CISR Publications

S. Su, G. Chhabra, M. Ndiaye, C. Singh, T. Ye, W. Huang, C. Dewey, V. Setaluri, and N. Ahmad (2021) PLK1 and NOTCH Positively Correlate in Melanoma and Their Combined Inhibition Results in Synergistic Modulations of Key Melanoma Pathways. Molecular Cancer Therapeutics. 20: 161-172. doi:10.1158/1535-7163.MCT-20-0654

Baschnagel AM, Kaushik S, Durmaz A, Goldstein S, Ong IM, Abel Lindsey, Clark PA, Gurel Z, Leal T, Buehler D, Iyer G, Scott JG, Kimple RJ. Development and characterization of patient-derived xenografts from non-small cell lung cancer brain metastases. Sci Rep. 2021 Jan 28;11(1):2520. doi: 10.1038/s41598-021-81832-1. Pubmed PMID: 33510214; Pubmed Central PMCID: PMC7843608

DK Singh, Z Lu, AM Kuehnl, R Welch, IM Ong, R Wen, X Pan. “A lineage-specific Requirement for YY1 Polycomb Group Protein Function in Early T cell Development”, ALFV Assumpcao, GFu, Development, 2021

Kubica, M. Lara-Velazquez, M. Bam, S. Sira, I. Ong, P. Liu, R. Priya, S. Salamat, R. R. Brutkiewicz, M. Dey, MR1 overexpression correlates with poor clinical prognosis in glioma patients. Neuro-Oncology Advances, vdab034 (2021). PMID: N/A; DOI: 10.1093/noajnl/vdab034

H. S. Jung, G. Uenishi, M. A. Park, P. Liu, K. Suknuntha, M. Raymond, Y. J. Choi, J. A. Thomson, I. M. Ong, I. I. Slukvin, SOX17 integrates HOXA and arterial programs in hemogenic endothelium to drive definitive lympho-myeloid hematopoiesis. Cell Rep. 34, 108758 (2021). PMID: 33596423; DOI: 10.1016/j.celrep.2021.108758

Liu, A. Soukup, E. Bresnick, C. Dewey, and S. Keles. (2020) PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments.Genome Research. 30: 1655-1666. doi:10.1101/gr.252445.119

McIlwain SJ, Wu Z, Wetzel M, Belongia D, Jin Y, Wenger K, Ong IM, Ge Y. Enhancing Top-Down Proteomics Data Analysis by Combining Deconvolution Results through a Machine Learning Strategy. J Am Soc Mass Spectrom. 2020 May 6;31(5):1104-1113. doi: 10.1021/jasms.0c00035. Epub 2020 Apr 8. PubMed PMID: 32223200; PubMed Central PMCID: PMC7909725.

Wu Z, Roberts DS, Melby JA, Wenger K, Wetzel M, Gu Y, Ramanathan SG, Bayne EF, Liu X, Sun R, Ong IM, McIlwain SJ, Ge Y. MASH Explorer: A Universal Software Environment for Top-Down Proteomics. J Proteome Res. 2020 Sep 4;19(9):3867-3876. doi: 10.1021/acs.jproteome.0c00469. Epub 2020 Aug 24. PubMed PMID: 32786689; PubMed Central PMCID: PMC7728713.

Fischer MM, Senthil Kumar G, Hu R, Goldstein S, Ong IM, Miller MC, Brennan SR, Kausik S, Abel L, Nickel KP, Iyer G, Harari PM, Kimple RJ, Baschnagel AM. Fibroblast Growth Factor Receptors as Targets for Radiosensitization in Head and Neck Squamous Cell Carcinomas. Int J Radiat Oncol Biol Phys. 2020 Jul 15;107(4):793-803. doi: 10.1016/j.ijrobp.2020.03.040. PubMed PMID: 32298810; PubMed Central PMCID: PMC7321889

M. Ivancic, B. Megna, S. Aleshin-Guendel, Y. Sverchkov, M. Craven, M. Reichelderfer, P. Pickhardt, M. Sussman, and G. Kennedy (2020). Noninvasive Detection of Colorectal Carcinomas Using Serum Protein Biomarkers. Journal of Surgical Research 246:160-169.

