Osvaldo Antonio Martin

Osvaldo Antonio Martin
National Scientific and Technical Research Council | conicet · IMASL Instituto de Matemática Aplicada de San Luis

PhD
I have interest in all aspects of the Bayesian Workflow. I colaborate with 3 Python OSS projects ArviZ, Bambi and PyMC.

About

61
Publications
9,054
Reads
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670
Citations
Additional affiliations
April 2014 - present
National Scientific and Technical Research Council
Position
  • Researcher (Investigador Asistente)
December 2013 - February 2014
Northwestern University
Position
  • Researcher
April 2013 - present
Position
  • Professor (Ad Honorem)
Description
  • We offer an elective course for Molecular Biologist undergrads. The course title is "Structural Bioinformatics" and is a primer about concepts and methods used in bioinformatics and structural biology.
Education
April 2007 - March 2012
Universidad Nacional de San Luis
Field of study
  • Structural Bioinformatics

Publications

Publications (61)
Preprint
Full-text available
Bayesian additive regression trees (BART) is a non-parametric method to approximate functions. It is a black-box method based on the sum of many trees where priors are used to regularize inference, mainly by restricting trees' learning capacity so that no individual tree is able to explain the data, but rather the sum of trees. We discuss BART in t...
Article
Full-text available
Many applied disciplines have recognized problems related to the practice of data analysis within their own communities. Some of them have even declared the existence of a statistical crisis that has raised doubts about findings that were once considered well established. In biological sciences, the recognition of misuse or poor reporting of statis...
Preprint
Specification of the prior distribution for a Bayesian model is a central part of the Bayesian workflow for data analysis, but it is often difficult even for statistical experts. Prior elicitation transforms domain knowledge of various kinds into well-defined prior distributions, and offers a solution to the prior specification problem, in principl...
Book
The full text is available online bayesiancomputationbook.com/
Article
We explore how ideas and practices common in Bayesian modeling can be applied to help assess the quality of 3D protein structural models. The basic premise of our approach is that the evaluation of a Bayesian statistical model's fit may reveal aspects of the quality of a structure when the fitted data is related to protein structural properties. Th...
Preprint
Full-text available
The popularity of Bayesian statistical methods has increased dramatically in recent years across many research areas and industrial applications. This is the result of a variety of methodological advances with faster and cheaper hardware as well as the development of new software tools. Here we introduce an open source Python package named Bambi (B...
Preprint
Full-text available
On the present work, we explore how ideas and practices common in Bayesian modeling can be applied in the context of protein structure assessment. We feature two different but related types of models in this work. The first is statistical while the second is related to the 3D structure of proteins. We fit a Bayesian hierarchical linear model to exp...
Article
Full-text available
Here we propose that the upper bound marginal stability of proteins is a universal property that includes macro-molecular complexes and is not affected by molecular changes such as mutations and post-translational modifications. We theorize that its existence is a consequence of Afinsen's thermodynamic hypothesis rather than a result of an evolutio...
Article
In the present work we explore three different approaches for the computation of the one-bond spin-spin coupling constants (SSCC) 1J CαH in proteins: DFT calculation, Karplus-like equation and Gaussian Process regression. The main motivation of this work is to select the best method for a fast and accurate computation of the 1J CαH SSCC, for its us...
Article
Full-text available
The conformational space of the ribose-phosphate backbone is very complex as it is defined in terms of six torsional angles. To help delimit the RNA backbone conformational preferences, 46 rotamers have been defined in terms of these torsional angles. In the present work, we use the ribose experimental and theoretical ¹³ C′ chemical shifts data and...
Article
Full-text available
There is abundant theoretical evidence indicating that a mirror image of Protein A may occur during the protein folding process. However, as to whether such mirror image exists in solution is an unsolved issue. Here we provide outline of an experimental design aimed to detect the mirror image of Protein A in solution. The proposal is based on compu...
Preprint
Full-text available
