Featured

Interview with… Natàlia Vilor Tejedor

Natàlia VilorNatàlia Vilor-Tejedor holds a BSc in Mathematics and Applied Statistics from the Universitat Autònoma de Barcelona. Additionally, she holds a MSc in Omics Data Analysis from the Universitat de Vic where she also worked at the Bioinformatics and Medical Statistics Research group developing new methods for analyzing the individual evidence of SNPs in biological pathways and was involved in some GWAS data analyses. Currently, she is a PhD student in the Biomedicine programme at the Universitat Pompeu Fabra. At the same time, she is working at the Barcelona Biomedical Research Park (in the Centre for Research in Environmental Epidemiology) where she is working on new statistical methods for integrating different types of Omics, Neuroimaging and Clinical Data from the European BREATHE project. She received one of the two Biostatnet prizes for the best presentations at the JEDE III conference for her talk on “Efficient and Powerful Testing for Gene Set Analysis in Genome-Wide Association Studies”.

Contact info: nvilor(at)creal(dot)cat  linkedin

  1. Why did you choose Biostatistics?

Because I enjoy my work and I think that my research can help to improve different aspects of biomedicine and, in general, the population’s life quality.

  1. Could you give us some insight into your current field of research?

Now I’m just starting my PhD thesis focused on the development of new mathematical methods to better understand the commonalities between Genetics and Neuroimaging, and how both affect Environmental phenotypes.

This is a relatively “new” area that has not been examined in depth, so I’m sure statistics can play an important role.

  1. Coming from a Mathematics/Statistics background, was it difficult to start in the area of Genomics?

The most difficult part is to find a good mentor who is an expert in both areas and who is willing to help you. After that, you need to become familiar and understand different biological concepts that probably you haven’t come across before. Then, you have to extrapolate these concepts to a mathematical point of view, and finally (what is the most important and hardest part), you have to be able convey the information to both, geneticists and mathematicians.

All of these steps require an extra effort that is often difficult to overcome.

  1. Which do you think are the main qualities of a good mentor?

I think the most important quality is knowing how to impart the indispensable knowledge whilst being clear and well organised, but also it is important to instill confidence and provide development opportunities.

  1. What do you think of the situation of young biostatisticians in Spain?

Although we are at a very delicate social-economic moment, I think we have a talented and very well prepared generation of young biostatisticians supported by important national institutions such as the Spanish Biometric Society and the Societat Catalana d’Estadística (in my case) and national networks such as BioStatNet and online resources like this blog that are helping us in our training.

  1. From your experience, would you recommend the area of Genomics as a professional option for statisticians?

I think this is a very interesting, motivating and emerging field of research where a lot of statisticians and mathematicians are required. From my personal experience, the vast majority of mathematicians/statisticians are not comfortable with biology, but I think that promoting interdisciplinarity is essential to ensure biomedical research.

  1. Finally, is there any topic you would like to see covered in the blog?

Of course, even more genetics!

Selected publication and projects:

Advertisements
Featured

Analysis of PubMed search results using R

Looking for information about meta-analysis in R (subject for an upcoming post as it has become a popular practice to analyze data from different Genome Wide Association studies) I came across  this tutorial from The R User Conference 2013 – I couldn´t make it this time, even when it was held so close, maybe Los Angeles next year…

Back to the topic at hand, that is how I found out about the RISmed package which is meant to retrieve information from PubMed. It looked really interesting because, as you may imagine,this is one of the most used resources in my daily routine.

Its use is quite straightforward. First, you define the query and download data from the database (be careful about your IP being blocked from accessing NCBI in the case of large jobs!) . Then, you might use the information to look for trends on a topic of interest or extracting specific information from abstracts, getting descriptives,…

In order to try it out, I decided to get data regarding what has been published relating to Next Generation Sequencing. For doing so, I adopted the search terms proposed in the paper by Jia et al. Through the following code we can get the PubMed results for these search terms since 1980:

library(RISmed)
query = "(exome OR whole OR deep OR high-throughput OR (next AND generation) OR (massively AND parallel)) AND sequencing"
ngs_search <- EUtilsSummary(query, type="esearch",db = "pubmed",mindate=1980, maxdate=2013, retmax=30000)
QueryCount(ngs_search)
ngs_records <- EUtilsGet(ngs_search)
years <- Year(ngs_records)
ngs_pubs_count <- as.data.frame(table(years))

