Generation of live mice from haploid ESCs with germline-DMR deletions or switch by Yongjian Ma, Meng Yan, Zhenfei Xie, Hongling Zhang, Zhoujie Li, Yuanyuan Li, Suming Yang, Meiling Zhang, Wen Li, Jinsong Li

“…Abstract Genomic imprinting is required for sexual reproduction and embryonic development of mammals, in which, differentially methylated regions (DMRs) regulate the parent-specific monoallelic expression of imprinted genes. …”
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Investigation of metabolic features of glioblastoma tissue and the peritumoral environment using targeted metabolomics screening by LC-MS/MS and gene network analysis by N. V. Basov, A. V. Adamovskaya, A. D. Rogachev, E. V. Gaisler, P. S. Demenkov, T. V. Ivanisenko, A. S. Venzel, S. V. Mishinov, V. V. Stupak, S. V. Cheresiz, O. S. Oleshko, E. A. Butikova, A. E. Osechkova, Yu. S. Sotnikova, Y. V. Patrushev, A. S. Pozdnyakov, I. N. Lavrik, V. A. Ivanisenko, A. G. Pokrovsky

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Real-World Outcomes of Pralsetinib in RET Fusion-Positive NSCLC by Francesca Lucibello, MD, Valérie Gounant, MD, PhD, Mihaela Aldea, MD, PhD, Michaël Duruisseaux, MD, PhD, Maurice Perol, MD, Christos Chouaid, MD, Jaafar Bennouna, MD, PhD, Vincent Fallet, MD, Aldo Renault, MD, Florian Guisier, MD, PhD, Etienne Giroux-Leprieur, MD, PhD, Marie Wislez, MD, PhD, Anne-Claire Toffart, MD, PhD, Julien Mazieres, MD, PhD, Clémence Basse, MD, PhD, Nadia Hegarat, PhD, Matthieu Carton, MD, Nicolas Girard, MD, PhD

“…We also observe the aggressive nature of disease progression, frequent utilization of chemotherapy and antiangiogenic agents as initial subsequent therapies, and limited insight into resistance mechanisms due to infrequent rebiopsy and genomic profiling at progression.…”
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The spatial landscape of cancer hallmarks reveals patterns of tumor ecological dynamics and drug sensitivity by Mustafa Sibai, Sergi Cervilla, Daniela Grases, Eva Musulen, Rossana Lazcano, Chia-Kuei Mo, Veronica Davalos, Arola Fortian, Adrià Bernat, Margarita Romeo, Collin Tokheim, Jordi Barretina, Alexander J. Lazar, Li Ding, Enrique Grande, Francisco X. Real, Manel Esteller, Matthew H. Bailey, Eduard Porta-Pardo, Enrique Grande, Teresa Alonso-Gordoa, Mario Álvarez-Maestro, Elena Andrada, Ainara Azueta, Raquel Benítez Javier Burgos, Daniel Castellano, M. Angel Climent, Mario Domínguez, Ignacio Durán Albert Font, Isabel Galante, Patricia Galván, Juan F. García, Xavier García del Muro, Félix Guerrero-Ramos, Núria Malats, Miriam Marqués, Pablo Maroto, Jaime Martínez de Villarreal, Ane Moreno-Oya, Jesús M. Paramio, Alvaro Pinto, Aleix Prat, Javier Puente, Oscar Reig, Francisco X. Real

“…Additionally, we discover that genomic distance between tumor subclones correlates with differences in hallmark activity, even leading to clone-hallmark specialization. …”
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Impact of donor CYP3A5 genotype on pharmacokinetics of tacrolimus in South African paediatric liver transplant patients by C Wheeler, C Masimirembwa, B Mthembu, J Botha, J Scholefield, J Fabian

“…Blood samples from 46 living liver donors were collected, their genomic DNA was extracted, and their CYP3A5 genotype was established (polymerase chain reaction and restriction fragment length polymorphism analysis, validated by Sanger sequencing). …”
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Standardization and validation of a novel reverse transcriptase polymerase chain reaction method for detecting virulent strains of the infectious bursal disease virus by Vladimir Longa-Bobadilla, Phillip Ormeño-Vásquez, Manuel Criollo-Orozco, Luis Tataje-Lavanda, Katherine Huamán-Gutierrez, Ángela Montalván, Mirko Zimic, Manolo Fernández-Sanchez, Manolo Fernández-Díaz

