Publications

Statistical Method Papers:

1. Xiaoyu Song*, Joselyn C. Chavez-Fuentes, Weiping Ma, Weijia Fu, Sujung Crystal Shin, Pei Wang, and Guo-Cheng Yuan*. "sCCIgen: A high-fidelity spatially resolved transcriptomics data simulator for cell-cell interaction studies." Genome Biology 26, 354 (2025). https://doi.org/10.1186/s13059-025-03762-9

2. Xiaoyu Song*, Yuqing Shang, Michelle Ehrlich, Panos Roussos, Guo-Cheng Yuan, and Pei Wang. "QuadST identifies cell-cell interaction-changed genes in spatially resolved transcriptomics data." Genome Research (2025): gr-279859. 

3. Weiping Ma, Xiaoyu Song, Guo-Cheng Yuan, and Pei Wang. "RECCIPE: A new framework assessing localized cell-cell interaction on gene expression in multicellular ST data." Frontiers in Genetics 15 (2024): 1322886.

4. Xiaoyu Song*, Jiayi Ji, Joseph H. Rothstein, Stacey E. Alexeeff, Lori C. Sakoda, Adriana Sistig, Ninah Achacoso, Eric Jorgenson, Neil Risch, Alice S. Whittemore, Robert J. Klein, Laurel A. Habel, Pei Wang*, Weiva Sieh*. ”MiXcan: A framework for cell-type specific transcriptome wide association study for breast cancer risk.” Nature Communications (2023).

5. Xiaoyu Song*,  Jiayi Ji, and Pei Wang. "iProMix: A decomposition model for studying the function of ACE2 based on bulk proteogenomic data for coronavirus pathogenesis." (2022) Journal of the American Statistical Association (Applications and Case Studies).

6. Mi Yang, Francesca Petralia, Zhi Li, Hongyang Li, Weiping Ma, Xiaoyu Song, Sunkyu Kim, Han Yu, Bora Lee, Sungsoo Park, Eunji Heo, Jan Kaczmarczyk, Piotr Stepniak, Michal􏰀 Warcho􏰀l, Thomas Yu, Anna P. Calinawan, Paul C. Boutros, Samuel H. Payne, Boris Reva, NCI-CPTAC-DREAM Consortium, Emily Boja, Henry Rodriguez, Gustavo Stolovitzky, Yuanfang Guan, Jaewoo Kang, Pei Wang, David Fenyo, Julio Saez-Rodriguez. “Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics.” Cell System 11, no. 2 (2020): 186-195.

7. Xiaoyu Song, Jiayi Ji, Kevin J. Gleason, Fan Yang, John A. Martignetti, Lin S. Chen, and Pei Wang. ”Insights into impact of DNA copy number alteration and methylation on the proteogenomic landscape in human ovarian cancer via a multi-omics integrative analysis.” Molecular & Cellular Proteomics (2019): mcp-RA118.

8. Xiaoyu Song*, Gen Li, Zhenwei Zhou, Xianling Wang, Iuliana Ionita-Laza, and Ying Wei. ”QRank: a novel quantile regression tool for eQTL discovery.” Bioinformatics 33, no. 14 (2017): 2123-2130.

9. Xiaoyu Song*, Iuliana Ionita-Laza, Mengling Liu, Joan Reibman, and Ying Wei. ”A general and robust framework for secondary traits analysis.” Genetics 202, no. 4 (2016): 1329-1343.

10. Ying Wei, Xiaoyu Song, Mengling Liu, Iuliana Ionita-Laza, and Joan Reibman. ”Quantile regression in the secondary analysis of case–control data.” Journal of the American Statistical Association (Theory and Methods) 111, no. 513 (2016): 344-354.

Leading Application Papers:

11. Xaoyu Song, Meng Ru, Zoe Steinsnyder, Kaitlyn Tkachuk, Zeynep Gumus, Ken Offit, Vijai Joseph, Robert J. Klein. ”SNPs at SMG7 associated with time from biochemical recurrence to prostate cancer death.” Cancer Epidemiology, Biomarkers & Prevention (2022).

12. Xiaoyu Song, Jiayi Ji, Boris Reva, Himanshu Joshi, Anna Pamela Calinawan, Madhu Mazumdar, Juan P. Wisnivesky, Emanuela Taioli, Pei Wang, and Rajwanth R. Veluswamy. ”Post-anticoagulant D-dimer is a highly prognostic biomarker of COVID-19 mortality.” ERJ Open Research (2021).