This code allow us to get published papers on this topic per year. By getting also data about the total number of publications per year, we are able to normalize the data. The complete R code, once the data are downloaded and edited can be found at  FreshBiostats GitHub Gist. In the next graph, we can see the publication trend for Next Generation Sequencing per year:

ngs_year

I was also curious about which ones would be the journals with the highest number of publications on this topic. Using the following code we can get the count of NGS publications per journal:

journal <- MedlineTA(ngs_records)
ngs_journal_count <- as.data.frame(table(journal))
ngs_journal_count_top25 <- ngs_journal_count[order(-ngs_journal_count[,2]),][1:25,]
Again, the complete code that allows us to normalize the data by the total number of publications per journal, as well as the following barplots showing the result, is available at our Gist:

ngs_publications_total

ngs_publications_normalized

You cand find some other examples using this package at Dave Tangs Bioinformatics blog. Additionally, some alternatives to the use of RISmed package can be found at R Chronicle and R Psychologist blogs.

Other potential applications of this package include creating a co-author network, as is described in Matthew Maenner´s blog.

Search and analyze carefully!

Featured

My impressions from the Workshop on the Future of the Statistical Sciences

An exciting workshop, organised as the capstone of the International Year of Statistics Statistics2013, was celebrated on the 11th and 12th of November at the Royal Statistical Society Headquarters in London, under the stimulating title of  “The Future of the Statistical Science”, science to which John Pullinger, president of the Royal Statistical Society, refers to as a quintessentially, multidisciplinary discipline. The workshop was indeed a good example of that.

Online attendance was welcomed to the event giving an additional opportunity to listen to highly reputed professionals in main areas of Statistics. Virtual participants were also allowed to pose their questions to the speakers, an innovation that worked very well as an excellent way to make these sorts of events available to a wider audience that would otherwise be excluded – I am already looking forward to more! -.

In case you missed it at the time, luckily the podcast is still available here.

True to its description, the event covered different areas of application, it showed the tools of the field for tackling a wide range of challenges, it portrayed potentially high impact examples of research, and in summary, was a great attention-grabbing exercise that will hopefully encourage other professionals to the area. A common vision of ubiquity and great relevance came across from the speeches and showed the field as a very attractive world to join. See my simplified summary below in form of a diagram certainly reflective of the great Statistics Views motto “Bringing Statistics Together”.

schematic_simpl

Fig 1. Some of the ideas discussed in the workshop

Particularly relevant to this blog and my particular interests were presentations on environmental Statistics and statistical Bioinformatics, as well as other health-related talks. Important lessons were taken on board from the rest of the speakers too.

The workshop started with a shared presentation on the hot topic “Statistical Bioinformatics” by Peter Bühlmann (ETH Zürich) and Martin Vingron (Free University of Berlin). In a fascinating talk, Bühlmann argued for the need of uncertainty quantification in an increasingly heterogeneous data world –examples of this are also appearing in other fields, e.g. in the study of autism disorders as Connie Kasari and Susan Murphy mentioned in “SMART Approaches to Combating Autism”- and for models to be the basis of the assignation of uncertainties – topic greatly covered by Andrew Gelman in “Living with uncertainty, yet still learning”-, while acknowledging that in the big data context, “confirmatory statistical inference is (even more) challenging”. Vingron followed by focusing on “Epigenomics as an example”, raising open questions to the audience on how to define causality in Biology where “most processes […] are feedback circular processes”, calling for models that are just complex enough so as to allow for mechanistic explanations, and for good definitions of null hypotheses.

In addition to the interesting points of the talk, I found its title particularly attractive in what it could be directly linked to a vibrant roundtable on “Genomics, Biostatistics and Bioinformatics” in the framework of the 2nd Biostatnet General Meeting, in which, as some of you might remember, the definitions of the terms Biostatistics and Bioinformatics were discussed. I wonder if the term “statistical Bioinformatics” would be indeed the solution to that dilemma? As a matter of fact, Bühlmann himself mentions at the start of his talk other options like Statistical Information Sciences, etc-

Michael Newton and David Schwartz from the University of Wisconsin-Madison also focused on the triumph of sequencing and “Millimeter-long DNA Molecules: Genomic Applications and Statistical Issues”. Breast cancer being one of the mentioned applications, this was followed by an introduction to “Statistics in Cancer Genomics” by Jason Carroll and Rory Stark (Cancer Research UK Cambridge Institute, University of Cambridge), particularly focusing on breast and prostate cancer and the process of targeting protein binding sites.  The latter, as a computational biologist, mentioned challenges on the translation of Statistics for the biologists and vice versa, and identified ”reproducibility as (the) most critical statistical challenge” in the area – also on the topic of reproducibility, it is especially worth watching “Statistics, Big Data and the Reproducibility of Published Research” by Emmanuel Candes (Stanford University) -.

