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Select item 110764931.

Whole-genome sequencing of Ganoderma boninense, the causal agent of basal stem rot disease in oil palm, via combined short- and long-read sequencing

Condro Utomo, Zulfikar Achmad Tanjung, Redi Aditama, Antonius Dony Madu Pratomo, Rika Fithri Nurani Buana, Hadi Septian Guna Putra, Reno Tryono, Tony Liwang

Sci Rep. 2024; 14: 10520. Published online 2024 May 8. doi: 10.1038/s41598-024-60713-3

PMCID:: PMC11076493

Article PDF–4.8M

Select item 110746942.

Lessons learned: overcoming common challenges in reconstructing the SARS-CoV-2 genome from short-read sequencing data via CoVpipe2

Marie Lataretu, Oliver Drechsel, René Kmiecinski, Kathrin Trappe, Martin Hölzer, Stephan Fuchs

Version 2. F1000Res. 2023; 12: 1091. Published online 2024 Apr 16. doi: 10.12688/f1000research.136683.2

PMCID:: PMC11074694

Article PDF–4.2M

Select item 110694653.

ESKEMAP: exact sketch-based read mapping

Tizian Schulz, Paul Medvedev

Algorithms Mol Biol. 2024; 19: 19. Published online 2024 May 4. doi: 10.1186/s13015-024-00261-7

PMCID:: PMC11069465

Article PDF–2.0M

Select item 110692054.

Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS gene

Elena Fernández-Suárez, María González-del Pozo, Cristina Méndez-Vidal, Marta Martín-Sánchez, Marcela Mena, Belén de la Morena-Barrio, Javier Corral, Salud Borrego, Guillermo Antiñolo

Mob DNA. 2024; 15: 9. Published online 2024 May 4. doi: 10.1186/s13100-024-00320-1

PMCID:: PMC11069205

Article PDF–2.7M

Select item 110691855.

A new long-read mitochondrial-genome protocol (PacBio HiFi) for haemosporidian parasites: a tool for population and biodiversity studies

M. Andreína Pacheco, Axl S. Cepeda, Erica A. Miller, Scott Beckerman, Mitchell Oswald, Evan London, Nohra E. Mateus-Pinilla, Ananias A. Escalante

Malar J. 2024; 23: 134. Published online 2024 May 4. doi: 10.1186/s12936-024-04961-8

PMCID:: PMC11069185

Article PDF–3.3M

Select item 110686746.

Community Assembly Processes of Deadwood Mycobiome in a Tropical Forest Revealed by Long-Read Third-Generation Sequencing

Witoon Purahong, Li Ji, Yu-Ting Wu

Microb Ecol. 2024; 87(1): 66. Published online 2024 May 3. doi: 10.1007/s00248-024-02372-5

PMCID:: PMC11068674

Article PDF–3.1M

Select item 110652847.

Deep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates

Chris Lauber, Xiaoyu Zhang, Josef Vaas, Franziska Klingler, Pascal Mutz, Arseny Dubin, Thomas Pietschmann, Olivia Roth, Benjamin W. Neuman, Alexander E. Gorbalenya, Ralf Bartenschlager, Stefan Seitz

PLoS Pathog. 2024 Apr; 20(4): e1012163. Published online 2024 Apr 22. doi: 10.1371/journal.ppat.1012163

PMCID:: PMC11065284

Article PDF–4.0M

Select item 110629468.

PHARE: a bioinformatics pipeline for compositional profiling of multiclonal Plasmodium falciparum infections from long-read Nanopore sequencing data

Salome Hosch, Philipp Wagner, Johanna Nouria Giger, Nina Dubach, Elis Saavedra, Carlo Federico Perno, Jean-Chrysostome Gody, Marilou Sonia Pagonendji, Carine Ngoagouni, Christophe Ndoua, Christian Nsanzabana, Ulrich Vickos, Claudia Daubenberger, Tobias Schindler

J Antimicrob Chemother. 2024 May; 79(5): 987–996. Published online 2024 Mar 19. doi: 10.1093/jac/dkae060

PMCID:: PMC11062946

Article PDF–912K

Select item 110596289.

