Yijun Sun PhD

Yijun Sun

Yijun Sun
PhD

Associate Professor of Bioinformatics

Department of Microbiology and Immunology

Jacobs School of Medicine & Biomedical Sciences


Specialty/Research Focus

Bioinformatics; Gene Expression; Genomics and proteomics

Contact Information
Room 5205
955 Main Street
Buffalo, New York 14203
Phone: 716 - 8811374
yijunsun@buffalo.edu



Professional Summary:

The recent development of high-throughput genomics technologies is revolutionizing many aspects of modern biology. However, the lack of computational algorithms and resources for analyzing massive data generated by these techniques has become a rate-limiting factor for scientific discoveries in biology research.

In my laboratory, we study machine learning, data mining and bioinformatics and their applications to cancer informatics and metagenomics. Our work is based on solid mathematical and statistical theories. The main focus of our research is on developing advanced algorithms to help biologists keep pace with the unprecedented growth of genomics datasets available today and enable them to make full use of their massive, high-dimensional data for various biological enquiries.

My research team is working on two major projects. The first is focused on metagenomics, currently funded by the National Institutes of Health (NIH), the National Science Foundation (NSF) and the Women’s Health Initiative. Our goal is to develop an integrated suite of computational and statistical algorithms to process millions or even hundreds of millions of microbial genome sequences to: 1) derive quantitative microbial signatures to characterize various infectious diseases, 2) interactively visualize the complex structure of a microbial community, 3) study microbe-microbe interactions and community dynamics and 4) identify novel species. We collaborate with researchers throughout the University at Buffalo, notably those in the School of Medicine and Biomedical Sciences, the School of Public Health and Health Professions and the College of Arts and Sciences.

The second project focuses on cancer progression modeling. We use advanced computational algorithms to integrate clinical and genetics data from thousands of tumor and normal tissue samples to build a model of cancer progression. Delineating the disease dynamic process and identifying the molecular events that drive stepwise progression to malignancy would provide a wealth of new insights. Results of this work also would guide the development of improved cancer diagnostics, prognostics and targeted therapeutics.

The bioinformatics algorithms and software developed in our lab have been used by more than 200 research institutes worldwide to process large, complex data sets that are core to a wide variety of biological and biomedical research.

Education and Training:

  • PhD, Electrical Engineering, University of Florida (2004)
  • MS, Electrical Engineering, University of Florida (2003)
  • BS, Electrical Engineering/Mechanical Engineering, Shanghai Jiao Tong University (1995)

Employment:

  • Associate Professor, Microbiology and Immunology, University at Buffalo, The State University of New York Jacobs School of Medicine & Biomedical Sciences (2017-present)
  • Adjunct Assistant Professor, Biostatistics, University at Buffalo, The State University of New York (2013-present)
  • Adjunct Assistant Professor, Computer Science, University at Buffalo, The State University of New York (2012-present)
  • Assistant Professor, Microbiology and Immunology, University at Buffalo, The State University of New York Jacobs School of Medicine & Biomedical Sciences (2012–2017)
  • Assistant Scientist, University of Florida The Interdisciplinary Center for Biotechnology Research (2005–2012)

Awards and Honors:

  • Spotlight Paper in the September 2010 issue of IEEE Trans. on Pattern Analysis and Machine Intelligence (2010)
  • IEEE M. Barry Carlton Best Transactions Paper Award (2005)

Research Expertise:

  • Bioinformatics: metagenomics, sequence analysis, microarray data analysis, microbial community analysis, molecular classification and genetic network modeling for cancer diagnosis and prognosis, microbial network analysis, phylogenetic analysis
  • Machine learning: large margin classification/regression, large-scale clustering analysis, ensemble learning, feature selection/extraction, computational learning theory, network analysis, graphical modeling and Bayesian network

Research Centers:

  • Center of Excellence in Bioinformatics and Life Sciences
  • Witebsky Center for Microbial Pathogenesis and Immunology

UB 2020 Strategic Strengths:

  • Molecular Recognition in Biological Systems and Bioinformatics

Grants and Sponsored Research:

