Jorge Finke
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View article: Unraveling Plant Recombination Patterns: Insights From Genome k‐mers
Unraveling Plant Recombination Patterns: Insights From Genome k‐mers Open
Crossover recombination is a pivotal event that takes place during meiosis of germinal cells, leading to the rearrangement of parental chromosomes and generating novel allele combinations, thereby enhancing genetic diversity. This process …
View article: Assessing drought stress in sugarcane with gene expression and phenomic data using CSI-OC
Assessing drought stress in sugarcane with gene expression and phenomic data using CSI-OC Open
Sugarcane, a prominent global crop utilized for sugar, bioethanol, and renewable bioenergy production, holds significant importance in Colombia. In 2022, it contributed to the production of 2.1 million tons of sugar, 347 million liters of …
View article: Methylomes as key features for predicting recombination in some plant species
Methylomes as key features for predicting recombination in some plant species Open
Knowing how chromosome recombination works is essential for plant breeding. It enables the design of crosses between different varieties to combine desirable traits and create new ones. This is because the meiotic crossovers between homolo…
View article: Prediction of crossover recombination using parental genomes
Prediction of crossover recombination using parental genomes Open
Meiotic recombination is a crucial cellular process, being one of the major drivers of evolution and adaptation of species. In plant breeding, crossing is used to introduce genetic variation among individuals and populations. While differe…
View article: Corrigendum: The ÓMICAS alliance, an international research program on multi-omics for crop breeding optimization
Corrigendum: The ÓMICAS alliance, an international research program on multi-omics for crop breeding optimization Open
[This corrects the article DOI: 10.3389/fpls.2022.992663.].
View article: Gene Expression Datasets for Two Versions of the Saccharum spontaneum AP85-441 Genome
Gene Expression Datasets for Two Versions of the Saccharum spontaneum AP85-441 Genome Open
Sugarcane is a species of tall grass with high biomass and sucrose production, and the world’s largest crop by production quantity. Its evolutionary environment adaptation and anthropogenic breeding response have resulted in a complex auto…
View article: Methylation in the CHH Context Allows to Predict Recombination in Rice
Methylation in the CHH Context Allows to Predict Recombination in Rice Open
DNA methylation is the most studied epigenetic trait. It is considered a key factor in regulating plant development and physiology, and has been associated with the regulation of several genomic features, including transposon silencing, re…
View article: The ÓMICAS alliance, an international research program on multi-omics for crop breeding optimization
The ÓMICAS alliance, an international research program on multi-omics for crop breeding optimization Open
The OMICAS alliance is part of the Colombian government’s Scientific Ecosystem, established between 2017-2018 to promote world-class research, technological advancement and improved competency of higher education across the nation. Since t…
View article: Hierarchy exploitation to detect missing annotations on hierarchical multi-label classification
Hierarchy exploitation to detect missing annotations on hierarchical multi-label classification Open
The availability of genomic data has grown exponentially in the last decade, mainly due to the development of new sequencing technologies. Based on the interactions between genes (and gene products) extracted from the increasing genomic da…
View article: Feature extraction with spectral clustering for gene function prediction using hierarchical multi-label classification
Feature extraction with spectral clustering for gene function prediction using hierarchical multi-label classification Open
View article: Feature extraction using Spectral Clustering for Gene Function Prediction using Hierarchical Multi-label Classification
Feature extraction using Spectral Clustering for Gene Function Prediction using Hierarchical Multi-label Classification Open
Gene annotation addresses the problem of predicting unknown associations between gene and functions (e.g., biological processes) of a specific organism. Despite recent advances, the cost and time demanded by annotation procedures that rely…
View article: A top-down supervised learning approach to hierarchical multi-label classification in networks
A top-down supervised learning approach to hierarchical multi-label classification in networks Open
View article: Identifying stress responsive genes using overlapping communities in co-expression networks
Identifying stress responsive genes using overlapping communities in co-expression networks Open
View article: Measuring event concentration in empirical networks with different types of degree distributions
Measuring event concentration in empirical networks with different types of degree distributions Open
Measuring event concentration often involves identifying clusters of events at various scales of resolution and across different regions. In the context of a city, for example, clusters may be characterized by the proximity of events in th…
View article: Characterizing the head of the degree distributions of growing networks
Characterizing the head of the degree distributions of growing networks Open
The analysis in this paper helps to explain the formation of growing networks with degree distributions that follow extended exponential or power-law tails. We present a generic model in which edge dynamics are driven by a continuous attac…
View article: Spectral Evolution with Approximated Eigenvalue Trajectories for Link\n Prediction
Spectral Evolution with Approximated Eigenvalue Trajectories for Link\n Prediction Open
The spectral evolution model aims to characterize the growth of large\nnetworks (i.e., how they evolve as new edges are established) in terms of the\neigenvalue decomposition of the adjacency matrices. It assumes that, while\neigenvectors …
View article: Spectral Evolution with Approximated Eigenvalue Trajectories for Link Prediction
Spectral Evolution with Approximated Eigenvalue Trajectories for Link Prediction Open
The spectral evolution model aims to characterize the growth of large networks (i.e., how they evolve as new edges are established) in terms of the eigenvalue decomposition of the adjacency matrices. It assumes that, while eigenvectors rem…
View article: Algorithmic Analysis of Blockchain Efficiency with Communication Delay
Algorithmic Analysis of Blockchain Efficiency with Communication Delay Open
A blockchain is a distributed hierarchical data structure. Widely-used applications of blockchain include digital currencies such as Bitcoin and Ethereum. This paper proposes an algorithmic approach to analyze the efficiency of a blockchai…
View article: A Random Network Model for the Analysis of Blockchain Designs with Communication Delay
A Random Network Model for the Analysis of Blockchain Designs with Communication Delay Open
This paper proposes a random network model for blockchains, a distributed hierarchical data structure of blocks that has found several applications in various industries. The model is parametric on two probability distribution functions go…
View article: Lyapunov–based Anomaly Detection in Preferential Attachment Networks
Lyapunov–based Anomaly Detection in Preferential Attachment Networks Open
Network models aim to explain patterns of empirical relationships based on mechanisms that operate under various principles for establishing and removing links. The principle of preferential attachment forms a basis for the well-known Bara…
View article: Community-Based Event Detection in Temporal Networks
Community-Based Event Detection in Temporal Networks Open
View article: Estimating formation mechanisms and degree distributions in mixed attachment networks
Estimating formation mechanisms and degree distributions in mixed attachment networks Open
Our work introduces an approach for estimating the contribution of attachment\nmechanisms to the formation of growing networks. We present a generic model in\nwhich growth is driven by the continuous attachment of new nodes according to\nr…
View article: Community-Based Event Detection in Temporal Networks
Community-Based Event Detection in Temporal Networks Open
This dataset contains daily tweets ids during April 2013. This is provided to facilitate reproducibility of results presented in the following paper: Pablo Moriano, Jorge Finke, and Yong-Yeol Ahn. "Community-Based Event Detection in Tempor…
View article: Community-Based Event Detection in Temporal Networks
Community-Based Event Detection in Temporal Networks Open
This dataset contains daily tweets ids during April 2013. This is provided to facilitate reproducibility of results presented in the following paper: Pablo Moriano, Jorge Finke, and Yong-Yeol Ahn. "Community-Based Event Detection in Tempor…
View article: Small-World Networks of corruption
Small-World Networks of corruption Open
Collective behavior forms and spreads through social contact. This thesis introduces a framework for understanding how the structure of social ties may impact the evolution of bribery. We represent relationships as highly clustered network…