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Shihua Zhang - Bioinformatician • Doctorate/PhD
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Shihua Zhang

Bioinformatician • Doctorate/PhD

Chinese Academy of Sciences • Academy of Mathematics and Systems Science • Beijing, China

Skills and expertise

Omics and technologies

  • ChIP-seq analysis
  • scRNA-seq analysis
  • Gene expression microarray analysis

Languages

  • Chinese

Tools maintained

CsreHMM

Algorithm

CsreHMM / cell type-specific regulatory elements by Hidden Markov Model

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Detects cell type-specific regulatory elements (CSREs). CsreHMM is an integrative and comparative method based on a hidden Markov model, that systematically reveals cell type-specific regulatory…
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PBLR

Desktop

PBLR / Population based Bounded Low-Rank

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Enables single-cell RNA sequencing (scRNA-seq) data imputation. PBLR is a cell sub-population based bounded low-rank method that can (1) recover transcriptomic level and dynamics masked by dropouts,…

MSTD

Desktop

MSTD / Multi-Scale Topological Domains

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Detects multi-scale topological domains (MSTD) from both asymmetric and symmetric 3D genomic datasets. MSTD provides two different method able to identify domains with or without possible overlapping…

CSMF

Desktop

CSMF / Common and Specific Matrix Factorization

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Allows extraction of common and specific patterns from the data of two or multiple biological interrelated conditions via matrix factorization. CSMF is a program that can be suitable for analyzing…

SAMO

Desktop

SAMO / Structure Alignment tool based on Multiple Objective optimization

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Aligns protein structures. SAMO is a general algorithm that reveals divergent evolution, detects circular permutations and identifies structural motifs. This method treats the structure alignment in…

JMF

Desktop

JMF / Joint Matrix Factorization

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Contains multi-view data. JMF integrates prior relationship knowledge to simplify pattern identification and data mining.
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ESPCA

Desktop

ESPCA / Edge-group Sparse PCA

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Assists users to analyze high dimensional gene expression data. ESPCA constrains the number of nonzero elements of each principal component (PC) loading via selecting gene interactions (edges). This…

dCMA

Desktop

dCMA / differential Chromatin Modification Analysis

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Identifies cell-type-specific regulatory elements (CSREs) in the human genome. dCMA is a computational framework capable of identifying genomic regions, containing distinctive chromatin modifications…

MIA

Desktop

MIA / Matrix Integration Analysis

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Detects multi-dimensitional modules in diverse genomics data as well as molecular network data. MIA is a MATLAB package that provides various types of genomic data as copy number variation, DNA…
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HTTMM

Desktop

HTTMM / Hierarchical Taxonomy Tree-based Mixture Model

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Estimates the abundance of taxon within a microbial community by incorporating the structure of the taxonomy tree. In this model, genome specific short reads and homologous short reads among genomes…
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SNMNMF

Desktop

SNMNMF

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Serves for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules. SNMNMF is a program that presents the following characteristics: (1) integrates…

SNPLS

Desktop

SNPLS / Sparse Network-regularized Partial Least Squares

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Identifies combinatorial gene-drug co-modules by integrating gene expression and drug response data across a set of cell lines as well as a gene interaction network. We first demonstrated the…