Publications

See Google Scholar for a complete list of publications.

44. He Zhang, Liang Zhang, Ang Lin, Congcong Xu, Ziyu Li, Kaibo Liu, Boxiang Liu, Xiaopin Ma, Fanfan Zhao, Huiling Jiang, Chunxiu Chen, Haifa Shen, Hangwen Li, David H. Mathews, Yujian Zhang & Liang Huang. (2023). Algorithm for Optimized mRNA Design Improves Stability and Immunogenicity. Nature [paper]

43. Hyun-Jung Kim, Paul Cheng, Stanislao Travisano, Chad Weldy, João P. Monteiro, Ramendra Kundu, Trieu Nguyen, Disha Sharma, Huitong Shi, Yi Lin, Boxiang Liu, Saptarsi Haldar, Simon Jackson, Thomas Quertermous. (2023). Molecular mechanisms of coronary artery disease risk at the PDGFD locus. Nature Communications [paper]

42.  Yunpeng Huang, Zhihui Wan, Yinglu Tang, Junxuan Xu, Bretton Laboret, Sree Nallamothu, Chenyu Yang, Boxiang Liu, Rongze Olivia Lu, Bingwei Lu, Juan Feng, Jing Cao, Susan Hayflick, Zhihao Wu, and Bing Zhou. (2022). Pantothenate Kinase 2 Interacts with PINK1 to Regulate Mitochondrial Quality Control via acetyl-CoA metabolism. Nature Communications [paper]  

41. Boxiang Liu1*, Yanjun Li1, Liang Zhang. (2022). Analysis and Visualization of Spatial Transcriptomic Data. Frontiers in Genetics [paper]

40.  Xingyu Cai, Yuchen Bian, Jiaji Huang, Boxiang Liu, Jiahong Yuan, Kenneth Church. (2021) SSPF: a Simple and Scalable Parameter Free Clustering Method. International Conference on Data Mining Workshops [paper]

39.  Sizhen Li, He Zhang, Liang Zhang, Kaibo Liu, Boxiang Liu, David H. Mathews, Liang Huang (2021). LinearTurboFold: Linear-Time RNA Structural Alignment and Conserved Structure Prediction with Applications to Coronaviruses. Proceedings of the National Academy of Sciences. [paper]

38.  Kenneth Church and Boxiang Liu. (2021). Multiword Expressions, Acronyms and Opportunities for Improving Deep Nets. Frontiers in Artificial Intelligence. [paper]

37.  Yingmei Li, Dina Polyak, Layton Lamsam, Ian David Connolly, Eli Johnson, Lina Khav Khoeur, Stephanie Andersen, Monica Granucci, Geoff Stanley, Boxiang Liu, Seema Nagpal, Melanie Hayden Gephart. (2021). Comprehensive RNA analysis of CSF reveals a role for CEACAM6 in lung cancer leptomeningeal metastases. npj Precision Oncology. [paper]

36.  Alvaro N Barbeira, Rodrigo Bonazzola, Eric R Gamazon, Yanyu Liang, YoSon Park, Sarah Kim-Hellmuth, Gao Wang, Zhuoxun Jiang, Dan Zhou, Farhad Hormozdiari, Boxiang Liu, Abhiram Rao, Andrew R Hamel, Milton D Pividori, François Aguet, Lisa Bastarache, Daniel M Jordan, Marie Verbanck, Ron Do, Matthew Stephens, Kristin Ardlie, Mark McCarthy, Stephen B Montgomery, Ayellet Segré, Christopher D Brown, Tuuli Lappalainen, Xiaoquan Wen, Hae Kyung Im, GTEx GWAS Working Group, GTEx Consortium. (2020). Exploiting the GTEx resources to decipher the mechanisms at GWAS loci. Genome Biology. [paper]

35.  Boxiang Liu, Liang Huang. (2021). ParaMed: A Parallel Corpus for English-Chinese Translation in the Biomedical Domain. BMC Medical Informatics and Decision Making. [paper]

34.  Boxiang Liu, Kaibo Liu, He Zhang, Liang Zhang, Yuchen Bian, Liang Huang. (2020). CoV-Seq, a New Tool for SARS-CoV-2 Genome Analysis and Visualization: Development and Usability Study. Journal of Medical Internet Research. [paper]

