Article
Biochemical Research Methods
Giovanni Marques de Castro, Zandora Hastenreiter, Thiago Augusto Silva Monteiro, Thieres Tayroni Martins da Silva, Francisco Pereira Lobo
Summary: This article presents and validates a machine learning strategy to predict essential genes in insects using sequence-based intrinsic attributes and transcriptomic data. Even models trained using only intrinsic attributes can predict genes in other insect species, including lineage-specific essential genes. Furthermore, the inclusion of RNA-Seq data contributes to increased classifier performance.
Article
Biochemical Research Methods
Lesong Wei, Xiucai Ye, Yuyang Xue, Tetsuya Sakurai, Leyi Wei
Summary: ATSE is a peptide toxicity predictor based on graph neural networks and attention mechanism, which accurately predicts the potential toxicity of peptides. By combining structural and evolutionary information, ATSE outperforms other methods and provides interpretable and visualizable features for further analysis.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Lin Yang, Feng Ding, Qiang Lin, Junhua Xie, Wei Fan, Fangyin Dai, Peng Cui, Wanfei Liu
Summary: PMPrimer is an automated tool for designing and evaluating multiplex PCR primer pairs for specific targets. It uses statistical filtering and multiple sequence alignment to design optimal primer pairs, and evaluates them based on template coverage, taxon specificity, and target specificity. PMPrimer showed outstanding performance and adaptability compared to existing tools.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Andreas Lange, Prajal H. Patel, Brennen Heames, Adam M. Damry, Thorsten Saenger, Colin J. Jackson, Geoffrey D. Findlay, Erich Bornberg-Bauer
Summary: By analyzing the function and structure of the gene goddard, which emerged de novo at least 50 million years ago within the Drosophila genus, it was found that the protein structure has remained largely unchanged over millions of years of evolution.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Alex Morehead, Chen Chen, Ada Sedova, Jianlin Cheng
Summary: In this work, we introduce DIPS-Plus, an enhanced dataset for machine learning of protein interfaces, which contains additional features compared to the original DIPS dataset. By training a state-of-the-art model on DIPS-Plus, we achieve better results than previous models trained on residue-level and atom-level encodings of protein complexes.
Article
Biochemical Research Methods
Jerome Tubiana, Dina Schneidman-Duhovny, Haim J. Wolfson
Summary: This study introduces ScanNet, a geometric deep learning model that learns features directly from the 3D structure of proteins to predict their functional sites. By training on protein-protein and protein-antibody binding sites, ScanNet demonstrates accuracy and interpretable learned features. Additionally, ScanNet successfully predicts antigenic epitopes of the SARS-CoV-2 spike protein.
Article
Multidisciplinary Sciences
Yiyu Hong, Jinung Song, Junsu Ko, Juyong Lee, Woong-Hee Shin
Summary: S-Pred is a powerful new tool that can predict secondary structures, accessible surface areas, and intrinsically disordered regions from a given protein sequence. The tool utilizes multiple sequence alignment and an attention mechanism protein language model for feature prediction, with final predictions generated by a long short-term memory. The program consistently provides accurate predictions for various test sets.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Physical
Jingzi Zhang, Zhuoxuan Zhu, X. -D. Xiang, Ke Zhang, Shangchao Huang, Chengquan Zhong, Hua-Jun Qiu, Kailong Hu, Xi Lin
Summary: This study introduces a structural descriptor called smooth overlap of atomic position (SOAP) into machine learning (ML) models to predict the T-c values of superconductors. The ML models achieved a high prediction accuracy using the SOAP descriptor and identified new high-temperature superconductors.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Biology
Xingyue Gu, Yijie Ding, Pengfeng Xiao
Summary: Protein sequence classification is an important field in bioinformatics that plays a vital role in functional annotation, structure prediction, and understanding protein function and interactions. However, existing machine learning methods have limitations in terms of accuracy, precision, and generalization capabilities for different types of proteins. In this study, a protein sequence classifier called MLapRVFL is proposed, which incorporates Multi-Laplacian and L2,1-norm regularization to improve the model's generalization performance, robustness, and accuracy. Experimental results demonstrate that MLapRVFL outperforms popular machine learning methods and achieves superior predictive performance compared to previous studies. Overall, the proposed MLapRVFL method makes significant contributions to protein sequence prediction.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biochemical Research Methods
Gokhan Ozsari, Ahmet Sureyya Rifaioglu, Ahmet Atakan, Tunca Dogan, Maria Jesus Martin, Rengul Cetin Atalay, Volkan Atalay
Summary: In this study, the researchers propose SLPred, an ensemble-based multi-view and multi-label protein subcellular localization prediction tool, which provides predictions for nine main subcellular locations using independent machine-learning models. The results show that SLPred outperforms other tools in most cases.
