Review
Agriculture, Dairy & Animal Science
Ying Gong, Yefang Li, Xuexue Liu, Yuehui Ma, Lin Jiang
Summary: As large-scale genomic studies progress, it has been found that a single reference genome cannot represent genetic diversity at the species level. The pangenome, on the other hand, contains all DNA sequences of a species and can reveal missing genetic components and large structural variants. Pangenomic studies have shown the importance of individual-specific sequences in biological adaptability and economic traits in domestic animals. The development of pangenome research with advanced technologies and methods will further contribute to understanding animal domestication, evolution, and breeding.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Brice Letcher, Martin Hunt, Zamin Iqbal
Summary: Genome graphs provide a general way to represent genetic variation, allowing for multiscale variation and transparency on different sequence backgrounds. The software gramtools can handle variant calls on multiple references and outperforms existing methods in genotyping SNPs overlapping large deletions.
Article
Biotechnology & Applied Microbiology
Anupam Bhattacharya, Sushmita Das, Maloyjo Joyraj Bhattacharjee, Ashis K. Mukherjee, Mojibur Rohman Khan
Summary: The study investigated the genomic features of different strains of Lactobacillus in the vaginal microbiome of healthy women. The findings revealed variations in gene functions among the strains, highlighting the importance of considering region-specific candidate strains for preventive measures against vaginal dysbiosis.
Article
Biochemistry & Molecular Biology
Fiona J. Whelan, Rebecca J. Hall, James O. McInerney
Summary: A pangenome consists of all genes within a phylogenetic Glade, with accessory genes being structured and maintained by selection. Genes that co-occur and/or avoid each other exhibit shared functional categories, simultaneous transcription, and interactions, suggesting a structured accessory genome. These findings may be applicable to other prokaryotic species with open pangenomes.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Andrea Monserrat Negrete-Paz, Gerardo Vazquez-Marrufo, Ana Gutierrez-Moraga, Ma Soledad Vazquez-Garciduenas
Summary: This study constructed the pangenome of Mycobacterium tuberculosis and identified genes associated with different clinical presentations of tuberculosis. The analysis revealed gene deletions that could lead to metabolic and stress response changes associated with pulmonary or extrapulmonary tuberculosis.
Article
Microbiology
Nicholas A. Pudlo, Karthik Urs, Ryan Crawford, Ali Pirani, Todd Atherly, Roberto Jimenez, Nicolas Terrapon, Bernard Henrissat, Daniel Peterson, Cherie Ziemer, Evan Snitkin, Eric C. Martens
Summary: Symbiotic bacteria in the human colon are responsible for the digestion of complex carbohydrates. Understanding the relationship between diet and gut microbial ecology is crucial, and a custom phenotyping array was used to determine carbohydrate utilization profiles of the Bacteroidetes phylum. The ability to utilize dietary polysaccharides and endogenous mucin glycans was negatively correlated, and genomic analyses revealed variability in gene clusters involved in polysaccharide metabolism. Some lineages of B. ovatus and B. xylanisolvens have lost the ability to utilize mucin, but still harbor residual gene clusters.
Article
Biochemistry & Molecular Biology
Francisco J. J. Mancebo, Marcos Parras-Molto, Estefani Garcia-Rios, Pilar Perez-Romero
Summary: CMV is a major cause of illness and death in immunocompromised individuals, but there is currently no available vaccine. In this study, we explored the CMV genome to identify potential viral envelope proteins with transmembrane domains, which could contribute to the development of a new vaccine.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Nashwa Ahmed, Payal Joglekar, Clayton Deming, Katherine P. Lemon, Heidi H. Kong, Julie A. Segre, Sean Conlan
Summary: This study investigated the distribution and genetic diversity of Corynebacterium species on the skin. It identified two distinct ribotypes of Corynebacterium tuberculostearicum and determined their characteristics through whole genome sequencing. The study also proposed a potential new species, Corynebacterium hallux, based on its preference for sites on the feet. The findings provide valuable insights into the diversity and characteristics of Corynebacterium on the skin.
Article
Genetics & Heredity
Zuyu Yang, Andrea Guarracino, Patrick J. Biggs, Michael A. Black, Nuzla Ismail, Jana Renee Wold, Tony R. Merriman, Pjotr Prins, Erik Garrison, Joep de Ligt
Summary: Whole genome sequencing has revolutionized infectious disease surveillance. However, using a linear reference genome may introduce biases when studying highly variable bacterial genomes. Pangenome graphs provide an efficient model for representing and analyzing multiple genomes and their variants, improving mapping rates and variant calling for pathogens such as Neisseria meningitidis.
