Article
Biochemical Research Methods
Margaret R. Woodhouse, Shatabdi Sen, David Schott, John L. Portwood, Michael Freeling, Justin W. Walley, Carson M. Andorf, James C. Schnable
Summary: RNA-Seq whole-genome sequencing has become a widely used method for measuring and understanding transcriptome-level changes in gene expression. The comparative gene expression tool qTeller has been revamped to take advantage of the growing number of public RNA-Seq datasets, enabling users to evaluate gene expression data in a defined genomic interval and perform two-gene comparisons across multiple user-chosen tissues. The updated qTeller now supports multiple genomes for intergenomic comparisons, and includes capabilities for both mRNA and protein abundance datasets, along with support for additional data formats and a modernized interface.
Article
Biochemistry & Molecular Biology
Juliana S. Bernardes, Raphael J. Eberle, Fabio R. J. Vieira, Monika A. Coronado
Summary: Analysis of the pan-genome of Corynebacterium pseudotuberculosis revealed that the equi biovar is more variable, with a higher number of biovar-specific domains associated with virulence mechanisms. Functional differences were identified between strains of the ovis and equi biovars, potentially related to niche-adaptation and virulence mechanisms. This may impact bacterial physiology and lifestyle, and could lead to the development of new diagnostics, vaccines, and treatments for C. pseudotuberculosis diseases.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Food Science & Technology
Xiayu Liu, Guangyu Liu, Yansha Wu, Xinxin Pang, Yajing Wu, Qinshu, Jianrui Niu, Qihe Chen, Xinglin Zhang
Summary: This article summarizes the common types and hazards of food-borne pathogens, the development of Tn-seq technology, and its applications in studying the physiology, pathogenesis, and environmental survival of food-borne pathogens.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2021)
Article
Biochemical Research Methods
Emilie Pasche, Anais Mottaz, Deborah Caucheteur, Julien Gobeill, Pierre-Andre Michel, Patrick Ruch
Summary: This article describes a system for identifying and interpreting clinically actionable variants, and triaging and prioritizing relevant publications. The system has been shown to be effective in searching and accurately identifying clinically actionable variants.
Article
Plant Sciences
Tong Yu, Xiao Ma, Zhuo Liu, Xuehuan Feng, Zhiyuan Wang, Jun Ren, Rui Cao, Yingchao Zhang, Fulei Nie, Xiaoming Song
Summary: This study constructed a comprehensive vegetable database, TVIR, based on the genomes of 59 vegetables. It includes gene annotations, functional gene data, and transcriptome data, as well as bioinformatic tools for comparative genomic analysis. TVIR is expected to become a key hub for global vegetable research.
HORTICULTURE RESEARCH
(2022)
Article
Computer Science, Information Systems
A. Velez-Estevez, I. J. Perez, P. Garcia-Sanchez, J. A. Moral-Munoz, M. J. Cobo
Summary: The science of science practice requires the analysis of large and complex bibliometric data. This study aims to establish a taxonomy and offer a comparative analysis of 44 bibliographic APIs from different organizations, analyzing their characteristics, metadata, possible bibliometric analyses, and API interoperability across different data categories. The study found that Clarivate Analytics and Elsevier offer versatile APIs, while non-profit organizations promote the Open Science philosophy. Most organizations provide free access to APIs for non-commercial purposes, but some have limitations on metadata retrieval.
INFORMATION PROCESSING & MANAGEMENT
(2023)
Review
Plant Sciences
Mutsumi Watanabe, Takayuki Tohge
Summary: Functional genomics approaches have successfully detected key metabolic polymorphisms in plant specialized metabolism through comparative omics analyses of wild-accessions and cultivars/wild species, as well as comparative genomic analyses in plant species focusing on gene clusters. In recent decades, intra-species specific metabolic polymorphisms, new functionalization of tandem duplicated genes, and metabolic gene clusters have been found as the main factors creating metabolic diversity of specialized metabolites in plants. However, strategic approaches depending on the target metabolic pathways are required for gene identification in plant specialized metabolism. The increasing availability of plant genome sequences and transcriptome data has facilitated inter-specific comparative analyses, including genomic analysis and gene co-expression network analysis. Here, we introduce functional genomics approaches with the integration of inter-/intra-species comparative metabolomics, their key roles in providing genomic signatures of metabolic evolution, and discuss future prospects of functional genomics on plant specialized metabolism.
