Article
Multidisciplinary Sciences
Jason M. Neal-McKinney, Kun C. Liu, Christopher M. Lock, Wen-Hsin Wu, Jinxin Hu
Summary: The study compared Campylobacter genome assemblies generated from MiSeq and MinION data independently, as well as hybrid genome assemblies combining both data types. SPAdes assemblies had the most accurate nucleotide identity, while hybrid assemblies were the most contiguous. Assemblies generated only from MinION data using Canu were the least accurate. The hybrid sequencing approach was the most useful for detecting plasmids, large genome rearrangements, and repetitive elements.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Timo Lassmann
Summary: SAMStat is an efficient program for extracting quality control metrics from fastq and SAM/BAM files. It displays sequence composition, base quality composition, and mapping error profiles based on mapping quality, allowing users to quickly identify reasons for poor mapping. A major update to SAMStat now supports paired-end and long-read data, with quality control plots drawn using the ploty javascript library.
Article
Genetics & Heredity
Christian Vogeley, Thach Nguyen, Selina Woeste, Jean Krutmann, Thomas Haarmann-Stemmann, Andrea Rossi
Summary: Transcriptome analysis experiments provide valuable insights into cell physiology and disease mechanisms. Oxford Nanopore Technologies (ONT) offers a fast, portable, and cost-effective alternative to next-generation sequencing (NGS). However, the availability of RNA-Seq data analysis software that is user-friendly and allows ONT data analysis without bioinformatics expertise is limited. To address this, we developed Duesselpore (TM), a user-friendly deep sequencing workflow that runs as a local webserver and enables ONT and NGS data analysis without the need for additional tools or internet connection.
FRONTIERS IN GENETICS
(2022)
Article
Forestry
Dwi Wahyuni, Fifi Gus Dwiyanti, Rahadian Pratama, Muhammad Majiidu, Henti Hendalastuti Rachmat, Iskandar Zulkarnaen Siregar
Summary: This study utilized ONT technology to generate a large amount of DNA sequence data for Kapur, successfully constructing a partial chloroplast genome and identifying the close genetic relationships between species of the genus Dryobalanops.
Article
Biotechnology & Applied Microbiology
Tomas Nohejl, Jana Palkovicova, Kristina Nesporova, Adam Valcek, Jarmila Lausova, Monika Dolejska
Summary: The fos operon enables bacteria to thrive in challenging environments, and its global distribution in bacterial genomes is still unknown. The presence of plasmid-harbored fos operons in resistant bacteria may contribute to the spread of antibiotic resistance.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Wei Zhang, Lei Wei, Jiaqi Huang, Bixi Zhong, Jiaqi Li, Hanwen Xu, Shuying He, Yu Liu, Juhong Liu, Hairong Lv, Xiaowo Wang
Summary: cfDNApipe is an easy-to-use and systematic python package for cfDNA whole-genome sequencing and whole-genome bisulfite sequencing data analysis, covering the entire analysis pipeline, quality control, and statistical analysis.
Article
Biotechnology & Applied Microbiology
Syeed Md Iskander, Yamrot M. Amha, Phillip Wang, Qin Dong, Juhe Liu, Michael Corbett, Adam L. Smith
Summary: Co-digestion of fats, oils, and grease (FOG) with food waste (FW) can improve energy recovery in anaerobic membrane bioreactors (AnMBRs), especially by introducing more biogas production through a two-phase (TP-MP) reactor. Co-digestion of FW with FOG can also significantly increase daily biogas production and have a positive impact on microbial communities.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Cardiac & Cardiovascular Systems
Tomoya Takashima, Sophie Brisset, Asuka Furukawa, Hirohisa Taniguchi, Rika Takeyasu, Akio Kawamura, Yuichi Tamura
Summary: The study demonstrated the feasibility of using MinION nanopore sequencer for genetic analysis of PAH patients, particularly in detecting BMPR2 mutations. The portable nanopore sequencer showed promise as a screening tool for BMPR2 mutations, especially in small laboratories and research groups.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2021)
Article
Biochemical Research Methods
Matthew Z. DeMaere, Aaron E. Darling
Summary: Hi-C is a sample preparation method that captures genome-wide spatial interactions between DNA molecules, and has been successfully applied to various challenging problems. Despite the complexity of preparing a Hi-C library, diligent quality management is crucial for successful outcomes. A new reference-free approach has been proposed to quantify Hi-C library quality, which is independent of other criteria and requires only a modest amount of sequencing data.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Obstetrics & Gynecology
Anna Oberle, Lara Urban, Stefanie Falch-Leis, Chiara Ennemoser, Yoko Nagai, Kyota Ashikawa, Patricia A. Ulm, Markus Hengstschlaeger, Michael Feichtinger
Summary: This study investigated the feasibility of using nanopore technology for full-length 16S rRNA gene sequencing as an alternative approach for endometrial microbiome analysis. Results from experiments on 33 patients seeking infertility treatment showed that nanopore sequencing was reliable and could accurately assess and compare the microbiome composition of different patients.
