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EMBL Interdisciplinary, International and Intersectorial Postdocs

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Publications

Structural Basis for Draxin-Modulated Axon Guidance and Fasciculation by Netrin-1 through DCC

Author(s): Ying Liu, Tuhin Bhowmick, Yiqiong Liu, Xuefan Gao, Haydyn D.T. Mertens, Dmitri I. Svergun, Junyu Xiao, Yan Zhang, Jia-huai Wang, Rob Meijers
Published in: Neuron, 97/6, 2018, Page(s) 1261-1267.e4, ISSN 0896-6273
Publisher: Cell Press
DOI: 10.1016/j.neuron.2018.02.010

Control of mechanical pain hypersensitivity in mice through ligand-targeted photoablation of TrkB-positive sensory neurons

Author(s): Rahul Dhandapani, Cynthia Mary Arokiaraj, Francisco J. Taberner, Paola Pacifico, Sruthi Raja, Linda Nocchi, Carla Portulano, Federica Franciosa, Mariano Maffei, Ahmad Fawzi Hussain, Fernanda de Castro Reis, Luc Reymond, Emerald Perlas, Simone Garcovich, Stefan Barth, Kai Johnsson, Stefan G. Lechner, Paul A. Heppenstall
Published in: Nature Communications, 9/1, 2018, Page(s) 1640, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-04049-3

Topology and enzymatic properties of a canonical Polycomb repressive complex 1 isoform

Author(s): Matteo Colombo, Ombeline Pessey, Marco Marcia
Published in: FEBS Letters, 593/14, 2019, Page(s) 1837-1848, ISSN 0014-5793
Publisher: Elsevier BV
DOI: 10.1002/1873-3468.13442

Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons

Author(s): Daria Bunina, Nade Abazova, Nichole Diaz, Kyung-Min Noh, Jeroen Krijgsveld, Judith B. Zaugg
Published in: Cell Systems, 10/6, 2020, Page(s) 480-494.e8, ISSN 2405-4712
Publisher: Cell Press
DOI: 10.1016/j.cels.2020.05.003

Properties of structural variants and short tandem repeats associated with gene expression and complex traits

Author(s): David Jakubosky, Matteo D’Antonio, Marc Jan Bonder, Craig Smail, Margaret K. R. Donovan, William W. Young Greenwald, Hiroko Matsui, Agnieszka D’Antonio-Chronowska, Oliver Stegle, Erin N. Smith, Stephen B. Montgomery, Christopher DeBoever, Kelly A. Frazer
Published in: Nature Communications, 11/1, 2020, Page(s) 2927, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-16482-4

Real-time 3D single-molecule localization using experimental point spread functions

Author(s): Yiming Li, Markus Mund, Philipp Hoess, Joran Deschamps, Ulf Matti, Bianca Nijmeijer, Vilma Jimenez Sabinina, Jan Ellenberg, Ingmar Schoen, Jonas Ries
Published in: Nature Methods, 15/5, 2018, Page(s) 367-369, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/nmeth.4661

Lumen Expansion Facilitates Epiblast-Primitive Endoderm Fate Specification during Mouse Blastocyst Formation

Author(s): Allyson Quinn Ryan, Chii Jou Chan, François Graner, Takashi Hiiragi
Published in: Developmental Cell, 51/6, 2019, Page(s) 684-697.e4, ISSN 1534-5807
Publisher: Cell Press
DOI: 10.1016/j.devcel.2019.10.011

A Tug-of-War between Cell Shape and Polarity Controls Division Orientation to Ensure Robust Patterning in the Mouse Blastocyst

Author(s): Ritsuya Niwayama, Prachiti Moghe, Yan-Jun Liu, Dimitri Fabrèges, Frank Buchholz, Matthieu Piel, Takashi Hiiragi
Published in: Developmental Cell, 51/5, 2019, Page(s) 564-574.e6, ISSN 1534-5807
Publisher: Cell Press
DOI: 10.1016/j.devcel.2019.10.012

Nanoscale subcellular architecture revealed by multicolor three-dimensional salvaged fluorescence imaging