Experimental evidence indicates that proteins are marginally stable. Unlike all previous proposals here we suggest, on a statistical thermodynamics basis, that the upper bound of the marginal stability of proteins also belongs to biomacromolecular complexes and its origin should be sought on fluctuations of the pairwise and many-body interactions o...
Article
Full-text available
Background. South America faces strong environmental pressures as a result of agriculture and infrastructure expansion and also of demographic growth, demanding immediate action to preserve natural assets by establishing protected areas. Currently, 7.1% of the (sub)continent is under strict conservation categories (I to IV, IUCN), but the spatial d...
Preprint
Full-text available
The conformational space of the ribose-phosphate backbone is very complex as is defined in terms of six torsional angles. To help delimit the RNA backbone conformational preferences 46 rotamers have been defined in terms of the these torsional angles. In the present work, we use the ribose experimental and theoretical 13C'; chemical shifts data and...
Preprint
Full-text available
There is abundant theoretical evidence indicating that a mirror image of Protein A may occur during the protein folding process. However, as to whether such mirror image exists in solution is an unsolved issue. Here we provide sound theoretical evidence indicating that the use of a mutant of protein A, namely Q10H, could be used to detect the mirro...
Preprint
Full-text available
Background South America faces strong environmental transformations due to agriculture and infrastructure expansion and due to demographic growth, demanding immediate action to preserve natural assets by means of the deployment of protected areas. Currently, 7.1% of the (sub)continent is under strict conservation categories (I to IV, IUCN), but the...
Article
Full-text available
Motivation: Chemical shifts (CS) are an important source of structural information of macromolecules such as RNA. In addition to the scarce availability of CS for RNA, the observed values are prone to errors due to a wrong re-calibration or miss assignments. Different groups have dedicated their efforts to correct CS systematic errors on RNA. Desp...
Article
Full-text available
There is a need to develop widely applicable tools to understand glycan organization, diversity and structure. We present a graph-theoretical study of a large sample of glycans in terms of finite dimension, a new metric which is an adaptation to finite sets of the classical Hausdorff "fractal" dimension. Every glycan in the sample is encoded, via f...
Article
Full-text available
Glycans are the most abundant and structurally diverse biomolecules in nature. The knowledge of the tridimensional structure of these molecules is necessary to understand in detail, at atomic level, the molecular processes in which they are involved. Chemical shifts (CS) are observables obtained from Nuclear Magnetic Resonance experiments and are h...
Article
Full-text available
Background Protected areas, regarded today as a cornerstone of nature conservation, result from an array of multiple motivations and opportunities. We explored at global and regional levels the current distribution of protected areas along biophysical, human, and biological gradients, and assessed to what extent protection has pursued (i) a balance...
Data
Background Protected areas, regarded today as a cornerstone of nature conservation, result from an array of multiple motivations and opportunities. We explored at global and regional levels the current distribution of protected areas along biophysical, human, and biological gradients, and assessed to what extent protection has pursued (i) a balance...
Article
Full-text available
Background. The establishment of protected areas, regarded today as a cornerstone of nature conservation, resulted from a multiple array of motivations and opportunities. We explore at global and regional levels, the current distribution of protected areas along biophysical, human, and biological gradients, and assess to what extent protection purs...
Preprint
Full-text available
Background. The establishment of protected areas, regarded today as a cornerstone of nature conservation, resulted from a multiple array of motivations and opportunities. We explore at global and regional levels, the current distribution of protected areas along biophysical, human, and biological gradients, and assess to what extent protection purs...
Article
Full-text available
Glycans are key molecules in many physiological and pathological processes. As with other molecules, like proteins, visualization of the 3D structures of glycans adds valuable information for understanding their biological function. Hence, here we introduce Azahar, a computing environment for the creation, visualization and analysis of glycan molec...