13. David J Clark, et all (including Xiaoyu Song as co-first author). “Integrated Proteogenomic Charac- terization of Clear Cell Renal Cell Carcinoma.” Cell 179, no. 4 (2019): 964-983.

14. Xiaoyu Song, Jonathan D. Klein, Hanying Yan, Marina Catallozzi, Xianling Wang, Jenifer Heitel, Kristen Kaseeska, Julie Gorzkowski, and John S. Santelli. ”Parent and adolescent attitudes towards preventive care and confidentiality.” Journal of Adolescent Health 64, no. 2 (2019): 235-241.

15. Xiaoyu Song, Stephanie A. Grilo, Sanyukta Mathur, Tom Lutalo, Robert Ssekubugu, Fred Nalugoda, and John S. Santelli. ”Differential Impacts of HIV status on short-term fertility desires among couples in Rakai, Uganda.” PloS one 14, no. 1 (2019): e0210935.

Collaborative Application Papers : 

- Cancer Proteogenomics 

16. Kołodziejczak-Guglas, Iga, et al (including Xiaoyu Song). "Proteomic-based stemness score measures oncogenic dedifferentiation and enables the identification of druggable targets." Cell Genomics 5.6 (2025).Rodrigues, 

17. Fernanda Martins, et al (including Xiaoyu Song). "Precision proteogenomics reveals pan-cancer impact of germline variants." Cell 188.9 (2025): 2312-2335.

18. Petralia, Francesca, et al (including Xiaoyu Song). "Pan-cancer proteogenomics characterization of tumor immunity." Cell (2024).

19. Chowdhury, Shrabanti, et al  (including Xiaoyu Song). "Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer." Cell 187.4 (2024): 1016.

20. Li, Yize, et al (including Xiaoyu Song). "Pan-cancer proteogenomics connects oncogenic drivers to functional states." Cell 186.18 (2023): 3921-3944. 

21. Geffen, Yifat, et al (including Xiaoyu Song). "Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation." Cell 186.18 (2023): 3945-3967. 

22. Liang, Wen-Wei, et al (including Xiaoyu Song). "Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin." Cancer Cell 41.9 (2023): 1567-1585.

23. Li, Yize, et al (including Xiaoyu Song). "Proteogenomic data and resources for pan-cancer analysis." Cancer Cell 41.8 (2023): 1397-1406.

24. Shankha Satpathy, et al (including Xiaoyu Song). ”A proteogenomic portrait of lung squamous cell carcinoma.” Cell 184, no. 16 (2021): 4348-4371.

25. Liang-Bo Wang, et al (including Xiaoyu Song). ”Proteogenomic and Metabolomic Characterization of Human Glioblastoma” Cancer Cell 39, no. 4 (2021): 509-528.

26. Chen Huang, et al (including Xiaoyu Song). ”Proteogenomics insights into the biology and treatment of HPV-negative head and neck cancer” Cancer Cell 39, no. 3 (2021): 361-379.

27. Francesca Petralia, et al (including Xiaoyu Song). ”Integrated Proteogenomic Characterization across Major Histological types of Pediatric Brain Cancer”Cell 183, no. 7 (2020): 1962-1985.

28. Michael A. Gillette , et all (including Xiaoyu Song). ”Proteogenomic characterization reveals therapeutic vulnerabilities in lung adenocarcinoma.” Cell 182, no. 1 (2020): 200-225.

29. Anna P. Calinawan, Xiaoyu Song, Jiayi Ji, Saravana Mohan Dhanasekaran, Francesca Petralia, Pei Wang, and Boris Reva. ”ProTrack: An Interactive Multi-Omics Data Browser for Proteogenomic Studies.” Proteomics (2020): 1900359.

30. Yongchao Dou, et al (including Xiaoyu Song). ”Proteogenomic Characterization of Endometrial Carcinoma.” Cell 180, no. 4 (2020): 729-748.

- AI image 

31. Wang, Joshua M., et al (including Xiaoyu Song). "Deep learning integrates histopathology and proteogenomics at a pan-cancer level." Cell Reports Medicine 4.9 (2023)

32. Li, Xueshen, et al (including Xiaoyu Song). "Generating virtual histology staining of human coronary OCT images using transformer-based neural network." Diagnostic and Therapeutic Applications of Light in Cardiology 2024. Vol. 12819. SPIE, 2024.

