Article
Biochemical Research Methods
Ann-Kristin Becker, Marcus Dorr, Stephan B. Felix, Fabian Frost, Hans J. Grabe, Markus M. Lerch, Matthias Nauck, Uwe Volker, Henry Volzke, Lars Kaderali
Summary: The study introduces an automated workflow combining network learning and clustering to reveal disease-associated biomarker networks from healthcare data. This approach automatically detects related feature groups and models their interactions, leading to easily analyzable network models.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Jun Yan, Hongning Zhai, Ling Zhu, Sasha Sa, Xiaojun Ding
Summary: obaDIA is a comprehensive automated tool for analyzing quantitative proteomics data, supporting various abundance matrices and providing rich result visualization and analysis functions.
Article
Multidisciplinary Sciences
Eric A. Jensen, Paul Wong, Mark S. Reed
Summary: This study examines the contribution of research data to non-academic impacts through analyzing high-scoring impact case studies from the UK's REF. The findings reveal that the most prevalent type of impact driven by research data is related to practice, followed by impacts on government. It is also highlighted that research data alone rarely generate impacts and necessitate additional interventions such as analysis, curation, and product development.
Article
Environmental Sciences
Dan E. Kelley, Jaimie Harbin, Clark Richards
Summary: The R package argoFloats facilitates identification, downloading, caching, and analysis of oceanographic data collected by Argo profiling floats. The package has close connections with the oce package, making it familiar to R users analyzing oceanographic data of other kinds. Benefits of using argoFloats in everyday tasks specific to Argo data, such as downloading data, quality control, and producing diagnostic plots, are outlined in the paper.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Biochemical Research Methods
Zuguang Gu, Daniel Huebschmann
Summary: Spiral layout has two major advantages in data visualization, improving visualization resolution and revealing periodic patterns. The R package spiralize provides a general solution with numerous graphics functions for users to easily implement self-defined high-level graphics.
Article
Biochemical Research Methods
Mireia Ramos-Rodriguez, Marc Subirana-Granes, Lorenzo Pasquali
Summary: UMI-4C is a technique that combines 4C and UMI to profile and quantitatively compare targeted chromosomal contact profiles. UMl4Cats is an R package developed to simplify processing, analyzing, and visualizing data obtained from UMI-4C experiments.
Article
Biochemistry & Molecular Biology
Piyal Karunarathne, Qiujie Zhou, Klaus Schliep, Pascal Milesi
Summary: Recent studies have emphasized the important role of copy number variants (CNVs) in phenotypic diversity, environmental adaptation, and species divergence in eukaryotes. The detection of CNVs in genomes poses a challenge, especially in non-model organisms. To address this, a statistical framework and an r software package ('rCNV') have been developed that utilize allelic-read depth from SNP data for accurate CNV detection. The framework improves sensitivity to sampling effects, addresses reference biases, and is compatible with various NGS technologies.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemical Research Methods
Antoine Bodein, Marie-Pier Scott-Boyer, Olivier Perin, Kim-Anh Le Cao, Arnaud Droit
Summary: This text introduces the R package timeOmics, a generic analytical framework for integrating longitudinal multi-omics data. The package includes functions for pre-processing, modeling, and clustering to help researchers identify molecular features strongly associated with time. It is demonstrated in a case study to detect seasonal patterns of various molecular and clinical variables in patients with diabetes mellitus.
Article
Biochemical Research Methods
Xiaoyu Liang, Ying Hu, Chunhua Yan, Ke Xu
Summary: The study introduces a novel R package, i2d, for simulating image data through digital convolution, enabling information extraction and analysis in biomedical and biological research. Additionally, the package includes efficient methods for graph clustering based on simulated data to dissect complex gene networks.
Article
Biotechnology & Applied Microbiology
Guan-Dong Shang, Zhou-Geng Xu, Mu-Chun Wan, Fu-Xiang Wang, Jia-Wei Wang
Summary: In this study, we introduce FindIT2, a software package that can process and analyze multi-omics data to infer influential transcription factors using ChIP-seq/ATAC-seq datasets. The package annotates ChIP-seq/ATAC-seq peaks, identifies transcription factor targets by combining ChIP-seq and RNA-seq data, and supports inference of influential transcription factors based on different types of data input. Moreover, FindIT2 is compatible with any species with genomic annotations, making it particularly useful for less well-studied non-model species.
