Machine Learning and Artificial Intelligence

• L. Yang, R. Chen, S. Goodison, Y. Sun (2021) An efficient and effective method to identify significantly perturbed subnetworks in cancer, Nature Computational Science, 1:79-88.

• W. Wei, J. Liang, X. Guo, P. Song, Y. Sun (2019) Hierarchical division clustering framework for categorical data, Neurocomputing, 341: 118-134.

• W. Zheng, L. Yang, R. Genco, J. Wactawski-Wende, M. Buck, Y. Sun (2019) SENSE: Siamese Neural Network for Sequence Embedding and Alignment-free Comparison, Bioinformatics, 35(11): 1820-1828. (impact factor: 5.5)

• W. Zheng, Q. Mao, R. Genco, J. Wactawski-Wende, M. Buck, Y. Cai, Y. Sun (2019) A Parallel Computational Framework for Ultra-large-scale Sequence Clustering Analysis, Bioinformatics, 35(3), 380-388. (impact factor: 5.5)

• W. Wei, X. Wu, J. Liang, J. Cui, Y. Sun (2018) Discernibility Matrix Based Incremental Attribute Reduction for Dynamic Data, Knowledge-Based Systems, 14: 142-157. (impact factor: 4.5)

• Q. Mao, L. Wang, I. W. Tsang, Y. Sun (2017) Principal Graph and Structure Learning Based on Reversed Graph Embedding, IEEE Trans. on Pattern Analysis and Machine Intelligence, 39(11): 2227-2241. (impact factor: 8.3)

• Q. Mao, W. Zheng, L. Wang, Y. Cai, V. Mai, Y. Sun (2015) Parallel Hierarchical Clustering in Linearithmic Time for Large-scale Sequence Analysis (regular paper), in Proc. IEEE International Conference on Data Mining (ICDM'15), 310-319. (acceptance rate: 19%. Regular paper: 8%)

• Q. Mao, L. Wang, S. Goodison, Y. Sun (2015) Dimensionality Reduction via Graph Structure Learning, in Proc. 21st ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD'15), 765-774. (acceptance rate: 159/819 = 19%)

• Q. Mao, L. Yang, L. Wang, S. Goodison, Y. Sun (2015) SimplePPT: A Simple Principal Tree Algorithm, in Proc. 15th SIAM International Conference on Data Mining (SDM'15), 792-800. (acceptance rate: 22%)

• Y. Sun, J. Yao, S. Goodison (2015) Feature Selection for Nonlinear Regression and its Application to Cancer Research, in Proc. 15th SIAM International Conference on Data Mining (SDM'15), 73-81. (acceptance rate: 22%)

• J. Yao, Q. Mao, V. Mai, S. Goodison, Y. Sun (2015) Feature Selection for Unsupervised Learning through Local Learning, Pattern Recognition Letters, 53: 100-107. (impact factor: 2.0)

• J. Wang, Y. Sun, X. Gao (2015) Sparse Structure Regularized Ranking, Multimedia Tools and Applications, 74(2): 635-654. (impact factor: 1.5)

• J. Wang, J. Huang, Y. Sun, X. Gao (2014) Feature Selection and Multi-kernel Learning for Adaptive Graph Regularized Nonnegative Matrix Factorization, Expert Systems With Applications, 42(3): 1278-1286. (impact factor: 2.3)

• J. Wang, Y. Sun (2014) From One Graph to Many: Ensemble Transduction for Content-based Database Retrieval, Knowledge-Based Systems, 65: 31-37. (impact factor: 2.9)

• J. Wang, Y. Sun, H. Bensmail (2014) Domain Transfer Nonnegative Matrix Factorization, in Proc. International Joint Conference on Neural Networks (IJCNN'14), pp. 3605-3612.

• J. Wang, J. Yao, Y. Sun (2014) Semi-supervised Local-learning-based Feature Selection, in Proc. International Joint Conference on Neural Networks (IJCNN'14), pp. 1942-1948.

• Y. Sun, S. Todorovic, S. Goodison (2010) Local Learning Based Feature Selection for High Dimensional Data Analysis, IEEE Trans. on Pattern Analysis and Machine Intelligence, 32(9): 1610-1626. (impact factor: 6.0, the overall top-ranked IEEE transactions journal) This paper is featured as Spotlight Paper in the September 2010 issue of the journal.

• Y. Cai, Y. Sun, Y. Cheng, J. Li, S. Goodison (2010) Fast Implementation of ℓ1 Regularized Learning Algorithms Using Gradient Descent Methods, in Proc 10th SIAM International Conference on Data Mining (SDM'10), pp. 862-871. (oral presentation/acceptance rate: 82/351 = 23%)

• Y. Cai, Y. Sun, J. Li, S. Goodison (2009) Online Feature Selection Algorithm with Bayesian L-1 Regularization, in Proc. 13th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD'09), pp. 401-413. (oral presentation: 39/338 = 12%)

• Y. Sun, D. Wu (2009) Feature Extraction through Local Learning, Statistical Analysis and Data Mining, 2(1): 34-47.

