Simon Whelan, Ph.D. - Related publications

Evolutionary Biology Uppsala University, Uppsala, Uppsala län, Sweden 
Molecular Evolution
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Bernard G, Stephens TG, González-Pech RA, Chan CX. Inferring Phylogenomic Relationship of Microbes Using Scalable Alignment-Free Methods. Methods in Molecular Biology (Clifton, N.J.). 2242: 69-76. PMID 33961218 DOI: 10.1007/978-1-0716-1099-2_5   
2021 De Maio N, Weilguny L, Walker CR, Turakhia Y, Corbett-Detig R, Goldman N. phastSim: efficient simulation of sequence evolution for pandemic-scale datasets. Biorxiv : the Preprint Server For Biology. PMID 33758852 DOI: 10.1101/2021.03.15.435416   
2021 Zhang D, Rheindt FE, She H, Cheng Y, Song G, Jia C, Qu Y, Alström P, Lei F. Most genomic loci misrepresent the phylogeny of an avian radiation because of ancient gene flow. Systematic Biology. PMID 33787929 DOI: 10.1093/sysbio/syab024   
2021 Knyshov A, Gordon ERL, Weirauch C. New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics. Peerj. 9: e11019. PMID 33850647 DOI: 10.7717/peerj.11019   
2021 Qian S, Zhang Y, Lee SY. Comparative Analysis of Complete Chloroplast Genome Sequences in (Thymelaeaceae) and New Insights Into Phylogenetic Relationships. Frontiers in Genetics. 12: 643552. PMID 33790948 DOI: 10.3389/fgene.2021.643552   
2021 Qian S, Zhang Y, Lee SY. Comparative Analysis of Complete Chloroplast Genome Sequences in (Thymelaeaceae) and New Insights Into Phylogenetic Relationships. Frontiers in Genetics. 12: 643552. PMID 33790948 DOI: 10.3389/fgene.2021.643552   
2021 Rossier V, Vesztrocy AW, Robinson-Rechavi M, Dessimoz C. OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches. Bioinformatics (Oxford, England). PMID 33787851 DOI: 10.1093/bioinformatics/btab219   
2021 Deng Z, Wang J, Zhang W, Geng Y, Zhao M, Gu C, Fu L, He M, Xiao Q, Xiao W, He L, Yang Q, Han J, Yan X, Yu Z. The Insights of Genomic Synteny and Codon Usage Preference on Genera Demarcation of Family. Frontiers in Microbiology. 12: 657887. PMID 33868215 DOI: 10.3389/fmicb.2021.657887   
2021 Zhou J, Zhang S, Wang J, Shen H, Ai B, Gao W, Zhang C, Fei Q, Yuan D, Wu Z, Tembrock LR, Li S, Gu C, Liao X. Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution. Scientific Reports. 11: 9471. PMID 33947883 DOI: 10.1038/s41598-021-88160-4   
2021 Walker CR, Scally A, De Maio N, Goldman N. Short-range template switching in great ape genomes explored using pair hidden Markov models. Plos Genetics. 17: e1009221. PMID 33651813 DOI: 10.1371/journal.pgen.1009221   
2021 Jiang M, Li Y, Chen H, Wang B, Liu C. Comparative and phylogenetic analysis of the complete chloroplast genome sequences of and . Mitochondrial Dna. Part B, Resources. 6: 1498-1506. PMID 33969207 DOI: 10.1080/23802359.2021.1911700   
2021 Zou Y, Zhu Y, Li Y, Wu FX, Wang J. Parallel computing for genome sequence processing. Briefings in Bioinformatics. PMID 33822883 DOI: 10.1093/bib/bbab070   
2021 Morales-Briones DF, Gehrke B, Huang CH, Liston A, Ma H, Marx HE, Tank DC, Yang Y. Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae). Systematic Biology. PMID 33978764 DOI: 10.1093/sysbio/syab032   
2021 Preuss M, Verbruggen H, West JA, Zuccarello GC. Divergence times and plastid phylogenomics within the intron-rich order erythropeltales (Compsopogonophyceae, Rhodophyta). Journal of Phycology. PMID 33657649 DOI: 10.1111/jpy.13159   
2021 Wei X, Li X, Chen T, Chen Z, Jin Y, Malik K, Li C. Complete chloroplast genomes of Achnatherum inebrians and comparative analyses with related species from Poaceae. Febs Open Bio. PMID 33932143 DOI: 10.1002/2211-5463.13170   
2021 Miao S, Luo Y, Bautista MAC, Chen T. Complete plastid genome characterization and phylogenetic analysis of Wallich ex Wight (Gentianales: Apocynaceae) from Guangdong, China. Mitochondrial Dna. Part B, Resources. 6: 858-859. PMID 33796657 DOI: 10.1080/23802359.2021.1885319   
