Article
Oncology
Luciano Giaco, Fernando Palluzzi, Davide Guido, Camilla Nero, Flavia Giacomini, Simona Duranti, Emilio Bria, Giampaolo Tortora, Tonia Cenci, Maurizio Martini, Elisa De Paolis, Maria Elisabetta Onori, Maria De Bonis, Nicola Normanno, Giovanni Scambia, Angelo Minucci
Summary: Comprehensive genomic profiling (CGP) is crucial for understanding solid tumors at the molecular level and providing personalized therapy. In this study, the performance of the Illumina TSO500 high-throughput assay was evaluated, showing consistent results with standard approaches and minor limitations, making it suitable for routine patient screening.
Review
Biochemistry & Molecular Biology
Paula Arribas, Carmelo Andujar, Martin I. Bidartondo, Kristine Bohmann, Eric Coissac, Simon Creer, Jeremy R. deWaard, Vasco Elbrecht, Gentile F. Ficetola, Marta Goberna, Susan Kennedy, Henrik Krehenwinkel, Florian Leese, Vojtech Novotny, Fredrik Ronquist, Douglas W. Yu, Lucie Zinger, Thomas J. Creedy, Emmanouil Meramveliotakis, Victor Noguerales, Isaac Overcast, Helene Morlon, Alfried P. Vogler, Anna Papadopoulou, Brent C. Emerson
Summary: High-throughput sequencing technology is increasingly used for biodiversity characterization and monitoring, offering a deeper understanding of global biodiversity when applied across broad geographical scales. International collaborative efforts are needed to maximize the potential of HTS data for global integration and synthesis, particularly in establishing an effective Genomic Observatories network for terrestrial biodiversity integration.
Article
Biochemical Research Methods
Goo Jun, Fritz Sedlazeck, Qihui Zhu, Adam English, Ginger Metcalf, Hyun Min Kang, Charles Lee, Richard Gibbs, Eric Boerwinkle
Summary: This study introduces muCNV, a software developed for joint genotyping of over 100,000 samples, showing high efficiency and accuracy in population-scale genotyping. Pilot results demonstrate very low Mendelian inconsistencies, with computational efficiencies highlighted when applied to large-scale projects in the cloud.
Article
Cell Biology
Pavel Katunin, Jianbo Zhou, Ola M. Shehata, Andrew A. Peden, Ashley Cadby, Anton Nikolaev
Summary: Modern data analysis methods, such as optimization algorithms or deep learning, have been successfully applied to biotechnological and medical questions, requiring a large number of high-quality and reproducible experiments with automation. An open-source hardware and low-cost framework has been introduced for automatic high-throughput generation of cell biology data, demonstrating flexibility and adaptability to individual experimental needs.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Maxime de Ronne, Gaetan Legare, Francois Belzile, Brian Boyle, Davoud Torkamaneh
Summary: 3D-GBS is an optimized GBS procedure that provides an ultra-high-throughput and ultra-low-cost genotyping solution for large-scale studies. It reduces the genotyping cost significantly and improves the efficiency of marker discovery.
Article
Biochemistry & Molecular Biology
Cyril Hammoud, Stephen Mulero, Bert Van Bocxlaer, Jerome Boissier, Dirk Verschuren, Christian Albrecht, Tine Huyse
Summary: The new workflow developed in this study utilizes high-throughput amplicon sequencing to simultaneously genotype snail hosts and their infecting trematode parasites. After stringent quality control, the workflow can identify snails and trematodes with high sensitivity, successfully detecting co-infections and providing new possibilities for studying parasite-parasite interactions.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Cornelis A. M. Wagemaker, Liesje Mommer, Eric J. W. Visser, Alexandra Weigelt, Thomas P. van Gurp, Maarten Postuma, Annemiek E. Smit-Tiekstra, Hans de Kroon
Summary: Plant interactions belowground are important and difficult to quantify accurately. The msGBS method presented in this study allows for high taxonomic resolution and parallel quantification of multiple species in root samples. Compared to qPCR, msGBS offers similar results with advantages in revealing hidden belowground interactions.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Multidisciplinary Sciences
Kelsy C. Cotto, Yang-Yang Feng, Avinash Ramu, Megan Richters, Sharon L. Freshour, Zachary L. Skidmore, Huiming Xia, Joshua F. McMichael, Jason Kunisaki, Katie M. Campbell, Timothy Hung-Po Chen, Emily B. Rozycki, Douglas Adkins, Siddhartha Devarakonda, Sumithra Sankararaman, Yiing Lin, William C. Chapman, Christopher A. Maher, Vivek Arora, Gavin P. Dunn, Ravindra Uppaluri, Ramaswamy Govindan, Obi L. Griffith, Malachi Griffith
Summary: RegTools is a software package that integrates genomic data with transcriptomic data to identify somatic variants that may cause aberrant splicing. It has been applied to over 9000 tumor samples and discovered numerous splice-associated variants.
