| Greengenes2 unifies microbial data in a single reference tree D McDonald, Y Jiang, M Balaban, K Cantrell, Q Zhu, A Gonzalez, ... Nature biotechnology 42 (5), 715-718, 2024 | 144 | 2024 |
| TreeCluster: Clustering biological sequences using phylogenetic trees M Balaban, N Moshiri, U Mai, X Jia, S Mirarab PloS one 14 (8), e0221068, 2019 | 134 | 2019 |
| Multi-level analysis of the gut–brain axis shows autism spectrum disorder-associated molecular and microbial profiles JT Morton, DM Jin, RH Mills, Y Shao, G Rahman, D McDonald, Q Zhu, ... Nature neuroscience 26 (7), 1208-1217, 2023 | 90 | 2023 |
| APPLES: scalable distance-based phylogenetic placement with or without alignments M Balaban, S Sarmashghi, S Mirarab Systematic Biology 69 (3), 566-578, 2020 | 70 | 2020 |
| Complexity of avian evolution revealed by family-level genomes J Stiller, S Feng, AA Chowdhury, I Rivas-González, DA Duchêne, Q Fang, ... Nature 629 (8013), 851-860, 2024 | 43 | 2024 |
| Fast and accurate distance‐based phylogenetic placement using divide and conquer M Balaban, Y Jiang, D Roush, Q Zhu, S Mirarab Molecular Ecology Resources 22 (3), 1213-1227, 2022 | 36 | 2022 |
| DEPP: deep learning enables extending species trees using single genes Y Jiang, M Balaban, Q Zhu, S Mirarab Systematic Biology 72 (1), 17-34, 2023 | 31 | 2023 |
| Greengenes2 enables a shared data universe for microbiome studies D McDonald, Y Jiang, M Balaban, K Cantrell, Q Zhu, A Gonzalez, ... bioRxiv, 2022.12. 19.520774, 2022 | 28 | 2022 |
| Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT S Sarmashghi, M Balaban, E Rachtman, B Touri, S Mirarab, V Bafna PLoS computational biology 17 (11), e1009449, 2021 | 28 | 2021 |
| In Vivo Imaging of the Segregation of the 2 Chromosomes and the Cell Division Proteins of Rhodobacter sphaeroides Reveals an Unexpected Role for MipZ N Dubarry, CR Willis, G Ball, C Lesterlin, JP Armitage MBio 10 (1), 10.1128/mbio. 02515-18, 2019 | 25 | 2019 |
| The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters E Rachtman, M Balaban, V Bafna, S Mirarab Molecular Ecology Resources 20 (3), 649-661, 2020 | 22 | 2020 |
| Phylogenetic double placement of mixed samples M Balaban, S Mirarab Bioinformatics 36 (Supplement_1), i335-i343, 2020 | 11 | 2020 |
| Generation of accurate, expandable phylogenomic trees with uDance M Balaban, Y Jiang, Q Zhu, D McDonald, R Knight, S Mirarab Nature biotechnology 42 (5), 768-777, 2024 | 10 | 2024 |
| Simulated annealing algorithm for graph coloring A Kose, BA Sonmez, M Balaban arXiv preprint arXiv:1712.00709, 2017 | 8 | 2017 |
| HATCHet2: clone-and haplotype-specific copy number inference from bulk tumor sequencing data MA Myers, BJ Arnold, V Bansal, M Balaban, KM Mullen, S Zaccaria, ... Genome biology 25 (1), 130, 2024 | 5 | 2024 |
| Author correction: Greengenes2 unifies microbial data in a single reference tree D McDonald, Y Jiang, M Balaban, K Cantrell, Q Zhu, A Gonzalez, ... nature biotechnology 42 (5), 813-813, 2024 | 5 | 2024 |
| The gene family-free median of three D Doerr, M Balaban, P Feijão, C Chauve Algorithms for Molecular Biology 12, 1-14, 2017 | 5 | 2017 |
| Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model M Balaban, NA Bristy, A Faisal, MS Bayzid, S Mirarab Bioinformatics Advances 2 (1), vbac055, 2022 | 4 | 2022 |
| Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics C Ma, M Balaban, J Liu, S Chen, MJ Wilson, CH Sun, L Ding, BJ Raphael Nature Methods, 1-9, 2024 | 2 | 2024 |
| Distance-based phylogenetic placement with statistical support NB Hasan, M Balaban, A Biswas, MS Bayzid, S Mirarab Biology 11 (8), 1212, 2022 | 2 | 2022 |
