Nuno Bandeira

ORCID

Publication Activity (10 Years)

Years Active: 2020-2023
Publications (10 Years): 23

Top Venues

Journal of proteome research

Nature methods

PNAS nexus

Nature communications

University of California San Diego

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of California San Diego

United States

Associate Professor :: CSE / SSPPS

Publications

Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research 22 (2) (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research 22 (2) (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research 22 (2) (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research 22 (2) (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research 22 (2) (2023)
Gilbert S Omenn, Lydie Lane, Christopher M Overall, Charles Pineau, Nicolle H Packer, Ileana M Cristea, Cecilia Lindskog, Susan T Weintraub, Sandra E Orchard, Michael H A Roehrl, Edouard Collins Nice, Siqi Liu, Nuno Bandeira, Yi-Ju Chen, Tiannan Guo, Ruedi Aebersold, Robert L Moritz, Eric W Deutsch
The 2022 Report on the Human Proteome from the HUPO Human Proteome Project. Journal of proteome research (2022)
Tiago F Leão, Mingxun Wang, Ricardo R da Silva, Alexey Gurevich, Anelize Bauermeister, Paulo Wender Portal Gomes, Asker Daniel Brejnrod, Evgenia Glukhov, Allegra T Aron, Joris J R Louwen, Hyun Woo Kim, Raphael Reher, Marli Fatima Fiore, Justin Johan Jozias van der Hooft, Lena Gerwick, William H Gerwick, Nuno Bandeira, Pieter C Dorrestein
NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters. PNAS nexus 1 (5) (2022)
Richard D LeDuc, Eric W Deutsch, Pierre-Alain Binz, Ryan T Fellers, Anthony J Cesnik, Joshua A Klein, Tim Van Den Bossche, Ralf Gabriels, Arshika Yalavarthi, Yasset Perez Riverol, Jeremy Carver, Wout Bittremieux, Shin Kawano, Benjamin Pullman, Nuno Bandeira, Neil L Kelleher, Paul M Thomas, Juan Antonio Vizcaino
Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms. Journal of proteome research 21 (4) (2022)
Tiago F Leão, Mingxun Wang, Ricardo R da Silva, Alexey Gurevich, Anelize Bauermeister, Paulo Wender Portal Gomes, Asker Daniel Brejnrod, Evgenia Glukhov, Allegra T Aron, Joris J R Louwen, Hyun Woo Kim, Raphael Reher, Marli Fatima Fiore, Justin Johan Jozias van der Hooft, Lena Gerwick, William H Gerwick, Nuno Bandeira, Pieter C Dorrestein
NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters. PNAS nexus 1 (5) (2022)
Wout Bittremieux, Charlotte Adams, Kris Laukens, Pieter C Dorrestein, Nuno Bandeira
Open Science Resources for the Mass Spectrometry-Based Analysis of SARS-CoV-2. Journal of proteome research 20 (3) (2021)
Eric W Deutsch, Yasset Perez Riverol, Jeremy Carver, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Pierre-Alain Binz, Benjamin Pullman, Zhi Sun, Jim Shofstahl, Wout Bittremieux, Tytus D Mak, Joshua Klein, Yunping Zhu, Henry H N Lam, Juan Antonio Vizcaino, Nuno Bandeira
Universal Spectrum Identifier for mass spectra. Nature methods 18 (7) (2021)
Tiago F Leao, Chase M Clark, Anelize Bauermeister, Emmanuel O Elijah, Emily C Gentry, Makhai Husband, Michelli F Oliveira, Nuno Bandeira, Mingxun Wang, Pieter C Dorrestein
Quick-start infrastructure for untargeted metabolomics analysis in GNPS. Nature metabolism 3 (7) (2021)
Gilbert S Omenn, Lydie Lane, Christopher M Overall, Young-Ki Paik, Ileana M Cristea, Fernando José Corrales, Cecilia Lindskog, Susan T Weintraub, Michael H A Roehrl, Siqi Liu, Nuno Bandeira, Sudhir Srivastava, Yi-Ju Chen, Ruedi Aebersold, Robert L Moritz, Eric W Deutsch
Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project. Journal of proteome research 20 (12) (2021)
Chengxin Dai, Anja Füllgrabe, Julianus Pfeuffer, Elizaveta M Solovyeva, Jingwen Deng, Pablo Moreno, Selvakumar Kamatchinathan, Deepti Jaiswal Kundu, Nancy George, Silvie Fexova, Bjoern Andreas Gruening, 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 Vizcaino, Mingze Bai, Timo Sachsenberg, Lev I Levitsky, Yasset Perez Riverol
A proteomics sample metadata representation for multiomics integration and big data analysis. Nature communications 12 (1) (2021)
Daniel Petras, Vanessa V Phelan, Deepa Acharya, Andrew Ellis Allen, Allegra T Aron, Nuno Bandeira, Benjamin P Bowen, Deirdre Belle-Oudry, Simon Boecker, Dale A Cummings, Jessica M Deutsch, Eoin Fahy, Neha Garg, Rachel Gregor, Jo Handelsman, Mirtha Navarro-Hoyos, Alan K Jarmusch, Scott Alexander Jarmusch, Katherine Louie, Katherine N Maloney, Michael Thomas Marty, Michael M Meijler, Itzhak Mizrahi, Rachel L Neve, Trent R Northen, Carlos Molina-Santiago, Morgan Panitchpakdi, Benjamin S Pullman, Aaron W Puri, Robin Schmid, Shankar Subramaniam, Monica Thukral, Felipe Vasquez-Castro, Pieter C Dorrestein, Mingxun Wang
GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nature methods (2021)
Meena Choi, Jeremy Carver, Cristina Chiva, Manuel Tzouros, Ting Huang, Tsung-Heng Tsai, Benjamin S Pullman, Oliver M Bernhardt, Ruth Hüttenhain, Guo Ci Teo, Yasset Perez Riverol, Jan Muntel, Maik Müller, Sandra Goetze, Maria Pavlou, Erik Verschueren, Bernd Wollscheid, Alexey I Nesvizhskii, Lukas Reiter, Tom Dunkley, Eduard Sabidó, Nuno Bandeira, Olga Vitek
MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets. Nature methods 17 (10) (2020)
Subash Adhikari, Edouard C Nice, Eric W Deutsch, Lydie Lane, Gilbert S Omenn, Stephen R Pennington, Young-Ki Paik, Christopher M Overall, Fernando J Corrales, Ileana M Cristea, Jennifer E Van Eyk, Mathias Uhlen, Cecilia Lindskog, Daniel W Chan, Amos Bairoch, James C Waddington, Joshua L Justice, Joshua LaBaer, Henry Rodriguez, Fuchu He, Markus Kostrzewa, Peipei Ping, Rebekah L Gundry, Peter Stewart, Sanjeeva Srivastava, Sudhir Srivastava, Fabio C S Nogueira, Gilberto B Domont, Yves Vandenbrouck, Maggie P Y Lam, Sara Wennersten, Juan Antonio Vizcaino, Marc R Wilkins, Jochen M Schwenk, Emma Lundberg, Nuno Bandeira, Gyorgy Marko-Varga, Susan T Weintraub, Charles Pineau, Ulrike Kusebauch, Robert L Moritz, Seong Beom Ahn, Magnus Palmblad, Michael Paul Snyder, Ruedi Aebersold, Mark S Baker
A high-stringency blueprint of the human proteome. Nature communications 11 (1) (2020)
Michael R Hoopmann, Ulrike Kusebauch, Magnus Palmblad, Nuno Bandeira, David D Shteynberg, Lingjie He, Bin Xia, Stoyan H Stoychev, Gilbert S Omenn, Susan T Weintraub, Robert L Moritz
Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project. Journal of proteome research 19 (12) (2020)
Alan K Jarmusch, Mingxun Wang, Christine M Aceves, Rohit S Advani, Shaden Aguirre, Alexander A Aksenov, Gajender Aleti, Allegra T Aron, Anelize Bauermeister, Sanjana Bolleddu, Amina Bouslimani, Andres Mauricio Caraballo Rodriguez, Rama Chaar, Roxana Coras, Emmanuel O Elijah, Madeleine Ernst, Julia M Gauglitz, Emily C Gentry, Makhai Husband, Scott A Jarmusch, Kenneth L Jones, Zdeněk Kameník, Audrey Le Gouëllec, Aileen Lu, Laura-Isobel McCall, Kerry L McPhail, Michael J Meehan, Alexey V Melnik, Riya C Menezes, Yessica Alejandra Montoya Giraldo, Ngoc Hung Nguyen, Louis-Felix Nothias, Mélissa Nothias-Esposito, Morgan Panitchpakdi, Daniel Petras, Robert A Quinn, Nicole Sikora, Justin Johan Jozias van der Hooft, Fernando Vargas, Alison Vrbanac, Kelly C Weldon, Rob Knight, Nuno Bandeira, Pieter C Dorrestein
ReDU: a framework to find and reanalyze public mass spectrometry data. Nature methods 17 (9) (2020)
Gilbert S Omenn, Lydie Lane, Christopher M Overall, Ileana M Cristea, Fernando José Corrales, Cecilia Lindskog, Young-Ki Paik, Jennifer E Van Eyk, Siqi Liu, Stephen R Pennington, Michael P Snyder, Mark S Baker, Nuno Bandeira, Ruedi Aebersold, Robert L Moritz, Eric W Deutsch
Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. Journal of proteome research 19 (12) (2020)
Louis-Félix Nothias, Daniel Petras, Robin Schmid, Kai Dührkop, Johannes Rainer, Abinesh Sarvepalli, Ivan Protsyuk, Madeleine Ernst, Hiroshi Tsugawa, Markus Fleischauer, Fabian Aicheler, Alexander A Aksenov, Oliver Alka, Pierre-Marie Allard, Aiko Barsch, Xavier Cachet, Andrés Mauricio Caraballo-Rodriguez, Ricardo R Da Silva, Tam Dang, Neha Garg, Julia M Gauglitz, Alexey Gurevich, Giorgis Isaac, Alan K Jarmusch, Zdeněk Kameník, Kyo-Bin Kang, Nikolas Kessler, Irina Koester, Ansgar Korf, Audrey Le Gouëllec, Marcus Ludwig, Christian Martin H, Laura-Isobel McCall, Jonathan McSayles, Sven W Meyer, Hosein Mohimani, Mustafa Morsy, Oriane Moyne, Steffen Neumann, Heiko Neuweger, Ngoc Hung Nguyen, Melissa Nothias-Esposito, Julien Paolini, Vanessa V Phelan, Tomáš Pluskal, Robert A Quinn, Simon Rogers, Bindesh Shrestha, Anupriya Tripathi, Justin Johan Jozias van der Hooft, Fernando Vargas, Kelly C Weldon, Michael Witting, Heejung Yang, Zheng Zhang, Florian Zubeil, Oliver Kohlbacher, Sebastian Böcker, Theodore Alexandrov, Nuno Bandeira, Mingxun Wang, Pieter C Dorrestein
Feature-based molecular networking in the GNPS analysis environment. Nature methods 17 (9) (2020)

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Publication Activity (10 Years)

Top Topics

Top Venues

Nuno Bandeira