NATURE COMMUNICATIONS
(2023)
Review
Chemistry, Multidisciplinary
Farhad Soheilmoghaddam, Madeleine Rumble, Justin Cooper-White
Summary: Many existing clinical treatments are limited in their ability to completely restore decreased or lost tissue and organ function. The increasing demand for new medical interventions has led to the development of promising fields such as gene therapy, tissue engineering, and regenerative medicine. Success in these fields relies on biomaterials that provide necessary biological cues for cell fate, necessitating a shift towards rapid synthesis and characterization practices.
Article
Microbiology
Gina Faraci, Sung Yong Park, Tanzy M. T. Love, Michael P. Dube, Ha Youn Lee
Summary: HIV microdrop sequencing is a powerful tool for large-scale and high-precision HIV genomic surveillance. The study successfully identified individuals with recent infections and achieved high detection accuracies. Moreover, the analysis of chronic HIV infection confirmed the false recency rate and estimated the time since infection with high consistency.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Yuanyuan Cheng, Catherine Grueber, Carolyn J. Hogg, Katherine Belov
Summary: The major histocompatibility complex (MHC) is crucial for the vertebrate immune system, but accurately characterizing MHC genetic diversity in non-model species is technically challenging due to gene duplication and diversification. A new long-read based MHC typing method has been developed to address these challenges and provide better solutions for high accuracy MHC typing in research. This approach allows for population-scale MHC typing in various species, revealing new insights into genetic diversity.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Engineering, Environmental
Rafaela S. Fontenele, Simona Kraberger, James Hadfield, Erin M. Driver, Devin Bowes, LaRinda A. Holland, Temitope O. C. Faleye, Sangeet Adhikari, Rahul Kumar, Rosa Inchausti, Wydale K. Holmes, Stephanie Deitrick, Philip Brown, Darrell Duty, Ted Smith, Aruni Bhatnagar, Ray A. Yeager, Rochelle H. Holm, Natalia Hoogesteijn von Reitzenstein, Elliott Wheeler, Kevin Dixon, Tim Constantine, Melissa A. Wilson, Efrem S. Lim, Xiaofang Jiang, Rolf U. Halden, Matthew Scotch, Arvind Varsani
Summary: The study analyzed 91 wastewater samples from 11 states in the USA, detecting a large number of new single-nucleotide variants of SARS-CoV-2, with half of them also being found in subsequent clinical data. The presence of more lineages in wastewater samples suggests a greater genetic diversity circulating within communities compared to clinical-derived data.
Article
Multidisciplinary Sciences
Ashley Osborne, Jody E. E. Phelan, Leen N. N. Vanheer, Alphaxard Manjurano, Jesse Gitaka, Christopher J. J. Drakeley, Akira Kaneko, Kiyoshi Kita, Susana Campino, Taane G. G. Clark
Summary: Malaria has had a significant impact on the human genome, leading to genetic conditions and defects. Our understanding of the genetic differences between different indigenous populations in Africa and their implications on disease is limited. However, advances in low-cost sequencing technologies have allowed for targeted genetic profiling and insights into genetic diversity.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Victoria Popic, Chris Rohlicek, Fabio Cunial, Iman Hajirasouliha, Dmitry Meleshko, Kiran Garimella, Anant Maheshwari
Summary: Cue achieves versatile and performant structural variant calling and genotyping using a deep-learning approach. It converts alignments to images that encode SV-informative signals and uses a stacked hourglass convolutional neural network to accurately predict the type, genotype, and genomic locus of the captured SVs. Cue outperforms existing state-of-the-art methods in detecting various classes of SVs on synthetic and real short-read data, and can be easily extended to other sequencing platforms.
Article
Materials Science, Multidisciplinary
Adrien Couet
Summary: This article introduces a novel, integrated, high-throughput (HTP) research framework aimed at developing radiation and corrosion tolerant materials for high-temperature nuclear structural applications and accelerating materials discovery. By utilizing in situ alloying techniques, automated heavy-ion irradiation experiments, and an innovative corrosion testing method, rapid data acquisition of irradiation and corrosion resistance of Compositionally Complex Alloys (CCAs) can be achieved. This approach enables the establishment of a robust database within a year.
