Article
Biochemical Research Methods
Sara Hetzel, Pay Giesselmann, Knut Reinert, Alexander Meissner, Helene Kretzmer
Summary: Bisulfite sequencing data can provide valuable information beyond simple methylation assessment by analyzing single-read patterns. To address the bottleneck of read-level analysis, a fast and scalable tool called RLM was developed to compute frequently used read-level methylation statistics efficiently. This tool supports standard alignment tools, is independent of reference genomes, and can handle various sequencing experiment designs.
Review
Biochemical Research Methods
Adam Nunn, Christian Otto, Peter F. Stadler, David Langenberger
Summary: Whole genome bisulfite sequencing has advanced epigenetic analysis by providing nucleotide-level resolution of 5-methylcytosine (5mC) on a genome-wide scale. Evaluations of nine short-read aligners suggest that BWA-meth and BSMAP are most effective in utilizing data during mapping. Downstream methylation analysis is influenced by handling multi-mapping reads and mapping quality.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Chemistry, Multidisciplinary
Yanfang Du, Ying Tang, Bingqian Lin, Xiaochen Xue, Yafen Wang, Yibin Liu
Summary: The mapping of DNA cytosine modifications is essential for understanding epigenetic regulation. While bisulfite sequencing has limitations, bisulfite-free methods have emerged as promising alternatives. This review provides an overview of both methods, discussing their advantages, limitations, and applications. Challenges and future perspectives for advancing bisulfite-free mapping methods are also explored.
SCIENCE CHINA-CHEMISTRY
(2023)
Article
Biochemical Research Methods
Arun Das, Michael C. Schatz
Summary: In modern sequencing experiments, accurately identifying the sources of the reads is crucial. This study investigates several sampling and sketching-based approaches for read classification. These approaches require limited preprocessing and are able to perform classification with high accuracy.
BMC BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Jeremy Fan, Steven Huang, Samuel D. Chorlton
Summary: BugSeq is a novel and highly accurate metagenomic classifier for nanopore reads, evaluated on simulated data, mock microbial communities, and real clinical samples. Compared to existing tools, BugSeq shows superior accuracy and run times, especially in producing higher concordance with microbiological culture and qPCR results in samples from patients with lower respiratory tract infections.
BMC BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Daniel Danis, Julius O. B. Jacobsen, Parithi Balachandran, Qihui Zhu, Feyza Yilmaz, Justin Reese, Matthias Haimel, Gholson J. Lyon, Ingo Helbig, Christopher J. Mungall, Christine R. Beck, Charles Lee, Damian Smedley, Peter N. Robinson
Summary: This paper introduces a method called SvAnna for structural variant annotation and analysis, which can effectively detect SVs, determine their effects on gene function and clinical phenotype, and provide prioritization rankings. This method contributes to the widespread adoption of long-read sequencing in diagnostic genomics.
Article
Biotechnology & Applied Microbiology
Mourdas Mohamed, Francois Sabot, Marion Varoqui, Bruno Mugat, Katell Audouin, Alain Pelisson, Anna-Sophie Fiston-Lavier, Severine Chambeyron
Summary: TrEMOLO is a new software that combines assembly- and mapping-based approaches to detect transposable elements (TEs) and estimate their allele frequency in populations. It outperforms other computational tools and has been validated with simulated and experimental datasets, making it a comprehensive and suitable tool for studying TE dynamics.
