Differences

This shows you the differences between two versions of the page.

--- start [2021/04/11 17:05]
pmoreno [People]
+++ start [2024/04/08 21:46] (current)
pmoreno [People]
@@ Line 1: / Line 1: @@
 ====== Our Group ======
-Our [[https://www.youtube.com/watch?v=v1cTNhiZ2_c | bioinformatics]] research group is located at the [[https://www.univalle.edu.co|Universidad del Valle]], Cali, Colombia. We are fascinated by microbiological and human genome questions and their complexity, and seek to contribute to their analysis and solution. We belong to the Computer Science Department ([[http://eisc.univalle.edu.co/|EISC]]) of our university, therefore our approaches are mainly informatics and computer oriented. \\ \\ Our main topics [[https://www.youtube.com/watch?v=0mqz94bRma8&t=30s|omics]][[https://www.youtube.com/watch?v=_AQMTJwLoqI|analyses]], gene finding and [[https://www.youtube.com/watch?v=gg7WjuFs8F4|protein structure prediction]], where we apply [[https://www.apd.es/tecnicas-de-la-inteligencia-artificial-cuales-son-y-para-que-se-utilizan/|artificial intelligence methods]], based on machine learning, [[https://www.youtube.com/watch?v=9RN2Wr8xvro|neural networks]] as well as data mining techniques, [[https://www.youtube.com/watch?v=ovJcsL7vyrk&t=84s|chaos theory approaches]], statistical analysis, and FPGA technology. We also work on [[https://www.youtube.com/watch?v=BC9sxqAEs2s|metagenomics]] to analyze Colombian Andean environments and human  health problems, such as breast cancer. Generally, our results include software and hardware tools which allow other users to apply our approaches to their specific context.  \\ \\ Our group is interdisciplinary, made up of professors, graduate and undergraduate students from different disciplines, especially from computer science, biology, and health sciences. That's why we feel capable to face complex problems using both: biological state-of-the-art knowledge and advanced computational methodologies.
+Our [[https://www.youtube.com/watch?v=v1cTNhiZ2_c | bioinformatics]] research group is located at the [[https://www.univalle.edu.co|Universidad del Valle]], Cali, Colombia. We are fascinated by microbiological and human genome questions and their complexity, and seek to contribute to their analysis and solution. We belong to the Computer Science Department ([[http://eisc.univalle.edu.co/|EISC]]) of our university, therefore our approaches are mainly informatics and computer oriented. \\ \\ Our main topics [[https://www.youtube.com/watch?v=0mqz94bRma8&t=30s|omics]][[https://www.youtube.com/watch?v=_AQMTJwLoqI|analyses]], gene finding and [[https://www.youtube.com/watch?v=gg7WjuFs8F4|protein structure prediction]], where we apply [[https://www.apd.es/tecnicas-de-la-inteligencia-artificial-cuales-son-y-para-que-se-utilizan/|artificial intelligence methods]], based on machine learning, [[https://www.youtube.com/watch?v=9RN2Wr8xvro|neural networks]] as well as data mining techniques, [[https://www.youtube.com/watch?v=ovJcsL7vyrk&t=84s|chaos theory approache (fractal and multifractal analysis)]], statistical analysis, and FPGA technology. We also work on [[https://www.youtube.com/watch?v=BC9sxqAEs2s|metagenomics]] to analyze Colombian Andean environments and human  health problems, such as breast cancer. Generally, our results include software and hardware tools which allow other users to apply our approaches to their specific context.  \\ \\ Our group is interdisciplinary, made up of professors, graduate and undergraduate students from different disciplines, especially from computer science, biology, and health sciences. That's why we feel capable to face complex problems using both: biological state-of-the-art knowledge and advanced computational methodologies.
 ----
 More information about our group at:\\ [[https://scienti.minciencias.gov.co/gruplac/jsp/visualiza/visualizagr.jsp?nro=00000000000759| GrupLac]], MinCiencias, Colombia.
 ====== People ======