S. S. Schoeff, X. Shi, W. G. Young, C. W. Whited, R. S. Soni, P. Liu, I. M. Ong, S. H. Dailey, N. V. Welham, Proteomic and Genomic Methylation Signatures of Idiopathic Subglottic Stenosis. Laryngoscope (2020). PMID: 32619300; DOI: 10.1002/lary.28851

P. Liu, A. A. Soukup, E. H. Bresnick, C. N. Dewey, S. Keleş, PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments. Genome Res. 30, 1655–1666 (2020). PMID: 32958497; DOI: 10.1101/gr.252445.119

K. D. Johnson, D. J. Conn, E. Shishkova, K. R. Katsumura, P. Liu, S. Shen, E. A. Ranheim, S. G. Kraus, W. Wang, K. R. Calvo, A. P. Hsu, S. M. Holland, J. J. Coon, S. Keles, E. H. Bresnick, Constructing and deconstructing GATA2-regulated cell fate programs to establish developmental trajectories. J Exp Med. 217 (2020). PMID: 32736380; DOI: 10.1084/jem.20191526

Kiblawi, D. Chasman, A. Henning, E. Park, H. Poon, M. Gould, P. Ahlquist and M. Craven (2019). Augmenting Subnetwork Inference with Information Extracted from the Scientific Literature. PLoS Computational Biology 15(6):e1006758.

A. A. Soukup, Y. Zheng, C. Mehta, J. Wu, P. Liu, M. Cao, I. Hofmann, Y. Zhou, J. Zhang, K. D. Johnson, K. Choi, S. Keles, E. H. Bresnick, Single-nucleotide human disease mutation inactivates a blood-regenerative GATA2 enhancer. J Clin Invest. 129, 1180–1192 (2019). PMID: 30620726; DOI: 10.1172/JCI122694

Pak HH, Cummings NE, Green CL, Brinkman JA, Yu D, Tomasiewicz JL, Yang SE, Boyle C, Konon EN, Ong IM, Lamming DW. The Metabolic Response to a Low Amino Acid Diet is Independent of Diet-Induced Shifts in the Composition of the Gut Microbiome. Sci Rep. 2019 Jan 11;9(1):67. doi: 10.1038/s41598-018-37177-3. PubMed PMID: 30635612; PubMed Central PMCID: PMC6329753.

Pasch CA, Favreau PF, Yueh AE, Babiarz CP, Gillette AA, Sharick JT, Karim MR, Nickel KP, DeZeeuw AK, Sprackling CM, Emmerich PB, DeStefanis RA, Pitera RT, Payne SN, Korkos DP, Clipson L, Walsh CM, Miller D, Carchman EH, Burkard ME, Lemmon KK, Matkowskyj KA, Newton MA, Ong IM, Bassetti MF, Kimple RJ, Skala MC, Deming DA. Patient-Derived Cancer Organoid Cultures to Predict Sensitivity to Chemotherapy and Radiation. Clin Cancer Res. 2019 Sep 1;25(17):5376-5387. doi: 10.1158/1078-0432.CCR-18-3590. Epub 2019 Jun 7. PubMed PMID: 31175091; PubMed Central PMCID: PMC6726566

Zahm CD, Colluru VT, McIlwain SJ, Ong IM, McNeel DG. TLR Stimulation during T-cell Activation Lowers PD-1 Expression on CD8⁺T Cells. Cancer Immunol Res. 2018 Nov;6(11):1364-1374. doi: 10.1158/2326-6066.CIR-18-0243. Epub 2018 Sep 10. PubMed PMID: 30201735; PubMed Central PMCID: PMC6215515.

Kim J, McIlwain S, Lee I, Ong I, Steve Cho, Prognostic value of baseline FDG PET/CT and MR images using machine learning algorithm in soft tissue sarcoma. Journal of nuclear medicine. 2018 May; 59(supplement 1):129.

