Literature DB >> 33893283

The VRNetzer platform enables interactive network analysis in Virtual Reality.

Sebastian Pirch1,2, Felix Müller1,2, Eugenia Iofinova1, Julia Pazmandi1,2,3, Christiane V R Hütter1,2, Martin Chiettini1,2, Celine Sin1,2, Kaan Boztug1,3,4,5,6, Iana Podkosova7, Hannes Kaufmann7, Jörg Menche8,9,10.   

Abstract

Networks provide a powerful representation of interacting components within complex systems, making them ideal for visually and analytically exploring big data. However, the size and complexity of many networks render static visualizations on typically-sized paper or screens impractical, resulting in proverbial 'hairballs'. Here, we introduce a Virtual Reality (VR) platform that overcomes these limitations by facilitating the thorough visual, and interactive, exploration of large networks. Our platform allows maximal customization and extendibility, through the import of custom code for data analysis, integration of external databases, and design of arbitrary user interface elements, among other features. As a proof of concept, we show how our platform can be used to interactively explore genome-scale molecular networks to identify genes associated with rare diseases and understand how they might contribute to disease development. Our platform represents a general purpose, VR-based data exploration platform for large and diverse data types by providing an interface that facilitates the interaction between human intuition and state-of-the-art analysis methods.

Entities:  

Year:  2021        PMID: 33893283     DOI: 10.1038/s41467-021-22570-w

Source DB:  PubMed          Journal:  Nat Commun        ISSN: 2041-1723            Impact factor:   14.919


  41 in total

1.  The immune system as a social network.

Authors:  Andreas Bergthaler; Jörg Menche
Journal:  Nat Immunol       Date:  2017-04-18       Impact factor: 25.606

2.  Basal ganglion calcification and hyperparathyroidism.

Authors:  P Siklos
Journal:  Miner Electrolyte Metab       Date:  1982-03

3.  Disease networks. Uncovering disease-disease relationships through the incomplete interactome.

Authors:  Jörg Menche; Amitabh Sharma; Maksim Kitsak; Susan Dina Ghiassian; Marc Vidal; Joseph Loscalzo; Albert-László Barabási
Journal:  Science       Date:  2015-02-20       Impact factor: 47.728

4.  A global genetic interaction network maps a wiring diagram of cellular function.

Authors:  Michael Costanzo; Benjamin VanderSluis; Elizabeth N Koch; Anastasia Baryshnikova; Carles Pons; Guihong Tan; Wen Wang; Matej Usaj; Julia Hanchard; Susan D Lee; Vicent Pelechano; Erin B Styles; Maximilian Billmann; Jolanda van Leeuwen; Nydia van Dyk; Zhen-Yuan Lin; Elena Kuzmin; Justin Nelson; Jeff S Piotrowski; Tharan Srikumar; Sondra Bahr; Yiqun Chen; Raamesh Deshpande; Christoph F Kurat; Sheena C Li; Zhijian Li; Mojca Mattiazzi Usaj; Hiroki Okada; Natasha Pascoe; Bryan-Joseph San Luis; Sara Sharifpoor; Emira Shuteriqi; Scott W Simpkins; Jamie Snider; Harsha Garadi Suresh; Yizhao Tan; Hongwei Zhu; Noel Malod-Dognin; Vuk Janjic; Natasa Przulj; Olga G Troyanskaya; Igor Stagljar; Tian Xia; Yoshikazu Ohya; Anne-Claude Gingras; Brian Raught; Michael Boutros; Lars M Steinmetz; Claire L Moore; Adam P Rosebrock; Amy A Caudy; Chad L Myers; Brenda Andrews; Charles Boone
Journal:  Science       Date:  2016-09-23       Impact factor: 47.728

5.  A DIseAse MOdule Detection (DIAMOnD) algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the human interactome.

Authors:  Susan Dina Ghiassian; Jörg Menche; Albert-László Barabási
Journal:  PLoS Comput Biol       Date:  2015-04-08       Impact factor: 4.475

6.  Uncovering disease mechanisms through network biology in the era of Next Generation Sequencing.

Authors:  Janet Piñero; Ariel Berenstein; Abel Gonzalez-Perez; Ariel Chernomoretz; Laura I Furlong
Journal:  Sci Rep       Date:  2016-04-15       Impact factor: 4.379

7.  The BioGRID interaction database: 2019 update.

Authors:  Rose Oughtred; Chris Stark; Bobby-Joe Breitkreutz; Jennifer Rust; Lorrie Boucher; Christie Chang; Nadine Kolas; Lara O'Donnell; Genie Leung; Rochelle McAdam; Frederick Zhang; Sonam Dolma; Andrew Willems; Jasmin Coulombe-Huntington; Andrew Chatr-Aryamontri; Kara Dolinski; Mike Tyers
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

8.  New approach for understanding genome variations in KEGG.

Authors:  Minoru Kanehisa; Yoko Sato; Miho Furumichi; Kanae Morishima; Mao Tanabe
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

9.  The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.

Authors:  Sandra Orchard; Mais Ammari; Bruno Aranda; Lionel Breuza; Leonardo Briganti; Fiona Broackes-Carter; Nancy H Campbell; Gayatri Chavali; Carol Chen; Noemi del-Toro; Margaret Duesbury; Marine Dumousseau; Eugenia Galeota; Ursula Hinz; Marta Iannuccelli; Sruthi Jagannathan; Rafael Jimenez; Jyoti Khadake; Astrid Lagreid; Luana Licata; Ruth C Lovering; Birgit Meldal; Anna N Melidoni; Mila Milagros; Daniele Peluso; Livia Perfetto; Pablo Porras; Arathi Raghunath; Sylvie Ricard-Blum; Bernd Roechert; Andre Stutz; Michael Tognolli; Kim van Roey; Gianni Cesareni; Henning Hermjakob
Journal:  Nucleic Acids Res       Date:  2013-11-13       Impact factor: 16.971

10.  Architecture of the human interactome defines protein communities and disease networks.

Authors:  Edward L Huttlin; Raphael J Bruckner; Joao A Paulo; Joe R Cannon; Lily Ting; Kurt Baltier; Greg Colby; Fana Gebreab; Melanie P Gygi; Hannah Parzen; John Szpyt; Stanley Tam; Gabriela Zarraga; Laura Pontano-Vaites; Sharan Swarup; Anne E White; Devin K Schweppe; Ramin Rad; Brian K Erickson; Robert A Obar; K G Guruharsha; Kejie Li; Spyros Artavanis-Tsakonas; Steven P Gygi; J Wade Harper
Journal:  Nature       Date:  2017-05-17       Impact factor: 49.962

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  1 in total

Review 1.  Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context.

Authors:  Vivian Robin; Antoine Bodein; Marie-Pier Scott-Boyer; Mickaël Leclercq; Olivier Périn; Arnaud Droit
Journal:  Front Mol Biosci       Date:  2022-09-08
  1 in total

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