Robersy Sanchez

Robersy Sanchez
Pennsylvania State University | Penn State · Department of Biology

See: http://orcid.org/0000-0002-5246-1453

About

67
Publications
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Introduction
To get better understanding of the evolutionary process and the genomic architecture, my research work in mathematical biology has been focused on the creation and development of the genome algebras, which resulted in several peer-reviewed publications about the subject. My mathematical biology studies have been extended to the field of Epigenomics. The creation of the theory on the information thermodynamic of cytosine DNA methylation (ITCDM) resulted from the collaborative research with Prof. Sally Mackenzie (Penn State). Results has been summarized (so far) in two published papers and implemented into a R package named Methyl-IT. Website: https://genomaths.com/

Publications

Publications (67)
Article
Full-text available
Crop resilience and yield stability are complex traits essential for food security. Sorghum bicolor is an important grain crop that shows promise for its natural resilience to drought and potential for marginal land production. We have developed sorghum lines in the Tx430 genetic background suppressed for MSH1 expression as a means of inducing de n...
Article
Full-text available
MSH1 is a plant-specific protein. RNAi suppression of MSH1 results in phenotype variability for developmental and stress response pathways. Segregation of the RNAi transgene produces non-genetic msh1 ‘memory’ with multi-generational inheritance. First-generation memory versus non-memory comparison, and six-generation inheritance studies, identifies...
Article
Full-text available
Genome-wide DNA methylation and gene expression are commonly altered in pediatric acute lymphoblastic leukemia (PALL). Integrated network analysis of cytosine methylation and expression datasets has the potential to provide deeper insights into the complex disease states and their causes than individual disconnected analyses. With the purpose of id...
Article
Full-text available
Advances in the study of human DNA methylation variation offer a new avenue for the translation of epigenetic research results to clinical applications. Although current approaches to methylome analysis have been helpful in revealing an epigenetic influence in major human diseases, this type of analysis has proven inadequate for the translation of...
Article
Full-text available
INFLUENCIA DE DIFERENTES MÉTODOS DE PLANTACIÓN EN LA INCIDENCIA DE LAS PUDRICIONES RADICALES DE LA YUCA (Manihot esculenta Crantz). RESUMEN La yuca forma parte del grupo de raíces y tubérculos que la población cubana denomina "viandas" y existe en Cuba desde épocas precolombinas; su elevado valor energético, destacada adaptabilidad a diferentes con...
Preprint
Full-text available
Genome-wide DNA methylation and gene expression are commonly altered in pediatric acute lymphoblastic leukemia (PALL). Integrated analysis of cytosine methylation and expression datasets has the potential to provide deeper insights into the complex disease states and their causes than individual disconnected analyses. Studies of protein-protein int...
Data
Figure S2 Gene expression changes and ReviGO terms associated with soybean severe MSH1‐RNAi lines.
Data
Figure S4 Schematic representation of crossing scheme in msh1 derived epigenetic breeding.
Data
Figure S5 Bar graph showing reduction in MSH1‐derived enhanced growth in epi F2:6.
Data
Figure S7 Reaction norm and AMMI plots showing grouping of epi‐F2:4 and wild type sub‐lines across four different environments.
Data
Figure S8 Genetic distance profiles using SNPs from transcriptome data of wild type and epi‐lines.
Data
Table S1 Spreadsheet containing differentially expressed genes in mild and severe soybean MSH1‐RNAi.
Data
Figure S1 Classification of MSH1 memory phenotypes into extreme (eMSH1), intermediate (iMSH1) and normal phenotype (nMSH1).
Data
Figure S3 Transcriptome changes in soybean MSH1‐RNAi lines and cross species comparison of MSH1‐RNAi gene expression changes.
Data
Figure S6 MSH1‐derived enhanced growth in S2 progenies of wild type scion grafted onto MSH1‐RNAi and msh1 memory rootstock.
Data
Table S3 Spreadsheet containing enriched GO terms for DEGs in soybean severe MSH1‐RNAi, tomato extreme MSH1‐RNAi, and Arabidopsis MSH1 T‐DNA insertion mutant.
Data
Table S7 Summary of variance components for total yield in wild type and epi‐F2:4 populations.
Data
Table S2 Significant GO term enrichment from DEGs in mild and severe soybean MSH1‐RNAi.
Data
Table S4 Summary of phenotypic data analysis for number of pods per plant, number of seeds per plant, seed weight, 100 seed weight, flowering time, and maturity time in reciprocal epi‐F2 population in the greenhouse.
Data
Table S8 Test of significant difference in variance for strain and plants within strains by ANOVA in wild type sub‐lines and three different epi‐F2:4 populations from single plant measurements of plant height, number of branches, and number of pods per plant.
Data