REPRODUCTIVE BIOMEDICINE ONLINE
(2021)
Article
Biochemical Research Methods
Steven A. Eschrich, Xiaoqing Yu, Jamie K. Teer
Summary: This article introduces a fast genotype comparison tool and develops a complete workflow to ensure high quality and robust results in sequencing studies.
BMC BIOINFORMATICS
(2023)
Article
Microbiology
Ansgar Schulz, Balal Sadeghi, Franziska Stoek, Jacqueline King, Kerstin Fischer, Anne Pohlmann, Martin Eiden, Martin H. Groschup
Summary: By sequencing samples of arboviruses circulating in Africa, we demonstrated the effectiveness of a nonspecific sequencing technique, SISPA, in generating complete genomes without the need for virus-specific whole-genome PCRs. The results of this study may contribute to a better understanding of the genetic diversity of neglected arboviruses.
Article
Biochemical Research Methods
David Morgenstern, Rotem Barzilay, Yishai Levin
Summary: The tool RawBeans generates visual and HTML-based reports to monitor the LC-MS system performance, aiding users in evaluating raw data quality.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Lifeng Yan, Zekun Yin, Hao Zhang, Zhan Zhao, Mingkai Wang, Andre Mueller, Felix Kallenborn, Alexander Wichmann, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu
Summary: RabbitQCPlus is an ultra-efficient quality control tool for modern multi-core systems, achieving substantial performance gains through vectorization, memory copy reduction, parallel (de)compression, and optimized data structures. It is faster than existing tools, with speed improvements ranging from 1.1 to 5.4 times, and requires fewer compute resources. It is also significantly faster than other applications when processing gzip-compressed FASTQ files and has a quick processing time for large amounts of sequencing data.
Article
Multidisciplinary Sciences
Renesh Bedre, Carlos Avila, Kranthi Mandadi
Summary: HTSQualC is a stand-alone, flexible, and easy-to-use software for one-step quality control analysis of raw HTS data. It can evaluate data quality, perform filtering and trimming analysis in a single run, and has significant benefits for processing large-scale samples.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Scott Ferguson, Ashley Jones, Kevin Murra, Benjamin Schwessinger, Justin O. Borevitz
Summary: Synteny loss, primarily caused by unequal homologous recombination, is commonly observed when comparing closely related species. In this study, the genomes of three closely related Eucalyptus species were analyzed, revealing that approximately 48% of the genomes remained syntenic while approximately 36% underwent rearrangements. It was found that rearrangements highly fragmented microsynteny and potentially altered the phenotypes of the Eucalyptus species. This study highlights the importance of using an unbiased framework in genomic variation studies and emphasizes the potential impact of rearrangements on species differentiation and adaptation.