FRONTIERS IN GENETICS
(2023)
Article
Biotechnology & Applied Microbiology
Sina Beier, Nicholas R. Thomson
Summary: Panakeia is an easy-to-use tool that provides a detailed view of the pangenome structure, allowing for the discovery and in-depth analysis of features of interest. It analyzes the synteny and structural patterns of the pangenome, providing insights into the biological diversity and evolution of the studied taxon.
Article
Microbiology
Wen-Jing Cui, Biliang Zhang, Ran Zhao, Li-Xue Liu, Jian Jiao, Ziding Zhang, Chang-Fu Tian
Summary: This study utilized gene editing to improve compatibility between rhizobium and soybean. Transcriptomics revealed consistent lineage-dependent transcriptional profiles of core pathways, predating the divergence of legumes and rhizobia. Additionally, low-efficiency nodules exhibited impaired antioxidant activity and energy status, restricting nitrogen fixation activity.
Article
Chemistry, Multidisciplinary
Loukas Kollias, Roger Rousseau, Vassiliki-Alexandra Glezakou, Matteo Salvalaglio
Summary: In this study, the collective assembly of building units during the early stages of metal-organic framework (MOF) nucleation was investigated using large-scale molecular dynamics simulations. The choice of solvent, introduction of ions, and relative populations of MOF building unit isomers were found to greatly influence the cluster formation process, leading to variations in shape, size, nucleation and growth rates, crystallinity, and order. Graph theory analysis revealed that only a few molecular descriptors were needed to understand MOF self-assembly and these descriptors can be experimentally observed. This approach provides valuable insights into the complex processes of MOF synthesis and scale-up.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Wenxia Xu, Lei Feng, Jun Ma
Summary: This study aims to provide insights into the driving distraction domain systematically using scientific knowledge graphs. Through bibliometric analysis and research content analysis, the study reveals the trends, significance, and future directions of this field.
Article
Biochemistry & Molecular Biology
Sarah Henaut-Jacobs, Hemanoel Passarelli-Araujo, Thiago M. Venancio
Summary: In this study, a network-based analysis of all publicly available Campylobacter genomes was conducted to explore the structure and diversity of the genus, revealing potential new species and elucidating genus features. The researchers also proposed a new species hypothesis and found a negative correlation between pangenome fluidity and saturation coefficient in different Campylobacter species, which could help estimate pangenome metrics of less sequenced genomes and understand their lifestyle and niche adaptation.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Review
Plant Sciences
Songtao Gui, Felix Juan Martinez-Rivas, Weiwei Wen, Minghui Meng, Jianbing Yan, Bjoern Usadel, Alisdair R. R. Fernie
Summary: Deep sequencing has become popular in recent years due to the collection and release of large amounts of high-quality genomic and transcriptomic data. This approach has greatly advanced our understanding of plant physiology, evolution, and crop domestication through both broad and deep sequencing.
Article
Biochemistry & Molecular Biology
Gwenola Manic, Martina Musella, Francesca Corradi, Antonella Sistigu, Sara Vitale, Sara Soliman Abdel Rehim, Luca Mattiello, Eva Malacaria, Claudia Galassi, Michele Signore, Matteo Pallocca, Stefano Scalera, Frauke Goeman, Francesca De Nicola, Andrea Guarracino, Rosa Pennisi, Fabrizio Antonangeli, Francesca Sperati, Marta Baiocchi, Mauro Biffoni, Maurizio Fanciulli, Marcello Maugeri-Sacca, Annapaola Franchitto, Pietro Pichierri, Ruggero De Maria, Ilio Vitale
Summary: This passage discusses the crucial role of cancer stem cells in colorectal cancer and the research findings on PARP1 and MRE11/RAD51, providing new insights for tumor treatment.