Author(s): Yongdeng Zhang, Lena K. Schroeder, Mark D. Lessard, Phylicia Kidd, Jeeyun Chung, Yuanbin Song, Lorena Benedetti, Yiming Li, Jonas Ries, Jonathan B. Grimm, Luke D. Lavis, Pietro De Camilli, James E. Rothman, David Baddeley, Joerg Bewersdorf
Published in: Nature Methods, 17/2, 2020, Page(s) 225-231, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-019-0676-4

Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow

Author(s): Olga Ponomarova 1 , Natalia Gabrielli 1 , Daniel C Sévin 2 , Michael Mülleder 3 , Katharina Zirngibl 1 , Katsiaryna Bulyha 1 , Sergej Andrejev 1 , Eleni Kafkia 1 , Athanasios Typas 1 , Uwe Sauer 2 , Markus Ralser 3 , Kiran Raosaheb Patil
Published in: Cell System, 2017 Oct 25;5(4):345-357.e6. doi: 10.1016/j.cels.2017.09.002. Epub 2017 Sep 27., 2017, Page(s) 2017 Oct 25;5(4):345-357.e6. doi: 10.1016/j.cels.2017.09.002. Epub 2017 Sep 27., ISSN 2405-4720
Publisher: Elsevier
DOI: 10.1016/j.cels.2017.09.002

Depth-dependent PSF calibration and aberration correction for 3D single-molecule localization

Author(s): Yiming Li, Yu-Le Wu, Philipp Hoess, Markus Mund, Jonas Ries
Published in: Biomedical Optics Express, 10/6, 2019, Page(s) 2708, ISSN 2156-7085
Publisher: The Optical Society
DOI: 10.1364/boe.10.002708

Proteasomes tether to two distinct sites at the nuclear pore complex.

Author(s): Sahradha Albert,a Miroslava Schaffer,a Florian Beck,a Shyamal Mosalaganti,b Shoh Asano,a,1 Henry F. Thomas,a Jürgen M. Plitzko,a Martin Beck,b Wolfgang Baumeister,a,2 and Benjamin D. Engela, Beck M2, Baumeister W3, Benjamin D Engel Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; baumeist@biochem.mpg.de baumeist@biochem.mpg.de
Published in: Proceedings of the National Academy of Sciences of the United States of America, 114(52):13726-13731, 2017, Page(s) 114(52):13726-13731, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1716305114

A General Small-Angle X-ray Scattering-Based Screening Protocol Validated for Protein-RNA Interactions

Author(s): Chen PC1, Masiewicz P1, Rybin V1, Svergun D2, Hennig J1
Published in: ACS Combinataorial Science, 23 Mar 2018, 2018, Page(s) 20(4):197-202, ISSN 2156-8944
Publisher: American Chemical Society
DOI: 10.1021/acscombsci.8b00007

Second-Shell Basic Residues Expand the Two-Metal-Ion Architecture of DNA and RNA Processing Enzymes

Author(s): Vito Genna,1,4 Matteo Colombo,2,4 Marco De Vivo,1,3,* and Marco Marcia2,5,**
Published in: Structure, 2018 Jan 2; 26(1): 40–50.e2., 2018, Page(s) 2018 Jan 2; 26(1): 40–50.e2., ISSN 0969-2126
Publisher: Elsevier
DOI: 10.1016/j.str.2017.11.008

Structural and functional characterization of the severe fever with thrombocytopenia syndrome virus L protein

Author(s): Dominik Vogel, Sigurdur Rafn Thorkelsson, Emmanuelle R J Quemin, Kristina Meier, Tomas Kouba, Nadja Gogrefe, Carola Busch, Sophia Reindl, Stephan Günther, Stephen Cusack, Kay Grünewald, Maria Rosenthal
Published in: Nucleic Acids Research, 48/10, 2020, Page(s) 5749-5765, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa253

Debugging Eukaryotic Genetic Code Expansion for Site-Specific Click-PAINT Super-Resolution Microscopy

Author(s): Ivana Nikić, Gemma Estrada Girona, Jun Hee Kang, Giulia Paci, Sofya Mikhaleva, Christine Koehler, Nataliia V. Shymanska, Camilla Ventura Santos, Daniel Spitz, Edward A. Lemke
Published in: Angewandte Chemie International Edition, 55/52, 2016, Page(s) 16172-16176, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201608284

Molecular architecture of the inner ring scaffold of the human nuclear pore complex

