Publications by authors named "Diogo Lima"

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Structural dynamics of the TPS/TPP complex in Saccharomyces cerevisiae: Insights from cross-linking mass spectrometry and computational modeling.
Renata M Santos, Viviane A Bastos, Felipe F M Bagatelli, Richard H Valente, Louise U Kurt, Diogo B Lima

J Proteomics· January 2026

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AIRPred: A Deep Learning Model Predictor for Peptide Intensity Ratios in Cross-Linking Mass Spectrometry Improves Cross-Link Spectrum Matching.
Zehong Zhang, Mei Wu, Max Ruwolt, Ying Zhu, Pin-Lian Jiang, Diogo Borges Lima

Anal Chem· November 2025

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Q2C: A software for managing mass spectrometry facilities.
Diogo B Lima, Max Ruwolt, Marlon D M Santos, Ke Pu, Fan Liu

J Proteomics· October 2025

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The association of ABC proteins with multidrug resistance in cancer.
Andrezza Viviany Lourenço Marques, Bruna Estelita Ruginsk, Larissa de Oliveira Prado, Diogo Eugênio de Lima, Isabelle Watanabe Daniel

Biochim Biophys Acta Mol Cell Res· February 2025

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Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics.
Milan Avila Clasen, Max Ruwolt, Cong Wang, Julia Ruta, Boris Bogdanow, Diogo Borges Lima

Nat Methods· December 2024

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RawVegetable 2.0: Refining XL-MS Data Acquisition through Enhanced Quality Control.
Louise Ulrich Kurt, Milan Avila Clasen, Ísis Venturi Biembengut, Max Ruwolt, Fan Liu, Diogo Borges Lima

J Proteome Res· August 2024

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Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies.
Ying Zhu, Kerem Can Akkaya, Julia Ruta, Nanako Yokoyama, Cong Wang, Diogo Borges Lima

Nat Commun· April 2024

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"Choose it, and remember it": The impact of choice on destination memory.
Diogo Lima, Pedro B Albuquerque, María Soledad Beato

Scand J Psychol· December 2023

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Correlation between levels of perceived stress and depressive symptoms in the functional disability of patients with fibromyalgia.
Luiz Gustavo Rachid Fernandes, Carolyn Maria de Geus Wenceslau, André Amaro Mamédio Dos Santos, Diogo Von Gaevernitz Lima, Luiz Henrique Junqueira Dieckmann

Rev Assoc Med Bras (1992)· November 2023

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The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber.
Emanuel Cunha, Miguel Silva, Inês Chaves, Huseyin Demirci, Davide Rafael Lagoa, Diogo Lima

PLoS Comput Biol· September 2023

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Remembering to whom we transmit information during pandemics: the effect of face masks on destination memory.
Raquel Pinto, Diogo Lima, Beatriz Mello, Pedro B Albuquerque

Cogn Process· May 2023

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DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters.
Marlon D M Santos, Amanda C Camillo-Andrade, Diogo B Lima, Tatiana A C B Souza, Juliana de S da G Fischer

J Proteomics· April 2023

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PatternLab V Handles Multiplex Spectra in Shotgun Proteomic Searches and Increases Identification.
Milan A Clasen, Marlon D M Santos, Louise Ulrich Kurt, Juliana Fischer, Amanda C Camillo-Andrade, Diogo Borges Lima

J Am Soc Mass Spectrom· April 2023

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Shigella IpaA mediates actin bundling through diffusible vinculin oligomers with activation imprint.
Cesar Valencia-Gallardo, Daniel-Isui Aguilar-Salvador, Hamed Khakzad, Benjamin Cocom-Chan, Charles Bou-Nader, Diogo Borges Lima

Cell Rep· April 2023

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The COVID-19 outbreak on dental practice in State of São Paulo, Brazil.
Thamires Diogo Lima, Laís Lima Pelozo, Silmara Aparecida Milori Corona, Claudio Souza Miranda, Aline Evangelista Souza-Gabriel

Int J Environ Health Res· December 2022

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Increasing confidence in proteomic spectral deconvolution through mass defect.
Milan A Clasen, Louise U Kurt, Marlon D M Santos, Diogo B Lima, Fan Liu

Bioinformatics· November 2022

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Two New Species of () from Soil in an Upland Forest in Northeastern Brazil with an Identification Key of from the Americas.
Catarina Letícia Ferreira de Lima, Joana D'arc Alves Leitão Lundgren, Thuong Thuong Thi Nguyen, Thalline Rafhaella Leite Cordeiro, Diogo Xavier Lima

J Fungi (Basel)· September 2022

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Simple, efficient and thorough shotgun proteomic analysis with PatternLab V.
Marlon D M Santos, Diogo B Lima, Juliana S G Fischer, Milan A Clasen, Louise U Kurt

Nat Protoc· July 2022

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merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models.
João Capela, Davide Lagoa, Ruben Rodrigues, Emanuel Cunha, Fernando Cruz, Diogo Lima

Nucleic Acids Res· June 2022

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Molecular Architecture of the Antiophidic Protein DM64 and its Binding Specificity to Myotoxin II From Venom.
Barbara S Soares, Surza Lucia G Rocha, Viviane A Bastos, Diogo B Lima, Paulo C Carvalho

Front Mol Biosci· January 2022

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Recognition and naming test of the Portuguese population for national and international celebrities.
Diogo Lima, Raquel Pinto, Pedro B Albuquerque

Behav Res Methods· December 2021

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Genomic Regions Associated with the Position and Number of Hair Whorls in Horses.
Diogo Felipe Pereira de Assis Lima, Valdecy Aparecida Rocha da Cruz, Guilherme Luís Pereira, Rogério Abdallah Curi, Raphael Bermal Costa

Animals (Basel)· October 2021

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Leveraging the partition selection bias to achieve a high-quality clustering of mass spectra.
André R F Silva, Diogo B Lima, Louise U Kurt, Mathieu Dupré, Julia Chamot-Rooke

J Proteomics· August 2021

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Evaluation of the Reproducibility of Lauge-Hansen, Danis-Weber, and AO Classifications for Ankle Fractures.
Lucas Sacramento Ramos, Henrique Mansur Gonçalves, Anderson Freitas, Marcio de Paiva Oliveira, Diogo Marcelino Santos Lima

Rev Bras Ortop (Sao Paulo)· June 2021

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XlinkCyNET: A Cytoscape Application for Visualization of Protein Interaction Networks Based on Cross-Linking Mass Spectrometry Identifications.
Diogo Borges Lima, Ying Zhu, Fan Liu

J Proteome Res· April 2021

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