A call for public archives for biological image data.
Jan Ellenberg,Jason R. Swedlow,Mary Barlow,Charles E. Cook,Ugis Sarkans,Ardan Patwardhan,Alvis Brazma,Ewan Birney +7 more
Reads0
Chats0
TLDR
The rationale for the construction of bioimage archives and their associated databases to underpin the next revolution in bioinformatics discovery is presented.Abstract:
Public data archives are the backbone of modern biological research. Biomolecular archives are well established, but bioimaging resources lag behind them. The technology required for imaging archives is now available, thus enabling the creation of the first public bioimage datasets. We present the rationale for the construction of bioimage archives and their associated databases to underpin the next revolution in bioinformatics discovery.read more
Citations
More filters
Journal ArticleDOI
Spatial proteomics: a powerful discovery tool for cell biology.
TL;DR: Spatial proteomics improves the understanding of protein function by revealing the subcellular localizations of proteins and their movement between compartments, and ways to improve integration of spatial proteomics data are discussed.
Journal ArticleDOI
Tutorial: guidance for quantitative confocal microscopy.
TL;DR: This tutorial and the accompanying poster provide a guide for performing quantitative fluorescence imaging using confocal microscopy, including advice and troubleshooting information from sample preparation and microscope setup to data analysis and statistics.
Journal ArticleDOI
Image-based profiling for drug discovery: due for a machine-learning upgrade?
TL;DR: How the application of machine learning is renewing interest in image-based profiling for all aspects of the drug discovery process, from understanding disease mechanisms to predicting a drug’s activity or mechanism of action is discussed.
Journal ArticleDOI
OpenCell: Endogenous tagging for the cartography of human cellular organization
Nathan H. Cho,Keith Cheveralls,Andreas D. Brunner,Ki Ha Kim,André C. Michaelis,Preethi Raghavan,Hirofumi Kobayashi,Laura Savy,Jason Y. Li,Hera Canaj,James Y. S. Kim,E. M. Stewart,Christian Gnann,Frank McCarthy,Joana P. Cabrera,Rachel M. Brunetti,Bryant B. Chhun,Greg Dingle,Marco Y. Hein,Bo Huang,Shalin B. Mehta,Jonathan S. Weissman,R. Gómez-Sjöberg,Daniel N. Itzhak,Loic Royer,Matthias Mann,Manuel D. Leonetti +26 more
TL;DR: This work combined genome engineering, confocal live-cell imaging, mass spectrometry, and data science to systematically map the localization and interactions of human proteins, and shows that proteins that bind RNA form a separate subgroup defined by specific localization and interaction signatures.
Journal ArticleDOI
Reproducibility standards for machine learning in the life sciences.
Benjamin J. Heil,Michael M. Hoffman,Florian Markowetz,Su-In Lee,Casey S. Greene,Stephanie C. Hicks +5 more
TL;DR: To make machine-learning analyses in the life sciences more computationally reproducible, standards based on data, model and code publication, programming best practices and workflow automation are proposed.
References
More filters
Journal ArticleDOI
DNA sequencing with chain-terminating inhibitors
TL;DR: A new method for determining nucleotide sequences in DNA is described, which makes use of the 2',3'-dideoxy and arabinon nucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase.
Journal ArticleDOI
Tissue-based map of the human proteome
Mathias Uhlén,Mathias Uhlén,Linn Fagerberg,Björn M. Hallström,Cecilia Lindskog,Per Oksvold,Adil Mardinoglu,Åsa Sivertsson,Caroline Kampf,Evelina Sjöstedt,Evelina Sjöstedt,Anna Asplund,IngMarie Olsson,Karolina Edlund,Emma Lundberg,Sanjay Navani,Cristina Al-Khalili Szigyarto,Jacob Odeberg,Dijana Djureinovic,Jenny Ottosson Takanen,Sophia Hober,Tove Alm,Per-Henrik Edqvist,Holger Berling,Hanna Tegel,Jan Mulder,Johan Rockberg,Peter Nilsson,Jochen M. Schwenk,Marica Hamsten,Kalle von Feilitzen,Mattias Forsberg,Lukas Persson,Fredric Johansson,Martin Zwahlen,Gunnar von Heijne,Jens Nielsen,Jens Nielsen,Fredrik Pontén +38 more
TL;DR: In this paper, a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level.
