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Jianhua Ruan, Ph.D. - Publications

Affiliations: 
2007 Washington University, Saint Louis, St. Louis, MO 
Area:
Computer Science, Bioinformatics Biology
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61 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Najnin T, Saimon SH, Sunter G, Ruan J. A Network-Based Approach for Improving Annotation of Transcription Factor Functions and Binding Sites in . Genes. 14. PMID 36833209 DOI: 10.3390/genes14020282  0.33
2020 Adnan N, Lei C, Ruan J. Robust edge-based biomarker discovery improves prediction of breast cancer metastasis. Bmc Bioinformatics. 21: 359. PMID 32998692 DOI: 10.1186/s12859-020-03692-2  0.781
2020 Guerrero J, Regedanz E, Lu L, Ruan J, Bisaro DM, Sunter G. Manipulation of the Plant Host by the Geminivirus AC2/C2 Protein, a Central Player in the Infection Cycle. Frontiers in Plant Science. 11: 591. PMID 32508858 DOI: 10.3389/Fpls.2020.00591  0.331
2020 Bi M, Zhang Z, Jiang YZ, Xue P, Wang H, Lai Z, Fu X, De Angelis C, Gong Y, Gao Z, Ruan J, Jin VX, Marangoni E, Montaudon E, Glass CK, et al. Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance. Nature Cell Biology. PMID 32424275 DOI: 10.1038/S41556-020-0514-Z  0.317
2020 Zand M, Ruan J. Network-Based Single-Cell RNA-Seq Data Imputation Enhances Cell Type Identification. Genes. 11. PMID 32244427 DOI: 10.3390/Genes11040377  0.431
2020 Adnan N, Liu Z, Huang THM, Ruan J. Comparative evaluation of network features for the prediction of breast cancer metastasis. Bmc Medical Genomics. 13: 40. PMID 32241278 DOI: 10.1186/S12920-020-0676-3  0.424
2020 Zand M, Ruan J. Spatial mapping of single cells in the Drosophila embryo from transcriptomic data based on topological consistency F1000research. 9: 1014. DOI: 10.12688/F1000Research.24163.1  0.387
2019 Wu Z, Yan J, Wang K, Liu X, Guo Y, Zhi D, Ruan J, Zhao Z. The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: genomics with bigger data and wider applications. Bmc Genomics. 20: 80. PMID 30712512 DOI: 10.1186/S12864-018-5369-3  0.316
2018 Wang K, Liu X, Guo Y, Wu Z, Zhi D, Ruan J, Zhao Z. The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: systems biology on diverse data types. Bmc Systems Biology. 12: 125. PMID 30577731 DOI: 10.1186/S12918-018-0648-9  0.312
2018 Polusani SR, Huang YW, Huang G, Chen CW, Wang CM, Lin LL, Osmulski P, Lucio ND, Liu L, Hsu YT, Zhou Y, Lin CL, Aguilera-Barrantes I, Valente PT, Kost ER, ... ... Ruan J, et al. Adipokines Deregulate Cellular Communication via Epigenetic Repression of Gap Junction Loci in Obese Endometrial Cancer. Cancer Research. PMID 30389702 DOI: 10.1158/0008-5472.Can-18-1615  0.315
2018 Horning AM, Lin C, Wang Y, Lieberman B, Mahalingam D, Gao M, Wang P, Wang C, Liu Z, Ruan J, Liss MA, Jin VX, Huang TH, Chen C. Abstract 3402: Castration resistance transcriptome in prostate cancer revealed by single-cell RNA-seq Cancer Research. 78: 3402-3402. DOI: 10.1158/1538-7445.Am2018-3402  0.312
2017 Liu L, Ruan J. Utilizing networks for differential analysis of chromatin interactions. Journal of Bioinformatics and Computational Biology. 1740008. PMID 29113562 DOI: 10.1142/S021972001740008X  0.381
2017 Liu L, Wei J, Ruan J. Pathway Enrichment Analysis with Networks. Genes. 8. PMID 28956817 DOI: 10.3390/Genes8100246  0.437
2017 Gao Z, Ruan J. Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning. Bioinformatics (Oxford, England). PMID 28334224 DOI: 10.1093/Bioinformatics/Btx115  0.321
2016 Hsu YT, Osmulski P, Wang Y, Huang YW, Liu L, Ruan J, Jin VX, Kirma NB, Gaczynska ME, Huang TH. EpCAM-Regulated Transcription Exerts Influences on Nanomechanical Properties of Endometrial Cancer Cells that Promote Epithelial-to-Mesenchymal Transition. Cancer Research. PMID 27569206 DOI: 10.1158/0008-5472.Can-16-0752  0.367
