Mary Yang, MS, MSECE, Ph.D.
Director of MidSouth Bioinformatics Center, Associate Professor and Director,
Joint Bioinformatics Ph.D. Program,
George Washington Donaghey College of Engineering and Information Technology,
University of Arkansas at Little Rock and University of Arkansas for Medical Sciences,
2801 S. University Avenue, Little Rock, Arkansas 72204 U.S.A.
mqyang (at) ualr.edu myang (at) uams.edu
Education and Fellowship
MSECE, Purdue University, West Lafayette, IN USA
M.S., Purdue University, West Lafayette, IN USA
Bilsland Dissertation Fellow and PRF Fellow, Purdue University, West Lafayette, IN USA
Graduate Biostatistics Studies, Johns Hopkins University, Baltimore, MD USA
Certificate of Completion of Post-Doctoral Fellowship, HHS/NIH/NHGRI, Bethesda, MD USA
NIH Fellow, NIH, Bethesda, MD USA
Research Fellow, National Human Genome Research Institute, Bethesda, MD USA
Currently Funded Research Projects:
DEVELOPING INTEGRATIVE APPROACHES FOR IDENTIFYING DISEASE-CAUSING GENES AND DYSFUNCTIONAL NETWORKS, National Institutes of Health, Role: PI.
Developing Integrative Approaches for Identifying Network-Based Cancer Biomarkers Utilizing Multi-Layer Whole-Genome Scale Data, Arkansas Science and Technology Authority, Role: PI
Partnership of Biomedical Research in Arkansas, Joint Bioinformatics Program of UALR-UAMS, National Institutes of Health, Role: Partnership lead research university support, joint bioinformatics graduate program director.
Research Partnership: HHS/FDA/NCTR in Arkansas, and HHS/NIH in Maryland.
Pathway Analysis and Experimental Technologies, Laboratory Rotations, Multivariate Statistics, Statistical Learning, Visual Programming, Algorithms, Data Mining, Machine Intelligence, Molecular Biophysics, Systems Genomics, Ph.D. Dissertation Supervision, Bioinformatics Undergraduate Curriculum, and Graduate Program Development.
Teaching Interest: Synergistic Teaching-Research Model in Integrative Genomics, Bioinformatics and Experimental Technologies, Laboratory Rotations, Multivariate Statistics, Statistical Learning, Visual Programming, Algorithms, Data Mining, Machine Intelligence, Molecular Biophysics, Systems Genomics, Ph.D. Dissertation Supervision, Bioinformatics Undergraduate Curriculum, and Graduate Program Development.
Bio: Dr. Mary Yang received the MS, MSECE and Ph.D. degrees all from Purdue University. She joined the National Human Genome Research Institute in 2005, where she has been working on various projects related to genomics and systems biology. She has been Founding Editor-in-Chief of International Journal of Computational Biology and Drug Design, a NIH PubMed fully indexed journal and is on editorial broads of Journal of Supercomputing and International Journal of Pattern Recognition and Artificial Intelligence. She was recruited to Arkansas as Associate Professor and Director of the Joint Bioinformatics Ph.D. Program of University of Arkansas Little Rock College of Engineering & Information Technology and University of Arkansas for Medical Sciences, and has served on the Steering Committee of NIH funded AR INBRE as bioinformatics core director for the NIH funded research network in the MidSouth region. She is the recipient of the Bilsland Dissertation Fellowship, the Purdue Research Foundation Fellowship, the IEEE and ISIBM Bioinformatics and Bioengineering Outstanding Achievement Awards, the NIH Academic Research Enhancement Award, NIH Fellows Award for Research Excellence and the Basic Science Research Award of Arkansas Science and Technology Authority. Dr. Yang’s systems genomics research laboratory is supported by HHS/NIH, HHS/FDA/NCTR and ASTA.
Selected Publications (from over one hundred peer-viewed publications by relevancy of intelligent computing)
Mary Yang, L Koehly, L Elnitski “Comprehensive Annotation of Bidirectional Promoters Identifies Co-Regulation among Breast and Ovarian Cancer Genes” PLoS Computational Biology (official journal of international society of computational biology), Vol. 3, issue 4. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1853124, Open Access, PubMed ID: 17447839, PubMed Central ID: 1853124. Digital Object Identifier, doi: 10.1371/journal.pcbi.0030072.eor, Public Library of Science, April 2007.