Single-molecule long-read methylation profiling reveals regional DNA methylation regulated by Elongator Complex Subunit 2 in Arabidopsis roots experiencing spaceflight

Mingqi Zhou, Alberto Riva, Marie-Pierre L. Gauthier, Michael P. Kladde, Robert J. Ferl, Anna-Lisa Paul

Biol Direct. 2024; 19: 33. Published online 2024 Apr 30. doi: 10.1186/s13062-024-00476-z

PMCID:: PMC11059628

Article PDF–7.7M

Select item 1105941810.

Pan-cancer identified ARPC1B as a promising target for tumor immunotherapy and prognostic biomarker, particularly in READ

Chenxiong Zhang, Hao Tan, Han Xu, Jiaming Ding, Huijuan Chen, Xiaohong Liu, Feng Sun

Heliyon. 2024 Apr 15; 10(7): e28005. Published online 2024 Mar 16. doi: 10.1016/j.heliyon.2024.e28005

PMCID:: PMC11059418

Article PDF–9.3M

Select item 1105635611.

Overexpression of SYNGAP1 suppresses the proliferation of rectal adenocarcinoma via Wnt/β-Catenin signaling pathway

Yun Xiao, Ying Zhu, Jiaojiao Chen, Mei Wu, Lan Wang, Li Su, Fei Feng, Yanli Hou

Discov Oncol. 2024 Dec; 15: 135. Published online 2024 Apr 29. doi: 10.1007/s12672-024-00997-z

PMCID:: PMC11056356

Article PDF–17M

Select item 1104863512.

IFN-Type-I Response and Systemic Immunity in Rectal Adenocarcinoma Patients Treated with Conventional or Hypofractionated Neoadjuvant Radiotherapy

Ioannis M. Koukourakis, Erasmia Xanthopoulou, Michael I. Koukourakis, Dina Tiniakos, Vassilis Kouloulias, Anna Zygogianni

Biomolecules. 2024 Apr; 14(4): 448. Published online 2024 Apr 6. doi: 10.3390/biom14040448

PMCID:: PMC11048635

Article PDF–1.8M

Select item 1104448013.

Long-read sequencing of extrachromosomal circular DNA and genome assembly of a Solanum lycopersicum breeding line revealed active LTR retrotransposons originating from S. Peruvianum L. introgressions

Pavel Merkulov, Melania Serganova, Georgy Petrov, Vladislav Mityukov, Ilya Kirov

BMC Genomics. 2024; 25: 404. Published online 2024 Apr 24. doi: 10.1186/s12864-024-10314-1

PMCID:: PMC11044480

Article PDF–6.8M

Select item 1104253314.

Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes

Mathieu Gand, Indre Navickaite, Lee-Julia Bartsch, Josephine Grützke, Søren Overballe-Petersen, Astrid Rasmussen, Saria Otani, Valeria Michelacci, Bosco Rodríguez Matamoros, Bruno González-Zorn, Michael S. M. Brouwer, Lisa Di Marcantonio, Bram Bloemen, Kevin Vanneste, Nancy H. C. J. Roosens, Manal AbuOun, Sigrid C. J. De Keersmaecker

Front Microbiol. 2024; 15: 1336532. Published online 2024 Apr 4. doi: 10.3389/fmicb.2024.1336532

PMCID:: PMC11042533

Article PDF–2.4M

Select item 1104226615.

Long-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project

Siegfried Schloissnig, Samarendra Pani, Bernardo Rodriguez-Martin, Jana Ebler, Carsten Hain, Vasiliki Tsapalou, Arda Söylev, Patrick Hüther, Hufsah Ashraf, Timofey Prodanov, Mila Asparuhova, Sarah Hunt, Tobias Rausch, Tobias Marschall, Jan O. Korbel

Version 1. bioRxiv. Preprint. 2024 Apr 20. doi: 10.1101/2024.04.18.590093