CURRENT OPINION IN PLANT BIOLOGY
(2023)
Article
Oncology
Anna Puiggros, Silvia Ramos-Campoy, Joanna Kamaso, Mireia de la Rosa, Marta Salido, Carme Melero, Maria Rodriguez-Rivera, Sandrine Bougeon, Rosa Collado, Eva Gimeno, Rocio Garcia-Serra, Sara Alonso, Marco Antonio Moro-Garcia, Maria Dolores Garcia-Malo, Xavier Calvo, Leonor Arenillas, Ana Ferrer, Tuomo Mantere, Alexander Hoischen, Jacqueline Schoumans, Blanca Espinet
Summary: This study investigated the use of optical genome mapping (OGM) in assessing the cytogenetics of chronic lymphocytic leukemia (CLL). The results showed that OGM can identify most known abnormalities and provide new structural information. OGM had better accuracy than current methods in predicting the time to first treatment. A complex OGM group defined by the number of abnormalities was associated with TP53 abnormalities and shorter time to first treatment.
Article
Microbiology
Qiqi Pan, Xudan Shen, Leilei Yu, Fengwei Tian, Jianxin Zhao, Hao Zhang, Wei Chen, Qixiao Zhai
Summary: The study explored common functional genes for bile salt resistance in 90 Lactobacillus salivarius strains, identifying genes related to peptidoglycan synthesis, phosphotransferase system, and stress response as key factors. A significant association was found between GATase1-encoding gene and bile salt tolerance. Additionally, global regulatory genes for bile salt tolerance were identified, offering a potential method for rapid screening of bile salt-tolerant L. salivarius strains based on PCR amplification of functional genes.
Article
Pharmacology & Pharmacy
Eric Savier, Lorena Simon-Gracia, Frederic Charlotte, Pierre Tuffery, Tambet Teesalu, Olivier Scatton, Angelita Rebollo
Summary: The study demonstrated that bi-functional tumor-penetrating and interfering peptides are internalized in malignant hepatocytes, inducing apoptosis, while having no effect on non-malignant cells. The degree of peptide internalization correlated with receptor expression levels and tumor aggressiveness.
Article
Multidisciplinary Sciences
Jun Li, Hengyu Lu, Patrick Kwok-Shing Ng, Angeliki Pantazi, Carman Ka Man Ip, Kang Jin Jeong, Bianca Amador, Richard Tran, Yiu Huen Tsang, Lixing Yang, Xingzhi Song, Turgut Dogruluk, Xiaojia Ren, Angela Hadjipanayis, Christopher A. Bristow, Semin Lee, Melanie Kucherlapati, Michael Parfenov, Jiabin Tang, Sahil Seth, Harshad S. Mahadeshwar, Kamalika Mojumdar, Dong Zeng, Jianhua Zhang, Alexei Protopopov, Jonathan G. Seidman, Chad J. Creighton, Yiling Lu, Nidhi Sahni, Kenna R. Shaw, Funda Meric-Bernstam, Andrew Futreal, Lynda Chin, Kenneth L. Scott, Raju Kucherlapati, Gordon B. Mills, Han Liang
Summary: The study introduces a new method to systematically identify fusion genes and evaluate their sensitivity to drugs, revealing that some of these genes have activating effects on tumor growth. It proposes an integrated, level-of-evidence classification system to prioritize gene fusions systematically.
Article
Multidisciplinary Sciences
Yiting Lim, Sonali Arora, Samantha L. Schuster, Lukas Corey, Matthew Fitzgibbon, Cynthia L. Wladyka, Xiaoying Wu, Ilsa M. Coleman, Jeffrey J. Delrow, Eva Corey, Lawrence D. True, Peter S. Nelson, Gavin Ha, Andrew C. Hsieh
Summary: The study explores the functional consequences of genetic variations in 5' untranslated regions (UTRs) in disease, focusing on prostate cancer. It introduces a high-throughput method called PLUMAGE to quantify the molecular effects of somatic mutations in 5' UTRs and identifies their impact on gene expression and clinical outcomes.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Yiwei Wang, Jiaxin Yang, Xinhao Zhuang, Yunchao Ling, Ruifang Cao, Qingwei Xu, Peng Wang, Ping Xu, Guoqing Zhang
Summary: This study collated and analyzed viral genomic and epidemiological data related to COVID-19, establishing an online database by integrating information from various sources. It provides assistance in identifying relevant knowledge and devising epidemic prevention and control policies.
