Chengbin Peng

Learn More
We analyze the passengers' traffic pattern for 1.58 million taxi trips of Shanghai, China. By employing the non-negative matrix factorization and optimization methods, we find that, people travel on workdays mainly for three purposes: commuting between home and workplace, traveling from workplace to workplace, and others such as leisure activities.(More)
Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k=8∼10); such comprehensive binding affinity data usually need to be reduced and(More)
MOTIVATION Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-Seq) measures the genome-wide occupancy of transcription factors in vivo. Different combinations of DNA-binding protein occupancies may result in a gene being expressed in different tissues or at different developmental stages. To fully understand the functions of(More)
The K-core of a graph is the largest subgraph within which each node has at least K connections. The key observation of this paper is that the K-core may be much smaller than the original graph while retaining its community structure. Building on this observation, we propose a framework that can accelerate community detection algorithms by first focusing on(More)
Protein-DNA bindings are essential activities. Understanding them forms the basis for further deciphering biological and genetic systems. In particular, the proteinDNA bindings between Transcription Factors (TFs) and Transcription Factor Binding Sites (TFBSs) play a central role in gene transcription. Comprehensive TF-TFBS binding sequence pairs have been(More)
With the prevalence of chromatin immunoprecipitation (ChIP) with sequencing (ChIP-Seq) technology, massive ChIP-Seq data has been accumulated. The ChIP-Seq technology measures the genome-wide occupancy of DNA-binding proteins <italic> in vivo</italic>. It is well-known that different DNA-binding protein occupancies may result in a gene being regulated in(More)
The protein-DNA interactions between transcription factors and transcription factor binding sites are essential activities in gene regulation. To decipher the binding codes, it is a long-standing challenge to understand the binding mechanism across different transcription factor DNA binding families. Past computational learning studies usually focus on(More)