• Y. Cheng, Y. Cai, Y. Sun, J. Li (2008) Semi-supervised Feature Selection under the Logistic I-RELIEF Framework, in Proc. 19th International Conference on Pattern Recognition (ICPR'08), pp. 1-4. (oral presentation: 18%)

• Y. Sun, D. Wu (2008) A RELIEF Based Feature Extraction Algorithm, in Proc. 8th SIAM International Conference on Data Mining (SDM'08), pp. 188-195. (oral presentation: 40/282 = 13%)

• Y. Sun, S. Todorovic, S. Goodison (2008) A Feature Selection Algorithm Capable of Handling Extremely Large Data Dimensionality, in Proc. 8th SIAM International Conference on Data Mining (SDM'08), pp. 530-540. (acceptance rate: 72/282 = 25%)

• Y. Sun (2007) Iterative RELIEF for Feature Weighting: Algorithms, Theories, and Applications [Website], IEEE Trans. on Pattern Analysis and Machine Intelligence, 29(6): 1035-1051. (impact factor: 6.0)

• Y. Sun, S. Todorovic, J. Li (2007) Unifying Multi-Class AdaBoost Algorithms with Binary Base Learners under the Margin Framework, Pattern Recognition Letters, 28(5): 631-643.

• Y. Sun (2007) Feature Weighting through Local Learning, Computational Methods of Feature Selection, H. Liu and H. Motoda (eds.), Chapman and Hall/CRC Press.

• Y. Sun, Z. Liu, S. Todorovic, J. Li (2007) Adaptive Boosting for Synthetic Aperture Radar Automatic Target Recognition, IEEE Trans. on Aerospace and Electronic Systems, 43(1): 112-125.

• Y. Sun, S. Todorovic, J. Li (2007) Increasing the Robustness of Boosting Algorithms within the Linear-Programming Framework, Journal of VLSI Signal Processing Systems, 48(1-2): 5-20.

• Y. Sun, S. Todorovic, J. Li (2006) Reducing the Overfitting of AdaBoost by Controlling its Data Distribution Skewness, International Journal of Pattern Recognition and Artificial Intelligence, 20(7): 1093-1116.

• Y. Sun, J. Li (2006) Iterative RELIEF for Feature Weighting, in Proc. International Conference on Machine Learning (ICML'06), pp. 1035-1051. (acceptance rate 140/700 = 20%)

• Y. Sun, S. Todorovic, J. Li, D. O. Wu (2005) Unifying Error-Correcting and Output-Code AdaBoost within the Margin Framework, in Proc. International Conference on Machine Learning (ICML'05), pp. 872-879. (acceptance rate 134/491 = 27%)

• Y. Sun, S. Todorovic, J. Li, D. O. Wu (2005) A Robust Linear-programming Based Boosting Algorithm, in Proc. IEEE International Workshop on Machine Learning for Signal Processing (MLSP'05), pp. 49-54.

• Y. Sun, J. Li, W. Hager (2004) Two New Regularized AdaBoost Algorithms, in Proc. International Conference on Machine Learning and Applications (ICMLA'04), pp. 41- 48.

Bioinformatics

• L. Yang, R. Chen, T Melendy, S. Goodison, Y. Sun (2023) Identifying significantly perturbed subnetworks using multiple protein-protein interaction networks, Cancers, 15 (16): 4090.

• A. Dubey, B. Tylec, A. Mishra, K. Sortino, R. Chen, Y. Sun, L. Read (2023) KREH1 RNA helicase activity promotes utilization of initiator gRNAs across multiple mRNAs in trypanosome RNA editing, Nucleic Acids Research, 5 (11): 5791–5809.

• K. Yeh, F. Parekh, I. Mombo, J. Leimer, R. Hewson, J. Fair, Y. Sun, J. Hay (2023) Climate change and infectious disease: a prologue on multidisciplinary cooperation and predictive analytics, Frontiers in Public Health, 11: 1018293.

• J. Sohn, L. Li, L. Zhang, R. Genco, K. Falkner, H. Tettelin, A. Rowsam, D. Smiraglia, J. Novak, P. Diaz, Y. Sun, K. Kirkwood (2022) Periodontal disease is associated with increased gut colonization of pathogenic Haemophilus parainfluenzae in Crohn's disease patients, Cell Reports, 42 (2), 112120.

• J. Chen, L. Yang, L. Li, S. Goodison, Y. Sun (2022) Alignment-free comparison of metagenomics sequences via approximate string matching, Bioinformatics Advances, 2 (1): vbac077.

