Article
Biochemistry & Molecular Biology
Ziyuan Wang, Junjie Tan, Yanling Long, Yijia Liu, Wenyan Lei, Jing Cai, Yi Yang, Zhibin Liu
Summary: Multiple DNA/RNA sequence alignment is a crucial tool in bioinformatics for phylogenetic tree construction. By optimizing a dynamic programming algorithm using the longest common substring method, we developed an efficient alignment tool that outperforms existing tools for large datasets and long sequences.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Furong Tang, Jiannan Chao, Yanming Wei, Fenglong Yang, Yixiao Zhai, Lei Xu, Quan Zou
Summary: HAlign is a cross-platform program for multiple sequence alignments based on the center star strategy. The major updates of HAlign 3 improved time efficiency and alignment quality, making it a specialized program for processing large numbers of similar DNA/RNA sequences.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemical Research Methods
Ryan D. Crawford, Evan S. Snitkin
Summary: cognac is a user-friendly software package for rapidly generating concatenated gene alignments for phylogenetic analysis, which can quickly identify phylogenetic marker genes using a data-driven approach. The tool efficiently generates concatenated gene alignments for very large genomic datasets in a short amount of time.
BMC BIOINFORMATICS
(2021)
Review
Biochemical Research Methods
Yongqing Zhang, Qiang Zhang, Jiliu Zhou, Quan Zou
Summary: Multiple sequence alignment (MSA) is an important aspect in bioinformatics, revealing potential information in biological sequences. However, MSA faces new challenges with the increasing sequence scale and demand for alignment accuracy. Developing an efficient and accurate MSA strategy has become a research hotspot in bioinformatics. This work summarizes MSA algorithms and their applications in bioinformatics, providing valuable insights for further research and contributions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Lang Zhou, Tingze Feng, Shuangbin Xu, Fangluan Gao, Tommy T. Lam, Qianwen Wang, Tianzhi Wu, Huina Huang, Li Zhan, Lin Li, Yi Guan, Zehan Dai, Guangchuang Yu
Summary: The identification of conserved and variable regions in multiple sequence alignment is crucial for accelerating gene function understanding. ggmsa, an R package, provides various display methods to mine comprehensive sequence features, supports correlation analysis, and offers a new visualization method for genome alignment, aiding researchers in discovering MSA patterns and making decisions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Elena Tea Russoid, Federico Barone, Alex Bateman, Stefano Cozzini, Marco Punta, Alessandro Laio
Summary: Automatic clustering using Density Peak Clustering algorithm was applied to the UniRef50 protein database, resulting in the identification of thousands of protein clusters. The classification results were compared with existing resources and revealed some unannotated protein families.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Vladimir Smirnov, Tandy Warnow
Summary: MAGUS is a new technique for computing large-scale alignments, similar to PASTA but faster and more accurate. It utilizes a divide-and-conquer approach and merges subset alignments using a Graph Clustering Merger.
Article
Biology
Gayathri Mahalingam, Russel Torres, Daniel Kapner, Eric T. Trautman, Tim Fliss, Shamishtaa Seshamani, Eric Perlman, Rob Young, Samuel Kinn, JoAnn Buchanan, Marc M. Takeno, Wenjing Yin, Daniel J. Bumbarger, Ryder P. Gwinn, Julie Nyhus, Ed Lein, Steven J. Smith, R. Clay Reid, Khaled A. Khairy, Stephan Saalfeld, Forrest Collman, Nuno Macarico da Costa
Summary: Serial-section electron microscopy is a high-resolution method for studying biological samples, with applications in reconstructing neural wiring diagrams. We present ASAP, a software pipeline that can handle large datasets in a distributed computational environment, offering high throughput and modular design.