Another area increasingly gaining attention in parallel with technologies improvements is Neuroimaging. Thomas Nichols (University of Warwick) lead the audience in a trip through classical examples of its application (from Phineas Gage´s accident to observational studies of the structural changes in the hippocampi of taxi drivers, and the brain´s reaction to politics) up to current exciting times, with great “Opportunities in Functional Data Analysis” which Jane-Ling Wang (University of California) promoted in her talk.

Also in the area of Health Statistics, different approaches to dietary patterns modelling were shown in “The Analysis of Dietary Patterns and its Application to Dietary Surveillance and Epidemiology” by Raymond J. Carroll (Texas A&M University), and Sue Krebs-Smith (NCI), with challenges in the area being; finding dietary patterns over the life course – e.g. special waves of data would appear in periods like pregnancy and menarchy for women-, and incorporation of technology to the studies as a new form of data collection –e.g., pictures of food connected to databases-.

Again with a focus on the challenges posed by technology, three talks on environmental Statistics outlined an evolution over time of the field. Starting from current times, Marian Scott (University of Glasgow) in “Environment – Present and Future” stated in her talk that “natural variability is more and more apparent” because we are now able to visualise it. This idea going back to the heterogeneity claimed by Bühlmann. Despite the great amounts of data being available, and initially caused by technological improvements but ultimately due to a public demand – “people are wanting what it is happening now”-, the future of the field is still subject to the basic questions: “how and where to sample.” Especially thought-provoking were Scott´s words on “the importance of people in the environmental arena” and the need for effective communication: “we have to communicate: socio-economic, hard science…, it all needs to be there because it all matters, it applies to all the world…”

Amongst other aims of this environmental focus such as living sustainably – both in urban and rural environments-, climate is a major worry/fascination which is being targeted through successful collaborations of specialists in its study and statisticians. “Climate: Past to Future” by Gabi Hegerl (University of Edinburgh) and Douglas Nychka (NCAR) covered “Regional Climate – Past, Present and Future” and showed relevant examples of these successful collaborations.

Susan Waldron (University of Glasgow), under the captivating speech title of “A Birefringent Future”, highlighted the need to address challenges in the communication of “multiple layers of information” too, Statistics appearing as the solution for doing this effectively –e.g. by creating “accessible visualisation of data” and by incorporating additional environmental variation in controversial green energy studies such as whether wind turbines create a microclimate-. Mark Hansen (Columbia University Journalism School) seconded Waldron´s arguments and called for journalists to play an important role in the challenge: “data are changing systems of power in our world and journalists. […] have to be able to think both critically as well as creatively with data”, so as to “provide much needed perspective”. Examples of this role are; terms such as “computational Journalism” already being coined and data visualisation tools being put in place -as a fascinating example, the New York Times´ Cascade tool builds a very attractive representation of the information flow in Social Media-. David Spiegelhalter (Cambridge University) also dealt with the topic in the great talk “Statistics for an Informed Public”, providing relevant examples (further explanation on the red meat example can be found here as well).

To encourage “elicitation of experts opinions (to reach a) rational consensus” and “to spend more time with regulators” came up as other useful recommendations in the presentation “Statistics, Risk and Regulation” by Michel Dacorogna (SCOR) and Paul Embrechts (ETH Zürich).

In a highly connected world inmersed in a data revolution, privacy becomes another major issue. Statistical challenges arising from networked data –e.g. historical interaction information modelling- were addressed by Steve Fienberg (Carnegie Mellon University) and Cynthia Dwork (Microsoft Research), who argued that “statisticians of the future will approach data and privacy (and its loss) in a fundamentally algorithmic fashion”, in doing so explicitly answering the quote by Sweeney: “Computer science got us into this mess, can computer science get us out of it?”. Michael I. Jordan (University of California-Berkeley) in “On the Computation/Statistics Interface and “Big Data”” also referred to “bring(ing)  algorithmic principles more fully into contact with statistical inference“.

I would like to make a final mention to one of the questions posed by the audience during the event. When Paul Embrechts was enquired about the differences between Econometrics and Statistics, a discussion  followed on how crossfertilisation between fields has happened back and forth. As a direct consequence of this contact, fields rediscover issues from other areas. For instance, Credit Risk Analysis models were mentioned as being inferred from Medical Statistics or back in Peter Bühlmann´s talk, links were also found between Behavioural Economics and Genetics. These ideas, from my point of view, bring together the essence of Statistics, i.e. its application and interaction with multiple disciplines as the foundations of its success.

Many other fascinating topics were conveyed in the workshop but unfortunately, I cannot fit here mentions to all the talks. I am sure you will all agree it was a fantastic event.