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Items: 13

1.

MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome.

Ma A, Sun M, McDermaid A, Liu B, Ma Q.

Bioinformatics. 2019 May 22. pii: btz414. doi: 10.1093/bioinformatics/btz414. [Epub ahead of print]

PMID:
31116375
2.

Rootstock effects on scion phenotypes in a 'Chambourcin' experimental vineyard.

Migicovsky Z, Harris ZN, Klein LL, Li M, McDermaid A, Chitwood DH, Fennell A, Kovacs LG, Kwasniewski M, Londo JP, Ma Q, Miller AJ.

Hortic Res. 2019 May 1;6:64. doi: 10.1038/s41438-019-0146-2. eCollection 2019.

3.

Improved Draft Genome Sequence of Pseudomonas poae A2-S9, a Strain with Plant Growth-Promoting Activity.

Xia Y, DeBolt S, Ma Q, McDermaid A, Wang C, Shapiro N, Woyke T, Kyrpides NC.

Microbiol Resour Announc. 2019 Apr 11;8(15). pii: e00275-19. doi: 10.1128/MRA.00275-19.

4.

Improved Draft Genome Sequence of Bacillus sp. Strain YF23, Which Has Plant Growth-Promoting Activity.

Xia Y, DeBolt S, Ma Q, McDermaid A, Wang C, Shapiro N, Woyke T, Kyrpides NC.

Microbiol Resour Announc. 2019 Apr 11;8(15). pii: e00099-19. doi: 10.1128/MRA.00099-19.

5.

Predicting outcomes of chronic kidney disease from EMR data based on Random Forest Regression.

Zhao J, Gu S, McDermaid A.

Math Biosci. 2019 Apr;310:24-30. doi: 10.1016/j.mbs.2019.02.001. Epub 2019 Feb 12.

PMID:
30768948
6.

IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis.

Monier B, McDermaid A, Wang C, Zhao J, Miller A, Fennell A, Ma Q.

PLoS Comput Biol. 2019 Feb 14;15(2):e1006792. doi: 10.1371/journal.pcbi.1006792. eCollection 2019 Feb.

7.

A New Machine Learning-Based Framework for Mapping Uncertainty Analysis in RNA-Seq Read Alignment and Gene Expression Estimation.

McDermaid A, Chen X, Zhang Y, Wang C, Gu S, Xie J, Ma Q.

Front Genet. 2018 Aug 14;9:313. doi: 10.3389/fgene.2018.00313. eCollection 2018.

8.

Interpretation of differential gene expression results of RNA-seq data: review and integration.

McDermaid A, Monier B, Zhao J, Liu B, Ma Q.

Brief Bioinform. 2018 Aug 6. doi: 10.1093/bib/bby067. [Epub ahead of print]

PMID:
30099484
9.

RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis.

Chen X, Ma A, McDermaid A, Zhang H, Liu C, Cao H, Ma Q.

Genes (Basel). 2018 May 30;9(6). pii: E278. doi: 10.3390/genes9060278.

10.

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes.

Niu SY, Yang J, McDermaid A, Zhao J, Kang Y, Ma Q.

Brief Bioinform. 2018 Mar 1;19(2):360. doi: 10.1093/bib/bby012. No abstract available.

PMID:
29481588
11.

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes.

Niu SY, Yang J, McDermaid A, Zhao J, Kang Y, Ma Q.

Brief Bioinform. 2018 Nov 27;19(6):1415-1429. doi: 10.1093/bib/bbx051. Review. Erratum in: Brief Bioinform. 2018 Mar 1;19(2):360.

PMID:
28481971
12.

DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses.

Yang J, Chen X, McDermaid A, Ma Q.

Bioinformatics. 2017 Aug 15;33(16):2586-2588. doi: 10.1093/bioinformatics/btx223.

PMID:
28419194
13.

An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data.

Liu B, Yang J, Li Y, McDermaid A, Ma Q.

Brief Bioinform. 2018 Sep 28;19(5):1069-1081. doi: 10.1093/bib/bbx026. Review.

PMID:
28334268

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