Article
Biochemical Research Methods
Anja Moesch, Dmitrij Frishman
Summary: The ability of T cells to recognize foreign peptides is determined by a single alpha and beta chain, with sometimes multiple chains being expressed but only one being functional. TCRpair is a method that predicts functional TCR pairs, which is crucial for high-throughput characterization of therapeutic TCRs.
Article
Engineering, Biomedical
Madhura Ingalhalikar, Sumeet Shinde, Arnav Karmarkar, Archith Rajan, D. Rangaprakash, Gopikrishna Deshpande
Summary: The study demonstrates that harmonization of multi-site neuroimaging data using ComBat technique improves diagnostic classification accuracy, especially for autism spectrum disorder. Insights into ASD pathology and connectivity networks were gained through network ablation analysis.
IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING
(2021)
Review
Pharmacology & Pharmacy
Masataka Kuroda, Reiko Watanabe, Tsuyoshi Esaki, Hitoshi Kawashima, Rikiya Ohashi, Tomohiro Sato, Teruki Honma, Hiroshi Komura, Kenji Mizuguchi
Summary: This article discusses one solution to address the shortage of publicly available data, which is to collect more quality-controlled data from the private sector through public-private partnerships. Using a case study in Japan, the technical aspects of these partnerships are reviewed, with a focus on data collection from multiple private sector companies and its impact on improving chemical space coverage and prediction performance when merged with public sector datasets.
DRUG DISCOVERY TODAY
(2022)
Article
Construction & Building Technology
Zhongnan Ye, Shu-Chien Hsu, Hsi-Hsien Wei
Summary: This study developed an FE-based machine learning framework for predicting structural displacement based on temperature data, with RF and GB models outperforming others in terms of predictive accuracy. The developed framework shows high potential for real-time structural response prediction during fire emergencies.
AUTOMATION IN CONSTRUCTION
(2022)
Article
Biochemistry & Molecular Biology
Veronique Geoffroy, Thomas Guignard, Arnaud Kress, Jean-Baptiste Gaillard, Tor Solli-Nowlan, Audrey Schalk, Vincent Gatinois, Helene Dollfus, Sophie Scheidecker, Jean Muller
Summary: This article introduces a web server dedicated to the annotation, ranking, visualization, and interpretation of human structural variations, integrating annotations from various sources and providing scoring and ranking of SV, which can help human geneticists identify pathogenic structural variations.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Infectious Diseases
Ingo Riederer, Daniella Areas Mendes-da-Cruz, Guilherme Cordenonsi da Fonseca, Mariela Natacha Gonzalez, Otavio Brustolini, Cassia Rocha, Guilherme Loss, Joseane Biso de Carvalho, Mariane Talon Menezes, Lidiane Menezes Souza Raphael, Alexandra Gerber, Myrna Cristina Bonaldo, Gillian Butler-Browne, Vincent Mouly, Vinicius Cotta-de-Almeida, Wilson Savino, Ana Tereza Ribeiro de Vasconcelos
Summary: This study investigated the mechanisms of Zika virus infection in human skeletal muscle using an in vitro model. The research found that myoblasts are permissive to ZIKV infection, while myotubes control viral replication. Gene expression profiling revealed differences between infected myoblasts and myotubes, with the latter showing pathways related to antiviral and innate immune responses. This study sheds light on potential antiviral mechanisms against ZIKV infection in skeletal muscle.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Microbiology
Aline da Rocha Matos, Braulia Costa Caetano, Joao Luiz de Almeida Filho, Jessica Santa Cruz de Carvalho Martins, Michele Gabrielle Pacheco de Oliveira, Thiago das Chagas Sousa, Marco Aurelio Pereira Horta, Marilda Mendonca Siqueira, Jorge Hernandez Fernandez
