Publications and presentations
#: Student supervised by Dr. Ruan
IF: ISI Journal Impact Factor
2017 and beyond
- L Liu, J Ruan, Utilizing networks for differential analysis of chromatin interactions, Journal of bioinformatics and computational biology 15 (06), 1740008
- K Mitsuya, AN Parker, L Liu, J Ruan, MCM Vissers, L Myatt, Alterations in the placental methylome with maternal obesity and evidence for metabolic regulation, PloS one 12 (10), e0186115
- Z Gao, L Liu, J Ruan, Logo2PWM: a tool to convert sequence logo to position weight matrix, BMC genomics 18 (6), 709
- L Liu, J Wei, J Ruan, Pathway Enrichment Analysis with Networks, Genes 8 (10), 246
- Z Gao, J Ruan, Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning, Bioinformatics 33 (14), 2097-2105
- J Ruan, MJ Jahid#, F Gu, C Lei#, YW Huang, YT Hsu, DG Mutch, CL Chen, NB Kirma, TH Huang, A novel algorithm for network-based prediction of cancer recurrence Genomics, 2016
SJ Nair, X Zhang, HC Chiang, MJ Jahid#, Y Wang, P Garza, C April, N Salathia, T Banerjee, FS Alenazi#, J Ruan, JB Fan, JD Parvin, VX Jin, Y Hu, R Li, Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development,
Nature communications7:10913, 2016
- DL Lovelace, Z Gao#, K Mutoji, YC Song, J Ruan, BP Hermann, The regulatory repertoire of PLZF and SALL4 in undifferentiated spermatogonia Development 143 (11), 1893-1906, 2016
- YT Hsu, P Osmulski, Y Wang, YW Huang, L Liu#, J Ruan, VX Jin, NB Kirma, Maria E Gaczynska, Tim HM Huang, EpCAM-Regulated Transcription Exerts Influences on Nanomechanical Properties of Endometrial Cancer Cells that Promote Epithelial-to-Mesenchymal Transition Cancer Research, canres. 0752.2016, 2016
- MJ Jahid#, J Ruan Structure-based prediction of drug side effects using a novel classification algorithm International Journal of Computational Biology and Drug Design 9 (1-2), 87-101, 2016
- Z Zhao, Y Liu, Y Huang, K Huang, J Ruan(corresponding author), Editorial: Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015, BMC Systems Biology 10 (S3), 61, 2016
- K Huang, Y Liu, Y Huang, L Li, L Cooper, J Ruan(co-corresponding author), Z Zhao, Editorial: Intelligent Biology and Medicine in 2015: advancing interdisciplinary education, collaboration, and data science, BMC genomics 17 (S7), 524, 2016
- Z Gao#, J Ruan A structure-based Multiple-Instance Learning approach to predicting in vitro transcription factor-DNA interaction BMC genomics 16 (S4), S3, 2015
- J Ruan, V Jin, Y Huang, H Xu, JS Edwards, Y Chen, Z Zhao, Education, collaboration, and innovation: intelligent biology and medicine in the era of big data BMC genomics 16 (Suppl 7), S1, 2015
- Zhao Z, Jin VX, Huang Y, Guda C, Ruan J(corresponding author). Frontiers in Integrative Genomics and Translational Bioinformatics. Biomed Res Int. 2015;2015:725491.
- L Liu#, HY Chung, G Lacatus, S Baliji, J Ruan (co-corresponding author), G Sunter, Altered expression of Arabidopsis genes in response to a multifunctional geminivirus pathogenicity protein BMC plant biology 14 (1), 302, 2014
- MJ Jahid#, TH Huang, and J Ruan, A Personalized Committee Classification Approach to Improving Prediction of Breast Cancer Metastasis, Bioinformatics, 2014 Mar 10. [Epub ahead of print].
- MJ Jahid# and J Ruan, An Ensemble Approach for Drug Side Effect Prediction, IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2013 (regular paper).
- L Liu# and J Ruan, Network-based Pathway Enrichment Analysis, IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2013 (short paper).
