Networks, Trees, and Landscapes

@article{Dony2019,

title = {Parametric and non-parametric gradient matching for network inference: a comparison},

author = {Leander Dony and Fei He and Michael P.H. Stumpf},

doi = {10.1186/s12859-018-2590-7},

issn = {1471-2105},

year  = {2019},

date = {2019-12-00},

urldate = {2019-12-00},

journal = {BMC Bioinformatics},

volume = {20},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {Networks | trees and cell structures},

pubstate = {published},

tppubtype = {article}

}

@article{Chan2017,

title = {Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures},

author = {Thalia E. Chan and Michael P.H. Stumpf and Ann C. Babtie},

doi = {10.1016/j.cels.2017.08.014},

issn = {2405-4712},

year  = {2017},

date = {2017-09-00},

urldate = {2017-09-00},

journal = {Cell Systems},

volume = {5},

number = {3},

pages = {251--267.e3},

publisher = {Elsevier BV},

keywords = {Networks | trees and cell structures},

pubstate = {published},

tppubtype = {article}

}

@article{Stumpf2008,

title = {Estimating the size of the human interactome},

author = {Michael P.H. Stumpf and Thomas Thorne and Eric de Silva and Ronald Stewart and Hyeong Jun An and Michael Lappe and Carsten Wiuf},

doi = {10.1073/pnas.0708078105},

issn = {1091-6490},

year  = {2008},

date = {2008-05-13},

urldate = {2008-05-13},

journal = {Proc. Natl. Acad. Sci. U.S.A.},

volume = {105},

number = {19},

pages = {6959--6964},

publisher = {Proceedings of the National Academy of Sciences},

abstract = {<jats:p>

            After the completion of the human and other genome projects it emerged that the number of genes in organisms as diverse as fruit flies, nematodes, and humans does not reflect our perception of their relative complexity. Here, we provide reliable evidence that the size of protein interaction networks in different organisms appears to correlate much better with their apparent biological complexity. We develop a stable and powerful, yet simple, statistical procedure to estimate the size of the whole network from subnet data. This approach is then applied to a range of eukaryotic organisms for which extensive protein interaction data have been collected and we estimate the number of interactions in humans to be ≈650,000. We find that the human interaction network is one order of magnitude bigger than the

            <jats:italic>Drosophila melanogaster</jats:italic>

            interactome and ≈3 times bigger than in

            <jats:italic>Caenorhabditis elegans</jats:italic>

            .

          </jats:p>},

keywords = {Networks | trees and cell structures},

pubstate = {published},

tppubtype = {article}

}