Master Computational Systems

PRACTICES/MASTER THESIS OFFER 2020 - 2021

Centro de Biotecnología y Genómica de Plantas
ID	Título	Tutor/es	Requisitos	Nº Plazas	Horas semanales	Horario	ESTADO
CBGP1	ESTUDIO DE LA DISTRIBUCIÓN ECOLÓGICA Y FILOGENÉTICA DE LOS SISTEMAS DE SECRECIÓN TIPO VI EN MICROBIOMAS MEDIOAMBIENTALES	Joaquin Giner Lamia	Estudiante de Máster de Biología Computacional. Conocimientos de programación en BASH, AWK, PYTHON y R. Uso de inglés fluido. Conocimientos de Filogenia, y de los sistemas de secreción en bacterias.	1	25	A convenir con el alumno	CERRADA
CBGP2	Microbiome dynamics simulations under interventions	Beatriz García Jiménez	- Computational Biology Master student - Programming knowledge in python, R and shell script	1	25	Flexible	CERRADA
CBGP3	Microbiomes prediction with Deep and Transfer Learning	Beatriz García Jiménez	- Computational Biology Master student - Programming knowledge in python, R and shell script	1	25	Flexible	CERRADA
CBGP4	Study of synthetic design parameters that maximize transgene expression in plants	Elena Caro Bernat	Estudiante de Master en Biología Computacional	1	20	Tele-trabajo a elección del estudiante
CBGP5	Inference and comparison of prokaryotic pangenomes: orthology vs sequence identity	Jaime Iranzo Sanz	Computational Biology Master student with computer programming skills (Python, C++, Matlab, etc). Knowledge of basic bioinformatic tools for comparative (meta)genomics and/or mathematical modeling is desirable, although these skills can be acquired during the training period.	1	25	A convenir	CERRADA
CBGP6	Identification of structural patterns involved in the development of allergy	María Garrido Arandia	Computational Biology Master Student Experience in Structural Bioinformatics	1	20	Tele-trabajo a elección del estudiante	CERRADA
CBGP7	Modeling epistasis and conditional selection on cancer driver mutations	Jaime Iranzo Sanz	Computational Biology Master student with strong computer programming skills (Python, C++, Matlab, etc). Familiarity with modelization and simulation of dynamical systems. Basic knowledge of linear algebra, calculus, statistics, and numerical methods is highly desirable.	1	25	A convenir	CERRADA
CBGP8	Accelerating sunflower breeding by Genomic Selection	Julio Isidro Sánchez	Master student with some background on R, bioinformatic and statistical modelling. English is mandatory.	1	25	5 horas al día	CERRADA
CBGP9	Evolutionary stasis in an antimicrobial resistance operon: a bioinformatic and experimental approach.	Alejandro Couce	Computational Biology Master student with basic bioinformatics skills (alignment software, R, Python…), motivated and curious about exploring fundamental questions in evolutionary genetics. Lab experience will be considered a plus (e.g. basic microbiology and molecular biology techniques), although if needed training will be provided by the host. Good command of scientific English, or good disposition to develop your language skills.	1	25	Flexible	CERRADA
CBGP10	Predicting the evolution of spontaneous multi-drug resistance in bacteria: a modelling approach.	Alejandro Couce	Computational Biology Master student with basic bioinformatics skills (alignment software, R, Python…), motivated and curious about exploring fundamental questions in evolutionary genetics. Modelling experience in R will be considered a plus, although if needed training will be provided by the host. Good command of scientific English, or good disposition to develop your language skills.	1	25	Flexible	CERRADA
Cluster of Excellence on Plant Sciences
ID	Título	Tutor/es	Requisitos	Nº Plazas	Horas semanales	Horario	ESTADO
CEPLAS1	Machine learning driven co-expression analysis of large-scale plant-fungal transcriptomic data	Alga Zuccaro	R, Linux and programming skills required, preferentially in Python. Genuine interest in plant microbe interactions and microbiome studies is advantageous. It is expected that the student is fluent in English.	1	Flexible	Flexible
CEPLAS2	Genome evolution in the aftermath of a host jump: comparative genomics of the fungal smut pathogen Melanopsychium pennsylvanicum with other smuts.		· Language: good written and verbal English skills. · Coding language: basic knowledge of Python Operating system: basic knowledge of Linux commands	1
CEPLAS3	Kinetic modelling of terpene synthase in specialised cells of tomato	Dr. Anna Matuszyńska	Programming skills required, preferentially in Python Strong understanding of calculus (in particular solving systems of ordinary differential equations) Genuine interest in plant biology and biochemistry is advantageous Working language: English	1
CEPLAS4	Microbiome manipulation by the soil-borne fungal plant pathogen Verticillium dahliae	Bart Thomma	· Proven proficiency in programming (e.g., Python and/or R) Basic knowledge on microbiology and/or microbial ecology	1	Flexible
CEPLAS5	Quantitative analysis and modelling of the Arabidopsis shoot apical meristem during the floral transition.	George Coupland	Experience in coding and scripting is required (most importantly Python and Matlab; C++ or C would be desirable). Some knowledge on modelling gene regulatory networks through ordinary differential equations would be helpful. It is expected that the student is fluent in English.	1	Flexible	Flexible.