Article
Multidisciplinary Sciences
Hyeunjeong Song, Ki-Tae Kim, Sook-Young Park, Gir-Won Lee, Jaeyoung Choi, Jongbum Jeon, Kyeongchae Cheong, Gobong Choi, Jae-Seoun Hur, Yong-Hwan Lee
Summary: By comparing the genomes of six lichen-forming fungi, this study reveals the reduction of dispensable genes and the acquisition of lineage-specific genes, providing insights into the symbiotic biology of lichens.
SCIENTIFIC REPORTS
(2022)
Review
Computer Science, Interdisciplinary Applications
Gregorius Satia Budhi, Raymond Chiong, Ilung Pranata, Zhongyi Hu
Summary: This paper introduces a novel framework for gauging the ratings of online reviews using machine learning techniques and evaluates different classifiers and feature extraction methods to find that linear-kernel support vector machine, logistic regression, and multilayer perceptron are the top three single classifiers. Furthermore, by leveraging these classifiers as base classifiers in ensemble models, their performance can be further enhanced. Additionally, various text pre-processing techniques and sentiment lexicons are explored to improve accuracy, with deep learning models also yielding promising results.
ARCHIVES OF COMPUTATIONAL METHODS IN ENGINEERING
(2021)
Article
Biochemical Research Methods
Clementine Decamps, Florian Prive, Raphael Bacher, Daniel Jost, Arthur Waguet, Sophie Achard, Sophie Achard, Elise Amblard, Raphael Bacher, Fabian Bergmann, Michael Blum, Yuna Blum, Guillaume Bottaz-Bosson, Lucile Broseus, Florent Chuffart, Clementine Decamps, Emilie Devijver, Ghislain Durif, Vassili Feofanov, Eugene Andres Houseman, Melina Gallopin, Paulina Jedynak, Vincent Jonchere, Ellen Van de Geer, Basile Jumentier, Tony Kaoma, Eugene Lurie, Pavlo Lutsik, Julia Markowski, Anna Melnykova, Jane Merlevede, Petr Nazarov, Ngoc Ha Nguyen, Olga Permiakova, Florian Prive, Magali Richard, Matthieu Rolland, Michael Scherer, Yannick Spill, Eugene Andres Houseman, Eugene Lurie, Pavlo Lutsik, Aleksandar Milosavljevic, Michael Scherer, Michael G. B. Blum, Magali Richard
BMC BIOINFORMATICS
(2020)
Article
Oncology
Miriam Marques, Robin Tranchant, Blanca Risa-Ebri, Maria L. Suarez-Solis, Luis C. Fernandez, Enrique Carrillo-de-Santa-Pau, Natalia Del Pozo, Jaime Martinez de Villarreal, Clement Meiller, Yves Allory, Yuna Blum, Christine Pirker, Balazs Hegedus, Simon T. Barry, Amancio Carnero, Walter Berger, Didier Jean, Francisco X. Real
Article
Oncology
Lisa Quetel, Clement Meiller, Jean-Baptiste Assie, Yuna Blum, Sandrine Imbeaud, Francois Montagne, Robin Tranchant, Julien de Wolf, Stefano Caruso, Marie-Christine Copin, Veronique Hofman, Laure Gibault, Cecile Badoual, Ecaterina Pintilie, Paul Hofman, Isabelle Monnet, Arnaud Scherpereel, Francoise Le Pimpec-Barthes, Jessica Zucman-Rossi, Marie-Claude Jaurand, Didier Jean
MOLECULAR ONCOLOGY
(2020)
Article
Multidisciplinary Sciences
Clara Savary, Artem Kim, Alexandra Lespagnol, Virginie Gandemer, Isabelle Pellier, Charlotte Andrieu, Gilles Pages, Marie-Dominique Galibert, Yuna Blum, Marie de Tayrac
