Explanipedia

Parecer prévio em perícia contábil: análise crítica da qualidade técnica e do impacto no contraditório técnico Open

Diogo Borges Lima, Cássio Miri Oliveira, A. Pinto da Costa · 2025

Os pareceres prévios desempenham um papel crucial no processo judicial e extrajudicial, contribuindo para o contraditório técnico ao antecipar questões relevantes e fornecer subsídios para a análise pericial. Este estudo analisou criticame…

AIRPred: A Deep Learning Model Predictor for Peptide Intensity Ratios in Cross-Linking Mass Spectrometry Improves Cross-Link Spectrum Matching Open

Zehong Zhang, Mei Wu, Max Ruwolt, Ying Zhu, Pin‐Lian Jiang , et al. · 2025

Cross-linking mass spectrometry (XL-MS) is a powerful tool in structural proteomics, offering insights into protein conformations, interactions and dynamics by linking spatially proximal residues. However, current cross-linked spectrum mat…

Tratamento do Transtorno Afetivo Bipolar Durante a Gravidez: Uma Revisão Crítica da Terapêutica Farmacológica Open

L. Andrade, Diogo Borges Lima, Harianne Vitoria Silva Borges, Aline Ramos da Silva, Isabela Fiorin Carmona , et al. · 2025

O transtorno afetivo bipolar (TAB) durante a gestação representa um desafio clínico significativo, pois exige equilíbrio entre eficácia terapêutica e segurança fetal. A descontinuação abrupta da medicação aumenta o risco de recaídas graves…

Abordagens Assistidas por Robótica na Cirurgia de Câncer Colorretal Open

Luiz A. Rocha, Diogo Borges Lima, Marta Coelho, Rita Pereira, Maria Clara de Queiroz Braz , et al. · 2025

O artigo apresenta uma revisão integrativa da literatura sobre a cirurgia robótica no tratamento do câncer colorretal, destacando que, embora essa técnica oferece inovações tecnológicas significativas—como visão tridimensional, maior preci…

Descrição da veia safena anterior: relato de caso Open

Helder Bindá Pimenta, Marta Coelho, Diogo Borges Lima, Giovanna Regina Melo Basilio, Evaldo Nascimento , et al. · 2025

O conhecimento aprofundado das variações anatômicas na drenagem venosa superficial do corpo humano é essencial para práticas clínicas e cirúrgicas de precisão. Neste estudo de caso, foi identificada a presença da veia safena anterior no se…

Prevenção da Obesidade Infantil: Uma Revisão Integrativa das Abordagens e Seus Resultados Open

Hugo Dionizio Gomes da Silva Berger, Diogo Borges Lima, Giovanna Tarsitani Eskinazi · 2024

A obesidade infantil tem se tornado um grave problema de saúde pública em diversos países, devido ao seu impacto negativo na saúde física e psicológica das crianças, além de aumentar o risco de doenças crônicas na vida adulta. A prevenção …

Duplicação unilateral de veia jugular interna Open

Helder Bindá Pimenta, Anna Rachel Bengaly Moita, Natasha Thais Dahrouge Alecrim, Zumma da Silva Lima Feijão, Ana Rafaela Barreto Matheus , et al. · 2024

A duplicação da veia jugular interna é um fenômeno pouco comum, com apenas vinte e um casos registrados em dezoito indivíduos até o momento. Aqui, relatamos um caso de duplicação unilateral da veia jugular interna. Ambas tributavam individ…

Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics Open

Milan Avila Clasen, Max Ruwolt, Cong Wang, Julia Ruta, Boris Bogdanow , et al. · 2024

Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies Open

Ying Zhu, Kerem Can Akkaya, Julia Ruta, Nanako Yokoyama, Cong Wang , et al. · 2024

RawVegetable 2.0: Refining XL-MS Data Acquisition through Enhanced Quality Control Open

Louise Ulrich Kurt, Milan Avila Clasen, Ísis Venturi Biembengut, Max Ruwolt, Fan Liu , et al. · 2024

We present RawVegetable 2.0, a software tailored for assessing mass spectrometry data quality and fine-tuned for cross-linking mass spectrometry (XL-MS) applications. Building upon the capabilities of its predecessor, RawVegetable 2.0 intr…

