Article
Biochemistry & Molecular Biology
Mark P. Simmons, John Gatesy
Summary: In this study, the impact of alternative methods for collapsing gene-tree branches on species-tree inference was quantified for seven empirical datasets. It was found that the choice of branch-collapsing methods significantly influences species-tree inference, with certain methods enhancing branch support.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Frederik Schulz, Dongying Wu, David Paez-Espino, I-Min Chen, Marcel Huntemann, Krishna Palaniappan, Joshua Ladau, Supratim Mukherjee, T. B. K. Reddy, Torben Nielsen, Edward Kirton, Jose P. Faria, Janaka N. Edirisinghe, Christopher S. Henry, Sean P. Jungbluth, Dylan Chivian, Paramvir Dehal, Elisha M. Wood-Charlson, Adam P. Arkin, Susannah G. Tringe, Axel Visel, Tanja Woyke, Nigel J. Mouncey, Natalia N. Ivanova, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh
Summary: Reconstructing bacterial and archaeal genomes from shotgun metagenomes has led to the creation of a comprehensive catalog representing a significant expansion of the known phylogenetic diversity of bacteria and archaea. This resource is available for streamlined comparative analyses, interactive exploration, metabolic modeling, and bulk download, demonstrating the utility of genome-centric approaches for understanding genomic properties of uncultivated microorganisms.
NATURE BIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
Thien Le, Aaron Sy, Erin K. Molloy, Qiuyi Zhang, Satish Rao, Tandy Warnow
Summary: Incremental tree building (INC) is a fast converging phylogeny estimation method, but has poor accuracy for gene tree estimation; Constrained-INC approaches the accuracy of the best methods for species tree estimation and is faster.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Plant Sciences
Vheena Mohankumar, Elizabeth K. Dann, Olufemi A. Akinsanmi
Summary: This study found that the causal agents of branch dieback in commercial macadamia orchards in different agroecological regions in Australia are similar, mainly consisting of Lasiodiplodia and Neofusicoccum fungi. Among them, L. pseudotheobromae is the most prevalent pathogen, while L. theobromae, N. luteum, and L. iraniensis are the most aggressive species.
Article
Plant Sciences
Shanshan Dong, Min Liu, Yang Liu, Fei Chen, Ting Yang, Lu Chen, Xingtan Zhang, Xing Guo, Dongming Fang, Linzhou Li, Tian Deng, Zhangxiu Yao, Xiaoan Lang, Yiqing Gong, Ernest Wu, Yaling Wang, Yamei Shen, Xun Gong, Huan Liu, Shouzhou Zhang
Summary: The chromosome-level reference genome of Magnolia biondii was successfully assembled using advanced sequencing technologies, providing valuable insights for evolutionary studies and ecological adaptability.
HORTICULTURE RESEARCH
(2021)
Article
Multidisciplinary Sciences
Jiawei Zhou, Shuo Zhang, Jie Wang, Hongmei Shen, Bin Ai, Wei Gao, Cuijun Zhang, Qili Fei, Daojun Yuan, Zhiqiang Wu, Luke R. Tembrock, Sen Li, Cuihua Gu, Xuezhu Liao
Summary: The study focused on the comprehensive analysis of chloroplast genomes in the Populus genus to understand chloroplast evolution in a widely studied lineage of angiosperms. Comparative analyses in Populus revealed variations in key genome features such as genome size, gene number, gene content, repeat type and number, and SSR abundance, providing insights into evolutionary patterns. Additionally, the study highlighted the utility of complete chloroplast genomes for phylogenetic analyses and the importance of population-level variations in pan-chloroplast genomes.
SCIENTIFIC REPORTS
(2021)
Article
Evolutionary Biology
Lenard L. Szantho, Nicolas Lartillot, Gergely J. Szollosi, Dominik Schrempf
Summary: Accurate phylogenies are crucial for understanding evolution. But deep evolutionary time scales with long branches have been controversial due to conflicting estimates from models of varying complexity. Inadequate modeling of compositional heterogeneity can lead to erroneous topologies. We introduce a method, compositional constraint analysis, to investigate the effect of amino acid constraints on phylogenetic inference. We show that more constrained sites and less constrained sites produce conflicting signals that can be resolved with more complex models.