  • September 2020–August 2025
    Bacterial sialometabolic activity impacts periodontal immunity and microbiota
    NIH
    Role: Co-Investigator
    $1,930,340
  • April 2020–March 2025
    Advanced computational approaches to delineating dynamic cancer progression processes by using massive static sample data
    NIH
    Role: Principal Investigator
    $1,964,300
  • August 2020–July 2022
    Identification of new or unrecognized virulence genes in hypervirulent Klebsiella pneumoniae and antivirulence genes in classical K. pneumoniae
    NIH
    Role: Co-Investigator
    $431,682
  • January 2019–July 2022
    The microbiome in the etiology and prevention of breast cancer
    NYS Department of Health
    Role: Co-Investigator
    $359,000
  • May 2017–April 2022
    Stress responsive reprogramming of translating mRNA pools in C. neoformans
    NIH
    Role: Co-Investigator
    $2,000,000
  • July 2016–June 2021
    Developing advanced algorithms to address major computational challenges in current microbiome research
    NIH
    Role: Principal Investigator
    $973,277
  • February 2019–April 2021
    Multiplexed protein biomarker-based assay for the detection of bladder cancer
    NIH
    Role: Principal Investigator
    $45,535
  • July 2014–July 2019
    Oral microbiome and periodontitis: a prospective study in postmenopausal women
    NIH
    Role: Co-Investigator
    $4,000,000
  • July 2016–June 2017
    The airway microbiome and lung cancer in a COPD cohort
    UB - GEM Pilot Study Program
    Role: Co-Investigator
    $34,000
  • July 2016–June 2017
    Methylglyoxal could mediate the relationship between infections and diabetes: a method development and feasibility study
    UB-the Innovative Micro-Programs Accelerating Collaboration in Themes Program
    Role: Co-Investigator
    $31,000
  • July 2016–June 2017
    Pilot study of the placental, oral and gut microbiome related to pregnancy outcomes
    UB - GEM Pilot Study Program
    Role: Co-Investigator
    $34,000
  • July 2016–June 2017
    PPI related gut microbiota dysbiosis role in diabetic nephropathy: A cross-sectional analysis
    UB - GEM Pilot Study Program
    Role: Co-Investigator
    $34,000
  • January 2014–December 2016
    Derivation of molecular signatures for accurate prostate cancer prognosis using both annotated and non-annotated tissue samples
    SUNY Research Foundation
    Role: Principal Investigator
    $96,495
  • February 2011–December 2016
    Microarray-Based Biomarkers in Juvenile Idiopathic Arthritis
    NIH/NIAMS
    Role: Co-Investigator
    $1,250,000
  • July 2015–July 2016
    Feasibility study to evaluate gut microbiome and CVD-related measures in older women
    Women's Health Initiative
    Role: Co-Investigator
    $29,400
  • July 2015–June 2016
    The neonatal microbiome study: a pilot study in Meru County, Kenya
    UB-the Innovative Micro-Programs Accelerating Collaboration in Themes Program
    Role: Co-Investigator
    $34,947
  • June 2011–December 2015
    Advanced computational algorithms for deep interrogation of microbial communities using millions of 16S rRNA pyrosequences
    NSF
    Role: Principal Investigator
    $657,300
  • July 2014–June 2015
    Expression-Based Biomarkers in Cystic Fibrosis
    University at Buffalo Clinical and Translational Research Fund
    Role: Co-Investigator
    $34,190
  • June 2011–June 2013
    Derivation of molecular signatures for accurate breast cancer prognosis
    Bankhead-Coley Cancer Program
    Role: Principal Investigator
    $203,696
  • September 2007–October 2010
    Accurate breast cancer prognosis
    Susan Komen Breast Cancer Foundation
    Role: Co-Principal Investigator
    $216,762
See all (10 more)

Journal Articles:

  • Sun Y, Todorovic S, Goodison S. (2010) Local-learning-based feature selection for high-dimensional data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence (Sep), 32(9): 1610-1616.
  • Yang L, Chen R, Goodison S, Sun Y. (2020) An efficient and effective method to identify significantly perturbed subnetworks in cancer. Nature Computational Science (Dec)(1): 79–88.
  • LaMonte MJ, Genco RJ, Buck MJ, McSkimming DI, Li L, Hovey KM, Andrews CA, Zheng W, Sun Y, Millen AE, Tsompana M, Banack HR, Wactawski-Wende J, Buck M. (2019) Composition and diversity of the subgingival microbiome and its relationship with age in postmenopausal women: an epidemiologic investigation. BMC Oral Health (Nov), 19(1): 246-246.
  • Poppenberg KE, Jiang K, Li L, Sun Y, Meng H, Wallace CA, Hennon TR, Jarvis JN. (2019) The feasibility of developing biomarkers from peripheral blood mononuclear cell RNAseq data in children with juvenile idiopathic arthritis using machine learning approaches. Arthritis Res Ther (Nov), 21(1): 230-230.
  • Genco RJ, LaMonte MJ, McSkimming DI, Buck MJ, Li L, Hovey KM, Andrews CA, Sun Y, Tsompana M, Zheng W, Banack HR, Murugaiyan V, Wactawski-Wende J, Buck M. (2019) The Subgingival Microbiome Relationship to Periodontal Disease in Older Women. J Dent Res (Jan), 98(9): 975-984.
  • Gordon JH, LaMonte MJ, Genco RJ, Zhao J, Li L, Hovey KM, Tsompana M, Buck MJ, Andrews CA, Mcskimming DI, Zheng W, Sun Y, Wactawski-Wende J, Buck M. (2019) Is the Oral Microbiome Associated with Blood Pressure in Older Women?. High Blood Press Cardiovasc Prev (Jun), 26(3): 217-225.
  • McAdams NM, Harrison GL, Tylec BL, Ammerman ML, Chen R, Sun Y, Read LK. (2019) MRB10130 is a RESC assembly factor that promotes kinetoplastid RNA editing initiation and progression. RNA (Jan), 25(9): 1177-1191.
  • Tylec BL, Simpson RM, Kirby LE, Chen R, Sun Y, Koslowsky DJ, Read LK. (2019) Intrinsic and regulated properties of minimally edited trypanosome mRNAs. Nucleic Acids Res (Jan), 47(7): 3640-3657.
  • Tutino VM, Poppenberg KE, Li L, Shallwani H, Jiang K, Jarvis JN, Sun Y, Snyder KV, Levy EI, Siddiqui AH, Kolega J, Meng H. (2018) Biomarkers from circulating neutrophil transcriptomes have potential to detect unruptured intracranial aneurysms. J Transl Med (Dec), 16(1): 373.
  • Banack HR, Genco RJ, LaMonte MJ, Millen AE, Buck MJ, Sun Y, Andrews CA, Hovey KM, Tsompana M, McSkimming DI, Zhao J, Wactawski-Wende J, Buck M. (2018) Cohort profile: the Buffalo OsteoPerio microbiome prospective cohort study. BMJ Open (Dec), 8(12): e024263.
  • LaMonte MJ, Genco RJ, Zheng W, McSkimming DI, Andrews CA, Hovey KM, Li L, Sun Y, Buck MJ, Millen AE, Falkner KL, Wactawski-Wende J, Buck M. (2018) Substantial Differences in the Subgingival Microbiome Measured by 16S Metagenomics According to Periodontitis Status in Older Women. Dentistry Journal (Oct), 4(6): 58.
  • Zheng W, Yang L, Genco RJ, Wactawski-Wende J, Buck M, Sun Y. (2019) SENSE: Siamese neural network for sequence embedding and alignment-free comparison. Bioinformatics (Jan), 35(11): 1820-1828.
  • Zheng W, Yang L, Genco RJ, Wactawski-Wende J, Buck M, Sun Y. (2019) SENSE: Siamese neural network for sequence embedding and alignment-free comparison. Bioinformatics (Jun)
  • Wang X, Yan F, Liu X, Wang P, Shao S, Sun Y, Sheng Z, Liu Q, Lovell JF, Zheng H. (2018) Enhanced drug delivery using sonoactivatable liposomes with membrane-embedded porphyrins. J Control Release (Jul).
  • Zheng W, Mao Q, Genco RJ, Wactawski-Wende J, Buck M, Cai Y, Sun Y. (2019) A parallel computational framework for ultra-large-scale sequence clustering analysis. Bioinformatics (Feb), 35(3): 380-388.
  • Chaves LD, McSkimming DI, Bryniarski MA, Honan AM, Abyad S, Thomas SA, Wells S, Buck M, Sun Y, Genco RJ, Quigg RJ, Yacoub R. (2018) Chronic Kidney Disease, Uremic Milieu, and its Effects on Gut Bacterial Microbiota Dysbiosis. Am J Physiol Renal Physiol (Sep), 315(3): 487-502.
  • Tutino VM, Poppenberg KE, Jiang K, Jarvis JN, Sun Y, Sonig A, Siddiqui AH, Snyder KV, Levy EI, Kolega J, Meng H. (2018) Circulating neutrophil transcriptome may reveal intracranial aneurysm signature. PLoS One (Jan), 13(1)
  • McAdams NM, Simpson RM, Chen R, Sun Y, Read LK. (2018) MRB7260 is essential for productive protein-RNA interactions within the RNA editing substrate binding complex during trypanosome RNA editing. RNA (Jan), 24(4): 540-556.
  • Yacoub R, Nugent M, Cai W, Nadkarni GN, Chaves LD, Abyad S, Honan AM, Thomas SA, Zheng W, Valiyaparambil SA, Bryniarski MA, Sun Y, Buck M, Genco RJ, Quigg RJ, He JC, Uribarri J. (2017) Advanced Glycation End Products Dietary Restriction Effects on Bacterial Gut Microbiota in Peritoneal Dialysis Patients; a Randomized Open Label Controlled Trial. PLoS One (Sep), 12(9): 0184789-0184789.
  • Simpson RM, Bruno AE, Chen R, Lott K, Tylec BL, Bard JE, Sun Y, Buck MJ, Read LK, Buck M. (2017) Trypanosome RNA Editing Mediator Complex proteins have distinct functions in gRNA utilization. Nucleic Acids Res (Jul), 45(13): 7965-7983.
  • Sun Y, Yao J, Yang L, Chen R, Nowak NJ, Goodison S. (2017) Computational approach for deriving cancer progression roadmaps from static sample data. Nucleic Acids Res (May), 45(9): 69-69.
  • Zheng W, Tsompana M, Ruscitto A, Sharma A, Genco R, Sun Y, Buck MJ. (2015) An accurate and efficient experimental approach for characterization of the complex oral microbiota. Microbiome (Oct), 3: 48-48.
  • Mai V, Torrazza RM, Ukhanova M, Wang X, Sun Y, Li N, Shuster J, Sharma R, Hudak ML, Neu J. (2013) Distortions in development of intestinal microbiota associated with late onset sepsis in preterm infants. PLoS ONE (Jan), 8(1): 1-10.
  • Raychoudhury R, Sen R, Cai Y, Sun Y, Lietze VU, Boucias DG, Scharf ME. (2013) Comparative metatranscriptomic signatures of wood and paper feeding in the gut of the termite Reticulitermes flavipes (Isoptera: Rhinotermitidae). Insect Molecular Biology (Apr), 22(2): 155-171.
  • Khairallah RJ, Shi G, Sbrana F, Prosser BL, Borroto C, Mazaitis MJ, Hoffman EP, Mahurkar A, Sachs F, Sun Y, Chen YW, Raiteri R, Lederer WJ, Dorsey SG, Ward CW. (2012) Microtubules underlie dysfunction in duchenne muscular dystrophy. Sci Signal (Aug), 5(236): 56-56.
  • Rice KL, Lin X, Wolniak K, Ebert BL, Berkofsky-Fessler W, Buzzai M, Sun Y, Xi C, Elkin P, Levine R, Golub T, Gilliland DG, Crispino JD, Licht JD, Zhang W. (2011) Analysis of genomic aberrations and gene expression profiling identifies novel lesions and pathways in myeloproliferative neoplasms. Blood Cancer J (Nov), 1(11): 40-40.
  • Yu H, Sun Y, Haycraft C, Palanisamy V, Kirkwood KL. (2011) MKP-1 regulates cytokine mRNA stability through selectively modulation subcellular translocation of AUF1. Cytokine (Nov), 56(2): 245-255.
  • Karakikes I, Kim M, Hadri L, Sakata S, Sun Y, Zhang W, Chemaly ER, Hajjar RJ, Lebeche D. (2009) Gene remodeling in type 2 diabetic cardiomyopathy and its phenotypic rescue with SERCA2a. PLoS One (Jul), 4(7): 6474-6474.
  • Qiao G, Lei M, Li Z, Sun Y, Minto A, Fu YX, Ying H, Quigg RJ, Zhang J. (2007) Negative Regulation of CD40-mediated B Cell Responses by E3 Ubiquitin Ligase Casitas-B-Lineage Lymphoma Protein-B. J Immunol (Oct), 179(7): 4473-4479.
  • Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, Li R, Xu Z, Li S, Li X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Wang J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren X, Wang J, Wang X, Li D, Liu D, Zhang X, Ji Z, Zhao W, Sun Y, Zhang Z, Bao J, Han Y, Dong L, Ji J, Chen P, Wu S, Liu J, Xiao Y, Bu D, Tan J, Yang L, Ye C, Zhang J, Xu J, Zhou Y, Yu Y, Zhang B, Zhuang S, Wei H, Liu B, Lei M, Yu H, Li Y, Xu H, Wei S, He X, Fang L, Zhang Z, Zhang Y, Huang X, Su Z, Tong W, Li J, Tong Z, Li S, Ye J, Wang L, Fang L, Lei T, Chen C, Chen H, Xu Z, Li H, Huang H, Zhang F, Xu H, Li N, Zhao C, Li S, Dong L, Huang Y, Li L, Xi Y, Qi Q, Li W, Zhang B, Hu W, Zhang Y, Tian X, Jiao Y, Liang X, Jin J, Gao L, Zheng W, Hao B, Liu S, Wang W, Yuan L, Cao M, McDermott J, Samudrala R, Wang J, Wong GK, Yang H. (2005) The Genomes of Oryza sativa: a history of duplications. PLoS Biol (Feb), 3(2): 38-38.
  • Boucias DG, Cai Y, Sun Y, Lietze VU, Sen R, Raychoudhury R, Scharf ME. (2013) The hindgut-lumen prokaryotic microbiota of the termite Reticulitermes flavipes and its responses to dietary lignocellulose composition. Molecular Ecology (Apr), 22(7): 1836-1853.
  • Sen R, Raychoudhury R, Cai Y, Sun Y, Lietze VU, Peterson BF, Scharf ME, Boucias DG. (2015) Molecular signatures of nicotinoid-pathogen synergy in the termite gut. PLoS ONE (Jan), 10(4): e0123.
  • Sun Y, Li J. (2003) Time-frequency analysis for plastic landmine detection via forward-looking ground penetrating radar. IEE Proceedings-Radar, Sonar and Navigation, (Aug), 150(4): 253-261.
  • Correll MJ, Pyle TP, Millar K, Sun Y, Yao J, Edelmann RE, Kiss J. (2013) Transcriptome analyses of Arabidopsis thaliana seedlings grown in space: implications for gravity-responsive genes. Planta (Jun), 238(3): 519-533.
  • Smith J, Doleželová E, Tylec B, Bard J, Chen R, Sun Y, Zikova A, Read L. (2020) Developmental regulation of edited CYb and COIII mitochondrial mRNAs is achieved by distinct mechanisms in Trypanosoma brucei. Nucleic Acids Research (Jul), 15(48): 8704–8723.
  • Wei W, Liang J, Guo X, Song P, Sun Y. (2019) Hierarchical division clustering framework for categorical data. Neurocomputing (May)(341): 118-134.
  • Paul AL, Zupanska AK, Ostrow DT, Zhang Y, Sun Y, Li JL, Shanker S, Farmerie WG, Amalfitano CE, Ferl RJ. (2012) Spaceflight transcriptomes: unique responses to a novel environment. Astrobiology (Jan), 12(1): 40-56.
  • Wang J, Sun Y, Gao, X. (2015) Sparse structure regularized ranking. Multimedia Tools and Applications (Jan), 74(2): 635-654.
  • Wang Y, An C, Zhang X, Yao J, Zhang Y, Sun Y, Yu F, Amador DM, Mou Z. (2013) The Arabidopsis elongator complex subunit2 epigenetically regulates plant immune responses. Plant Cell (Feb), 25(2): 762-776.
  • Wang C, Ding Y, Yao J, Zhang Y, Sun Y, Colee J, Mou Z. (2015) The Arabidopsis elongator subunit 2 positively contributes to resistance to the Necrotrophic fungal pathogens botrytis cinerea and alternaria brassicicola. The Plant Journal (Jan), 83(6): 1019-1033.
  • Wang C, Yao J, Zhang Y, Sun Y, Rollins J, Mou Z. (2015) The Arabidopsis mediator complex subunit16 is a key regulator of basal resistance against the necrotrophic fungal pathogen sclerotinia sclerotiorum. Plant Physiology (Jan), 169(1): 856-872.
  • Sun Y, Goodison S. (2009) Optimizing molecular signatures for predicting prostate cancer recurrence. Prostate (Jul), 69(10): 1119-1127.
  • Chung A, Li Q, Blair SJ, Jesus MD, Dennis KL, LeVea C, Yao J, Sun Y, Conway TF, Virtuoso LP, Battaglia NG, Furtado S, Mathiowitz E, Mantis NJ, Khazaie K, Egilmez N. (2014) Oral interleukin-10 alleviates polyposis via neutralization of pathogenic T-regulatory cells. Cancer Research (Jan), 74(19): 5377-5385.
  • Wang X, Cai Y, Sun Y, Knight R, Mai V. (2012) Secondary structure information does not improve OTU picking for 16S rRNA sequences. The ISME Journal (Jul), 6(7): 1277-1278.
  • Sun Y. (2007) Iterative RELIEF for feature weighting: algorithms, theories, and applications. IEEE Transactions on Pattern Analysis and Machine Intelligence (Jun), 29(6): 1035-1051.
  • Wang X, Yao J, Sun Y, Mai V. (2013) M-pick, a modularity-based method for OTU picking of 16S rRNA sequences. BMC Bioinformatics (Feb), 14(1): 1-14.
  • Yu F, Sun Y, Liu L, Farmerie W. (2009) GSTaxClassifier: a genomic signature based taxonomic classifier for metagenomic data analysis. Bioinformation (Jan), 4(1): 46-49.
  • Ukhanova M, Culpepper T, Baer D, Gordon D, Kanahori S, Valentine J, Neu J, Sun Y, Wang X, Mai V. (2012) Gut microbiota correlates with energy gain from a dietary fiber and appears associated with acute and chronic intestinal diseases. Clinical Microbiology and Infection (Jul)62-66.
  • Yin L, Liu L, Sun Y, Hou W, Lowe AC, Gardner BP, Salemi M, Williams WB, Farmerie WG, Sleasman JW, Goodenow MM. (2012) High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems. Retrovirology (Dec), 9: 108-107.
  • Sun Y, Goodison S, Li J, Liu L, Farmerie W. (2007) Improved breast cancer prognosis through the combination of clinical and genetic markers. Bioinformatics (Jun), 23(1): 30-37.
  • Duan Y, Zhou L, Hall DG, Li W, Doddapaneni H, Lin H, Liu L, Vahling CM, Gabriel DW, Williams KP, Dickerman A, Sun Y, Gottwald T. (2009) Complete genome sequence of citrus huanglongbing bacterium, `Candidatus Liberibacter asiaticus' obtained through metagenomics. Molecular Plant-Microbe Interactions (Aug), 22(8): 1011-1020.
  • Sun Y, Todorovic S, Li J. (2007) Unifying multi-class AdaBoost algorithms with binary base learners under the margin framework. Pattern Recognition Letters (Jun), 28(5): 631-643.
  • Furuya H, Tamashiro PM, Shimizu Y, Peres R, Chen R, Sun Y, Iino K, Hannun YA, Obeid LM, Kawamori T. (2017) Sphingosine kinase 1 expression in peritoneal macrophages is required for colon carcinogenesis. Carcinogenesis (Dec), 38(12): 1218-1227.
  • Goodison S, Sherman ME, Sun Y. (2020) Computational disease progression modeling can provide insights into cancer evolution. Oncoscience (May), 3-4(7): 21-22.
  • LaMonte MJ, Genco RJ, Buck MJ, McSkimming DI, Li L, Hovey KM, Andrews CA, Zheng W, Sun Y, Millen AE, Tsompana M, Banack HR, Wactawski-Wende J. (2019) Composition and diversity of the subgingival microbiome and its relationship with age in postmenopausal women: an epidemiologic investigation. BMC Oral Health (Nov)(19): 246.
  • ME Scharf, Y Cai, Y Sun, R Sen, R Raychoudhury, DG Boucias. (2017) A meta-analysis testing eusocial co-option theories in termite gut physiology and symbiosis. Communicative and Integrative Biology (Apr), 10(2): e1295187.
  • Mao Q, Wang L, Tsang I, Sun Y. (2017) Principal graph and structure learning based on reversed graph embedding. IEEE Transactions on Pattern Analysis and Machine Intelligence (Nov), 39(11): 2227-2241.
  • Furuya H, Hayashi K, Shimizu Y, Kim N, Tsukikawa Y, Chen R, Sun Y, Chan O, Pagano I, Peres R, Hokutan K, Igari F, Chan KS, Rosser CJ. (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 (Feb)(18): 57.
  • Chen R, Yang L, Goodison S, Sun Y. (2020) Deep learning approach to identifying cancer subtypes using high-dimensional genomic data. Bioinformatics (Mar), 5(36): 1476–1483.
