misMM: An Integrated Pipeline for Misassembly Detection Using Genotyping-by-Sequencing and Its Validation with BAC End Library Sequences and Gene Synteny by Young-Joon Ko, Jung Sun Kim, Sangsoo Kim

“…As next-generation sequencing technologies have advanced, enormous amounts of whole-genome sequence information in various species have been released. …”
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Germline structural variant as the cause of Lynch Syndrome in a family from Ecuador by Gemma Llargués-Sistac, Laia Bonjoch, Jenifer Muñoz, Xavier Domínguez-Rovira, Teresa Ocaña, Maria Isabel Alvarez-Mora, Celia Badenas, Anna Esteve-Codina, Carlos Reyes-Silva, Gabriela Jaramillo-Koupermann, Maria Teresa Rodrigo, Sandra López-Prades, Miriam Cuatrecasas, Antoni Castells, Francesc Balaguer, Leticia Moreira, Guerau Fernandez, Sergi Castellví-Bel

“…We report the identification and characterization of a novel germline structural variant encompassing 48.757 kb, involving the 3’-ends of the MLH1 and LRRFIP2 genes, as the cause of LS in a family of Ecuador. Whole-genome sequencing and transcriptomics allowed the identification of the genomic rearrangement and highlights the importance of the use of these additional approaches to achieve a comprehensive molecular diagnosis in some LS patients.…”
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Assembly and characterization of the complete mitogenome of Bauhinia purpurea (Leguminosae) by Siqi Xie, Yong Chen, Danjing Zheng, Shukai Luo, Shiyuan Meng, Yan Zhong

“…Abstract Objective Mitochondrial genome sequences are very useful for understanding the mitogenome evolution itself and reconstructing phylogeny of different plant lineages. …”
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Analysis of Protein-Ligand Interactions of SARS-CoV-2 Against Selective Drug Using Deep Neural Networks by Natarajan Yuvaraj, Kannan Srihari, Selvaraj Chandragandhi, Rajan Arshath Raja, Gaurav Dhiman, Amandeep Kaur

“…The DNN senses the response of protein-ligand interactions for a specific drug and identifies which drug makes the interaction that combats effectively the virus. With limited genome sequence of Indian patients submitted to the GISAID database, we find that the DNN system is effective in identifying the protein-ligand interactions for a specific drug.…”
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Recent Advances in Antimicrobial Resistance: Insights from <i>Escherichia coli</i> as a Model Organism by Zhaoyang Zhang, Minliang Wei, Bin Jia, Yingjin Yuan

“…This review explores recent advances for investigating AMR in <i>E. coli</i>, including machine learning for resistance pattern analysis, laboratory evolution to generate resistant mutants, mutant library construction, and genome sequencing for in-depth characterization. Key resistance mechanisms are discussed, including drug inactivation, target modification, altered transport, and metabolic adaptation. …”
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The high cancer incidence in young people in Italy: do genetic signatures reveal their environmental causes? by Ruggero Ridolfi

“…Today, the whole genome sequencing techniques for human cancers can help to formulate a map of mutational signatures in individual tumours, and a list of mutational fingerprints showing exposure to specific environmental mutagens is being developed. …”
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Colistin Resistance and Management of Drug Resistant Infections by Juhi Sharma, Divakar Sharma, Amit Singh, Kumari Sunita

“…Researchers focus on the most advanced genomics (whole genome sequencing), proteomics, and bioinformatics approaches to explore the question of colistin resistance. …”
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Psychrophilic Enzymes: From Folding to Function and Biotechnology by Georges Feller

“…Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. …”
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First isolation and characterization of SARS-CoV-2 from COVID-19 patient of North East India by Aniruddha Jakharia, Biswajyoti Borkakoty, Sumi Pait, Gautam Baruah, Rahul Hazarika, Dipankar Biswas

“…Phylogenetic analyses of the whole genome sequences of the SARS-CoV-2 isolate (EPI_ISL_2501532 | 2020-05-19) showed monophyletic clade G and lineage B.1.1.…”
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Genomic analysis of antimicrobial resistant Escherichia coli isolated from manure and manured agricultural grasslands by C. Tyrrell, C. M. Burgess, F. P. Brennan, D. Münzenmaier, D. Drissner, R. J. Leigh, F. Walsh

“…The E. coli isolates were phenotypically antimicrobial resistant, predominantly multidrug resistant. Whole genome sequencing identified 31 antimicrobial resistance genes, and mutations in the gyrA, parC, and parE genes, conferring fluoroquinolone resistance. …”
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Protein-Protein Interactions Inferred from Domain-Domain Interactions in Genogroup II Genotype 4 Norovirus Sequences by Chuan-Ching Huang, Chuan Yi Tang

