Hagen E, Beaulieu J
Ann Bot. 2024; 134(6):923-932.
PMID: 39297611
PMC: 11687621.
DOI: 10.1093/aob/mcae143.
Akther S, Mongodin E, Morgan R, Di L, Yang X, Golovchenko M
mBio. 2024; 15(9):e0174924.
PMID: 39145656
PMC: 11389397.
DOI: 10.1128/mbio.01749-24.
Shempela D, Chambaro H, Sikalima J, Cham F, Njuguna M, Morrison L
Int J Mol Sci. 2024; 25(12).
PMID: 38928045
PMC: 11203853.
DOI: 10.3390/ijms25126338.
Patane J, Martins Jr J, Setubal J
Methods Mol Biol. 2024; 2802:267-345.
PMID: 38819564
DOI: 10.1007/978-1-0716-3838-5_11.
Fields P, Jalinsky J, Bankers L, McElroy K, Sharbrough J, Higgins C
Genome Biol Evol. 2024; 16(5).
PMID: 38776329
PMC: 11110935.
DOI: 10.1093/gbe/evae091.
Comparative genomics and phylogenomics of the genus (Fabaceae) based on chloroplast genomes.
Wu L, Fan P, Cai J, Zang C, Lin Y, Xu Z
Front Pharmacol. 2024; 15:1371390.
PMID: 38515836
PMC: 10955637.
DOI: 10.3389/fphar.2024.1371390.
ContScout: sensitive detection and removal of contamination from annotated genomes.
Balint B, Merenyi Z, Hegedus B, Grigoriev I, Hou Z, Foldi C
Nat Commun. 2024; 15(1):936.
PMID: 38296951
PMC: 10831095.
DOI: 10.1038/s41467-024-45024-5.
Phylogenomics of the Ecdysteroid Kinase-like (EcKL) Gene Family in Insects Highlights Roles in Both Steroid Hormone Metabolism and Detoxification.
Scanlan J, Robin C
Genome Biol Evol. 2024; 16(2).
PMID: 38291829
PMC: 10859841.
DOI: 10.1093/gbe/evae019.
Automatic annotation of the bHLH gene family in plants.
Thoben C, Pucker B
BMC Genomics. 2023; 24(1):780.
PMID: 38102570
PMC: 10722790.
DOI: 10.1186/s12864-023-09877-2.
Phylogenetic inference of the emergence of sequence modules and protein-protein interactions in the ADAMTS-TSL family.
Dennler O, Coste F, Blanquart S, Belleannee C, Theret N
PLoS Comput Biol. 2023; 19(8):e1011404.
PMID: 37651409
PMC: 10499240.
DOI: 10.1371/journal.pcbi.1011404.
Incongruence in the phylogenomics era.
Steenwyk J, Li Y, Zhou X, Shen X, Rokas A
Nat Rev Genet. 2023; 24(12):834-850.
PMID: 37369847
PMC: 11499941.
DOI: 10.1038/s41576-023-00620-x.
Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree.
Dylus D, Altenhoff A, Majidian S, Sedlazeck F, Dessimoz C
Nat Biotechnol. 2023; 42(1):139-147.
PMID: 37081138
PMC: 10791578.
DOI: 10.1038/s41587-023-01753-4.
Mutation-driven parallel evolution in emergence of ACE2-utilizing sarbecoviruses.
Gao B, Zhu S
Front Microbiol. 2023; 14:1118025.
PMID: 36910184
PMC: 9996049.
DOI: 10.3389/fmicb.2023.1118025.
The Structure of Evolutionary Model Space for Proteins across the Tree of Life.
Scolaro G, Braun E
Biology (Basel). 2023; 12(2).
PMID: 36829559
PMC: 9952988.
DOI: 10.3390/biology12020282.
Four principles to establish a universal virus taxonomy.
Simmonds P, Adriaenssens E, Zerbini F, Abrescia N, Aiewsakun P, Alfenas-Zerbini P
PLoS Biol. 2023; 21(2):e3001922.
PMID: 36780432
PMC: 9925010.
DOI: 10.1371/journal.pbio.3001922.
Read2Tree: scalable and accurate phylogenetic trees from raw reads.
Dylus D, Altenhoff A, Majidian S, Sedlazeck F, Dessimoz C
bioRxiv. 2022; .
PMID: 36561179
PMC: 9774205.
DOI: 10.1101/2022.04.18.488678.
Phylogenomic analysis of 20S proteasome gene family reveals stress-responsive patterns in rapeseed ( L.).
Kumar V, Sharma H, Saini L, Tyagi A, Jain P, Singh Y
Front Plant Sci. 2022; 13:1037206.
PMID: 36388569
PMC: 9659873.
DOI: 10.3389/fpls.2022.1037206.
Progress and Challenges in Studying the Ecophysiology of Archaea.
Adam P, Bornemann T, Probst A
Methods Mol Biol. 2022; 2522:469-486.
PMID: 36125771
DOI: 10.1007/978-1-0716-2445-6_32.
Defining hierarchical protein interaction networks from spectral analysis of bacterial proteomes.
Zaydman M, Little A, Haro F, Aksianiuk V, Buchser W, DiAntonio A
Elife. 2022; 11.
PMID: 35976223
PMC: 9427106.
DOI: 10.7554/eLife.74104.
A Practical Guide to Design and Assess a Phylogenomic Study.
Lozano-Fernandez J
Genome Biol Evol. 2022; 14(9).
PMID: 35946263
PMC: 9452790.
DOI: 10.1093/gbe/evac129.
