Article
Biochemical Research Methods
Tiago Cabral Borelli, Gabriel Santos Arini, Luis G. P. Feitosa, Pieter C. Dorrestein, Norberto Peporine Lopes, Ricardo R. da Silva
Summary: Annotation of mass signals remains a major challenge in untargeted mass spectrometry analysis. We introduce ChemWalker, a Python library that expands annotation propagation to nodes not directly connected to spectral matches, overcoming the limitations of Network Annotation Propagation (NAP). Compared to NAP, ChemWalker has achieved improvements in running time, scalability, and maintainability, and is available as a standalone Python package.
Article
Biochemistry & Molecular Biology
Yaqiang Cao, Shuai Liu, Gang Ren, Qingsong Tang, Keji Zhao
Summary: Investigating chromatin interactions between regulatory regions is important for understanding gene expression regulation. Emerging 3D mapping technologies like TrAC-looping provide cost-effective and high-resolution data for cis-regulatory elements. The versatile tool cLoops2 was developed for comprehensive analysis of 3D chromatin interaction data, with core modules for peak-calling and loop-calling, and additional features for resolution estimation and visualization.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biophysics
Meng Gao, Yue Han, Yifan Zeng, Zhengding Su, Yongqi Huang
Summary: The study examined the impact of introducing intrinsic disorder on the electrostatic steering of the E3/Im3 complex, finding that the ordered complex showed greater response to changes in salt concentration compared to the disordered complex. Mechanistic analysis revealed similar native contact interactions for ordered and disordered forms of E3 in both encounter state and transition state, suggesting that the difference in electrostatic steering between ordered and disordered forms may be attributed to their conformational differences rather than binding mechanisms.
BIOPHYSICAL JOURNAL
(2021)
Article
Engineering, Environmental
Yuquan Li, Pengyong Li, Xing Yang, Chang-Yu Hsieh, Shengyu Zhang, Xiaorui Wang, Ruiqiang Lu, Huanxiang Liu, Xiaojun Yao
Summary: The BGNN algorithm, a deep learning approach, can approximate the molecular properties of many-body quantum systems by extracting useful interactions between target atoms and neighboring atomic groups. It outperformed other graph model variants in tasks on large molecular datasets QM9 and Alchemy, showing great potential for applications in bioactivity prediction, drug discovery, and materials design.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Computer Science, Interdisciplinary Applications
Richard Olsen
Summary: To perform atomistic calculations, it is necessary to construct and define the molecular system of interest. After simulations or calculations, large sets of data containing atomic trajectories and relevant information are obtained. MolTwister is an open source software platform that assists in the construction of molecular systems, visualization, input file generation, and calculation of properties from atomistic simulation data.
COMPUTER PHYSICS COMMUNICATIONS
(2023)
Article
Mathematics
Nihat Akgunes, Busra Aydin
Summary: New graph invariants, called exponential Zagreb indices, are introduced for various Zagreb indices. They are used to obtain equality results and new bounds on special graphs, as well as for certain graph operations.
JOURNAL OF MATHEMATICS
(2021)
Article
Biochemical Research Methods
Elena Kuzmin, Mahfuzur Rahman, Benjamin VanderSluis, Michael Costanzo, Chad L. Myers, Brenda J. Andrews, Charles Boone
Summary: Systematic complex genetic interaction studies have provided insight into high-order functional redundancies and genetic network wiring of the cell. A method for screening and quantifying trigenic interactions from ordered arrays of yeast strains grown on agar plates as individual colonies is described. The protocol instructs users on a technique for high-throughput screens, which involves construction of double-mutant query strains and parallel screening of single-mutant control query strains in two replicates. Large-scale screen computational analysis is achieved by using MATLAB pipelines to score raw colony size data and produce tau-SGA interaction scores.
Article
Biology
Giulia Agostinetto, Alberto Brusati, Anna Sandionigi, Adam Chahed, Elena Parladori, Bachir Balech, Antonia Bruno, Dario Pescini, Maurizio Casiraghi
Summary: ExTaxsI can easily retrieve molecular data and its metadata with an explorable visualization, aiming to assist researchers in improving experimental designs and highlighting the main gaps in the coverage of available data.