• K. Sortino, B. L. Tylec, R. Chen, Y. Sun, L. K. Read (2022) Conserved and transcript-specific functions of the RESC factors, RESC13 and RESC14, in kinetoplastid RNA editing, RNA, 28: 1496-1508.

• R. Chen, I. Pagano, Y. Sun, K. Murakami, S. Goodison, R. Vairavan, M. Tahsin, P.C. Black, C. J. Rosser, H. Furuya (2022) A diagnostic gene expression signature for bladder cancer can stratify cases into prescribed molecular subtypes and predict outcome, Diagnostics, 12 (8): 1801.

• H. Furuya, Y. Sasaki, R. Chen, R. Peres, K. Hokutan, K. Murakami, N. Kim, O. Chan, I. Pagano, L. Dyrskjøt, J. B. Jensen, P. Malmstrom, U. Segersten, Y. Sun, A. Arab, H. Goodarzi, S. Goodison, C. J. Rosser (2022) PAI-1 is a potential transcriptional silencer that supports bladder cancer cell activity. Scientific Reports, 12: 12186.

• A. Soliman, A. Millen, C. Andrews, K. Hovey, M. Buck, M. LaMonte, P. Diaz, Y. Sun, J. Wactawski-Wende (2022) Relationship between the subgingival microbiome and menopausal hormone therapy use: the Buffalo OsteoPerio study, Journal of Periodontology, 93 (11): 1635-1648.

• L. Li, J. Sohn, R. Genco, J. Wactawski-Wende, S. Goodison, P. Diaz, Y. Sun (2022) Computational approach to modeling microbiome landscapes associated with chronic human disease progression, PLoS Computational Biology, 18(8): e1010373.

• A. Millen, R. Dahhan, J. Freudenheim, K. Hovey, L. Li, D. McSkimming, C. Andrews, M. Buck, M. LaMonte, K. Kirkwood, Y. Sun, V. Murugaiyan, M. Tsompana, J. Wactawski‑Wende (2022) Dietary carbohydrate intake is associated with the subgingival plaque oral microbiome abundance and diversity in a cohort of postmenopausal women, Scientific Reports, 12:2643.

• J. Sohn, L. Li, L. Zhang, R. Settem, K. Honma, A. Sharma, K. Falkner, J. Novak, Y. Sun, K. Kirkwood (2022) Porphyromonas gingivalis ­ indirectly elicits intestinal inflammation by altering the gut microbiota and disrupting epithelial barrier function through IL9-producing CD4 + T cells, Molecular Oral Microbiology, 37(2): 42-52.

• K. Murakami, A. Kamat, Y. Dai, I. Pagano, R. Chen, Y. Sun, A. Gupta, S. Goodison, C. Rosser, H. Furuya (2021) Application of a multiplex urinalysis test for the prediction of intravesical BCG treatment response: a pilot study, Cancer Biomarkers, 1-7.

• K. Murakami, I. Pagano, R. Chen, Y. Sun, S. Goodison, C. Rosser, H. Furuya (2021) Influencing factors on the Oncuria Urinalysis assay: an experimental model, Diagnostics, 11(6):1023.

• Y. Hirasawa, I. Pagano, R. Chen,Y. Sun, Y. Dai, A. Gupta, S. Tikhonenkov, C. Rosser, H. Furuya (2021) Diagnostic performance of Oncuria, a urinalysis test for bladder cancer, Journal of Translational Medicine, 19:141.

• L. Yang, R. Chen, S. Goodison, Y. Sun (2021) An efficient and effective method to identify significantly perturbed subnetworks in cancer, Nature Computational Science, 1:79-88.

• M. LaMonte, C. Andrews, K. Hovey, M. Buck, L. Li, D. McSkimming, H. Banack, J. Rotterman, Y. Sun, K. Kirkwood, J. Wactawski-Wende (2021) Subgingival microbiome is associated with alveolar bone loss measured 5-years later in postmenopausal women, Journal of Periodontology, 92 (5): 648-661.

• K. E. Poppenberg, V. M. Tutino, L. Li, M. Waqas, A. June, L. Chaves, K. Jiang, J. N. Jarvis, Y. Sun, K. V. Snyder, E. I. Levy, A. H. Siddiqui, J. Kolega, H. Meng (2020) Classification models using circulating neutrophil transcripts can detect unruptured intracranial aneurysm, Journal of Translational Medicine, 18:392.

• K. E. Poppenberg, L. Li, M. Waqas, N. Paliwal, K. Jiang, J. N. Jarvis, Y. Sun, K. V. Snyder, E. I. Levy, A. H. Siddiqui, J. Kolega, H. Meng, V. M. Tutino (2020) Whole blood transcriptome biomarkers of unruptured intracranial aneurysm, PLOS One, 15(11): e0241838.

