EMBL Interdisciplinary, International and Intersectorial Postdocs

Publications

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

Auteurs: Ying Liu, Tuhin Bhowmick, Yiqiong Liu, Xuefan Gao, Haydyn D.T. Mertens, Dmitri I. Svergun, Junyu Xiao, Yan Zhang, Jia-huai Wang, Rob Meijers
Publié dans: Neuron, Numéro 97/6, 2018, Page(s) 1261-1267.e4, ISSN 0896-6273
Éditeur: 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

Auteurs: 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
Publié dans: Nature Communications, Numéro 9/1, 2018, Page(s) 1640, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-018-04049-3

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

Auteurs: Matteo Colombo, Ombeline Pessey, Marco Marcia
Publié dans: FEBS Letters, Numéro 593/14, 2019, Page(s) 1837-1848, ISSN 0014-5793
Éditeur: Elsevier BV
DOI: 10.1002/1873-3468.13442

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

Auteurs: Daria Bunina, Nade Abazova, Nichole Diaz, Kyung-Min Noh, Jeroen Krijgsveld, Judith B. Zaugg
Publié dans: Cell Systems, Numéro 10/6, 2020, Page(s) 480-494.e8, ISSN 2405-4712
Éditeur: 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

Auteurs: 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
Publié dans: Nature Communications, Numéro 11/1, 2020, Page(s) 2927, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-16482-4

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

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

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

Auteurs: Allyson Quinn Ryan, Chii Jou Chan, François Graner, Takashi Hiiragi
Publié dans: Developmental Cell, Numéro 51/6, 2019, Page(s) 684-697.e4, ISSN 1534-5807
Éditeur: 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

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

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

Auteurs: 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
Publié dans: Nature Methods, Numéro 17/2, 2020, Page(s) 225-231, ISSN 1548-7091
Éditeur: Nature Publishing Group
DOI: 10.1038/s41592-019-0676-4

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

Auteurs: 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
Publié dans: Cell System, Numéro 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
Éditeur: Elsevier
DOI: 10.1016/j.cels.2017.09.002

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

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

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

Auteurs: 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
Publié dans: Proceedings of the National Academy of Sciences of the United States of America, Numéro 114(52):13726-13731, 2017, Page(s) 114(52):13726-13731, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.1716305114

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

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

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

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

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

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro 48/10, 2020, Page(s) 5749-5765, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkaa253

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

Auteurs: 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
Publié dans: Angewandte Chemie International Edition, Numéro 55/52, 2016, Page(s) 16172-16176, ISSN 1433-7851
Éditeur: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201608284

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

Auteurs: 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
Publié dans: Science, Numéro 352/6283, 2016, Page(s) 363-365, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.aaf0643

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

Auteurs: 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
Publié dans: Proceedings of the National Academy of Sciences, Numéro 117/36, 2020, Page(s) 22157-22166, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.2005301117

In situ architecture of the algal nuclear pore complex

Auteurs: 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
Publié dans: Nature Communications, Numéro 9/1, 2018, Page(s) 2361, ISSN 2041-1723
Éditeur: 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

Auteurs: 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
Publié dans: Nature Communications, Numéro 11/1, 2020, Page(s) 810, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-14457-z

Nuclear pores as versatile reference standards for quantitative superresolution microscopy

Auteurs: 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
Publié dans: Nature Methods, Numéro 16/10, 2019, Page(s) 1045-1053, ISSN 1548-7091
Éditeur: Nature Publishing Group
DOI: 10.1038/s41592-019-0574-9

Population-scale proteome variation in human induced pluripotent stem cells

Auteurs: 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
Publié dans: eLife, Numéro 9, 2020, Page(s) e57390, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.7554/elife.57390

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

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

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

Auteurs: Po-chia Chen, Janosch Hennig
Publié dans: Biophysical Reviews, Numéro 10/5, 2018, Page(s) 1295-1310, ISSN 1867-2450
Éditeur: Springer Verlag
DOI: 10.1007/s12551-018-0464-x

Revisiting the role of metabolism during development

Auteurs: Hidenobu Miyazawa, Alexander Aulehla
Publié dans: Development, Numéro 145/19, 2018, Page(s) dev131110, ISSN 0950-1991
Éditeur: The Company of Biologists Ltd.
DOI: 10.1242/dev.131110

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