Article
Multidisciplinary Sciences
Bryan D. Ryder, Irina Matlahov, Sofia Bali, Jaime Vaquer-Alicea, Patrick C. A. van der Wel, Lukasz A. Joachimiak
Summary: This study investigates the domain interactions of Hsp40 DnaJB8 and their impact on Hsp70 recruitment, revealing an interaction mechanism between the J-Domain and C-terminal domain that prevents Hsp70 binding, proposing a model for DnaJB8-Hsp70 recruitment.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Tobias M. Hain, Michal Bykowski, Matthias Saba, Myfanwy E. Evans, Gerd E. Schroeder-Turk, Lucja Kowalewska
Summary: Bicontinuous membranes in cell organelles demonstrate nature's ability to create complex nanostructures, with the SPIRE tool being able to accurately identify and analyze their features. Studying the structure of etioplasts reveals insights into storage capacities with different volume proportions and the role of plastid ribosome localization in their functioning.
Article
Biochemistry & Molecular Biology
Sergio Peignier, Federica Calevro
Summary: Self-expressiveness is a mathematical property that characterizes the relationship between instances in a dataset. It has been successfully applied in various domains but not explicitly used to infer gene networks.
Article
Oncology
Fanny S. Krebs, Vincent Zoete, Maxence Trottet, Timothee Pouchon, Christophe Bovigny, Olivier Michielin
Summary: Swiss-PO is a new web tool designed to map gene mutations on the 3D structure of corresponding proteins and assess the structural implications of protein variants for precision oncology. It is constructed around a manually curated database of 3D structures, variant annotations, and sequence alignments for a list of 50 genes. The importance of mutated residues for protein structure and activity can be evaluated based on molecular interactions, conservation in orthologs, and known effects of mutations.
NPJ PRECISION ONCOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Yongqing Zhang, Qingyuan Chen, Meiqin Gong, Yuanqi Zeng, Dongrui Gao
Summary: This study proposes constructing gene regulatory networks under different molecular subtypes of MIBC and analyzing the regulatory differences. Differential expression analysis and network analysis revealed significant differences in expression and regulatory relationships of genes such as SERPINI1, NOTUM, and FGFR1. Pathway enrichment analysis showed pathways like Neuroactive ligand-receptor interaction and Cytokine-cytokine receptor interaction are significantly enriched with diverse genes in bladder cancer subtypes.
Article
Biochemistry & Molecular Biology
Elisa Salviato, Vera Djordjilovic, Judith Mary Hariprakash, Ilario Tagliaferri, Koustav Pal, Francesco Ferrari
Summary: This study introduces a new perspective based on the definition of multi-scale structural chromatin domains integrated in a statistical framework to improve the accuracy of ETG pairing. The method developed in this work leverages functional genomics data to reconstruct a comprehensive map of ETG pairs and was extensively benchmarked against previous solutions, showing promising results in annotating and interpreting sequence variants in distal non-coding regulatory elements.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Elisa Salviato, Vera Djordjilovi, Judith Mary Hariprakash, Ilario Tagliaferri, Koustav Pal, Francesco Ferrari
Summary: This study introduces a new perspective on defining gene regulatory relationships by integrating multi-scale structural chromatin domains and statistical frameworks. The incorporation of chromatin 3D architecture information has been shown to improve the accuracy of gene pair matching, which holds significance for clinical applications of whole genome sequencing in cancer and undiagnosed genetic diseases research.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Cell Biology
Naghmeh Hoghoughi, Sophie Barral, Sandrine Curtet, Florent Chuffart, Guillaume Charbonnier, Denis Puthier, Thierry Buchou, Sophie Rousseaux, Saadi Khochbin
Article
Medicine, Research & Experimental
Carole Robert, Jean Imbert, Mohamed Lajnef, Camille Nous, Gilbert Cabiran, Serge Robert, Francoise Cabiran, Flavie Mathieu
Summary: To address the challenge of medical knowledge democratization, various initiatives including patient education and research collaborations have been developed. However, only a few collaborations are initiated by patients directly, highlighting the potential for further research in this area.