Rhoads TW, Burhans MS, Chen VB, Hutchins PD, Rush MJP, Clark JP, Stark JL, McIlwain SJ, Eghbalnia HR, Pavelec DM, Ong IM, Denu JM, Markley JL, Coon JJ, Colman RJ, Anderson RM. Caloric Restriction Engages Hepatic RNA Processing Mechanisms in Rhesus Monkeys. Cell Metab. 2018 Mar 6;27(3):677-688.e5. doi: 10.1016/j.cmet.2018.01.014. PubMed PMID: 29514073; PubMed Central PMCID: PMC5844481.

Ong IM, Gonzalez JG, McIlwain SJ, Sawin EA, Schoen AJ, Adluru N, Alexander AL, Yu JJ. Gut microbiome populations are associated with structure-specific changes in white matter architecture. Transl Psychiatry. 2018 Jan 10;8(1):6. doi: 10.1038/s41398-017-0022-5. PubMed PMID: 29317592; PubMed Central PMCID: PMC5802560.

Feld SI, Woo KM, Alexandridis R, Wu Y, Liu J, Peissig P, Onitilo AA, Cox J, Page CD, Burnside ES. Improving Breast Cancer Risk Prediction by Using Demographic Risk Factors, Abnormality Features on Mammograms and Genetic Variants. AMIA Annu Symp Proc. 2018 Dec 5; 1252-1262. PubMed PMID: 30815167; PubMed Central PMCID: PMC6371301

Adam Swick, Andrew Stein, Timothy McCulloch, Gregory Hartig, Irene M. Ong, Emmanuel Sampene, Prashanth Prabakaran, Cheng Liu, Randall Kimple “Defining the boundaries and expanding the utility of head and neck cancer patient derived xenografts” Oral Oncology 2017.

Adam Swick, Prashanth J. Prabakaran, Margot Miller, Amal Javaid, Michael Fisher, Emmanuel Sampene, Irene M. Ong, Mari Iida, Deric L Wheeler, Kwangok Nickel, Justine Y Bruce, and Randall J. Kimple “Co-targeting mTORC and EGFR signaling as a therapeutic strategy in HNSCC” Molecular Cancer Therapeutics 2017.

Alice Chakanira, Pamela Westmark, Irene Ong, John Sheehan “Tissue Factor-Factor VIIa Complex triggers Protease Activated Receptor 2-dependent Growth Factor Release and Migration in Ovarian Cancer” To appear in Gynecologic Oncology 2017.

Cai, W.; Tucholski, T.; Chen, B.; Alpert, A. J.; McIlwain, S.; Kohmoto, T.; Jin, S.; Ge, Y. Top–down Proteomics of Large Proteins up to 223 kDa Enabled by Serial Size Exclusion Chromatography Strategy. Anal Chem., 2017, 89, 5467-5475.

Chen, B.; Guo, X.; Tucholski, T.; Lin, Z.; Mcilwain, S.; Ge, Y. The impact of phosphorylation on electron capture dissociation of proteins: a top-down perspective. J. Am. Soc. Mass Spectrom., 2017, DOI: 10.1007/s13361-017-1710-3.

Feld SI, Cobian AG, Tevis SE, Kennedy GD, Craven MW. Modeling the Temporal Evolution of Postoperative Complications. AMIA Annual Symposium proceedings AMIA Symposium. 2016;2016:551-9. Epub 2017/03/09. PubMed PMID: 28269851; PMCID: PMC5333217.

Swick AD, Prabakaran PJ, Miller MC, Javaid AM, Fisher MM, Sampene E, Ong IM, Hu R, Iida M, Nickel KP, Bruce JY, Wheeler DL, Kimple RJ. Co-targeting mTORC and EGFR signaling as a therapeutic strategy in HNSCC. Mol Cancer Ther. 2017. doi: 10.1158/1535-7163.MCT-17-0115. PubMed PMID: 28446642; PMCID: PMC5505754.

Swick AD, Stein AP, McCulloch TM, Hartig GK, Ong IM, Sampene E, Prabakaran PJ, Liu CZ, Kimple RJ. Defining the boundaries and expanding the utility of head and neck cancer patient derived xenografts. Oral Oncol. 2017;64:65-72. doi: 10.1016/j.oraloncology.2016.11.017. PubMed PMID: 28024726; PMCID: PMC5218527.

