diff --git a/.DS_Store b/.DS_Store index 3b7c51f752ed471877ab1bc455666cf436314247..1761bf85748cd7ef72d5b1c27f079f64f201e9f0 100644 Binary files a/.DS_Store and b/.DS_Store differ diff --git a/Publication I/Pub I methodology.svg b/Publication I/Pub I methodology.svg new file mode 100644 index 0000000000000000000000000000000000000000..40fd531f464cad5a4a8d2ad853296fe87bdf30be --- /dev/null +++ b/Publication I/Pub I methodology.svg @@ -0,0 +1 @@ +F1F2F3…FmD1100…0D2000…1………………Dn110…0F1F2F3FmD1D2Dn1)Disease–featureassociations(weightedornot)2) Featurematrices formedbybinaryornumericalfeaturevectorsa. Datasetsstructurationin featurematrices Disease feature vectorDiseasesComplete list (for each feature)Inner list (for all features)Biological featuresGenesProteinsPathwaysVariantsb. Computing distancematricesD1D2…DnD10D2…DnD1D2…DnD10D2…DnD1D2…DnD101…0,5D20…1…0…Dn0Metrics•Binaryvectors:-dice-hamming-jaccard-sokalsneath•Numericvectors:-correlation-cosine-euclidean-minkowskic. Clusteringimplementationand evaluationClusteringalgorithms-DBSCAN-HDBSCAN-OPTICS-KMeans-HierarchicalEvaluation-Numberofclusters-Noise-Silhouette-Calinski-Harabasz-Davies-Bouldin-SSE \ No newline at end of file diff --git a/Publication I/README.md b/Publication I/README.md index 4c318b42ee2f2c425dd8f929fc1a2deb8d4f08f2..dd4d4efb100ca4c788b890cea04d0f17855336ee 100644 --- a/Publication I/README.md +++ b/Publication I/README.md @@ -4,4 +4,12 @@ L. Prieto Santamaría, E. P. García del Valle, M. Zanin, G. S. Hernández Chan, :point_right: Go to [online publication](https://www.nature.com/articles/s41598-021-00554-6) -:point_right: Go to [repository of the publication](https://medal.ctb.upm.es/internal/gitlab/disnet/nosologic-models-paper) \ No newline at end of file +:point_right: Go to [repository of the publication](https://medal.ctb.upm.es/internal/gitlab/disnet/nosologic-models-paper) + +:point_right: Go to [PDF with the manuscript](https://medal.ctb.upm.es/internal/gitlab/lprieto/phd-thesis-luciaprietosantamaria/blob/master/Publication%20I/Publication%20I.pdf) + +:point_right: Go to [supplementary information](https://medal.ctb.upm.es/internal/gitlab/lprieto/phd-thesis-luciaprietosantamaria/blob/master/Publication%20I/SM%20-%20Publication%20I.pdf) + +The broad methodology used in this publications is summarized in the following figure: + + \ No newline at end of file diff --git a/Publication II/Pub II methodology.svg b/Publication II/Pub II methodology.svg new file mode 100644 index 0000000000000000000000000000000000000000..d177bfa745757b56519489b0de7256c4183fcc52 --- /dev/null +++ b/Publication II/Pub II methodology.svg @@ -0,0 +1,12183 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Publication II/README.md b/Publication II/README.md new file mode 100644 index 0000000000000000000000000000000000000000..c5097bce46ad98699e357c301c252710d5bde360 --- /dev/null +++ b/Publication II/README.md @@ -0,0 +1,16 @@ +# Publication II + +L. Prieto Santamaría*, E. Ugarte Carro*, M. Díaz Uzquiano, E. Menasalvas Ruiz, Y. Pérez Gallardo, and A. Rodríguez-González, «A data-driven methodology towards evaluating the potential of drug repurposing hypotheses», Computational and Structural Biotechnology Journal, vol. 19, pp. 4559–4573, 2021, doi: 10.1016/j.csbj.2021.08.003. + +:point_right: Go to [online publication](https://www.sciencedirect.com/science/article/pii/S2001037021003342) + +:point_right: Go to [supplementary data](https://www.sciencedirect.com/science/article/pii/S2001037021003342#s0075) + +:point_right: Go to [PDF with the manuscript](https://medal.ctb.upm.es/internal/gitlab/lprieto/phd-thesis-luciaprietosantamaria/tree/master/Publication%20II) + +:point_right: Go to [supplementary information](https://medal.ctb.upm.es/internal/gitlab/lprieto/phd-thesis-luciaprietosantamaria/blob/master/Publication%20II/SM%20-%20Publication%20II.pdf) + + +The broad methodology used in this publications is summarized in the following figure: + + \ No newline at end of file diff --git a/Publication III/Pub III methodology.svg b/Publication III/Pub III methodology.svg new file mode 100644 index 0000000000000000000000000000000000000000..d190f992e3938ab989a994b7eff197e83f8b30fd --- /dev/null +++ b/Publication III/Pub III methodology.