JOURNAL OF NUCLEAR MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Andrea Parra-Salazar, Jorge Gomez, Daniela Lozano-Arce, Paula H. Reyes-Herrera, Jorge Duitama
Summary: Genotyping-by-sequencing (GBS) is a cost-effective technique for obtaining genetic markers from populations, and reference-free approaches are needed for species without a reference genome. However, available tools for de novo analysis of GBS reads face usability and accuracy issues. The novel algorithm NGSEP shows better accuracy and computational efficiency in benchmark experiments, making it a useful tool for population genetic studies in various species.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Genetics & Heredity
Daniel Mahecha, Haydemar Nunez, Maria C. Lattig, Jorge Duitama
Summary: This manuscript compares three machine learning methods for classifying VUS as Pathogenic or No pathogenic and creates an open-source software tool for prioritizing VUS using a Random Forest model, thus improving the process of genetic diagnosis.
Article
Green & Sustainable Science & Technology
Caroline L. Perez, Lais P. R. da C. Pereira, Thais S. Milessi, Juliana P. Sandri, Mekonnen Demeke, Maria R. Foulquie-Moreno, Johan M. Thevelein, Teresa C. Zangirolami
Summary: A strategy based on strain evaluation and integration with 1G ethanol production was used to develop a robust and scalable process for 2G ethanol production. The study found that using mixed medium of crude bagasse hydrolysate and molasses achieved high ethanol concentrations and long-term stability.
Review
Biochemistry & Molecular Biology
Laura Vanderwaeren, Ruveyda Dok, Karin Voordeckers, Sandra Nuyts, Kevin J. Verstrepen
Summary: Yeast is an important enzyme source for bread and beer production and is an ideal model organism for studying eukaryotic cell biology and genetics. This review discusses the characteristics that make yeast such a widely used model organism, with a focus on the DNA damage response pathway as an example of its contribution to elucidating highly conserved biological processes. Differences in the DNA damage response of yeast and humans are also highlighted, along with the challenges of using yeast as a model system.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Liesbet Wilberts, Jozsef Vuts, John C. Caulfield, Gareth Thomas, Michael A. Birkett, Beatriz Herrera-Malaver, Kevin J. Verstrepen, Islam S. Sobhy, Hans Jacquemyn, Bart Lievens
Summary: This study investigated whether root inoculation of sweet pepper with entomopathogenic fungi can improve resistance against the tobacco peach aphid. The results showed that plants inoculated with Akanthomyces muscarius significantly attracted aphids and negatively affected their life history traits. However, plants inoculated with B. bassiana did not have a significant effect on aphids.
Review
Microbiology
Lieselotte Vermeersch, Lloyd Cool, Anton Gorkovskiy, Karin Voordeckers, Tom Wenseleers, Kevin J. Verstrepen
Summary: Microbes need to respond properly to environmental cues for cellular functioning. Past exposure to environmental cues can accelerate the response even in daughter cells. This behavior is mainly epigenetic and is often accompanied by heterogeneity in response between cells of the same population.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Applied
Fabio Herrera-Rocha, Monica P. Cala, Ana Maria Leon-Inga, Jenny Lorena Aguirre Mejia, Claudia M. Rodriguez-Lopez, Sergio Leonardo Florez, Maria Jose Chica, Hector Hugo Olarte, Jorge Duitama, Andres Fernando Gonzalez Barrios, Miguel Fernandez-Nino
Summary: This study analyzed the lipidome of fine-flavor cocoa fermentation using LC-MS-QTOF and developed a Machine Learning model to assess potential bioactivity. The results showed that the cocoa lipidome, mainly consisting of fatty acyls and glycerophospholipids, remained stable during fermentation. The K-Nearest Neighbors algorithm exhibited the best performance and classified 28 identified lipids as potential bioactive compounds. None of these compounds have been previously reported as bioactive.
Article
Chemistry, Applied
Ruben Wauters, Beatriz Herrera-Malaver, Michiel Schreurs, Peter Bircham, Charlotte Cautereels, Jeroen Cortebeeck, Paul M. Duffin, Jan Steensels, Kevin J. Verstrepen
Summary: This study demonstrates that refermentation can reduce the accumulation of staling aldehydes in beer. By using high-throughput screening and breeding, novel S. cerevisiae hybrids that survive for over a year in beer were developed, significantly increasing beer flavor stability.