Article
Biochemistry & Molecular Biology
Kevin R. Cope, Erica T. Prates, John I. Miller, Omar N. A. Demerdash, Manesh Shah, David Kainer, Ashley Cliff, Kyle A. Sullivan, Mikaela Cashman, Matthew Lane, Anna Matthiadis, Jesse Labbe, Timothy J. Tschaplinski, Daniel A. Jacobson, Udaya C. Kalluri
Summary: For plants, differentiating between mutualistic and pathogenic microbes is crucial for survival. Lysin motif receptor-like kinases (LysM-RLKs) play a vital role in perceiving microbe-associated molecular patterns (MAMPs) and triggering a response to specific MAMPs. In this study, we analyzed LysM-RLKs in the Populus genome and predicted their function. Our findings provide insights into the role of LysM-RLKs in Populus-microbe interactions and establish a starting point for future research on microbial perception mechanisms.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Ecology
Daniel Powell, Benjamin Schwessinger, Celine H. Frere
Summary: Researchers uncover new information on the evolutionary relationship of emerging fungal pathogens through mitochondrial genome sequencing and phylogenetic analysis of seven species. They also develop a species-specific qPCR assay for rapid detection and demonstrate its application in a wild urban population of a dragon lizard.
ECOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Jaclyn M. Noshay, Tyler Walker, William G. Alexander, Dawn M. Klingeman, Jonathon Romero, Angelica M. Walker, Erica Prates, Carrie Eckert, Stephan Irle, David Kainer, Daniel A. Jacobson
Summary: Empirical rules-of-thumb for sgRNA efficiency are limited, and this study introduces a new feature set and public resource for interpreting and predicting sgRNA efficiency using quantum chemical tensors. The study identifies important traits for sgRNA design in bacterial species and captures intricate interactions in local and neighboring nucleotides of the target DNA by encoding quantitative attributes of position-specific sequences using quantum descriptors. These novel encodings enhance our understanding of the quantum biological processes involved in CRISPR-Cas9 machinery.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Patricia M. B. Saint-Vincent, Anna Furches, Stephanie Galanie, Erica Teixeira Prates, Jessa L. L. Aldridge, Audrey Labbe, Nan Zhao, Madhavi Z. Z. Martin, Priya Ranjan, Piet Jones, David Kainer, Udaya C. C. Kalluri, Jin-Gui Chen, Wellington Muchero, Daniel A. A. Jacobson, Timothy J. J. Tschaplinski
Summary: Metabolite genome-wide association studies (mGWASs) are important in plant genetics and metabolomics, but there is a lack of experimental validation. This study presents a functional genomics workflow for validating mGWAS-predicted enzyme-substrate relationships. Through high-throughput enzyme activity testing and metabolite screening, the study provides evidence for the role of UGTs in P. trichocarpa and identifies potential implications for sustainable biomass crop production.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Neurosciences
Xin Wang, Qian Sun, Weiwen Wang, Baohui Liu, Ying Gu, Liang Chen
Summary: In this study, single-cell RNA-sequencing data from 36 patient-matched primary and recurrent glioblastoma (GBM) specimens were used to explore molecular alterations at recurrence. Genes involved in extracellular matrix (ECM) organization were found to be enriched in recurrent GBM cells, with MAFK highlighted as a potential regulator. A unique subpopulation of GBM cells that highly expresses ECM and mesenchyme related genes was also identified, suggesting its contribution to the molecular transition of recurrent GBM. Transcription factors, such as NFATC4 and activator protein 1 members, were identified as potential hub regulators. The study provides new insights into the molecular understanding of GBM relapse and candidate targets for recurrent GBM treatment.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2023)
Article
Public, Environmental & Occupational Health
Robyn N. Hall, Ashley Jones, Emma Crean, Victoria Marriott, Nevada Pingault, Alexandra Marmor, Timothy Sloan-Gardner, Karina Kennedy, Kerryn Coleman, Vanessa Johnston, Benjamin Schwessinger
Summary: The Australian Capital Territory (ACT) detected an incursion of the SARS-CoV-2 Delta variant. Public health interventions, including a territory-wide lockdown and comprehensive contact tracing, were rapidly implemented. Genomic sequencing revealed at least 13 independent incursions with onward spread in the community, and different incursions affected distinct cohorts.