  • LaMonte MJ, Andrews CA, Hovey KM, Buck MJ, Li L, McSkimming DI, Banack HR, Rotterman J, Sun Y, Kirkwood K, Wactawski-Wende J. (2020) Subgingival microbiome is associated with alveolar bone loss measured 5-years later in postmenopausal women. Journal of Periodontology (Oct)
  • Sohn J, Sun Y, Genco RJ, Kirkwood KL. (2020) The periodontal microenvironment: a potential reservoir for intestinal pathobionts in Crohn’s disease. Current Oral Health Reports (Jan)(7): 37-44.
  • Zheng W, Wang K, Sun Y, Kuo SM. (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 (Oct), 10(13): e0205055.
  • Rossetti S, Ren M, Visconti N, Corlazzoli F, Gagliostro V, Somenzi G, Yao J, Sun Y, Sacchi N. (2016) Tracing anti-cancer and cancer-promoting actions of all-trans retinoic acid in breast cancer to a RARa epigenetic mechanism of mammary epithelial cell fate. Oncotarget (Dec), 7(52): 87064-87080.
  • Cai Y, Zheng W, Yao J, Yang Y, Mai V, Mao Q, Sun Y. (2017) ESPRIT-Forest: parallel clustering of massive amplicon sequence data in subquadratic time. PLOS Computational Biology (Apr), 13(4): e1005518.
  • Poppenberg KE, Tutino VM, Li L, Waqas M, June A, Chaves L, Jiang K, Jarvis JN, Sun Y, Snyder KV, Levy EI, Siddiqui AH, Kolega J, Meng H. (2020) Classification Models using Circulating Neutrophil Transcripts Can Detect Unruptured Intracranial Aneurysm. Journal of Translational Medicine (Oct)(18): 392.
  • Sun Y, Cai Y, Mai V, Farmerie W, Yu F, Li J, Goodison S. (2010) Advanced computational algorithms for microbial community analysis using massive 16S rRNA sequence data. Nucleic Acids Research (Dec), 38(22).
  • Poppenberg KE, Li L, Waqas M, Paliwal N, Jiang K, Jarvis JN, Sun Y, Snyder KV, Levy EI, Siddiqui AH, Kolega J, Meng H, Tutino VM. (2020) Whole blood transcriptome biomarkers of unruptured intracranial aneurysm. PLOS One (Nov), 11(15): e0241838.
  • Lott K, Mukhopadhyay S, Li J, Wang J, Yao J, Sun Y, Qu J, Read L. (2015) Arginine methylation of DRBD18 differentially impacts its opposing effects on the trypanosome transcriptome. Nucleic Acids Research (Jun), 43(11): 5501-5523.
  • Rosser CJ, Liu L, Sun Y, Villicana P, McCullers M, Porvasnik S, Young PR, Parker AS, Goodison S. (2009) Bladder cancer-associated gene expression signatures identified by profiling of exfoliated urothelia. Cancer Epidemiology, Biomarkers and Prevention (Feb), 18(2): 444-453.
  • Sun Y, Yao J, Nowak N, Goodison S. (2014) Cancer progression modeling using static sample data. Genome Biology (Jan), 15(8): 440-456.
  • Zheng W, Tsompana M, Ruscitto A, Sharma A, Genco R, Sun Y*, Buck M*. (2015) An accurate and efficient experimental approach for characterization of the complex oral microbiota. Microbiome (Jan), 3(48).
  • Sun Y, Liu Z, Todorovic S, Li J. (2007) Adaptive boosting for SAR automatic target recognition. IEEE Transactions on Aerospace and Electronic Systems (Jan), 43(1): 112-125.
  • Urquidi V, Goodison S, Cai Y, Sun Y, Rosser CJ. (2012) A candidate molecular biomarker panel for the detection of bladder cancer. Cancer Epidemiology, Biomarkers and Prevention (Dec), 21(12): 2149-2158.
  • Wang Y, Sun Y, Li J, Stoica P. (2005) Adaptive imaging for forward-looking ground penetrating radar. IEEE Transactions on Aerospace and Electronic Systems (Jul), 41(3): 922-936.
  • Sun Y, Li J. (2005) Adaptive learning approach to landmine detection. IEEE Transactions on Aerospace and Electronic Systems (Jul), 41(3): 973-985.
  • Sun Y, Li X, Li J. (2005) Practical landmine detector using forward-looking ground penetrating radar. Electronics Letters (Jan), 41(2): 97-98.
  • Sun Y, Todorovic S, Li J. (2006) Reducing the overfitting of AdaBoost by controlling its data distribution skewness. International Journal of Pattern Recognition and Artificial Intelligence (Nov), 20(7): 1093-1116.
  • Zhang X, Wang C, Zhang Y, Sun Y, Mou Z. (2012) The Arabidopsis mediator complex subunit16 positively regulates salicylate-mediated systemic acquired resistance and jasmonate/ethylene-induced defense pathways. Plant Cell (Oct), 24(10): 4294-4309.
  • Zhang X, Yao J, Zhang Y, Sun Y, Mou Z. (2013) The Arabidopsis mediator complex subunits MED14/SWP and MED16/SFR6/IEN1 differentially regulate defense gene expression in plant immune responses. The Plant Journal (Apr), 75(3): 484-497.
  • Hickman D, Jones MK, Zhu S, Kirkpatrick E, Ostrov DA, Wang X, Ukhanova M, Sun Y, Mai V, Salemi M. (2014) The effect of malnutrition on norovirus infection. mBio (Jan), 5(2): e0103-13.
  • Chen R, Goodison S, Sun Y. (2020) Molecular profiles of matched primary and metastatic tumor samples support a linear evolutionary model of breast cancer. Cancer Research (Jan)(80): 170-174.
  • Wei W, Wu X, Liang J, Cui J, Sun Y. (2018) Discernibility matrix based incremental attribute reduction for dynamic data. Knowledge-Based Systems (Jan)(14): 142-157.
  • Sun Y, Cai Y, Huse SM, Knight R, Farmerie WG, Wang X, Mai V. (2012) A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. Briefings in Bioinformatics (Jan), 13(1): 107-121.
  • Goodison S, Sun Y, Urquidi V. (2010) Derivation of cancer diagnostic and prognostic signatures from gene expression data. Bioanalysis (May), 2(5): 855-862.
  • Sun Y, Urquidi V, Goodison S. (2010) Derivation of molecular signatures for breast cancer recurrence prediction using a two-way validation approach. Breast Cancer Research and Treatment (Feb), 119(3): 593-599.
  • Sen R, Raychoudhury R, Cai Y, Sun Y, Lietze VU, Boucias DG, Scharf ME. (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 (Jul), 14: 491-500.
  • Sun Y, Todorovic S, Li J. (2007) Increasing the robustness of boosting algorithms within the linear-programming framework. The Journal of VLSI Signal Processing (Jun), 48(1): 5-20.
  • Bandyopadhyay N, Kahveci T, Goodison S, Sun Y, Ranka S. (2010) Pathway-based feature selection algorithm for cancer microarray data. Advances in Bioinformatics (Mar), 3: 53298.
  • Bandyopadhyay N, Kahveci T, Goodison S, Sun Y, Ranka S. (2009) Pathway-based feature selection algorithm for cancer microarray data. Advances in Bioinformatics (Jan)53298.
  • Cai, Y, Sun Y. (2011) ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time. Nucleic Acids Research (Aug), 39(14): e95.
  • Sun Y, Cai Y, Liu L, Yu F, Farrell ML, McKendree W, Farmerie W. (2009) ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Research (Jun), 37(10).
  • Sun Y, Wu D. (2009) Feature extraction through local learning. Statistical Analysis and Data Mining (Jan), 2(1): 34-47.
  • Wang J, Huang J, Sun Y, Gao X . (2015) Feature selection and multi-kernel learning for adaptive graph regularized nonnegative matrix factorization. Expert Systems With Applications (Jan), 42(3): 1278-1286.
  • Yao J, Mao Q, Mai V, Goodison S, Sun Y. (2015) Feature selection for unsupervised learning through local learning. Pattern Recognition Letters (Jan), 53(1): 100-107.
  • Mai V, Young CM, Ukhanova M, Wang X, Sun Y, Casella G, Theriaque D, Li N, Sharma R, Hudak M, Neu J. (2011) Fecal microbiota in premature infants prior to necrotizing enterocolitis. PLoS One (Jan), 6(6).
  • Wang J, Sun Y. (2014) From one graph to many: ensemble transduction for content-based database retrieval. Knowledge-Based Systems (Jan), 65: 31-37.
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Books and Book Chapters:

  • Sun Y, Cai Y. (2011) Handbook of Molecular Microbial Ecology: Metagenomics and Complementary Approaches. In: Estimating Species Richness Using Large Collections of 16S rRNA Pyrosequences. Wiley-Blackwell, 461-471.
  • Sun Y. (2007) Computational Methods of Feature Selection. In: Feature Weighting through Local Learning. Chapman and Hall/CRC Press

Abstracts:

  • Sun Y, Goodison S. (2007) Predicting Breast Cancer Metastasis by Integrating Both Clinical and Genetic Markers. (Jun) 229-235
  • Sun Y, Todorovic S, Goodison S. (2008) A Feature Selection Algorithm Capable of Handling Extremely Large Data Dimensionality. (Apr) 530-540
  • Sun Y, Wu D. (2008) A RELIEF Based Feature Extraction Algorithm. (Apr) 188-195
  • Sun Y, Todorovic S, Li J, Wu D. (2005) A Robust Linear-programming Based Boosting Algorithm. (Sep) 49-54
  • Sun Y, Cai Y, Goodison S. (2008) Combining Nomogram and Microarray Data for Predicting Prostate Cancer Recurrence. (Oct) 1-7
  • Mammen MJ, Buck M, Sun Y, Waldron N, Valiyaparambil S, Wrona C, Sethi S. (2018) Distinct Airway Microbiome Patterns Associated with Lung Cancer Development in a COPD Cohort. (May)
  • Sun Y, Yu F, Liu L, Farmerie W. (2007) Estimating Microbial Population Densities Based on Genomic Signatures. (Jun) 163-168
  • Sun Y, Liu L, Popp M, Farmerie W. (2006) Estimation of Cross-hybridization Signals Using Support Vector Regression. (Jun) 17-21
  • Cai Y, Sun Y, Cheng Y, Li J, Goodison S. (2010) Fast Implementation of l1 Regularized Learning Algorithms Using Gradient Descent Methods. (Apr) 862-871
  • Sun Y, Li J. (2006) Iterative RELIEF for Feature Weighting. (Jun) 1035-1051
  • Cai Y, Sun Y, Li J, Goodison S. (2009) Online Feature Selection Algorithm with Bayesian L-1 Regularization. (Apr) 401-413
  • Cheng Y, Cai Y, Sun Y, Li J. (2008) Semi-supervised Feature Selection under the Logistic I-RELIEF Framework. (Dec) 1-4
  • Sun Y, Li L, Hager W. (2004) Two New Regularized AdaBoost Algorithms. (Dec) 41-48
  • Sun Y, Todorovic S, Li J, Wu D. (2005) Unifying Error-Correcting and Output-Code AdaBoost within the Margin Framework. (Aug) 872-879
  • Pascoe C, Lawande A, Lam H, George A, Sun Y, Farmerie W, Herbordt M. (2010) Reconfigurable Supercomputing with Scalable Systolic Arrays and In-Stream Control for Wavefront Genomics Processing. (Jul) 1-6
  • Millen AE, Hall K, Kamm KB, Liu Z, Krajewski BJ, Wactawski-Wende J, Lema G, Buck M, Blair RH, Sun Y, McSkimming D, Mares JA. (2019) Mail-based stool collection in women with and without age-related macular degeneration (AMD). 2019 ARVO Annual Meeting. Vancouver, (Jul) 56-56Poster
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Presentations:

  • "Cancer progression modeling using massive static sample data" UB Cancer Research Consortium (2020)
  • "Cancer progression modeling using massive static sample data" Department of Biological Data Science, Dartmouth College (2020)
  • "Cancer progression modeling using massive static sample data" Department of Microbiology and Immunology, SUNY Buffalo (2016)
  • "Parallel hierarchical clustering in linearithmic time for large-scale sequence analysis" International Conference on Data Mining (2015)
  • "Feature selection for nonlinear regression and its application to cancer research" 15th SIAM International Conference on Data Mining (2015)
  • "Machine learning approaches to cancer progression modeling" Roswell Park Cancer Research Institute (2013)
  • "Bioinformatics approaches to studying tumor progression" The UB2020 strength in Molecular Recognition in Biological Systems and Bioinformatics (2013)
  • "Toward optimal feature selection through local learning" Department of Computer Science, SUNY Buffalo (2012)
  • "Advanced computational algorithms for deep interrogation of the hidden microbial world" Virginia Commonwealth University (2011)
  • "Derivation of molecular signatures for accurate breast cancer prognosis" Cancer Topics Seminar Series; University of Florida (2011)
  • "Derivation of molecular signatures for accurate breast cancer prognosis" The University of Florida Cancer Topics Seminar Series (2011)
  • "Pyrosequencing technology for microbial community analysis" Summer School; Marine Biological Laboratory (2011)
  • "Advanced computational algorithms for mining massive high-dimensional biological data" H. Lee Moffitt Cancer Center & Research Institute; Biomedical Informatics Department (2011)
  • "Advanced computational algorithms for deep interrogation of microbial communities" International Census of Marine Microbes Workshop; Max Planck Institute for Marine Microbiology (2011)
  • "Advanced computational algorithms for deep interrogation of microbial communities" International Census of Marine Microbes Workshop; University of Southern California (2010)
  • "Molecular classification for breast cancer prognosis" MD Anderson Cancer Center (2008)
  • "Predicting breast cancer metastasis by integrating both clinical and genetic markers" International Conference on Bioinformatics and Computational Biology (2008)
  • "Machine learning techniques for biomarker identification" National Cancer Institute (2007)
  • "A robust linear-programming based boosting algorithm" IEEE International Workshop on Machine Learning for Signal Processing (2005)
See all (9 more)

