21 Papers
14 Citations
Mingze Bai is an academic researcher from Chongqing University of Posts and Telecommunications. The author has contributed to research in topics: Computer science & Metadata. The author has an hindex of 6, co-authored 16 publications. Previous affiliations of Mingze Bai include European Bioinformatics Institute & Protein Sciences.
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Papers
iProX: an integrated proteome resource.
Jie Ma,Tao Chen,Songfeng Wu,Chunyuan Yang,Mingze Bai,Kunxian Shu,Kenli Li,Guoqing Zhang,Zhong Jin,Fuchu He,Henning Hermjakob,Henning Hermjakob,Yunping Zhu +12 more
TL;DR: iProX will facilitate worldwide data analysis and sharing of proteomics experiments, and is based on a high availability architecture and has been deployed as part of the proteomics infrastructure of China, ensuring long-term and stable resource support.
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BioContainers: an open-source and community-driven framework for software standardization.
Felipe da Veiga Leprevost,Björn Grüning,Saulo Alves Aflitos,Hannes L. Röst,Julian Uszkoreit,Harald Barsnes,Marc Vaudel,Marc Vaudel,Pablo Moreno,Laurent Gatto,Jonas Weber,Mingze Bai,Rafael C. Jimenez,Timo Sachsenberg,Julianus Pfeuffer,Roberto Vera Alvarez,Johannes Griss,Johannes Griss,Alexey I. Nesvizhskii,Yasset Perez-Riverol +19 more
TL;DR: This paper presents BioContainers, an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software, and provides infrastructure and basic guidelines to create, manage and distribute bioInformatics containers with a special focus on omics technologies.
A proteomics sample metadata representation for multiomics integration and big data analysis.
Chengxin Dai,Anja Füllgrabe,Julianus Pfeuffer,Julianus Pfeuffer,Elizaveta M. Solovyeva,Elizaveta M. Solovyeva,Jingwen Deng,Pablo Moreno,Selvakumar Kamatchinathan,Deepti J. Kundu,Nancy George,Silvie Fexova,Björn Grüning,Melanie Christine Föll,Melanie Christine Föll,Johannes Griss,Marc Vaudel,Enrique Audain,Marie Locard-Paulet,Michael Turewicz,Martin Eisenacher,Julian Uszkoreit,Tim Van Den Bossche,Veit Schwämmle,Henry Webel,Stefan Schulze,David Bouyssié,Savita Jayaram,Vinay Kumar Duggineni,Patroklos Samaras,Mathias Wilhelm,Meena Choi,Mingxun Wang,Oliver Kohlbacher,Alvis Brazma,Irene Papatheodorou,Nuno Bandeira,Eric W. Deutsch,Juan Antonio Vizcaíno,Mingze Bai,Mingze Bai,Timo Sachsenberg,Lev I. Levitsky,Yasset Perez-Riverol +43 more
TL;DR: In this article, the authors propose a standard representation for proteomics sample metadata, called MAGE-TAB-Proteomics, which is used to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis.
Deep learning embedder method and tool for mass spectra similarity search.
Chunyuan Qin,Xiyang Luo,Chuan Deng,Kunxian Shu,Weimin Zhu,Johannes Griss,Henning Hermjakob,Mingze Bai,Mingze Bai,Yasset Perez-Riverol +9 more
TL;DR: A new tool mslookup is proposed that enables the researcher to find spectra previously identified in public data that is faster for future comparisons and large-scale data and a human database is released to enable bioinformaticians and biologists to search for identified spectra in their machines.
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Omics Discovery Index - Discovering and Linking Public Omics Datasets
Yasset Perez-Riverol,Mingze Bai,Felipe da Veiga Leprevost,Silvano Squizzato,Y Park Mi,O Haug,AJ Carroll,Dylan Spalding,Justin Paschall,Mingxun Wang,Noemi del-Toro,Tobias Ternent,Peng Zhang,Nicola Buso,Nuno Bandeira,Eric W. Deutsch,David S. Campbell,Ronald C. Beavis,Reza M. Salek,Alexey I. Nesvizhskii,Susanna Sansone,Christoph Steinbeck,Rodrigo Lopez,Juan Antonio Vizcaíno,Peipei Ping,Henning Hermjakob +25 more
TL;DR: There is a great need for development of new platforms and applications to make possible to search datasets across different omics fields, making such information accessible to the end-user.