Timothy W. Rhoads, Maggie S. Burhans, Vincent B. Chen, Paul D. Hutchins, Sean J. McIlwain, Hamid R. Eghbalnia, Derek M. Pavelec, Irene M. Ong, John M. Denu, John L. Markley, Joshua J. Coon, Ricki J. Colman, and Rozalyn M. Anderson.  Caloric restriction engages RNA processing pathways to reprogram metabolism. To appear Cell Metabolism 2017.

Wu CG, Chen H, Guo F, Yadav VK, McIlwain SJ, Rowse M, Choudhary A, Lin Z, Li Y, Gu T, Zhen A, Xu Q, Lee W, Resch E, Johnson B, Ge Y, Ong IM, Burkard M, Ivarsson Y, Xing Y.  PP2A-B’ holoenzyme substrate recognition, regulation, and role in cytokinesis. To appear Cell Discovery 2017.

Ashok Singh, Estelle Willems, Anupama Singh, Bilal Bin Hafeez, Irene Ong, Suresh L. Mehta and Ajit Kumar Verma “Ultraviolet radiation-induced tumor necrosis factor alpha, which is linked to the development of cutaneous SCC, modulates differential epidermal microRNAs expression.” Oncotarget, 2016. PMID: 26918454.

Ashok Singh, Estelle Willems, Anupama Singh, Irene Ong, and Ajit Kumar Verma “Ultraviolet radiation-induced differential microRNA expression in the skin of hairless SKH1 mice, a widely used mouse model for dermatology research.” Oncotarget, 2016.

Baar EL, Carbajal KA, Ong IM, Lamming DW. Sex- and tissue-specific changes in mTOR signaling with age in C57BL/6J mice. Aging cell. 2016;15(1):155-66. Epub 2015/12/24. doi: 10.1111/acel.12425. PubMed PMID: 26695882; PMCID: PMC4717274.

Cevik M, Ergun MA, Stout NK, Trentham-Dietz A, Craven M, Alagoz O. Using Active Learning for Speeding up Calibration in Simulation Models. Medical decision making : an international journal of the Society for Medical Decision Making. 2016;36(5):581-93. Epub 2015/10/17. doi: 10.1177/0272989×15611359. PubMed PMID: 26471190; PMCID: PMC4833719.

Craven M, Page CD. Big Data in Healthcare: Opportunities and Challenges. Big data. 2015;3(4):209-10. Epub 2016/07/22. doi: 10.1089/big.2015.29001.mcr. PubMed PMID: 27441403.

Fan J, Wu Y, Yuan M, Page D, Liu J, Ong IM, Peissig P, Burnside E. Structure-Leveraged Methods in Breast Cancer Risk Prediction. J Mach Learn Res. 2016;17. PubMed PMID: 28559747; PMCID: PMC5446896.

Fan, J., Wu, Y., Yuan, M., Page, D., Liu, J., Ong, I.M., Peissig, P., and Burnside, E.S. “Structure-leveraged methods in breast cancer risk prediction.” To appear in Journal of Machine Learning Research Special Issue 2016.

Feld SI, Tevis SE, Cobian AG, Craven MW, Kennedy GD. Multiple postoperative complications: Making sense of the trajectories. Surgery. 2016;160(6):1666-74. Epub 2016/10/23. doi: 10.1016/j.surg.2016.08.047. PubMed PMID: 27769659.

Hao L, Greer T, Page D, Shi Y, Vezina CM, Macoska JA, Marker PC, Bjorling DE, Bushman W, Ricke WA, Li L. In-Depth Characterization and Validation of Human Urine Metabolomes Reveal Novel Metabolic Signatures of Lower Urinary Tract Symptoms. Scientific reports. 2016;6:30869. Epub 2016/08/10. doi: 10.1038/srep30869. PubMed PMID: 27502322; PMCID: PMC4977550.

Jiang P, Nelson JD, Leng N, Collins M, Swanson S, Dewey CN, Thomson JA, Stewart R. Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability. Developmental biology. 2016. Epub 2016/08/01. doi: 10.1016/j.ydbio.2016.05.024. PubMed PMID: 27475628; PMCID: PMC5272911.

