong to the group of histone acetyltransferases and histone deacetylases. These enzymes are involved in the reverse epigenetic regulation mechanisms linked to the regulation of PTK2, NF\u03baB, and p53 signaling interaction subnetworks of the extended PIN7. The analysis emphasized the role of PTK2 signaling, which functions upstream of the p53 signaling pathway, and its interaction network includes all top rank protein nodes of the extended PIN7 and all members of the sirtuin family (SIRT1-SIRT7). Further, the analysis suggests the involvement of molecular mechanisms related to metastatic cancer (prostate cancer, small cell lung cancer), hemostasis, the regulation of the thyroid hormones, and the cell cycle G1/S checkpoint. The additional data-mining analysis shows that the protein interaction network MYBBP1A-p53-TPPII-SIRT6-CD147 controls the Warburg effect, and MYBBP1A-p53-TPPII-SIRT7-CD147 influences mTOR signaling and autophagy. The proposed insights into the molecular mechanisms of aging and age-related diseases could be valuable for the discovery of new controlling interaction clusters, which could contribute to the development of the multitarget therapeutical strategies.", "doi": "10.1016/j.jtbi.2019.110124", "pmid": "31863763", "labels": [], "xrefs": [{"db": "pii", "key": "S0022-5193(19)30493-X"}], "notes": [], "created": "2026-09-23T13:27:27.279Z", "modified": "2026-09-23T13:27:27.293Z"}, {"entity": "publication", "iuid": "82b4c256019643aa80866e18794a6d07", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/82b4c256019643aa80866e18794a6d07.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/82b4c256019643aa80866e18794a6d07"}}, "title": "An informational transition in conditioned Markov chains: Applied to genetics and evolution.", "authors": [{"family": "Zhao", "given": "Lei", "initials": "L"}, {"family": "Lascoux", "given": "Martin", "initials": "M"}, {"family": "Waxman", "given": "David", "initials": "D"}], "type": "journal article", "published": "2016-08-07", "journal": {"title": "J Theor Biol", "issn": "1095-8541", "volume": "402", "pages": "158-170", "issn-l": null}, "abstract": "In this work we assume that we have some knowledge about the state of a population at two known times, when the dynamics is governed by a Markov chain such as a Wright-Fisher model. Such knowledge could be obtained, for example, from observations made on ancient and contemporary DNA, or during laboratory experiments involving long term evolution. A natural assumption is that the behaviour of the population, between observations, is related to (or constrained by) what was actually observed. The present work shows that this assumption has limited validity. When the time interval between observations is larger than a characteristic value, which is a property of the population under consideration, there is a range of intermediate times where the behaviour of the population has reduced or no dependence on what was observed and an equilibrium-like distribution applies. Thus, for example, if the frequency of an allele is observed at two different times, then for a large enough time interval between observations, the population has reduced or no dependence on the two observed frequencies for a range of intermediate times. Given observations of a population at two times, we provide a general theoretical analysis of the behaviour of the population at all intermediate times, and determine an expression for the characteristic time interval, beyond which the observations do not constrain the population's behaviour over a range of intermediate times. The findings of this work relate to what can be meaningfully inferred about a population at intermediate times, given knowledge of terminal states.", "doi": "10.1016/j.jtbi.2016.04.021", "pmid": "27105672", "labels": [], "xrefs": [{"db": "pii", "key": "S0022-5193(16)30049-2"}], "notes": [], "created": "2026-09-23T13:12:41.920Z", "modified": "2026-09-23T13:12:41.961Z"}], "created": "2026-09-23T13:12:41.927Z", "modified": "2026-09-23T13:12:41.927Z"}