CEPLAS6	Identification of transcriptional modules coordinating nutrient homeostasis in plants.	Stanislav Kopriva	Is expected that the student is fluent in English. Experience in coding and scripting is essential. Previous experience is RNA-Seq. analysis is desirable. Motivation to learn about plants is advantageous.	1	Flexible	Flexible
CEPLAS7	Discovery of cis-regulatory motifs with epigenetic signature in plants	Franziska Turck	The student should be familiar with using and adapting established bioinformatics pipelines that are used in genomics (Bowtie2/MEME suite/Homer suite/Deeptools/various R pipelines). All pipelines will be run as command line tools on the MPIPZ compute cluster. Bash scripting and writing plugins e.g. using R/Bash scripting/Python should be done autonomously, solid statistical background is a plus. The group members are mostly experimental biologists with a strong background in epigenetics, but there will be a second Master student from the University of Cologne with a data analysis project. The student can expect ample training in epigenetics, but should be rather self-sufficient in computational approaches.	1	40	9:00-18:00
Centro Nacional de Investigaciones Oncológicas
ID	Título	Tutor/es	Requisitos	Nº Plazas	Horas semanales	Horario	ESTADO
CNIO1	Predicting copy number signatures using DNA methylation status	Geoff Macintyre	Student in the Master of Computational Biology, Orientation, basic knowledge of linux; experience with python or R; basic knowledge of high-performance computing systems (e.g. slurm) and ability to work as part of a team.	1	A convenir con el alumno	A convenir con el alumno	CERRADA
Centro de Investigaciones Biológicas Margarita Salas
ID	Título	Tutor/es	Requisitos	Nº Plazas	Horas semanales	Horario	ESTADO
CSIC1	Análisis de las poblaciones microbianas presentes en el intestino de insectos	Federica Bertocchini	- Estudiante de Máster en Biología Computacional. - Conocimientos de Python, Matlab y shell script.	1	25	A convenir con el alumno	CERRADA
CSIC2	Estudios filogenéticos sobre la evolución de la resistencia a antibióticos en aislados hospitalarios	Daniel López Serrano	Estudiante de Grado Biología	1	25	A convenir con el alumno	CERRADA
CSIC3	Creación de flujos de trabajo en dinámica molecular	María Garrido Arandia	Conocimientos de programación en python	1	20	9-13
CSIC4	Análisis de datos en Biología Computacional	José Ramón Valverde Carrillo	Estudiante de Grado relacionado con Ciencias de la Vida y/o la Salud.	1	40	9-17	CERRADA
CSIC5	Análisis genómico en hongos liquenizados y su interactoma	Sergio Pérez Ortega	Grado en Biología, Máster en Biodiversidad: Conservación y Evolución, experiencia en biología molecular y conocimientos en bioinformática.	1	25		CERRADA
Centro de Tecnología Biomédica
ID	Título	Tutor/es	Requisitos	Nº Plazas	Horas semanales	Horario	ESTADO
CTB1	SEM-DISNET: Semantization of a multi-layer disease networks by reusing existing ontological approaches	Alejandro Rodríguez González	Computational Biology Master student	1	25-30h	A convenir con el alumno
CTB2	Study and integration of new biological features data from public sources in the context of human complex disease networks	Alejandro Rodríguez González	Computational Biology Master student	1	25-30h	A convenir con el alumno	CERRADA
HI-Iberia
ID	Título	Tutor/es	Requisitos	Nº Plazas	Horas semanales	Horario	ESTADO
HI1	8ai :: Proyectos de Inteligencia Artificial aplicados a la Industria	Roberto G.E. Martín	• Conocimiento básico de Machine Learning (no necesario pero valorable) • Conocimientos de librerías: scikit-learn, numpy, pandas, …	2	25h	8-14	CERRADA
IECISA
ID	Título	Tutor/es	Requisitos	Nº Plazas	Horas semanales	Horario	ESTADO
IECISA1	Desarrollo de aplicaciones para el entorno salud: Aplicación de asistencia a enfermería, con chatbot asistente integrado.	Ana Moraga Ferreira	Estudiante de Máster en Biología Computacional	1	25	8:00-13:00	CERRADA
IGBMC – University of Strasbourg
ID	Título	Tutor/es	Requisitos	Nº Plazas	Horas semanales	Horario	ESTADO