“…For many years, the development of molecular techniques for either diagnostic purposes or surveillance of the appearance of new pathogenic strains has mainly focused on targeting the VP2 genomic region. However, due to the constant necessity for the discrimination between already prevalent vaccine strains and new pathogenic strains of this virus, it becomes imperative to have an immediate molecular method targeting a consensus sequence to achieve this task using field samples to reduce costs. …”
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Detection of fusion events by RNA sequencing in FFPE versus freshly frozen colorectal cancer tissue samples by Maxim Sorokin, Maxim Sorokin, Maxim Sorokin, Maxim Sorokin, Vladimir Lyadov, Vladimir Lyadov, Vladimir Lyadov, Maria Suntsova, Marat Garipov, Anna Semenova, Natalia Popova, Egor Guguchkin, Rustam Heydarov, Marianna Zolotovskaia, Xiaowen Zhao, Qing Yan, Ye Wang, Evgeny Karpulevich, Anton Buzdin, Anton Buzdin, Anton Buzdin, Anton Buzdin

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Small RNA CjNC110 regulates the activated methyl cycle to enable optimal chicken colonization by Campylobacter jejuni by Brandon Ruddell, Alan Hassall, Orhan Sahin, Paul J. Plummer, Qijing Zhang, Amanda J. Kreuder

“…Depending on the strain examined and accessory genomic content present, conserved regulatory actions might be masked, thus investigation in multiple strains may be warranted.…”
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The role of artificial intelligence and machine learning in predicting and combating antimicrobial resistance by Hazrat Bilal, Muhammad Nadeem Khan, Sabir Khan, Muhammad Shafiq, Wenjie Fang, Rahat Ullah Khan, Mujeeb Ur Rahman, Xiaohui Li, Qiao-Li Lv, Bin Xu

“…AI/ML models can use various data sources, such as clinical information, genomic sequences, microbiome insights, and epidemiological data for predicting AMR outbreaks. …”
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Stratification system with dual human endogenous retroviruses for predicting immunotherapy efficacy in metastatic clear-cell renal cell carcinoma by Li Xu, Stephane Oudard, Catherine Sautes-Fridman, Xiaoping Su, Gabriel G. Malouf, Virginie Verkarre, Salma Kotti, Fangrong Yan, Yann-Alexandre Vano, Wolf Herve Fridman, Cheng-Ming Sun, Xiaofan Lu, Wenxuan Cheng

“…Background Endogenous retrovirus (ERV) elements are genomic footprints of ancestral retroviral infections within the human genome. …”
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Dealing With the Complexity of Effective Population Size in Conservation Practice by Ancuta Fedorca, Joachim Mergeay, Adejoke O. Akinyele, Tamer Albayrak, Iris Biebach, Alice Brambilla, Pamela A. Burger, Elena Buzan, Ino Curik, Roberta Gargiulo, José A. Godoy, Santiago C. González‐Martínez, Christine Grossen, Myriam Heuertz, Sean Hoban, Jo Howard‐McCombe, Maria Kachamakova, Peter Klinga, Viktoria Köppä, Elenora Neugebauer, Ivan Paz‐Vinas, Peter B. Pearman, Laia Pérez‐Sorribes, Baruch Rinkevich, Isa‐Rita M. Russo, Adélaïde Theraroz, Nia E. Thomas, Marjana Westergren, Sven Winter, Linda Laikre, Alexander Kopatz

“…To address the challenges associated with estimating Ne for conservation purposes, the COST Action 18134, Genomic Biodiversity Knowledge for Resilient Ecosystems (G‐BiKE), organized an international workshop that met in August 2022 in Brașov, Romania. …”
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Network and systems biology approaches help investigate gene regulatory interactions between Salmonella disease and host in chickens: Model‐based in silico evidence combined with g... by Reza Tohidi, Hoda Javaheri Bargourooshi, Arash Javanmard

“…To start, we used free computational tools and online bioinformatics resources, including predicting gene function using a multiple association network integration algorithm (geneMania), the Kyoto Encyclopedia of Genes and Genomes, the Annotation, Visualization and Integrated Discovery (DAVID) database and the stimulator of interferon genes. …”
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Selective utilization of medicinal polysaccharides by human gut Bacteroides and Parabacteroides species by Zepeng Qu, Hongbin Liu, Ji Yang, Linggang Zheng, Jumin Huang, Ziming Wang, Chun Xie, Wenlong Zuo, Xiong Xia, Lin Sun, Yifa Zhou, Ying Xie, Jingguang Lu, Yizhun Zhu, Lili Yu, Lihua Liu, Hua Zhou, Lei Dai, Elaine Lai-Han Leung

“…This distinct utilization profile was associated with genomic variation in carbohydrate-active enzymes, rather than monosaccharides composition variation among medicinal polysaccharides. …”
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Multi-omics unveils strain-specific neuroactive metabolite production linked to inflammation modulation by Bacteroides and their extracellular vesicles by Basit Yousuf, Walid Mottawea, Galal Ali Esmail, Nazila Nazemof, Nour Elhouda Bouhlel, Emmanuel Njoku, Yingxi Li, Xu Zhang, Zoran Minic, Riadh Hammami