Summary: The COVID-19 pandemic has had a significant impact on the global economy and public health. In this study, Hypericin, a compound found in Hypericum perforatum, was identified as a potential drug with anti-SARS-CoV-2 properties. It showed high affinity for viral main-protease (Mpro) and RNA dependent RNA polymerase (RdRp). In vitro experiments demonstrated that Hypericin inhibited viral replication in a dose dependent manner without significant cytotoxicity. These findings suggest that Hypericin is a promising candidate for repurposing in the treatment of COVID-19.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Ana Valesca Fernandes Gilson Silva, Diego Menezes, Filipe Romero Rebello Moreira, Octavio Alcantara Torres, Paula Luize Camargos Fonseca, Rennan Garcias Moreira, Hugo Jose Alves, Vivian Ribeiro Alves, Tania Maria de Resende Amaral, Adriano Neves Coelho, Julia Maria Saraiva Duarte, Augusto Viana da Rocha, Luiz Gonzaga Paula de Almeida, Joao Locke Ferreira de Araujo, Hilton Soares de Oliveira, Nova Jersey Claudio de Oliveira, Camila Zolini, Josy Hubner de Sousa, Elizangela Goncalves de Souza, Rafael Marques de Souza, Luciana de Lima Ferreira, Alexandra Lehmkuhl Gerber, Ana Paula de Campos Guimaraes, Paulo Henrique Silva Maia, Fernanda Martins Marim, Lucyene Miguita, Cristiane Campos Monteiro, Tuffi Saliba Neto, Fabricia Soares Freire Pugedo, Daniel Costa Queiroz, Damares Nigia Alborguetti Cuzzuol Queiroz, Luciana Cunha Resende-Moreira, Franciele Martins Santos, Erika Fernanda Carlos Souza, Carolina Moreira Voloch, Ana Tereza Vasconcelos, Renato Santana de Aguiar, Renan Pedra de Souza
Summary: This study conducted epidemiological monitoring using diverse strategies to describe the initial stages of the COVID-19 pandemic in Betim City, Brazil. The results revealed the prevalence of the virus, risk factors for positivity, and multiple viral introductions.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biology
Emma J. Griffiths, Ruth E. Timme, Catarina Ines Mendes, Andrew J. Page, Nabil-Fareed Alikhan, Dan Fornika, Finlay Maguire, Josefina Campos, Daniel Park, Idowu B. Olawoye, Paul E. Oluniyi, Dominique Anderson, Alan Christoffels, Anders Goncalves da Silva, Rhiannon Cameron, Damion Dooley, Lee S. Katz, Allison Black, Ilene Karsch-Mizrachi, Tanya Barrett, Anjanette Johnston, Thomas R. Connor, Samuel M. Nicholls, Adam A. Witney, Gregory H. Tyson, Simon H. Tausch, Amogelang R. Raphenya, Brian Alcock, David M. Aanensen, Emma Hodcroft, William W. L. Hsiao, Ana Tereza R. Vasconcelos, Duncan R. MacCannell
Summary: PHA4GE is a global coalition working to improve openness, interoperability, and consistency in public health microbial bioinformatics. They have developed a SARS-CoV-2 contextual data specification package to support data collection and harmonization in public biorepositories.
Article
Infectious Diseases
Ana Paula Streling, Rodrigo Cayo, Carolina S. Nodari, Luiz G. P. Almeida, Felipe Bronze, Andre Valencio Siqueira, Adriana P. Matos, Vitor Oliveira, Ana Tereza R. Vasconcelos, Marcelo F. M. Marcondes, Ana Cristina Gales
Summary: Pseudomonas aeruginosa is often associated with life-threatening infections due to its intrinsic and acquired antimicrobial mechanisms, including different types of beta-lactamases. The study found that OXA-488 has a higher catalytic efficiency for benzylpenicillin and imipenem compared to OXA-50, although its carbapenemase activity is considered weak. Additionally, OXA-488 and OXA-494 have increased affinity for penicillins, contributing to improved catalytic efficiency against ampicillin.
