Computational Biology: 
Post-doctoral positions

Computational Biologist

Candidates would join a team of three computational biologists in the lab.

One main project in the lab is to use computational tools to model gene expression and translation integrating the signals from multiple regulatory mechanisms that we have discovered in the lab, including microRNA regulation, RNA binding proteins activity, Translation, upstreamORF regulation, and codon mediated regulation.

Other reas of study in computational biology are in areas of Epigenetics, long non-coding RNAs, Structure-seq, RNA-seq, Ribosome profiling, iClip, Gene networks and expression analysis

Description of project: Several postdoctoral position in computational biology are available to study:

-Modeling gene expression and translation in vivo by integrating regulatory inputs from transcription, and post-transcriptional regulation: miRNA, uORF, RNAbinding protein, stabilizing and destabilizing sequences and codon optimality

  1. -The regulatory motifs and the RNA binding proteins that control translation, transcription and mRNA decay during development.

  1. -RNA structure in vivo combining high throughput sequencing and genetics in vertebrate model systems.

  1. -Epigenetic regulation during embryonic development

The Giraldez laboratory provides an integrated environment for computational biologists and experimental biologists to develop these projects.

Applicants require a strong background in Bioinformatics, machine learning, sequence analysis, statistics and programming.  Currently there are three other computational biologists in the Giraldez laboratory.


Please e-mail CV, summary and relevance of your current research (500 word max), why you are interested in the giraldez lab (200 word max) and names of three references to:

Include “Computational Biology postdoctoral applicant” in the subject of the email

These are some of the papers recently published by the laboratory relevant to these topics:

  1. 1.Johnstone TG, Bazzini AA, Giraldez AJ. Upstream ORFs are prevalent translational repressors in vertebrates. EMBO J. 2016 Feb 19. pii: e201592759.

  2. 2.Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC, Giraldez AJ. Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation.EMBO J. 2014 May 2;33(9):981-93.

  3. 3.Lee MT*, Bonneau AR*, Takacs CM, Bazzini AA, Divito KR, Fleming ES, Giraldez AJ Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition. Nature. 2013 Sep 22. 

  4. 4.Bazzini AA, Lee MT, Giraldez AJ‡. Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish. Science 13 April 2012: 233-237.

  5. 5.Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson N, Wolfe S, Giraldez AJ‡. A novel miRNA processing pathway independent of Dicer requires Argonaute2. Science. 2010, Jun 25

  6. 6.Giraldez AJ‡, Mishima Y, Rihel J, Grocock R, van Dongen S, Inoue, K, Enright A, and Schier AF‡. Zebrafish miR-430 promotes deadenylation and clearance of maternal mRNAs. Science. 2006 Apr 7