- Hsu YT, Gu F, Huang YW, Liu J, Ruan J, Huang RL, Wang CM, Chen CL, Jadhav R, Lai HC, Mutch DG, Goodfellow PJ, Thompson IM Jr, Kirma NB, Huang TH., Promoter hypomethylation of EpCAM-regulated bone morphogenetic protein gene family in recurrent endometrial cancer. Clin Cancer Res. 2013 Sep 27. (IF = 7.837)
- Z Gao#, J Ruan, A structure-based approach to predicting in vitro transcription factor-dna interaction, 2013 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS'11), Nov 17-19 2013, Houston, TX
- C Lei#, S Tamim#, AJR Bishop and J Ruan, Fully automated protein complex prediction based on topological similarity and community structure, Proteome Science, 11(S1):S9 (IF = 2.42)
- RL Huang, F Gu, NB Kirma, J Ruan, CL Chen, HC Wang, YP Liao, CC Chang, MH Yu, JM Pilrose, IM Thompson, HC Huang, THM Huang, HC Lai and KP Nephew, Comprehensive methylome analysis of ovarian tumors reveals hedgehog signaling pathway regulators as prognostic DNA methylation biomarkers, Epigenetics, 8(6):624-634, 2013 (IF = 4.58)
- S Ghosh, K Ashcraft, MJ Jahid#, C April, C Ghajar, J Ruan, H Wang, M Foster, D Hughes, A Ramirez, T Huang, JB Fan, Y Hu, R Li, Regulation of adipose oestrogen output by mechanical stress, Nature Communications, 4:1821, 2013. (IF = 10.015)
- MT Weirauch, A Cote, ..., DREAM5 Consortium (..., C Lei#, ..., J Ruan, ..., ), ..., QD Morris, ML Bulyk, G Stolovitzky, and TR Hughes, Evaluation of methods for the modeling of transcription factor sequence specificity. Nature Biotechnology, 31:126-134, 2013. (IF = 23.3)
- C. Lei# and J. Ruan, A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity, Bioinformatics, 29(3): 355-364, 2013. (IF = 5.47).
- Z Gao#, R Zhao#, and J Ruan, A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks, BMC Genomics, 14 (S1):S4, 2013. This was also presented at the Eleventh Asia Pacific Bioinformatics Conference (APBC) 2013, January 21-23, Vancouver, BC, Canada, 2013. Acceptance rate: 40/105 = 38.1%.
- J Ruan, MJ Jahid#, F Gu, C Lei#, Y Huang, Y Hsu, D Mutch, C Chen, NB Kirma, T Huang. Network-based classification of recurrent endometrial cancers using DNA methylation data. ACM Conference of Bioinformatics, Computational Biology and Biomedicine (ACM BCB), October 7-10, Orlando, Florida, USA 2012 . Acceptance rate: 64/159=40.2%.
- MJ Jahid# and J Ruan, A Steiner tree-based method for biomarker discovery and classification in breast cancer metastasis, BMC Genomics, 13 (S6):S8 (IF = 4.07)
- C Lei# and J Ruan , A random walk based approach for improving protein-protein interaction network and protein complex prediction, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), October 4 - 7, Philadephia, PA, USA 2012 . Acceptance rate: 59/299=19.9%.
- J Sun, H Pan, C Lei#, B Yuan, SJ Nair, C April, B Parameswaran, B Klotzle, JB Fan, J Ruan (co-corresponding author) and R Li. Genetic and genomic analyses of an RNA polymerase II-pausing factor in regulation of mammalian transcription and cell growth, Journal of Biological Chemistry, 286(42):36248-36257 (IF=5.328)
- P.J. Uren, S.C. Burns, J Ruan, K.K. Singh, A.D. Smith and L.O.F. Penalva, Genomic analyses of the RNA binding protein Hu Antigen R (HuR) identify a complex network of target genes and novel characteristics of its binding sites, Journal of Biological Chemistry, 286(43):37063-37066 (IF=5.328)
- J. Ruan, J. Perez#, B. Hernandez#, C. Lei#, G. Sunter and V.M. Sponsel. Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana, BMC Bioinformatics, 12 (Suppl 12):S2.