2016 Ruan J, Jahid MJ, Gu F, Lei C, Huang YW, Hsu YT, Mutch DG, Chen CL, Kirma NB, Huang TH. A novel algorithm for network-based prediction of cancer recurrence. Genomics. PMID 27453286 DOI: 10.1016/J.Ygeno.2016.07.005  0.78
2016 Zhang W, Zhu M, Wang F, Cao D, Ruan JJ, Su W, Ruan BH. Mono-sulfonated tetrazolium salt based NAD(P)H detection reagents suitable for dehydrogenase and real-time cell viability assays. Analytical Biochemistry. PMID 27387057 DOI: 10.1016/j.ab.2016.06.026  0.311
2016 Lovelace DL, Gao Z, Mutoji K, Song YC, Ruan J, Hermann BP. The regulatory repertoire of PLZF and SALL4 in undifferentiated spermatogonia. Development (Cambridge, England). PMID 27068105 DOI: 10.1242/Dev.132761  0.357
2016 Nair SJ, Zhang X, Chiang HC, Jahid MJ, Wang Y, Garza P, April C, Salathia N, Banerjee T, Alenazi FS, Ruan J, Fan JB, Parvin JD, Jin VX, Hu Y, et al. Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development. Nature Communications. 7: 10913. PMID 26941120 DOI: 10.1038/Ncomms10913  0.339
2016 Zhang X, Nair SJ, Chiang H, Wang Y, Jahid J, Ruan J, Jin VX, Hu Y, Li R. Abstract 2874: Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development Cancer Research. 76: 2874-2874. DOI: 10.1158/1538-7445.Am2016-2874  0.33
2015 Zhao Z, Jin VX, Huang Y, Guda C, Ruan J. Frontiers in Integrative Genomics and Translational Bioinformatics. Biomed Research International. 2015: 725491. PMID 26605336 DOI: 10.1155/2015/725491  0.318
2015 Gao Z, Ruan J. A structure-based Multiple-Instance Learning approach to predicting in vitro transcription factor-DNA interaction. Bmc Genomics. 16: S3. PMID 25917392 DOI: 10.1186/1471-2164-16-S4-S3  0.344
2014 Liu L, Chung HY, Lacatus G, Baliji S, Ruan J, Sunter G. Altered expression of Arabidopsis genes in response to a multifunctional geminivirus pathogenicity protein. Bmc Plant Biology. 14: 302. PMID 25403083 DOI: 10.1186/S12870-014-0302-7  0.338
2014 Zeng YX, Zhang W, Qian CN, Xu RH, Ruan J. The Chinese Journal of Cancer is indexed in Science Citation Index (SCI) expanded. Chinese Journal of Cancer. 33: 367-8. PMID 25313411 DOI: 10.5732/Cjc.014.10115  0.33
2014 Jahid MJ, Huang TH, Ruan J. A personalized committee classification approach to improving prediction of breast cancer metastasis. Bioinformatics (Oxford, England). 30: 1858-66. PMID 24618465 DOI: 10.1093/Bioinformatics/Btu128  0.304
2014 Hsu Y, Gu F, Huang Y, Liu J, Ruan J, Huang R, Wang C, Chen C, Jadhav RR, Wang Y, Jin VX, Lai H, Mutch DG, Goodfellow PJ, Thompson IM, et al. Abstract 1376: EpCAM-mediated hypomethylation of BMP and cell adhesion genes is associated with advanced endometrial cancer Cancer Research. 74: 1376-1376. DOI: 10.1158/1538-7445.Am2014-1376  0.383
2013 Liu L, Ruan J. Network-based Pathway Enrichment Analysis. Proceedings. Ieee International Conference On Bioinformatics and Biomedicine. 218-221. PMID 25327472 DOI: 10.1109/BIBM.2013.6732493  0.326
2013 Lei C, Tamim S, Bishop AJ, Ruan J. Fully automated protein complex prediction based on topological similarity and community structure. Proteome Science. 11: S9. PMID 24564887 DOI: 10.1186/1477-5956-11-S1-S9  0.76
2013 Hsu YT, Gu F, Huang YW, Liu J, Ruan J, Huang RL, Wang CM, Chen CL, Jadhav RR, Lai HC, Mutch DG, Goodfellow PJ, Thompson IM, Kirma NB, Huang TH. Promoter hypomethylation of EpCAM-regulated bone morphogenetic protein gene family in recurrent endometrial cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 19: 6272-85. PMID 24077349 DOI: 10.1158/1078-0432.Ccr-13-1734  0.343