Article
Microbiology
Sophia David, Joshua L. C. Wong, Julia Sanchez-Garrido, Hok-Sau Kwong, Wen Wen Low, Fabio Morecchiato, Tommaso Giani, Gian Maria Rossolini, Stephen J. Brett, Abigail Clements, Konstantinos Beis, David M. Aanensen, Gad Frankel
Summary: Mutations in outer membrane porins act in synergy with carbapenemase enzymes to increase carbapenem resistance in Klebsiella pneumoniae. The diversity, spread and impact of different insertions in the extracellular loop 3 region of OmpK36 were characterized. The study found that different insertions resulted in varying degrees of pore constriction and resistance to antibiotics.
Article
Multidisciplinary Sciences
Yejin Lee, Dong U. Woo, Yang Jae Kang
Summary: Due to the advancement of sequencing technology and decreased cost, numerous whole genome sequences have been obtained, leading to the discovery of extensive genetic variations. The aim of this research was to verify and establish a reliable set of SNPs through different reference genomes and publicly available databases, resulting in the creation of an accessible database.
SCIENTIFIC REPORTS
(2023)
Article
Plant Sciences
Xiaojuan Liu, Qin Gong, Chenning Zhao, Dengliang Wang, Xianming Ye, Guixia Zheng, Yue Wang, Jinping Cao, Chongde Sun
Summary: In this study, a comprehensive genome-wide analysis of the CYP superfamily in Citrus clementina genome was conducted, identifying 301 CYP genes grouped into ten clans and 49 families. The reliability of the phylogenetic relationship was supported by the characteristics of gene structures and motif compositions. The expression patterns of CYP genes in citrus fruit peel during development and in response to UV-B were elucidated through RNA-seq data. Furthermore, a UV-B-induced CYP gene (CitF3 ' H) was characterized as a flavonoid 3'-hydroxylase, providing insights into the biosynthesis of 3'-hydroxylated flavonoids in citrus.
HORTICULTURE RESEARCH
(2023)
Article
Biochemical Research Methods
Anna Klimovskaia Susmelj, Yani Ren, Yann Vander Meersche, Jean-Christophe Gelly, Tatiana Galochkina
Summary: In the era of increasing protein data, a relevant and interpretable visualization is crucial. Poincare disk projection has shown its efficiency in visualizing single-cell RNAseq data. Here, we introduce PoincareMSA, a new method for visualizing complex relationships between protein sequences using Poincare maps embedding. It demonstrates efficiency in visualizing protein family topology and annotating unknown sequences. PoincareMSA is implemented in open source Python code with available interactive Google Colab notebooks.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Maksim Shegay, Vytas K. Svedas, Vladimir V. Voevodin, Dmitry A. Suplatov, Nina N. Popova
Summary: With the increasing availability of 3D data, there is a shift towards content-rich 3D alignments in comparative bioinformatic analysis, leading to the need for new ways to improve 3D superimposition accuracy. The proposed guide tree optimization with genetic algorithm (GA) significantly improves alignment quality for multiple protein 3D structures. Implementation of the GA-based approach in M3DSA algorithms demonstrates statistically significant improvements in TM-score quality indicators on various datasets, showing potential for optimizing 3D alignments across diverse protein superfamilies.
Article
Biochemistry & Molecular Biology
Dimitrii O. Kostenko, Eugene Korotkov
Summary: The aim of this study was to compare the performance of multiple alignment methods in aligning highly divergent amino acid sequences. The results showed that although MAHDS had slightly lower quality alignments compared to other algorithms, it compensated with greater statistical significance. Additionally, MAHDS outperformed other methods in constructing statistically significant alignments for highly divergent protein sequences.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Giacomo Janson, Alessandro Paiardini
Summary: The PyMod project serves as an integrated interface between PyMOL and popular tools for structural bioinformatics. The latest release, PyMod 3, features a new graphical interface and expanded functionalities for users to perform homology modeling processes and other tasks in the PyMOL environment.