SYSTEMATIC BIOLOGY
(2023)
Article
Geochemistry & Geophysics
Yufeng Cui, Yong-Liang Wang, Weijian Liu, Qinglei Du, Jun Liu
Summary: This letter considers the problem of detecting a signal in a nonhomogeneity environment caused by random unknown interference. An effective detector is proposed based on the criteria of the two-step Durbin test or the two-step Wald test. Simulation results demonstrate that the proposed detector achieves slightly better performance compared to existing detectors while maintaining similar computational load under both hypothetical interference conditions and other interference conditions.
IEEE GEOSCIENCE AND REMOTE SENSING LETTERS
(2022)
Review
Biology
Paul Zaharias, Tandy Warnow
Summary: This article introduces some recent advances in highly accurate phylogeny estimation on large datasets, including divide-and-conquer techniques, methods for estimating species trees from multi-locus datasets and addressing heterogeneity, and methods for adding sequences into large gene trees or species trees.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Microbiology
L. Thiberio Rangel, Gregory P. Fournier
Summary: Contrary to the assumption, even fast-evolving sites in conserved proteins contain reliable and valuable phylogenetic information. Trimming such sites can negatively impact the accuracy of phylogenetic reconstruction. Slow-evolving sites are less likely to recover true bipartitions compared to even the fastest-evolving sites.
Article
Biochemistry & Molecular Biology
David Diaz-Escandon, Gulnara Tagirdzhanova, Dan Vanderpool, Carmen C. G. Allen, Andre Aptroot, Oluna Ceska, David L. Hawksworth, Alejandro Huereca, Kerry Knudsen, Jana Kocourkova, Robert Luecking, Philipp Resl, Toby Spribille
Summary: Ascomycota account for a significant proportion of named fungal species. By analyzing previously undersampled and uncultured lineages, researchers have discovered a new clade within Pezizomycotina that diverged over 300 million years ago. This clade, known as Lichinomycetes, includes diverse symbionts, endophytes, and mycorrhizae, and challenges traditional taxonomic classifications.
Article
Evolutionary Biology
Anthony Cognato, William Taft, Rachel K. Osborn, Daniel Rubinoff
Summary: Sesiids are a diverse group of diurnal moths, many of which mimic Hymenoptera. The relationships among these moths are poorly understood. A multi-gene phylogenetic analysis of 48 North American sesiid species confirmed traditional taxonomic ranks, showed that Carmenta and Synanthedon are not monophyletic, and provided limited resolution within and between North American and European groups. The CAD gene showed inconsistent phylogenetic signal compared to other genes, but its removal did not significantly change the initial results. The lack of resolution using informative genes at the species level suggests a rapid radiation of species in Carmenta/Synanthedon. This group's mimicry strategies and hostplant usage could be valuable for future research.
Article
Multidisciplinary Sciences
Sanea Sheikh, Faheema Kalsoom Khan, Mohammad Bahram, Martin Ryberg
Summary: In this study, the evolution of ectomycorrhiza (ECM) fungi was analyzed using different models. The results showed that models with variable rates provide a better fit to the data, and the conclusion about the relative rate between ECM and non-ECM depends on whether rate shifts are allowed or not. It was concluded that standard constant-rate ancestral state reconstruction models are not suitable for the analysis of ECM fungal evolution.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Rafaela Jorge Trad, Fernanda Nunes Cabral, Volker Bittrich, Saura Rodrigues da Silva, Maria do Carmo Estanislau do Amaral
Summary: This study compared and analyzed the plastomes of clusioid plants, revealing evolutionary patterns and specific structural characteristics, particularly in the Calophyllaceae family. The research identified regions for evolutionary studies and highlighted genic rearrangements in Calophyllaceae, as well as unique changes in Clusiaceae and Podostemaceae. Phylogenetic analyses confirmed the monophyletic nature of clusioids and the five families, while also addressing conflicts in relationships reported in previous literature.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Analytical
Marielle Crozet, Cedric Rivier, Valerie Lourenco, Severine Demeyer
Summary: In order to improve the management of contaminated materials in nuclear facilities, a methodology for coordinated interlaboratory comparisons (ILC) is proposed to assess the performance and uncertainty of measurement techniques. The study demonstrates the effectiveness of this methodology in the case of BR3 and highlights the importance of using reference materials with reported uncertainties for performance evaluation and monitoring.