2013 Huang RL, Gu F, Kirma NB, Ruan J, Chen CL, Wang HC, Liao YP, Chang CC, Yu MH, Pilrose JM, Thompson IM, Huang HC, Huang TH, Lai HC, Nephew KP. Comprehensive methylome analysis of ovarian tumors reveals hedgehog signaling pathway regulators as prognostic DNA methylation biomarkers. Epigenetics : Official Journal of the Dna Methylation Society. 8: 624-34. PMID 23774800 DOI: 10.4161/Epi.24816  0.326
2013 Gao Z, Zhao R, Ruan J. A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks. Bmc Genomics. 14: S4. PMID 23368633 DOI: 10.1186/1471-2164-14-S1-S4  0.396
2013 Lei C, Ruan J. A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity. Bioinformatics (Oxford, England). 29: 355-64. PMID 23235927 DOI: 10.1093/Bioinformatics/Bts688  0.762
2012 Jahid MJ, Ruan J. A Steiner tree-based method for biomarker discovery and classification in breast cancer metastasis. Bmc Genomics. 13: S8. PMID 23134806 DOI: 10.1186/1471-2164-13-S6-S8  0.351
2012 Lei Y, Chen J, Zhang W, Fu W, Wu G, Wei H, Wang Q, Ruan J. In vivo investigation on the potential of galangin, kaempferol and myricetin for protection of D-galactose-induced cognitive impairment. Food Chemistry. 135: 2702-7. PMID 22980861 DOI: 10.1016/j.foodchem.2012.07.043  0.301
2012 Zhang WJ, Santini CL, Bernadac A, Ruan J, Zhang SD, Kato T, Li Y, Namba K, Wu LF. Complex spatial organization and flagellin composition of flagellar propeller from marine magnetotactic ovoid strain MO-1. Journal of Molecular Biology. 416: 558-70. PMID 22245577 DOI: 10.1016/j.jmb.2011.12.065  0.345
2012 Wang JG, Ruan J, Li CY, Wang JM, Li Y, Zhai WT, Zhang W, Ye H, Shen NH, Lei KF, Chen XF, Yang XY. Connective tissue growth factor, a regulator related with 10-hydroxy-2-decenoic acid down-regulate MMPs in rheumatoid arthritis. Rheumatology International. 32: 2791-9. PMID 21850473 DOI: 10.1007/s00296-011-1960-5  0.356
2012 Lei C, Ruan J. A random walk based approach for improving protein-protein interaction network and protein complex prediction Proceedings - 2012 Ieee International Conference On Bioinformatics and Biomedicine, Bibm 2012. 337-342. DOI: 10.1109/BIBM.2012.6392693  0.334
2011 Ruan J, Perez J, Hernandez B, Lei C, Sunter G, Sponsel VM. Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana. Bmc Bioinformatics. 12: S2. PMID 22168340 DOI: 10.1186/1471-2105-12-S12-S2  0.763
2011 Huang J, Ruan J, Tang X, Zhang W, Ma H, Zou S. Comparative proteomics and phosphoproteomics analyses of DHEA-induced on hepatic lipid metabolism in broiler chickens. Steroids. 76: 1566-74. PMID 21971421 DOI: 10.1016/j.steroids.2011.09.009  0.346
2011 Uren PJ, Burns SC, Ruan J, Singh KK, Smith AD, Penalva LO. 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. The Journal of Biological Chemistry. 286: 37063-6. PMID 21890634 DOI: 10.1074/Jbc.C111.266882  0.349
2011 Sun J, Pan H, Lei C, Yuan B, Nair SJ, April C, Parameswaran B, Klotzle B, Fan JB, Ruan J, Li R. Genetic and genomic analyses of RNA polymerase II-pausing factor in regulation of mammalian transcription and cell growth. The Journal of Biological Chemistry. 286: 36248-57. PMID 21865163 DOI: 10.1074/Jbc.M111.269167  0.744
2011 Jahid MJ, Ruan J. Identification of biomarkers in breast cancer metastasis by integrating protein-protein interaction network and gene expression data Proceedings - Ieee International Workshop On Genomic Signal Processing and Statistics. 60-63.  0.354
2010 Lei C, Ruan J. A particle swarm optimization-based algorithm for finding gapped motifs. Biodata Mining. 3: 9. PMID 21144057 DOI: 10.1186/1756-0381-3-9  0.774
2010 Ghosh S, Dean A, Walter M, Bao Y, Hu Y, Ruan J, Li R. Cell density-dependent transcriptional activation of endocrine-related genes in human adipose tissue-derived stem cells. Experimental Cell Research. 316: 2087-98. PMID 20420826 DOI: 10.1016/J.Yexcr.2010.04.015  0.332
