A re-assessment of Taxomyces andreanae, the alleged taxol-producing fungus, using comparative genomics by Tian Cheng, Miroslav Kolařík, Luis Quijada, Marc Stadler

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A GDPR-compliant solution for analysis of large-scale genomics datasets on HPC cloud infrastructure by Silvia Gioiosa, Beatrice Chiavarini, Mattia D’Antonio, Giuseppe Trotta, Balasubramanian Chandramouli, Juan Mata Naranjo, Giuseppa Muscianisi, Mirko Cestari, Elisa Rossi

“…This solution has been successfully applied to the Network for Italian Genomes use-case, demonstrating scalability to other hospitals and universities involved in research projects dealing with sensitive genomic data.…”
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Design and implementation of an asynchronous online course-based undergraduate research experience (CURE) in computational genomics. by Seema B Plaisier, Danielle O Alarid, Joelle A Denning, Sara E Brownell, Kenneth H Buetow, Katelyn M Cooper, Melissa A Wilson

“…As genomics technologies advance, there is a growing demand for computational biologists trained for genomics analysis but instructors face significant hurdles in providing formal training in computer programming, statistics, and genomics to biology students. …”
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PathoGD: an integrative genomics approach to primer and guide RNA design for CRISPR-based diagnostics by Soo Jen Low, Matthew O’Neill, William J. Kerry, Natasha Wild, Marcelina Krysiak, Yi Nong, Francesca Azzato, Eileen Hor, Lewis Williams, George Taiaroa, Eike Steinig, Shivani Pasricha, Deborah A. Williamson

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Retrotrans-genomics identifies aberrant THE1B endogenous retrovirus fusion transcripts in the pathogenesis of sarcoidosis by Shunsuke Funaguma, Aritoshi Iida, Yoshihiko Saito, Jantima Tanboon, Francia Victoria De Los Reyes, Kyuto Sonehara, Yu-ichi Goto, Yukinori Okada, Shinichiro Hayashi, Ichizo Nishino

“…Abstract Transposon-like human element 1B (THE1B) originates from ancient retroviral sequences integrated into the primate genome approximately 50 million years ago, now accounting for at least 27,233 copies in the human genome, suggesting their extensive influence on human genomic architecture. …”
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The concept of natural genome reconstruction. Part 1. Basic provisions of the “natural genome reconstruction” concept.... by L. A. Yakubov, O. S. Taranov, S. V. Sidorov, S. D. Nikonov, A. A. Ostanin, E. R. Chernykh, N. A. Kolchanov, S. S. Bogachev

“…The occurrence of pangenomic single-strand breaks and restoration of genome (genomic DNA) integrity are associated with activation of a “recombinogenic situation” in the cell; during its active phase, stochastic homologous recombination or other recombination events between extracellular fragments localized in the nucleus and chromosomal DNA are possible. …”
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Genome-Wide Expression of MicroRNAs Is Regulated by DNA Methylation in Hepatocarcinogenesis by Jing Shen, Shuang Wang, Abby B. Siegel, Helen Remotti, Qiao Wang, Iryna Sirosh, Regina M. Santella

“…Previous studies, including ours, have examined the regulation of microRNAs (miRNAs) by DNA methylation, but whether this regulation occurs at a genome-wide level in hepatocellular carcinoma (HCC) is unclear. …”
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Chromosome-level genome assembly of Cyperus iria, an aggressive weed of rice by Siyu Yang, Qingyi Cao, Zexin Wen, Aoxue Wang, Shiyao Shi, Zhuoying Liang, Shuying Li, Wenjun Gui, Jinwen Zhu

“…Until now, the reference genome of C. iria has not been published. Here, we completed the chromosome-level genome assembly of C. iria based on Illumina, PacBio and Hi-C reads. …”
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Genomic Alterations in Primary Gastric Adenocarcinomas Correlate with Clinicopathological Characteristics and Survival by Marjan M. Weiss, Ernst J. Kuipers, Cindy Postma, Antoine M. Snijders, Daniel Pinkel, Stefan G. M. Meuwissen, Donna Albertson, Gerrit A. Meijer

