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Ramón Díaz-Uriarte



I am an Associate Professor at the Department of Biochemistry, Universidad Autónoma de Madrid (UAM). Before that, and for nine years, I was a researcher at the Spanish National Cancer Center (CNIO). My research (at UAM and CNIO) has been in the broad areas of bioinformatics and statistical computing applied to bioinformatics problems. My background is a mix of biology (BSc. in Biology, PhD Zoology) and statistics (MSc. Biometry, MSc. Statistics). After finishing my PhD and before coming to the CNIO I worked as statistician in a company that developed artifical intelligence software and in a marketing research company, and I have also done some "for-hire" private statistical consulting.

A more formal, but outdated, CV in English (publications, education, etc). A more verbose CV in Spanish. My ResearcherID, ORCID ID and Google Scholar links.

PGP public key: 0xE89B3462 (download key).

If you send me attachments, please do not use proprietary and non-standard formats. In particular, since I do not use a certain Operating System, do not send Microsoft Word or Excel files. It is painful for me to open, read, modify, or print those files. You can use many of the great and open ways to exchange editable text (including format) such as LaTeX, rST, rtf, or even plain ASCII for documents, and plain ASCII for data (or you can send data as binary R RData files -).). Documents not intended to be modified by me can be sent as postscript or PDF. You can read more about why sending word attachments is a bad idea, and what we can do to end it: We Can Put an End to Word Attachments, by R. Stallman.

Main research interests

In the last 10 years I've worked mainly in the use of statistics and statistical computing in bioinformatics problems. For instance, I've worked on classification problems (e.g., the random forest and GeneSrF papers), as well as gene differential expression (e.g., Pomelo paper, and several collaborative papers), on the usage of parallel computing for web-based stats applications for bioinformatics problems (the papers about Asterias, SignS, etc), and on the identification of DNA copy number alterations from aCGH data (e.g., the HMM and the recurrent regions papers).

My main current research interest include:

Information for prospective students

Currently, I have openings in my lab (but no funding for salaries). If you think you could be interested in working with me (masters project, PhD, postdoc, short stay, etc), send me an email letting me know what problems interest you, how they match/overlap my main research areas, and why you think our working together could be interesting for you (and for me). Please provide some information about your background in biology and your computing and statistical skills (or lack thereof, but how you'd deal with it), as well as how you plan to support yourself (funding, etc).

A few miscellaneous and unstructured links

An important part of my job was to provide statistical support at CNIO. You can check the CNIO Stats Consulting Guidelines. I also maintain a CNIO Stats FAQ. (This is actually outdated; should probably move it out of here.)

The R statistical computing project. R is a mature, flexible and extensible language for statistical analysis and graphics. It provides "out-of-the-box" access to a wide variety of statistical techniques, and is widely used for statistical research and bioinformatics (see the Bioconductor project). R is Free Software, released under the GNU GPL license.

The directory of Open Access Journals and the Public Library of Science, which provide access to free, full text, peer-reviewed scientific journals. Because readers and instituions do not have to pay for access, scientific results can be more widely disseminated, and are accessible to all (with an internet connection). Related projects are Samizdat Press, Creative Commons, Project Gutemberg and Eldritch Press; Creative Commons is a wide ranging project that intends to make creative work (of any kind, including of course science) available to others, so that it can be built upon and shared, and they offer (at no charge) a set of licenses that "(...) intends to help people express this preference for sharing" (from their FAQ); the later two sites are focused on making general literature, not necessarily science, available to all. I have some related notes and comments under this link.

Why settle for any lesser operating system when there is GNU/Linux? (You might want to give Debian GNU/Linux a try.)

The GNU project.

The Spanish section of Amnesty International, Amnistía Internacional.

Intermón Oxfam.

The hunger site

Like "The hunger site" for children in Argentina

Medicos sin fronteras (doctors without borders)

Statistics and human rights. This site contains bibliography and links to other sites. The American Statistical Association has a Committeee on Scientific Freedom and Human Rights. Interesting enough, what used to be the AAAS Science and Human Rights Program has a short article titled Human rights, human values, and technology: why human rights advocates need to use free software. And here is a very recent post in Amstat News about StatAid, a non-profit statistical organization.

More on science and human rights. Check the "On-call" scientists initiative of the AAAS Science and Human Rights Program that "connects scientists interested in volunteering their skills and knowledge with human rights organizations that are in need of scientific expertise."

Todos contra el canon. Here you can read about the outrageous attempts (some successful) by the SGAE, the Spanish equivalent of the RIAA, to force you to pay for "crimes" in advance ("el canon"), or to severely curtail internet freedom by allowing them (the SGAE and friends) to censor internet contents. In that page you'll also learn about ongoing campaigns to stop these abuses.

Atheism and secularism. Richard Dawkins's page contains a lot of links and resources to start with. I generally enjoyed his book "The God Delusion", by the way (though I have some complaints about the style and tone of some of his attacks). An excellent volume is "Philosophers without Gods: Meditations on Atheism and the Secular Life", edited by L. M. Antony, that includes articles by 20 US and UK philosophers involving a range of issues (from "personal journeys" to questions of ethics, respect, and reasonable disagreements).

Some notes on revision control systems (or version control systems, or code control systems). A brief and biased set of notes I took while searching for a revision control system.

Using idutils and others with R and Python: notes on systems for indexing and tagging, in particular with R and Python in mind, and an R scanner for IDutils.

Using Mendeley and Zotero with a tablet: notes on using PDF reference management software with a tablet and my computers.

LaTeX bst files

LaTeX bst (bibliography styles) files for Public Library of Science, Biology and Genome Biology. The PLoS one I use with the natbib package (with \usepackage[authoryear, round, sort]{natbib} in the preamble. The GB one does not use natbib. To use either, include

      \bibliography{the.name.of.the.bib.file}
      \bibliographystyle{GenomeBiology} %% or PLoS
      

where you want the bibliography to appear. I prepared these bst files using makebst.tex, with a little manual editing. (makebst.tex is available, I think, as standard in all LaTeX installations for GNU/Linux, and also from CTAN). If you find any errors, I'd appreciate if you can let me know.

More on LaTeX, with very useful links, bibliography style files, etc, at BiBTeX Bibliography and LaTeX Style Formats for Molecular Biologists.



Creative
Commons License
This page and, unless explicitly stated, all other pages in this web site, are copyright, , by Ramon Diaz-Uriarte, and are licensed under a Creative Commons License.

Ramon Diaz-Uriarte (rdiaz02 %at% gmail.com)
Ramon Diaz-Uriarte (ramon.diaz %at% iib.uam.es)
Last modified: November 2012

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