Selected Publications

derfinder analysis using expressed region-level and single base-level approaches provides a compromise between full transcript reconstruction and feature-level analysis. The package is available from Bioconductor.

We describe Rail-RNA, a cloud-enabled spliced aligner that analyzes many samples at once. Rail-RNA eliminates redundant work across samples, making it more efficient as samples are added. For many samples, Rail-RNA is more accurate than annotation-assisted aligners.

recount provides a valuable and user-friendly resource of processed RNA-seq datasets to draw additional biological insights from existing public data.

Recent Publications

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Recent Posts

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Have you ever had to explore a table with data? I believe the answer is yes for most people that work at a computer or even just use it for communicating with their friends and family. Tables of data pop up everywhere, for example in personal finance. Websites like allow you to download your transactions in a CSV file called transactions.csv. CSV is one of the many formats for storing tables and most likely when you try to open the transactions.


Over the weekend my brother wanted to figure out his class schedule for the next semester. He is a veterinary medicine and zootechnology student at UNAM. For this upcoming semester there is a set of classes he has to take and each has 8 or so instructor options. The website where he finds the class times lists about 8 pre-constructed class schedules. So he normally finds one he likes quite a bit, and then manually starts checking if he can change X instructor for Y for a given class.


Today the UNAM community at large mourns the passing of Federico Sánchez Rodríguez. He got his bachelor’s degree from the School of Chemistry - UNAM, masters and PhD degrees from Biomedicas - UNAM, postdoc from UCSF, was a member of CIFN-UNAM now called CCG-UNAM (it’s his affiliation in this 1983 paper), and worked most of his career at IBT-UNAM. I’m sure that he made many friends, trained many students at all levels, and had a highly productive academic career as evidenced on his homepage where he lists many papers, patents, etc.


This has been a busy week. I just flew in last night from #ENAR2016 and I’m getting ready for a postdoc interview tomorrow, which means that I’m also flying today. On the flight back from #ENAR2016 I started reading a book my friend John Muschelli bought for me. It’s called The Happiness Advantage by Shawn Anchor and so far I’m loving it. There are several things that it talks about that I’ve done in the past, but maybe not in the past year.


It’s the morning of the first day of oral conferences at #ENAR2016. I feel like I have a spidey sense since I woke up 3 min after an email from Jeff Leek; just a funny coincidence. Anyhow, I promised Valerie Obenchain at #Bioc2014 that I would write a post about one of my favorite Bioconductor packages: BiocParallel (Morgan, Obenchain, Lang, and Thompson, 2016). By now it’s on the top 5% of downloaded Bioconductor packages, so many people know about it or are unaware that their favorite package uses it behind the scenes.


Curriculum Vitae

Download my cv or view it at GitHub.




  1. Biostatistics and Stata instructor at a workshop for Kandahar University Faculty, organized by Johns Hopkins University.
  2. Invited instructor for the Genomeeting 2016 course at INMEGEN, Mexico City, Mexico.



  1. Teaching assistant and guest lecturer for Introduction to R for Public Health Researchers
  2. Teaching assistant for Statistical Methods in Public Health I (140.621)
  3. Lead teaching assistant for Statistical Methods in Public Health II (140.622).
  4. Teaching assistant for the MPH capstone project.


  1. Lead teaching assistant for Statistical Methods in Public Health I (140.621) and II (140.622).
  2. Teaching assistant for the MPH capstone project.


  1. Teaching assistant for Statistical Methods in Public Health I (140.621) and II (140.622).
  2. Teaching assistant for the MPH capstone project. Developed a shiny application that allows students to sign up for a TA session (code) and wrote a report of the number of TA sessions available here.


  1. Teaching assistant for Statistical Methods in Public Health I (140.621), II (140.622), III (140.623), and IV (140.624) courses.



While working at Winter Genomics I taught two courses for students of the Biomedical Sciences PhD Program (PDCB) from the National Autonomous University of Mexico (UNAM).

  1. Analysis of High-Throughput Sequencing data with Bioconductor Aug-Dec 2010.
  2. Introduction to R and Biostatistics (along with two other teachers).


While I was at the Institute of Biotechnology (UNAM) working with the Winter Genomics crew I organized two courses. One was a series of various bioinformatics and biology mini-courses and another one involved members of different institutions.

  1. Introduction to R for bench biologists Oct-Nov 2009. This mini-course has quite a bit of material on learning how to make plots with R.
  2. Métodos Estadísticos y Analíticos de Datos Genómicos (Statistical Methods and Analysis of Genomic Data) Jan 2010. This one week course had lectures about Perl, using a Cluster, high-throughput technologies, R and Bioconductor, C, and biology overviews.


I taught three courses during my undergrad stage at the Undergraduate Program on Genomic Sciences (LCG). Each of these courses has its own website organizing the material. These are:

  1. Intensive course on R/Bioconductor Oct-Nov 2008 (backup)
  2. Principles of Statistics Feb-June 2009 (backup)
  3. Seminar III: R/Bioconductor Aug-Dec 2009 (backup)