Software

WaVPeak is a wavelet smoothing and volume filtering-based method for automatic peak picking in NMR spectra. The program below has three options for the denoising step: 1) wavelet denoising; 2) median-modifie-Wiener-filter (MMWF)-based denoising; and 3) MMWF*-based denoising, where MMWF* is a novel variation of MMWF.

Reference: 

1. Zhi Liu, Ahmed Abbas, Bing-Yi Jing, and Xin Gao. WaVPeak: picking NMR peaks through wavelet transform and volume-based filtering. Bioinformatics (2012), 28(7): 914-920.

2. Carlo V. Cannistraci, Ahmed Abbas, and Xin Gao. Median modified Wiener filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra. Submitted.

SECOM is a rapid and sensitive genome-scale protein domain identification method. 

Reference:

1. Ming Fan, Ka-Chun Wong, Taewoo Ryu, Timothy Ravasi, and Xin Gao. SECOM: a novel hash seed and community detection-based approach for genome-scale protein domain identification. PLoS ONE (2012), doi:  10.1371/journal.pone.0039475

KAUSTNMF is a maximum correntropy criterion-based non-negative matrix factorization package.

Reference:

1. Jingyan Wang, Xiaolei Wang, Quanquan Wang, Xinge You, Yongping Li, and Xin Gao. Non-negative matrix factorization by maximizing correntropy for cancer clustering. BMC Bioinformatics (2013). 14:107.

The program is able to predict the 12 main variants of human poly(A) motifs, i.e., AATAAA, ATTAAA, AAAAAG, AAGAAA, TATAAA, AATACA, AGTAAA, ACTAAA, GATAAA, CATAAA, AATATA, and AATAGA.

Reference:

1. B. Xie, B. Jankovic, V. Bajic, L. Song and X. Gao. Prediction of poly(A) motifs in human DNA sequences. Bioinformatics. (2013). 29(13): i316-i325.

Reference:

1. Hiroyuki Kuwahara, Ming Fan, Suojin Wang and Xin Gao. A framework for scalable parameter estimation of gene
circuit models using structural information. Bioinformatics. (2013). 29(13): i98-i107. [Highlighted by Nature Middle East: http://www.nature.com/nmiddleeast/2013/130731/full/nmiddleeast.2013.118.html]

Reference:

1. Peng Chen, Jinyan Li, Limsoon Wong, Hiroyuki Kuwahara, Jianhua Huang, and Xin Gao. Accurate prediction of hot spot residues through
physicochemical characteristics of amino acid sequences. PROTEINS. (2013). 81(8): 1351-1362.

LigandRFs is a random forest-based approach to predict protein-ligand binding sites.

Reference:

1. Peng Chen, Jianhua Huang, and Xin Gao. LigandRFs: predict ligand-binding sites from sequence information through random forests. Submitted.

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iDTP is a novel integrated strucutre- and system-based approach of drug-target prediction to enable the large-scale discovery of new targets for small molecules, such as pharmaceutical drugs, co-factors and metabolites.

Reference:

1. Hammad Naveed, Umar Hameed, Deborah Harrus, William Bourguet, Stefan Arold, and Xin Gao. "An integrated structure- and system-based framework to identify new targets of metabolites and known drugs". Bioinformatics. In press. 

This is a method to form spin systems using 13C labeled NMR spectra, i.e., CBCACON and CBCANCO.

Reference:

1. Ahmed Abbas, Meshri Alazmi, Xianrong Guo, and Xin Gao. A novel slice-based spin system forming method for 13C NMR spectra. Submitted.

Gracob is a deterministic graph-based biclustering method that is designed to find maximal constant-column biclusters in any given two-dimensional data matrix, particularly growth phenotype data in which each row represents a gene deletion strain and each column represents a stress condition.

Reference:

1. Majed Alzahrani, Hiroyuki Kuwahara, Wei Wang, and Xin Gao. Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data. Submitted.

CMsearch is a protein homology detection method that simultaneously explore protein sequence space and protein structure space by cross-modal learning. 

Reference:

1. Xuefeng Cui, Zhiwu Lu, Sheng Wang, Jingyan Wang, and Xin Gao. CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also structure prediction. Submitted.