## GIT: Page Not Found

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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.

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About me

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** Published:**

I decided to revamp my website with something that was more easily manageble. Talking with collegues I decided to give Jekyll a try. Setting the site up is taking longer than I thought, but I am slowly getting there. Hopefully this winter break will be helpful. Stay tuned!

** Published:**

Since I moved to IUNI as an Assistant Research Scientist, I have been struggling to communicate in a precise scientific language with network scientist in Sociology. The main problem being that the same terms I have learned from network scientists in Informatics do not always mean exactly the same thing in the two disciplines.

So here I am going to try and put together a list of resources for Informatics/Physics trained network scientist to better navigate the long history of Social Network Analysis in Sociology.

** Published:**

I decided to add a layered graph drawing algorithm to my Mapper code [citation missing] So i have been looking for descriptions of the Sugiyama Method online, here are the best i found:

https://github.com/erikbrinkman/d3-dag

https://www.csd.uoc.gr/~hy583/papers/ch10.pdf

http://www.it.usyd.edu.au/~shhong/fab.pdf

http://publications.lib.chalmers.se/records/fulltext/161388.pdf

http://www.graphviz.org/Documentation/TSE93.pdf

https://blog.disy.net/sugiyama-method/

https://pdfs.semanticscholar.org/9d5e/62920365f339e9121e6e62f4cdc7a10ed058.pdf

** Published:**

New work out, together with collaborators at King’s College London, Imperial College London and ISI Foundation. We applied the Mapper algorithm to the AHBA (Allen Human Brain Atlas). Our results suggest that topological network descriptions can be a powerful tool to explore the relationships between genetic pathways and their association with brain function and its perturbation due to illness and/or pharmacological challenge.

A small script that looks for unread Google Scholar Alerts emails in your Gmail account and saves each paper in a Google Spreadsheet as:

Title/ Authors - Journal/ Google Scholar link/ Date/ number of Alerts that contained the paper

Code for reproducing results in the paper “Topological gene-expression networks recapitulate brain anatomy and function”.

We present a pipeline based on the Mapper algorithm, a topological simplification tool, to produce and analyze genes co-expression data.

The code contains an implementation of the Mapper algorithm with 2 filters and to compute the agreement edge density matrices for the optimal parameters.

Short description of portfolio item number 1

Short description of portfolio item number 2

Vaccarino, F., Patania, A., & Petri, G. (2017). "P-persistent homology of finite topological spaces." *Rendiconti Sem. Mat. Univ. Pol. Torino*. Vol. 74, 1. 27 - 45. __Rendiconti Sem. Mat. Univ. Pol. Torino__, 2015

We show that for any P-persistent object X in the category of finite topological spaces, there is a P− weighted graph whose clique complex has the same P-persistent homology as X.

Gurciullo, S., Smallegan, M., Pereda, M., Battiston, F., Patania, A., Poledna, S., ... & Mikhaylov, S. (2015). "Complex politics: A quantitative semantic and topological analysis of uk house of commons debates." *arXiv preprint*. arXiv:1510.03797. __arXiv:1510.03797.__, 2015

An exploratory attempt to use quantitative semantics techniques and topological analysis to analyze systemic patterns arising in a complex political system.

Young, J. G., Petri, G., Vaccarino, F., & Patania, A. (2017). "Construction of and efficient sampling from the simplicial configuration model." *Physical Review E*. 96(3), 032312. __Physical Review E__, 2017

We propose the simplicial configuration model and use it to build null models to investigate the topology of real systems.

Patania, A., Vaccarino, F., & Petri, G. (2017). "Topological analysis of data." *EPJ Data Science*. 6(1), 7. __EPJ Data Science__, 2017

An editorial where we briefly present the TDA paradigm and some applications, in order to highlight its relevance to the data science community.

Patania, A., Petri, G., & Vaccarino, F. (2017). "The shape of collaborations." *EPJ Data Science*. 6(1), 18. __EPJ Data Science__, 2017

A study on the structure of scientific collaborations using simplicial descriptions of publications. We extend the concept of triadic closure to simplicial complexes and introduce a new way of dealing with large simplex sizes when computing homology.

Patania, A., Selvaggi, P., Veronese, M., DiPasquale, O., Expert, P., & Petri, G. (2018). "Topological gene-expression networks recapitulate brain anatomy and function." *arXiv preprint*. bioRxiv, 476382. __bioRxiv, 476382__, 2018

We present a pipeline based on Mapper to analyze genes co-expression data. We find that co-expression networks produced by Mapper returned a structure that matches the well-known anatomy of the dopaminergic pathway.

** Published:**

Undergraduate course, *University 1, Department*, 2014

This is a description of a teaching experience. You can use markdown like any other post.

Workshop, *University 1, Department*, 2015

This is a description of a teaching experience. You can use markdown like any other post.