Care was taken to form groups balanced in terms of the students' educational background. This encouraged students to help one another.

All students

José António Almeida Costa Da Cruz


Having finished my degree in Informatics and Computer Engineering of Instituto Superior Tecnico (Lisbon) in 1996, I founded (with three other partners) a software company to explore the newborn field of Web Development.
11 years, uncountable sleepless nights, 80 employees, a wife and 2 kids later I decided to take a challenge and start a new career in the field of bioinformatics research applying to and joining the PDBC program.
From October 2008 to September 2011 we, my family and me, lived in Strasbourg where I searched for models of ncRNA structure and evolution in Eric Westhof's Lab at the Institut de biologie moléculaire et cellulaire du CNRS.
Presently I am the Head of the Scientific Computing and Software Platform, Champalimaud Neuroscience Programme

PhD Project

Supervisor: Eric Westhof

Laboratory: IBMC - Institut de biologie moléculaire et cellulaire du CNRS

University: Université de Strasbourg


Development of Evolutionary Models for Non-Coding RNAs. Université de Strasbourg (2011) pp.196. [pdf]


Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S, Das R, Ding F, Dokholyan NV, Flores SC, Huang L, Lavender CA, Lisi V, Major F, Mikolajczak K, Patel DJ, Philips A, Puton T, Santalucia J, Sijenyi F, Hermann T, Rother K, Rother M, Serganov A, Skorupski M, Soltysinski T, Sripakdeevong P, Tuszynska I, Weeks KM, Waldsich C, Wildauer M, Leontis NB, Westhof E.. RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction. RNA (2012) 18, 610-625.

Cruz JA & Westhof E. Identification and annotation of noncoding RNAs in Saccharomycotina. Comptes Rendus Biologies (2011) 334, 671-678.

Cruz JA & Westhof E. Sequence-based identification of 3D structural modules in RNA with RMDetect. Nature Methods (2011) 8, 513-519.

Cruz JA & E Westhof. The dynamic landscapes of RNA architecture. Cell (2009) 136, 604-609.

Parisien M, Cruz JA, Westhof E and Major F. New Metrics for Comparing and Assessing Discrepancies Between RNA 3D Structures and Models. RNA (2009) 15, 1875-1885.