TriVote - a novel python package in selecting methylome biomarkers. Submitted.
Manual of TriVote: TriVote-manual.pdf
Python package of TriVote, including the example data and code: TriVote-1-0-0.tar.gz
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MUSTv2: an improved de novo miniature inverted repeat transposable element (MITE) detection program. Submitted.
Supplementary tables S1: MUSTv2-supp.pdf
The software MUSTv2: MUST.r2-4-002.Release.tar.gz
The simulated genome: before and after the insertions of 150 MITE copies.
The software NCBI BLAST version 2.2.11 may be downloaded from here or locally.
The software BLAT version 3.5 may be downloaded from here or locally.
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Dongli Ma, Shan Zhong, Xiaorong Liu, Huirong Mai, Guoqin Mai, Cheng Xu, Fengfeng Zhou#. CD3D and PRKCQ work together to discriminate between B-cell and T-cell acute lymphoblastic leukemia. Computers in Biology and Medicine 77, 16-22.
Supplementary material: bALLt-supp-r2.pdf
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Ruiquan Ge, Guoqin Mai, Pu Wang, Manli Zhou, Youxi Luo, Y Cai, Fengfeng Zhou#. CRISPRdigger: detecting CRISPRs with better direct repeat annotations. Scientific Reports, 2016; 6: 32942.
CRISPR annotation pipeline version 1.007: CRISPRdigger-pipe-v1-007.rar
A package including all the dependent softwares (~350MB): CRISPRdigger-software.rar
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Guoqin Mai, Ruiquan Ge, Guoquan Sun, Qinghan Meng, Fengfeng Zhou#. A comprehensive curation demonstrates the dynamic evolutionary patterns of prokaryotic CRISPRs. BioMed Research International 2016; 2016: 7237053.
Supplementary information: caCRISPR-supp.pdf
Curated CRISPR annotations in FASTA: caCRISPR_20151001.fna
Curated CRISPR annotations in GFF3: caCRISPR_20151001.gff3.rar
DR sequences of curated CRISPR annotations: caCRISPR_dbDR_20151001.fasta
Spacer sequences of curated CRISPR annotations: caCRISPR_dbSpacer_20151001.fasta
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SubLasso: a feature selection and classification R package with a fixed feature subset. Submitted.
Supplementary information: SubLasso-supp.pdf
R packages: SubLasso_1.2.zip (windows) and SubLasso_1.2.tar.gz (linux)
Manual: SubLasso.pdf
Example dataset: GSE9574.rar
Example R scripts: exSubLasso.R and testSubLasso.R
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Miaomiao Zhao, Zhao Zhang, Guoqin Mai, Youxi Luo, Fengfeng Zhou#. jEcho: an Evolved weight vector to CHaracterize the protein's post-translational modification mOtifs. Interdisciplinary Sciences: Computational Life Sciences 7 (2), 194-199.
Supplementary table S1 and figure S1: jEcho-supp.pdf
Software: jEcho.v1
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Zhao Zhang, Ze Wang, Guoqin Mai, Youxi Luo, Miaomiao Zhao, Fengfeng Zhou#. Evolutionary optimization of transcription factor binding motif detection. Advance in Structural Bioinformatics 827, 261-274.
Supplementary figure S1: bDNA-supp.pdf
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Pi Guo, Youxi Luo, Guoqin Mai, Ming Zhang, Guoqing Wang, Miaomiao Zhao, Liming Gao, Fan Li, Fengfeng
Zhou#. Gene Expression Profile based Classification Models of Psoriasis. Genomics.103(1):48-55, 2014.
Supplementary figures S1-S2 and tables S1-S2: cPsoriasis-supp.pdf
3rd rank in the SBV IMPROVER Challenge 2012: cPsoriasis-SBV.pdf
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Meixue Yang, Bin Liu, Miaomiao Zhao, Fan Li, Guoqing Wang, Fengfeng Zhou#. Normalizing electrocardiograms of both healthy persons and cardiovascular disease patients for biometric authentication. PLoS ONE 8(8):e71523, 2013.
Supplementary table S1: STable1.pdf
Matlab source code: bECG-src.rar
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Kaishi Li, Meixue Yang, Gaurav
Sablok, Jianping Fan, Fengfeng
Zhou#. Screening features to improve the class prediction
of acute myeloid leukemia and myelodysplastic syndrome. Gene.
2013 Jan 10;512(2):348-54.
Supplementary data matrix: AML-MDS.data-matrix.1-00.arff.gz
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