Dr. Mary Yang

MS, MSECE, PhD.

Selected Publications

Comprehensive Annotation of Bidirectional Promoters Identifies Co-Regulation among Breast and Ovarian Cancer Genes

Mary Yang, L Koehly, L Elnitski

PLoS Computational Biology (official journal of international society of computational biology), Vol. 3, issue 4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1853124 PubMed ID: 17447839, PubMed Central ID: 1853124. Digital Object Identifier, doi: 10.1371/journal.pcbi.0030072.eor, Public Library of Science, April 2007.

Genome-wide detection of a TFIID localization element from an initial human disease mutation

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

Nucleic Acids Research (NAR). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064768, PubMed ID: 21071415. DOI: 10.1093/nar/gkq1035, Oxford, November 2010.

The genome sequence of taurine cattle: a window to ruminant biology and evolution

C Elsik, R Tellam ...Mary Yang, L Chen ...J Yang, F Zhao (The Bovine Genome Sequencing and Analysis Consortium)

Science, Volume 324 issue 5926, p.p. 522-528. PubMed ID: 19390049, https://www.ncbi.nlm.nih.gov/pubmed/19390049 April 2009

Cross-species mapping of bidirectional promoters enables prediction of unannotated 5" UTRs and identification of species-specific transcripts

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

https://GenomeBiology.com/1471-2164/10/189 BMC Genomics, Vol. 10, 189, DOI: 10.1186/1471-2164-10-189. PubMed: 19393065, PubMed Central: PMC2688522, April 2009

Orthology-driven mapping of bidirectional promoters in human and mouse genomics

Mary Yang and L Elnitski

BMC Bioinformatics, Vol. 15. PubMed ID: 25559261, https://www.ncbi.nlm.nih.gov/pubmed/25559261, BioMed Central, December 16, 2014

Invited Talk: A Computational Study of Bidirectional Promoters in the Human Genome.

Mary Yang and L Elnitski

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. https://link.springer.com/chapter/10.1007%2F978-3-540-72031-7_33 Springer May 2007

Diversity of core promoter elements comprising human bidirectional promoters

Mary Yang and L Elnitski

BMC Genomics, Vol. 9, PubMed: 1883179, PubMed Central ID: PMC2559893. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559893, September 2008

Classifying Protein Single Labeled, Multiple Labeled with Protein Functional Classes

Mary Yang, J Yang, O Ersoy

International Journal of General Systems, Volume 36, issue 1, p.p. 91-109. DOI: 10.1080/03081070600950868, Taylor & Francis, January, 2007. https://www.tandfonline.com/doi/abs/10.1080/03081070600950868

The emerging genomics and systems biology research lead to systems genomics studies

Mary Yang, K Yoshigoe, W Yang, X Qin, K. Dunker, Z Chen, H Arabnia, J. Liu, A Niemierko, J. Yang

BMC Genomics, Volume 15, PubMed ID: 25558922, https://www.ncbi.nlm.nih.gov/pubmed/25558922, BioMed Central, 2014

Sequential Bifurcation Methods to Learning Gene Functional Classes

Mary Yang, J Yang, O Ersoy

Advances in Bioinformatics and its Applications, Series in Mathematical Biology and Medicine, Vol. 8, p.p. 264-275, ISBN: 981-256-148-X. https://www.worldscientific.com/doi/abs/10.1142/9789812702098_0024 World Scientific 2005.

Feature Characterization and Testing of Bidirectional Promoters in the Human Genome - Significance and Applications in Human Genome Research

Mary Yang, D King, L Elnitski

Wiley Book: Machine Learning in Bioinformatics, ISBN: 978-0-470-11662-3. Wiley Book Series in Bioinformatics. DOI: 10.1002/9780470397428.ch15. Wiley 2008. https://onlinelibrary.wiley.com/doi/10.1002/9780470397428.ch15/summary

Functional analysis of a novel cis-acting regulatory region within the human ankyrin (ANK-1) gene promoter

K Kaflamme, A Owen, E Devlin, Mary Yang, C. Wong, L Steiner, L Elnitski, P Gallagher, D Bordine

Molecular Cell Biology (MCB), Vol. 30, Issue 14, p.p. 3493-3502,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2897556 DOI: 10.1128/MCB.00119-10. PubMed ID: 20479128 Official journal of American Society of Microbiology, July 2010

MicroRNA and messenger RNA profiling reveals new biomarkers and mechanisms for RDX induced neurotoxicity

Y Deng, J Ai, X Guan, Z Wang, B Yan, D Zhang, C Liu, M Wilbanks, B Escalon, S Meyers, Mary Yang, E Perkins

https://GenomeBiology.com/1471-2164/15/S11/S1, BMC Genomics, Vol. 15. Digital Object Identifier: 10.1186 /1471-2164-15-S11-S1, BioMed Central, 2014

Differential Expression of Human Telomerase Catalytic Subunit mRNA by In Situ Hybridization in Pheochromocytomas

Z Luo, J Li, Y Qin, Y Ma, X Liang, J Xian, D Lu, M Wei, J Yang, Mary Yang, Z. He

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, https://www.ncbi.nlm.nih.gov/pubmed/17525487 Springer December 2006.