“…This study investigated the strain-specific production of neuroactive metabolites by 18 Bacteroidetes (12 Bacteroides, 4 Phocaeicola, and 2 Parabacteroides) using multi-omics approaches. Genomic analysis revealed a significant potential for producing GABA, tryptophan, tyrosine, and histidine metabolism-linked neuroactive compounds. …”
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Adjuvant Autologous Melanoma Vaccine for Macroscopic Stage III Disease: Survival, Biomarkers, and Improved Response to CTLA-4 Blockade by Michal Lotem, Sharon Merims, Stephen Frank, Tamar Hamburger, Aviram Nissan, Luna Kadouri, Jonathan Cohen, Ravid Straussman, Galit Eisenberg, Shoshana Frankenburg, Einat Carmon, Bilal Alaiyan, Shlomo Shneibaum, Zeynep Ozge Ayyildiz, Murat Isbilen, Kerem Mert Senses, Ilan Ron, Hanna Steinberg, Yoav Smith, Eitan Shiloni, Ali Osmay Gure, Tamar Peretz

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Construction and Pathogenicity Analysis of a GFPuv-labeled Peanut Ralstonia solanacearum Strain by Jinling HUANG, Yushuang WU, Huiquan TANG, Minyi HUANG, Ruixue YANG, Qiang WANG, Yong YANG, Xiaodan TAN

“…【Method】Through whole-genome analysis of R. solanacearum PeaFJ1 strain, the insertion sites for exogenous gene were selected. …”
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Molecular Epidemiology, Drug-Resistant Variants, and Therapeutic Implications of Hepatitis B Virus and Hepatitis D Virus Prevalence in Nigeria: A National Study by Oludare ‘Sunbo Adewuyi, Muhammad Shakir Balogun, Hirono Otomaru, Alash’le Abimiku, Anthony Agbakizu Ahumibe, Elsie Ilori, Que Anh Luong, Nwando Mba, James Christopher Avong, John Olaide, Oyeladun Okunromade, Adama Ahmad, Afolabi Akinpelu, Chinwe Lucia Ochu, Babatunde Olajumoke, Haruka Abe, Chikwe Ihekweazu, Adetifa Ifedayo, Michiko Toizumi, Hiroyuki Moriuchi, Katsunori Yanagihara, Jide Idris, Lay-Myint Yoshida

“…Information on circulating HBV (sub-)genotype, variants, and hepatitis D virus (HDV) coinfection, which vary by geographical area, is crucial for the efficient control and management of HBV. We investigated the genomic characteristics of HBV (with a prevalence of 8.1%) and the prevalence of HDV in Nigeria. …”
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Implementation of a genotyped African population cohort, with virtual follow-up: A feasibility study in the Western Cape Province, South Africa [version 2; peer review: 2 approved,... by Robert J Wilkinson, Francisco Lakay, Nicki Tiffin, Joel A Dave, Catherine Riou, Peter Raubenheimer, Anna K Coussens, Tsaone Tamuhla, Melissa J Blumenthal, Maleeka Abrahams

“…We demonstrated feasibility of nested case control genome wide association studies using these data for phenotypes type 2 diabetes mellitus (T2DM) and severe COVID-19. …”
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Association of Irisin with Fat Mass, Resting Energy Expenditure, and Daily Activity in Conditions of Extreme Body Mass Index by María Pardo, Ana B. Crujeiras, María Amil, Zaida Aguera, Susana Jiménez-Murcia, Rosa Baños, Cristina Botella, Rafael de la Torre, Xavier Estivill, Ana B. Fagundo, Jose M. Fernández-Real, José C. Fernández-García, Gema Fruhbeck, Javier Gómez-Ambrosi, Roser Rodríguez, Francisco J. Tinahones, Fernando Fernández-Aranda, Felipe F. Casanueva

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Spatial and temporal epidemiology of SARS-CoV-2 virus lineages in Teesside, UK, in 2020: effects of socio-economic deprivation, weather, and lockdown on lineage dynamics by Moss, E.D., Rushton, S.P., Baker, P., Bashton, M., Crown, M.R., dos Santos, R.N., Nelson, A., O’Brien, S.J., Richards, Z., Sanderson, R.A., Yew, W.C., Young, G.R., McCann, C.M., Smith, D.L.

“…As the outbreak continued, new variants were detected through two national monitoring programmes that conducted genomic sequencing. This study aimed to determine the effects of weather, demographic features, and national and local COVID-19 restrictions on positive PCR tests at a sub-regional scale. …”
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