The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models. by Ahmed Daoud, Asa Ben-Hur

“…By providing pre-trained models that can be fine-tuned for specific applications, they enable researchers to create accurate models with minimal effort and computational resources. Large scale genomics deep learning models come in two flavors: the first are large language models of DNA sequences trained in a self-supervised fashion, similar to the corresponding natural language models; the second are supervised learning models that leverage large scale genomics datasets from ENCODE and other sources. …”
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Prevalence and methodologies for detection, characterization and subtyping of Listeria monocytogenes and L. ivanovii in foods and environmental sources by Jin-Qiang Chen, Patrick Regan, Pongpan Laksanalamai, Stephanie Healey, Zonglin Hu

“…In this review, we (A) described L. monocytogenes and L. ivanovii, world-wide incidence of listeriosis, and prevalence of various L. monocytogenes strains in food and environmental sources; (B) comprehensively reviewed different types of traditional and newly developed methodologies, including culture-based, antigen/antibody-based, LOOP-mediated isothermal amplification, matrix-assisted laser desorption ionization-time of flight-mass spectrometry, DNA microarray, and genomic sequencing for detection and characterization of L. monocytogenes in foods and environmental sources; (C) comprehensively summarized different subtyping methodologies, including pulsed-field gel electrophoresis, multi-locus sequence typing, ribotyping, and phage-typing, and whole genomic sequencing etc. for subtyping of L. monocytogenes strains from food and environmental sources; and (D) described the applications of these methodologies in detection and subtyping of L. monocytogenes in foods and food processing facilities.…”
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Evaluation of the Effects of Different Bacteroides vulgatus Strains against DSS-Induced Colitis by Sijia Li, Chen Wang, Chengcheng Zhang, Yanhong Luo, Qianqian Cheng, Leilei Yu, Zhen Sun

“…In this study, we selected four B. vulgatus strains (FTJS5K1, FTJS7K1, FSDTA11B14, and FSDLZ51K1) with different genomic characteristics and evaluated their protective roles against dextran sulfate sodium- (DSS-) induced colitis. …”
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An ultra-simplified protocol for PCR template preparation from both unsporulated and sporulated Eimeria oocysts by Aruto Takano, Dennis V. Umali, April H. Wardhana, Dyah H. Sawitri, Isao Teramoto, Toshimitsu Hatabu, Yasutoshi Kido, Akira Kaneko, Kazumi Sasai, Hiromitsu Katoh, Makoto Matsubayashi

“…Our data revealed that whereas neither pretreatment of oocysts with sodium hypochlorite nor purification of genomic DNA with commercial kits improved the limit of detection of PCR, disruption of oocysts was a critical step in the preparation of PCR templates. …”
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Hairy transcriptional repression targets and cofactor recruitment in Drosophila. by Daniella Bianchi-Frias, Amir Orian, Jeffrey J Delrow, Julio Vazquez, Alicia E Rosales-Nieves, Susan M Parkhurst

“…This approach identified 40 novel genomic targets for Hairy in Kc cells, as well as 155 loci recruiting Groucho, 107 loci recruiting dSir2, and wide genomic binding of dCtBP to 496 loci. …”
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The Role of PDGFs and PDGFRs in Colorectal Cancer by Roberta M. Manzat Saplacan, Loredana Balacescu, Claudia Gherman, Romeo I. Chira, Anca Craiu, Petru A. Mircea, Cosmin Lisencu, Ovidiu Balacescu

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Watermelon Germplasm with Resistance to Whitefly-transmitted Viruses by Alex Luckew, Nebahat Sari, Swikriti Pandey, Ted McAvoy, Alvin M. Simmons, Geoffrey Meru, Cecilia McGregor

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Interaction of human neutrophils with Trichomonas vaginalis protozoan highlights lactoferrin secretion by Wei-Hung Cheng, Ruei-Min Chen, Seow-Chin Ong, Yuan-Ming Yeh, Po-Jung Huang, Chi-Ching Lee

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An Effective and Safe Maize Seed Chipping Protocol Using Clipping Pliers With Applications in Small-Scale Genotyping and Marker-Assisted Breeding by Brian Zebosi, John Ssengo, Lander Geadelmann, Erica Unger-Wallace, Erik Vollbrecht

