| Interpretation of differential gene expression results of RNA-seq data: review and integration A McDermaid, B Monier, J Zhao, B Liu, Q Ma Briefings in bioinformatics 20 (6), 2044-2054, 2019 | 218 | 2019 |
| Integrative methods and practical challenges for single-cell multi-omics A Ma, A McDermaid, J Xu, Y Chang, Q Ma Trends in biotechnology 38 (9), 1007-1022, 2020 | 155 | 2020 |
| Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes SY Niu, J Yang, A McDermaid, J Zhao, Y Kang, Q Ma Briefings in bioinformatics 19 (6), 1415-1429, 2018 | 78 | 2018 |
| DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses J Yang, X Chen, A McDermaid, Q Ma Bioinformatics 33 (16), 2586-2588, 2017 | 58 | 2017 |
| Predicting outcomes of chronic kidney disease from EMR data based on Random Forest Regression J Zhao, S Gu, A McDermaid Mathematical biosciences 310, 24-30, 2019 | 48 | 2019 |
| An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data B Liu, J Yang, Y Li, A McDermaid, Q Ma Briefings in bioinformatics 19 (5), 1069-1081, 2018 | 47 | 2018 |
| Rootstock effects on scion phenotypes in a ‘Chambourcin’experimental vineyard Z Migicovsky, ZN Harris, LL Klein, M Li, A McDermaid, DH Chitwood, ... Horticulture Research 6, 2019 | 41 | 2019 |
| IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq A Ma, C Wang, Y Chang, FH Brennan, A McDermaid, B Liu, C Zhang, ... Nucleic acids research 48 (W1), W275-W286, 2020 | 35 | 2020 |
| IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis B Monier, A McDermaid, C Wang, J Zhao, A Miller, A Fennell, Q Ma PLoS computational biology 15 (2), e1006792, 2019 | 30 | 2019 |
| A new machine learning-based framework for mapping uncertainty analysis in RNA-Seq read alignment and gene expression estimation A McDermaid, X Chen, Y Zhang, C Wang, S Gu, J Xie, Q Ma Frontiers in Genetics 9, 313, 2018 | 24 | 2018 |
| Differential gene expression in non-transgenic and transgenic “M. 26” apple overexpressing a peach CBF gene during the transition from eco-dormancy to bud break T Artlip, A McDermaid, Q Ma, M Wisniewski Horticulture Research 6, 2019 | 23 | 2019 |
| MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome A Ma, M Sun, A McDermaid, B Liu, Q Ma Bioinformatics 35 (21), 4474-4477, 2019 | 10 | 2019 |
| Improved draft genome sequence of Pseudomonas poae A2-S9, a strain with plant growth-promoting activity Y Xia, S DeBolt, Q Ma, A McDermaid, C Wang, N Shapiro, T Woyke, ... Microbiology resource announcements 8 (15), 10.1128/mra. 00275-19, 2019 | 10 | 2019 |
| ViDGER: An R package for integrative interpretation of differential gene expression results of RNA-seq data A McDermaid, B Monier, J Zhao, Q Ma bioRxiv, 268896, 2018 | 8 | 2018 |
| RECTA: regulon identification based on comparative genomics and transcriptomics analysis X Chen, A Ma, A McDermaid, H Zhang, C Liu, H Cao, Q Ma Genes 9 (6), 278, 2018 | 4 | 2018 |
| GeneQC: A quality control tool for gene expression estimation based on RNA-sequencing reads mapping A McDermaid, X Chen, Y Zhang, J Xie, C Wang, Q Ma BioRxiv, 266445, 2018 | 3 | 2018 |
| IRIS-DGE: an integrated RNA-seq data analysis and interpretation system for differential gene expression B Monier, A McDermaid, J Zhao, A Fennell, Q Ma | 2 | 2018 |
| Improved Draft Genome Sequence of Bacillus sp. Strain YF23, Which Has Plant Growth-Promoting Activity Y Xia, S DeBolt, Q Ma, A McDermaid, C Wang, N Shapiro, T Woyke, ... Microbiology resource announcements 8 (15), 10.1128/mra. 00099-19, 2019 | 1 | 2019 |
| Improved draft genome sequence of Pseudomonas poae A2-S9, a strain with plant growth-promoting activity. Microbiol Resour Announc 8: e00275-19 Y Xia, S DeBolt, Q Ma, A McDermaid, C Wang, N Shapiro, T Woyke, ... | 1 | 2019 |
| Rootstock Effects on Shoot System Phenotypes in Grafted Grapevines Z Migicovsky, A Bozzolo, D Chitwood, A Fennell, Z Harris, LL Klein, ... Plant and Animal Genome XXVII Conference (January 12-16, 2019), 2019 | | 2019 |