Mary Yang, K Laflamme, V Gotea, C Joiner, N Seidel, C Wong, H Petrykowska, J Lichtenberg, S Lee, L Welch, P Gallagher, D Bodine, L Elnitski “Genome-wide detection of a TFIID localization element from an initial human disease mutation." Nucleic Acids Research (NAR). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064768, Open Access, PubMed ID: 21071415. DOI: 10.1093/nar/gkq1035, Oxford, November 2010.
C Elsik, R Tellam …….Mary Yang, L Chen ….. J Yang, F Zhao (The Bovine Genome Sequencing and Analysis Consortium) “The genome sequence of taurine cattle: a window to ruminant biology and evolution”. Science, Volume 324 issue 5926, p.p. 522-528. PubMed ID: 19390049, http://www.ncbi.nlm.nih.gov/pubmed/19390049 April 2009
H Piontkivska*, Mary Yang* (*equal contribution, stated co-first authors, companion expansion paper to the above Science journal paper), D Larkin, H Lewin, J Reecy, L Elnitski “Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts” Highly accessed http://GenomeBiology.com/1471-2164/10/189 BMC Genomics, Vol. 10, 189, DOI: 10.1186/1471-2164-10-189. Open Access, PubMed: 19393065, PubMed Central: PMC2688522, April 2009
Mary Yang and L Elnitski “Orthology-driven mapping of bidirectional promoters in human and mouse genomics” BMC Bioinformatics, Vol. 15. PubMed ID: 25559261, http://www.ncbi.nlm.nih.gov/pubmed/25559261, Open Access, BioMed Central, December 16, 2014
Mary Yang, L Elnitski “Invited Talk: A Computational Study of Bidirectional Promoters in the Human Genome.” Lecture Notes in Bioinformatics (LNBI), p.p. 361-371, ISBN: 978-3-540-72030-0. Lecture Notes in Computer Science series (LNCS), Volume 4463, DOI: 10.1007/978-3-540-72031-7_33, PubMed ID 20333320, NIH Medline, NIHMSID: NIHMS111963. NIH/NLM PubMed Central ID: PMC2843096. http://link.springer.com/chapter/10.1007%2F978-3-540-72031-7_33 Springer May 2007
Mary Yang, L Elnitski "Diversity of core promoter elements comprising human bidirectional promoters." BMC Genomics, Vol. 9, PubMed: 1883179, PubMed Central ID: PMC2559893. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559893, Open Access, September 2008
Mary Yang, J Yang, O Ersoy “Classifying Protein Single Labeled, Multiple Labeled with Protein Functional Classes.” International Journal of General Systems, Volume 36, issue 1, p.p. 91-109. DOI: 10.1080/03081070600950868, Taylor & Francis, January, 2007. http://www.tandfonline.com/doi/abs/10.1080/03081070600950868
Mary Yang, J Taylor, L Elnitski “Comparative analyses of bidirectional promoters in vertebrates” BMC Bioinformatics, Vol. 9, PubMed ID: 18541062, PubMed Central ID, PMC2423431, http://www.pubfacts.com/detail/18541062/Comparative-analyses-of-bidirectional-promoters-in-vertebrates. Open Access, May 2008
Mary Yang, L Elnitski “Prediction-based approaches to characterize bidirectional promoters in the mammalian genome” BMC Genomics. Vol. 9, PubMed ID: 18366609, PubMed Central ID: PMC2386062, http://www.ncbi.nlm.nih.gov/pubmed/18366609, Open Access, BioMed Central, March 2008
Mary Yang, J Yang, C Codrington “Identification of Transmembrane Proteins Using Variants of the Self-Organizing Feature Map Algorithm” Knowledge Discovery in Bioinformatics: Techniques, Methods, and Applications, Wiley Book Series on Bioinformatics: Computational Techniques and Engineering, Wiley Online Library ISBN: 047177796X, DOI:10.1002/9780470124642.ch14, http://onlinelibrary.wiley.com/doi/10.1002/9780470124642.ch14/summary Wiley, December, 2006.
Mary Yang, K Yoshigoe, W Yang, X Qin, K. Dunker, Z Chen, H Arabnia, J. Liu, A Niemierko, J. Yang “The emerging genomics and systems biology research lead to systems genomics studies” BMC Genomics, Volume 15, PubMed ID: 25558922, http://www.ncbi.nlm.nih.gov/pubmed/25558922, Open Access, BioMed Central, 2014
Mary Yang, J Yang, O Ersoy “Sequential Bifurcation Methods to Learning Gene Functional Classes” Advances in Bioinformatics and its Applications, Series in Mathematical Biology and Medicine, Vol. 8, p.p. 264-275, ISBN: 981-256-148-X. http://www.worldscientific.com/doi/abs/10.1142/9789812702098_0024 World Scientific 2005.