Katsumura KR, Ong IM, DeVilbiss AW, Sanalkumar R, Bresnick EH. GATA Factor-Dependent Positive-Feedback Circuit in Acute Myeloid Leukemia Cells. Cell reports. 2016;16(9):2428-41. Epub 2016/08/23. doi: 10.1016/j.celrep.2016.07.058. PubMed PMID: 27545880; PMCID: PMC5154384.

Koichi Katsumura, Irene Ong, Andrew DeVilbiss, Rajendran Sanalkumar, Emery Bresnick “GATA factor-dependent positive-feedback circuit controls acute myeloid leukemia cell proliferation” American Society of Hematology. 2016. Vol. 128 no. 22 1706.

Kolb AW, Lee K, Larsen I, Craven M, Brandt CR. Quantitative Trait Locus Based Virulence Determinant Mapping of the HSV-1 Genome in Murine Ocular Infection: Genes Involved in Viral Regulatory and Innate Immune Networks Contribute to Virulence. PLoS pathogens. 2016;12(3):e1005499. Epub 2016/03/11. doi: 10.1371/journal.ppat.1005499. PubMed PMID: 26962864; PMCID: PMC4786273.

Kuang Z, Thomson J, Caldwell M, Peissig P, Stewart R, Page D. Computational Drug Repositioning Using Continuous Self-Controlled Case Series. KDD. 2016;2016:491-500. doi: 10.1145/2939672.2939715. PubMed PMID: 28316874; PMCID: PMC5351812.

Lee K, Kolb AW, Larsen I, Craven M, Brandt CR. Mapping Murine Corneal Neovascularization and Weight Loss Virulence Determinants in the Herpes Simplex Virus 1 Genome and the Detection of an Epistatic Interaction between the UL and IRS/US Regions. Journal of virology. 2016;90(18):8115-31. Epub 2016/07/08. doi: 10.1128/jvi.00821-16. PubMed PMID: 27384650; PMCID: PMC5008079.

Liu P, Sanalkumar R, Bresnick EH, Keles S, Dewey CN. Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq. Genome research. 2016;26(8):1124-33. Epub 2016/07/14. doi: 10.1101/gr.199174.115. PubMed PMID: 27405803; PMCID: PMC4971760.

McIver SC, Katsumura KR, Davids E, Liu P, Kang YA, Yang D, Bresnick EH. Exosome complex orchestrates developmental signaling to balance proliferation and differentiation during erythropoiesis. eLife. 2016;5. Epub 2016/08/21. doi: 10.7554/eLife.17877. PubMed PMID: 27543448; PMCID: PMC5040589.

Skye C. McIver, Koichi R. Katsumura, Elsa Davids, Peng Liu, Yoon-A Kang, David Yang, Emery H. Bresnick. “Exosome complex orchestrates developmental signaling to balance proliferation and differentiation during erythropoiesis.” eLife 2016.

Somnay YR, Craven M, McCoy KL, Carty SE, Wang TS, Greenberg CC, Schneider DF. Improving diagnostic recognition of primary hyperparathyroidism with machine learning. Surgery. 2017;161(4):1113-21. Epub 2016/12/19. doi: 10.1016/j.surg.2016.09.044. PubMed PMID: 27989606; PMCID: PMC5367958.

Tanimura N, Miller E, Igarashi K, Yang D, Burstyn JN, Dewey CN, Bresnick EH. Mechanism governing heme synthesis reveals a GATA factor/heme circuit that controls differentiation. EMBO reports. 2016;17(2):249-65. Epub 2015/12/25. doi: 10.15252/embr.201541465. PubMed PMID: 26698166; PMCID: PMC5290819.

Tevis SE, Cobian AG, Truong HP, Craven MW, Kennedy GD. Implications of Multiple Complications on the Postoperative Recovery of General Surgery Patients. Annals of surgery. 2016;263(6):1213-8. Epub 2016/05/12. doi: 10.1097/sla.0000000000001390. PubMed PMID: 27167563.