Article
Evolutionary Biology
Keren Halabi, Eli Levy Karin, Laurent Gueguen, Itay Mayrose
Summary: The article introduces a new phylogenetic model called TraitRELAX, which can accurately detect changes in selection patterns of protein-coding genes, overcoming strong assumptions about the evolution of traits in previous methods.
SYSTEMATIC BIOLOGY
(2021)
Article
Biochemical Research Methods
Oren Avram, Aya Kigel, Anna Vaisman-Mentesh, Sharon Kligsberg, Shai Rosenstein, Yael Dror, Tal Pupko, Yariv Wine
Summary: The proteomics of serum antibodies (Ig-Seq) combines BCR-Seq and high-resolution mass-spectrometry, providing a comprehensive characterization of the humoral response. The PASA web server offers a robust computational platform for analyzing and integrating data from proteomics of serum antibodies, making it accessible to non-expert users.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
David Ruano-Gallego, Julia Sanchez-Garrido, Zuzanna Kozik, Elena Nunez-Berrueco, Massiel Cepeda-Molero, Caroline Mullineaux-Sanders, Jasmine Naemi-Baghshomali Clark, Sabrina L. Slater, Naama Wagner, Izabela Glegola-Madejska, Theodoros Roumeliotis, Tal Pupko, Luis Angel Fernandez, Alfonso Rodriguez-Paton, Jyoti S. Choudhary, Gad Frankel
Summary: The study demonstrates the extreme robustness of both T3SS effector networks and host responses, as pathogenicity can be maintained even with a 60% contraction in the effector network. Different effector networks induce varying colonic cytokine profiles, yet all can induce protective immunity, implicating the importance of effector networks in host adaptation.
Article
Immunology
Smadar Hada-Neeman, Yael Weiss-Ottolenghi, Naama Wagner, Oren Avram, Haim Ashkenazy, Yaakov Maor, Ella H. Sklan, Dmitry Shcherbakov, Tal Pupko, Jonathan M. Gershoni
Summary: The study utilizes phage-display epitope arrays for sero-diagnosis, measuring serum binding to multiple epitopes using Next-generation sequencing (NGS). Machine learning classification distinguishes healthy individuals from those infected with HIV-1 or HCV, accurately identifying the contributing domains.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemical Research Methods
Ruoshi Zhang, Milot Mirdita, Eli Levy Karin, Clovis Norroy, Clovis Galiez, Johannes Soeding
Summary: SpacePHARER is a sensitive and fast tool for predicting phage-host relationships by comparing spacers and phages at the protein level, optimizing scores for matching short sequences, and combining evidence from multiple matches.
Article
Biochemical Research Methods
M. Mirdita, M. Steinegger, F. Breitwieser, J. Soeding, E. Levy Karin
Summary: MMseqs2 taxonomy is a new tool for assigning taxonomic labels to metagenomic contigs. It extracts protein fragments from each contig, retains those relevant for taxonomic annotation, and determines the taxonomic identity using weighted voting. MMseqs2 is 2-18 times faster than existing tools and includes modules for creating and manipulating taxonomic reference databases.
Article
Multidisciplinary Sciences
Tridib Mahata, Shahar Molshanski-Mor, Moran G. Goren, Biswanath Jana, Miriam Kohen-Manor, Ido Yosef, Oren Avram, Tal Pupko, Dor Salomon, Udi Qimron
Summary: Bacteriophages have evolved efficient means to take over the machinery of the bacterial host. Through the study of a bacterial growth inhibitor gene product T5.015 encoded by the T5 phage, it was found that growth inhibition mediated by T5.015 depends on the uracil-excision activity of Ung, leading to DNA replication and cell division arrest.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Naama Wagner, Oren Avram, Dafna Gold-Binshtok, Ben Zerah, Doron Teper, Tal Pupko
Summary: Effectidor is a user-friendly web server that utilizes multiple machine-learning techniques to predict T3Es within bacterial genomes and performs well in terms of accuracy.