• J. Smith, E. Doleželová, B. Tylec, J. Bard, R. Chen, Y. Sun, A. Zikova, L. Read (2020) Developmental regulation of edited CY b and COIII mitochondrial mRNAs is achieved by distinct mechanisms in Trypanosoma brucei, Nucleic Acids Research, 48(15), 8704–8723.

• S. Goodison, M. E. Sherman, Y. Sun (2020) Computational disease progression modeling can provide insights into cancer evolution, Oncoscience, 7(3-4), 21-22.

• J. Sohn, Y. Sun, R. J. Genco, K. L. Kirkwood (2020) The periodontal microenvironment: a potential reservoir for intestinal pathobionts in Crohn’s disease, Current Oral Health Reports, 7, 37-44.

• H. Furuya, K. Hayashi, Y. Shimizu, N. Kim, Y. Tsukikawa, R. Chen, Y. Sun, O. Chan, I. Pagano, R. Peres; K. Hokutan, F. Igari, K. S. Chan, C. J. Rosser (2020) Plasminogen activator inhibitor-2 (PAI-2) overexpression supports bladder cancer development in PAI-1 knockout mice in N-butyl-N-(4-hydroxybutyl)-nitrosamine-induced bladder cancer mouse model, Journal of Translational Medicine, 15, 57.

• R. Chen, S. Goodison, Y. Sun (2020) Molecular profiles of matched primary and metastatic tumor samples support a linear evolutionary model of breast cancer, Cancer Research, 80:170–174. (impact factor: 9.1)

• R. Chen, L. Yang, S. Goodison, Y. Sun (2020) Deep learning approach to identifying breast cancer subtypes using high-dimensional genomic data, Bioinformatics, 36(5), 1476–1483. (impact factor: 4.5)

• M. J. LaMonte, R. J. Genco, M. J. Buck, D. I. McSkimming, L. Li, K. M. Hovey, C. A. Andrews, W. Zheng, Y. Sun, A. E. Millen, M. Tsompana, H. R. Banack, J. Wactawski-Wende (2019) Composition and diversity of the subgingival microbiome and its relationship with age in postmenopausal women: an epidemiologic investigation, BMC Oral Health, 19:246.

• K. E. Poppenberg, K. Jiang, L. Li, Y. Sun, H. Meng, C. A. Wallace, T. Hennon, J. N. Jarvis (2019) The feasibility of developing biomarkers from peripheral blood mononuclear cell RNAseq data in children with juvenile idiopathic arthritis using machine learning approaches, Arthritis Research & Therapy, 21:230. (impact factor: 4.3)

• J. H. Gordon, M. J. LaMonte, R. J. Genco, J. Zhao, L. Li, K. M. Hovey, M. Tsompana, M. J. Buck, C. A. Andrews, D. I. McSkimming, W. Zheng, Y. Sun, J. Wactawski-Wende (2019) Is the oral microbiome associated with blood pressure in older women? High Blood Pressure & Cardiovascular Prevention, 26(3): 217–225.​

• N. M. McAdams, G. L. Harrison, B. L. Tylec, M. L. Ammerman, R. Chen, Y. Sun, R. K. Read (2019) MRB10130 is a RESC assembly factor that promotes kinetoplastid RNA editing initiation and progression, RNA, 25(9), 1177-1191. (impact factor: 4.9)

• R. J. Genco, M. J. LaMonte, D. I. McSkimming, M. J. Buck, L. Li, K. M. Hovey, C. A. Andrews, Y. Sun, M. Tsompana, W. Zheng, H. R. Banack, V. Murugaiyan, J. Wactawski-Wende (2019) The subgingival microbiome in relationship to periodontal disease in older women, Journal of Dental Research, 98(9): 975-984. (impact factor: 4.6)

• B. Tylec, R. Simpson, L. Kirby, R. Chen, Y. Sun, D. Koslowsky, L. Read (2019) Intrinsic and Regulated Properties of Minimally Edited Trypanosome mRNAs, Nucleic Acids Research, 47(7): 3640-3657. (impact factor: 11.6)

• W. Zheng, L. Yang, R. Genco, J. Wactawski-Wende, M. Buck, Y. Sun (2019) SENSE: Siamese Neural Network for Sequence Embedding and Alignment-free Comparison, Bioinformatics, 35(11):1820-1828. (impact factor: 5.5)

• W. Zheng, Q. Mao, R. Genco, J. Wactawski-Wende, M. Buck, Y. Cai, Y. Sun (2018) A Parallel Computational Framework for Ultra-large-scale Sequence Clustering Analysis, Bioinformatics, 35(3), 380-388. (impact factor: 5.5)

• V. M. Tutino, K. E. Poppenberg, L. Li, H. Shallwani, K. Jiang, J. N. Jarvis, Y. Sun, K. V. Snyder, E. I. Levy, A. H. Siddiqui, J. Kolega, H. Meng (2018) Biomarkers from Circulating Neutrophil Transcriptomes Have Potential to Detect Unruptured Intracranial Aneurysms, Journal of Translational Medicine, 16: 373.