“…In order to investigate the patterns of chromosomal aberrations in gastric carcinomas, we performed genome‐wide microarray based comparative genomic hybridisation (microarray CGH). …”
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Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures by Clairet, Colin, Lapalu, Nicolas, Simon, Adeline, Soyer, Jessica L., Viaud, Muriel, Zehraoui, Enric, Dalmais, Berengère, Fudal, Isabelle, Ponts, Nadia

“…Control of fungal diseases on crops necessitates a global understanding of fungal pathogenicity determinants and their expression during infection. Genomes of phytopathogenic fungi are often compartmentalized: the core genome contains housekeeping genes whereas the fast-evolving genome mainly contains transposable elements and species-specific genes. …”
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From the Cytoplasm into the Nucleus—Hepatitis B Virus Travel and Genome Repair by Johan Ringlander, Gustaf E. Rydell, Michael Kann

“…Understanding the intracellular transport and genome repair mechanisms of HBV is crucial for developing new drugs, which—in combination with immune modulators—may contribute to potential cures. …”
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Genome-Wide Expression Difference of MicroRNAs in Basal Cell Carcinoma by Hai-Peng Wei, Song Zhan, Qing-An Zhu, Zhen-Juan Chen, Xian Feng, Jun-Yuan Chen, Qi-Lin Zhang, Jingjie Zhao, Lingzhang Meng

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3C-BASED METHODS FOR 3D GENOME ORGANIZATION ANALYSIS by N. R. Battulin, V. S. Fishman, Yu. L. Orlov, A. G. Menzorov, D. A. Afonnikov, O. L. Serov

Subjects: “…3d genome organization…”
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The complete mitochondrial genome of Ophiocordyceps gracilis and its comparison with related species by Aifeire Abuduaini, Yuan-Bing Wang, Hui-Ying Zhou, Rui-Ping Kang, Ming-Liang Ding, Yu Jiang, Fei-Ya Suo, Luo-Dong Huang

Subjects: “…Mitochondrial genome…”
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A phenomenological model of non-genomic variability of luminescent bacterial cells by S. I. Bartsev

Subjects: “…non-genomic variability…”
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Development and Validation of a Bordetella pertussis Whole-Genome Screening Strategy by Ricardo da Silva Antunes, Lorenzo G. Quiambao, Aaron Sutherland, Ferran Soldevila, Sandeep Kumar Dhanda, Sandra K. Armstrong, Timothy J. Brickman, Tod Merkel, Bjoern Peters, Alessandro Sette

“…Here, we compare the T cell reactivity of original aP and wP priming for different antigens contained or not contained in the aP vaccine and define the basis of a full-scale genomic map of memory T cell reactivity to BP antigens in humans. …”
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Corrigendum: In-depth analysis of IS6110 genomic variability in the Mycobacterium tuberculosis complex by Jessica Comín, Jessica Comín, Isabel Otal, Isabel Otal, Isabel Otal, Sofía Samper, Sofía Samper, Sofía Samper

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Draft genome sequence of Kei apple, an underutilized African tree crop by Robert Kariba, Bernice Waweru, Isaac Njaci, Linly Banda, Jenniffer W. Mwangi, Antso Harimanantsoa R, Samuel Muthemba, Jonathan Featherstone, Prasad Hendre, Ramni Jamnadass, Allen Van Deynze, Jean-Baka Domelevo Entfellner, Oluwaseyi Shorinola

“…We also annotated the genome and identified 27,449 protein-coding genes. …”
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Reversing the Negative Genomic Effects of Aging with Short-Term Calorie Restriction by Stephen R. Spindler

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Genome assembly of Hawaiian flower thrips Thrips hawaiiensis (Thysanoptera: Thripidae) by Xiaodi Hu, Houjun Tian, Yixin Chen, Yueqin Zheng, Hui Wei, Jian-Ping Chen, Chuan-Xi Zhang, Yong Chen, Yiyuan Li

“…Here, we sequenced the genome of T. hawaiiensis using Oxford Nanopore sequencing technology, Illumina, and Hi-C technology, yielding a genome assembly of 287.59 Mb with scaffold N50 of 13.84 Mb. …”
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