-|[[people:people|Leaders]] | [[people:people|PhD]]| [[people:people|Master]]| [[people:people|Undergraduate]]|[[people:people|We wait for you here!]]|[[Lab´s pictures]]|
+|[[people:people|Leaders]]| [[people:people|PhD]]| [[people:people|Master]]| [[people:people|Undergraduate]]|[[people:people|We wait for you here!]]|Lab´s pictures]]
+|{{:visita_ashwin.png?200|}}\\ MFA and human genome project-2007||{{:proyecto_gebix.png?200|}}\\ GeBiX project-2012||{{:dscn6962.jpg?200|}}\\ Breast cancer and Omics I project-2015||{{:fpga.gif?200|}}\\ Human genome FPGA project-2018||{{:nature.png?200|}}\\ Cenicaña project-2018|{{:nueva_docente_velez.jpg?200|}}\\ Human gene regulation project-2018||{{:eisc-table.png?200|}}\\ EISC teachers and students-2019||{{:met_3d.png?200|}}\\ In silico antimalarial molecules project-2020||{{:protein_folding_2_.jpeg?200|}}\\ Protein folding project-2021||{{:reunion_proj_enfs_raras.jpeg?200|}}\\ Rare diseases project-2022||{{:riabio2023.jpeg?400|}}\\ RIABIO network project-2023|{{:xxxx |}}\\ Breast cancer and Omics II project-2023||{{:xxxx |}}\\ ALAN project-2023||
-|{{ :dscn6962.jpg?200 |}}\\ Omics team|{{:eisc-table.png?200|}}\\ EISC teachers and students|{{ :visita_ashwin.png?200|}}\\ Ashwin´s visit to BIMAC|{{ :soibio_2020.png?200 |}}\\ RIABIO meet|
 ====== Research Fields ======
@@ Line 65: / Line 67: @@
 <hidden>
-<hidden {{:green-expand.gif?nolink,14x14|more}} **UTILIZACIÓN DE UNA ESTRATEGIA MULTIDISCIPLINARIA PARA LA IDENTIFICACIÓN DE NUEVOS COMPUESTOS HETEROCÍCLICOS SINTÉTICOS CON ACTIVIDAD ANTIMALÁRICA (2021 - Approved)></hidden>
+<hidden {{:green-expand.gif?nolink,14x14|more}} **Análisis Ómico, Multifractal y Ancestría En Medicina Personalizada y de Precisión con Impacto en el Cáncer de Mama></hidden>
+<hidden {{:green-expand.gif?nolink,14x14|more}} **Implementación y evaluación de un modelo predictivo de asociación genómica para Enfermedades Raras basado en configuraciones de repeticiones ADN y variantes estructurales></hidden>
+<hidden {{:green-expand.gif?nolink,14x14|more}} **UTILIZACIÓN DE UNA ESTRATEGIA MULTIDISCIPLINARIA PARA LA IDENTIFICACIÓN DE NUEVOS COMPUESTOS HETEROCÍCLICOS SINTÉTICOS CON ACTIVIDAD ANTIMALÁRICA (2021 - 2024)></hidden>
 <hidden {{:green-expand.gif?nolink,14x14|more}} **Análisis de imágenes de pacientes con ca. mamario mediante IA**. Vélez PE., Spetale F., Tapia E., Moreno PA. (2021 - Sent to the RIABIO network)></hidden>
-<hidden {{:green-expand.gif?nolink,14x14|more}} ** Platform in omics sciences and breast cancer health states (Phase II) and modeling with artificial intelligence techniques.** Universidad del Cauca, Universidad del Valle; Bioinformatics and Biocomputation,(2021-Submitted)>
+<hidden {{:green-expand.gif?nolink,14x14|more}} ** Platform in omics sciences and breast cancer health states (Phase II) and modeling with artificial intelligence techniques.** Universidad del Cauca, Universidad del Valle; Bioinformatics and Biocomputation,(2021-2024)>
 Original title: "PLATAFORMA EN CIENCIAS ÓMICAS DEL CÁNCER MAMARIO, SUR-OCCIDENTE (FASE II) Y MODELAMIENTO CON TÉCNICAS DE INTELIGENCIA ARTIFICIAL ". \\ Convocatoria 890 - MinCiencias. Universidad del Valle.
 </hidden>
@@ Line 131: / Line 137: @@
 ====== Courses  ======
 <hidden>
-<hidden {{:green-expand.gif?nolink,14x14|more}} ** Herramientas computacionales de bases de datos biológicas ** > {{ :750107m_herramientas_de_bases_de_datos_biolo_gicas.png?200 |}}
+<hidden {{:green-expand.gif?nolink,14x14|more}} ** Herramientas computacionales de bases de datos biológicas ** > {{ :750107m_herramientas_de_bases_de_datos_biolo_gicas.xxx?200|}}
 </hidden>
@@ Line 166: / Line 172: @@
 <hidden {{:green-expand.gif?nolink,14x14|more}} ** Restricted Molecular Dynamics ** >
-Molecular dynamics (MC), the computer simulation of movements of atoms and molecules, is frequently applied to biomolecules (DNA or RNA sequences, proteins). Based on numerical methods, MD calculates their time-depend behavior. Generally, it is used to study the  molecule's structure and understand the dynamics of the formation, functioning and interaction. In proteomics, MD is used to analyze a protein's stability