Service Activities:

  • Biomedical Computing and Health Informatics (BCHI) Study Section, National Institutes of Health; ad hoc reviewer (2020)
  • CTSI Translational Pilot Studies Program; Reviewer (2020)
  • Faculty Council; Faculty Council Member (2019–present)
  • Research Reports (2017–present)
  • IMPACT Funding Program; Reviewer (2016)
  • CTSA Translational Pilot Study Program; Reviewer (2016)
  • Bioinformatics Research Scientist Search Committee (2016)
  • Metagenomics Faculty Search Committee (2014)
  • Computational Biology Program/CISE Directorate, National Science Foundation; ad hoc reviewer (2014–2019)
  • International Conference on Machine Learning; Program Committee Member (2013–2014)
  • Bioinformatics service and informal consultations provided to UB colleagues (2012–present)
  • MD-PhD and PPBS Program Admissions; Discussant (2012–present)
  • Frontiers in Evolutionary and Genomic Microbiology (2012–present)
  • Frontiers in Genetics (2012–present)
  • SIAM International Conference on Data Mining; Program Committee Member (2011)
  • Nucleic Acids Research, Genome Biology, Genome Research, PLoS ONE, BMC Bioinformatics, PLoS Computational Biology, Bioinformatics, Frontiers in Biosciences, Applied and Environmental Microbiology, The ISME Journal, IEEE Transactions on Pattern Analysis and Machine Intelligence, IEEE Transactions on Neural Networks, IEEE Transactions on Knowledge and Data Engineering, IEEE Trans. on Fuzzy Systems, Journal of Pattern Recognition Research, Neurocomputing, Pattern Recognition, Pattern Recognition Letters, Computational Optimization and Applications, IEE Proceedings-Radar, Sonar and Navigation, IEEE Signal Processing Letters, IEEE Transactions on Aerospace and Electronic Systems, IEEE Transactions on Instrumentation and Measurement, IEEE Transactions on Geoscience and Remote Sensing, Biomedical Signal Processing and Control, Chinese Optics Letters, Knowledge and Information Systems, Artificial Intelligence, International Journal of Data Mining and Bioinformatics, Scientific Reports, Microbiome, Journal of Machine Learning Research, Molecular Informatics, IEEE/ACM Transactions on Computational Biology and Bioinformatics; ad hoc reviewer (2010–present)
  • IEEE International Conference on Bioinformatics and Bioengineering; Program Committee Member (2007)

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Contact Information

Room 5205
955 Main Street
Buffalo, New York 14203
Phone: 716 - 8811374
yijunsun@buffalo.edu