MICROBIAL DRUG RESISTANCE
(2022)
Article
Virology
Dalal Nour, Rayane Rafei, Alessandra P. Lamarca, Luiz G. P. de Almeida, Marwan Osman, Mohamad Bachar Ismail, Hassan Mallat, Atika Berry, Gwendolyne Burfin, Quentin Semanas, Laurence Josset, Hamad Hassan, Fouad Dabboussi, Bruno Lina, Philippe Colson, Ana Tereza R. Vasconcelos, Monzer Hamze
Summary: This study provides a retrospective genomic surveillance of the SARS-CoV-2 pandemic in Lebanon, revealing the dominance of four different lineages and the role of Lebanon as a dispersal center for lineage B.1.398. The district of Tripoli in Lebanon was identified as a significant source of dispersal within the country. These findings highlight the potential role of developing countries in the emergence of new variants.
Article
Multidisciplinary Sciences
Leandro Nascimento Lemos, Fabiola Marques de Carvalho, Fernanda Fernandes Santos, Tiago Barcelos Valiatti, Dandara Cassu Corsi, Alessandro Conrado de Oliveira Silveira, Alexandra Gerber, Ana Paula C. Guimaraes, Cintya de Oliveira Souza, Danielle Murici Brasiliense, Debora de Souza Collares Maia Castelo-Branco, Eleine Kuroki Anzai, Francisco Ozorio Bessa-Neto, Glaucia Morgana de Melo, Gleyce Hellen de Souza, Lucio Fabio Caldas Ferraz, Marcia de Nazare Miranda Bahia, Marcia Soares Mattos, Ramon Giovani Brandao da Silva, Ruanita Veiga, Simone Simionatto, Walter Aparecido Pimentel Monteiro, William Alencar de Oliveira Lima, Carlos Roberto Veiga Kiffer, Rodrigo Cayo, Ana Cristina Gales, Ana Tereza Ribeiro de Vasconcelos
Summary: This article presents a dataset based on metagenome-assembled genomes (MAGs) from the gut microbiomes of humans and animals. It aims to study the relationship between human and animal health and the transfer of pathogens between these systems. The dataset contains many potential pathogens and novel species with potential biotechnological applications.
Article
Biochemistry & Molecular Biology
Liliane Tavares de Faria Cavalcante, Guilherme Cordenonsi da Fonseca, Luciane Almeida Amado Leon, Andreza Lemos Salvio, Otavio Jose Brustolini, Alexandra Lehmkuhl Gerber, Ana Paula de Campos Guimaraes, Carla Augusta Barreto Marques, Renan Amphilophio Fernandes, Carlos Henrique Ferreira Ramos Filho, Rafael Lopes Kader, Marisa Pimentel Amaro, Joao Paulo da Costa Goncalves, Soniza Vieira Alves-Leon, Ana Tereza Ribeiro Vasconcelos
Summary: Transcriptome studies have identified dysregulated cell cycle-related genes and global inhibition of host mRNA translation in COVID-19 cases. This study used RNA-seq to analyze the differential expression of genes in buffy coat cells between two groups: (a) Mild cases with mild symptoms, and (b) SARS cases admitted to the intensive care unit. The analysis revealed up-regulated and down-regulated genes, including long non-coding RNAs, in the SARS group. The down-regulated genes were enriched in ribosome and cell cycle pathways. The differentially expressed genes were involved in transport dysregulation, proteasome degradation, interferon response, cytokinesis failure, and host translation inhibition. Fibrillarin was identified as a key gene affected by SARS-CoV-2, interacting with the N protein and long non-coding RNAs to affect transcription, translation, and ribosomal processes. Severe COVID-19 outcomes are associated with dysregulated translation and cell cycle pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Virology
Fernando Luz de Castro, Otavio Jose Bernandes Brustolini, Victor Emmanuel Viana Geddes, Jorge Paes Barreto Marcondes de Souza, Soniza Vieira Alves-Leon, Renato Santana Aguiar, Ana Tereza Ribeiro Vasconcelos
Summary: This study analyzed RNAseq data from human primary astrocytes infected with Zika, Mayaro, Oropouche, and Chikungunya viruses, and evaluated the modulation of HERVs and nearby genes. The results showed that these viruses collectively regulated the expression of certain HERVs and genes related to cellular processes and antiviral response. These findings support the role of HERVs induction in the transcription regulation of genes during arboviral infections.