• H. Banack, R. Genco, M. LaMonte, A. Millen, M. Buck, Y. Sun, C. Andrews, K. Hovey, M. Tsompana, D. McSkimming, J. Zhao, J. Wactawski-Wende (2018) Cohort Profile: the Buffalo OsteoPerio Microbiome Prospective Cohort Study, BMJ Open, 8: e024263.

• M. LaMonte, R. Genco, W. Zheng, D. McSkimming, C. Andrews, K. Hovey, L. Li, Y. Sun, M. Buck, A. Millen, K. Falkner, J. Wactawski-Wende (2018) Does the Subgingival Microbiome Differ by Periodontitis Status in Older Postmenopausal Women? Dentistry Journal, 6 (4): 58.

• W. Zheng, K. Wang, Y. Sun, S. M. Kuo (2018) Dietary or Supplemental Fermentable Fiber Intake Reduces the Presence of Clostridium XI in Mouse Intestinal Microbiota: the Importance of Higher Fecal Bacterial Load and Density, PLoS ONE, 13 (10): e0205055.

• L. Chaves, D. McSkimming, M. Bryniarski, A. Honan, S. Abyad, S. Thomas, S. Wells, M. Buck, Y. Sun, R. Genco, R. Quigg, R. Yacoub (2018) Chronic Kidney Disease, Uremic Milieu, and its Effects on Gut Bacterial Microbiota Dysbiosis, American Journal of Physiology-Renal Physiology, 315(3): F487-F502.

• N. M. McAdams, R. M. Simpson, R. Chen, Y. Sun, L. K. Read (2018) MRB7260 is Essential for Productive Protein-RNA Interactions within the RNA Editing Substrate Binding Complex during Trypanosome RNA Editing, RNA, 24: 540-556. (impact factor: 4.3)

• V. Tutino, K. Poppenberg, K. Jiang, J. Jarvis, Y. Sun, A. Sonig, A. Siddiqui, K. Snyder, E. Levy, J. Kolega, H. Meng (2018) Circulating Neutrophil Transcriptome May Reveal Intracranial Aneurysm Signature, PLoS ONE, 13(1): e0191407.

• H. Furuya, P. M. Tamashiro, Y. Shimizu, R. Peres, R. Chen, Y. Sun, K. Iino, Y. A. Hannun, L. M. Obeid, T. Kawamori (2017) Sphingosine Kinase 1 Expression in Peritoneal Macrophages is Required for Colon Carcinogenesis, Carcinogenesis, 38(12): 1218-1227. (impact factor: 5.3)

• R. Yacoub, M. Nugent, W. Cai, G. N. Nadkarni, L. D. Chaves, S. Abyad, A. M. Honan, S. A. Thomas, W. Zheng, S. A. Valiyaparambil, M. A. Bryniarski, Y. Sun, M. Buck, R. J. Genco, R. J. Quigg, J. He, J. Uribarri (2017) Advanced Glycation End Products Dietary Restriction Effects on Bacterial Gut Microbiota in Peritoneal Dialysis Patients: a Randomized Open Label Controlled Trial, PLoS ONE, 12(9): e0184789.

• R. Simpson, A. Bruno, R. Chen, K Lott, B. Tylec, J. Bard, Y. Sun, M. Buck, L. Read (2017) Trypanosome RNA Editing Mediator Complex Proteins Have Distinct Functions in gRNA Utilization, Nucleic Acids Research, 45(13):7965-7983. (impact factor: 10.2)

• M. E. Scharf, Y. Cai, Y. Sun, R. Sen, R. Raychoudhury, D. G. Boucias (2017) A Meta-analysis Testing Eusocial Co-option Theories in Termite Gut Physiology and Symbiosis, Communicative and Integrative Biology, 10(2): e1295187.

• Y. Cai*, W. Zheng, J. Yao, Y. Yang, V. Mai, Q. Mao, Y. Sun* (2017) ESPRIT-Forest: Parallel Clustering of Massive Amplicon Sequence Data in Subquadratic Time, PLoS Computational Biology, 13(4): e1005518. (impact factor: 4.6)

• Y. Sun*, J. Yao, L. Yang, R. Chen, N. Nowak, S. Goodison* (2017) Computational Approach for Deriving Cancer Progression Roadmaps from Static Sample Data, Nucleic Acids Research, 45(9): e69. (impact factor: 10.2)

• S. Rossetti, M. Ren, N. Visconti, F. Corlazzoli, V. Gagliostro, G. Somenzi, J. Yao, Y. Sun, N. Sacchi (2017) Tracing Anti-cancer and Cancer-promoting Actions of All-transretinoic Acid in Breast Cancer to a RAR Epigenetic Mechanism of Mammary Epithelial Cell Fate, Oncotarget, 7(52): 87064-87080. (impact factor: 6.4)