+Molecular dynamics (MC), the computer simulation of movements of atoms and molecules, is frequently applied to biomolecules (DNA or RNA sequences, proteins). Based on numerical methods, MD calculates their time-depend behavior. Generally, it is used to study the  molecule's structure and understand the dynamics of the formation, functioning and interaction. In proteomics, MD is used to analyze a protein's stability and allows to model the complex processes a protein to perform fulfilling its function.
+The objective of this course is to provide an overview of the theoretical fundamentals of classical molecular dynamics, discuss some practical aspects and show some specific applications of energy minimization and dynamics simulation of proteins or nucleotide sequences in order to illustrate the theoretical concepts. Students will be able to deepen their understanding of principles of macromolecular structure and function, to gain practical experience in the  of molecular model construction and evaluation and to get familiar with standard MD algorithms.
+{{:dinamicamolecular.pdf|course outline}}
+<hidden see __Spanish version__  >
+** Dinámica molecular restringida. **
+Una de las herramientas para estudiar las macromoléculas de interés biológico (secuencias de
+ADN o ARN, proteínas) es la dinámica molecular. La dinámica molecular calcula el comportamiento
+de un sistema molecular en dependencia del tiempo. Este método se emplea hoy día en forma rutinaria
+para investigar la estructura y entender la dinámica en los procesos de formación, operación e interacci
+ón de estas macromoléculas. En el campo de la proteómica, se usa la dinámica molecular para
+analizar la estabilidad de una proteína, su plegamiento y sus cambios conformacionales, la interacción
+con otras proteínas u otras biomoléculas, y permite describir y modelar los procesos complejos que
+aplican las proteínas para poder cumplir con su función, como por ejemplo la unión de ligados, el
+transporte de iones y la inserción en membranas.
+El objetivo del presente curso es dar una visión general de los fundamentos teóricos de la dinámica
+molecular clásica, discutir algunos aspectos prácticos, y mostrar algunas aplicaciones específicas de
+la minimización de energía y la simulación dinámica de proteínas o secuencia de nucleótidos. Estos
+temas de aplicación acompa˜naran e ilustrarán la exposición de los conceptos teóricos a lo largo del
+curso. Se espera poder profundizar el entendimiento del estudiante en los principios de la estructura
+macromolecular y su relación con su función, generar experiencia práctica en el proceso de construcci
+ón y evaluación de modelos moleculares y familiarizar el estudiante con el uso de los algoritmos
+estándares de la dinámica molecular.</hidden> </hidden>
+<hidden {{:green-expand.gif?nolink,14x14|more}} ** Machine Learning in Bioinformatics ** >
+Machine learning (ML), a branch of artificial intelligence, comprises techniques that allow computers to learn. ML seeks to optimize a performance criterion in order to describe information contained in data. In bioinformatics, ML is able to retrieve information from the increasing biological databases. From an informatics perspective, the ML techniques are classified in different groups, among them: Classification y Clustering, Feature selection, Biological sequence analysis and phylogenetic inference.
+The proposed course applies a theoretical-practical approach. The theoretical part introduces the relevant biological and computational concepts,  explains the main ML techniques and points out biologicas problemas, where these techniques are successful. The practical part, exemplary problems are solved, based on ML software ( for example BioMall). The student should not only apply these techniques but  also draw consistent informatic and biologic conclusions. {{:aprendizajemaquina.pdf|course outline}}