Mary Yang, D King, L Elnitski “Feature Characterization and Testing of Bidirectional Promoters in the Human Genome - Significance and Applications in Human Genome Research”. Wiley Book: Machine Learning in Bioinformatics, ISBN: 978-0-470-11662-3. Wiley Book Series in Bioinformatics. DOI: 10.1002/9780470397428.ch15. Wiley 2008. http://onlinelibrary.wiley.com/doi/10.1002/9780470397428.ch15/summary
K Kaflamme, A Owen, E Devlin, Mary Yang, C. Wong, L Steiner, L Elnitski, P Gallagher, D Bordine "Functional analysis of a novel cis-acting regulatory region within the human ankyrin (ANK-1) gene promoter." Molecular Cell Biology (MCB), Vol. 30, Issue 14, p.p. 3493-3502, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2897556 Open Access, DOI: 10.1128/MCB.00119-10. PubMed ID: 20479128 Official journal of American Society of Microbiology, July 2010
Y Deng, J Ai, X Guan, Z Wang, B Yan, D Zhang, C Liu, M Wilbanks, B Escalon, S Meyers, Mary Yang, E Perkins “MicroRNA and messenger RNA profiling reveals new biomarkers and mechanisms for RDX induced neurotoxicity” Highly accessed http://GenomeBiology.com/1471-2164/15/S11/S1, BMC Genomics, Vol. 15. Open Access, Digital Object Identifier: 10.1186 /1471-2164-15-S11-S1, BioMed Central, 2014
Z Luo, J Li, Y Qin, Y Ma, X Liang, J Xian, D Lu, M Wei, J Yang, Mary Yang, Z. He “Differential Expression of Human Telomerase Catalytic Subunit mRNA by In Situ Hybridization in Pheochromocytomas”. Endocrine Pathology (Official Journal of the Endocrine Pathology Society), Volume 17, Issue 4, pp. 3387-3398, PubMed ID: 17525487, DOI: 10.1007/s12022-006-0010-4, http://www.ncbi.nlm.nih.gov/pubmed/17525487 Springer December 2006.
W Yang, K Yoshigoe, X Qin, J Liu, J Yang, A Niemierko, Y Deng, Y Liu, A Dunker, Z Chen, L Wang, D Xu, H Arabnia, W Tong, Mary Yang “Identification of genes and pathways involved in kidney renal clear cell carcinoma” http://GenomeBiology.com/1471-2105/15/S17/S2, Highly accessed BMC Bioinformatics, Vol. 15, Open Access, Digital Object Identifier: 10.1186 /1471-2105-15-S17-S2, BioMed Central, 2014
M Pirooznia, J Yang, Mary Yang, Y Deng “A Comparative Study of Different Machine Learning Methods on Microarray Gene Expression Data”, Highly accessed, http://GenomeBiology.com/1471-2164/9/S1/S13, BMC Genomics, Vol. 9, PudMed ID18366602, PubMed Central ID: PMC2386055 Open Access, BioMed Central, March 2008
L Wang, C Huang, Mary Yang, J Yang "BindN + for Accurate prediction of DNA and RNA-binding residues from protein sequence features" BMC Systems Biology, Vol. 4. PubMed ID: 20522253, PubMed Central ID: PMC2880409. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880409, Open Access, May 2010
C Oldfield1, J Meng1, J Yang, Mary Yang, V Uversky, A Dunker “Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners” BMC Genomics, Vol. 9. PubMed ID: 18366598, PubMed Central ID: PMC2386051 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386051 Open Access, BioMed Central, March 2008
G Li, H Meng, Mary Yang, J Yang “Combining Support Vector Regression with Feature Selection for Multivariate Calibration” Neural Computing & Applications, Vol. 17. Issue 7, pp 813-820. DOI: 10.1007/s00521-008-0202-6 http://link.springer.com/article/10.1007%2Fs00521-008-0202-6 Springer September 2008.