33.  Quanyi Zhao, Michael Dacre, Trieu Nguyen, Milos Pjanic, Boxiang Liu, Dharini Iyer, Paul Cheng, Robert Wirka, Juyong Brian Kim, Hunter B Fraser, Thomas Quertermous (2020). Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping. Genome Biology. [paper]

32.  M Ryan Corces, Anna Shcherbina, Soumya Kundu, Michael J Gloudemans, Laure Frésard, Jeffrey M Granja, Bryan H Louie, Tiffany Eulalio, Shadi Shams, S Tansu Bagdatli, Maxwell R Mumbach, Boxiang Liu, Kathleen S Montine, William J Greenleaf, Anshul Kundaje, Stephen B Montgomery, Howard Y Chang, Thomas J Montine. (2020). Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases. Nature Genetics. [paper]

31.  Md Bahadur Badsha1, Rui Li1, Boxiang Liu1, Yang I Li, Min Xian, Nicholas E Banovich, Audrey Qiuyan Fu. (2020). Imputation of single-cell gene expression with an autoencoder neural network. Quantitative Biology. [paper]

30.  Brunilda Balliu, Matthew Durrant, Olivia de Goede, Nathan Abell, Xin Li, Boxiang Liu, Michael J. Gloudemans, Naomi L. Cook, Kevin S. Smith, David A. Knowles, Mauro Pala, Francesco Cucca, David Schlessinger, Siddhartha Jaiswal, Chiara Sabatti, Lars Lind, Erik Ingelsson & Stephen B. Montgomery. (2019). Genetic dysregulation of gene expression and splicing during a ten-year period of human aging. Genome Biology [paper]

29.  Boxiang Liu*, and Stephen B. Montgomery*. Identifying causal variants and genes using functional genomics in specialized cell types and contexts. (2019). Human Genetics. [paper]

28.  Laure Frésard, Craig Smail, Nicole M. Ferraro, Nicole A. Teran, Xin Li, Kevin S. Smith, Devon Bonner, Kristin D. Kernohan, Shruti Marwaha, Zachary Zappala, Brunilda Balliu, Joe R. Davis, Boxiang Liu, Cameron J. Prybol, Jennefer N. Kohler, Diane B. Zastrow, Chloe M. Reuter, Dianna G. Fisk, Megan E. Grove, Jean M. Davidson, Taila Hartley, Ruchi Joshi, Benjamin J. Strober, Sowmithri Utiramerur, Undiagnosed Diseases Network, Care4Rare Canada Consortium, Lars Lind, Erik Ingelsson, Alexis Battle, Gill Bejerano, Jonathan A. Bernstein, Euan A. Ashley, Kym M. Boycott, Jason D. Merker, Matthew T. Wheeler & Stephen B. Montgomery. (2019). Identification of rare-disease genes in diverse undiagnosed cases using whole blood transcriptome sequencing and large control cohorts. Nature Medicine. [paper]

27.  Zhongdong Liu, Boxiang Liu, Gaowei Chen. (2019). Retrospective analysis of the development history of the Chinese food additive standards system based on the CODEX principles. npj Science of Food. [paper]

26.  Boxiang Liu1*, Michael J. Gloudemans1, Abhiram S. Rao, Erik Ingelsson, and Stephen B. Montgomery*. (2019). Abundant associations with gene expression complicate GWAS follow-up. Nature Genetics, 51(5), 768-769. [paper]

25.  Mengfei Wan, Zhongdong Liu, Yongfu Chen, Caiyuan Lu, Kechang Li, Fahe Wang, Xiaomei Wang, Boxiang Liu. (2019). Preparation of pure gum raw materials-low brown algae application. Journal of Oceanology and Limnology. [paper]

24.  Robert C. Wirka, Dhananjay Wagh, David T. Paik, Milos Pjanic, Trieu Nguyen, Clint L. Miller, Ramen Kundu, Manabu Nagao, John Coller, Tiffany K. Koyano, Robyn Fong, Y. Joseph Woo, Boxiang Liu, Stephen B. Montgomery, Joseph C. Wu, Kuixi Zhu, Rui Chang, Melissa Alamprese, Michelle D. Tallquist, Juyong B. Kim & Thomas Quertermous. (2019). Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis. Nature Medicine. [paper]

23.  Boxiang Liu1, Melissa A. Calton1, Nathan S. Abell, Gillie Benchorin, Michael J. Gloudemans, Ming Chen, Jane Hu, Xin Li, Brunilda Balliu, Dean Bok, Stephen B. Montgomery, Douglas Vollrath. (2019). Genetic analyses of human fetal retinal pigment epithelium gene expression suggest ocular disease mechanisms. Communications Biology. [paper]