PROTEOME-SCALE RECOMBINANT STANDARDS AND A ROBUST HIGH-SPEED SEARCH ENGINE TO ADVANCE CROSS-LINKING MS-BASED INTERACTOMICS Open

Milan Avila Clasen, Max Ruwolt, Louise Ulrich Kurt, Fábio C. Gozzo, Shuai Wang , et al. · 2023

A bstract Advancing data analysis tools for proteome-wide cross-linking mass spectrometry (XL-MS) requires ground-truth standards that mimic biological complexity. Here, we develop wellcontrolled XL-MS standards comprising hundreds of reco…

Shigella IpaA mediates actin bundling through diffusible vinculin oligomers with activation imprint Open

Cesar Valencia‐Gallardo, Daniel-Isui Aguilar-Salvador, Hamed Khakzad, Benjamin Cocom-Chan, Charles Bou‐Nader , et al. · 2023

Upon activation, vinculin reinforces cytoskeletal anchorage during cell adhesion. Activating ligands classically disrupt intramolecular interactions between the vinculin head and tail domains that bind to actin filaments. Here, we show tha…

PatternLab V Handles Multiplex Spectra in Shotgun Proteomic Searches and Increases Identification Open

Milan Avila Clasen, Marlon Dias Mariano Santos, Louise Ulrich Kurt, Juliana de Saldanha da Gama Fischer, Amanda C. Camillo-Andrade , et al. · 2023

Complex protein mixtures typically generate many tandem mass spectra produced by different peptides coisolated in the gas phase. Widely adopted proteomic data analysis environments usually fail to identify most of these spectra, succeeding…

Real-Time Library Search Increases Cross-Link Identification Depth across All Levels of Sample Complexity Open

Max Ruwolt, Yi He, Diogo Borges Lima, William D. Barshop, Johannes Broichhagen , et al. · 2023

Cross-linking mass spectrometry (XL-MS) is a universal tool for probing structural dynamics and protein-protein interactions in vitro and in vivo. Although cross-linked peptides are naturally less abundant than their unlinked…

DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters Open

Marlon Dias Mariano Santos, Amanda C. Camillo-Andrade, Diogo Borges Lima, T.A.C.B. Souza, Juliana de Saldanha da Gama Fischer , et al. · 2023

DiagnoMass and related documentation, including a usage protocol, are available at http://www.diagnomass.com.

Real-time library search increases cross-link identification depth across all levels of sample complexity Open

Max Ruwolt, Yi He, Diogo Borges Lima, William D. Barshop, Johannes Broichhagen , et al. · 2022

Cross-linking mass spectrometry (XL-MS) is a universal tool for probing structural dynamics and protein-protein interactions in vitro and in vivo . Although cross-linked peptides are naturally less abundant than their unlinked counterparts…

<i>Shigella</i>ipaA mediates actin bundling through diffusible vinculin oligomers with activation imprint Open

Cesar Valencia‐Gallardo, Daniel-Isui Aguilar-Salvador, Hamed Khakzad, Benjamin Cocom-Chan, Charles Bou‐Nader , et al. · 2022

Upon activation, vinculin reinforces cytoskeletal anchorage during cell adhesion. Activating ligands classically disrupt intramolecular interactions between the vinculin head and tail domain that binds to actin filaments. Here, we show tha…

Increasing confidence in proteomic spectral deconvolution through mass defect Open

Milan Avila Clasen, Louise Ulrich Kurt, Marlon Dias Mariano Santos, Diogo Borges Lima, Fan Liu , et al. · 2022

Motivation Confident deconvolution of proteomic spectra is critical for several applications such as de novo sequencing, cross-linking mass spectrometry and handling chimeric mass spectra. Results In general, all deconvolution algorithms m…

Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topology Open

Ying Zhu, Kerem Can Akkaya, Diogo Borges Lima, Cong Wang, Martin Lehmann , et al. · 2022

The specific functions of cellular organelles and sub-compartments depend on their protein content, which can be characterized by spatial proteomics approaches. However, many spatial proteomics methods are limited in their ability to resol…

Molecular Architecture of the Antiophidic Protein DM64 and its Binding Specificity to Myotoxin II From Bothrops asper Venom Open

