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Jose Sergio Hleap

Jose Sergio Hleap
SHARCNET

Ph.D.

About

30
Publications
57,337
Reads
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106
Citations
Citations since 2016
8 Research Items
76 Citations
20162017201820192020202120220510152025
20162017201820192020202120220510152025
20162017201820192020202120220510152025
20162017201820192020202120220510152025
Introduction
My main interest is understanding evolution. I work with quantitative genetics, population genetics, molecular biology, and phylogeny of elasmobranches, as well as with protein structure evolution, trying to assess the modular evolution of protein structures. I was involved in theoretical human population genetics, GWAS, IBD mapping and Admixture mapping as well as with environmental DNA and evolutionary Genomics at McGill university. I am interested in most aspects of bioinformatics.
Additional affiliations
July 2016 - present
McGill University
Position
  • PostDoc Position
Description
  • Postdoc in theorethical population genetics
March 2016 - July 2016
Fisheries and Oceans Canada
Position
  • Research Associate
Description
  • Based at the Bedford Institute of Oceanography and Dalhousie University.
September 2015 - December 2015
Dalhousie University
Position
  • Co-Lecturer
Description
  • Developing course material, evaluation and lecturing of Bioinformatics (CSCI 4180 / CSCI 6801) in the Computer Science Faculty. The course is a fourth year / Graduate course. My contribution was on metabolic network analysis.
Education
September 2010 - December 2015
Dalhousie University
Field of study
  • Biochemistry and molecular biology
August 2007 - June 2010
August 1999 - June 2005