Table S10 Spreadsheet containing DEGs in soybean MSH1 epi‐lines R‐10 and P‐37 in F2:4, F2:5 and F2:6 generation compared to respective wild type control.
Data
Figure S9 Overlap of genes and associated pathways in two epi‐lines R‐10 and P‐37 with enhanced growth.
Data
Table S5 Summary of phenotypic data analysis for number of pods per plant, days to flowering, and plant height in three epi‐F2 population compared to wild type in the greenhouse.
Data
Table S6 Summary of phenotypic data analysis for total yield, maturity, plant height, protein concentration, and oil concentration in wild type and epi‐F2:4 lines.
Data
Table S9 Table containing summary of phenotypic data analysis for total yield, maturity date, plant height, protein, and oil concentration in wild type and enhanced growth epi‐F2:5 lines.
Article
Full-text available
Plastids comprise a complex set of organelles in plants that can undergo distinctive patterns of differentiation and redifferentiation during their lifespan. Plastids localized to the epidermis and vascular parenchyma are distinctive in size, structural features and functions. These plastids are termed 'sensory' plastids, and here we show their pro...
Article
Full-text available
We have developed a novel methylome analysis procedure, Methyl-IT, based on information thermodynamics and signal detection. Methylation analysis involves a signal detection problem, and the method was designed to discriminate methylation regulatory signal from background noise induced by thermal fluctuations. Comparison with three commonly used pr...
Article
Full-text available
Epigenetic variation has been associated with a wide range of adaptive phenotypes in plants, but there exist few direct means for exploiting this variation. RNAi suppression of the plant‐specific gene, MutS HOMOLOG1 (MSH1), in multiple plant species produces a range of developmental changes accompanied by modulation of defense, phytohormone, and ab...
Method
Full-text available
Methyl-IT, a novel methylome analysis procedure based on information thermodynamics and signal detection was recently released. Methylation analysis involves a signal detection problem, and the method was designed to discriminate methylation regulatory signal from background noise induced by thermal fluctuations. Methyl-IT enhances the resolution of...
Preprint
This material is supporting information for the paper “Symmetric Group of the Genetic-Code Cubes. Effect of the Genetic-Code Architecture on the Evolutionary Process” (Sanchez 2018). The derivation of the algebraic structure of the symmetric group of the genetic-code cubes (GC, o) is given in the manuscript. A deep complexity of the quantitative re...
Article
Full-text available
The current evidence supports that the genetic code architecture is optimized to minimize the transcriptional and translational errors and to preserve amino-acid hydrophobicity during mutational events. The genetic code is mathematically equivalent to a cube inserted in the ordinary three-dimensional (3D) space, which leads to consistent phylogenet...
Preprint
Full-text available
Epigenetic variation has been associated with a wide range of adaptive phenotypes in plants, but there exist few direct means for exploiting this variation. RNAi suppression of the plant-specific gene, MutS HOMOLOG1 ( MSH1 ), in multiple plant species produces a range of developmental changes accompanied by modulation of defense, phytohormone, and...
Article
Full-text available
Background Proper regulation of nuclear-encoded, organelle-targeted genes is crucial for plastid and mitochondrial function. Among these genes, MutS Homolog 1 (MSH1) is notable for generating an assortment of mutant phenotypes with varying degrees of penetrance and pleiotropy. Stronger phenotypes have been connected to stress tolerance and epigenet...
Article
Full-text available
Cytosine DNA methylation (CDM) is a highly abundant, heritable but reversible chemical modification to the genome. Herein, a machine learning approach was applied to analyze the accumulation of epigenetic marks in methylomes of 152 ecotypes and 85 silencing mutants of Arabidopsis thaliana. In an information-thermodynamics framework, two measurement...
Article
Full-text available
Cytosine DNA methylation (CDM) is a stable epigenetic modification to the genome and a widespread regulatory process in living organisms that involves multicomponent molecular machines. Genome-wide cytosine methylation patterning participates in the epigenetic reprogramming of a cell, suggesting that the biological information contained within meth...
Conference Paper
Full-text available
Cytosine DNA methylation (CDM) is a highly abundant epigenetic heritable but reversible chemical modification to the genome. Herein, a machine learning approach, was applied to analyze the accumulation of epigenetic marks in 150 methylomes from Arabidopsis thaliana ecotypes. We hypothesize that these marks are chromosomal footprints that account fo...
Article
Full-text available