Barbara S. Soares, Sabine Borges da Rocha, Viviane A. Bastos, Diogo Borges Lima, Paulo C. Carvalho , et al. · 2022

DM64 is a toxin-neutralizing serum glycoprotein isolated from Didelphis aurita , an ophiophagous marsupial naturally resistant to snake envenomation. This 64 kDa antitoxin targets myotoxic phospholipases A 2 , which account for most local …

TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics Open

Jonathan Dhenin, Diogo Borges Lima, Mathieu Dupré, Julia Chamot‐Rooke · 2021

Motivation We present a new software-tool allowing an easy visualization of fragment ions and thus a rapid evaluation of key experimental parameters on the sequence coverage obtained for the MS/MS (tandem mass spectrometry) analysis of int…

TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics Open

Jonathan Dhenin, Diogo Borges Lima, Mathieu Dupré, Julia Chamot‐Rooke · 2021

Motivation We present a new software-tool allowing an easy visualization of fragment ions and thus a rapid evaluation of key experimental parameters on the sequence coverage obtained for the MS/MS analysis of intact proteins. Our tool can …

Leveraging the partition selection bias to achieve a high-quality clustering of mass spectra Open

André R.F. Silva, Diogo Borges Lima, Louise Ulrich Kurt, Mathieu Dupré, Julia Chamot‐Rooke , et al. · 2021

In proteomics, the identification of peptides from mass spectral data can be mathematically described as the partitioning of mass spectra into clusters (i.e., groups of spectra derived from the same peptide). The way partitions are validat…

Using TDFragMapper: a high-performance tool to assess experimental parameters in top-down proteomics Open

Diogo Borges Lima, Jonathan Dhenin, Mathieu Dupré, Julia Chamot‐Rooke · 2021

Here we present a new software-tool for visualizing fragment ions and sequence coverage of intact proteins in top-down mass spectrometry. TDFragMapper combines the data arising from multiple and diverse tandem mass spectrometry experiments…

DiagnoTop: A Computational Pipeline for Discriminating Bacterial Pathogens without Database Search Open

Diogo Borges Lima, Mathieu Dupré, Marlon Dias Mariano Santos, Paulo C. Carvalho, Julia Chamot‐Rooke · 2021

Pathogen identification is crucial to confirm bacterial infections and guide antimicrobial therapy. Although MALDI-TOF mass spectrometry (MS) serves as foundation for tools that enable rapid microbial identification, some bacteria remain c…

Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition Open

Louise Ulrich Kurt, Milan Avila Clasen, Marlon Dias Mariano Santos, Eduardo S B Lyra, Luana Oliveira dos Santos , et al. · 2021

Motivation Chemical cross-linking coupled to mass spectrometry (XLMS) emerged as a powerful technique for studying protein structures and large-scale protein-protein interactions. Nonetheless, XLMS lacks software tailored toward dealing wi…

<i>Shigella</i> ipaA Mediates Actin Bundling Through Diffusible Vinculin Oligomers With Activation Imprint Open

Daniel-Isui Aguilar-Salvador, Cesar Valencia‐Gallardo, Hamed Khakzad, Charles Bou‐Nader, Christophe Le Clainche , et al. · 2021

XlinkCyNET: a Cytoscape application for visualization of protein interaction networks based on cross-linking mass-spectrometry identifications Open

Diogo Borges Lima, Ying Zhu, Fan Liu · 2020

Software tools that allow visualization and analysis of protein interaction networks are essential for studies in systems biology. One of the most popular network visualization tools in biology is Cytoscape, which offers a large selection …

Using XlinkCyNET to visualize protein cross-links in Cytoscape software Open

Diogo Borges Lima, Ying Zhu, Fan Liu · 2020

We present a high-performance app for Cytoscape to visualize cross-linking mass-spectrometry (XL-MS) data. XlinkCyNET is an open-source Java plugin that generates residue-to-residue connections provided by XL-MS in protein interaction netw…

ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment Open

Diogo Borges Lima, Mathieu Dupré, Magalie Duchateau, Quentin Giai Gianetto, Martial Rey , et al. · 2020

Motivation We present a high-performance software integrating shotgun with top-down proteomic data. The tool can deal with multiple experiments and search engines. Enable rapid and easy visualization, manual validation and comparison of th…

Diogo Borges Lima YOU? Author Swipe