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Detailed cytogenetic analysis of three duck species (the northern pintail, mallard, and common goldeneye) and karyotype evolution in the family Anatidae (Anseriformes, Aves) by V. R. Beklemisheva, K. V. Tishakova, S. A. Romanenko, D. A. Andreushkova, V. A. Yudkin, E. А. Interesova, F. Yang, M. A. Ferguson-Smith, A. S. Graphodatsky, A. A. Proskuryakova

“…The results indicated a high level of syntenic group conservation among the duck genomes. The two Anas species share their macrochromosome number, whereas in B. clangula, this number is increased due to fissions of two ancestral elements. …”
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Uncovering Molecular Mechanisms of Feed Efficiency in Pigs Through Multi-Omics Analysis of the Jejunum by Saixian Zhang, Yue Xiang, Yaobang Jian, Qiulin Zhao, Jiahui Sun, Yi Huang, Jing Xu, Xiaolong Qi, Jingjin Li, Zhuqing Zheng, Liangliang Fu, Yuwen Liu, Xinyun Li

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Computational identification of promising genetic markers associated with molecular mechanisms of reduced rice resistance to <i>Rhizoctonia solani</i> under excess nitrogen fertili... by E. A. Antropova, A. R. Volyanskaya, A. V. Adamovskaya, P. S. Demenkov, I. V. Yatsyk, T. V. Ivanisenko, Y. L. Orlov, Ch. Haoyu, M. Chen, V. A. Ivanisenko

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Gene networks for use in metabolomic data analysis of blood plasma from patients with postoperative delirium by V. A. Ivanisenko, N. V. Basov, A. A. Makarova, A. S. Venzel, A. D. Rogachev, P. S. Demenkov, T.  V. Ivanisenko, M. A. Kleshchev, E. V. Gaisler, G. B. Moroz, V. V. Plesko, Y. S. Sotnikova, Y. V. Patrushev, V. V. Lomivorotov, N. A. Kolchanov, A. G. Pokrovsky

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The Role of Organelle Stresses in Diabetes Mellitus and Obesity: Implication for Treatment by Yi-Cheng Chang, Siow-Wey Hee, Meng-Lun Hsieh, Yung-Ming Jeng, Lee-Ming Chuang

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APPLICATION OF THE ELECTROPHORESIS OF COTYLEDON PROTEINS AND ISSR-MARKERS TO THE IDENTIFICATION OF HYBRIDS BETWEEN SORBUS SIBIRICA HEDL. AND SORBOCOTONEASTER POZDNJAKOVII POJARK. by S. V. Asbaganov, E. V. Kobozeva, A. V. Agafonov

“…Recombination of molecular and morphological characters was observed in hybrids, which proves close relationships of the parental genomes and, as a consequence, the potential of utilizing Sorbocotoneaster pozdnjakovii genotypes in breeding of Sorbus cultivars. …”
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Relationship between Abnormal Lipid Metabolism and Gallstone Formation by Xiang Li, Xiaodan Yin, Jun Xu, Lei Geng, Zhengtao Liu

“…This study aimed to determine the role of lipid metabolism in the pathogenesis of gallstones and provide insights for future studies using previous research in genomics, metabolomics, transcriptomics, and other fields.…”
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A BRAF V600E Mutation in RET-Negative Medullary Thyroid Cancer by Richard J. Robbins, Jessica S. Thomas, Patricia Mejia Osuna, Jawairia Shakil

“…We report the case of a woman with a sporadic medullary thyroid carcinoma. Genomic analysis found that her tumor did not contain any common RET mutations but did harbor a BRAF V600E mutation. …”
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Tracking des transferts des bactéries porteuses de résistances entre animal, homme et environnement by Meyer, Sylvain, Laval, Lucie, Pimenta, Mélanie, González-Flores, Yolanda, Gaschet, Margaux, Couvé-Deacon, Elodie, Barraud, Olivier, Dagot, Christophe, Ploy, Marie-Cécile

“…Various targeted or pan-genomic molecular biology techniques can be used to better characterise the dissemination of bacterial clones and to identify exchanges of genes and mobile genetic elements between ecosystems.…”
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Glioblastoma drives protease-independent extracellular matrix invasion of microglia by Chia-Wen Chang, Ashwin Bale, Rohit Bhargava, Brendan A.C. Harley

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Toward measurements of absolute membrane potential in Bacillus subtilis using fluorescence lifetime by Debjit Roy, Xavier Michalet, Evan W. Miller, Kiran Bharadwaj, Shimon Weiss

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