Jianhua Ruan

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Chengwei Lei, Ph.D.Department of Computer & Electrical Engineering/Computer Science, California State UniversityVerified email at csub.edu
Lu LiuNorth Dakota State UniversityVerified email at ndsu.edu
Jin, VictorLinda T. and John A. Mellows Endowed Chair, Professor of Biostatistics, Medical College of WisconsinVerified email at mcw.edu
Gary D StormoDept of Genetics, Washington University School of MedicineVerified email at wustl.edu
Chun-Liang ChenProfessorVerified email at uthscsa.edu
Fei GuChildren's hospital boston, Harvard medical schoolVerified email at childrens.harvard.edu
Zhongming ZhaoUniversity of Texas Health Science Center at HoustonVerified email at uth.tmc.edu
Alexander BishopProfessor Cell Systems and Anatomy, University of Texas Health Science Center at San AntonioVerified email at uthscsa.edu
Rui-Lan HuangDpt. of OB/GYN, School of Medicine, College of Medicine and Dpt. of OB/GYN, Shuang Ho Hospital, TMUVerified email at s.tmu.edu.tw
Timothy R. HughesUniversity of TorontoVerified email at utoronto.ca
Raquel NorelResearch Staff Member, IBMVerified email at us.ibm.com
Matthew T. WeirauchProfessor, Cincinnati Children's HospitalVerified email at cchmc.org
Thomas CokelaerInstitut PasteurVerified email at pasteur.fr
Julio Saez RodriguezHeidelberg UniversityVerified email at uni-heidelberg.de
Harmen J. BussemakerColumbia UniversityVerified email at columbia.edu
Philip J UrenChief Technology Officer, Episona, Inc.Verified email at episona.com
Tuan-hua David HoDistinguished Research Fellow, Institute of Plant and Microbial Biology, Academia SinicaVerified email at biology.wustl.edu
Rohit JadhavJuvena TherapeuticsVerified email at juvenatherapeutics.com
Andrew D SmithProfessor of Biological Sciences, University of Southern CaliforniaVerified email at smithlabresearch.org
J. Perren Cobb, MD, FACS, FCCMKeck Medicine of USC, Los Angeles, CA, USAVerified email at usc.edu

Jianhua Ruan

Professor at University of Texas - San Antonio

Verified email at cs.utsa.edu

Bioinformatics and Computational Biology


Title Sort by citations Sort by year Sort by title	Cited by Cited by	Year
Characterization and identification of microRNA core promoters in four model species X Zhou, J Ruan, G Wang, W Zhang PLoS computational biology 3 (3), e37, 2007	401	2007
Evaluation of methods for modeling transcription factor sequence specificity MT Weirauch, A Cote, R Norel, M Annala, Y Zhao, TR Riley, ... Nature biotechnology 31 (2), 126-134, 2013	398	2013
An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots J Ruan, GD Stormo, W Zhang Bioinformatics 20 (1), 58-66, 2004	292	2004
A general co-expression network-based approach to gene expression analysis: comparison and applications J Ruan, AK Dean, W Zhang BMC systems biology 4 (1), 8, 2010	268	2010
Identifying network communities with a high resolution J Ruan, W Zhang Physical Review E 77 (1), 016104, 2008	238	2008
A novel link prediction algorithm for reconstructing protein–protein interaction networks by topological similarity C Lei, J Ruan Bioinformatics 29 (3), 355-364, 2013	206	2013
Cis-regulatory element based targeted gene finding: genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana W Zhang, J Ruan, TD Ho, Y You, T Yu, RS Quatrano Bioinformatics 21 (14), 3074-3081, 2005	199	2005
An efficient spectral algorithm for network community discovery and its applications to biological and social networks J Ruan, W Zhang Seventh IEEE international conference on data mining (ICDM 2007), 643-648, 2007	167	2007
Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases M Ray, J Ruan, W Zhang Genome biology 9, 1-14, 2008	124	2008
The regulatory repertoire of PLZF and SALL4 in undifferentiated spermatogonia DL Lovelace, Z Gao, K Mutoji, YC Song, J Ruan, BP Hermann Development 143 (11), 1893-1906, 2016	92	2016
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 PJ Uren, SC Burns, J Ruan, KK Singh, AD Smith, LOF Penalva Journal of Biological Chemistry 286 (43), 37063-37066, 2011	92	2011
Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance M Bi, Z Zhang, YZ Jiang, P Xue, H Wang, Z Lai, X Fu, C De Angelis, ... Nature cell biology 22 (6), 701-715, 2020	85	2020
Plasticity of the systemic inflammatory response to acute infection during critical illness: development of the riboleukogram JE McDunn, KD Husain, AD Polpitiya, A Burykin, J Ruan, Q Li, ... PloS one 3 (2), e1564, 2008	79	2008
Building and analyzing protein interactome networks by cross-species comparisons AM Wiles, M Doderer, J Ruan, TT Gu, D Ravi, B Blackman, AJR Bishop BMC systems biology 4, 1-16, 2010	75	2010
Alterations in the placental methylome with maternal obesity and evidence for metabolic regulation K Mitsuya, AN Parker, L Liu, J Ruan, MCM Vissers, L Myatt PloS one 12 (10), e0186115, 2017	71	2017
Comprehensive methylome analysis of ovarian tumors reveals hedgehog signaling pathway regulators as prognostic DNA methylation biomarkers RL Huang, F Gu, NB Kirma, J Ruan, CL Chen, HC Wang, YP Liao, ... Epigenetics 8 (6), 624-634, 2013	69	2013
A network of conserved damage survival pathways revealed by a genomic RNAi screen D Ravi, AM Wiles, S Bhavani, J Ruan, P Leder, AJR Bishop PLoS genetics 5 (6), e1000527, 2009	65	2009
Intratumoral CD56bright natural killer cells are associated with improved survival in bladder cancer N Mukherjee, N Ji, V Hurez, TJ Curiel, MO Montgomery, AJ Braun, ... Oncotarget 9 (92), 36492, 2018	56	2018
EpCAM-regulated transcription exerts influences on nanomechanical properties of endometrial cancer cells that promote epithelial-to-mesenchymal transition YT Hsu, P Osmulski, Y Wang, YW Huang, L Liu, J Ruan, VX Jin, NB Kirma, ... Cancer research 76 (21), 6171-6182, 2016	55	2016
ILM: a web server for predicting RNA secondary structures with pseudoknots J Ruan, GD Stormo, W Zhang Nucleic acids research 32 (suppl_2), W146-W149, 2004	50	2004

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