Article
Biochemical Research Methods
Evan A. Martin, James M. Fulcher, Mowei Zhou, Matthew E. Monroe, Vladislav A. Petyuk
Summary: Top-down proteomics is a developing field that analyzes proteins in their intact form without proteolysis. However, limitations in instrumentation and data interpretation have hindered its progress. TopPICR is a companion R package that extends the capabilities of the popular proteoform identification tool, TopPIC, to label-free proteoform quantification. The pipeline includes several key steps, such as filtering identifications and compiling feature intensities, and the output is compatible with downstream data analysis packages from the Bioconductor project.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Zachary B. Abrams, Dwayne G. Tally, Lynne Abruzzo, Kevin R. Coombes
Summary: Cytogenetics data, stored as karyotypes, are now being analyzed on a large scale thanks to tools like CytoGPS. The development of RCytoGPS further facilitates the analysis and visualization of karyotype data, advancing the field of computational cytogenetic pathology.
Article
Multidisciplinary Sciences
Wikum Dinalankara, Qian Ke, Donald Geman, Luigi Marchionni
Summary: Divergence analysis is a novel framework that transforms high-dimensional omics data into digitized codes, facilitating simple and effective analysis on different omics platforms.
Article
Environmental Sciences
Aude Ratier, Virgile Baudrot, Milena Kaag, Aurelie Siberchicot, Christelle Lopes, Sandrine Charles
Summary: This paper introduces the functions and applications of the R-package rbioacc, which can be used to analyze data from bioaccumulation tests. The package provides TK parameter estimates, bioaccumulation metrics, and supports environmental risk assessment, in compliance with regulatory requirements.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Article
Biochemical Research Methods
Marzia Settino, Mario Cannataro
Summary: MMRFBiolinks is a tool package for integrating and analyzing data from MMRF and NCI-GDC, providing comprehensive analysis through various methods and visualizations. Through two case studies, it demonstrates how the tool overcomes the limitations of other analysis tools, making the retrieval, downloading, and analysis of MMRF data more comprehensive.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Jeehyun Yoon, Oleg Grinchuk, Roberto Tirado-Magallanes, Zhen Kai Ngian, Emmy Xue Yun Tay, You Heng Chuah, Bernice Woon Li Lee, Jia Feng, Karen Carmelina Crasta, Chin Tong Ong, Touati Benoukraf, Derrick Sek Tong Ong
Summary: The histone variant H2AZ is overexpressed in glioblastomas (GBM) and glioma stem cells (GSCs), promoting their proliferation and tumorigenicity. E2F1 and STAT3 synergistically activate H2AZ gene transcription in GSCs, and an E2F/STAT3 inhibitor combination shows promise in suppressing GSC tumorigenicity in GBM treatment.
CELL DEATH AND DIFFERENTIATION
(2022)
Article
Cell & Tissue Engineering
Katharina Schoenberger, Nadine Obier, Mari Carmen Romero-Mulero, Pierre Cauchy, Julian Mess, Polina Pavlovich, Yu Wei Zhang, Michael Mitterer, Jasmin Rettkowski, Maria-Eleni Lalioti, Karin Jaecklein, Jonathan D. Curtis, Betty Feret, Pia Sommerkamp, Claudia Morganti, Keisuke Ito, Norbert B. Ghyselinck, Eirini Trompouki, Joerg M. Buescher, Erika L. Pearce, Nina Cabezas-Wallscheid
Summary: This study investigates the complex regulatory networks that preserve stemness in hematopoietic stem cells and uncovers a non-classical retinoic acid signaling axis that controls their function. The findings highlight the importance of a single metabolite in controlling stem cell fate through epigenetic and transcriptional attributes.
Article
Engineering, Biomedical
Joanne Tze Chin Lim, Leng Gek Kwang, Nicholas Ching Wei Ho, Clarissa Chin Min Toh, Nathaniel Sheng Hua Too, Lissa Hooi, Touati Benoukraf, Pierce Kah-Hoe Chow, Yock Young Dan, Edward Kai-Hua Chow, Tan Boon Toh, Eliza Li Shan Fong
Summary: Hepatocellular carcinoma (HCC) is a common and deadly form of cancer. Despite advancements in treatment, the impact of anti-angiogenic therapies on overall survival of HCC patients is limited. This study demonstrates that endothelial cells have roles beyond angiogenesis in supporting tumor progression and generating an inflammatory microenvironment. These findings highlight the importance of understanding the interplay between angiogenesis and the immune milieu in HCC.