Identification of genes and pathways involved in kidney renal clear cell carcinoma

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

https://GenomeBiology.com/1471-2105/15/S17/S2, BMC Bioinformatics, Vol. 15, Digital Object Identifier: 10.1186 /1471-2105-15-S17-S2, BioMed Central, 2014

A Comparative Study of Different Machine Learning Methods on Microarray Gene Expression Data

M Pirooznia, J Yang, Mary Yang, Y Deng

https://GenomeBiology.com/1471-2164/9/S1/S13, BMC Genomics, Vol. 9, PudMed ID18366602, PubMed Central ID: PMC2386055 BioMed Central, March 2008

BindN + for Accurate prediction of DNA and RNA-binding residues from protein sequence features

L Wang, C Huang, Mary Yang, J Yang

BMC Systems Biology, Vol. 4. PubMed ID: 20522253, PubMed Central ID: PMC2880409. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880409, May 2010

Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners

C Oldfield1, J Meng1, J Yang, Mary Yang, V Uversky, A Dunker

BMC Genomics, Vol. 9. PubMed ID: 18366598, PubMed Central ID: PMC2386051 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386051 BioMed Central, March 2008

Combining Support Vector Regression with Feature Selection for Multivariate Calibration

G Li, H Meng, Mary Yang, J Yang

Neural Computing & Applications, Vol. 17. Issue 7, pp 813-820. DOI: 10.1007/s00521-008-0202-6 https://link.springer.com/article/10.1007%2Fs00521-008-0202-6 Springer September 2008.

3D Protein structure prediction with genetic tabu search algorithm

X Zhang, T Wang, H Luo, J Yang, J Tang, Mary Yang

BMC Systems Biology, Vol. 4, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880412 PubMed ID 20522256, PubMed Central ID PMC2880412, BioMed Central May 2010

Prediction of DNA-binding residues from protein sequence information using random forest

L Wang, Mary Yang, J Yang

BMC Genomics, Vol. 10. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709252, PubMed ID: 19594868, PubMed Central ID: PMC2709252. July 2010

Ensemble Voting System for Multi-class Protein Fold Recognition

Y Chen, F Chen, J Yang, Mary Yang

International Journal of Pattern Recognition and Artificial Intelligence. Vol. 22, Issue 4. p.p. 747-763, DOI: 10.1142/S0218001408006454, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709252 World Scientific, June 2008.

A hybrid machine learning-based method for classifying the Cushing’s Syndrome with comorbid adrenocortical lesions

J Yang, Mary Yang, Z Luo, Y Ma, J Li, Y Deng, X Huang

BMC Genomics. Vol. 9, PubMed ID: 18366613, PubMed Central ID: PMC2386065 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386065, BioMed Central, 2008.

A new statistical approach to combining p-values using gamma distribution and its application to genome-wide association study

Z Chen, W Yang, Q Liu, J Yang, J Li, Mary Yang

BMC Bioinformatics, Vol. 15. PubMed ID: 25559433, https://www.ncbi.nlm.nih.gov/pubmed/25559433, Digital Object Identifier: 10.1186 /1471-2164-15-S11-S3, BioMed Central, December 2014.

Selecting subsets of newly extracted features from PCA and PLS in microarray data analysis

G Li, H Bu, Mary Yang, X Zeng, J Yang

BMC Genomics, Vol. 9, PubMed: 18831790, PubMed Central ID: PMC2559889, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559889, BioMed Central, 2008.

Identification of Intrinsically Unstructured Proteins using hierarchical classifier

J Yang, Mary Yang

International Journal of Data Mining and Bioinformatics, Vol. 2, Issue 2. p.p. 121-133, 10.1504/IJDMB.2008.019093, PubMed ID: 18767350. https://www.ncbi.nlm.nih.gov/pubmed/18767350, InderScience 2008.

Comparison of feature selection and classification of MALDI-MS data

Q Liu, A Sung, M Qiao, Z Chen, J Yang, Mary Yang, X Huang, Y Deng

BMC Genomics. Vol. 10, PubMed ID: 19594880, PubMed Central ID: PMC2709264 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709264, BioMed Central, July 2009.

Exploring Protein Functional Relationships Using Genomic Information and Data Mining Techniques

J Yang, Mary Yang, O Ersoy

Lecture Notes in Computer Science, Volume 2714, pp 1073-1080. https://link.springer.com/chapter/10.1007%2F3-540-44989-2_128, Springer, 2003

Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms

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

BMC Bioinformatics, Vol. 15, PubMed ID: 25559210, https://www.ncbi.nlm.nih.gov/pubmed/25559210, BioMed Central, 2014

An Enhanced Lipschitz Embedding Classifier for Multi-Emotion Speech Analysis

M You, G Li, J Yang, Mary Yang

International Journal of Pattern Recognition and Artificial Intelligence, Vol. 23, Issue 8, pp 1685-1700. Digital Object Identifier: 10.1142/S021800140900764. https://www.worldscientific.com/doi/abs/10.1142/S0218001409007764 World Scientific. December, 2009.

Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research

J Yang, Mary Yang, H Arabnia, Y Deng

https://GenomeBiology.com/1471-2164/9/S2/I1 BMC Genomics, Vol. 9. PubMed ID: 18831773, PubMed Central ID: PMC3226104 BioMed Central, 2008.

Dimension reduction with redundant gene elimination for tumor classification

X Zeng, G Li, J Yang, Mary Yang, G Wu

BMC Bioinformatics, Vol. 9, PubMed: 18541601, PubMed Central ID: PMC2423430. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2423430, May 2008

Analyzing adjuvant radiotherapy suggests a non monotonic radio-sensitivity over tumor volumes

J Yang, A Niemierko, Mary Yang, Y Deng

BMC Genomics, Vol. 9, PubMed: 18831800, PubMed Central ID: PMC255899. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559899, May 2008

Irrelevant gene elimination for Partial Least Squares based Dimension Reduction by using feature probes

X Zeng, G Li, G Wu, J Yang, Mary Yang

International Journal of Data Mining and Bioinformatics. Vol. 3, Issue 1. p.p 82-103, https://www.ncbi.nlm.nih.gov/pubmed/19432378 PubMed ID, 19432378. DOI: 10.1504/IJDMB.2009.023886. 2009

Improving predication accuracy of tumor classification by reducing genes discarded during gene selection

J Yang, G Li, H Meng, Mary Yang, Y Deng

BMC Genomics, Vol. 9, PubMed: 183366616, PubMed Central ID: PMC2386068. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386068, BioMed Central, 2008

Asymmetric Bagging and Feature Selection for Activities Prediction of Drug Molecules

G Li, H Meng, W Lu, J Yang, Mary Yang

BMC Bioinformatics, Vol. 9, PubMed ID: 19594877, PubMed Central ID: PMC2709261, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709261, BioMed Central, 2009.

Word-based characterization of promoters involved in human DNA repair pathways

J Lichtenberg, E Jacox, J Welch, K Kurz, X Liang, Mary Yang, F Drews, K Ecker, S Lee, L Elnitski, L Welch

BMC Genomics, Vol. 10, PubMed ID: 18541060, PubMed Central ID: PMC2423448, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2423448, BioMed Central, May 2008.

Feature selection for the imbalanced QSAR problems by using EasyEnsemble

T Liu, G Li, J Yang, Mary Yang

International Journal of Computational Biology and Drug Design, Vol. 1, Issue 4, pp 334-346. PubMed ID: 20063462. https://www.ncbi.nlm.nih.gov/pubmed/20063462, DOI: 10.1504/IJCBDD.2008.022206. Official Journal of International Society of Intelligent Biological Medicine, 2008.

Predicting Protein Disorder by Analyzing Amino Acid Sequence

J Yang, Mary Yang

BMC Genomics. Vol. 9, PubMed ID: 18831799, PubMed Central ID: PMC2559898. SCI-ISI IDS Number: V92JQ. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559898, BioMed Central, September 2008

Developing discriminate model and comparative analysis of differentially expressed genes and pathways for bloodstream samples of diabetes mellitus type 2

C Liu, L Lu, Q Kong, Y Li, H Wu, W Yang, S Xu, X Yang, X Song, J Yang, Mary Yang, Y Deng

BMC Bioinformatics, Vol. 15, PubMed ID: 25559614, https://www.ncbi.nlm.nih.gov/pubmed/25559614, BioMed Central, 2014.

Supervised learning-based tagSNP selection for genome-wide disease classifications

Q Liu, J Yang, Z Chen, Mary Yang, A Sung, X Huang

BMC Genomics. Vol. 9, PubMed ID: 18366619, PubMed Central ID: PMC2386071 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386071, BioMed Central, 2008

Lecture Notes: 2010 and beyond: the decade of high-performance computing for next-generation sequence analysis

Mary Yang, J. Yang

International Journal of Computational Biology and Drug Design, Vol. 2, Issue 2, PubMed ID: 20090171 https://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.

High-throughput next-generation sequencing technologies foster new cutting-edge computing techniques in bioinformatics

Mary Yang, B Athey, H Arabnia, A Sung, Q Liu, J Yang, J Mao, Y Deng

https://GenomeBiology.com/1471-2164/10/S1/I1, BMC Genomics. Vol. 10. PubMed ID: 19594867, PubMed Central ID: PMC2709251. BioMed Central, 2009

Gene regulation mediated by microRNAs in response to green tea polyphenol EGCG in mouse lung cancer

H Zhou, J Chen, C Yang, Mary Yang, Y Deng, H Wang

BMC Genomics, Vol. 15. PubMed ID: 25559244, https://www.ncbi.nlm.nih.gov/pubmed/25559244, Digital Object Identifier: 10.1186 /1471-2164-15-S11-S3, BioMed Central, 2014

Predicting Protein Structure and Function using Machine Learning

Mary Yang, J Yang, O Ersoy

Purdue University School of Electrical and Computer Engineering, On-Line Public Technical Report TR-ECE-05-15. https://docs.lib.purdue.edu/ecetr/69/ Purdue University, West Lafayette, IN, USA 2005.