Article
Biochemical Research Methods
Rachael M. Zemek, Vanessa S. Fear, Cath Forbes, Emma de Jong, Thomas H. Casey, Louis Boon, Timo Lassmann, Anthony Bosco, Michael J. Millward, Anna K. Nowak, Richard A. Lake, W. Joost Lesterhuis
Article
Multidisciplinary Sciences
Alexia L. Weeks, Heather A. D'Antoine, Melita McKinnon, Genevieve Syn, Dawn Bessarab, Ngiare Brown, Steven Y. C. Tong, Bo Remenyi, Andrew Steer, Lesley-Ann Gray, Michael Inouye, Jonathan R. Carapetis, Jenefer M. Blackwell, Timo Lassmann
Article
Biochemistry & Molecular Biology
Tanvir Alam, Saumya Agrawal, Jessica Severin, Robert S. Young, Robin Andersson, Erik Arner, Akira Hasegawa, Marina Lizio, Jordan A. Ramilowski, Imad Abugessaisa, Yuri Ishizu, Shohei Noma, Hiroshi Tarui, Martin S. Taylor, Timo Lassmann, Masayoshi Itoh, Takeya Kasukawa, Hideya Kawaji, Luigi Marchionni, Guojun Sheng, Alistair R. R. Forrest, Levon M. Khachigian, Yoshihide Hayashizaki, Piero Carninci, Michiel J. L. de Hoon
Article
Immunology
Kak-Ming Ling, Luke W. Garratt, Erin E. Gill, Amy H. Y. Lee, Patricia Agudelo-Romero, Erika N. Sutanto, Thomas Iosifidis, Tim Rosenow, Stuart E. Turvey, Timo Lassmann, Robert E. W. Hancock, Anthony Kicic, Stephen M. Stick
FRONTIERS IN IMMUNOLOGY
(2020)
Review
Immunology
Joel Kidman, Nicola Principe, Mark Watson, Timo Lassmann, Robert A. Holt, Anna K. Nowak, Willem Joost Lesterhuis, Richard A. Lake, Jonathan Chee
FRONTIERS IN IMMUNOLOGY
(2020)
Article
Multidisciplinary Sciences
Alexia L. Weeks, Richard W. Francis, Joao I. C. F. Neri, Nathaly M. C. Costa, Nivea M. R. Arrais, Timo Lassmann, Jenefer M. Blackwell, Selma M. B. Jeronimo
Article
Immunology
Sarra E. Jamieson, Michaela Fakiola, Dave Tang, Elizabeth Scaman, Genevieve Syn, Richard W. Francis, Harvey L. Coates, Denise Anderson, Timo Lassmann, Heather J. Cordell, Jenefer M. Blackwell
Summary: This study identified plausible genetic risk loci for severe otitis media in Aboriginal Australian children, including NR3C1 and NREP genes. Analysis also showed associations with variants influencing protein coding and pathways related to abnormal hair cell morphology, ear issues, integrin interactions, and cell projection phenotypes.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Multidisciplinary Sciences
Mathys Grapotte, Manu Saraswat, Chloe Bessiere, Christophe Menichelli, Jordan A. Ramilowski, Jessica Severin, Yoshihide Hayashizaki, Masayoshi Itoh, Michihira Tagami, Mitsuyoshi Murata, Miki Kojima-Ishiyamas, Shohei Noma, Shuhei Noguchi, Takeya Kasukawa, Akira Hasegawa, Harukazu Suzuki, Hiromi Nishiyori-Sueki, Martin C. Frith, Clement Chatelain, Piero Carninci, Michiel J. L. de Hoom, Wyeth W. Wasserman, Laurent Brehelin, Charles-Henri Lecellieree
Summary: The FANTOM5 consortium used CAGE technology to map transcription start sites, finding that a large portion of non-coding transcription initiates at microsatellites. They developed Cap Trap RNA-seq to confirm this transcription, and trained deep learning models to predict CAGE signal at STRs with high accuracy. These models revealed the importance of STR surrounding sequences for distinguishing STR classes and predicting transcription initiation levels.