- M. J. Jahid# and J. Ruan, Identification of biomarkers in breast cancer metastasis by integrating protein-protein interaction network and gene expression data, 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS'11), Dec 4-6 2011, San Antonio, TX
- C. Lei# and J. Ruan, A particle swarm optimization-based algorithm for finding gapped motifs, BioData Mining, 3:9, 2010
- J. Ruan, A.K. Dean# and W. Zhang, A general co-expression network-based approach to gene expression analysis: Comparison and applications, BMC Systems Biology, 4:8, 2010. (IF = 4.06)
- AM Wiles*, M Doderer*, J Ruan (*joint-first author), TT Gu, D Ravi, B Blackman and AJR Bishop, Building and Analyzing Protein Interactome Networks by Cross-species Comparisons, BMC Systems Biology, 4:36, 2010. (IF = 4.06) web server
- J. Ruan, A top-performing algorithm for the DREAM3 gene expression prediction challenge, PLoS ONE 5(2): e8944, 2010 (IF = 4.38)
- S Ghosh, AK Dean#, M Walter, Y Bao, Y Hu, J Ruan and Rong Li, Cell Density-Dependent Transcriptional Activation of Endocrine-Related Genes in Human Adipose Tissue-Derived Stem Cells, Experimental Cell Research, 316(13):2087-2098, 2010. (IF = 3.71)
- J. Ruan, J. Perez#, B. Hernandez#, G. Sunter and V.M. Sponsel. Systematic construction and analysis of co-expression networks for identification of functional modules and cis-regulatory elements, 9th International Workshop on Data Mining in Bioinformatics (BIOKDD'10) , July 25-28 2010, Washington DC, USA, accepted as a full paper. Acceptance rate: 7/29=24%.
- C. Lei# and J. Ruan, Finding gapped motifs by a novel evolutionary algorithm, Proc. of the 8th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBio'10), Istanbul, Turkey, April 7-9 2010. Acceptance rate: 15/40=38%. Best paper award nominee.
- X. Zhou, J. Ruan, W. Zhang, Promoter prediction based on a multiple instance learning scheme , ACM Intern. Conf. on Bioinformatics and Computational Biology (ACM-BCB), Aug. 2-4, 2010, Niagara Falls, NY, USA, accepted as a full paper. Acceptance rate: 37/136=28%.
- A.K. Dean#, S.E. Harris, I. Kalajzic and J. Ruan, A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes, BMC Bioinformatics, 10 (S9):S5, 2009 (IF = 3.78)
- D. Ravi, A.M. Wiles, S. Bhavani, J. Ruan, P. Leder, and A.J.R. Bishop, A network of conserved damage survival pathways revealed by a genomic RNAi screen, PLoS Genetics, 5(6): e1000527, 2009. (IF = 8.88)
- J. Ruan, Y Deng, E.J. Perkins and W. Zhang, An ensemble learning approach to reverse-engineering transcriptional regulatory networks from time-series gene expression data, BMC Genomics, 10(S1):S8, 2009. (IF = 3.93)
- C. Lei# and J. Ruan, A novel swarm intelligence algorithm for finding DNA motifs, International Journal of Computational Biology and Drug Design, 2(4):323 - 339, 2009
- J. Ruan, A fully automated method for discovering community structures in high dimensional data, Proc. of IEEE International Conference on Data Mining (ICDM'09), Miami, FL, USA, Dec. 6-9, 2009. Acceptance rate: 140/786=18%.
- A.K. Dean#, S.E. Harris and J. Ruan, A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes, AMIA Summit on Translational Bioinformatics, San Francisco, CA, March 2009. acceptance rate 17/68 = 25%. (An extended version appared in BMC Bioinformatics, 10 (S9):S5, 2009.)