33. Li, Xueshen, et al (including Xiaoyu Song). "Structurally constrained and pathology-aware convolutional transformer generative adversarial network for virtual histology staining of human coronary optical coherence tomography images." Journal of Biomedical Optics29.3 (2024): 036004-036004.

34. Liu, Hongshan, et al  (including Xiaoyu Song). "Toward reliable calcification detection: calibration of uncertainty in object detection from coronary optical coherence tomography images." Journal of Biomedical Optics 28.3 (2023): 036008-036008.

35. Xueshen Li, Shengting Cao, Hongshan Liu, Xinwen Yao, Brigitta C. Brott, Silvio H. Litovsky, Xiaoyu Song, Yuye Ling, and Yu Gan. ”Multi-scale reconstruction of undersampled spectral-spatial OCT data for coronary imaging using deep learning.” IEEE Transactions on Biomedical Engineering (2022).

- Other Cancer Research

36. Layne, Tracy M., Joseph H. Rothstein, Xiaoyu Song, Shaneda Warren Andersen, Emma KT Benn, Weiva Sieh, and Robert J. Klein. "Vitamin D-related genetic variants and prostate cancer risk in Black men." Cancer Epidemiology 95 (2025): 102742.

37. Habel, Laurel A., et al (including Xiaoyu Song). "Examination of fully automated mammographic density measures using LIBRA and breast cancer risk in a cohort of 21,000 non-Hispanic white women." Breast Cancer Research 25.1 (2023): 92.

38. Thomas U. Marron, et al (including Xiaoyu Song). ”Neoadjuvant cancer clinical trials provide a window of opportunity to demystify how novel immunotherapies work.” Nature Medicine 28, no. 4 (2022): 626-629.

39. Pedro Henrique Alves da Silva, Samantha Xing, Andriana G. Kotini, Eirini P. Papapetrou, Xiaoyu Song, Kai W. Wucherpfennig, John Mascarenhas, and Lucas Ferrari de Andrade. ”MICA/B antibody induces macrophage-mediated immunity against acute myeloid leukemia.” Blood, The Journal of the American Society of Hematology 139, no. 2 (2022): 205-216.

40. Samuel Terkper Ahuno, et al (including Xiaoyu Song). ”Circulating tumor DNA is readily detectable among Ghanaian breast cancer patients supporting non-invasive cancer genomic studies in Africa.” npj Precision Oncology  5, no. 1 (2021): 1-8.

41. Russell B McBride, Kezhen Fei, Joseph H. Rothstein, Stacey E. Alexeeff, Xiaoyu Song, Lori C. Sakoda, Valerie McGuire, Ninah Achacoso, Luana Acton, Rhea Y. Liang, Jafi A. Lipson, Martin J. Yaffe, Daniel L. Rubin, Alice S Whittermore, Laurel A. Habel, and Weiva Sieh. “Alcohol and tobacco use in relation to mammographic density in 23,456 women.” Cancer Epidemiology, Biomarkers & Prevention 29, no. 5 (2020): 1039-1048.

- Public Health (e.g. Adolescent Health, Reproductive Health, HIV/AIDS, Cardiovasncular Health, Environmental Health)

42. John S. Santelli, Jonathan D. Klein, Xiaoyu Song, Jennifer Heitel, Stephanie Grilo, Mengru Wang, Hanying Yan et al. ”Discussion of potentially sensitive topics with young people.” Pediatrics 143, no. 2 (2019): e20181403.

43. Stephanie A. Grilo, Marina Catallozzi, John S. Santelli, Hanying Yan, Xiaoyu Song, Jennifer Heitel, Kristen Kaseeska, Julie Gorzkowski, Alexandra E. Dereix, and Jonathan D. Klein. ”Confidentiality discussions and private time with a health-care provider for youth, United States, 2016.” Journal of Adolescent Health 64, no. 3 (2019): 311-318.

44. Stephanie A. Grilo, Xiaoyu Song, Tom Lutalo, Margo Mullinax, Sanyukta Mathur, and John Santelli. ”Facing HIV infection and unintended pregnancy: Rakai, Uganda, 2001–2013.” BMC Women’s health 18, no. 1 (2018): 46.

45. Fanfan Zheng, Baoliang Zhong, Xiaoyu Song, and Wuxiang Xie. ”Persistent depressive symptoms and cognitive decline in older adults.” The British Journal of Psychiatry 213, no. 5 (2018): 638-644.

