Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package [PDF]
Methods in Ecology and Evolution, 2023 Comparative genomics has become an indispensable part of modern biology due to the advancements in high‐throughput sequencing technologies and the accumulation of genomic data in public databases.
Fabricio Almeida-Silva +1 more
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OrthoML2GO: homology-based protein function prediction using orthogroups and machine learning [PDF]
Вавиловский журнал генетики и селекцииIn recent years, the rapid growth of sequencing data has exacerbated the problem of functional annotation of protein sequences, as traditional homology-based methods face limitations when working with distant homologs, making it difficult to accurately ...
E. V. Malyugin, D. A. Afonnikov
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Sequence-based comparative secretome analysis reveals conserved core effectors and host lineage-specific divergence between monocot- and dicot-associated powdery mildew lineages [PDF]
Frontiers in Plant SciencePowdery mildew fungi are obligate biotrophs that parasitize living plant tissues and deploy secreted proteins to support host colonization. We compared predicted secretomes from 26 powdery mildew isolates representing five genera (Blumeria, Erysiphe ...
Noman Ali, Nan Wu, Mahinur S. Akkaya
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Finding Species-Specific Extracellular Surface-Facing Proteomes in Toxic Dinoflagellates
Toxins, 2021 As a sequel to our previous report of the existence of species-specific protein/peptide expression profiles (PEPs) acquired by mass spectrometry in some dinoflagellates, we established, with the help of a plasma-membrane-impermeable labeling agent, a ...
Hang-Kin Kong +2 more
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OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy [PDF]
Genome Biology, 2015 AbstractIdentifying homology relationships between sequences is fundamental to biological research. Here we provide a novel orthogroup inference algorithm called OrthoFinder that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy.
Emms, D, Kelly, S
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Comparative genomics of microalgae: molecular mechanisms underlying efficient CO₂ assimilation [PDF]
BMC GenomicsRising atmospheric CO₂ levels necessitate the development of effective carbon capture strategies. Some species of microalgae, with their high growth rates and exceptional CO₂ fixation efficiency—up to 10–50 times greater than terrestrial plants—represent
Jessica Di Martino +11 more
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RedoxiBase: A database for ROS homeostasis regulated proteins
Redox Biology, 2019 We present a new database, specifically devoted to ROS homeostasis regulated proteins. This database replaced our previous database, the PeroxiBase, which was focused only on various peroxidase families.
Qiang Li +2 more
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Applications in Plant SciencesPremise Orthology inference is crucial for comparative genomics, and multiple algorithms have been developed to identify putative orthologs for downstream analyses.
Irene T. Liao +3 more
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BMC Genomics, 2019 Background Salmonid fishes are characterised by a very high level of variation in trophic, ecological, physiological, and life history adaptations. Some salmonid taxa show exceptional potential for fast, within-lake diversification into morphologically ...
Kevin Schneider +2 more
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PLoS ONEThe colonial green microalga Botryococcus braunii is well known for producing liquid hydrocarbons that can be utilized as biofuel feedstocks. B. braunii is taxonomically classified as a single species made up of three chemical races, A, B, and L, that ...
Timothy P Devarenne +2 more
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