Article
Multidisciplinary Sciences
Douglas Terra Machado, Otavio Jose Bernardes Brustolini, Yasmmin Cortes Martins, Marco Antonio Grivet Mattoso Maia, Ana Tereza Ribeiro de Vasconcelos
Summary: DEGRE is a user-friendly tool that considers fixed and random effects on individuals in the experimental design of RNA-Seq research to infer differentially expressed genes (DEGs). It preprocesses the data and applies generalized linear mixed models (GLMMs) to provide inference for DEGs. This tool efficiently removes genes that could impact the inference and offers improved assessment measures in cases with higher biological variability.
Article
Biology
Rafael Mina Piergiorge, Ronaldo da Silva Francisco Junior, Ana Tereza Ribeiro de Vasconcelos, Cintia Barros Santos-Reboucas
Summary: This study identified a complex ceRNA network involved in late-onset AD and highlighted the Fragile X Messenger Ribonucleoprotein 1 (FMR1) as a driver gene in this network. The findings enhance our understanding of ceRNA regulatory pathways in AD and provide potential targets for early biomarkers and therapeutic interventions.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Guilherme C. da Fonseca, Liliane T. F. Cavalcante, Otavio J. Brustolini, Paula M. Luz, Debora C. Pires, Emilia M. Jalil, Eduardo M. Peixoto, Beatriz Grinsztejn, Valdilea G. Veloso, Sandro Nazer, Carlos A. M. Costa, Daniel A. M. Villela, Guilherme T. Goedert, Cleber V. B. D. Santos, Nadia C. P. Rodrigues, Fernando do Couto Motta, Marilda Mendonca Siqueira, Lara E. Coelho, Claudio J. Struchiner, Ana Tereza R. Vasconcelos
Summary: This article investigates the impact of the Gamma and Delta variants of SARS-CoV-2 on the host immune system, finding that Delta can more effectively activate the IFN-I response, while Gamma evades the host immune system by inhibiting the interferon response pathway.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Mariana Rocha, Luisa Massarani, Sandro Jose de Souza, Ana Tereza R. de Vasconcelos
Summary: Brazil has a high rate of scientific production and ranks ninth in genome-sequencing projects. This study aims to understand the current situation and future prospects of bioinformatics and genomics research in Brazil. Through analyzing the views of 576 researchers, it was found that most researchers have a positive perception of this research area but are concerned about the lack of funding for equipment and professional training.
GENETICS AND MOLECULAR BIOLOGY
(2022)
Article
Virology
Sofia G. Seabra, Pieter J. K. Libin, Kristof Theys, Anna Zhukova, Barney Potter, Hanna Nebenzahl-Guimaraes, Alexander E. Gorbalenya, Igor A. Sidorov, Victor Pimentel, Marta Pingarilho, Ana T. R. de Vasconcelos, Simon Dellicour, Ricardo Khouri, Olivier Gascuel, Anne-Mieke Vandamme, Guy Baele, Lize Cuypers, Ana B. Abecasis
Summary: This study characterized the genetic diversity and phylodynamics of the Zika virus and proposed a dynamic classification system that reflects its divergence levels. Through comprehensive analyses of the full-length coding region of the virus, the study identified genetic groups and differentiation patterns.
Letter
Virology
Alessandra P. Lamarca, Luiz G. P. de Almeida, Ronaldo da Silva Francisco, Liliane Cavalcante, Douglas Terra Machado, Otavio Brustolini, Alexandra L. Gerber, Ana Paula de C. Guimaraes, Cintia Policarpo, Gleidson da Silva de Oliveira, Lidia Theodoro Boullosa, Isabelle Vasconcellos de Souza, Erika Martins de Carvalho, Mario Sergio Ribeiro, Silvia Carvalho, Flavio Dias da Silva, Marcio Henrique de Oliveira Garcia, Leandro Magalhaes de Souza, Cristiane Gomes Da Silva, Caio Luiz Pereira Ribeiro, Andrea Cony Cavalcanti, Claudia Maria Braga de Mello, Amilcar Tanuri, Ana Tereza R. Vasconcelosa
JOURNAL OF VIROLOGY
(2022)