Our Services

BioKDE (Biomedical Knowledge Discovery Engine) is a powerful Galaxy instance for integrative genomics data analysis, providing a platform for scientists to cope with the big data challenges in biomedical field.

Below is a list of services we currently offer:

RNA-seq, integrative differential gene expression analysis (iDGEA)

We perform several analyses including gene level DGEA, gene set enrichment analysis, GO term enrichment analysis, pathway analysis and network based analysis.

• Y Shi, A Steppi, Y Cao, J Wang, MM He, L Li, J Zhang. Integrative comparison of mRNA expression patterns in breast cancers from Caucasian and Asian Americans with implications for precision medicine. Cancer Research, 2017; 77(2):423-433.
• Yan Li, Albert Steppi, Yidong Zhou, Feng Mao, Philip Craig Miller, Max M. He, Tingting Zhao, Qiang Sun, Jinfeng Zhang*. Tumoral expression of drug and xenobiotic metabolizing enzymes in breast cancer patients of different ethnicities with implications to personalized medicine . Scientific Reports, 2017 7:4747. doi:10.1038/s41598-017-04250-2.
• Paul A. Stewart, Jennifer Luks, Mark D. Roycik, Qing-Xiang Amy Sang, and Jinfeng Zhang (2013) Differentially Expressed Transcripts and Dysregulated Signaling Pathways and Networks in African American Breast Cancer. PLoS One, 8(12): e82460.
• Hamdy EA Ali, Pei-Yau Lung, Andrew B Sholl, Shaimaa A Gad, Juan J Bustamante, Hamed I Ali, Johng S Rhim, Gagan Deep, Jinfeng Zhang, Zakaria Y Abd Elmageed, Dysregulated gene expression predicts tumor aggressiveness in African-American prostate cancer patients, Scientific Reports, 2018, 8, 16335.
• Yuhang Liu, Jinfeng Zhang*, Xing Qiu*. Super-delta: a new differential gene expression analysis procedure with robust data normalization BMC Bioinformatics, 2017, 18:582, https://doi.org/10.1186/s12859-017-1992-2.

Precision medicine, biomarker discovery

Machine learning and deep learning methods will be used to discovery biomarkers for diagnosis and patient stratification.

• Chemotherapy regimen selection, Jinfeng Zhang, Kaixian Yu, Amy Sang, USPTO, 61/950,498, pending.
• Kaixian Yu*, Qing-Xiang Amy Sang, Pei-Yau Lung, Winston Tan, Ty Lively, Cedric Sheffield, Mayassa Bou Dargham, Jun S. Liu*, Jinfeng Zhang*, Personalized chemotherapy selection for breast cancer using gene expression profiles., Scientific Reports, 2017 3;7:43294. doi: 10.1038/srep43294.

DNA methylation

• A DNA methylation pipeline is available on our BioKDE platform.

Segmentation of genomics and epigenomics profiles

An efficient segmentation algorithm has been developed recently by our scientists and showed superior performance than existing methods for peak calling and segmentation. The method can be used to analyze a wide variety of genomics and epigenomics data, including DNA copy number variation, ChIP-seq, DNA-seq, and nucleosome occupancy data.

• Senthil Girimurugan, Yuhang Liu, Pei-Yau Lung, Daniel Vera, Jonathan Dennis, Hank Bass, Jinfeng Zhang, iSeg: an efficient algorithm for segmentation of genomic and epigenomic data. BMC Bioinformatics, 2018, 19(1):131. doi: 10.1186/s12859-018-2140-3.
• Daniel L. Vera, Thelma F. Madzima, Jonathan D. Labonne, Mohammad P. Alam, Gregg G. Hoffman, S.B. Girimurugan, Jinfeng Zhang, Karen M. McGinnis, Jonathan H. Dennis and Hank W. Bass.Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize. The Plant Cell, 2014, 26(10):3883-93.
• Zachary M. Turpin, Daniel L. Vera, Savannah D. Savadel, Pei-Yau Lung, Emily E. Wear, Leigh Mickelson-Young, William F. Thompson, Linda Hanley-Bowdoin, Jonathan H. Dennis, Jinfeng Zhang, Hank W. Bass, Chromatin Structure Profile Data from DNS-seq: Differential Nuclease Sensitivity Mapping of Four Reference Tissues of B73 Maize (Zea mays L). Data in Brief, 2018.
• Sexton, B.S., Avey, D., Druliner, B. R., Fincher, J. A., Grau, D. J., Borowsky, M. L., Gupta, S., Girimurugan, S., Chicken, E., Zhang , J., Noble, W.S., Zhu, F., Kingston, R. E., and Dennis, J. H. (2013) The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed. Genome Research, 10.1101/gr.160150.113.

DNA replication timing data

A proprietary method was developed for cell type identification using DNA replication timing data.

• Fingerprint for cell identity and pluripotency, USPTO, 9,245,090, David Gilbert, Tyrone Ryba, Jinfeng Zhang, 2016.
• Tyrone Ryba, Ichiro Hiratani, Dana Battaglia, Micheal Kulik, Jinfeng Zhang, Stephen Dalton, and David M Gilbert.Replication timing: a fingerprint for cell identity and pluripotency, PLoS Computational Biology, 2011, 7(10): e1002225.
• Tyrone Ryba, Ichiro Hiratani, Junjie Lu, Mari Itoh, Michael Kulik, Jinfeng Zhang, Stephen Dalton, David M. Gilbert. Evolutionarily conserved replication timing profiles distinguish closely related cell types and predict long range chromatin interactions , Genome Research, 20(6):761-70 (2010).

Text mining, information extraction, knowledge discovery

We have developed innovative text mining methods to extract bio-entity relationship information and build knowledge base for automatic hypothesis generation and knowledge discovery.

• Automatic extraction of Bio-entity relationships from literature, USPTO, 8,886,522, Jinfeng Zhang, 2014. USPTO No. 9,542,528, 2017.
• Rajesh Chowdhary, Jinfeng Zhang, Jun S Liu. Bayesian Inference of Protein-protein Interactions from Biological Literature , Bioinformatics, 25(12), 1536-1542 (2009).
• Lindsey Bell, Rajesh Chowdhary, Jun S Liu, Xufeng Niu, Jinfeng Zhang. Integrated bio-entity network: a system for biological knowledge discovery. PLoS ONE, 2011, 6(6): e21474, doi:10.1371/journal.pone.0021474.
• Kaixian Yu, Pei-Yau Lung, Tingting Zhao, Peixiang Zhao, Yan-Yuan Tseng and Jinfeng Zhang. Automatic extraction of protein-protein interactions using grammatical relationship graph, BMC Medical Informatics and Decision Making, 2018, 18 (Suppl 2) :42

DNA-seq and variant calling