Journal ArticleDOI
The FAIR Guiding Principles for scientific data management and stewardship
Mark Wilkinson,Michel Dumontier,IJsbrand Jan Aalbersberg,Gabrielle Appleton,Myles Axton,Arie Baak,Niklas Blomberg,Jan-Willem Boiten,Luiz Olavo Bonino da Silva Santos,Philip E. Bourne,Jildau Bouwman,Anthony J. Brookes,Timothy Clark,Mercè Crosas,Ingrid Dillo,Olivier G. Dumon,Scott C. Edmunds,Chris T. Evelo,Richard Finkers,Alejandra Gonzalez-Beltran,Alasdair J. G. Gray,Paul Groth,Carole Goble,Jeffrey S. Grethe,Jaap Heringa,Peter A C 't Hoen,Rob Hooft,Tobias Kuhn,Ruben Kok,Joost N. Kok,Scott J. Lusher,Maryann E. Martone,Albert Mons,Abel L. Packer,Bengt Persson,Philippe Rocca-Serra,Marco Roos,Rene van Schaik,Susanna-Assunta Sansone,Erik Anthony Schultes,Thierry Sengstag,Ted Slater,George Strawn,Morris A. Swertz,Mark Thompson,Johan van der Lei,Erik M. van Mulligen,Jan Velterop,Andra Waagmeester,Peter Wittenburg,Katherine Wolstencroft,Jun Zhao,Barend Mons,Barend Mons +53 more
TL;DR: The FAIR Data Principles as mentioned in this paper are a set of data reuse principles that focus on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals.
Journal ArticleDOI
A new method for sequencing DNA
Allan M. Maxam,Walter Gilbert +1 more
TL;DR: Reactions that cleave DNA preferentially at guanines, at adenines,At cytosines and thymines equally, and at cytosine alone are described.
Journal ArticleDOI
From core referencing to data re-use: two French national initiatives to reinforce paleodata stewardship (National Cyber Core Repository and LTER France Retro-Observatory)
Fabien Arnaud,Cécile Pignol,Pierre Stéphan,Anne-Lise Develle,Pierre Sabatier,Olivier Evrard,Brice Mourier,Maxime Debret,Cécile Grobois,Laurent Millet,Damien Rius,Dominique Marguerie,Mathias Rouan,Elodie Godinho,Bruno Galabertier,Arnaud Caillo +15 more
TL;DR: ROZA was developed under the umbrella of LTER-France (Long Term Ecological Research) in order to facilitate the re-use of data and samples and will favor to use of paleodata by non-paleodata scientists, in particular ecologists.
Related Papers (5)
The FAIR Guiding Principles for scientific data management and stewardship
Mark Wilkinson,Michel Dumontier,IJsbrand Jan Aalbersberg,Gabrielle Appleton,Myles Axton,Arie Baak,Niklas Blomberg,Jan-Willem Boiten,Luiz Olavo Bonino da Silva Santos,Philip E. Bourne,Jildau Bouwman,Anthony J. Brookes,Timothy Clark,Mercè Crosas,Ingrid Dillo,Olivier G. Dumon,Scott C. Edmunds,Chris T. Evelo,Richard Finkers,Alejandra Gonzalez-Beltran,Alasdair J. G. Gray,Paul Groth,Carole Goble,Jeffrey S. Grethe,Jaap Heringa,Peter A C 't Hoen,Rob Hooft,Tobias Kuhn,Ruben Kok,Joost N. Kok,Scott J. Lusher,Maryann E. Martone,Albert Mons,Abel L. Packer,Bengt Persson,Philippe Rocca-Serra,Marco Roos,Rene van Schaik,Susanna-Assunta Sansone,Erik Anthony Schultes,Thierry Sengstag,Ted Slater,George Strawn,Morris A. Swertz,Mark Thompson,Johan van der Lei,Erik M. van Mulligen,Jan Velterop,Andra Waagmeester,Peter Wittenburg,Katherine Wolstencroft,Jun Zhao,Barend Mons,Barend Mons +53 more
OMERO: flexible, model-driven data management for experimental biology
Chris Allan,Jean-Marie Burel,Josh Moore,Colin Blackburn,Melissa Linkert,Scott Loynton,Donald MacDonald,William J. Moore,Carlos H. Neves,Andrew J. Patterson,Michael Porter,Aleksandra Tarkowska,Brian Loranger,Jerome Avondo,Ingvar Lagerstedt,Luca Lianas,Simone Leo,Katherine Hands,Ronald T. Hay,Ardan Patwardhan,Christoph Best,Christoph Best,Gerard J. Kleywegt,Gianluigi Zanetti,Jason R. Swedlow +24 more