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XMIPP: a new generation of an open-source image processing package for electron microscopy.
X-windows based microscopy image processing package (Xmipp) is a specialized suit of image processing programs, primarily aimed at obtaining the 3D reconstruction of biological specimens from large sets of projection images acquired by transmission electron microscopy. Expand
GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information
GeneCodis is a web server application for functional analysis of gene lists that integrates different sources of information and finds modular patterns of interrelated annotations. Expand
Image processing for electron microscopy single-particle analysis using XMIPP
We describe a collection of standardized image processing protocols for electron microscopy single-particle analysis using the XMIPP software package. These protocols allow performing the entireExpand
Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization
Although three-dimensional electron microscopy (3D-EM) permits structural characterization of macromolecular assemblies in distinct functional states, the inability to classify projections fromExpand
Crystal structure of a near-full-length archaeal MCM: Functional insights for an AAA+ hexameric helicase
The minichromosome maintenance protein (MCM) complex is an essential replicative helicase for DNA replication in Archaea and Eukaryotes. Whereas the eukaryotic complex consists of 6 homologousExpand
Phylogenetic Reconstruction Using an Unsupervised Growing Neural Network That Adopts the Topology of a Phylogenetic Tree
Abstract. We propose a new type of unsupervised, growing, self-organizing neural network that expands itself by following the taxonomic relationships that exist among the sequences being classified.Expand
GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists
We present GENECODIS, a web-based tool that integrates different sources of information to search for annotations that frequently co-occur in a set of genes and rank them by statistical significance.Expand
Xmipp 3.0: an improved software suite for image processing in electron microscopy.
Xmipp is a specialized software package for image processing in electron microscopy, and that is mainly focused on 3D reconstruction of macromolecules. Expand
Nonsmooth nonnegative matrix factorization (nsNMF)
We propose a novel nonnegative matrix factorization model that aims at finding localized, part-based, representations of nonnegative multivariate data items. Expand
Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization
We present a new image registration algorithm for the alignment of histological sections that combines the ideas of B-spline based elastic registration and consistent image registration, to allow simultaneous registration of images in two directions. Expand