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Supplementary materials of HILab publications

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* co-first authors. # corresponding authors.

pyHIVE, a Health-related Image Feature Extraction system using Python. Submitted.
  • Manual of pyHIVE: pyHIVE-manual-v1-0-3.pdf
  • Python package of pyHIVE, including the example data and code: pyHIVE-v1-0-3.rar (28Mb)
  • Rheumatoid arthritis and schizophrenia epigenetic biomarkers detected by a feature refining algorithm, TriVote. Submitted.
  • Manual of TriVote: TriVote-manual.pdf
  • Python package of TriVote, including the example data and code: TriVote-v1.rar (218Mb)
  • 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.

  • 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

  • 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
  • The pipeline may also be found at GitHub: CRISPRdigger

  • 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

  • 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

    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

    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

    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

    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

  • 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




    © Fengfeng Zhou, Health Informatics Lab, College of Computer Science and Technology, Jilin University.
    Last update: August 7, 2017.