NATURE COMMUNICATIONS
(2021)
Article
Medicine, General & Internal
Anna P. Ralph, Rachel Webb, Nicole J. Moreland, Reuben McGregor, Anthony Bosco, David Broadhurst, Timo Lassmann, Timothy C. Barnett, Rym Benothman, Jennifer Yan, Bo Remenyi, Julie Bennett, Nigel Wilson, Mark Mayo, Glenn Pearson, Tobias Kollmann, Jonathan R. Carapetis
Summary: The absence of a diagnostic test for acute rheumatic fever (ARF) is a major impediment in managing this serious childhood condition, which is the precursor to rheumatic heart disease (RHD), a leading cause of health inequity and premature mortality for Indigenous peoples. The 'Searching for a Technology-Driven Acute Rheumatic Fever Test' (START) study aims to discover biomarkers that can distinguish ARF cases from non-ARF cases and potentially transform the approach to ARF diagnosis and RHD prevention.
Article
Cell & Tissue Engineering
Vanessa S. Fear, Catherine A. Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Sarra Jamieson, Michelle Ward, Gareth Baynam, Timo Lassmann
Summary: This study proposes a rapid genetic variant assessment pipeline utilizing CRISPR technology and functional genomics to support rare disease diagnosis and identify key disease mechanisms. The results demonstrate the effectiveness of the pipeline in identifying specific genetic variants associated with Kleefstra syndrome and revealing potential transcription factors relevant to disease pathogenesis.
STEM CELL RESEARCH & THERAPY
(2022)
Article
Genetics & Heredity
Vanessa S. Fear, Catherine A. Forbes, Denise Anderson, Sebastian Rauschert, Genevieve Syn, Nicole Shaw, Matthew E. Jones, Alistair R. R. Forrest, Gareth Baynam, Timo Lassmann
Summary: This study investigates the use of CRISPR gene editing and genome-wide transcriptomic profiling to facilitate patient diagnosis. The introduction of a variant in the EHMT1 gene allowed the researchers to identify gene expression changes related to Kleefstra syndrome and gain insight into the disease mechanism.
Article
Genetics & Heredity
Denise Anderson, Timo Lassmann
Summary: Identifying causal variants for genetic disease diagnosis is challenging, and variant prioritization tools can assist in this task. Our study found that these tools show differences in performance across different disease contexts, and we recommend three standout tools.
Article
Multidisciplinary Sciences
Rachael M. Zemek, Wee Loong Chin, Vanessa S. Fear, Ben Wylie, Thomas H. Casey, Cath Forbes, Caitlin M. Tilsed, Louis Boon, Belinda B. Guo, Anthony Bosco, Alistair R. R. Forrest, Michael J. Millward, Anna K. Nowak, Richard A. Lake, Timo Lassmann, W. Joost Lesterhuis
Summary: The biological determinants of the response to immune checkpoint blockade (ICB) in cancer are not fully understood. This study shows that responding tumors are associated with transient IFN-beta signaling, which can promote the anti-tumor response. The authors also identify inflammatory monocytes as the primary source of IFN beta and find that active type-I-IFN signaling in tumor-infiltrating inflammatory monocytes is associated with T cell expansion in patients treated with ICB.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Caitlin M. Tilsed, Nicola Principe, Joel Kidman, Wee Loong Chin, M. Lizeth Orozco Morales, Rachael M. Zemek, Jonathan Chee, Rasa Islam, Vanessa S. Fear, Catherine Forbes, Wayne J. Aston, Maud Jansen, Abha Chopra, Timo Lassmann, Anna K. Nowak, Scott A. Fisher, Richard A. Lake, W. Joost Lesterhuis
Summary: This study characterizes the chemotherapy-responsive tumor microenvironment in mice through RNA sequencing analysis on tumors before and after chemotherapy. It reveals that responsive tumors have a highly immune infiltrated and inflammatory pre-treatment tumor microenvironment. The same gene expression profile is also associated with response to cyclophosphamide-based chemotherapy in breast cancer patients.
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.