Tuncbag N, Gosline SJ, Kedaigle A, Soltis AR, Gitter A, Fraenkel E. Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package. PLoS computational biology. 2016;12(4):e1004879. Epub 2016/04/21. doi: 10.1371/journal.pcbi.1004879. PubMed PMID: 27096930; PMCID: PMC4838263.

Wu Y, Abbey CK, Chen X, Liu J, Page DC, Alagoz O, Peissig P, Onitilo AA, Burnside ES. Developing a utility decision framework to evaluate predictive models in breast cancer risk estimation. Journal of medical imaging (Bellingham, Wash). 2015;2(4):041005. Epub 2016/02/03. doi: 10.1117/1.jmi.2.4.041005. PubMed PMID: 26835489; PMCID: PMC4718446.

Wu Y, Abbey CK, Liu J, Ong I, Peissig P, Onitilo AA, Fan J, Yuan M, Burnside ES. Discriminatory power of common genetic variants in personalized breast cancer diagnosis. Proceedings of SPIE–the International Society for Optical Engineering. 2016;9787. Epub 2016/06/10. doi: 10.1117/12.2217030. PubMed PMID: 27279675; PMCID: PMC4894298.

Wu, Yirong, Abbey, Craig K., Liu, Jie, Ong, I.M., Peissig, Peggy, Onitilo, Adedayo A., Fan, Jun, Yuan, Ming, and Burnside, Elizabeth S. “Discriminatory power of common genetic variants in personalized breast cancer diagnosis.” SPIE Medical Imaging 2016.

Burnside ES, Liu J, Wu Y, Onitilo AA, McCarty CA, Page CD, Peissig PL, Trentham-Dietz A, Kitchner T, Fan J, Yuan M. Comparing Mammography Abnormality Features to Genetic Variants in the Prediction of Breast Cancer in Women Recommended for Breast Biopsy. Academic radiology. 2016;23(1):62-9. Epub 2015/10/31. doi: 10.1016/j.acra.2015.09.007. PubMed PMID: 26514439; PMCID: PMC4684977.

Ferreira P, Fonseca NA, Dutra I, Woods R, Burnside E. Predicting malignancy from mammography findings and image-guided core biopsies. International journal of data mining and bioinformatics. 2015;11(3):257-76. Epub 2015/09/04. PubMed PMID: 26333262; PMCID: PMC4764253.

Hewitt KJ, Kim DH, Devadas P, Prathibha R, Zuo C, Sanalkumar R, Johnson KD, Kang YA, Kim JS, Dewey CN, Keles S, Bresnick EH. Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome. Molecular cell. 2015;59(1):62-74. Epub 2015/06/16. doi: 10.1016/j.molcel.2015.05.020. PubMed PMID: 26073540; PMCID: PMC4499333.

J. Liu, Y. Wu,I. Ong,D. Page, P. Peissig, C. McCarty, A.A. Onitilo, E. Burnside. Leveraging Interaction between Genetic Variants and Mammographic Findings for Personalized Breast Cancer Diagnosis. AMIA Jt Summits Transl Sci Proc. 2015; 2015: 107–111.

Johnson KD, Kong G, Gao X, Chang YI, Hewitt KJ, Sanalkumar R, Prathibha R, Ranheim EA, Dewey CN, Zhang J, Bresnick EH. Cis-regulatory mechanisms governing stem and progenitor cell transitions. Science advances. 2015;1(8):e1500503. Epub 2015/11/26. doi: 10.1126/sciadv.1500503. PubMed PMID: 26601269; PMCID: PMC4643771.

Kuusisto F, Dutra I, Elezaby M, Mendonca EA, Shavlik J, Burnside ES. Leveraging Expert Knowledge to Improve Machine-Learned Decision Support Systems. AMIA Joint Summits on Translational Science proceedings AMIA Joint Summits on Translational Science. 2015;2015:87-91. Epub 2015/08/26. PubMed PMID: 26306246; PMCID: PMC4525246.

Lee K, Kolb AW, Sverchkov Y, Cuellar JA, Craven M, Brandt CR. Recombination Analysis of Herpes Simplex Virus 1 Reveals a Bias toward GC Content and the Inverted Repeat Regions. Journal of virology. 2015;89(14):7214-23. Epub 2015/05/01. doi: 10.1128/jvi.00880-15. PubMed PMID: 25926637; PMCID: PMC4473588.