Article
Genetics & Heredity
Justin A. Pater, Cindy Penney, Darren D. O'Rielly, Anne Griffin, Lara Kamal, Zippora Brownstein, Barbara Vona, Chana Vinkler, Mordechai Shohat, Ortal Barel, Curtis R. French, Sushma Singh, Salem Werdyani, Taylor Burt, Nelly Abdelfatah, Jim Houston, Lance P. Doucette, Jessica Squires, Fabian Glaser, Nicole M. Roslin, Daniel Vincent, Pascale Marquis, Geoffrey Woodland, Touati Benoukraf, Alexia Hawkey-Noble, Karen B. Avraham, Susan G. Stanton, Terry-Lynn Young
Summary: A new DFNA gene, ATP11A, was identified in a Newfoundland family with bilateral sensorineural hearing loss (SNHL). Two additional families from Israel with similar hearing loss were also found to have a mutation in ATP11A. ATP11A is a type of P4-ATPase gene involved in phospholipid flipping in cell membranes.
Article
Immunology
Claude Gregoire, Lionel Spinelli, Sergio Villazala-Merino, Laurine Gil, Maria Pia Holgado, Myriam Moussa, Chuang Dong, Ana Zarubica, Mathieu Fallet, Jean-Marc Navarro, Bernard Malissen, Pierre Milpied, Mauro Gaya
Summary: This study investigated lung-resident memory B cells and identified two distinct transcriptional subsets with class switching, somatic mutation, and biased differentiation fate. The analysis of antigen specificity and B cell receptor repertoire revealed virus-specific and bystander subsets. The findings suggest that the transcriptional programs in MBCs are related to the immune system's strategies for providing protection and diversifying the B cell repertoire.
Article
Immunology
Julie Rebejac, Elisa Eme-Scolan, Laurie Arnaud Paroutaud, Sarah Kharbouche, Matei Teleman, Lionel Spinelli, Emeline Gallo, Annie Roussel-Queval, Ana Zarubica, Amandine Sansoni, Quentin Bardin, Philippe Hoest, Marie-Cecile Michallet, Carine Brousse, Karine Crozat, Monica Manglani, Zhaoyuan Liu, Florent Ginhoux, Dorian B. McGavern, Marc Dalod, Bernard Malissen, Toby Lawrence, Rejane Rua
Summary: Meningeal macrophages (MMs) play a protective role in viral infection and may serve as potential targets for therapeutic intervention. High viral load correlates with low numbers of MHC-II+ MMs.
Article
Immunology
Aurelie Lenaerts, Iwo Kucinski, Ward Deboutte, Marta Derecka, Pierre Cauchy, Thomas Manke, Berthold Gottgens, Rudolf Grosschedl
Summary: This study implicates EBF1 in regulating myeloid/lymphoid fate bias in MPPs by constraining C/EBP alpha-driven myelopoiesis and priming the B-lymphoid fate specifically in MPP3 cells.