X Zhang, T Wang, H Luo, J Yang, J Tang, Mary Yang “3D Protein structure prediction with genetic tabu search algorithm” BMC Systems Biology, Vol. 4, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880412 Open Access, PubMed ID 20522256, PubMed Central ID PMC2880412, BioMed Central May 2010
L Wang, Mary Yang, J Yang "Prediction of DNA-binding residues from protein sequence information using random forest" BMC Genomics, Vol. 10. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709252, Open Access, PubMed ID: 19594868, PubMed Central ID: PMC2709252. July 2010
Y Chen, F Chen, J Yang, Mary Yang “Ensemble Voting System for Multi-class Protein Fold Recognition” International Journal of Pattern Recognition and Artificial Intelligence. Vol. 22, Issue 4. p.p. 747-763, DOI: 10.1142/S0218001408006454, http://www.worldscientific.com/doi/abs/10.1142/S0218001408006454 World Scientific, June 2008.
J Yang, Mary Yang, Z Luo, Y Ma, J Li, Y Deng, X Huang "A hybrid machine learning-based method for classifying the Cushing’s Syndrome with comorbid adrenocortical lesions" BMC Genomics. Vol. 9, PubMed ID: 18366613, PubMed Central ID: PMC2386065 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386065, Open Access, BioMed Central, 2008.
Z Chen, W Yang, Q Liu, J Yang, J Li, Mary Yang “A new statistical approach to combining p-values using gamma distribution and its application to genome-wide association study” BMC Bioinformatics, Vol. 15. PubMed ID: 25559433, http://www.ncbi.nlm.nih.gov/pubmed/25559433, Digital Object Identifier: 10.1186 /1471-2164-15-S11-S3, Open Access, BioMed Central, December 2014.
G Li, H Bu, Mary Yang, X Zeng, J Yang "Selecting subsets of newly extracted features from PCA and PLS in microarray data analysis" BMC Genomics, Vol. 9, PubMed: 18831790, PubMed Central ID: PMC2559889, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559889, Open Access, BioMed Central, 2008.
J Yang, Mary Yang “Identification of Intrinsically Unstructured Proteins using hierarchical classifier” International Journal of Data Mining and Bioinformatics, Vol. 2, Issue 2. p.p. 121-133, 10.1504/IJDMB.2008.019093, PubMed ID: 18767350. http://www.ncbi.nlm.nih.gov/pubmed/18767350, InderScience 2008.
Q Liu, A Sung, M Qiao, Z Chen, J Yang, Mary Yang, X Huang, Y Deng "Comparison of feature selection and classification of MALDI-MS data" BMC Genomics. Vol. 10, PubMed ID: 19594880, PubMed Central ID: PMC2709264 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709264, Open Access, BioMed Central, July 2009.
J Yang, Mary Yang, O Ersoy “Exploring Protein Functional Relationships Using Genomic Information and Data Mining Techniques” Lecture Notes in Computer Science, Volume 2714, pp 1073-1080. http://link.springer.com/chapter/10.1007%2F3-540-44989-2_128, Springer, 2003
J Yang, K Dunker, J Liu, X Qin, H Arabnia, W Yang, A Niemierko, Z Chen, Z Luo, L Wang, Y Liu, D Xu, Y Deng, W Tong, Mary Yang “Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms” BMC Bioinformatics, Vol. 15, PubMed ID: 25559210, http://www.ncbi.nlm.nih.gov/pubmed/25559210, Open Access, BioMed Central, 2014
M You, G Li, J Yang, Mary Yang “An Enhanced Lipschitz Embedding Classifier for Multi-Emotion Speech Analysis” International Journal of Pattern Recognition and Artificial Intelligence, Vol. 23, Issue 8, pp 1685-1700. Digital Object Identifier: 10.1142/S021800140900764. http://www.worldscientific.com/doi/abs/10.1142/S0218001409007764 World Scientific. December, 2009.
J Yang, Mary Yang, H Arabnia, Y Deng “Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research” http://GenomeBiology.com/1471-2164/9/S2/I1 Highly accessed, BMC Genomics, Vol. 9. PubMed ID: 18831773, PubMed Central ID: PMC3226104 Open Access, BioMed Central, 2008.
