Johannes Schöneberg PhD

Assistant Professor, UCSD

Roger Tsien Chancellor’s Faculty Fellow

Departments of Pharmacology and Chemistry & Biochemistry

University of California, San Diego

jschoeneberg@health.ucsd.edu

Head of the

4D CELL Biology Lab

4D Computer Science, Engineering, Lattice Light-Sheet, Biology Laboratory



Full CV

Professional Experience and Education

UC San Diego

2020 - present

PI of the 4D CELL Biology Lab

UC Berkeley

2017 - 2020

Postdoc in lattice light-sheet microscopy, organoids and AI-based data analysis, Betzig Lab & Drubin Lab

2015 - 2017

Postdoc in optical engineering and membrane biophysics, Hurley Lab & Bustamante Lab

Max Planck Institute of Biophysics

2014 - 2017

Postdoc in computational biophysics, Hummer Lab

Max Planck Institute for Molecular Genetics Berlin / Free University Berlin

2009 - 2014

PhD Computer Science / Biophysics

IMPRS PhD Student

Computational Molecular Biology, Prof. Frank Noé

Thesis: 'Reaction-diffusion dynamics in biologial systems - theory, computation, modeling and simulation. Application to the visual cascade and the synaptic vesicle cycle.'

2009

MSc Bioinformatics

Completion in one year (instead of two as listed in the curriculum).

Thesis: 'Investigation of the reaction-diffusion processes of rod cell disc membrane photoactivation with single-particle resolution'

Advisor: Frank Noé

2008 - 2009

Fast Track program for outstanding young researchers

(Skip masters degree and advance to PhD with the BSc immediately. The Fast Track program included 1 year of courses before an exam would grant immediate advance to the PhD. I chose to do the 2 year MSc curriculum in that year. I successfully passed the Fast Track and additionally got the MSc.)

Saarland University

2005 - 2008

BSc Bioinformatics

Thesis: 'MHC:peptide structure prediction' with fast constraint based MD-Simulation substitute

Advisor: Rainer Böckmann

Prior Research

Scope Engineering and Optical Tweezing

I combined confocal microscopy with optical trapping to measure force and fluorescence of proteins acting on small membrane nanotubes (pulled from e.g. a giant unilamellar vesicles (GUV)). These nanotubes allow studying protein-membrane biophysics in tubular, highly curved topologies. They resemble vesicle necks found e.g. in normal topology budding (e.g. Clathrin mediated endocytosis) and reverse topology budding (ESCRT system).

The Confleezers: Left:The Confleezers 1.0 that combines confocal microscopy with optical tweezing. Right: Membrane nanotubes pulled from model membranes using micromanipulators (top) and the trap of the Confleezers (bottom).

See our applications on the ESCRT system and our review:

J Schöneberg, M R Pavlin*, S Yan*, M Righini, I-H Lee, L-A Carlson, A H Bahrami, D H Goldman, X Ren, G Hummer, C Bustamante and J H Hurley (2018) ATP-dependent force generation and membrane scission by ESCRT-III and Vps4, Science, 362 (6421), 1423-1428. * equal contribution.

J Schöneberg*, Lee IH*, Iwasa JH, Hurley JH, (2016) Reverse-topology membrane scission by the ESCRT proteins. Nature Reviews Molecular Cell Biology, doi: 10.1038/nrm.2016.12. (*equal contribution).

Reaction-Diffusion Simulation

https://www.nature.com/articles/ncomms15873

J Schöneberg*, M Lehmann*, A Ullrich, Y Posor, W-T Lo, G Lichtner, J Schmoranzer, V Haucke, F Noé, (2017) Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nature Communications 8, 15873 doi: 10.1038/ncomms15873. (*equal contribution).

https://youtu.be/9OKo29iQQ5g

ReaDDy

ReaDDy is a particle-based reaction-diffusion simulation software. It features

  1. simulation in and on arbitrary geometries (i.e. 3D, 2D, spherical,...),

  2. spatial confinement (walls, boxes, tubes, ...),

  3. excluded volume of particles (crowding effects) and

  4. particle-particle interaction potentials (repulsion, attraction, clustering, ...).

See more under readdy-project.org, contribute under gitHub/readdy and read the paper under Schöneberg and Noé, PLOS ONE, 2013. Also check out the newest ReaDDy developments here.

Awards and Honors

2019

2018

2018

2017

2015

2015

2014

2013

2012

2009

2009

2008

2006

2006

2005

2005

2004

2003


Best Presentation, Developmental and Cell Biology Division Posters, Asilomar

BIDS data science Fellowship

Siebel Scholars Stem Cell Fellowship

Elected Chair of the 2019 GRS Gordon Research Seminar on 'Molecular Membrane Biology'

Tiburtius Annerkennungs Prize for best PhD thesis of the universities of Berlin

Marie Skłodowska-Curie postdoctoral fellowship

Poster Award, 4th International caesar Conference

Steering committee member Junges Wissenschaftsforum Dahlem, FU-Berlin

Chosen student, Excellence Initiative Proposal , FU-Berlin

Best Poster Award, IMPRS-CBSC, MPI-Molgen Berlin

IMPRS-CBSC fellowship for doctoral studies, MPI-Molgen Berlin

Fast Track fellowship, IMPRS-CBSC, MPI-Molgen Berlin

Konrad Adenauer fellowship for undergraduate studies

German Federal Cultural Foundation grant

Barmer Award for best high school diploma in biology

Scheffel Award for best high school diploma in German

Young Leaders Academy

Saarland Academy for highly gifted people


Leadership

2017 - 2019



The 2019 GRS with its 53 participants and including our Keynote Speaker Randy Schekman and our Career Mentors Roberto Zoncu and Laura Lackner.

Liz and me with the freshly elected chairs of the 2021 meeting. (Left to right: Raquel Salvador Gallego, Joh Schöneberg, Liz Costa, Priya Gurumoorthy)

2017 - 2018




2015 - 2016




2011 - 2014

Co-Founder and West Coast Regional Coordinator

Marie Curie Alumni Association North America Chapter

MCAA, Washington, DC, USA


Co-Chair

Berkeley Postdoctoral Entrepreneurship Program (BPEP)

UC Berkeley, CA, USA


Co-Founder and Member

Young Science Forum Dahlem (German Research Excellence Initiative)

FU Berlin, Germany