Publications

Publications (30)
Article
Full-text available
Assessing protein modularity is important to understand protein evolution. Still the question of the existence of a sub-domain modular architecture remains. We propose a graph-theory approach with significance and power testing to identify modules in protein structures. In the first step, clusters are determined by optimizing the partition that max...
Article
Full-text available
Community structure detection is an important tool in graph analysis. This can be done, among other ways, by solving for the partition set which optimizes the modularity scores . Here it is shown that topological constraints in correlation graphs induce over-fragmentation of community structures. A refinement step to this optimization based on Line...
Article
Full-text available
Protein structures can be conceptualized as context-aware self-organizing systems. One of its emerging properties is a modular architecture. Such modular architecture has been identified as domains and defined as its units of evolution and function. However, this modular architecture is not exclusively defined by domains. Also, the definition of a...
Article
Full-text available
The 5S rDNA gene is a non-coding RNA that can be found in two copies (type I and type II) in bony and cartilaginous fish. Previous studies have pointed out that type II gene is a paralog derived from type I. We analyzed the molecular organization of 5S rDNA type II in elasmobranchs. Although the structure of the 5S rDNA is supposed to be highly con...
Article
Efforts to build representative studies are defeated when scientists discard data from certain groups. Instead, researchers should work to balance statistical needs with fairness. Efforts to build representative studies are defeated when scientists discard data from certain groups. Instead, researchers should work to balance statistical needs with...
Article
Full-text available
The Glycoside Hydrolase Family 13 (GH13) is both evolutionarily diverse and relevant to many industrial applications. Its members hydrolyze starch into smaller carbohydrates and members of the family have been bioengineered to improve catalytic function under industrial environments. We introduce a framework to analyze the response to selection of...
Data
Supplementary note. Supplementary methods (A) and results (B) testing the feasibility of the of the linear mixed model and Bayesian mixed model implementations. (PDF)
Data
Fitness surface of the MD simulations in the 34 structures dataset. Fitness in the Z axis is defined as ΔG°^. (PNG)
Preprint
Full-text available
A phenotype is defined as an organism's physical traits. In the macroscopic world, an animal's shape is a phenotype. Geometric morphometrics (GM) can be used to analyze its shape. Let's pose protein structures as microscopic three dimensional shapes, and apply principles of GM to the analysis of macromolecules. In this paper we introduce a way to 1...
Preprint
Full-text available
The Glycoside Hydrolase Family 13 (GH13) is both evolutionary diverse and relevant to many industrial applications. Its members perform the hydrolysis of starch into smaller carbohydrates. Members of the family have been bioengineered to improve catalytic function under industrial environments. We introduce a framework to analyze the response to se...
Preprint
Full-text available
Glycoside Hydrolase Family 13 (GH13) structures are responsible for the hydrolysis of starch into smaller carbohydrates. They important in industrial applications and evolutionary studies. This family has been thoroughly documented in the the Carbohydrate-Active enZYmes Database (CAZY), and divided into subfamilies based mainly in sequence informat...
Article
Full-text available
In order to investigate zoogeographical patterns of the marine elasmobranch species of Colombia, species richness of the Pacific and Caribbean and their subareas (Coastal Pacific, Oceanic Pacific, Coastal Caribbean, Oceanic Caribbean) was analyzed. The areas shared 10 families, 10 genera and 16 species of sharks, and eight families, three genera an...
Conference Paper
Assessing protein modularity is important to understand protein evolution. We propose a graph-theory approach with significance and power testing to identify sub-domain architecture (SDA). 1) clusters are determined by maximizing the modularity score; 2) clusters are tested for significance. We present here a methodology to identify SDA robustly, b...
Conference Paper
Full-text available
A central strategy in structural biology is to find the optimal alignment for a set of many homologous protein structures. This task is not trivial and is still not particularly scalable to large datasets. Several structural alignment programs have been developed in the last few years. They mainly differ on the definition of homology or the optimiz...
Article
Full-text available
Urotrygon rogersi is a stingray of the order Myliobatiformes, with benthic habits and trophic preference for crustaceans, is frequently caught in trawling fisheries. Such frequency could change the morphometric relationships (possible associations between variables) in this species; therefore, the 41 morphometric variables more commonly used in bat...
Article
Full-text available
Urotrygon rogersi is a stingray of the order Myliobatiformes, with benthic habits and trophic preference for crustaceans, is frequently caught in trawling fisheries. Such frequency could change the morphometric relationships (possible associations between variables) in this species; therefore, the 41 morphometric variables more commonly used in bat...
Conference Paper
Full-text available
There is a relationship between function, stability and the evolutionary process. One barrier to establish this relationship is to define functional and evolutionary units, or module in 3D data. It is possible to evaluate the correlation of residues across a sample of aligned homologous structures. Here, we define an evolutionary module as a subset...
Conference Paper
Full-text available
Defining modules in biological datasets is of increase interest in several branches of biological and medical sciences. Here, an evolutionary module is defined as a subset of landmarks that correlate significantly more with each other, than to the rest of the configuration (i.e. shape), in a evolutionary sampling (sampling across a phylogenetic tre...
Conference Paper
Full-text available
Domains are commonly regarded as coarse grained evolutionary units of protein structures. The next lower level is that of residues. Here, we propose a robust and rigorous analysis of evolutionary modules in protein structures. Our test system is α-Amylase, a TIM-barrel protein with a wide sample of homologous structures. We demonstrate that there a...
Conference Paper
Full-text available
We define here modules as substructures which shape variation across samples of homologous proteins is significantly small. These modules are relevant to the understanding of the interdependence across sites in evolving proteins folds. Our approach is inspired by the analysis of shapes in geometric morphometric, but applied to molecular data in 3 d...
Chapter
Full-text available
Article
Full-text available
Se describe la ontogenia y la esporogénesis en H. brevifolia, en material recolectado en el Parque Nacional Natural El Cocuy (Boyacá-Colombia) a 4200m de altitud. Los esporangios se desarrollan de forma basípeta sobre el eje caulinar: los iniciales y juveniles se localizan en el ápice y los adultos a maduros, en la base. El desarrollo se inicia a p...
Article
Full-text available
Huperzia brevifolia is one of the dominant species of the genus Huperzia living in paramos and superparamos from the Colombian Andes. A detailed study of the sporangium's ontogeny and sporogenesis was carried out using specimens collected at 4200m above sea level, in Parque Natural Nacional El Cocuy, Colombia. Small pieces of caulinar axis bearing...
Article
Full-text available
Conservation of tissue samples and quality of the DNA are crucial for the molecular techniques to work properly. For this reason, the standardization of the methods for tissue preservation and DNA extraction is basic, considering the availability of resources and its replicability. Five tissue preservation methods, two tissue types and five extract...

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Projects

Projects (3)
Project
We are about to release SPOCK, a bioinformatics tool which aims to facilitate the accurate identification of gene orthologs and their manual curation during functional annotation of genomes. In this protocol, we have combined state-of-the-art tools and designed decision-making-algorithms that provide the most relevant information for a set of query proteins in a scientifically rigorous, time efficient and unsupervised manner.
Project
To identify functional and structural modules in protein structures
Project
This project involve the annotation of two genome assemblies based Illumina Hi-seq reads.