+<hidden see __Spanish version__  >  ** Aprendizaje de máquina en bioinformática.**
+Aprendizaje de máquina, una rama de la inteligencia artificial, trata de las técnicas que permiten
+que los computadores aprendan. Está basado en datos y busca optimizar un criterio de desempe˜no, para
+lograr describir la información contenida en ellos. Tiene importancia especial en bioinformática, área
+que puede ser considerada como la aplicación de tecnologías de información a la biología molecular.
+La cantidad de datos biológicos almacenados en bases de datos crece exponencialmente, y la mayor
+ía de ellos está públicamente disponible. En varios campos biológicos como genómica, proteómica
+y biología de sistemas, se aplican con éxito técnicas de aprendizaje de máquina. Desde el enfoque
+informático, las técnicas de aprendizaje se pueden clasificar en grupos grandes, entre ellos los que
+son objetivos de esta asignación: Clasificación y agrupamiento, selección de características, análisis
+de secuencias biológicas e inferencia filogenética.
+La asignación propuesta tiene un enfoque teórico—práctico. En la parte teórica se introducen
+los conceptos de ambos campos involucrados, se explican las principales técnicas de aprendizaje de
+máquina y se se˜nalan los problemas bioinformáticos, donde se pueden aplicar exitosamente estas
+técnicas. La parte práctica consiste en la solución de problemas ejemplares, basado en un software de
+aprendizaje de máquina (por ejemplo BioMall), donde el estudiante, basándose en datos biológicos, no
+sólo aplica las técnicas, sino que está motivado a sacar conclusiones de tipo informático y biológico.
+</hidden></hidden>
+</hidden>
+====== Thesis ======
+|[[thesis:PhD|PhD Thesis]] | [[thesis:Master|Master Thesis]] | [[thesis:Undergraduate|Undergraduate Thesis]] | [[thesis:New|Ongoing Projects and Opportunities]] |
+====== Publications ======
+[[publications:publi_2021|2021]] | [[publications:publi_2020|2020]] | [[publications:publi_2019|2019]] | [[publications:publi_2018|2018]] | [[publications:publi_2017|2017]] | [[publications:publi_2016|2016]] |[[publications:publi_2015|2015]] | [[publications:publi_2014|2014]] | [[publications:publi_2013|2013]] | [[publications:publi_2011|2011]] | [[publications:publi_2010|2010]] | [[publications:publi_2009|2009]] | [[publications:publi_2008|2008]] | [[publications:publi_2007|2007]] | [[publications:publi_2006|2006]] | [[:publications:publi_before_2006| before 2006]] |
+====== Software  ======
+|[[software:soft_2011|2011]] | [[software:soft_before_2011|before 2011]]|
+====== Videos and Links======
+*[[https://en.wikipedia.org/wiki/Multifractal_system | Multifractal System]]\\
+*[[https://www.youtube.com/watch?v=bz3ZksC92_0  | Análisis multifractal de genomas]]\\
+*[[http://eiscapp.univalle.edu.co/omicas/ | Proyecto "ómicas" en Cáncer mamario]]\\
+*[[ http://eisc.univalle.edu.co/index.php/grupos-investigacion/bioinformatica | Bioinformatics group at EISC]]\\
+*[[http://eisc.univalle.edu.co  | Programas acadèmicos de posgrados - EISC]]\\
+*[[https://cisgebi.com/cisgebi/introduccion/  | CISGEBI]]\\
+====== Contact ======
+|Bioinformática y Biocomputación \\ \\ pedro.moreno@correounivalle.edu.co\\ Teléfono: (57) 2 3212100 Ext. 2283\\ \\ Edificio B13, Lab 3005\\ Ciudad Universitaria Meléndez\\ Calle 13 No 100-00\\ \\ Universidad del Valle \\ Cali, Colombia \\ [[https://www.timetoast.com/timelines/historia-eis-univalle| Línea de tiempo EISC]]|{{ :eisc-aero.jpeg?300|}}[[http://media.utp.edu.co/sue/archivos/V%20ENCUENTRO%20PRESENTACIONES%20PONENCIAS/SALA%201%20BLOQUE%20Y/Ponencia%2011%20Universidad%20del%20Valle%20Gestión%20de%20la%20Planta%20F%C3%ADsica.pdf|Planta física UniValle]]||{{ :captura_de_pantalla_2021-01-05_a_la_s_4.35.06_p._m..png?400|}}|

Bioinformatics Research Group at Universidad del Valle

User Tools

Site Tools

Differences

Page Tools