Article
Biotechnology & Applied Microbiology
David Dylus, Adrian Altenhoff, Sina Majidian, Fritz J. Sedlazeck, Christophe Dessimoz
Summary: Current methods for phylogenetic tree inference are computationally expensive and laborious, with limitations in sequencing coverage, assembly and annotation quality. To address this, Read2Tree directly processes raw sequencing reads into gene groups, bypassing traditional steps in phylogeny inference, and achieves high accuracy. It outperforms assembly-based approaches in terms of speed and accuracy across various datasets, including a yeast tree of life and classification of Coronaviridae samples. Read2Tree enables comparative genomics at scale without genome assembly or annotation.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Kez Cleal, Duncan M. Baird
Summary: Structural variation (SV) is important in genome evolution and disease, and Dysgu is a tool that accurately detects SVs using paired-end or long-read sequencing, with high sensitivity and fast running speed.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Prakash Chourasia, Sarwan Ali, Simone Ciccolella, Gianluca Della Vedova, Murray Patterson
Summary: The massive amount of genomic data for SARS-CoV-2 has led to the development of new methods like Pangolin. In this article, Reads2Vec, an alignment-free embedding approach, is proposed to generate feature vectors directly from raw sequencing reads without assembly. Experimental results show that Reads2Vec outperforms existing alignment-free methods in classification and clustering.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Lucas Czech, Moises Exposito-Alonso
Summary: grenepipe is an all-in-one workflow that streamlines the data processing from raw high-throughput sequencing data to genotype variant calls. It integrates popular software tools, automatically installs dependencies, and is highly scalable and easy to run.
Article
Biology
Fan Zhang, Hyun Min Kang
Summary: The study developed rapid and accurate methods to generate comprehensive quality metrics directly from a subset of raw sequence reads without full genome alignment. These methods offer faster turnaround time and provide sophisticated quality metrics, including estimates of genetic ancestry and cross-sample contamination, compared to existing full alignment-based methods.
Article
Biotechnology & Applied Microbiology
Hyunji Lee, Jun Kim, Junho Lee
Summary: Recent advances in long-read sequencing technologies have enabled accurate identification of genetic variants. In this study, two Caenorhabditis elegans strains were used to compare the performance of two long-read sequencing platforms, HiFi and CLR. HiFi identified more true-positive variants and fewer false-positive variants compared to CLR. Additionally, assembly-based variant calling was shown to be effective for detection of large insertions using accurate long-read sequencing data.
Article
Multidisciplinary Sciences
Fanny-Dhelia Pajuste, Maido Remm
Summary: The study developed a computational method GeneToCN that can infer gene copy number based on gene-specific k-mer frequencies. The method was validated using experimental data and showed strong correlation with experimentally determined copy numbers. Additionally, the method showed good agreement with previous studies and performed consistently across different sequencing technologies.
SCIENTIFIC REPORTS
(2023)
Article
Environmental Sciences
Mengyang Xu, Lidong Guo, Yanwei Qi, Chengcheng Shi, Xiaochuan Liu, Jianwei Chen, Jinglin Han, Li Deng, Xin Liu, Guangyi Fan
Summary: We present a reference-free approach, Symbiont-Screener, to identify high-confidence host's long reads from symbionts and contaminants and overcome the low sequencing accuracy. It maintains higher precision and recall rates compared to other tools, enabling high-quality reconstruction of the host genome and associated metagenomes. Application of this method on a real host-microbe system demonstrates improved host assembly and symbiotic microbiome profiling, providing a novel perspective on symbiotic research.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Biochemical Research Methods
Niema Moshiri
Summary: In viral molecular epidemiology, it is crucial to reconstruct consensus genomes from sequence data to track mutations and variants of concern. However, as the number of sequenced samples increases rapidly, the computational resources required for genome reconstruction can become prohibitively large. ViralConsensus is a fast and memory-efficient tool that directly calls viral consensus genome sequences from read alignment data.
Review
Biochemical Research Methods
Xiaoyu He, Shanyu Chen, Ruilin Li, Xinyin Han, Zhipeng He, Danyang Yuan, Shuying Zhang, Xiaohong Duan, Beifang Niu
Summary: NGS technology has revolutionized human cancer research by detecting genomic variants efficiently, but the challenges of software selection and multidimensional QC in cancer genome sequencing need to be systematically evaluated. This review investigates widely used software, provides guidance for software and pipeline selection, and discusses the prospects and new research directions in cancer genomics.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Lauris Kaplinski, Mart Mols, Tarmo Puurand, Fanny-Dhelia Pajuste, Maido Remm
Summary: KATK is a fast and accurate software tool for calling variants directly from raw next-generation sequencing reads. It uses predefined k-mers to retrieve reads and align them locally, achieving a high sensitivity and low false discovery rate.