“…However, no efficient vaccine for NoVs exists because of their variable genome sequences. This study investigates the infection processes in protein-protein interactions between hosts and NoVs. …”
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Hypermutability bypasses genetic constraints in SCV phenotypic switching in Pseudomonas aeruginosa biofilms by Romina A. Tobares, Román A. Martino, Claudia A. Colque, Gaston L. Castillo Moro, Alejandro J. Moyano, Andrea G. Albarracín Orio, Andrea M. Smania

“…Through experimental evolution and whole-genome sequencing, we show that both wild-type and mutator strains undergo parallel evolution by accumulating compensatory mutations in factors regulating intracellular c-di-GMP levels, particularly in the Wsp and Yfi systems. …”
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A study on the codon usage bias of arenavirus common genes by Pablo Daniel Thomas, María Florencia Ferrer, Mauricio J. Lozano, Ricardo Martín Gómez

“…The codon usage bias between the different genera has not yet been studied comparatively.MethodsWe retrieved the arenavirus genome sequences from public databases and used bioinformatics tools to compare the codon usage bias between the different genera for the GPC, NP and L proteins, common to all arenaviruses.Results and discussionHartmaniviruses show a larger codon usage bias, which can be partially explained by mutational bias. …”
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Genomic characteristics of ST6115 carbapenem-resistant Klebsiella pneumoniae coharboring blaNDM-1 and blaIMP-4 by Xiaofang Xie, Xiaofang Xie, Yaxuan Zhai, Zhichen Zhu, Feinan Qian, Feinan Qian, Jie Zhu, Qizhao Gao, Hong Du, Hong Du

“…ObjectivesThe aim of this study is to characterize the genomic features of ST6115 carbapenem-resistant Klebsiella pneumoniae (CRKP) co-harboring blaNDM-1 and blaIMP-4.MethodsThe genome sequences of one ST6115 Klebsiella pneumoniae (KP) strain and 12 ST17 KP strain were obtained through whole genome sequencing (WGS). …”
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In Vivo Resistance to Ceftolozane/Tazobactam in Pseudomonas aeruginosa Arising by AmpC- and Non-AmpC-Mediated Pathways by Erik Skoglund, Henrietta Abodakpi, Rafael Rios, Lorena Diaz, Elsa De La Cadena, An Q. Dinh, Javier Ardila, William R. Miller, Jose M. Munita, Cesar A. Arias, Vincent H. Tam, Truc T. Tran

“…The genetic basis of ceftolozane/tazobactam resistance was evaluated, and β-lactam-resistant mechanisms were assessed by phenotypic assays. Whole genome sequencing identified mutations in AmpC including the mutation (V213A) and a deletion of 7 amino acids (P210–G216) in the Ω-loop. …”
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Beta-HCG Secretion by a Pulmonary Choriocarcinoma in a Male Patient by Brecht Devos, Cedric Willemse, Mira Sterckx, Johan Debruyne, Inge Stappaerts, Tom Van den Mooter, Marjan Hertoghs, Pascale Abrams

“…Its biology, origin, and treatment remain to be elucidated. Cancer genome sequencing is necessary for the identification of the origin and seeking treatment.…”
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Multi-locus CRISPRi targeting with a single truncated guide RNA by Molly M. Moore, Siddarth Wekhande, Robbyn Issner, Alejandro Collins, Anna J. Cruz, Yanjing V. Liu, Nauman Javed, Salvador Casaní-Galdón, Jason D. Buenrostro, Charles B. Epstein, Eugenio Mattei, John G. Doench, Bradley E. Bernstein, Noam Shoresh, Fadi J. Najm

“…This approach can be a valuable screening step for testing transcription factor binding motifs or other repeated genomic sequences and is easily implemented with existing tools.…”
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Short-term evolutionary implications of an introgressed size-determining supergene in a vulnerable population by Pierre Lesturgie, John S. S. Denton, Lei Yang, Shannon Corrigan, Jeff Kneebone, Romuald Laso-Jadart, Arve Lynghammar, Olivier Fedrigo, Stefano Mona, Gavin J. P. Naylor

“…We conducted whole genome sequencing of samples collected across its range. …”
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Research Note: Novel reassortant avian influenza A(H9N2) Viruses in Wild Birds in Shanghai, China, 2020–2023 by Jie Hu, Yuting Xu, Min Ma, Chenyao Zhao, Yue Yuan, Guimei He

“…To better understand the genetic characteristics of these H9N2 viruses in Shanghai, the whole genome sequences were analyzed. Phylogenetical analysis showed that the nine H9N2 viruses have undergone complicated reassortment with waterfowl viruses along the East Asian-Australasian flyways. …”
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Infectious disease phylodynamics with occurrence data by Leo A. Featherstone, Francesca Di Giallonardo, Edward C. Holmes, Timothy G. Vaughan, Sebastián Duchêne

“…Abstract Phylodynamic models use pathogen genome sequence data to infer epidemiological dynamics. …”
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