- M. Ray*, J. Ruan (*joint first author) and W. Zhang, Variations in the transcriptome of Alzheimer's disease reveal modular networks involved in cardiovascular diseases, Genome Biology, 9:R148, 2008. (IF = 6.15)
- J.E. McDunn, K.D. Husain, A.D. Polpitiya, A. Burykin, J. Ruan, Q. Li, W. Schierding, N. Lin, D. Dixon, W. Zhang, C.M. Coopersmith, W.M. Dunne, M. Colonna, B.K. Ghosh, and P. Cobb. Plasticity of the systemic inflammatory response to acute infection during critical illness: Development of the Riboleukogram, PLoS ONE, 3(2):e1564, 2008. (21 Citations)
- J. Ruan and W Zhang, Identifying network community structures with a high resolution, Physical Review E, 77:016104, 2008.(49 Citations)
Supplemental file | Matlab code | In the news | Selected by Virtual Journal of Biological Physics Research.
- C. Lei# and J. Ruan, A Particle Swarm Optimization Algorithm for Finding DNA Sequence Motifs, 1st Workshop on Data Mining in Functional Genomics, in Conjunction with IEEE International Conference on Bioinformatics and Biomedicine (BIBM'08 workshops), Philadelphia, PA, USA, Nov. 5-7, 2008. Acceptance rate: 12/24=50%. (An extended version appeared in International Journal of Computational Biology and Drug Design, 2(4):323 - 339, 2009.)
2007 and before
- X. Zhou*, J. Ruan (*joint first author), G. Wang and W. Zhang, Characterization and identification of microRNA core promoters in four model species, PLoS Computational Biology, 3(3):e37, 2007. (114 Citations)
- J. Ruan and W. Zhang, A Bi-dimensional Regression Tree Approach to the Modeling of Gene Expression Regulation, Bioinformatics, 22(3):332-40, 2006. (16 Citations) Supplementary file
- W. Zhang, J. Ruan , T-h. D. Ho, Y. You, T. Yu and R.S. Quatrano, Cis-regulatory element based targeted gene finding: Genome-wide identification of ABA- and abiotic stress-responsive genes in Arabidopsis thaliana, Bioinformatics, 21(14):3074-81, 2005. (68 Citations)
- J. Ruan and W. Zhang, CAGER: Classification Analysis for Gene Expression Regulation, BMC Bioinformatics, 6:114, 2005. (IF = 4.96) web server
- J. Ruan , G.D. Stormo and W. Zhang, ILM: a web server for predicting RNA secondary structures with pseudoknots, Nucleic Acids Research, 32, W146-9, 2004. (29 Citations) web server
- J. Ruan , G.D. Stormo and W. Zhang, An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots, Bioinformatics, 20(1), 58-66, 2004. (155 Citations) Download software
- J. Ruan and W. Zhang, An efficient spectral algorithm for network community discovery and its applications to biological and social networks, Proc. of IEEE International Conference on Data Mining ( ICDM'07), Omaha, NE, USA, Oct. 28-31, 2007. Acceptance rate: 19%
- J. Ruan and W. Zhang, Identification and evaluation of weak community structures in networks, Proc. of National Conference on Artificial Intelligence (AAAI'06), Boston, MA, July 2006. Acceptance rate: 22% (oral presentation).
- J. Ruan and W. Zhang, Identification and evaluation of functional modules in gene co-expression networks, Proc. of RECOMB Satellite Conference on Systems Biology, San Diego, CA, Dec 2006. Acceptance rate: 40%.
- X. Zhou*, J. Ruan (*joint first author), G. Wang and W. Zhang, Characterization of the promoters of microRNA genes: A genome-scale analysis on C. elegans, A. thaliana and H. sapiens, Proc. of RECOMB Satellite Conference on Regulatory Genomics, San Diego, CA, Dec. 2005. Acceptance rate: 50%. (An extended version appared in PLoS Computational Biology, 3(3):e37, 2007.)