Two Project Scientist positions are available in my group in the Molecular Biophysics and Integrated Bioimaging (MBIB) Division at Lawrence Berkeley National Lab.

Bioimaging Project Scientist

Position Summary:

We have an exciting opportunity for a Bioimaging Project Scientist who will apply neuromorphic computing techniques to structural biology problems in X-ray diffraction, CryoEM, and CryoET.  This will be a cross-disciplinary effort between MBIB and the Computational Research (CRD) Division at Lawrence Berkeley National Laboratory.  The research group will include investigators Nick Sauter (X-ray Crystallography), Karen Davies (CryoEM/ET), and Chao Yang (Scalable Solvers).


Specific Responsibilities:

  • Investigate how to apply deep learning algorithms to specific data processing and data interpretation problems in structural biology.

  • Implement convolutional neural network (CNN) code on neuromorphic computing hardware such as the IBM TrueNorth chip.  Example problems include the identification of positive diffraction events in X-ray free-electron laser diffraction, conformational classification in CryoEM single particle reconstruction, and the identification of 3D sections for CryoET subtomogram averaging.

  • Use tools such as MatConvNet, CAFFE, THEANO or TensorFlow to construct and train CNNs that can be used to optimally classify experimental data.  


Required Qualifications:

  • Research experience in Structural Biology, with expertise in allied fields such as Bioinformatics, Mathematics, Computer Science, or Engineering (Ph.D. + 3 years or equivalent)

  • Strong background in image analysis and machine learning, including neural networks.

  • Working knowledge of image classification and/or other image processing techniques.

  • Proficient programming skills in MATLAB and/or Python.

  • Working knowledge of performance optimization for scientific codes.


Algorithm Developer Project Scientist


Position Summary: 

We are seeking an algorithm developer for the increasingly complex analysis of large diffraction datasets in structural biology.  Current projects utilize XFEL crystallography and spectroscopy to investigate the photosynthetic mechanism of water splitting and to probe other metalloenzyme reactions.  We also wish to test whether diffuse scattering can reveal correlated atomic motions in crystals.  Many problems remain to be solved, including the details of how to optimally merge datasets from thousands of crystals.  Our software development projects (including packages such as DIALS and cctbx.xfel) have been highlighted in several high-impact publications listed HERE.

 

Specific Responsibilities:

  • Continue work on the DIALS data integration suite.
  • Test new algorithms for optimally characterizing and merging data from serial crystallography experiments.
  • Analyze anomalous scattering from metalloenzymes using XFEL diffraction.
  • Investigate whether diffuse scattering can reveal correlated atomic motions in crystals.


Required Qualifications:

  • Expertise in one or more computational techniques including, but not limited to, ray tracing to test underlying physical models of the diffraction, Bayesian approaches for refining model parameters, macromolecular modeling and refinement, neural networks for interpreting image features, as well as signal processing and denoising methods.  
  • Extensive data analysis experience in crystallography or from more general bioimaging backgrounds are welcome. 
  • We particularly encourage strong mathematical intuition and a track record of bringing new ideas and tools to fruition, as evidenced through written publication and clear presentation.

Candidates should send an expression of interest, CV, and list of three references to Nick Sauter, nksauter@lbl.gov. Further details are posted at https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=82554.


Nicholas K. Sauter, Ph. D.
Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 33R0345
Berkeley, CA 94720