Oscar Saiz

New Position Open: CryoEM Image Processing Specialist

Description: The Biocomputing Unit/Instruct Image Processing Center is looking for an image processing specialist with clear experience in the processing of cryoEM images from a variety of specimens and approaches, including Single Particle Analysis and/or Tomography. No method development experience is needed, but the candidate should be familiarized with different processing suites and also willing to keep exploring more approaches. A doctoral degree is expected, although it would not be essential considering similar practical experience

The candidate will be immersed in a vibrant community in which top image processing developers sit side by side with application specialists addressing challenging international projects in the context of the Integrative Infrastructure for Structural Biology Instruct-ERIC

Location: Madrid

Required Skills:

  • Experience in cryoEM image processing.
  • Proficiency in different software packages and workflows for cryo-electron microscopy data analysis.
  • PhD degree in a related field (Structural Biology, Bioinformatics, Engineering, Physics, etc.) or equivalent practical experience demonstrating the required technical skills

Interested candidates should send their CV’s and letter of interest to blanca@cnb.csic.es

Artificial intelligence for macromolecular analysis and pharmaceutical ligands design

What we are looking for:
We are looking for PhDs in engineering, physics, mathematics, computing science or any related scientific domain with a strong will to apply the AI methods to Structural Biology and Drug Screening. Knowledge of Python and Deep learning libraries are a must. Previous knowledge of Bioinformatics or Biology is highly appreciated, although not compulsory. The Postdoc must propose a research proposal aligned to the presented challenge.

The context:
Structural biology is key to understanding biological macromolecules like proteins and nucleic acids, crucial for biological functions and diseases. Cryo-electron microscopy (cryoEM) revolutionizes this field by visualizing macromolecules at near-atomic resolution, facilitating their study in native states. Simultaneously, computational prediction of ligand binding is vital for drug discovery, helping identify therapeutic candidates by how they interact with biomolecules. The synergy of AI tools for cryoEM and ligand prediction accelerates understanding biological systems and developing new treatments.

The problem to address:
The journey from pixelated snapshots to precise atomic models is fraught with computational hurdles, requiring a blend of innovative AI techniques and a deep understanding of molecular landscapes. Parallel to this endeavor is the quest to discover ligands that snugly fit into these newly revealed structures, a critical step in the design of new drugs. This challenge involves sifting through vast chemical libraries to find those rare molecules that can bind with high affinity to target sites on the macromolecule.

Objectives:

  • Elucidating the complex structures of biological macromolecules from CryoEM images.
  • Discover ligands that fit into the structures revealed for new drug design.

Expected Outcomes:

  • Robust algorithms and workflows to tackle both problems.

APPLY HERE
(Deadline 20 Dec 2024)

Diseño estadístico de experimentos con animales

Lugar: Centro Nacional de Biotecnología, C. Darwin, 3, Fuencarral-El Pardo, 28049 Madrid – Sala B.6

Fecha: 11 de octubre de 2024

Este evento está dirigido a los asesores estadísticos que colaboran con comités de ética en experimentación animal y tiene como objetivo explorar y mejorar las prácticas de diseño estadístico en este ámbito. Durante la reunión, discutiremos cómo optimizar los diseños experimentales a través de cursos de formación y recursos comunes. También abordaremos el uso de programas específicos para solicitantes y la creación de un foro de dudas para el diseño experimental. Además, presentaremos la plataforma 3Rs, enfocada en la reducción del uso de animales en la investigación, y exploraremos la posibilidad de organizar un curso de verano para profundizar en estos temas. Únete a nosotros para compartir experiencias, aprender y contribuir a prácticas más éticas y efectivas en la experimentación animal.

Contenido

  • Intercambio de experiencias y mejores prácticas
  • ¿Cómo se puede mejorar el diseño estadístico de los experimentos? ¿Cursos existentes? ¿Formación online asíncrona?
  • ¿Foro de dudas de diseño?
  • Recursos comunes
  • Programas que pueden usar los solicitantes
  • Curso de verano
  • Participación plataforma 3Rs (Reducción) diseño experimental

Agenda

10:00 – 10:15Presentación de la jornada
10:15 – 11:30Presentaciones de los asistentes
11:30 – 12:00Café
12:00 – 14:00Discusión

 

PhD position in Single Particle Analysis and CLEM Correlative Imaging.

Description: We are looking for a candidate with a PhD in Computer Science, Mathematics, Engineering, Physics or equivalent with software development skills, preferrably applied to Structural Biology, Biomedical Imaging, or Imaging in general.

The candidate will work on the development of image processing algorithms for Single Particle Analysis (especially, continuous heterogeneity analysis) and CLEM Correlative imaging (especially, image alignment and segmentation). The contract is for 4 years and will be developed along with Dr. Eva Nogales (from Univ. Calif. Berkeley) in the context of the JAE-CHAIR grant “ALLCRYO. Technical developments for the improvement of the cryoEM workflow, and their application for the structural characterisation of conformationally and compositionally heterogeneous samples in vitro and in vivo.

Location: Madrid

Required Skills:

  • PhD in Computer Science, Mathematics, Engineering, Physics or equivalent
  • Programming experience with Python
  • Experience in Linux
  • Experience in Structural Biology, Biomedical Imaging, General Imaging or Bioinformatics

Interested candidates should send their CV’s and letter of interest to i2pc@cnb.csic.es

PhD position in fluorescence microscopy image processing.

The Biocomputing Unit of the National Biotechnology Centre is looking for excellent master students in Engineering, Physics, Mathematics or any other field related to data analysis. The PhD would be in fluorescence microscopy image processing.

This project involves several fast-growing technologies: electron cryo-microscopy and deep learning. Our laboratory is located at the Centro Nacional de Biotecnología in Madrid, a reference institute in Spain in cryo-EM, with highly advanced fluorescence microscopy facilities. Moreover, our group is a world reference in this field. In this work we intend to follow two main lines of work:

  • Spatio-temporal analysis, which will allow a more accurate detection and quantification of dynamic phenomena at the cellular level, thus facilitating the exploration of complex biological processes in real time
  • Correlative microscopy: To implement and refine correlative microscopy techniques to efficiently integrate data obtained through different fluorescence microscopy modalities, as well as scanning electron microscopy (SEM) and transmission electron microscopy (TEM).

Latest publications

  1. Cayuela, P. Conesa, A. Oña, J.A. Gómez-Pedrero, C.O.S. Sorzano. Real-Time Correction of Chromatic Aberration in Optical Fluorescence Microscopy. Methods and Applications in Fluorescence, 11: 045001 (2023)
  2. Cayuela-López, J.A. Gómez-Pedrero, A.M. Oña Blanco, C.O.S. Sorzano. Cell-TypeAnalyzer: A flexible Fiji/ImageJ plugin to classify cells according to user-defined criteria. Biological Imaging, 2: e5 (2022)
  3. Cayuela, E. García-Cuesta, J.A. Gomez-Pedrero, S.R. Gardeta, J.M. Rodriguez-Frade, M. Mellado, C.O.S. Sorzano. TrackAnalyzer: A Toolbox for a holistic analysis of Single-Particle Tracks. Biological Imaging, 3: e18 (2023)

Interested candidates should send their CV’s and letter of interest to: blanca@cnb.csic.es or coss@cnb.csic.es