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Sequencing techniques

Next-generation sequencing protocol of hematopoietic stem cells (HSCs). Step-by-step overview and troubleshooting guide

Justyna Jarczak, Kamila Bujko, Katarzyna Brzeźniakiewicz-Janus, Mariusz Ratajczak, Magdalena Kucia

published 09 Jan 2025

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tomoseqr: A Bioconductor package for spatial reconstruction and visualization of 3D gene expression patterns based on RNA tomography

Ryosuke Matsuzawa, Daichi Kawahara, Makoto Kashima, Hiromi Hirata, Haruka Ozaki

published 08 Jan 2025

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Clonal phylogenies inferred from bulk, single cell, and spatial transcriptomic analysis of epithelial cancers

Andrew Erickson, Sandy Figiel, Timothy Rajakumar, Srinivasa Rao, Wencheng Yin, Dimitrios Doultsinos, Anette Magnussen, Reema Singh, Ninu Poulose, Richard J. Bryant, Olivier Cussenot, Freddie C. Hamdy, Dan Woodcock, Ian G. Mills, Alastair D. Lamb

published 03 Jan 2025

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Whole genome sequences of nine Taylorella equigenitalis strains isolated in the Czech Republic between 1982–2021: Molecular dating suggests a common ancestor at the time of Roman Empire

Matěj Hrala, Petr Andrla, Juraj Bosák, Pavla Fedrová, Amir Mugutdinov, Renata Karpíšková, Kateřina Nedbalcová, Jitka Raichová, Martin Faldyna, Petr Hořín, David Šmajs

published 03 Jan 2025

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Site-specific prediction of O-GlcNAc modification in proteins using evolutionary scale model

Ayesha Khalid, Afshan Kaleem, Wajahat Qazi, Roheena Abdullah, Mehwish Iqtedar, Shagufta Naz

published 31 Dec 2024

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Loss of Mfn1 but not Mfn2 enhances adipogenesis

Jake P. Mann, Luis Carlos Tábara, Satish Patel, Pushpa Pushpa, Anna Alvarez-Guaita, Liang Dong, Afreen Haider, Koini Lim, Panna Tandon, Fabio Scurria, James E. N. Minchin, Stephen O’Rahilly S., Daniel J. Fazakerley, Julien Prudent, Robert K. Semple, David B. Savage

published 31 Dec 2024

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Comparing subsampling strategies for metagenomic analysis in microbial studies using amplicon sequence variants versus operational taxonomic units

Daniel Segura, Divya Sharma, Osvaldo Espin-Garcia

published 30 Dec 2024

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Plasmodium falciparum surf_4.1 in clinical isolates: From genetic variation and variant diversity to in silico design immunopeptides for vaccine development

Nitchakarn Noranate, Jariya Sripanomphong, Fingani Annie Mphande- Nyasulu, Suwanna Chaorattanakawee

published 30 Dec 2024

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Bioinformatics analysis of myelin-microbe interactions suggests multiple types of molecular mimicry in the pathogenesis of multiple sclerosis

Ali Bigdeli, Mostafa Ghaderi-Zefrehei, Bluma J. Lesch, Mehrdad Behmanesh, S. Shahriar Arab

published 30 Dec 2024

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Optimizing RNA extraction methods for high-throughput transcriptome sequencing of formalin-fixed paraffin-embedded cardiac tissue specimens

Nkechi Martina Odogwu, Jin Sung Jang, Sabrina Albertson, Clinton Hagen, Boyd Rasmussen, Oommen Saji, Timothy J. Nelson, the Wanek Program Preclinical Pipeline

published 26 Dec 2024

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Phenotypic and molecular characterization of the largest worldwide cluster of hereditary angioedema type 1

Juan Sebastian Arias-Flórez, Sandra Ximena Ramirez, Bibiana Bayona-Gomez, Lina Castro-Castillo, Valeria Correa-Martinez, Yasmín Sanchez-Gomez, William Usaquén-Martínez, Lilian Andrea Casas-Vargas, Carlos Eduardo Olmos Olmos, Nora Contreras Bravo, Camilo Andres Velandia-Piedrahita, Adrien Morel, Rodrigo Cabrera-Perez, Natalia Santiago-Tovar, Cristian Camilo Gaviria-Sabogal, Ingrid Tatyana Bernal, Dora Janeth Fonseca-Mendoza, Carlos M. Restrepo

published 26 Dec 2024

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Comparison of qPCR protocols for quantification of “Candidatus Saccharibacteria”, belonging to the Candidate Phyla Radiation, suggests that 23S rRNA is a better target than 16S rRNA

Stella Papaleo, Riccardo Nodari, Lodovico Sterzi, Enza D’Auria, Camilla Cattaneo, Giorgia Bettoni, Clara Bonaiti, Ella Pagliarini, Gianvincenzo Zuccotti, Simona Panelli, Francesco Comandatore

published 26 Dec 2024

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Molecular monitoring of short- and long-term transcriptional effects of hair growth stimulating agents

Sabrina K. Henne, Lara M. Hochfeld, Werner Bartmann, Thomas Welss, Markus M. Nöthen, Stefanie Heilmann-Heimbach

published 23 Dec 2024

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