SCIENTIFIC REPORTS
(2020)
Article
Medicine, General & Internal
Remy Nicolle, Yuna Blum, Pauline Duconseil, Charles Vanbrugghe, Nicolas Brandone, Flora Poizat, Julie Roques, Martin Bigonnet, Odile Gayet, Marion Rubis, Nabila Elarouci, Lucile Armenoult, Mira Ayadi, Aurelien de Reynies, Marc Giovannini, Philippe Grandval, Stephane Garcia, Cindy Canivet, Jerome Cros, Barbara Bournet, Louis Buscail, Vincent Moutardier, Marine Gilabert, Juan Iovanna, Nelson Dusetti
Article
Oncology
R. Nicolle, O. Gayet, P. Duconseil, C. Vanbrugghe, J. Roques, M. Bigonnet, Y. Blum, N. Elarouci, L. Armenoult, M. Ayadi, A. de Reynies, F. Puleo, J. Augustin, J. F. Emile, M. Svrcek, T. Arsenijevic, P. Hammel, M. Giovannini, P. Grandval, L. Dahan, V Moutardier, M. Gilabert, J. L. Van Laethem, J. B. Bachet, J. Cros, J. Iovanna, N. J. Dusetti
Summary: The study demonstrates that the RNA-based GemPred stratification can predict the benefit of adjuvant gemcitabine in PDAC patients.
ANNALS OF ONCOLOGY
(2021)
Article
Oncology
Jerome Raffenne, Fernando A. Martin, Remy Nicolle, Marina Konta, Yuna Blum, Jerome Torrisani, Francesco Puleo, Jean Baptiste Bachet, Magali Svrcek, Armel Bardier-Dupas, Jean Francois Emile, Peter Demetter, Miroslav Radman, Jean Luc Van Laethem, Pascal Hammel, Vinciane Rebours, Valerie Paradis, Anne Couvelard, Jerome Cros
Summary: Pancreatic ductal adenocarcinoma (PDAC) is typically diagnosed in the 7th decade, but around 10% of patients are diagnosed before the age of 55. Molecular features of early-onset tumors (<= 55 y.o.) were found to be similar to late-onset tumors (>= 70 y.o.), indicating that younger patients can serve as a good molecular surrogate model for the general older population with PDAC. The study also highlighted the impact of ageing on DNA methylation and proteome integrity, as well as the association of oxidative stress responses with PDAC.
Article
Gastroenterology & Hepatology
Sarra Smati, Arnaud Polizzi, Anne Fougerat, Sandrine Ellero-Simatos, Yuna Blum, Yannick Lippi, Marion Regnier, Alexia Laroyenne, Marine Huillet, Muhammad Arif, Cheng Zhang, Frederic Lasserre, Alain Marrot, Talal Al Saati, JingHong Wan, Caroline Sommer, Claire Naylies, Aurelie Batut, Celine Lukowicz, Tiffany Fougeray, Blandine Tramunt, Patricia Dubot, Lorraine Smith, Justine Bertrand-Michel, Nathalie Hennuyer, Jean-Philippe Pradere, Bart Staels, Remy Burcelin, Francoise Lenfant, Jean-Francois Arnal, Thierry Levade, Laurence Gamet-Payrastre, Sandrine Lagarrigue, Nicolas Loiseau, Sophie Lotersztajn, Catherine Postic, Walter Wahli, Christophe Bureau, Maeva Guillaume, Adil Mardinoglu, Alexandra Montagner, Pierre Gourdy, Herve Guillou
Summary: The study found that different diets induced more severe NAFLD in male mice, characterized by lipid accumulation and inflammation/fibrosis. Sex-biased hepatic gene signatures showed different responses to various dietary challenges, with Peroxisome proliferator-activated receptor alpha (PPAR alpha) playing a key role in gender-specific and NAFLD pathophysiology.