M S-MEDECINE SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Mohamed Belhocine, Mathieu Simonin, Jose David Abad Flores, Agata Cieslak, Iris Manosalva, Lydie Pradel, Charlotte Smith, Eve-Lyne Mathieu, Guillaume Charbonnier, Joost H. A. Martens, Hendrik G. Stunnenberg, Muhammad Ahmad Maqbool, Aneta Mikulasova, Lisa J. Russell, Daniel Rico, Denis Puthier, Pierre Ferrier, Vahid Asnafi, Salvatore Spicuglia
Summary: Broad H3K4 methylation domains are associated with T cell differentiation and T cell acute lymphoblastic leukemia. The varying breadth of these domains can distinguish between normal and neoplastic cells, and the genes associated with broad domains are deregulated in T-ALL. The ectopic expression of T-ALL oncogenic transcription factor affects the expression of broad domain-associated genes in preleukemic cells. Additionally, an H3K4me3 demethylase inhibitor selectively targets T-ALL cell lines depending on the extent and number of broad domains.
Article
Biochemistry & Molecular Biology
Florian Rosier, Audrey Brisebarre, Claire Dupuis, Sabrina Baaklini, Denis Puthier, Christine Brun, Lydie C. Pradel, Pascal Rihet, Didier Payen
Summary: Through two genome-wide association studies, the research identified an association between SNP within the CISH gene and death in septic shock patients. Further investigation revealed rs143356980 as a key regulatory candidate that modulates pathways related to death, increasing the risk of mortality in patients with septic shock.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Mengqing Gao, Jin Wang, Sophie Rousseaux, Minjia Tan, Lulu Pan, Lijun Peng, Sisi Wang, Wenqian Xu, Jiayi Ren, Yuanfang Liu, Martin Spinck, Sophie Barral, Tao Wang, Florent Chuffart, Ekaterina Bourova-Flin, Denis Puthier, Sandrine Curtet, Lisa Bargier, Zhongyi Cheng, Heinz Neumann, Jian Li, Yingming Zhao, Jian-Qing Mi, Saadi Khochbin
Summary: This study shows that mitochondrial activity can regulate the balance between histone acetylation and longer-chain acylations, impacting the function of histone H4K5. An increase in non-acetyl acylations over acetylation weakens the chromatin interaction of bromodomain containing protein 4 (BRD4), leading to enhanced nuclear mobility and binding at transcription start sites of active genes. This suggests that metabolism-driven control of the histone acetylation/longer-chain acylation(s) ratio may be a common mechanism regulating the genomic distribution of bromodomain factors.
Article
Biochemical Research Methods
Quentin Ferre, Jeanne Cheneby, Denis Puthier, Cecile Capponi, Benoit Ballester
Summary: Accurate identification of Transcriptional Regulator binding locations is crucial for analyzing genomic regions, and the method developed in this study leverages multiple experimental series to mark atypical peaks using deep learning. By compressing genomic regions' representations and identifying correlation groups, the approach successfully evaluates CRE completeness and detects peaks lacking known biological correlators in real data. The proposed normalization methods are useful for interpreting black-box models, and the approach can be extended to similar problems, implemented in an open-source tool called atyPeak.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Fayrouz Hammal, Pierre de Langen, Aurelie Bergon, Fabrice Lopez, Benoit Ballester
Summary: ReMap 2022 provides manually curated, high-quality catalogs of regulatory regions from Human, Arabidopsis, Mouse, and Fly, including hundreds of transcription factors and regulators. The update also introduces new regulatory catalogs for Mouse and Fly, enriching research resources for scientists. Users can browse the four regulatory catalogs through track hubs at UCSC, Ensembl, and NCBI genome browsers.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Immunology
Aritania Sousa Santos, Edecio Cunha-Neto, Nelson Vinicius Gonfinetti, Fernanda Bernardi Bertonha, Pauline Brochet, Aurelie Bergon, Carlos Alberto Moreira-Filho, Christophe Chevillard, Maria Elizabeth Rossi da Silva
Summary: Our study investigated the global gene expression in PBMC of recent-onset T1D patients from a highly admixed Brazilian population, revealing 474 differentially expressed genes between groups. The most expressed genes in T1D patients favored host defense, inflammatory and cell cycle progression, while immune-regulatory pathways were downregulated. These findings suggest immune activation and differential genetic profiles in recent-onset T1D patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Kaj Chokeshaiusaha, Thanida Sananmuang, Denis Puthier, Catherine Nguyen
Summary: This study investigated the application of exosome-derived miRNA in cross-species tumor diagnosis, successfully identifying and utilizing human-dog miRNA orthologs for differential tumor cell line classification. These findings shed light on a novel non-invasive tumor diagnostic tool that could be used in both human and veterinary medicine in the future.
