Meijers M, Ruchnewitz D, Eberhardt J, Karmakar M, Luksza M, Lassig M
Methods Mol Biol. 2025; 2890:253-290.
PMID: 39890732
DOI: 10.1007/978-1-0716-4326-6_14.
Ratcliff J, Merritt B, Gooden H, Siegers J, Srikanth A, Yann S
Microbiol Spectr. 2024; :e0188024.
PMID: 39508569
PMC: 11623064.
DOI: 10.1128/spectrum.01880-24.
Petros B
Proc Natl Acad Sci U S A. 2024; 121(28):e2410274121.
PMID: 38935582
PMC: 11252975.
DOI: 10.1073/pnas.2410274121.
Meijers M, Ruchnewitz D, Eberhardt J, Karmakar M, Luksza M, Lassig M
bioRxiv. 2024; .
PMID: 38746108
PMC: 11092427.
DOI: 10.1101/2024.03.19.585703.
Meijers M, Ruchnewitz D, Eberhardt J, Karmakar M, Luksza M, Lassig M
ArXiv. 2024; .
PMID: 38745695
PMC: 11092678.
Virus sequencing performance during the SARS-CoV-2 pandemic: a retrospective analysis of data from multiple rounds of external quality assessment in Austria.
Camp J, Puchhammer-Stockl E, Aberle S, Buchta C
Front Mol Biosci. 2024; 11:1327699.
PMID: 38375507
PMC: 10875003.
DOI: 10.3389/fmolb.2024.1327699.
A framework for automated scalable designation of viral pathogen lineages from genomic data.
McBroome J, de Bernardi Schneider A, Roemer C, Wolfinger M, Hinrichs A, OToole A
Nat Microbiol. 2024; 9(2):550-560.
PMID: 38316930
PMC: 10847047.
DOI: 10.1038/s41564-023-01587-5.
The ongoing evolution of UShER during the SARS-CoV-2 pandemic.
Hinrichs A, Ye C, Turakhia Y, Corbett-Detig R
Nat Genet. 2023; 56(1):4-7.
PMID: 38155331
DOI: 10.1038/s41588-023-01622-5.
Fast and Accurate Maximum-Likelihood Estimation of Multi-Type Birth-Death Epidemiological Models from Phylogenetic Trees.
Zhukova A, Hecht F, Maday Y, Gascuel O
Syst Biol. 2023; 72(6):1387-1402.
PMID: 37703335
PMC: 10924745.
DOI: 10.1093/sysbio/syad059.
Immune landscape and redox imbalance during neurological disorders in COVID-19.
Thakur A, Sharma V, Averbek S, Liang L, Pandya N, Kumar G
Cell Death Dis. 2023; 14(9):593.
PMID: 37673862
PMC: 10482955.
DOI: 10.1038/s41419-023-06102-6.
Whole-Genome Sequencing Revealed the Fusion Plasmids Capable of Transmission and Acquisition of Both Antimicrobial Resistance and Hypervirulence Determinants in Multidrug-Resistant Isolates.
Shelenkov A, Mikhaylova Y, Voskanyan S, Egorova A, Akimkin V
Microorganisms. 2023; 11(5).
PMID: 37317293
PMC: 10222915.
DOI: 10.3390/microorganisms11051314.
LAPIS is a fast web API for massive open virus sequencing data.
Chen C, Taepper A, Engelniederhammer F, Kellerer J, Roemer C, Stadler T
BMC Bioinformatics. 2023; 24(1):232.
PMID: 37277732
PMC: 10240112.
DOI: 10.1186/s12859-023-05364-3.
Web Resources for SARS-CoV-2 Genomic Database, Annotation, Analysis and Variant Tracking.
Cheng Y, Ji C, Zhou H, Zheng H, Wu A
Viruses. 2023; 15(5).
PMID: 37243244
PMC: 10222785.
DOI: 10.3390/v15051158.
HaploCoV: unsupervised classification and rapid detection of novel emerging variants of SARS-CoV-2.
Chiara M, Horner D, Ferrandi E, Gissi C, Pesole G
Commun Biol. 2023; 6(1):443.
PMID: 37087497
PMC: 10122080.
DOI: 10.1038/s42003-023-04784-4.
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.
Inferring phylogenies from pandemic-scale genome datasets.
Nat Genet. 2023; 55(5):734-735.
PMID: 37045912
PMC: 10092920.
DOI: 10.1038/s41588-023-01370-6.
Maximum likelihood pandemic-scale phylogenetics.
De Maio N, Kalaghatgi P, Turakhia Y, Corbett-Detig R, Minh B, Goldman N
Nat Genet. 2023; 55(5):746-752.
PMID: 37038003
PMC: 10181937.
DOI: 10.1038/s41588-023-01368-0.
Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations.
Layan M, Muller N, Dellicour S, De Maio N, Bourhy H, Cauchemez S
Virus Evol. 2023; 9(1):vead010.
PMID: 36860641
PMC: 9969415.
DOI: 10.1093/ve/vead010.
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations.
Gangavarapu K, Latif A, Mullen J, Alkuzweny M, Hufbauer E, Tsueng G
Nat Methods. 2023; 20(4):512-522.
PMID: 36823332
PMC: 10399614.
DOI: 10.1038/s41592-023-01769-3.
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.