Plant phenotypes respond to environmental change, an adaptive capacity that is at least partly transgenerational. However, epigenetic components of this interplay are difficult to measure. Depletion of the nuclear-encoded protein MSH1 causes dramatic and heritable changes in plant development, and here we show that crossing these altered plants wit...
Article
The right estimation of the evolutionary distance between DNA or protein sequences is the cornerstone of the current phylogenetic analysis based on distance methods. Herein, it is demonstrated that the Manhattan distance , weighted by the evolutionary importance of the nucleotide bases in the codon, is a naturally derived metric in the standard gen...
Article
Herein, we analyze the 24 different ways of constructing a 6-dimensional binary vector space, or a 3-dimensional GF(4) − vector space of the 64 triplets of the Standard Genetic
Article
El presente trabajo tiene como objetivo fundamental corroborar la eficacia de una estrategia que combina diferentes métodos multivariados para clasificar un grupo de genotipos de plátanos (Musa spp.) y malanga (Xanthosoma spp.) a partir de la evaluación de la variables cualitativas y cuantitativas, de los rasgos que los caracterizan. El análisis de...
Article
Full-text available
A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D,A,C,G,U}, where symbol D represents one or more hypothetical bases with unspecific pairings. We hypothesized that the high degeneration of a primeval genetic code with five bases and the gr...
Article
Full-text available
Digital Signal Processing (DSP) applications in Bioinformatics have received great attention in recent years, where new effective methods for genomic sequence analysis, such as the detection of coding regions, have been devel-oped. The use of DSP principles to analyze genomic sequences requires defining an adequate representation of the nucleo-tide...
Article
A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D, G, A, U, C}, where the letter D represents one or more hypothetical bases with unspecific pairing. We hypothesized that the high degeneration of a primeval genetic code with five bases and...
Book
Full-text available
Authors had reported before two dual Boolean algebras to understand the underlying logic of the genetic code structure. In such Boolean structures, deductions have physico-chemical meaning. We summarize here that these algebraic structures can help us to describe the gene evolution process. Particularly in the experimental confrontation, it was fou...
Conference Paper
Full-text available
In this paper we investigate the usage of a clustering algorithm as a feature extraction technique to find new features to represent the protein sequence. In particular, our work focuses on the prediction of HIV protease resistance to drugs. We use a biologically motivated similarity function based on the contact energy of the amino acid and the po...
Article
Full-text available
Starting from the four DNA bases order in the Boolean lattice, a novel Lie Algebra of the genetic code is proposed. Here, the main partitions of the genetic code table were obtained as equivalent classes of quotient spaces of the genetic code vector space over the Galois field of the four DNA bases. The new algebraic structure shows strong connecti...
Article
Full-text available
Motivation: Its well known the use of electric current in the cleaning of viral diseases in plants instead a deep knowledge of this phenomenas theoretical basis is not yet available. The description of the real causes of nucleoprotein inactivation, will contribute to the optimization of further experiments in order to obtain more and more efficient...
Article
A novel algebraic structure of the genetic code is proposed. Here, the principal partitions of the genetic code table were obtained as equivalent classes of quotient spaces of the genetic code vector space over the Galois field of the four DNA bases. The new algebraic structure shows strong connections among algebraic relationships, codon assignmen...
Article
Full-text available
The Z_64-algebra of the genetic code and DNA sequences of length N was recently stated. In order to beat the limits of this structure such as the impossibility of non-coding region analysis in genomes and the impossibility of the insertions and deletions analysis (indel mutations), we have develop a cycle group structure over the of extended base t...
Article
Full-text available
By considering the energy cost of messages carried by proteins as proportional to their information content we found experimental proof that proteins from all living organisms tend to have their estimated semantic content of information per unit mass, statistically, close to a constant. Thus, in the message carried by proteins -to achieve minimum e...
Conference Paper
Authors had reported before two dual Boolean algebras to understand the underlying logic of the genetic code structure. In such Boolean structures, deductions have physico-chemical meaning. We summarize here that these algebraic structures can help us to describe the gene evolution process. Particularly in the experimental confrontation, it was fou...
Article
Full-text available
