EMBL Interdisciplinary, International and Intersectorial Postdocs

Pubblicazioni

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

Autori: Ying Liu, Tuhin Bhowmick, Yiqiong Liu, Xuefan Gao, Haydyn D.T. Mertens, Dmitri I. Svergun, Junyu Xiao, Yan Zhang, Jia-huai Wang, Rob Meijers
Pubblicato in: Neuron, Numero 97/6, 2018, Pagina/e 1261-1267.e4, ISSN 0896-6273
Editore: 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

Autori: 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
Pubblicato in: Nature Communications, Numero 9/1, 2018, Pagina/e 1640, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-018-04049-3

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

Autori: Matteo Colombo, Ombeline Pessey, Marco Marcia
Pubblicato in: FEBS Letters, Numero 593/14, 2019, Pagina/e 1837-1848, ISSN 0014-5793
Editore: Elsevier BV
DOI: 10.1002/1873-3468.13442

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

Autori: Daria Bunina, Nade Abazova, Nichole Diaz, Kyung-Min Noh, Jeroen Krijgsveld, Judith B. Zaugg
Pubblicato in: Cell Systems, Numero 10/6, 2020, Pagina/e 480-494.e8, ISSN 2405-4712
Editore: 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

Autori: 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
Pubblicato in: Nature Communications, Numero 11/1, 2020, Pagina/e 2927, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-020-16482-4

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

Autori: Yiming Li, Markus Mund, Philipp Hoess, Joran Deschamps, Ulf Matti, Bianca Nijmeijer, Vilma Jimenez Sabinina, Jan Ellenberg, Ingmar Schoen, Jonas Ries
Pubblicato in: Nature Methods, Numero 15/5, 2018, Pagina/e 367-369, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/nmeth.4661

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

Autori: Allyson Quinn Ryan, Chii Jou Chan, François Graner, Takashi Hiiragi
Pubblicato in: Developmental Cell, Numero 51/6, 2019, Pagina/e 684-697.e4, ISSN 1534-5807
Editore: 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

Autori: Ritsuya Niwayama, Prachiti Moghe, Yan-Jun Liu, Dimitri Fabrèges, Frank Buchholz, Matthieu Piel, Takashi Hiiragi
Pubblicato in: Developmental Cell, Numero 51/5, 2019, Pagina/e 564-574.e6, ISSN 1534-5807
Editore: Cell Press
DOI: 10.1016/j.devcel.2019.10.012

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

Autori: 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
Pubblicato in: Nature Methods, Numero 17/2, 2020, Pagina/e 225-231, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-019-0676-4

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

Autori: 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
Pubblicato in: Cell System, Numero 2017 Oct 25;5(4):345-357.e6. doi: 10.1016/j.cels.2017.09.002. Epub 2017 Sep 27., 2017, Pagina/e 2017 Oct 25;5(4):345-357.e6. doi: 10.1016/j.cels.2017.09.002. Epub 2017 Sep 27., ISSN 2405-4720
Editore: Elsevier
DOI: 10.1016/j.cels.2017.09.002

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

Autori: Yiming Li, Yu-Le Wu, Philipp Hoess, Markus Mund, Jonas Ries
Pubblicato in: Biomedical Optics Express, Numero 10/6, 2019, Pagina/e 2708, ISSN 2156-7085
Editore: The Optical Society
DOI: 10.1364/boe.10.002708

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

Autori: 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
Pubblicato in: Proceedings of the National Academy of Sciences of the United States of America, Numero 114(52):13726-13731, 2017, Pagina/e 114(52):13726-13731, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.1716305114

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

Autori: Chen PC1, Masiewicz P1, Rybin V1, Svergun D2, Hennig J1
Pubblicato in: ACS Combinataorial Science, Numero 23 Mar 2018, 2018, Pagina/e 20(4):197-202, ISSN 2156-8944
Editore: American Chemical Society
DOI: 10.1021/acscombsci.8b00007

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

Autori: Vito Genna,1,4 Matteo Colombo,2,4 Marco De Vivo,1,3,* and Marco Marcia2,5,**
Pubblicato in: Structure, Numero 2018 Jan 2; 26(1): 40–50.e2., 2018, Pagina/e 2018 Jan 2; 26(1): 40–50.e2., ISSN 0969-2126
Editore: Elsevier
DOI: 10.1016/j.str.2017.11.008

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

Autori: 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
Pubblicato in: Nucleic Acids Research, Numero 48/10, 2020, Pagina/e 5749-5765, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkaa253

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

Autori: 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
Pubblicato in: Angewandte Chemie International Edition, Numero 55/52, 2016, Pagina/e 16172-16176, ISSN 1433-7851
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201608284

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

Autori: 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
Pubblicato in: Science, Numero 352/6283, 2016, Pagina/e 363-365, ISSN 0036-8075
Editore: American Association for the Advancement of Science
DOI: 10.1126/science.aaf0643

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

Autori: 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
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 117/36, 2020, Pagina/e 22157-22166, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2005301117

In situ architecture of the algal nuclear pore complex

Autori: 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
Pubblicato in: Nature Communications, Numero 9/1, 2018, Pagina/e 2361, ISSN 2041-1723
Editore: 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

Autori: 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
Pubblicato in: Nature Communications, Numero 11/1, 2020, Pagina/e 810, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-020-14457-z

Nuclear pores as versatile reference standards for quantitative superresolution microscopy

Autori: 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
Pubblicato in: Nature Methods, Numero 16/10, 2019, Pagina/e 1045-1053, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-019-0574-9

Population-scale proteome variation in human induced pluripotent stem cells

Autori: 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
Pubblicato in: eLife, Numero 9, 2020, Pagina/e e57390, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.57390

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

Autori: Po-chia Chen, Maggy Hologne, Olivier Walker, Janosch Hennig
Pubblicato in: Journal of Chemical Theory and Computation, Numero 14/2, 2018, Pagina/e 1009-1019, ISSN 1549-9618
Editore: American Chemical Society
DOI: 10.1021/acs.jctc.7b00750

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

Autori: Po-chia Chen, Janosch Hennig
Pubblicato in: Biophysical Reviews, Numero 10/5, 2018, Pagina/e 1295-1310, ISSN 1867-2450
Editore: Springer Verlag
DOI: 10.1007/s12551-018-0464-x

Revisiting the role of metabolism during development

Autori: Hidenobu Miyazawa, Alexander Aulehla
Pubblicato in: Development, Numero 145/19, 2018, Pagina/e dev131110, ISSN 0950-1991
Editore: The Company of Biologists Ltd.
DOI: 10.1242/dev.131110

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