Article
Biochemical Research Methods
Noa Ecker, Dana Azouri, Ben Bettisworth, Alexandros Stamatakis, Yishay Mansour, Itay Mayrose, Tal Pupko
Summary: In large-scale sequence alignment for phylogenetic reconstruction, we propose an artificial intelligence-based method that selects the optimal subset of sites and computes the log-likelihood of the entire data based on this subset by constraining the number of sites used. We show that computing the likelihood based on 5% of the sites already provides an accurate approximation of the tree likelihood based on the entire data. Furthermore, using this Lasso-based approximation significantly reduces the running time during a tree search while maintaining the same tree-search performance.
Article
Biochemistry & Molecular Biology
Asher Moshe, Elya Wygoda, Noa Ecker, Gil Loewenthal, Oren Avram, Omer Israeli, Einat Hazkani-Covo, Itsik Pe'er, Tal Pupko
Summary: This study developed a probabilistic approach to infer genome rearrangement rate parameters and used an Approximate Bayesian Computation framework for inference. The method can help elucidate the role of genome rearrangement in evolution and simulate genomes with empirical dynamics.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Barak Yariv, Elon Yariv, Amit Kessel, Gal Masrati, Adi Ben Chorin, Eric Martz, Itay Mayrose, Tal Pupko, Nir Ben-Tal
Summary: The ConSurf web-server is used for analyzing proteins, RNA, and DNA, and provides a quick and accurate estimation of per-site evolutionary rate among homologues. It has a user-friendly interface and improved visualization of results. By analyzing a set of homologous sequences, ConSurf calculates evolutionary rates using hidden Markov model-based search tools and assembles a representative set of effective homologues for informative analysis. The availability of AlphaFold model structures makes ConSurf particularly relevant to the research community. Python re-implementation of the computational pipeline and standalone version download are significant improvements.
Article
Biochemistry & Molecular Biology
Gil Loewenthal, Elya Wygoda, Natan Nagar, Lior Glick, Itay Mayrose, Tal Pupko
Summary: The article discusses the evolutionary events of insertions and deletions of short DNA segments, proposes the phenomenon of border-induced selection, and develops corresponding dynamic models to explore the topic.
Article
Biochemistry & Molecular Biology
Edo Dotan, Michael Alburquerque, Elya Wygoda, Dorothee Huchon, Tal Pupko
Summary: In the last decade, advances in sequencing technology have resulted in a significant increase in genomic data, transforming our understanding of gene and genome evolution and function. However, identifying contaminated reads remains challenging. To address this, GenomeFLTR is introduced as a web server that filters contaminated reads by comparing them against relevant sequence databases, allowing users to investigate the source and frequency of contamination and generate a contamination-free file.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Natan Nagar, Jerome Tubiana, Gil Loewenthal, Haim J. Wolfson, Nir Ben Tal, Tal Pupko
Summary: MSAs are important tools in molecular evolution and structural biology research, allowing inference of tolerated amino acids at each site during protein evolution. EvoRator2, a deep-learning algorithm trained on protein structures, can predict tolerated amino acids at any given site based on protein structural information. It shows satisfying results for position-weighted scoring matrices (PSSM) prediction and near state-of-the-art performance in predicting mutation effects in deep mutation scanning (DMS) experiments.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Genetics & Heredity
Sapir Labes, Doron Stupp, Naama Wagner, Idit Bloch, Michal Lotem, Ephrat L. Lahad, Paz Polak, Tal Pupko, Yuval Tabach
Summary: This study analyzed the association between complex conservation patterns and the pathogenicity of Single-Nucleotide Variants (SNVs). The results showed that conservation is not always accurate and its effectiveness depends on the species and genes being analyzed. The findings led to the development of a new approach called EvoDiagnostics, which outperforms traditional conservation algorithms in predicting variant pathogenicity.
NAR GENOMICS AND BIOINFORMATICS
(2022)