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Federico Morán

Bio: Federico Morán is an academic researcher from Complutense University of Madrid. The author has contributed to research in topics: Circular dichroism & Self-organizing map. The author has an hindex of 22, co-authored 88 publications receiving 3152 citations. Previous affiliations of Federico Morán include NASA Astrobiology Institute & Spanish National Research Council.


Papers
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Journal ArticleDOI
TL;DR: An optimized self-organizing map algorithm has been used to obtain protein topological (proteinotopic) maps and analysis of the proteinotopic map reveals that the network extracts the main secondary structure features even with the small number of examples used.
Abstract: An optimized self-organizing map algorithm has been used to obtain protein topological (proteinotopic) maps. A neural network is able to arrange a set of proteins depending on their ultraviolet circular dichroism spectra in a completely unsupervised learning process. Analysis of the proteinotopic map reveals that the network extracts the main secondary structure features even with the small number of examples used. Some methods to use the proteinotopic map for protein secondary structure prediction are tested showing a good performance in the 200-240 nm wavelength range that is likely to increase as new protein structures are known.

1,010 citations

Journal ArticleDOI
TL;DR: A computational study of protein folding predicts that proteins in Buchnera, as well as proteins of other intracellular bacteria, are generally characterized by smaller folding efficiency compared with proteins of free living bacteria.
Abstract: We have sequenced the genome of the intracellular symbiont Buchnera aphidicola from the aphid Baizongia pistacea. This strain diverged 80–150 million years ago from the common ancestor of two previously sequenced Buchnera strains. Here, a field-collected, nonclonal sample of insects was used as source material for laboratory procedures. As a consequence, the genome assembly unveiled intrapopulational variation, consisting of ≈1,200 polymorphic sites. Comparison of the 618-kb (kbp) genome with the two other Buchnera genomes revealed a nearly perfect gene-order conservation, indicating that the onset of genomic stasis coincided closely with establishment of the symbiosis with aphids, ≈200 million years ago. Extensive genome reduction also predates the synchronous diversification of Buchnera and its host; but, at a slower rate, gene loss continues among the extant lineages. A computational study of protein folding predicts that proteins in Buchnera, as well as proteins of other intracellular bacteria, are generally characterized by smaller folding efficiency compared with proteins of free living bacteria. These and other degenerative genomic features are discussed in light of compensatory processes and theoretical predictions on the long-term evolutionary fate of symbionts like Buchnera.

501 citations

Journal ArticleDOI
TL;DR: Small-angle x-ray solution scattering (SAXS) is analyzed with a new method to retrieve convergent model structures that fit the scattering profiles, and the low-resolution solution structure of lysozyme has been directly modeled from its experimental SAXS profile.

270 citations

Journal ArticleDOI
TL;DR: A system based on Kohonen's SOM (Self-Organizing Map) for protein classification according to Circular Dichroism (CD) spectra is described, and proteins with different secondary structures are clearly separated through a completely unsupervised training process.

131 citations

Journal ArticleDOI
TL;DR: A new genetic algorithm is designed which gradually explores a discrete search space and evolves convergent models made of several hundred beads best fitting the scattering profile upon Debye calculation, without geometrical constraints or penalty for loose beads.

126 citations


Cited by
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Journal ArticleDOI
TL;DR: This historical survey compactly summarizes relevant work, much of it from the previous millennium, review deep supervised learning, unsupervised learning, reinforcement learning & evolutionary computation, and indirect search for short programs encoding deep and large networks.

14,635 citations

Journal ArticleDOI
TL;DR: The work package JSpecies is examined as a user-friendly, biologist-oriented interface to calculate ANI and the correlation of the tetranucleotide signatures between pairwise genomic comparisons, and results agreed with the use of ANI to substitute DDH.
Abstract: DNA-DNA hybridization (DDH) has been used for nearly 50 years as the gold standard for prokaryotic species circumscriptions at the genomic level. It has been the only taxonomic method that offered a numerical and relatively stable species boundary, and its use has had a paramount influence on how the current classification has been constructed. However, now, in the era of genomics, DDH appears to be an outdated method for classification that needs to be substituted. The average nucleotide identity (ANI) between two genomes seems the most promising method since it mirrors DDH closely. Here we examine the work package JSpecies as a user-friendly, biologist-oriented interface to calculate ANI and the correlation of the tetranucleotide signatures between pairwise genomic comparisons. The results agreed with the use of ANI to substitute DDH, with a narrowed boundary that could be set at ≈95–96%. In addition, the JSpecies package implemented the tetranucleotide signature correlation index, an alignment-free parameter that generally correlates with ANI and that can be of help in deciding when a given pair of organisms should be classified in the same species. Moreover, for taxonomic purposes, the analyses can be produced by simply randomly sequencing at least 20% of the genome of the query strains rather than obtaining their full sequence.

4,527 citations

Journal ArticleDOI
TL;DR: In this paper, the authors describe the rules of the ring, the ring population, and the need to get off the ring in order to measure the movement of a cyclic clock.
Abstract: 1980 Preface * 1999 Preface * 1999 Acknowledgements * Introduction * 1 Circular Logic * 2 Phase Singularities (Screwy Results of Circular Logic) * 3 The Rules of the Ring * 4 Ring Populations * 5 Getting Off the Ring * 6 Attracting Cycles and Isochrons * 7 Measuring the Trajectories of a Circadian Clock * 8 Populations of Attractor Cycle Oscillators * 9 Excitable Kinetics and Excitable Media * 10 The Varieties of Phaseless Experience: In Which the Geometrical Orderliness of Rhythmic Organization Breaks Down in Diverse Ways * 11 The Firefly Machine 12 Energy Metabolism in Cells * 13 The Malonic Acid Reagent ('Sodium Geometrate') * 14 Electrical Rhythmicity and Excitability in Cell Membranes * 15 The Aggregation of Slime Mold Amoebae * 16 Numerical Organizing Centers * 17 Electrical Singular Filaments in the Heart Wall * 18 Pattern Formation in the Fungi * 19 Circadian Rhythms in General * 20 The Circadian Clocks of Insect Eclosion * 21 The Flower of Kalanchoe * 22 The Cell Mitotic Cycle * 23 The Female Cycle * References * Index of Names * Index of Subjects

3,424 citations

Book ChapterDOI
C. Stan Tsai1
14 Apr 2006

3,340 citations

Journal ArticleDOI
TL;DR: This protocol details the basic steps of obtaining and interpreting CD data, and methods for analyzing spectra to estimate the secondary structural composition of proteins.
Abstract: Circular dichroism (CD) is an excellent tool for rapid determination of the secondary structure and folding properties of proteins that have been obtained using recombinant techniques or purified from tissues. The most widely used applications of protein CD are to determine whether an expressed, purified protein is folded, or if a mutation affects its conformation or stability. In addition, it can be used to study protein interactions. This protocol details the basic steps of obtaining and interpreting CD data, and methods for analyzing spectra to estimate the secondary structural composition of proteins. CD has the advantage that measurements may be made on multiple samples containing < or =20 microg of proteins in physiological buffers in a few hours. However, it does not give the residue-specific information that can be obtained by x-ray crystallography or NMR.

3,093 citations