laboratory of computational biology

Our resources BARLEYMAP
footprintDB
3d-footprint logo
TFmodeller
more

blog: #!/perl/bioinfo

postal address
Laboratorio de Biología Computacional, Estación Experimental de Aula Dei / CSIC, Av. Montañana 1.005, 50059 Zaragoza (Spain)

phone (+34) 976716089

public transport logohow to get here
bicilogo rutas en bicicleta de Zaragoza al campus de Aula Dei
Research topics/objetivos del labo
  • genomics and transcriptional regulation of grasses, in collaboration with Ana Casas, Ernesto Igartua and Pilar Catalán
  • evolutionary and structural analysis of transcription factors and disordered proteins in plants
  • phylogenomic analyses and markers for breeding, molecular diagnostics and metagenomics, in collaboration with Pablo Vinuesa (UNAM,México)
interface annotation in footDB

Annotation of interface residues in footprintDB.

interfaces of R2R3 MYB TFs

(A) Sequence logos of the R2 and R3 recognition α-helices of Arabidopsis thaliana R2R3-MYB DBD subgroups (left) and of the bound cis-elements assayed on the Y1H experiments, classified into two groups (right).

BARLEYMAP pipeline

BARLEYMAP pipeline

plant disorder

Distribution of predicted disordered segments with length>30 in plants. Disorder in chloroplast (Cp), mitochondria (Mt) and nuclear (Nu) proteomes are shown.

footprint logo of restriction enzyme BamHI

footprint of dimeric complex 2bam_AB
(enzyme BamHI)

active transcriptional subnetworks in Escherichia coli

A few active transcriptional subnetworks in Escherichia coli (details here)

ML tree of plant-like FADS proteins

ML tree of plant-like FADS proteins (details here)

Multiple interface alignment of zinc fingers

Multiple interface alignment of zinc fingers (details here)

flowchart of DNAPROT footprint algorithm

DNAPROT algorithm (details here)

3D-fooprint of a comparative model of Escherichia coli FNR

structure-based position weight matrix for Escherichia coli FNR, modelled with TFmodeller
(read more here)

TFmodeller homology model of a protein-DNA complex

comparative model of a protein-DNA complex
(read more here)

evolutionary correlation between binding specificity and regulatory role in Bacteria

conceptual model of evolutionary role of binding specificity in bacterial regulatory networks
(read more here)

alpha parameter and codon usage table primers4clades benchmark

genomic benchmark of primers4clades
(read more here)

phylogenetic congruence heatmap

congruence of tree topologies derived from single and concatenated loci of Bradyrhizobium
(read more here)

flowchart of fragment-based homology modelling

benchmark of fragment-based comparative modelling approaches
(read more here)