2021 Snipen L, Angell IL, Rognes T, Rudi K. Reduced metagenome sequencing for strain-resolution taxonomic profiles. Microbiome. 9: 79. PMID 33781324 DOI: 10.1186/s40168-021-01019-8   
2021 Pereira J. GCsnap: interactive snapshots for the comparison of protein-coding genomic contexts. Journal of Molecular Biology. 166943. PMID 33737026 DOI: 10.1016/j.jmb.2021.166943   
2021 Tian P, Xiao J, Jia Z, Guo F, Wang X, Wang W, Wang J, Huang D, Niu W. Complete mitochondrial DNA sequence of the (Scleractinia, Psammocoridae): mitogenome characterisation and phylogenetic implications. Biodiversity Data Journal. 9: e62395. PMID 33911915 DOI: 10.3897/BDJ.9.e62395   
2021 Vasiljevic N, Lim M, Humble E, Seah A, Kratzer A, Morf NV, Prost S, Ogden R. Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification. Forensic Science International. Genetics. 53: 102493. PMID 33770699 DOI: 10.1016/j.fsigen.2021.102493   
2021 Liu B, Sun H, Zhan Q, Gai Y. The complete mitochondrial genome of (Lepidoptera: Pyralidae). Mitochondrial Dna. Part B, Resources. 6: 821-823. PMID 33763590 DOI: 10.1080/23802359.2021.1884016   
2021 Fehrer J, Slavíková R, Paštová L, Josefiová J, Mráz P, Chrtek J, Bertrand YJK. Molecular Evolution and Organization of Ribosomal DNA in the Hawkweed Tribe Hieraciinae (Cichorieae, Asteraceae). Frontiers in Plant Science. 12: 647375. PMID 33777082 DOI: 10.3389/fpls.2021.647375   
2021 Gu H, Zhang P, Xu M, Liang D. Amplicon genome fishing (AGF): a rapid and efficient method for sequencing target cis-regulatory regions in nonmodel organisms. Molecular Genetics and Genomics : Mgg. PMID 33797587 DOI: 10.1007/s00438-021-01775-0   
2021 Li N, Bai JQ, Gao S, Yang L, Li J, Du SB, Wang XP. The complete molecular sequence of chloroplast genome of (L.) Sweet. Mitochondrial Dna. Part B, Resources. 6: 758-759. PMID 33763570 DOI: 10.1080/23802359.2021.1878958   
2021 van Kruistum H, Nijland R, Reznick DN, Groenen MAM, Megens HJ, Pollux BJA. Parallel genomic changes drive repeated evolution of placentas in live-bearing fish. Molecular Biology and Evolution. PMID 33620468 DOI: 10.1093/molbev/msab057   
2021 Lücking R, Aime MC, Robbertse B, Miller AN, Aoki T, Ariyawansa HA, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, et al. Fungal taxonomy and sequence-based nomenclature. Nature Microbiology. PMID 33903746 DOI: 10.1038/s41564-021-00888-x   
2021 Misztal I, Aguilar I, Lourenco D, Ma L, Steibel J, Toro M. Emerging issues in genomic selection. Journal of Animal Science. PMID 33773494 DOI: 10.1093/jas/skab092   
2021 Chase MA, Ellegren H, Mugal CF. Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs. Evolution; International Journal of Organic Evolution. PMID 33851440 DOI: 10.1111/evo.14234   
2021 Ling Q, Cheng L, Li Z, Zhao Y, Wang Y. Characterization of the complete chloroplast genome of a Chinese Endangered species . Mitochondrial Dna. Part B, Resources. 6: 708-709. PMID 33796643 DOI: 10.1080/23802359.2020.1851152   
2021 Perrin A, Rocha EPC. PanACoTA: a modular tool for massive microbial comparative genomics. Nar Genomics and Bioinformatics. 3: lqaa106. PMID 33575648 DOI: 10.1093/nargab/lqaa106   
2021 Park TH. Complete chloroplast genome sequence of the wild diploid potato relative, . Mitochondrial Dna. Part B, Resources. 6: 1189-1191. PMID 33829083 DOI: 10.1080/23802359.2021.1902414   
2021 Zhao Y, Xi Q, Wei X, Fu J, Wang Q, He H, Ling C, Chang T, Zhao Y. The complete chloroplast genome of (L.) Lassen. Mitochondrial Dna. Part B, Resources. 6: 900-901. PMID 33796673 DOI: 10.1080/23802359.2021.1886018   
2021 Ramazzotti D, Angaroni F, Maspero D, Gambacorti-Passerini C, Antoniotti M, Graudenzi A, Piazza R. VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples. Patterns (New York, N.Y.). 2: 100212. PMID 33728416 DOI: 10.1016/j.patter.2021.100212   
2021 Park BK, Ghimire B, Ha YH, Son DC, Kim DK. Complete chloroplast genome of (Ranunculaceae), an endemic species from South Korea. Mitochondrial Dna. Part B, Resources. 6: 1496-1497. PMID 33969206 DOI: 10.1080/23802359.2021.1910080   