Leng N, Li Y, McIntosh BE, Nguyen BK, Duffin B, Tian S, Thomson JA, Dewey CN, Stewart R, Kendziorski C. EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments. Bioinformatics (Oxford, England). 2015;31(16):2614-22. Epub 2015/04/08. doi: 10.1093/bioinformatics/btv193. PubMed PMID: 25847007; PMCID: PMC4528625.

Li B, Fillmore N, Bai Y, Collins M, Thomson JA, Stewart R, Dewey CN. Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome biology. 2014;15(12):553. Epub 2015/01/23. doi: 10.1186/s13059-014-0553-5. PubMed PMID: 25608678; PMCID: PMC4298084.

Liu J, Page D, Peissig P, McCarty C, Onitilo AA, Trentham-Dietz A, Burnside E. New genetic variants improve personalized breast cancer diagnosis. AMIA Joint Summits on Translational Science proceedings AMIA Joint Summits on Translational Science. 2014;2014:83-9. Epub 2015/02/27. PubMed PMID: 25717406; PMCID: PMC4333695.

Liu J, Wu Y, Ong I, Page D, Peissig P, McCarty C, Onitilo AA, Burnside E. Leveraging Interaction between Genetic Variants and Mammographic Findings for Personalized Breast Cancer Diagnosis. AMIA Joint Summits on Translational Science proceedings AMIA Joint Summits on Translational Science. 2015;2015:107-11. Epub 2015/08/26. PubMed PMID: 26306250; PMCID: PMC4525263.

Phillip O, Vishal B, Tushar K, David P, Sriraam N. Artificial Intelligence in Medicine. springer. 2015;9105:195-204. doi: 10.1007/978-3-319-19551-3_26.

Schwartz MP, Hou Z, Propson NE, Zhang J, Engstrom CJ, Santos Costa V, Jiang P, Nguyen BK, Bolin JM, Daly W, Wang Y, Stewart R, Page CD, Murphy WL, Thomson JA. Human pluripotent stem cell-derived neural constructs for predicting neural toxicity. Proceedings of the National Academy of Sciences of the United States of America. 2015;112(40):12516-21. Epub 2015/09/24. doi: 10.1073/pnas.1516645112. PubMed PMID: 26392547; PMCID: PMC4603492.

Weiss J, Kuusisto F, Boyd K, Liu J, Page D. Machine Learning for Treatment Assignment: Improving Individualized Risk Attribution. AMIA Annual Symposium proceedings AMIA Symposium. 2015;2015:1306-15. Epub 2015/01/01. PubMed PMID: 26958271; PMCID: PMC4765638.

Wu Y, Liu J, Del Rio AM, Page DC, Alagoz O, Peissig P, Onitilo AA, Burnside ES. Developing a clinical utility framework to evaluate prediction models in radiogenomics. Proceedings of SPIE–the International Society for Optical Engineering. 2015;9416. Epub 2015/02/21. doi: 10.1117/12.2081954. PubMed PMID: 27095854; PMCID: PMC4834184.

Zeng X, Li B, Welch R, Rojo C, Zheng Y, Dewey CN, Keles S. Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping. PLoS computational biology. 2015;11(10):e1004491. Epub 2015/10/21. doi: 10.1371/journal.pcbi.1004491. PubMed PMID: 26484757; PMCID: PMC4618727.

Almeida E, Ferreira P, Vinhoza T, Dutra I, Li J, Wu Y, Burnside E. ExpertBayes: Automatically refining manually built Bayesian networks. Proceedings of the International Conference on Machine Learning and Applications International Conference on Machine Learning and Applications. 2014;2014:362-6. Epub 2014/12/01. doi: 10.1109/icmla.2014.64. PubMed PMID: 27066596; PMCID: PMC4826063.

Chasman D, Gancarz B, Hao L, Ferris M, Ahlquist P, Craven M. Inferring host gene subnetworks involved in viral replication. PLoS computational biology. 2014;10(5):e1003626. Epub 2014/05/31. doi: 10.1371/journal.pcbi.1003626. PubMed PMID: 24874113; PMCID: PMC4038467.