Article
Cell Biology
Xubin Zheng, Qiong Wu, Haonan Wu, Kwong-Sak Leung, Man-Hon Wong, Xueyan Liu, Lixin Cheng
Summary: This study introduced the most prevalent methods for processing bisulfite sequencing data and evaluated the consistency of the data acquired from different measurements in liver cancer. Differential methylated genes measured by various bisulfite sequencing assays and 450 k beadchip were consistently hypo-methylated in liver cancer with high functional similarity.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Lei Zhao, Rasmus Nielsen, Thorfinn Sand Korneliussen
Summary: Commonly used methods for inferring phylogenies are not well-suited for handling challenges associated with noisy, diploid sequencing data. To address this problem, we introduce two new probabilistic approaches, distAngsd-geno and distAngsd-nuc, that account for uncertainty in genotype calling and are specifically designed for next-generation sequencing data.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemical Research Methods
Nastassia Gobet, Maxime Jan, Paul Franken, Ioannis Xenarios
Summary: Genetic variations have an impact on behavior and disease, but understanding how these variations contribute to complex traits is still a question. One common approach is to link genetic variants to intermediate phenotypes, such as the transcriptome, using RNA-sequencing. However, the variants between samples are often ignored in the initial analysis, which can lead to biased transcriptome estimation. In this study, the researchers assessed the impact of reference-based analysis on the transcriptome and expression quantitative trait locus (eQTLs) in a mouse genetic population. They found that using custom references improved downstream analysis compared to using the classical genome reference.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biology
Colin Farrell, Michael Thompson, Anela Tosevska, Adewale Oyetunde, Matteo Pellegrini
Summary: BSBoIt is a fast and scalable bisulfite sequencing analysis platform that efficiently handles asymmetrical libraries. Compared to existing bisulfite alignment tools, BSBoIt outperforms in terms of alignment and methylation calling accuracy.
Article
Biology
Yan Zheng, Xuequn Shang, Wing-Kin Sung
Summary: Structural variations (SVs) are genomic rearrangements larger than 50bp, and they are important in genetic diseases and evolution mechanisms. Existing long-read SV callers often fail to detect true SVs or mistakenly detect false SVs in repetitive regions and regions with multi-allelic SVs, primarily due to messy alignments caused by high error rate in ONT long reads. To address this, we propose a novel method called SVsearcher, which greatly improves SV detection accuracy and is capable of identifying a high percentage of multi-allelic SVs.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Microbiology
Jiaxiong Zeng, Qichao Tu, Xiaoli Yu, Lu Qian, Cheng Wang, Longfei Shu, Fei Liu, Shengwei Liu, Zhijian Huang, Jianguo He, Qingyun Yan, Zhili He
Summary: In this study, a well-curated phosphorus cycling database (PCycDB) was constructed, covering various phosphorus cycling genes (PCGs) and microorganisms (PCMs). Compared to other orthology databases, PCycDB showed higher accuracy and faster analysis speed. The study demonstrated that PCycDB is a powerful tool for advancing our understanding of microbially driven phosphorus cycling.
Article
Biochemical Research Methods
Maia H. Malonzo, Viivi Halla-Aho, Mikko Konki, Riikka J. Lund, Harri Lahdesmaki
Summary: This study developed a probabilistic method and software, LuxRep, that improves the accuracy of DNA methylation level estimation and detection of differentially methylated sites by considering technical replicates with varying bisulfite conversion rates. The use of variational inference also speeds up computation time necessary for whole genome analysis.
BMC BIOINFORMATICS
(2022)
Article
Computer Science, Software Engineering
Sebastian Deorowicz, Adam Gudys
Summary: Identifying genetic variants is crucial in the era of precision medicine, and Whisper 2 is a short-read-mapping software that provides high-quality indel variant calling. It is among the fastest tools available.