22.  Vivek Nanda, Ting Wang, Milos Pjanic, Boxiang Liu, Trieu Nguyen, Ljubica Perisic Matic, Ulf Hedin, Simon Koplev, Lijiang Ma, Oscar Franzén, Arno Ruusalepp, Eric E. Schadt, Johan L. M. Björkegren, Stephen B. Montgomery, Michael P. Snyder, Thomas Quertermous, Nicholas J. Leeper, Clint L. Miller (2018). Functional Regulatory Mechanism of Smooth Muscle Cell-Restricted LMOD1 Coronary Artery Disease Locus. PLOS Genetics. [paper]

21.  Bina Kakusa, Summer Han, Sonya Aggarwal, Boxiang Liu, Gordon Li, Scott Soltys and Melanie Hayden Gephart. (2018). Clinical Factors Associated with Mortality Within Three Months After Radiosurgery of Small, Asymptomatic Brain Metastases from Non-small Cell Lung Cancer. Journal of Neuro-Oncology. [paper]

20.  Dharini Iyer, Quanyi Zhao, Robert Wirka, Ameay Naravane, Trieu Nguyen, Boxiang Liu, Manabu Nagao, Paul Cheng, Clint L. Miller, Juyong Brian Kim, Milos Pjanic, Thomas Quertermous. (2018). Coronary artery disease genes SMAD3 and TCF21 promote opposing interactive genetic programs that regulate smooth muscle cell differentiation and disease risk. PLOS Genetics. [paper]

19.  Boxiang Liu, Milos Pjanic, Ting Wang, Trieu Nguyen, Michael Gloudemans, Abhiram Rao, Victor G. Castano, Sylvia Nurnberg, Daniel J Rader, Susannah Elwyn, Erik Ingelsson, Stephen B Montgomery, Clint L Miller, Thomas Quertermous. (2018). Genetic regulatory mechanisms of smooth muscle cells map to coronary artery disease risk loci. American Journal of Human Genetics. [paper]

18.  Boxiang Liu*, and Thomas Quertermous. (2017). Approximating the sum of independent non-identical binomial random variables. R Journal [paper]

17.  Li, Yingmei1, Boxiang Liu1, Ian David Connolly1, Bina Wasunga Kakusa, Wenying Pan, Seema Nagpal, Stephen B. Montgomery, and Melanie Hayden Gephart. (2018). Recurrently mutated genes differ between leptomeningeal and solid lung cancer brain metastases. Journal of Thoracic Oncology. [paper]

16.  Boxiang Liu, Nadine Hussami, Avanti Shrikumar, Tyler Shimko, Salil Bhate, Scott Longwell, Stephen Montgomery, and Anshul Kundaje. (2017) A multi-modal neural network for learning cis and trans regulation of stress response in yeast. NeurIPS Machine Learning in Computational Biology Workshop [paper]

15.  Juyong Brian Kim, Milos Pjanic, Trieu Nguyen, Clint L Miller, Dharini Iyer, Boxiang Liu, Ting Wang, Olga Sazonova, Ivan Carcamo-Orive, Ljubica Perisic Matic, Lars Maegdefessel, Ulf Hedin, Thomas Quertermous. (2017). TCF21 and the environmental sensor aryl-hydrocarbon receptor cooperate to activate a pro-inflammatory gene expression program in coronary artery smooth muscle cells. PLOS Genetics. [paper]

14.  GTEx Consortium. (2017). Genetic effects on gene expression across human tissues. Nature. [paper] Note: GTEx Consortium is a multi-institutional collaboration with 200+ authors. Boxiang Liu is involved with the eQTL Manuscript Working Group and Statistical Methods Group

13.  Xin Li, Yungil Kim, Emily K. Tsang, Joe R. Davis, Farhan N. Damani, Colby Chiang, Gaelen T. Hess, Zachary Zappala, Benjamin J. Strober, Alexandra J. Scott, Amy Li, Andrea Ganna, Michael C. Bassik, Jason D. Merker, GTEx Consortium, Ira M. Hall, Alexis Battle & Stephen B. Montgomery (2017). The impact of rare variation on gene expression across tissues. Nature [paper]