• W. Zheng, M. Tsompana, A. Ruscitto, A. Sharma, R. Genco, Y. Sun*, M. Buck* (2015) An Accurate and Efficient Experimental Approach for Characterization of the Complex Oral Microbiota, Microbiome, 3:48. (impact factor: 9.0)

• Q. Mao, W. Zheng, L. Wang, Y. Cai, V. Mai, Y. Sun (2015) Parallel Hierarchical Clustering in Linearithmic Time for Large-scale Sequence Analysis (regular paper), in Proc. IEEE International Conference on Data Mining (ICDM'15), 310-319. (acceptance rate: 19%. Regular paper: 8%)

• C. Wang, Y. Ding, J. Yao, Y. Zhang, Y. Sun, J. Colee, Z. Mou (2015) The Arabidopsis Elongator Subunit 2 Positively Contributes to Resistance to the Necrotrophic Fungal Pathogens Botrytis Cinerea and Alternaria Brassicicola, The Plant Journal, 83(6): 1019-1033. (impact factor: 5.9)

• C. Wang, J. Yao, Y. Zhang, Y. Sun, J. Rollins, Z. Mou (2015) The Arabidopsis Mediator Complex Subunit16 is a Key Regulator of Basal Resistance against the Necrotrophic Fungal Pathogen Sclerotinia Sclerotiorum, Plant Physiology, 169(1): 856-872. (impact factor: 7.4)

• K. Lott, S. Mukhopadhyay, J. Li, J. Wang, J. Yao, Y. Sun, J. Qu, L. Read (2015) Arginine Methylation of DRBD18 Differentially Impacts its Opposing Effects on the Trypanosome Transcriptome, Nucleic Acids Research, 43(11): 5501-5523. (impact factor: 8.8. Selected as F1000Prime)

• R. Sen, R. Raychoudhury, Y. Cai, Y. Sun, V. U. Lietze, B. F. Peterson, M. E. Scharf, D. G. Boucias (2015) Molecular Signatures of Nicotinoid-pathogen Synergy in the Termite Gut, PLoS ONE, 10(4):e0123391. (impact factor: 3.5)

• T. Culpepper, M. Ukhanova, X. Wang, Y. Sun, V. Mai (2014) Associations between Diet, Gut Microbiota and Markers of CRC Risk, Cancer & Metabolism, 2:1.

• Y. Sun*, J. Yao*, N. Nowak, S. Goodison* (2014) Cancer Progression Modeling Using Static Sample Data, Genome Biology, 15(8): 440-442. (impact factor: 10.5)

• A. Chung, Q. Li, S. J. Blair, M. D. Jesus, K. L. Dennis, C. LeVea, J. Yao, Y. Sun, T. F. Conway, L. P. Virtuoso, N. G. Battaglia, S. Furtado, E. Mathiowitz, N. J. Mantis, K. Khazaie, N. K. Egilmez (2014) Oral interleukin-10 Alleviates Polyposis via Neutralization of Pathogenic T-regulatory Cells, Cancer Research, 74(19): 5377-5385. (impact factor: 9.3)

• D. Hickman, M. K. Jones, S. Zhu, E. Kirkpatrick, D. A. Ostrov, X. Wang, M. Ukhanova, Y. Sun, V. Mai, M. Salemi (2014) The Effect of Malnutrition on Norovirus Infection, mBio, 5(2): e01032-13. (impact factor: 5.6)

• M. J. Correll, T. P. Pyle, K. Millar, Y. Sun, J. Yao, R. E. Edelmann, J. Z. Kiss (2013) Transcriptome Analyses of Arabidopsis Thaliana Seedlings Grown in Space: Implications for Gravity-responsive Genes, Planta, 238(3):519-533. (impact factor: 3.0)

• R. Sen, R. Raychoudhury, Y. Cai, Y. Sun, V. U. Lietze, D. G. Boucias, M. E. Scharf (2013) Differential Impacts of Juvenile Hormone, Soldier Head Extract and Alternate Caste Phenotypes on Host and Symbiont Transcriptome Composition in The Gut of The Termite Reticulitermes Flavipes, BMC Genomics, 14(1): 491. (impact factor: 4.4)

• X. Zhang, J. Yao, Y. Zhang, Y. Sun, Z. Mou (2013) The Arabidopsis Mediator Complex Subunits MED14/SWP and MED16/SFR6/IEN1 Differentially Regulate Defense Gene Expression in Plant Immune Responses, The Plant Journal, 75(3): 484-497. (impact factor: 6.2)

