Publications

(selected from 90 journal and 28 conference papers) [Google Scholar]

Machine Learning

  • L. Yang, R. Chen, S. Goodison, Y. Sun (2020) FDRNet: A novel method to identify significantly mutated subnetworks in cancer, Nature Computational Science, accepted.
  • W. Wei, J. Liang, X. Guo, P. Song, Y. Sun (2019) Hierarchical division clustering framework for categorical data, Neurocomputing, 341: 118-134.
  • 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)
  • 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 (2007) Feature Weighting through Local Learning, Computational Methods of Feature Selection, H. Liu and H. Motoda (eds.), Chapman and Hall/CRC Press.
  • 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.

Bioinformatics

  • L. Yang, R. Chen, S. Goodison, Y. Sun (2020) FDRNet: A novel method to identify significantly mutated subnetworks in cancer, Nature Computational Science, accepted.
  • M. LaMonte, C. Andrews, K. Hovey, M. Buck, L. Li, D. McSkimming, H. Banack, J. Rotterman, Y. Sun, K. Kirkwood, J. Wactawski-Wende (2020) Subgingival microbiome is associated with alveolar bone loss measured 5-years later in postmenopausal women, Journal of Periodontology, accepted.
  • 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, in press.
  • 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)
  • 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.
  • 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.
  • 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)
  • 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.
  • 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. 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 (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%)