Article
Oncology
Laetitia Marisa, Yuna Blum, Julien Taieb, Mira Ayadi, Camilla Pilati, Karine Le Malicot, Come Lepage, Ramon Salazar, Daniela Aust, Alex Duval, Helene Blons, Valerie Taly, David Gentien, Audrey Rapinat, Janick Selves, Sophie Mouillet-Richard, Valerie Boige, Jean-Francois Emile, Aurelien de Reynies, Pierre Laurent-Puig
Summary: The study demonstrates that intratumor heterogeneity (ITH) in colon cancer, decoded based on consensus molecular subtypes (CMS), is common and impacts prognosis. Combinations of different CMSs are associated with poorer outcomes, with ITH being a significant factor in disease-free survival variance. Additionally, cellular analysis suggests that ITH could reflect distinct functional statuses of colon cancer cells, implying potential plasticity between different cell populations related to CMS. Further evaluation of transcriptomic ITH is warranted in the context of personalized medicine.
CLINICAL CANCER RESEARCH
(2021)
Article
Genetics & Heredity
Clement Meiller, Francois Montagne, Theo Z. Hirsch, Stefano Caruso, Julien de Wolf, Quentin Bayard, Jean-Baptiste Assie, Lea Meunier, Yuna Blum, Lisa Quetel, Laure Gibault, Ecaterina Pintilie, Cecile Badoual, Sarah Humez, Francoise Galateau-Salle, Marie-Christine Copin, Eric Letouze, Arnaud Scherpereel, Jessica Zucman-Rossi, Francoise Le Pimpec-Barthes, Marie-Claude Jaurand, Didier Jean
Summary: This study investigated intra-tumor heterogeneity in malignant pleural mesothelioma (MPM) using the largest series to date and multi-omics profiling of a substantial series of multi-site tumor samples. The results revealed patient-dependent spatial heterogeneity at genetic, transcriptomic, and epigenetic levels, as well as changes in the immune landscape of the tumor microenvironment, supporting the need for multi-sampling for precision medicine.
Article
Genetics & Heredity
Fabien Degalez, Frederic Jehl, Kevin Muret, Maria Bernard, Frederic Lecerf, Laetitia Lagoutte, Colette Desert, Frederique Pitel, Christophe Klopp, Sandrine Lagarrigue
Summary: Most single-nucleotide polymorphisms (SNPs) are located in non-coding regions, but the fraction usually studied is in protein-coding regions to predict impacts on proteins. Haplotype-aware variant annotation is valuable in considering multi-nucleotide variants (MNVs) in coding regions for severe functional consequences such as stop-gained variants.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Frederic Jehl, Fabien Degalez, Maria Bernard, Frederic Lecerf, Laetitia Lagoutte, Colette Desert, Manon Coulee, Olivier Bouchez, Sophie Leroux, Behnam Abasht, Michele Tixier-Boichard, Bertrand Bed'hom, Thierry Burlot, David Gourichon, Philippe Bardou, Herve Acloque, Sylvain Foissac, Sarah Djebali, Elisabetta Giuffra, Tatiana Zerjal, Frederique Pitel, Christophe Klopp, Sandrine Lagarrigue
Summary: RNA-seq data is a valuable yet unexploited resource for detecting SNPs and genotypes in various populations, especially in livestock species. This study compared SNP calling results using RNA-seq data in two chicken populations, proposing thresholds for genotype calling consistency and demonstrating the potential of RNA-seq data for gene expression regulation and population genetic analysis.
FRONTIERS IN GENETICS
(2021)
Article
Biochemical Research Methods
Clementine Decamps, Alexis Arnaud, Florent Petitprez, Mira Ayadi, Aurelia Baures, Lucile Armenoult, Sergio Escalera, Isabelle Guyon, Remy Nicolle, Richard Tomasini, Aurelien de Reynies, Jerome Cros, Yuna Blum, Magali Richard
Summary: DECONbench is a standardized resource for evaluating computational methods quantifying cell-type heterogeneity in cancer. It includes simulated benchmark datasets and baseline deconvolution methods, allowing continuous submission of new methods for evaluation.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Sandrine Lagarrigue, Matthias Lorthiois, Fabien Degalez, David Gilot, Thomas Derrien
Summary: Animal genomes produce a large number of lncRNAs, which are transcripts longer than 200 nucleotides with low coding-potential capabilities. Studying lncRNAs in domestic animals can help understand the roles of protein-coding and non-coding RNAs in phenotypic variations. This review covers the current knowledge on transcriptome-based catalogues of lncRNAs in major domesticated animals, comparing them to human and mouse lncRNA catalogues across a wide phylogenetic scale.