• Y. Wang, C. An, X. Zhang, J. Yao, Y. Zhang, Y. Sun, F. Yu, D. M. Amador, Z. Mou (2013) The Arabidopsis Elongator Complex Subunit2 Epigenetically Regulates Plant Immune Responses, The Plant Cell, 25(2): 762-776. (impact factor: 10.2)

• X. Wang, J. Yao, Y. Sun*, V. Mai* (2013) M-pick, a Modularity-based Method for OTU Picking of 16S rRNA Sequences, BMC Bioinformatics, 14(1): 43. (impact factor: 2.8)

• V. Mai, R.M. Torrazza, M. Ukhanova, X. Wang, Y. Sun, N. Li, J. Shuster, R. Sharma, M.L. Hudak, J. Neu (2013) Distortions in Development of Intestinal Microbiota Associated with Late Onset Sepsis in Preterm Infants, PLoS ONE, 8(1): e52876. (impact factor: 4.1)

• D. G. Boucias, Y. Cai, Y. Sun, V. U. Lietze, R. Sen, R. Raychoudhury, M. E. Scharf (2013) The Hindgut-Lumen Prokaryotic Microbiota of the Lignocellulose-Degrading Termite Reticulitermes Flavipes and its Responses to Dietary Lignocellulose Composition, Molecular Ecology, 22(7): 1836-1853. (impact factor: 5.5)

• L. Yin, L. Liu, Y. Sun, W. Hou, A. C. Lowe, B. P. Gardner, M. Salemi, W. B. Williams, W. G. Farmerie, J. W. Sleasman, M. M. Goodenow (2012) Novel High Resolution Deep Sequencing Analysis Reveals HIV-1 Biodiversity, Population Structure, and Persistence during Natural History of Infection, Retrovirology, 9(1): 108. (impact factor: 6.5)

• V. Urquidi, S. Goodison, Y. Cai, Y. Sun, C. J. Rosser (2012) A Candidate Molecular Biomarker Panel for the Detection of Bladder Cancer, Cancer Epidemiology Biomarkers & Prevention, 21(12): 2149-2158. (impact factor: 4.6)

• V. Urquidi, S. Goodison, Y. Cai, Y. Sun, C. Rosser (2012) Molecular Biomarker Signature for the Non-invasive Detection of Bladder Cancer, The Journal of Urology, 187(4): e512. (impact factor: 3.7)

• R. Raychoudhury, R. Sen, Y. Cai, Y. Sun, V. Ulrike-Lietze, D. Boucias, M. Scharf (2013) Comparative Metatranscriptomic Signatures of Wood and Paper Feeding in the Gut of the Termite Reticulitermes flavipes (Isoptera: Rhinotermitidae), Insect Molecular Biology, 22(2): 155-171. (impact factor: 2.5)

• X. Zhang, C. Wang, Y. Zhang, Y. Sun,, Z. Mou (2012) The Arabidopsis Mediator Complex Subunit 16 Positively Regulates Salicylate-Mediated Systemic Acquired Resistance and Jasmonate/Ethylene-Induced Defense Pathways, The Plant Cell, 24(10): 4294-4309. (impact factor: 10.2)

• A-L. Paul, A. Zupanska, D. Ostrow, Y. Zhang, Y. Sun, J. Li, S. Shanker, W. Farmerie, C. Amalfitano, R. J. Ferl (2012) Spaceflight Transcriptomes: Unique Responses to a Novel Environment, Astrobiology, 12(1): 40-56. (impact factor: 2.4)

• M. Ukhanova, T. Culpepper, D. Baer, D. Gordon, S. Kanahori, J. Valentine, J. Neu, Y. Sun, X. Wang, V. Mai (2012) Gut Microbiota Correlates with Energy Gain from a Dietary Fiber and Appears Associated with Acute and Chronic Intestinal Diseases, Clinical Microbiology and Infection, 4: 62-66. (impact factor: 4.8)

• X. Wang, Y. Cai, Y. Sun, R. Knight, V. Mai (2012) Secondary Structure Information Does not Improve OTU Picking for 16S rRNA Sequences, The ISME Journal, 6(7): 1277-1280. (impact factor: 9.3)

• Y. Sun*, Y. Cai*, S. Huse, R. Knight, W. Farmerie, X. Wang, V. Mai (2012) A Large-scale Benchmark Study of Existing Algorithms for Taxonomy-Independent Microbial Community Analysis, Briefings in Bioinformatics, 13(1): 107-121. (impact factor: 9.3)

• V. Mai, C. M. Young, M. Ukhanova, X. Wang, Y. Sun, G. Casella, D. Theriaque, N. Li, R. Sharma, M. Hudak, J. Neu (2011) Fecal Microbiota in Premature Infants Prior to Necrotizing Enterocolitis, PLoS ONE, 6(6): e20647. (impact factor: 4.4)

• Y. Cai*, Y. Sun* (2011) [Website] ESPRIT-Tree: Hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasilinear Time, Nucleic Acids Research, 39(14): e95. (impact factor: 7.8)

• Y. Sun, Y. Cai (2011) Estimating Species Richness Using Large Collections of 16S rRNA Pyrosequences, Handbook of Molecular Microbial Ecology: Metagenomics and Complementary Approaches (Edited by Frans J. de Bruijn), Wiley-Blackwell.

