| ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference JL Steenwyk, TJ Buida III, Y Li, XX Shen, A Rokas PLoS biology 18 (12), e3001007, 2020 | 365 | 2020 |
| A genome-scale phylogeny of the kingdom Fungi Y Li, JL Steenwyk, Y Chang, Y Wang, TY James, JE Stajich, JW Spatafora, ... Current Biology 31 (8), 1653-1665. e5, 2021 | 260 | 2021 |
| Rooting the animal tree of life Y Li, XX Shen, B Evans, CW Dunn, A Rokas Molecular Biology and Evolution, msab170, 2021 | 139 | 2021 |
| Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota XX Shen, JL Steenwyk, AL LaBella, DA Opulente, X Zhou, J Kominek, Y Li, ... Science Advances 6 (45), eabd0079, 2020 | 129 | 2020 |
| PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data JL Steenwyk, TJ Buida III, AL Labella, Y Li, XX Shen, A Rokas Bioinformatics 37 (16), 2325-2331, 2021 | 126 | 2021 |
| Incongruence in the phylogenomics era JL Steenwyk, Y Li, X Zhou, XX Shen, A Rokas Nature Reviews Genetics 24 (12), 834-850, 2023 | 103 | 2023 |
| Mitogenomics reveals phylogeny and repeated motifs in control regions of the deep-sea family Siboglinidae (Annelida) Y Li, KM Kocot, C Schander, SR Santos, DJ Thornhill, KM Halanych Molecular Phylogenetics and Evolution 85, 221-229, 2015 | 77 | 2015 |
| A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina M Groenewald, CT Hittinger, K Bensch, DA Opulente, XX Shen, Y Li, ... Studies in Mycology 105 (1), 1-22, 2023 | 59 | 2023 |
| Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation N Li, L Bao, T Zhou, Z Yuan, S Liu, R Dunham, Y Li, K Wang, X Xu, Y Jin, ... BMC genomics 19, 1-16, 2018 | 57 | 2018 |
| An investigation of irreproducibility in maximum likelihood phylogenetic inference XX Shen, Y Li, CT Hittinger, X Chen, A Rokas Nature communications 11 (1), 6096, 2020 | 52 | 2020 |
| Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods Y Li, KM Kocot, NV Whelan, SR Santos, DS Waits, DJ Thornhill, ... Zoologica Scripta 46 (2), 200-213, 2017 | 51 | 2017 |
| Mitogenomics reveals phylogenetic relationships of Arcoida (Mollusca, Bivalvia) and multiple independent expansions and contractions in mitochondrial genome size L Kong, Y Li, KM Kocot, Y Yang, L Qi, Q Li, KM Halanych Molecular Phylogenetics and Evolution 150, 106857, 2020 | 49 | 2020 |
| Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi Y Li, MG Tassia, DS Waits, VE Bogantes, KT David, KM Halanych Bmc Biology 17, 1-14, 2019 | 49 | 2019 |
| Endosymbiont genomes yield clues of tubeworm success Y Li, MR Liles, KM Halanych The ISME Journal 12 (11), 2785-2795, 2018 | 48 | 2018 |
| Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates of Aspergillus fumigatus JL Steenwyk, ME Mead, PA de Castro, C Valero, A Damasio, ... Microbiology spectrum 9 (1), 10.1128/spectrum. 00010-21, 2021 | 46 | 2021 |
| Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts DA Opulente, AL LaBella, MC Harrison, JF Wolters, C Liu, Y Li, J Kominek, ... Science 384 (6694), eadj4503, 2024 | 41* | 2024 |
| Metagenomic evidence for the microbial transformation of carboxyl-rich alicyclic molecules: A long-term macrocosm experiment C He, J Liu, R Wang, Y Li, Q Zheng, F Jiao, C He, Q Shi, Y Xu, R Zhang, ... Water Research 216, 118281, 2022 | 28 | 2022 |
| Mitogenomics reveals a novel genetic code in Hemichordata Y Li, KM Kocot, MG Tassia, JT Cannon, M Bernt, KM Halanych Genome biology and evolution 11 (1), 29-40, 2019 | 28 | 2019 |
| Conservation of mitochondrial genome arrangements in brittle stars (Echinodermata, Ophiuroidea) MP Galaska, Y Li, KM Kocot, AR Mahon, KM Halanych Molecular Phylogenetics and Evolution 130, 115-120, 2019 | 25 | 2019 |
| Extensive intragenomic variation in the internal transcribed spacer region of fungi MJ Bradshaw, MC Aime, A Rokas, A Maust, S Moparthi, K Jellings, ... IScience 26 (8), 2023 | 24 | 2023 |
Antonis RokasCornelius Vanderbilt Chair in Biological Sciences, Vanderbilt UniversityVerifierad e-postadress på vanderbilt.edu