EPIDEMIOLOGY AND INFECTION
(2023)
Article
Agronomy
John Lagergren, Mirko Pavicic, Hari B. Chhetri, Larry M. York, Doug Hyatt, David Kainer, Erica M. Rutter, Kevin Flores, Jack Bailey-Bale, Marie Klein, Gail Taylor, Daniel Jacobson, Jared Streich
Summary: This study applies few-shot learning and convolutional neural networks to segment Populus trichocarpa leaf images, extracting features related to leaf morphology and vein topology for genome-wide association study. The work provides the plant phenotyping community with fast and accurate image-based feature extraction methods and a dataset containing diverse leaf phenotypes.
Article
Biochemistry & Molecular Biology
Zhicheng Xu, Weiwen Wang, Tao Yang, Ling Li, Xizheng Ma, Jing Chen, Jieyu Wang, Yan Huang, Joshua Gould, Huifang Lu, Wensi Du, Sunil Kumar Sahu, Fan Yang, Zhiyong Li, Qingjiang Hu, Cong Hua, Shoujie Hu, Yiqun Liu, Jia Cai, Lijin You, Yong Zhang, Yuxiang Li, Wenjun Zeng, Ao Chen, Bo Wang, Longqi Liu, Fengzhen Chen, Kailong Ma, Xun Xu, Xiaofeng Wei
Summary: Recent technological developments in spatial transcriptomics have enabled researchers to measure gene expression and spatial locations at the single-cell level, providing detailed biological insights. A comprehensive database like STOmicsDB can facilitate data sharing and streamline the data acquisition process, promoting research efficiency.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Muralikrishnan Gopalakrishnan Meena, Matthew J. Lane, Joanna Tannous, Alyssa A. Carrell, Paul E. Abraham, Richard J. Giannone, Jean-Michel Ane, Nancy P. Keller, Jesse L. Labbe, Armin G. Geiger, David Kainer, Daniel A. Jacobson, Tomas A. Rush
Summary: Fungal specialized metabolites are important sources of beneficial compounds. This study introduces a data-driven algorithm based on network analysis to characterize the production of specialized fungal metabolites triggered by different exogenous compounds. The algorithm consists of two routes, the direct route and the auxiliary route, which provide insights into the influence of treatments on metabolite production. The algorithm was validated using chitooligosaccharides and lipids on the fungal pathogen Aspergillus fumigatus, and it was found to be effective in discovering new compounds for drug discovery.
Article
Biochemical Research Methods
Weiwen Wang, James Barbetti, Thomas Wong, Bryan Thornlow, Russ Corbett-Detig, Yatish Turakhia, Robert Lanfear, Bui Quang Minh
Summary: DecentTree is a highly optimized and parallel implementation of the Neighbour-Joining phylogenetic inference method, which shows similar or improved performance compared to existing software, especially for handling very large sequence alignments.
Article
Biochemical Research Methods
Jiri C. Moravec, Robert Lanfear, David L. Spector, Sarah D. Diermeier, Alex Gavryushkin
Summary: This article demonstrates for the first time that scRNA-seq data contain sufficient evolutionary signal and can be utilized for phylogenetic analyses. Both expression levels and SNVs derived from scRNA-seq data are shown to be useful for reconstructing phylogenetic relationships between cells and reflecting the clonal composition of a tumor.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Yu K. Mo, Robert Lanfear, Matthew W. Hahn, Bui Quang Minh
Summary: In this study, a new method for calculating site concordance factors (sCFs) is introduced. The updated version uses likelihood to generate probability distributions of ancestral states at internal nodes, thus reducing the effects of homoplasy and taxon sampling.
Article
Genetics & Heredity
David Kainer, Alan R. Templeton, Erica T. Prates, Daniel Jacboson, Euan R. O. Allan, Sharlee Climer, Michael R. Garvin
Summary: This study identifies structural variations in non-Mendelian inheritance patterns that may contribute to the heritability of autism spectrum disorder. These variations, mostly located in non-coding genic space, affect gene regulation and overlap with differentially expressed genes in the postmortem brain tissue of ASD individuals. Additionally, specific structural variations in certain genes are significantly associated with the non-verbal ASD phenotype.
HUMAN GENETICS AND GENOMICS ADVANCES
(2023)