JOURNAL OF EXPERIMENTAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Saswati Saha, Laurent Perrin, Laurence Roder, Christine Brun, Lionel Spinelli
Summary: In this article, a novel method called epiMEIF is proposed for detecting higher-order epistatic interactions from GWAS data, improving the detection of genetic architecture underlying complex phenotypes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Immunology
Pauline Brochet, Barbara Ianni, Joao P. S. Nunes, Amanda F. Frade, Priscila C. Teixeira, Charles Mady, Ludmila R. P. Ferreira, Andreia Kuramoto, Cristina W. Pissetti, Bruno Saba, Darlan D. S. Candido, Fabricio Dias, Marcelo Sampaio, Jose A. Marin-Neto, Abilio Fragata, Ricardo C. F. Zaniratto, Sergio Siqueira, Giselle D. L. Peixoto, Vagner O. C. Rigaud, Paula Buck, Rafael R. Almeida, Hui Tzu Lin-Wang, Andre Schmidt, Martino Martinelli, Mario H. Hirata, Eduardo Donadi, Virmondes Rodrigues Junior, Alexandre C. Pereira, Jorge Kalil, Lionel Spinelli, Edecio Cunha-Neto, Christophe Chevillard
Summary: This study proposes two sets of DNA methylation biomarkers that can predict the occurrence and stage of Chagas disease cardiomyopathy. Using machine learning algorithms, predictions in a test cohort achieved an accuracy of over 95%. These biomarkers are also associated with immune response, nervous system, ion transport, and ATP synthesis pathways.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biology
Xinhui Zhao, Boris Bartholdy, Yukiya Yamamoto, Erica K. Evans, Meritxell Alberich-Jorda, Philipp B. Staber, Touati Benoukraf, Pu Zhang, Junyan Zhang, Bon Q. Trinh, John D. Crispino, Trang Hoang, Mahmoud A. Bassal, Daniel G. Tenen
Summary: The transcription factor PU.1 recruits c-Jun as a co-activator to promoters without AP-1 binding sites, which is crucial for macrophage differentiation.
COMMUNICATIONS BIOLOGY
(2022)
Article
Immunology
Cynthia Arroyo Portilla, Romain Fenouil, Camille Wagner, Cecilia Luciani, Margaux Lagier, Clement Da Silva, Fanny Hidalgo-Villeda, Lionel Spinelli, Mathieu Fallet, Julie Tomas, Jean-Pierre Gorvel, Hugues Lelouard
Summary: Peyer's patches (PPs) are lymphoid organs that interact with the intestinal lumen, allowing the study of phagocyte differentiation and activation. The study found that monocyte-derived Lysozyme-expressing dendritic cells (LysoDCs) have different activation patterns compared to macrophages. They also identified gene sets that distinguish PP cDCs from other cell populations and identified markers for different stages of PP phagocyte maturation. Additionally, the study found that the type of stimulus, phagocyte subset, and initial location of the cells influence their activation profile and immune response.
MUCOSAL IMMUNOLOGY
(2023)
Letter
Biochemical Research Methods
Cheng Yong Tham, Touati Benoukraf
Summary: This paper investigates the guidelines for long-read sequencing settings in structural variation (SV) calling and benchmarks the performance of various SV calling tools. However, the results contradict the findings of a previous study, showing that the performance of NanoVar was underestimated. Additionally, detrimental errors encountered during the analysis were identified, which were not addressed in the previous study.
BMC BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Matthew Dyer, Quy Xiao Xuan Lin, Sofiia Shapoval, Denis Thieffry, Touati Benoukraf
Summary: MethMotif is a publicly available database that provides a comprehensive repository of transcription factor-binding profiles with DNA methylation patterns. The latest release includes over 700 position weight matrices, segregated based on their cofactors and DNA methylation status. The database also offers precomputed GO annotations for human TFs and TF-co-TF complexes, allowing for a comprehensive analysis of TF functions in their context with cofactors. Furthermore, MethMotif has been expanded to include data for two additional species, increasing its applicability and value to the scientific community.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Mathematical & Computational Biology
Pauline Brochet, Jean-Christophe Mouren, Laurent Hannouche, Fabrice Lopez, Benoit Ballester, Edecio Cunha-Neto, Lionel Spinelli, Christophe Chevillard
Summary: Chagas disease is a parasitic disease caused by Trypanosoma cruzi, affecting approximately 7 million people worldwide. About 10,000 people die from this disease annually, with 30% developing severe chronic forms that currently have no treatment. To facilitate research on Chagas disease, a manual curation of all relevant papers on PubMed was conducted, and a database called ChagasDB was created to include all deregulated molecules in host organisms following T. cruzi infection. A website has also been developed for easy accessibility to this database, and this article provides detailed information on its construction, contents, and usage.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Cell Biology
Pierre de Langen, Fayrouz Hammal, Elise Gueret, Jean-Christophe Mouren, Lionel Spinelli, Benoit Ballester
Summary: This study reveals the pervasive intergenic transcription in normal and cancerous tissues through data analysis and integration. By constructing an RNAPII atlas and integrating other datasets, tissue and disease-specific transcriptional activities were discovered, and intergenic transcription was identified as a biomarker associated with cancer subtypes and survival.