IGBMC1	Modeling Gene Regulation with an Interpretable Variational Autoencoder	Nacho Molina	Enrolling in a Master in Computer Science, Computational Biology, Biophysics or similar will be required. Very good programming skills will be expected. Good background in mathematics will be a plus. Prior knowledge in biology is not required but certain degree of curiosity to learn new fields will be desirable.	1	35	TBD
Instituto Nacional de Investigación en Salud y Medicina de Francia
ID	Título	Tutor/es	Requisitos	Nº Plazas	Horas semanales	Horario	ESTADO
INSERM1	Machine-learning scoring functions for structure-based virtual screening	Pedro Ballester	The ideal candidate will be: · Skilled in the implementation of python (numPy/SciPy/scikit-learn) scripts for scientific data analysis. · Previously exposed to supervised learning algorithms. · Familiar with open-source chemoinformatics toolkits (e.g. RDKit) and medicinal chemistry databases (e.g. ChEMBL). Trained in structural bioinformatics and/or computational drug design		35
Universidad Carlos III de Madrid
ID	Título	Tutor/es	Requisitos	Nº Plazas	Horas semanales	Horario	ESTADO
UC3M1	Análisis bioinformático e integrativo de la respuesta metabolómica y transcriptómica al tratamiento con MSCs de pacientes con Epidermolisis Bullosa Distrófica Recesiva	Carlos León Canseco	Estudiante de Máster de Biología Computacional. Conocimientos de tecnologías ómicas (transcriptómica y metabolómica), y de terapias biomédicas avanzadas (medicina traslacional). Conocimientos de programación en R.	1	25	A convenir
Universidad Complutense de Madrid
ID	Título	Tutor/es	Requisitos	Nº Plazas	Horas semanales	Horario	ESTADO
UCM1	Computational Model-Data Integration in Physical Biology	FRANCISCO MONROY MUÑOZ / HORACIO LOPEZ MENENDEZ	Grado en Ciencias o Ingeniería, Orientación biofísica y/o biología computacional. Informática: Conocimientos de programación en MATLAB y/o MATHEMATICA	1
UCM2	Computational tool for monitoring the cellular nucleus activity.	FRANCISCO MONROY MUÑOZ / HORACIO LOPEZ MENENDEZ	Grado en Ciencias o Ingeniería, Orientación biofísica y/o biología computacional. Informática: Conocimientos de programación en MATLAB y/o MATHEMATICA	1			CERRADA
UCM3	Holographic Optical Tweezers for controlling the cellular cycle Pinzas ópticas holográficas para controlar el ciclo celular	FRANCISCO MONROY MUÑOZ / HORACIO LOPEZ MENENDEZ	Grado en Ciencias o Ingeniería, Orientación biofísica y/o biología computacional. Informática: Conocimientos de programación en MATLAB y/o MATHEMATICA	1
UCM4	Modelado predictivo de complicaciones derivadas de preeclamsia en madres gestantes a partir de datos clínicos	José Luis Ayala Rodrigo	Estudiante de máster. Conocimientos de bioinformática, programación, inglés. Capacidad de trabajo en equipo.	1	15	9:00-12:00, o 15:00-18:00	CERRADA
UCM5	Detección de alteraciones cognitivas en Esclerosis Múltiple a partir de Imágenes de Resonancia Magnética	José Luis Ayala Rodrigo	Estudiante de máster. Conocimientos de bioinformática, programación, inglés. Capacidad de trabajo en equipo.	1	15	9:00-12:00, o 15:00-18:00	CERRADA
UCM6	Study of the contribution of phylogenetic and environmental factors on the trait diversity of flower and pollinator-associated microorganisms.	Sergio Álvarez Pérez	Students of the Master Program on Computational Biology. Previous knowledge on R/Python programming and machine learning. Proficiency in English. It is expected that the students will maintain frequent communication (e.g. by email and/or Skype) with the supervisor at UCM.	2	A convenir	A convenir	CERRADAS1/2
Universidad de Córdoba
ID	Título	Tutor/es	Requisitos	Nº Plazas	Horas semanales	Horario	ESTADO
UC1	Bioinformatic analysis of hemiptera insects present in the olea europea population in Andalusia	Antonio Rodríguez Franco / Meelad Yousef Yuosef	Student in the Grade of ……., Orientation, course…. A degree with a student having knowledge and skills on bioinformatics and basic System Biology	1	25	9:00-14:00	CERRADA