CELL DEATH AND DIFFERENTIATION
(2021)
Article
Cell Biology
Giuseppe Novelli, Jing Liu, Michela Biancolella, Tonino Alonzi, Antonio Novelli, J. J. Patten, Dario Cocciadiferro, Emanuele Agolini, Vito Luigi Colona, Barbara Rizzacasa, Rosalinda Giannini, Benedetta Bigio, Delia Goletti, Maria Rosaria Capobianchi, Sandro Grelli, Justin Mann, Trevor D. McKee, Ke Cheng, Fatima Amanat, Florian Krammer, Andrea Guarracino, Gerardo Pepe, Carlo Tomino, Yacine Tandjaoui-Lambiotte, Yurdagul Uzunhan, Sarah Tubiana, Jade Ghosn, Luigi D. Notarangelo, Helen C. Su, Laurent Abel, Aurelie Cobat, Gai Elhanan, Joseph J. Grzymski, Andrea Latini, Sachdev S. Sidhu, Suresh Jain, Robert A. Davey, Jean-Laurent Casanova, Wenyi Wei, Pier Paolo Pandolfi
Summary: HECT family E3 ligases are identified as potential biomarkers for COVID-19, with rare germline activating variants in NEDD4 and WWP1 genes associated with severe cases. Natural inhibitors I3C from Brassicaceae show potent antiviral effects against SARS-CoV-2, making them potential targets for therapeutic strategies easily testable in clinical trials.
CELL DEATH & DISEASE
(2021)
Article
Biochemistry & Molecular Biology
Andrea Guarracino, Gerardo Pepe, Francesco Ballesio, Marta Adinolfi, Marco Pietrosanto, Elisa Sangiovanni, Ilio Vitale, Gabriele Ausiello, Manuela Helmer-Citterich
Summary: The interaction between RNA and RNA-binding proteins is crucial in gene expression regulation and other biological processes. BRIO is a new web server designed to identify sequence and structure RNA-binding motifs in RNA molecules, providing access to over 2508 sequence motifs and 2296 secondary structure motifs identified in humans and mice.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
G. Pepe, A. Guarracino, F. Ballesio, L. Parca, G. Ausiello, M. Helmer-Citterich
Summary: This study explores the potential interactions between human miRNAs and coronaviruses. The findings suggest that certain miRNA binding sites may be associated with deep vein thrombosis and cardiovascular diseases, particularly in SARS-CoV-2 and other pathogenic viruses.
NON-CODING RNA RESEARCH
(2022)
Article
Oncology
Simon Heumos, Sandra Dehn, Konstantin Braeutigam, Marius C. Codrea, Christian M. Schuerch, Ulrich M. Lauer, Sven Nahnsen, Michael Schindler
Summary: This study identified specific cell surface receptor biomarkers for colon and renal cancer through analyzing the surface receptors of tumor cells, with CD106 (VCAM1) identified as a promising novel immunotherapeutic target for renal cancer treatment.
CANCER CELL INTERNATIONAL
(2022)
Article
Immunology
Martina Musella, Andrea Guarracino, Nicoletta Manduca, Claudia Galassi, Eliana Ruggiero, Alessia Potenza, Ester Maccafeo, Gwenola Manic, Luca Mattiello, Sara Soliman Abdel Rehim, Michele Signore, Marco Pietrosanto, Manuela Helmer-Citterich, Matteo Pallocca, Maurizio Fanciulli, Tiziana Bruno, Francesca De Nicola, Giacomo Corleone, Anna Di Benedetto, Cristiana Ercolani, Edoardo Pescarmona, Laura Pizzuti, Francesco Guidi, Francesca Sperati, Sara Vitale, Daniele Macchia, Massimo Spada, Giovanna Schiavoni, Fabrizio Mattei, Adele De Ninno, Luca Businaro, Valeria Lucarini, Laura Bracci, Eleonora Arico, Giovanna Ziccheddu, Francesco Facchiano, Stefania Rossi, Massimo Sanchez, Alessandra Boe, Mauro Biffoni, Ruggero De Maria, Ilio Vitale, Antonella Sistigu
Summary: The study demonstrates that type I interferons can promote the formation of cancer stem cells by upregulating the chromatin remodeling factor KDM1B. Inhibition of KDM1B could potentially prevent stem cell expansion and increase the long-term benefit of therapy.