Article
Immunology
Pauline Brochet, Barbara Maria Ianni, Laurie Laugier, Amanda Farage Frade, Joao Paulo Silva Nunes, Priscila Camillo Teixeira, Charles Mady, Ludmila Rodrigues Pinto Ferreira, Quentin Ferre, Ronaldo Honorato Barros Santos, Andreia Kuramoto, Sandrine Cabantous, Samuel Steffen, Antonio Noedir Stolf, Pablo Pomerantzeff, Alfredo Inacio Fiorelli, Edimar Alcides Bocchi, Cristina Wide Pissetti, Bruno Saba, Darlan da Silva Candido, Fabricio C. Dias, Marcelo Ferraz Sampaio, Fabio Antonio Gaiotto, Jose Antonio Marin-Neto, Abilio Fragata, Ricardo Costa Fernandes Zaniratto, Sergio Siqueira, Giselle De Lima Peixoto, Vagner Oliveira-Carvalho Rigaud, Fernando Bacal, Paula Buck, Rafael Ribeiro Almeida, Hui Tzu Lin-Wang, Andre Schmidt, Martino Martinelli, Mario Hiroyuki Hirata, Eduardo Antonio Donadi, Alexandre Costa Pereira, Virmondes Rodrigues Junior, Denis Puthier, Jorge Kalil, Lionel Spinelli, Edecio Cunha-Neto, Christophe Chevillard
Summary: In this study, the genetic and epigenetic deregulations associated with moderate and severe stages of Chagas disease were investigated using bulk RNA-seq and DNA methylation analysis. The results revealed differentially expressed transcripts and regulatory differentially methylated regions in the heart tissue of CCC patients. Transcription factors binding sites affected by DNA methylation were also identified. The study identified biological processes affected by severe CCC and highlighted the importance of ion transport and the nervous system in the development of the disease.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Kaj Chokeshaiusaha, Thanida Sananmuang, Denis Puthier, Catherine Nguyen
Summary: This study identified potential cross-species genes and transcript isoforms in humans and chickens that may play a significant role in the development and progression of fatty liver disease.
Article
Medicine, Research & Experimental
Lamia Madaci, Charlyne Gard, Sebastien Nin, Geoffroy Venton, Pascal Rihet, Denis Puthier, Beatrice Loriod, Regis Costello
Summary: This article discusses the importance of personalized treatment for acute myeloid leukemia. The use of targeted drugs is crucial in differentiating between different types of cell targets, but cell-by-cell analysis poses challenges. The study demonstrates the applicability of the cell hashing technique for analyzing acute myeloid leukemia cells and compares it to standard single cell analysis, showing strong correlation in various parameters.
Article
Genetics & Heredity
Quentin Ferre, Cecile Capponi, Denis Puthier
Summary: The method introduces a new approach to infer functional associations between different genomic regions, improving resolution and interpretability of the results. It utilizes Monte Carlo method and machine learning techniques, and has been experimentally validated for feasibility.
NAR GENOMICS AND BIOINFORMATICS
(2021)
Article
Veterinary Sciences
Natthaporn Kuendee, Denis Puthier, Catherine Nguyen, Kaj Chokeshaiusaha
Summary: The study reveals that in canine AD, NK cells express genes related to cell apoptosis regulation, similar to those in human AD patients, supporting the idea of AD inducing AICD of canine NK cells.
THAI JOURNAL OF VETERINARY MEDICINE
(2021)