Article
Genetics & Heredity
Ze-Gang Wei, Xing-Guo Fan, Hao Zhang, Xiao-Dan Zhang, Fei Liu, Yu Qian, Shao-Wu Zhang
Summary: In this paper, a novel mapper called kngMap is introduced for aligning long noisy SMS reads to a reference sequence using a k-mer neighborhood graph. Experimental results show that kngMap has higher sensitivity and can produce consecutive alignments for the whole read.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Angana Chakraborty, Burkhard Morgenstern, Sanghamitra Bandyopadhyay
Summary: The newly developed S-conLSH mapping tool uses spaced-context based Locality Sensitive Hashing to achieve faster mapping speed and higher sensitivity on 5 different real and simulated datasets. By utilizing multiple spaced patterns, S-conLSH enables gapped mapping of noisy long reads to the corresponding target locations of a reference genome, making it a promising direction towards alignment-free sequence analysis.
BMC BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Chaokun Yan, Junyi He, Junwei Luo, Jianlin Wang, Ge Zhang, Huimin Luo
Summary: A novel insertion detection approach called SIns is proposed in this study, which accurately calls insertions by extracting breakpoints and determining insertion locations from soft-clipped reads, and uses Minia to assemble insertion sequences. Experimental results show that SIns achieves better performance in terms of the F-score value compared to other methods for simulated and true datasets.
FRONTIERS IN GENETICS
(2021)
Review
Genetics & Heredity
Dhrithi Deshpande, Karishma Chhugani, Yutong Chang, Aaron Karlsberg, Caitlin Loeffler, Jinyang Zhang, Agata Muszynska, Viorel Munteanu, Harry Yang, Jeremy Rotman, Laura Tao, Brunilda Balliu, Elizabeth Tseng, Eleazar Eskin, Fangqing Zhao, Pejman Mohammadi, Pawel P. Labaj, Serghei Mangul
Summary: RNA-seq has become a widely used technology in biology and clinical science due to the development of accurate computational tools by the bioinformatics community. These tools enable the analysis of large amounts of transcriptomic data and help to detect novel exons, assess gene expression, and study alternative splicing. However, it can be challenging to obtain meaningful biological signals from raw RNA-seq data due to the scale of the data and limitations of sequencing technologies. The rapid development of novel computational tools has helped to overcome these challenges and unlock the full potential of RNA-seq.
FRONTIERS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Tonis Tasa, Kristi Krebs, Mart Kals, Reedik Magi, Volker M. Lauschke, Toomas Haller, Tarmo Puurand, Maido Remm, Tonu Esko, Andres Metspalu, Jaak Vilo, Lili Milani
EUROPEAN JOURNAL OF HUMAN GENETICS
(2019)
Article
Biochemistry & Molecular Biology
Lehti Saag, Margot Laneman, Liivi Varul, Martin Malve, Heiki Valk, Maria A. Razzak, Ivan G. Shirobokov, Valeri I. Khartanovich, Elena R. Mikhaylova, Alena Kushniarevich, Christiana Lyn Scheib, Anu Solnik, Tuuli Reisberg, Juri Parik, Lauri Saag, Ene Metspalu, Siiri Rootsi, Francesco Montinaro, Maido Remm, Reedik Magi, Eugenia D'Atanasio, Enrico Ryunosuke Crema, David Diez-del-Molino, Mark G. Thomas, Aivar Kriiska, Toomas Kivisild, Richard Villems, Valter Lang, Mait Metspalu, Kristiina Tambets
Article
Plant Sciences
Kairi Raime, Kaarel Krjutskov, Maido Remm
FRONTIERS IN PLANT SCIENCE
(2020)
Article
Multidisciplinary Sciences
Sirli Rosendahl, Hedvig Tamman, Age Brauer, Maido Remm, Rita Horak
SCIENTIFIC REPORTS
(2020)
Article
Genetics & Heredity
Tiit Ord, Tarmo Puurand, Daima Ord, Tarmo Annilo, Mart Mols, Maido Remm, Tonis Ord
Article
Microbiology
Kaidi Telling, Age Brauer, Mailis Laht, Piret Kalmus, Karolin Toompere, Veljo Kisand, Matti Maimets, Maido Remm, Tanel Tenson, Irja Lutsar
Article
Genetics & Heredity
Lauris Kaplinski, Mart Mols, Tarmo Puurand, Fanny-Dhelia Pajuste, Maido Remm
Summary: KATK is a fast and accurate software tool for calling variants directly from raw next-generation sequencing reads. It uses predefined k-mers to retrieve reads and align them locally, achieving a high sensitivity and low false discovery rate.
