Research Fellow/Professor  |  Lin, Chung-Yen  
lab (New window)
Other Achievements
  • POWER, phylogenetics web repeater, NAR, 2005,, Accumulative visits: 16,200, processed sequences: 400,000, since July, 2005, Collected by Expasy phylogenetic platform and other bioinformatic portals.
  • Database of Protein Interactome of Helicobacter pylori, Bioinformatics, 2005,, Accumulative visits: 28,500 since April 2005
  • Database of Protein Interactome of Drosophila melanogaster, BMC bioinformatics, 2006,, Accumulative visits: 120,800 since Dec 2006. And selected by Nucleic Acid Research as one of 2006 Databases collection.
  • PALM, Phylogenetic reconstruction by Automatic Likelihood Model Selector, PLoS ONE, 2009, , Accumulative visits: 3,200 Since Dec, 2009
  • Shrimp Genome Database , PAGE, Marine Biotechnology, 2010,, Accumulated visits: ~900
  • UPS, unique probe selector, for microarray and hybridization probe design, BMC Bioinformatics, 2008,, Accumulative visits: 1930 and processed sequences: 853,000, since Jan 2008
  • myBLAST: A BLAST Web Service and Standalone Program for Customized Databases and Result Analyzer with Parallel Computing, Standalone verion,  Submitted
  • AfterGenBank is an updated, value-added data portal for gene/ protein information derived from the GenBank database.
  • UPS 2.0, Unique Probe Selector for Probe Design and Oligonucleotide Microarrays at the Pangenomic/ Genomic Level,, BMC Genomics, 2010, Accumuative visits: ~1,800
  • Aftergenbank: Extraction of feature sequences from Genbank, Website:
  • Hubba, Hub object analyzer for network biology, NAR 2008,, Accumulative Visits: over 1,950, Since July, 2008. Cited by Nature Review Genetics, Trends in Immunology, Molecular Systems Biology, etc.
  • cytoHubba plug-in for Cytoscape to explore important nodes/hubs in a complex biological network with 11 topological analysis algorithms including Degree, Edge Percolated Component (EPC), Maximum Neighborhood Component (MNC), Density of Maximum Neighborhood Component (DMNC), Maximal Clique Centrality (MCC), Bottleneck (BN), EcCentricity, Closeness, Radiality, Betweenness, and Stress. The number of download activity is around 2,700 since 2009.
  • Primer design Assistant (PDA), for PCR primer design, NAR 2003,, Accumulative visits: ~185,000 and processed sequences: 1,160,000 since July 2003. And several pathogens detection kits were developed by this platform, like SARS, Vibrio parahaemolyticusMicrosporum audouinii and etc.
  • Spotlight is web based framework by implemented an integration method to capture protein complex from biological networks.
  • Multiā€Omics onLine Analysis System (MOLAS): this platform derived from this system will be transferred to Welgene Inc. on early 2015 to serve as transcriptome web database online portal and provide realtime analyses on human  and mouse expression experiments. Reference website:
  • Evidence: EnteroVirus in Deep Conception,  Recombination detection and Genome typing
  • TEA: The epigenomics platform for Arabidopsis
  • Transcriptomics of Coral pocillopora damicornis with symbiodinium
  • Database for Transcriptome of the Acorn Worm
  • Genome and Transcriptome database for Giant Grouper
  • Genome & Transcriptome for Japanese Eel
  • Database for Genome & Transcriptome of Agarwood
  • Cytohubba for Cytoscape 3.0. Since Jan 2017, there are near 4,000 times of downloads from world wide. Meanwhile, the citations related with this work are more than 200 times. For the statistics, please visit