Data
Supplemental Information file The information provided in the Supplemental Information includes: (i) the Kernel Density Estimation of the D values for Lys and Arg (Figs. S1 and S2); (ii) the probability profile distribution to detect glycosylation of Ser, Thr and Asn (Figs. S3–S5), and (iii) the ball and stick representation of a glycan-amino acidi...
Article
Full-text available
Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new...
Article
Full-text available
Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new...
Article
Full-text available
Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new...
Article
Full-text available
Knowledge of the three-dimensional structures of glycans and glycoproteins is useful for a full understanding of molecular processes in which glycans are involved, such as antigen-recognition and virus infection, to name a few. Among the ubiquitous nuclei in glycan molecules, the 13C nucleus is an attractive candidate for computation of theoretical...
Article
Full-text available
By using local (free-energy profiles along the amino acid sequence and (13)C(α) chemical shifts) and global (principal component) analyses to examine the molecular dynamics of protein-folding trajectories, generated with the coarse-grained united-residue force field, for the B domain of staphylococcal protein A, we are able to (i) provide the main...
Article
Full-text available
The goal of this study is twofold. First, to investigate the relative influence of the main structural factors affecting the computation of the (13) C' shielding, namely, the conformation of the residue itself and the next nearest-neighbor effects. Second, to determine whether calculation of the (13) C' shielding at the density functional level of...
Article
Full-text available
A better understanding of protein aggregation is bound to translate into critical advances in several areas, including the treatment of misfolded protein disorders and the development of self-assembling biomaterials for novel commercial applications. Because of its ubiquity and clinical potential, albumin is one of the best-characterized models in...
Article
Full-text available
A method that makes use of information provided by the combination of (13)C(α) and (13)C(β) chemical shifts, computed at the density functional level of theory, enables one to (i) validate, at the residue level, conformations of proteins and detect backbone or side-chain flaws by taking into account an ensemble average of chemical shifts over all o...
Article
Full-text available
Summary: The differences between observed and predicted 13Cα chemical shifts can be used as a sensitive probe with which to detect possible local flaws in protein structures. For this reason, we previously introduced CheShift, a Web server for protein structure validation. Now, we present CheShift-2 in which a graphical user interface is implemente...
Article
Full-text available
In this work, a novel catalpol derivative (6,10,2',6'-tetraacetyl-O-catalpol), which was previously obtained by our group and shown experimentally to inhibit a type of Taq DNA polymerase, was studied in silico. Studies of the interaction of 6,10,2',6'-tetraacetyl-O-catalpol with the Klentaq fragment of the Taq DNA polymerase I from Thermus aquaticu...
Article
Full-text available
Cysteines possess a unique property among the 20 naturally occurring amino acids: it can be present in proteins in either the reduced or oxidized form, and can regulate the activity of some proteins. Consequently, to augment our previous treatment of the other types of residues, the 13Calpha and 13Cbeta chemical shifts of 837 cysteines in disulfide...
Article
Full-text available
A server (CheShift) has been developed to predict (13)C(alpha) chemical shifts of protein structures. It is based on the generation of 696,916 conformations as a function of the phi, psi, omega, chi1 and chi2 torsional angles for all 20 naturally occurring amino acids. Their (13)C(alpha) chemical shifts were computed at the DFT level of theory with...
Article
Full-text available
The room-temperature X-ray structures of ubiquitin (PDB code 1ubq) and of the RNA-binding domain of nonstructural protein 1 of influenza A virus (PDB code 1ail) solved at 1.8 and 1.9 Å resolution, respectively, were used to investigate whether a set of conformations rather than a single X-ray structure provides better agreement with both the X-ray...
Article
Full-text available
The acidic C-terminal peptides from Trypanosoma cruzi ribosomal P proteins are the major target of the antibody response in patients suffering Chagas chronic heart disease. It has been proposed that the disease is triggered by the cross-reaction of these antibodies with the second extra cellular loop of the β1-adrenoreceptor, brought about by the m...

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