12.  Meng How Tan, Qin Li, Raghuvaran Shanmugam, Robert Piskol, Jennefer Kohler, Amy N. Young, Kaiwen Ivy Liu, Rui Zhang, Gokul Ramaswami, Kentaro Ariyoshi, Ankita Gupte, Liam P. Keegan, Cyril X. George, Avinash Ramu, Ni Huang, Elizabeth A. Pollina, Dena S. Leeman, Alessandra Rustighi, Y. P. Sharon Goh, GTEx Consortium, Ajay Chawla, Giannino Del Sal, Gary Peltz, Anne Brunet, Donald F. Conrad, Charles E. Samuel, Mary A. O’Connell, Carl R. Walkley, Kazuko Nishikura & Jin Billy Li. (2017). Nature. [paper]

11.  Taru Tukiainen, Alexandra-Chloé Villani, Angela Yen, Manuel A. Rivas, Jamie L. Marshall, Rahul Satija, Matt Aguirre, Laura Gauthier, Mark Fleharty, Andrew Kirby, Beryl B. Cummings, Stephane E. Castel, Konrad J. Karczewski, François Aguet, Andrea Byrnes, GTEx Consortium, Tuuli Lappalainen, Aviv Regev, Kristin G. Ardlie, Nir Hacohen & Daniel G. MacArthur. (2017) Landscape of X chromosome inactivation across human tissues. Nature. [paper]

10.  Halit Ongen, Andrew A Brown, Olivier Delaneau, Nikolaos I Panousis, Alexandra C Nica, GTEx Consortium, Emmanouil T Dermitzakis (2017). Estimating the causal tissues for complex traits and diseases. Nature Genetics [paper]

9.  Zhihao Wu, Yan Wang, Junghyun Lim, Boxiang Liu, Yanping Li, Rasika Vartak, Trisha Stankiewicz, Stephen Montgomery, Bingwei Lu. (2017). Ubiquitination of ABCE1 by NOT4 in Response to Mitochondrial Damage Links Co-translational Quality Control to PINK1-Directed Mitophagy. Cell Metabolism. [paper]

8.  Zhongdong Liu, Boxiang Liu, Mengxing Li, Min Wei, Hua Li, Peng Liu, Tuo Wan. (2013). Scanning probe acoustic microscopy of extruded starch materials: Direct visual evidence of starch crystal. Carbohydrate Polymers. [paper]

7.  Zhongdong Liu, Benqian Gong, Liang Zhang, Hongjie An, Boxiang Liu. (2012). The influence of emulsifiers on retrogradation properties of waxy starch. Advances in Computational Environment Science. [paper]

6.  Zhongdong Liu, Lizheng Bi, Guojin Yan, Shijie Yang, Chao Yang, Boxiang Liu. (2012). The Effects of Protein Content to Starch’s Enzymolysis Character. Advances in Computational Environment Science [paper]

5.  Min Wei, Yong Liu, Changxiao Ju, Boxiang Liu, Zhongdong Liu. (2012). Studies on the Preparation, Structure and Characteristics of Magnetic Starch. Advances in Computational Environment Science. [paper]

4.  Zhongdong Liu, Junhui Ou, Zhaotang Zhang, Yiwei Deng, Peng Wang, Boxiang Liu, Jinhui Peng, Zhaotan Chen, Xiaoyun Li, Guangzong Zhou. (2011). Undulator (Pump) Mechanism of Ultraviolet Microwave Synergistic Gain and Design of Microwave-UV Ovens. Journal of Kunming University of Science and Technology [paper]

3.  Min Wei, Yong Liu, Boxiang Liu, Xiaoling Lv, Pin Sun, Zesheng Zhang, Fengshou Zhang, Su Yin, Zhongdong Liu (2011). Preparation and Application of Starch Phosphate with a Low Degree of Substitution. Phosphorus, Sulfur, and Silicon and the Related Elements. [paper]

2.  Zhongdong Liu, Benqian Gong, Yaqiang He, Zhenxing Li, Boxiang Liu. (2011). A new method for the non-destructive determination of fish freshness by nuclear imaging. IEEE/ICME International Conference on Complex Medical Engineering. [paper]

1.  Hua Li, Zhong-Dong Liu, Boxiang Liu, Jian-Hui Chen, You-Ning Sun, Xiao-Ling Lv, Ze-Sheng Zhang, Pin Sun, Pin Zhang, Yang-Li Wang (2009). Application of the Molecular Combing Technique to Starch Granules. Molecules. [paper]