Author(s): J. Kosinski, S. Mosalaganti, A. von Appen, R. Teimer, A. L. DiGuilio, W. Wan, K. H. Bui, W. J. H. Hagen, J. A. G. Briggs, J. S. Glavy, E. Hurt, M. Beck
Published in: Science, 352/6283, 2016, Page(s) 363-365, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aaf0643

Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress

Author(s): Ye Zhou, Panagiotis L. Kastritis, Shannon E. Dougherty, Jonathan Bouvette, Allen L. Hsu, Laura Burbaum, Shyamal Mosalaganti, Stefan Pfeffer, Wim J. H. Hagen, Friedrich Förster, Mario J. Borgnia, Christine Vogel, Martin Beck, Alberto Bartesaghi, Gustavo M. Silva
Published in: Proceedings of the National Academy of Sciences, 117/36, 2020, Page(s) 22157-22166, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2005301117

In situ architecture of the algal nuclear pore complex

Author(s): Shyamal Mosalaganti, Jan Kosinski, Sahradha Albert, Miroslava Schaffer, Daniela Strenkert, Patrice A. Salomé, Sabeeha S. Merchant, Jürgen M. Plitzko, Wolfgang Baumeister, Benjamin D. Engel, Martin Beck
Published in: Nature Communications, 9/1, 2018, Page(s) 2361, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-04739-y

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

Author(s): Anna S. E. Cuomo, Daniel D. Seaton, Davis J. McCarthy, Iker Martinez, Marc Jan Bonder, Jose Garcia-Bernardo, Shradha Amatya, Pedro Madrigal, Abigail Isaacson, Florian Buettner, Andrew Knights, Kedar Nath Natarajan, Ludovic Vallier, John C. Marioni, Mariya Chhatriwala, Oliver Stegle
Published in: Nature Communications, 11/1, 2020, Page(s) 810, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-14457-z

Nuclear pores as versatile reference standards for quantitative superresolution microscopy

Author(s): Jervis Vermal Thevathasan, Maurice Kahnwald, Konstanty Cieśliński, Philipp Hoess, Sudheer Kumar Peneti, Manuel Reitberger, Daniel Heid, Krishna Chaitanya Kasuba, Sarah Janice Hoerner, Yiming Li, Yu-Le Wu, Markus Mund, Ulf Matti, Pedro Matos Pereira, Ricardo Henriques, Bianca Nijmeijer, Moritz Kueblbeck, Vilma Jimenez Sabinina, Jan Ellenberg, Jonas Ries
Published in: Nature Methods, 16/10, 2019, Page(s) 1045-1053, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-019-0574-9

Population-scale proteome variation in human induced pluripotent stem cells

Author(s): Bogdan Andrei Mirauta, Daniel D Seaton, Dalila Bensaddek, Alejandro Brenes, Marc Jan Bonder, Helena Kilpinen, Chukwuma A Agu, Alex Alderton, Petr Danecek, Rachel Denton, Richard Durbin, Daniel J Gaffney, Angela Goncalves, Reena Halai, Sarah Harper, Christopher M Kirton, Anja Kolb-Kokocinski, Andreas Leha, Shane A McCarthy, Yasin Memari, Minal Patel, Ewan Birney, Francesco Paolo Casale, Laura Clark
Published in: eLife, 9, 2020, Page(s) e57390, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.57390

Ab Initio Prediction of NMR Spin Relaxation Parameters from Molecular Dynamics Simulations

Author(s): Po-chia Chen, Maggy Hologne, Olivier Walker, Janosch Hennig
Published in: Journal of Chemical Theory and Computation, 14/2, 2018, Page(s) 1009-1019, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.7b00750

The role of small-angle scattering in structure-based screening applications

Author(s): Po-chia Chen, Janosch Hennig
Published in: Biophysical Reviews, 10/5, 2018, Page(s) 1295-1310, ISSN 1867-2450
Publisher: Springer Verlag
DOI: 10.1007/s12551-018-0464-x

Revisiting the role of metabolism during development

Author(s): Hidenobu Miyazawa, Alexander Aulehla
Published in: Development, 145/19, 2018, Page(s) dev131110, ISSN 0950-1991
Publisher: The Company of Biologists Ltd.
DOI: 10.1242/dev.131110