Article
Biotechnology & Applied Microbiology
Glenn Hickey, Jean Monlong, Jana Ebler, Adam M. Novak, Jordan M. Eizenga, Yan Gao, Tobias Marschall, Heng Li, Benedict Paten, Haley J. Abel, Lucinda L. Antonacci-Fulton, Mobin Asri, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Guillaume Bourque, Silvia Buonaiuto, Andrew Carroll, Mark J. P. Chaisson, Pi-Chuan Chang, Xian H. Chang, Haoyu Cheng, Justin Chu, Sarah Cody, Vincenza Colonna, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Daniel Doerr, Peter Ebert, Jana Ebler, Evan E. Eichler, Jordan M. Eizenga, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Xiaowen Feng, Christian Fischer, Paul Flicek, Giulio Formenti, Adam Frankish, Robert S. Fulton, Yan Gao, Shilpa Garg, Erik Garrison, Nanibaa' A. Garrison, Carlos Garcia Giron, Richard E. Green, Cristian Groza, Andrea Guarracino, Leanne Haggerty, Ira M. Hall, William T. Harvey, Marina Haukness, David Haussler, Simon Heumos, Glenn Hickey, Kendra Hoekzema, Thibaut Hourlier, Kerstin Howe, Miten Jain, Erich D. Jarvis, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Wen-Wei Liao, Shuangjia Lu, Tsung-Yu Lu, Julian K. Lucas, Magalhaes Hugo, Marco-Sola Santiago, Pierre Marijon, Charles Markello, Tobias Marschall, Fergal J. Martin, Ann McCartney, Jennifer McDaniel, Karen H. Miga, Matthew W. Mitchell, Jean Monlong, Jacquelyn Mountcastle, Katherine M. Munson, Moses Njagi Mwaniki, Maria Nattestad, Adam M. Novak, Sergey Nurk, Hugh E. Olsen, Nathan D. Olson, Trevor Pesout, Adam M. Phillippy, Alice B. Popejoy, David Porubsky, Pjotr Prins, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen Schultz, Kishwar Shafin, Jonas A. Sibbesen, Jouni Siren, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Francoise Thibaud-Nissen, Chad Tomlinson, Francesca Floriana Tricomi, Flavia Villani, Mitchell R. Vollger, Justin Wagner, Brian Walenz, Ting Wang, Jonathan M. D. Wood, Aleksey Zimin, Justin M. Zook
Summary: Genome assemblies are used to directly construct genome graphs, which can represent various forms of genetic variation and improve analysis accuracy by overcoming single-reference bias.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Santiago Marco-Sola, Jordan M. Eizenga, Andrea Guarracino, Benedict Paten, Erik Garrison, Miquel Moreto
Summary: Pairwise sequence alignment is a fundamental problem in computational biology and bioinformatics. Recent advances in genomics and sequencing technologies call for faster and scalable algorithms to handle longer sequences. The wavefront alignment algorithm (WFA) proposed an efficient approach to perform exact gap-affine alignment, but its memory requirements were computationally impractical for genome-scale alignments. In this study, the bidirectional WFA algorithm is introduced, which can compute optimal alignments with significantly reduced memory usage while maintaining the time complexity of WFA.
Article
Biotechnology & Applied Microbiology
Noe Cochetel, Andrea Minio, Andrea Guarracino, Jadran F. Garcia, Rosa Figueroa-Balderas, Melanie Massonnet, Takao Kasuga, Jason P. Londo, Erik Garrison, Brandon S. Gaut, Dario Cantu
Summary: This study reports the sequencing, assembly, and annotation of wild North American grape genomes, and demonstrates the utility of a reference-unbiased super-pangenome in mapping short reads and identifying loci associated with salt tolerance. It highlights the importance of capturing the genetic diversity of wild relatives for crop improvement research.
Article
Biochemical Research Methods
Erik Garrison, Andrea Guarracino
Summary: This study presents the seqwish algorithm, which can build a variation graph from a set of sequences and their alignments. By transforming the alignment set into a tree-based representation and querying this representation, the algorithm constructs a variation graph, resulting in a pangenome variation graph. The method is scalable and has been successfully applied to build pangenome graphs for multiple species.
Article
Genetics & Heredity
Sabrina Krakau, Daniel Straub, Hadrien Gourle, Gisela Gabernet, Sven Nahnsen
Summary: The study presents the nf-core/mag pipeline for metagenome assembly, binning, and taxonomic classification. The pipeline is characterized by its ease of installation, portability, and reproducibility, and it utilizes sample-wise group information to enhance assembly continuity.
NAR GENOMICS AND BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Marco Pietrosanto, Marta Adinolfi, Andrea Guarracino, Fabrizio Ferre, Gabriele Ausiello, Ilio Vitale, Manuela Helmer-Citterich
Summary: The study introduces a method for modeling the structural features of RNA, expanding alignment sets and introducing a new scoring metric to encode RNA structural information at different granularities. These approaches can be used in conjunction with other tools to gain insights into the structural elements of RNA.
NAR GENOMICS AND BIOINFORMATICS
(2021)