Article
Genetics & Heredity
Erica L. Larson, Dan Vanderpool, Sara Keeble, Meng Zhou, Brice A. J. Sarver, Andrew D. Smith, Matthew D. Dean, Jeffrey M. Good
Article
Biochemistry & Molecular Biology
Philip J. Uren, Emad Bahrami-Samani, Patricia Rosa de Araujo, Christine Vogel, Mei Qiao, Suzanne C. Burns, Andrew D. Smith, Luiz O. F. Penalva
Article
Microbiology
Nathan G. Walworth, David A. Hutchins, Egor Dolzhenko, Michael D. Lee, Feixue Fu, Andrew D. Smith, Eric A. Webb
ENVIRONMENTAL MICROBIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Jianghan Qu, Emily Hodges, Antoine Molaro, Pascal Gagneux, Matthew D. Dean, Gregory J. Hannon, Andrew D. Smith
Article
Biochemistry & Molecular Biology
Benjamin E. Decato, Jorge Lopez-Tello, Amanda N. Sferruzzi-Perri, Andrew D. Smith, Matthew D. Dean
MOLECULAR BIOLOGY AND EVOLUTION
(2017)
Article
Cell Biology
Nils O. Lindstrom, Guilherme De Sena Brandine, Tracy Tran, Andrew Ransick, Gio Suh, Jinjin Guo, Albert D. Kim, Riana K. Parvez, Seth W. Ruffins, Elisabeth A. Rutledge, Matthew E. Thornton, Brendan Grubbs, Jill A. McMahon, Andrew D. Smith, Andrew P. McMahon
DEVELOPMENTAL CELL
(2018)
Correction
Biochemistry & Molecular Biology
Jianghan Qu, Emily Hodges, Antoine Molaro, Pascal Gagneux, Matthew D. Dean, Gregory J. Hannon, Andrew D. Smith
Article
Urology & Nephrology
Nils O. Lindstrom, Jinjin Guo, Albert D. Kim, Tracy Tran, Qiuyu Guo, Guilherme De Sena Brandine, Andrew Ransick, Riana K. Parvez, Matthew E. Thornton, Laurence Basking, Brendan Grubbs, Jill A. McMahon, Andrew D. Smith, Andrew P. McMahon
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2018)
Article
Multidisciplinary Sciences
Yu-Hsiang Tu, Alexander J. Cooper, Bochuan Teng, Rui B. Chang, Daniel J. Artiga, Heather N. Turner, Eric M. Mulhall, Wenlei Ye, Andrew D. Smith, Emily R. Liman
Article
Genetics & Heredity
Lori L. O'Brien, Qiuyu Guo, Emad Bahrami-Samani, Joo-Seop Park, Sean M. Hasso, Young-Jin Lee, Alan Fang, Albert D. Kim, Jinjin Guo, Trudy M. Hong, Kevin A. Peterson, Scott Lozanoff, Ramya Raviram, Bing Ren, Ben Fogelgren, Andrew D. Smith, Anton Valouev, Andrew P. McMahon
Article
Biotechnology & Applied Microbiology
Serghei Mangul, Harry Taegyun Yang, Nicolas Strauli, Franziska Gruhl, Hagit T. Porath, Kevin Hsieh, Linus Chen, Timothy Daley, Stephanie Christenson, Agata Wesolowska-Andersen, Roberto Spreafico, Cydney Rios, Celeste Eng, Andrew D. Smith, Ryan D. Hernandez, Roel A. Ophoff, Jose Rodriguez Santana, Erez Y. Levanon, Prescott G. Woodruff, Esteban Burchard, Max A. Seibold, Sagiv Shifman, Eleazar Eskin, Noah Zaitlen
Article
Biology
M. Joaquina Delas, Leah R. Sabin, Egor Dolzhenko, Simon R. V. Knott, Ester Munera Maravilla, Benjamin T. Jackson, Sophia A. Wild, Tatjana Kovacevic, Eva Maria Stork, Meng Zhou, Nicolas Erard, Emily Lee, David R. Kelleys, Mareike Roth, Ines A. M. Barbosa, Johannes Zuber, John L. Rinn, Andrew D. Smith, Gregory J. Hannon
Article
Medicine, Research & Experimental
Jing Liu, Sanjeev Kumar, Egor Dolzhenko, Gregory F. Alvarado, Jinjin Guo, Can Lu, Yibu Chen, Meng Li, Mark C. Dessing, Riana K. Parvez, Pietro E. Cippa, Michaela Krautzberger, Gohar Saribekyan, Andrew D. Smith, Andrew P. McMahon
Article
Biochemical Research Methods
Wenzheng Li, Weili Wang, Philip J. Uren, Luiz O. F. Penalva, Andrew D. Smith