X Zeng, G Li, J Yang, Mary Yang, G Wu "Dimension reduction with redundant gene elimination for tumor classification" BMC Bioinformatics, Vol. 9, PubMed: 18541601, PubMed Central ID: PMC2423430. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2423430, Open Access, May 2008
J Yang, A Niemierko, Mary Yang, Y Deng “Analyzing adjuvant radiotherapy suggests a non monotonic radio-sensitivity over tumor volumes” BMC Genomics, Vol. 9, PubMed: 18831800, PubMed Central ID: PMC255899. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559899, Open Access, May 2008
X Zeng, G Li, G Wu, J Yang, Mary Yang “Irrelevant gene elimination for Partial Least Squares based Dimension Reduction by using feature probes.” International Journal of Data Mining and Bioinformatics. Vol. 3, Issue 1. p.p 82-103, http://www.ncbi.nlm.nih.gov/pubmed/19432378 PubMed ID, 19432378. DOI: 10.1504/IJDMB.2009.023886. 2009
J Yang, G Li, H Meng, Mary Yang, Y Deng "Improving predication accuracy of tumor classification by reducing genes discarded during gene selection" BMC Genomics, Vol. 9, PubMed: 183366616, PubMed Central ID: PMC2386068. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386068, Open Access, BioMed Central, 2008
G Li, H Meng, W Lu, J Yang, Mary Yang “Asymmetric Bagging and Feature Selection for Activities Prediction of Drug Molecules”. BMC Bioinformatics, Vol. 9, PubMed ID: 19594877, PubMed Central ID: PMC2709261, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709261, Open Access, BioMed Central, 2009.
J Lichtenberg, E Jacox, J Welch, K Kurz, X Liang, Mary Yang, F Drews, K Ecker, S Lee, L Elnitski, L Welch “Word-based characterization of promoters involved in human DNA repair pathways” BMC Genomics, Vol. 10, PubMed ID: 18541060, PubMed Central ID: PMC2423448, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2423448, Open Access, BioMed Central, May 2008.
T Liu, G Li, J Yang, Mary Yang “Feature selection for the imbalanced QSAR problems by using EasyEnsemble” International Journal of Computational Biology and Drug Design, Vol. 1, Issue 4, pp 334-346. PubMed ID: 20063462. http://www.ncbi.nlm.nih.gov/pubmed/20063462, DOI: 10.1504/IJCBDD.2008.022206. Official Journal of International Society of Intelligent Biological Medicine, 2008.
J Yang, Mary Yang “Predicting Protein Disorder by Analyzing Amino Acid Sequence” BMC Genomics. Vol. 9, PubMed ID: 18831799, PubMed Central ID: PMC2559898. SCI-ISI IDS Number: V92JQ. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559898, Open Access, BioMed Central, September 2008
C Liu, L Lu, Q Kong, Y Li, H Wu, W Yang, S Xu, X Yang, X Song, J Yang, Mary Yang, Y Deng “Developing discriminate model and comparative analysis of differentially expressed genes and pathways for bloodstream samples of diabetes mellitus type 2”. BMC Bioinformatics, Vol. 15, PubMed ID: 25559614, http://www.ncbi.nlm.nih.gov/pubmed/25559614, Open Access, BioMed Central, 2014.
Q Liu, J Yang, Z Chen, Mary Yang, A Sung, X Huang "Supervised learning-based tagSNP selection for genome-wide disease classifications" BMC Genomics. Vol. 9, PubMed ID: 18366619, PubMed Central ID: PMC2386071 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386071, Open Access, BioMed Central, 2008
Mary Yang, J. Yang “Lecture Notes: 2010 and beyond: the decade of high-performance computing for next-generation sequence analysis” International Journal of Computational Biology and Drug Design, Vol. 2, Issue 2, PubMed ID: 20090171 http://www.ncbi.nlm.nih.gov/pubmed/20090171, DOI:10.1504/IJCBDD.2008.028824, DBLP:journals/ijcbdd/YangY09. Official Journal of International Society of Intelligent Biological Medicine, 2009.
Mary Yang, B Athey, H Arabnia, A Sung, Q Liu, J Yang, J Mao, Y Deng “High-throughput next-generation sequencing technologies foster new cutting-edge computing techniques in bioinformatics”, Highly accessed http://GenomeBiology.com/1471-2164/10/S1/I1, BMC Genomics. Vol. 10. PubMed ID: 19594867, PubMed Central ID: PMC2709251.Open Access, BioMed Central, 2009
H Zhou, J Chen, C Yang, Mary Yang, Y Deng, H Wang “Gene regulation mediated by microRNAs in response to green tea polyphenol EGCG in mouse lung cancer” BMC Genomics, Vol. 15. PubMed ID: 25559244, http://www.ncbi.nlm.nih.gov/pubmed/25559244, Open Access, Digital Object Identifier: 10.1186 /1471-2164-15-S11-S3, BioMed Central, 2014
Mary Yang, J Yang, O Ersoy “Predicting Protein Structure and Function using Machine Learning” Purdue University School of Electrical and Computer Engineering, On-Line Public Technical Report TR-ECE-05-15. http://docs.lib.purdue.edu/ecetr/69/ Open Access, Purdue University, West Lafayette, IN, USA 2005.