2021 Tian L, Mazloom R, Heath LS, Vinatzer BA. LINflow: a computational pipeline that combines an alignment-free with an alignment-based method to accelerate generation of similarity matrices for prokaryotic genomes. Peerj. 9: e10906. PMID 33828908 DOI: 10.7717/peerj.10906   
2021 Jia H, Xu H, Xian W, Li Y, Zhang H. The complete mitochondrial genome of the spiny red gurnard McClelland, 1844 (Scorpaeniformes: Triglidae). Mitochondrial Dna. Part B, Resources. 6: 980-982. PMID 33796707 DOI: 10.1080/23802359.2021.1889412   
2021 Bhattacharyya T, Sowdhamini R. Genome-wide survey of tyrosine phosphatases in thirty mammalian genomes. Cellular Signalling. 110009. PMID 33848580 DOI: 10.1016/j.cellsig.2021.110009   
2021 Sigwart JD, Lindberg DR, Chen C, Sun J. Molluscan phylogenomics requires strategically selected genomes. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 376: 20200161. PMID 33813889 DOI: 10.1098/rstb.2020.0161   
2021 Albanaz ATS, Gerasimov ES, Shaw JJ, Sádlová J, Lukeš J, Volf P, Opperdoes FR, Kostygov AY, Butenko A, Yurchenko V. Genome Analysis of and spp., Closest Phylogenetic Relatives of , Highlights the Role of Amastins in Shaping Pathogenicity. Genes. 12. PMID 33804709 DOI: 10.3390/genes12030444   
2021 Calvelage S, Freuling CM, Fooks AR, Höper D, Marston DA, McElhinney L, Rasmussen TB, Finke S, Beer M, Müller T. Full-Genome Sequences and Phylogenetic Analysis of Archived Danish European Bat Lyssavirus 1 (EBLV-1) Emphasize a Higher Genetic Resolution and Spatial Segregation for Sublineage 1a. Viruses. 13. PMID 33917139 DOI: 10.3390/v13040634   
2021 Lim SY, Jang JH, Lee HJ, Park SS, Kim SR, Lee KM, Kim JK, Park H, Jung HK. Characteristics and phylogenetic analysis of the complete chloroplast genome of (Paeoniaceae). Mitochondrial Dna. Part B, Resources. 6: 734-735. PMID 33763563 DOI: 10.1080/23802359.2020.1860718   
2021 Liu K, Liu S, Chen Y, Liu F, Zhao Y, Chen N. Complete mitochondrial genome of (Mediophyceae, Bacillariophyta). Mitochondrial Dna. Part B, Resources. 6: 1560-1562. PMID 33969218 DOI: 10.1080/23802359.2021.1916409   
2021 Lu H, Tang J, Li D. The complete chloroplast genome sequences of (Cornaceae). Mitochondrial Dna. Part B, Resources. 6: 931-932. PMID 33796687 DOI: 10.1080/23802359.2021.1888333   
2021 Hong J, Gao R, Yang Y. CrepHAN: Cross-species prediction of enhancers by using hierarchical attention networks. Bioinformatics (Oxford, England). PMID 33978703 DOI: 10.1093/bioinformatics/btab349   
2021 Hao Y, Mabry ME, Edger PP, Freeling M, Zheng C, Jin L, VanBuren R, Colle M, An H, Abrahams RS, Washburn JD, Qi X, Barry K, Daum C, Shu S, et al. The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible. Genome Research. PMID 33863805 DOI: 10.1101/gr.270033.120   
2021 Wu H, Ma PF, Li HT, Hu GX, Li DZ. Comparative plastomic analysis and insights into the phylogeny of (Lamiaceae). Plant Diversity. 43: 15-26. PMID 33778221 DOI: 10.1016/j.pld.2020.07.004   
2021 Puri A, Bajaj A, Lal S, Singh Y, Lal R. Phylogenomic Framework for Taxonomic Delineation of spp. and Exploration of Core-Pan Genome. Indian Journal of Microbiology. 61: 180-194. PMID 33927459 DOI: 10.1007/s12088-021-00929-3   
2021 Marchi N, Schlichta F, Excoffier L. Demographic inference. Current Biology : Cb. 31: R276-R279. PMID 33756135 DOI: 10.1016/j.cub.2021.01.053   
2021 Sylverken AA, El-Duah P, Owusu M, Schneider J, Yeboah R, Ayisi-Boateng NK, Gorman R, Adu E, Kwarteng A, Frimpong M, Binger T, Aryeetey S, Asamoah JA, Amoako YA, Amuasi JH, et al. Transmission of SARS-CoV-2 in northern Ghana: insights from whole-genome sequencing. Archives of Virology. PMID 33723631 DOI: 10.1007/s00705-021-04986-3   
2021 Horesh G, Blackwell GA, Tonkin-Hill G, Corander J, Heinz E, Thomson NR. A comprehensive and high-quality collection of genomes and their genes. Microbial Genomics. 7. PMID 33417534 DOI: 10.1099/mgen.0.000499