Chasman D, Ho YH, Berry DB, Nemec CM, MacGilvray ME, Hose J, Merrill AE, Lee MV, Will JL, Coon JJ, Ansari AZ, Craven M, Gasch AP. Pathway connectivity and signaling coordination in the yeast stress-activated signaling network. Molecular systems biology. 2014;10:759. Epub 2014/11/21. doi: 10.15252/msb.20145120. PubMed PMID: 25411400; PMCID: PMC4299600.

Glarner CE, Hu YY, Chen CH, Radwin RG, Zhao Q, Craven MW, Wiegmann DA, Pugh CM, Carty MJ, Greenberg CC. Quantifying technical skills during open operations using video-based motion analysis. Surgery. 2014;156(3):729-34. Epub 2014/06/26. doi: 10.1016/j.surg.2014.04.054. PubMed PMID: 24962187; PMCID: PMC4150845.

Hou Z, Zhang J, Schwartz MP, Stewart R, Page CD, Murphy WL, Thomson JA. A human pluripotent stem cell platform for assessing developmental neural toxicity screening. Stem cell research & therapy. 2013;4 Suppl 1:S12. Epub 2014/02/26. doi: 10.1186/scrt373. PubMed PMID: 24565336; PMCID: PMC3983661.

Kuusisto F, Santos Costa V, Nassif H, Burnside E, Page D, Shavlik J. Support Vector Machines for Differential Prediction. Machine learning and knowledge discovery in databases : European Conference, ECML PKDD : proceedings ECML PKDD (Conference). 2014;8725:50-65. Epub 2014/01/01. doi: 10.1007/978-3-662-44851-9_4. PubMed PMID: 26158123; PMCID: PMC4492338.

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Wu Y, Liu J, Page D, Peissig P, McCarty C, Onitilo AA, Burnside ES. Comparing the value of mammographic features and genetic variants in breast cancer risk prediction. AMIA Annual Symposium proceedings AMIA Symposium. 2014;2014:1228-37. Epub 2014/01/01. PubMed PMID: 25954434; PMCID: PMC4419896.

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Gao X, Johnson KD, Chang YI, Boyer ME, Dewey CN, Zhang J, Bresnick EH. Gata2 cis-element is required for hematopoietic stem cell generation in the mammalian embryo. The Journal of experimental medicine. 2013;210(13):2833-42. Epub 2013/12/04. doi: 10.1084/jem.20130733. PubMed PMID: 24297994; PMCID: PMC3865483.

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Nassif H, Kuusisto F, Burnside ES, Page D, Shavlik J, Costa VS. Score As You Lift (SAYL): A Statistical Relational Learning Approach to Uplift Modeling. Machine learning and knowledge discovery in databases : European Conference, ECML PKDD : proceedings ECML PKDD (Conference). 2013;8190:595-611. Epub 2013/01/01. doi: 10.1007/978-3-642-40994-3_38. PubMed PMID: 26158122; PMCID: PMC4492311.

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Liu J, Peissig P, Zhang C, Burnside E, McCarty C, Page D. Graphical-model Based Multiple Testing under Dependence, with Applications to Genome-wide Association Studies. Uncertainty in artificial intelligence : proceedings of the conference Conference on Uncertainty in Artificial Intelligence. 2012;2012:511-22. Epub 2012/01/01. PubMed PMID: 25285046; PMCID: PMC4184466.

Nassif H, Cunha F, Moreira IC, Cruz-Correia R, Sousa E, Page D, Burnside E, Dutra I. Extracting BI-RADS Features from Portuguese Clinical Texts. Proceedings IEEE International Conference on Bioinformatics and Biomedicine. 2012:1-4. Epub 2012/01/01. PubMed PMID: 23797461; PMCID: PMC3688645.

Nassif H, Wu Y, Page D, Burnside E. Logical Differential Prediction Bayes Net, improving breast cancer diagnosis for older women. AMIA Annual Symposium proceedings AMIA Symposium. 2012;2012:1330-9. Epub 2013/01/11. PubMed PMID: 23304412; PMCID: PMC3540455.

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