In the vector space of DNA sequences over the Galois field of the 64 codons (GF (64)), recently published, deletions and insertions (indel) could not be analyzed. Now, in order to include these kinds of mutations, we have defined a new Galois field over the set of extended triplets X1X 2X3 (C125), where Xi ∈ {O, A, C, G, U}. Taking the polynomial c...
Book
In this paper we investigate the usage of a clustering algorithm as a feature extraction technique to find new features to represent the protein sequence. In particular, our work focuses on the prediction of HIV protease resistance to drugs. We use a biologically motivated similarity function based on the contact energy of the amino acid and the po...
Article
Full-text available
A new N-dimensional vector space of DNA sequences over the Galois field of the 64 codons (GF(64)) was recently presented. Now, in order to include deletions and insertions (indel mutations), we have defined a new Galois field over the set of elements X1X2X3 (C125), where Xi belong to {O, A, C, G, C}. We have called this set, the extended triplet se...
Article
Full-text available
By considering two important factors involved in the codon-anticodon interactions, the hydrogen bond number and the chemical type of bases, a codon array of the genetic code table as an increasing code scale of interaction energies of amino acids in proteins was obtained. Next, in order to consecutively obtain all codons from the codon AAC, a sum o...
Article
Full-text available
The current understanding of supernova and gamma-ray burst events suggests important effects on the biosphere if one of more of them happened to strike the earth in the past. In this paper we evaluate the possibility that life extinctions which probably occurred due to excess of radiation occurring in the geologic past might have left a genetic sig...
Article
A Boolean structure of the genetic code where Boolean deductions have biological and physicochemical meanings was discussed in a previous paper. Now, from these Boolean deductions we propose to define the value of amino acid information in order to consider the genetic information system as a communication system and to introduce the semantic conte...
Article
This paper proposes a genetic code Boolean structure derived from hydrogen bond numbers and chemical types of bases, purines and pyrimidines. It shows that in such Boolean structure, deductions comprise physico-chemical meaning. In particular, codons with adenine as a second base coding to hydrophilic amino acids are not deductible from codons with...
Article
Full-text available
A new n-dimensional vector space of the DNA sequences on the Galois field of the 64 codons (GF(64)) is proposed. In this vector space gene mutations can be considered linear transformations or translations of the wild type gene. In particular, the set of translations that preserve the chemical type of the third base position in the codon is a subgr...
Article
Full-text available
Las estructuras boolenas del código genético constituyen modelos matemáticos minimales y muy simplificados que nos ayudan a comprender mejor la lógica subyacente del código genético. Más específicamente, estas estructuras reflejan una fuerte conexión entre los órdenes del código genético y las propiedades físico-químicas de los aminoácidos. En este...
Article
Full-text available
The algebraic structures of the genetic code are most important to obtain additional information about the semantic code and its applications. In this paper we define two dual Boolean codon lattices of the genetic code using hydrogen bond numbers and the chemical types of bases: purines and pyrimidines. The Boolean lattices reflect the role of hydr...
Article
Full-text available
A new N-dimensional vector space of DNA sequences over the Galois field of the 64 codons (GF (64)) was recently presented. Although in this vector space, gene point mutations were considered linear transformations or translations of the wild type gene, deletions and insertions (indel) could not be considered. Now, in order to include indel mutation...

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Project
MOL2NET: FROM MOLECULES TO NETWORKS, Conf. Series on Mol., Biomed. & Comput. Sci. and Eng., ISSN: 2624-5078, MDPI SciForum, Basel, Switzerland, Since 2015: https://sciforum.net/conferences?text=mol2net MOL2NET is a trans-Atlantic conference series with >10 associated congresses. These are North America-Europe inter-university congresses organized by professors hired/endowed by North America and Europe centers like: University of Minnesota (UMN), Duluth, USA; Miami Dade College (MDC), USA; University of California (UC), Irvine, USA; Virginia Commonwealth University (VCU), USA; North Dakota State University (NDSU); University of Rostock, Germany; and CNAM, CNRS, Université Paris-Sud, France, IKERBASQUE, Basque Foundation for Science, and University of Basque Country (UPV/EHU), etc. Chairperson: Humbert G. Díaz, IKERBASQUE Professor, (1) Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU , 48940, Leioa, Biscay, Spain. (2) IKERBASQUE, Basque Foundation for Science , 48011, Bilbao, Biscay, Spain. mol2net.chair@gmail.com