• Y. Sun*, Y. Cai*, V. Mai, W. Farmerie, F. Yu, J. Li, S. Goodison (2010) Advanced Computational Algorithms for Microbial Community Analysis Using Massive 16S rRNA Sequence Data, Nucleic Acids Research, 38(22): e205. (impact factor: 7.8)

• S. Goodison, Y. Sun, V. Urquidi (2010) Review: Derivation of Cancer Diagnostic and Prognostic Signatures from Gene Expression Data, Bioanalysis, 2(5): 855-862.

• Y. Sun, V. Urquidi, S. Goodison (2010) Derivation of Molecular Signatures for Breast Cancer Recurrence Prediction Using a Two-way Validation Approach, Breast Cancer Research and Treatment, 119(3): 593-599. (impact factor: 5.7)

• C. Pascoe, A. Lawande, H. Lam, A. George, Y. Sun, W. Farmerie, H. Martin (2010) Reconfigurable Supercomputing with Scalable Systolic Arrays and In-Stream Control for Wavefront Genomics Processing, in Proc. 2010 Symposium on Application Accelerators in High-Performance Computing (SAAHPC'10), pp. 1-6. (oral presentation)

• Y. Sun*, Y. Cai*, L. Liu, F. Yu, M. L. Farrell, W. McKendree, W. Farmerie (2009) ESPRIT: Estimating Species Richness Using Large Collections of 16S rRNA Pyrosequences, Nucleic Acids Research, 37(10): e76. (impact factor: 7.8) The algorithm has been used by more than 200 major research institutes worldwide.

• F. Yu*, Y. Sun*, L. Liu, W. Farmerie (2009) GSTaxClassifier: A Genomic Signature Based Taxonomic Classifier for Metagenomics Data Analysis, Bioinformation, 4(1): 46-49.

• Y. Duan, L. Zhou, D. Hall, W. Li, H. Doddapaneni, H. Lin, L. Liu, C. Vahling, D. Gabriel, K. Williams, A. Dickerman, Y. Sun, T. Gottwald (2009) Complete Genome Sequence of Citrus Huanglongbing Bacterium, Candidatus Liberibacter Asiaticus Obtained through Metagenomics, Molecular Plant-Microbe Interactions, 22(8): 1011-1020. (impact factor: 4.3)

• N. Bandyopadhyay, T. Kahveci, S. Ranka, Y. Sun, S. Goodison (2009) Pathway based Feature Selection Algorithm for Cancer Microarray Data, Advances in Bioinformatics, 532989.

• Y. Sun* , S. Goodison* (2009) Optimizing Molecular Signatures for Predicting Prostate Cancer Recurrence, The Prostate, 69(10): 1119-1127. (impact factor: 3.7) This paper was featured in Medical News Today.

• C. Rosser, L. Liu, Y. Sun, P. Villicana, M. McCullers, S. Porvasnik, S. Goodison (2009) Bladder Cancer Associated Gene Expression Signatures Identified by Profiling of Exfoliated Urothelia, Cancer Epidemiology, Biomarkers and Prevention, 18(2): 444-453. (impact factor: 4.8)

• Y. Sun, Y. Cai, S. Goodison (2008) Combining Nomogram and Microarray Data for Predicting Prostate Cancer Recurrence, in Proc. 8th IEEE International Conference on Bioinformatics and Bioengineering (BIBE'08), pp. 1-7.

• Y. Sun, S. Goodison, J. Li, L. Liu, W. Farmerie (2007) Improved Breast Cancer Prognosis through the Combination of Clinical and Genetic Markers, Bioinformatics, 23(1): 30-37. (impact factor: 5.0)
This paper was among the 50 most-frequently read articles in Bioinformatics, and featured in MATLAB Digest - Biotech and Pharmaceutical Edition (vol. 1, no. 2, June 2007).

• Y. Sun, S. Goodison (2007) Predicting Breast Cancer Metastasis by Integrating Both Clinical and Genetic Markers, in Proc. International Conference on Bioinformatics and Computational Biology (BIOCOMP'07), pp. 229-235. (acceptance rate = 27%)

• Y. Sun, F. Yu, L. Liu, W. Farmerie (2007) Estimating Microbial Population Densities Based on Genomic Signatures, in Proc. International Conference on Bioinformatics and Computational Biology (BIOCOMP'07), pp. 163-168. (acceptance rate = 27%)