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/Publication III/README.md b/Publication III/README.md new file mode 100644 index 0000000000000000000000000000000000000000..dda25355c4a486024f80f3fca96864f9c3129780 --- /dev/null +++ b/Publication III/README.md @@ -0,0 +1,16 @@ +# Publication III + +L. Prieto Santamaría*, M. Díaz Uzquiano*, E. Ugarte Carro, N. Ortiz-Roldán, Y. Pérez Gallardo, and A. Rodríguez-González, «Integrating heterogeneous data to facilitate COVID-19 drug repurposing», Drug Discovery Today, vol. 27, no. 2, pp. 558–566, Feb. 2022, doi: 10.1016/j.drudis.2021.10.002. + +:point_right: Go to [online publication](https://www.sciencedirect.com/science/article/pii/S1359644621004384) + +:point_right: Go to [repository of the publication](https://medal.ctb.upm.es/internal/gitlab/disnet/disnet_covid_paper) + +:point_right: Go to [PDF with the manuscript](https://medal.ctb.upm.es/internal/gitlab/lprieto/phd-thesis-luciaprietosantamaria/tree/master/Publication%20III) + +:point_right: Go to [supplementary information](https://medal.ctb.upm.es/internal/gitlab/lprieto/phd-thesis-luciaprietosantamaria/blob/master/Publication%20III/SM%20-%20Publication%20III.pdf) + + +The broad methodology used in this publications is summarized in the following figure: + + \ No newline at end of file diff --git a/README.md b/README.md index 75e5d7ff9231c36bebaaf5340d797236f853de60..e40c403345155e5a27ab67568069ba6a8c888b5e 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,22 @@ -# PhD Thesis LuciaPrietoSantamaria +# PhD Thesis - Lucía Prieto Santamaría (2023) + +This repository brings together the resources, materials and code generated for and in relation to the doctoral thesis of [Lucía Prieto Santamaría](https://luciaprietosantamaria.es/). + +The title of the thesis is: + +--- +Creation, integration, and analysis of disease networks towards a better disease understanding and drug repurposing +--- + +The supervisors of this thesis have been [Alejandro Rodríguez González](https://www.alejandrorg.com/) and [Yuliana Pérez Gallardo](https://scholar.google.com/citations?user=1bF8dTwAAAAJ&hl=en). The doctoral program in which the thesis has been carried out is the[PhD. in Software, Systems and Computing](https://dssc.fi.upm.es/), which takes place at the Escuela Técnica Superior de Ingenieros Informáticos ([ETSIInf](https://www.etsiinf.upm.es/)) of the Universidad Politécnica de Madrid ([UPM](https://www.upm.es/)), Spain. + +The thesis has been developed under the scope of the [DISNET project](https://disnet.ctb.upm.es/), executed at the Medical Data Analytics Laboratory ([MEDAL](https://medal.ctb.upm.es/)) of the Center for Biomedical Technology ([CTB](http://www.ctb.upm.es/)). The thesis is a result of an industrial doctorate in conjunction with [Ezeris Networks Global Services, S.L.](http://www.ezeris.com/) + +The thesis is presented as a compendium of 3 publications: + +* [Publication I](https://medal.ctb.upm.es/internal/gitlab/lprieto/phd-thesis-luciaprietosantamaria/tree/master/Publication%20I) + +* [Publication II](https://medal.ctb.upm.es/internal/gitlab/lprieto/phd-thesis-luciaprietosantamaria/tree/master/Publication%20II) + +* [Publication III](https://medal.ctb.upm.es/internal/gitlab/lprieto/phd-thesis-luciaprietosantamaria/tree/master/Publication%20III) -This repository brings together the resources, materials and code generated for and in relation to the doctoral thesis of Lucía Prieto Santamaría. \ No newline at end of file