Article
Biochemistry & Molecular Biology
Sara Deleu, Kaline Arnauts, Lowie Deprez, Kathleen Machiels, Marc Ferrante, Geert R. B. Huys, Johan M. M. Thevelein, Jeroen Raes, Severine Vermeire
Summary: Short-chain fatty acids and their bacterial producers are gaining increasing attention in inflammatory bowel diseases. Acetate, although less studied compared to butyrate, shows potential in being less toxic to epithelial cells, stimulating butyrate-producing bacteria, and having anti-inflammatory and barrier-protective properties. In a study using organoid-based monolayer cultures from ulcerative colitis patients, high acetate concentrations were found to improve epithelial resistance, decrease pro-inflammatory markers, and enhance barrier gene expression. These findings suggest that acetate may offer a promising approach for managing barrier defects and inflammation in IBD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Daniel Tello, Laura Natalia Gonzalez-Garcia, Jorge Gomez, Juan Camilo Zuluaga-Monares, Rogelio Garcia, Ricardo Angel, Daniel Mahecha, Erick Duarte, Maria del Rosario Leon, Fernando Reyes, Camilo Escobar-Velasquez, Mario Linares-Vasquez, Nicolas Cardozo, Jorge Duitama
Summary: The article introduces the latest functionalities implemented in NGSEP 4 for identifying orthogroups and conducting whole genome alignments. NGSEP 4 also includes a new graphical user interface based on JavaFX technology. These new developments are expected to be very useful for studies in evolutionary biology and population genomics.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Chemistry, Physical
Andrea Steinmann, Maurice Finger, Christian Nowacki, Davide Decembrino, Georg Hubmann, Marco Girhard, Vlada B. Urlacher, Stephan Luetz
Summary: This study investigated the biotransformation of coniferyl alcohol to secoisolariciresinol using recombinant Escherichia coli in a stirred-tank reactor. The researchers optimized the production conditions by monitoring the lignan pathway activity and metabolite concentrations. The results showed that copper concentration and substrate-feeding strategy had a significant impact on lignan production.
Review
Food Science & Technology
Fabio Herrera-Rocha, Miguel Fernandez-Nino, Monica P. Cala, Jorge Duitama, Andres Fernando Gonzalez Barrios
Summary: The global market of chocolate has experienced significant growth over the past decade and is projected to reach a value of USD 200 billion by 2028. Chocolate production involves a complex process that requires extensive post-harvesting, particularly cocoa bean fermentation, drying, and roasting. Improving cocoa processing is a current challenge in order to enhance global production of high-quality cocoa and subsequently improve chocolate quality.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Plant Sciences
Laura Natalia Gonzalez-Garcia, Daniela Lozano-Arce, Juan Pablo Londono, Romain Guyot, Jorge Duitama
Summary: We propose a new method using the Next-Generation Sequencing Experience Platform (NGSEP) for efficient homology-based transposable element (TE) annotation. Our algorithm performs well on genome assemblies of different plant species, outperforming traditional homology-based annotation tools in speed by a factor of three to >20, reducing the annotation time of the T. aestivum genome from months to hours, and recovering up to 80% of TEs annotated with RepeatMasker with a precision of up to 0.95.
APPLICATIONS IN PLANT SCIENCES
(2023)
Article
Biology
Laura Gonzalez-Garcia, David Guevara-Barrientos, Daniela Lozano-Arce, Juanita Gil, Jorge Diaz-Riano, Erick Duarte, German Andrade, Juan Camilo Bojaca, Maria Camila Hoyos-Sanchez, Christian Chavarro, Natalia Guayazan, Luis Alberto Chica, Maria Camila Buitrago Acosta, Edwin Bautista, Miller Trujillo, Jorge Duitama
Summary: Building de novo genome assemblies for complex genomes is possible with long-read DNA sequencing technologies. New algorithms are developed to assemble long DNA sequencing reads from haploid and diploid organisms. The algorithms demonstrate competitive accuracy and computational efficiency compared with other software currently used. This development is expected to be useful for researchers building genome assemblies for different species.
LIFE SCIENCE ALLIANCE
(2023)
Article
Biology
Daniela Lozano-Arce, Tatiana Garcia, Laura Natalia Gonzalez-Garcia, Romain Guyot, Maria Isabel Chacon-Sanchez, Jorge Duitama
Summary: The complete catalog of transposable elements in the lima bean genome sheds light on the dual domestication events in the Mesoamerican and Andean gene pools. These events make lima bean an ideal model for studying convergent evolution. The mechanisms of adaptation and the genes involved in these processes are not well understood, and this study demonstrates the potential role of transposable elements in shaping gene functions. The analysis of whole-genome sequencing data reveals the genetic structure of lima bean and provides insights into its demographic history and selection processes during domestication.
COMMUNICATIONS BIOLOGY
(2023)
