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 | 243 | 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 | 199 | 2021 |
Rooting the animal tree of life Y Li, XX Shen, B Evans, CW Dunn, A Rokas Molecular Biology and Evolution, msab170, 2021 | 121 | 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 | 112 | 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 | 81 | 2021 |
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 | 68 | 2015 |
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 | 48 | 2020 |
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 | 48 | 2018 |
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 | 47 | 2017 |
Endosymbiont genomes yield clues of tubeworm success Y Li, MR Liles, KM Halanych The ISME Journal 12 (11), 2785-2795, 2018 | 43 | 2018 |
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 | 39 | 2020 |
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 | 38 | 2021 |
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 | 38 | 2019 |
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 | 32 | 2023 |
Incongruence in the phylogenomics era JL Steenwyk, Y Li, X Zhou, XX Shen, A Rokas Nature Reviews Genetics 24 (12), 834-850, 2023 | 31 | 2023 |
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 | 26 | 2019 |
Multiple introns in a deep-sea Annelid (Decemunciger: Ampharetidae) mitochondrial genome AF Bernardino, Y Li, CR Smith, KM Halanych Scientific reports 7 (1), 4295, 2017 | 23 | 2017 |
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 | 21 | 2019 |
Life in wood: preliminary phylogeny of deep-sea wood-boring bivalves (Xylophagaidae), with descriptions of three new genera and one new species JR Voight, BA Marshall, J Judge, KM Halanych, Y Li, AF Bernardino, ... Journal of Molluscan Studies 85 (2), 232-243, 2019 | 16 | 2019 |
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 | 14* | 2024 |