2010 Wiles AM, Doderer M, Ruan J, Gu TT, Ravi D, Blackman B, Bishop AJ. Building and analyzing protein interactome networks by cross-species comparisons. Bmc Systems Biology. 4: 36. PMID 20353594 DOI: 10.1186/1752-0509-4-36  0.344
2010 Ruan J. A top-performing algorithm for the DREAM3 gene expression prediction challenge. Plos One. 5: e8944. PMID 20140212 DOI: 10.1371/Journal.Pone.0008944  0.416
2010 Ruan J, Dean AK, Zhang W. A general co-expression network-based approach to gene expression analysis: comparison and applications. Bmc Systems Biology. 4: 8. PMID 20122284 DOI: 10.1186/1752-0509-4-8  0.532
2009 Lei C, Ruan J. A novel swarm intelligence algorithm for finding DNA motifs. International Journal of Computational Biology and Drug Design. 2: 323-39. PMID 20090174 DOI: 10.1504/Ijcbdd.2009.030764  0.766
2009 Dean AK, Harris SE, Kalajzic I, Ruan J. A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes. Bmc Bioinformatics. 10: S5. PMID 19761575 DOI: 10.1186/1471-2105-10-S9-S5  0.307
2009 Ruan J, Deng Y, Perkins EJ, Zhang W. An ensemble learning approach to reverse-engineering transcriptional regulatory networks from time-series gene expression data. Bmc Genomics. 10: S8. PMID 19594885 DOI: 10.1186/1471-2164-10-S1-S8  0.531
2009 Ravi D, Wiles AM, Bhavani S, Ruan J, Leder P, Bishop AJ. A network of conserved damage survival pathways revealed by a genomic RNAi screen. Plos Genetics. 5: e1000527. PMID 19543366 DOI: 10.1371/Journal.Pgen.1000527  0.354
2008 Ray M, Ruan J, Zhang W. Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases. Genome Biology. 9: R148. PMID 18842138 DOI: 10.1186/Gb-2008-9-10-R148  0.664
2008 Ruan J, Zhang W. Identifying network communities with a high resolution. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 77: 016104. PMID 18351912 DOI: 10.1103/Physreve.77.016104  0.492
2008 McDunn JE, Husain KD, Polpitiya AD, Burykin A, Ruan J, Li Q, Schierding W, Lin N, Dixon D, Zhang W, Coopersmith CM, Dunne WM, Colonna M, Ghosh BK, Cobb JP. Plasticity of the systemic inflammatory response to acute infection during critical illness: development of the riboleukogram. Plos One. 3: e1564. PMID 18270561 DOI: 10.1371/Journal.Pone.0001564  0.371
2007 Zhou X, Ruan J, Wang G, Zhang W. Characterization and identification of microRNA core promoters in four model species. Plos Computational Biology. 3: e37. PMID 17352530 DOI: 10.1371/Journal.Pcbi.0030037  0.605
2007 Ruan J, Zhang W. Identification and evaluation of functional modules in gene co-expression networks Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4532: 57-76.  0.345
2006 Ruan J, Zhang W. A bi-dimensional regression tree approach to the modeling of gene expression regulation. Bioinformatics (Oxford, England). 22: 332-40. PMID 16303796 DOI: 10.1093/Bioinformatics/Bti792  0.503
2005 Zhang W, Ruan J, Ho TH, You Y, Yu T, Quatrano RS. Cis-regulatory element based targeted gene finding: genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana. Bioinformatics (Oxford, England). 21: 3074-81. PMID 15890746 DOI: 10.1093/Bioinformatics/Bti490  0.514
2005 Ruan J, Zhang W. CAGER: classification analysis of gene expression regulation using multiple information sources. Bmc Bioinformatics. 6: 114. PMID 15890068 DOI: 10.1186/1471-2105-6-114  0.507
2004 Ruan J, Stormo GD, Zhang W. ILM: a web server for predicting RNA secondary structures with pseudoknots. Nucleic Acids Research. 32: W146-9. PMID 15215368 DOI: 10.1093/Nar/Gkh444  0.426
2004 Ruan J, Stormo GD, Zhang W. An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics (Oxford, England). 20: 58-66. PMID 14693809 DOI: 10.1093/Bioinformatics/Btg373  0.448
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