Article
Food Science & Technology
J. Mildenberger, M. Remm, M. Atanassova
Summary: Hydrogels based on marine natural biopolymers, such as peptide fractions from Parastichopus tremulus, have been characterized for their antioxidant activity and self-assembly capacity. The study identified potential peptide sequences with auto-assembly capacity, providing new materials for tissue engineering in regenerative medicine.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Microbiology
Erki Aun, Veljo Kisand, Mailis Laht, Kaidi Telling, Piret Kalmus, Ulo Vali, Age Brauer, Maido Remm, Tanel Tenson
Summary: This study characterized the population structure, drug resistance mechanisms, and virulence genes of Enterococcus isolates in Estonia. The findings revealed closely related strains isolated from different host species, indicating potential interspecies spread of strains and transfer of antibiotic resistance. Genomic context analysis of the resistance genes showed frequent association with plasmids and mobile genetic elements, suggesting the occurrence of transfer events.
FRONTIERS IN MICROBIOLOGY
(2021)
Editorial Material
Biology
Maria Vittoria Modica, Rafi Ahmad, Stuart Ainsworth, Gregor Anderluh, Agostinho Antunes, Dimitris Beis, Figen Caliskan, Mauro Dalla Serra, Sebastien Dutertre, Yehu Moran, Ayse Nalbantsoy, Naoual Oukkache, Stano Pekar, Maido Remm, Bjoern Marcus von Reumont, Yiannis Sarigiannis, Andrea Tarallo, Jan Tytgat, Eivind Andreas Baste Undheim, Yuri Utkin, Aida Verdes, Aude Violette, Giulia Zancolli
Summary: Venom research is a highly multidisciplinary field involving various subfields of biology, informatics, pharmacology, medicine, and other areas. However, lack of coordination among different research teams hampers the full development of venom investigation and applications. The recently launched European Venom Network aims to promote synergistic interactions among stakeholders and foster venom research at the European level.
Article
Microbiology
Agnese Bellabarba, Giovanni Bacci, Francesca Decorosi, Erki Aun, Elisa Azzarello, Maido Remm, Luciana Giovannetti, Carlo Viti, Alessio Mengoni, Francesco Pini
Summary: The association between leguminous plants and symbiotic nitrogen-fixing rhizobia showcases mutualism between eukaryotic hosts and prokaryotic microbes. While this symbiosis is somewhat species-specific, different rhizobial strains can co-colonize the same nodule. Through a bacterial genome-wide association (GWAS) analysis, the study identified genomic determinants related to competitive capabilities in Sinorhizobium meliloti strains.
Correction
Biology
Maria Vittoria Modica, Rafi Ahmad, Stuart Ainsworth, Gregor Anderluh, Agostinho Antunes, Dimitris Beis, Figen Caliskan, Mauro Dalla Serra, Sebastien Dutertre, Yehu Moran, Ayse Nalbantsoy, Naoual Oukkache, Stano Pekar, Maido Remm, Bjoern Marcus von Reumont, Yiannis Sarigiannis, Andrea Tarallo, Jan Tytgat, Eivind Andreas Baste Undheim, Yuri Utkin, Aida Verdes, Aude Violette, Giulia Zancolli
Article
Biotechnology & Applied Microbiology
Nemailla Bonturi, Marina Julio Pinheiro, Paola Monteiro de Oliveira, Eka Rusadze, Tobias Eichinger, Gintare Liudziute, Juliano Sabedotti De Biaggi, Age Brauer, Maido Remm, Everson Alves Miranda, Rodrigo Ledesma-Amaro, Petri-Jaan Lahtvee
Summary: This study successfully applied the Golden Gate DNA assembly system to the oleaginous yeast R. toruloides, establishing an efficient genome engineering platform. Using this platform, researchers designed complex metabolic pathways and achieved overexpression of the carotenoid production pathway, resulting in a 41% increase in carotenoid concentration.
METABOLIC ENGINEERING COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Fanny-Dhelia Pajuste, Maido Remm
Summary: The study developed a computational method GeneToCN that can infer gene copy number based on gene-specific k-mer frequencies. The method was validated using experimental data and showed strong correlation with experimentally determined copy numbers. Additionally, the method showed good agreement with previous studies and performed consistently across different sequencing technologies.
SCIENTIFIC REPORTS
(2023)