46. Craig J. Heck, Stephanie A. Grilo, Xiaoyu Song, Tom Lutalo, Neema Nakyanjo, and John S. Santelli. ”“It is my business”: A Mixed-Methods Analysis of Covert Contraceptive Use among Women in Rakai, Uganda.” Contraception 98, no. 1 (2018): 41-46.

47. Margo Mullinax, Stephanie A. Grilo, Xiaoyu Song, Jennifer Wagman, Sanyukta Mathur, Fred Nalu- goda, Tom Lutalo, and John Santelli. ”HIV-risk behaviors of men who perpetrate intimate partner violence in Rakai, Uganda.” AIDS Education and Prevention 29, no. 6 (2017): 527-539.

48. John S. Santelli, Xiaoyu Song, Samantha Garbers, Vinit Sharma, and Russell M. Viner. ”Global trends in adolescent fertility, 1990–2012, in relation to national wealth, income inequalities, and educational expenditures.” Journal of Adolescent Health 60, no. 2 (2017): 161-168.

49. Wuxiang Xie, Fanfan Zheng, Xiaoyu Song, Baoliang Zhong, and Li Yan. ”Renin–angiotensin–aldosterone system blockers for heart failure with reduced ejection fraction or left ventricular dysfunction: Network meta-analysis.” International Journal of Cardiology 205 (2016): 65-71.

50. Sanyukta Mathur, Ying Wei, Xiaobo Zhong, Xiaoyu Song, Fred Nalugoda, Tom Lutalo, Maria Wawer, Ron Gray, David Serwadda, and John S. Santelli. ”Partner characteristics associated with HIV acqui- sition among youth in Rakai, Uganda.” Journal of Acquired immune Deficiency Syndromes 69, no. 1 (2015): 75.

51. John S. Santelli, Xiaoyu Song, Inge K. Holden, Kristin Wunder, Xiaobo Zhong, Ying Wei, Sanyukta Mathur et al. ”Prevalence of sexual experience and initiation of sexual intercourse among adolescents, Rakai District, Uganda, 1994–2011.” Journal of Adolescent Health 57, no. 5 (2015): 496-505.

52. John S. Santelli, Sanyukta Mathur, Xiaoyu Song, Tzu Jung Huang, Ying Wei, Tom Lutalo, Fred Nalugoda, Ron Gray, and David Serwadda. ”Rising school enrollment and declining HIV and pregnancy risk among adolescents in Rakai District, Uganda, 1994–2013.” Global Social Welfare 2, no. 2 (2015): 87-103.

53. John S. Santelli, Zoe R. Edelstein, Ying Wei, Sanyukta Mathur, Xiaoyu Song, Ashley Schuyler, Fred Nalugoda et al. ”Trends in HIV acquisition, risk factors and prevention policies among youth in Uganda, 1999–2011.” AIDS 29, no. 2 (2015): 211-219.

54. Wuxiang Xie, Fanfan Zheng, Baoliang Zhong, and Xiaoyu Song. ”Long-term antiplatelet mono-and dual therapies after ischemic stroke or transient ischemic attack: network meta-analysis.” Journal of the American Heart Association 4, no. 8 (2015): e002259.

55. Zoe R. Edelstein, John S. Santelli, Stephane Helleringer, Ashley C. Schuyler, Ying Wei, Sanyukta Mathur, Xiaoyu Song et al. ”Factors associated with incident HIV infection versus prevalent infection among youth in Rakai, Uganda.” Journal of Epidemiology and Global Health 5, no. 1 (2015): 85-91.

56. Wuxiang Xie, Fanfan Zheng, and Xiaoyu Song. ”Obstructive sleep apnea and serious adverse outcomes in patients with cardiovascular or cerebrovascular disease: a PRISMA-compliant systematic review and meta-analysis.” Medicine 93, no. 29 (2014).

57. Peter Muennig, Xiaoyu Song, Devon C. Payne-Sturges, and Gilbert C. Gee. ”Blood and urine levels of long half-life toxicants by nativity among immigrants to the United States.” Science of the Total Environment 412 (2011): 109-113.

Editor Invited:

58. Xiaoyu Song. "Unlocking Cellular Insights Through Cell-Type Decomposition." Statistics in Biosciences 15, no. 3 (2023): 734-736.

59. Xiaoyu Song. "Statistical and Computational Methods for Proteogenomic Data Analysis." In Statistical Genomics, pp. 271-303. New York, NY: Springer US, 2023.