Research

My research interests include statistical learning from high-dimensional and small sample size problems, optimization, structured variable selection, density estimation, functional data analysis, and their applications such as data mining, learning, detection, etc. In particular, I am interested in developing novel methodologies motivated by real-world problems.

An overview of the research topics can be found by clicking [here].


Publications

Preprints and unpublished work   (*: authors with equal contributions)

  • T.-Y. Liu, M. Perlman, A. O. Hero, M. Roth, I. Rajapakse.   Chromosome conformation during suspended animation and reversible stopping of biological time, in preparation.
  • T.-Y. Liu, A. O. Hero.   A Structured Sparse Multi-class Classifier, to be submitted.
  • T.-Y. Liu, L. Trinchera, A. Tenenhaus, D. Wei, and A. O. Hero.   Jointly Sparse Global SIMPLS Regression, submitted. [html]

Papers published   (*: authors with equal contributions)

  • T.-Y. Liu*, H. H. Huang*, D. Wheeler, Y. Xu, J. A. Wells, Y. S. Song, A. P. Wiita.   Time-resolved proteomics extends ribosomal profiling-based measurements of protein synthesis dynamics, Cell Systems, Vol. 4, No. 6, pp. 636-644, 2017. (This is a cover article.) [html]
  • T.-Y. Liu, Y. S. Song.   Prediction of Ribosome Footprint Profile Shapes from Transcript Sequences, Bioinformatics,Vol. 32, No. 12, pp. i183-i191, doi:10.1093/bioinformatics/btw253, 2016. [html]
  • T.-Y. Liu*, A. E. Dodson*, J. Terhorst, Y. S. Song and J. Rine.   Riches of Phenotype Computationally Extracted from Microbial Colonies, Proceedings of the National Academy of Sciences, Vol. 113, No. 20, pp. E2822-E2831, doi:10.1073/pnas.1523295113, 2016. [html]
  • M. T. McClain, B. P. Nicholson, L. P. Park, T.-Y. Liu, A. O. Hero III, E. Tsalik, A. K. Zaas, T. Veldman, L. L. Hudson, R. Lambkin-Williams, A. Gilbert, G. S. Ginsburg and C. W. Woods.   A Genomic Signature of Influenza Infection Shows Potential for Presymptomatic Detection, Guiding Early Therapy, and Monitoring Clinical Responses, Open Forum Infectious Diseases, Vol. 3, No. 1, doi:10.1093/ofid/ofw007, 2016. [html]
  • T.-Y. Liu, T. Burke, L. P. Park, C. W. Woods, A. K. Zaas, G. S. Ginsburg and A. O. Hero.   An individualized predictor of health and disease using paired reference and target samples, BMC bioinformatics, Vol. 17, No. 1, pp. 1-15, 2016. [html]
  • T.-Y. Liu, A. Wiesel, and A. O. Hero.   A Sparse Multi-class Classifier for Biomarker Screening. Global Conference on Signal and Information Processing (GlobalSIP) Proceedings, IEEE, pp. 77-80, 2014.[html]
  • A. Dufour, T.-Y. Liu, C. Ducroz, R. Tournemenne, B. Cummings, R. Thibeaux, N. Guillen, A. O. Hero III, and Jean-Christophe Olivo-Marin.   Signal Processing Challenges in Quantitative 3-D Cell Morphology. IEEE Signal Processing Magazine, pp. 30-40, 2014. [html]
  • T.-Y. Liu, L. Trinchera, A. Tenenhaus, D. Wei, and A. O. Hero.   Globally Sparse PLS Regression. New Perspectives in Partial Least Squares and Related Methods, Springer Proceedings in Mathematics and Statistics, Vol. 56, pp. 117-127, 2013. [html]
  • M. Yokokawa*, T.-Y. Liu*, K. Yoshida, C. Scott, A. O. Hero, E. Good, F. Morady, and F. Bogun.   Automated analysis of the 12-lead electrocardiogram to identify the exit site of postinfarction ventricular tachycardia. Heart Rhythm, Vol. 9, No. 3, pp. 330-334, 2012. [html]
  • K. Yoshida*, T.-Y. Liu*, C. Scott, A. Hero, M. Yokokawa, S. Gupta, E. Good, F. Morady, F. Bogun.   The Value of Defibrillator Electrograms for Recognition of Clinical Ventricular Tachycardias and for Pace-Mapping Of Post-Infarction Ventricular Tachycardia. Journal of the American College of Cardiology, Vol. 56, No. 12, pp. 969-979, 2010. [html]
  • T. S. Baman, D. C. Lange, K. J. Ilg, S. K. Gupta, T.-Y. Liu, C. Alguire, W. Armstrong, E. Good, A. Chugh, K. Jongnarangsin, F. Pelosi Jr., T. Crawford, M. Ebinger, H. Oral, F. Morady, F. Bogun.   Relationship between burden of premature ventricular complexes and left ventricular function. Heart Rhythm Vol. 7, No. 7, pp. 865-869, 2010. [html]

Ph.D. dissertation

  • Statistical Learning for Sample-Limited High-dimensional Problems with Application to Biomedical Data. [pdf file]

Conference Presentations, including talks and posters

  • T.-Y. Liu, H. H. Huang, D. Wheeler, Y. Xu, J. A. Wells, Y. S. Song, A. P. Wiita. "Translational dynamics revealed by ribosome occupancy and time-resolved proteomics during chemotherapeutic response". Cold Spring Harbor Meeting: The Biology of Genomes, 2017.
  • T.-Y. Liu, Y. S. Song. "Prediction of Ribosome Footprint Profile Shapes from Transcript Sequences". Intelligent Systems for Molecular Biology (ISMB), 2016 (oral presentation).
  • T.-Y. Liu, H. H. Huang, D. Wheeler, Y. S. Song, A. P. Wiita. "Direct measurement and modeling of protein synthesis and degradation dynamics during chemotherapeutic response in multiple myeloma". American Society for Mass Spectrometry (ASMS), 2016.
  • T.-Y. Liu, Y. S. Song. "Prediction of Ribosome Footprint Distributions from Transcript Sequences via Multiresolution Analysis". Neural Information Processing Systems (NIPS) workshop on Machine Learning in Computational Biology (MLCB), 2015 (oral presentation).
  • T.-Y. Liu, Y. S. Song. "Can you predict the shape of Ribosome profiles? Marginal Probability Density Estimation of Ribosome Footprints". Cold Spring Harbor Laboratory (CSHL) Probabilistic Modeling in Genomics, 2015.
  • T.-Y. Liu, H. H. Huang, D. Wheeler, J. A. Wells, Y. S. Song, A. P. Wiita. "Integrative longitudinal analysis of ribosome occupancy and protein synthesis during chemotherapeutic response reveals complex translational dynamics". American Society of Human Genetics Annual Meeting (ASHG), 2015.
  • T.-Y. Liu, A. Wiesel, and A. O. Hero. "A Sparse Multi-class Classifier for Biomarker Screening". Global Conference on Signal and Information Processing (GlobalSIP), IEEE, 2014.
  • T.-Y. Liu, L. Trinchera, A. Tenenhaus, D. Wei, and A. O. Hero. "Global Criteria for Sparse Penalized Partial Least Squares". World Statistics Congress, 2013.
  • T.-Y. Liu, L. Trinchera, A. Tenenhaus, D. Wei, and A. O. Hero."Globally Sparse PLS Regression with Application to Gene Expression Analysis". Information Theory and Applications Workshop (ITA), 2013.
  • T.-Y. Liu, L. Trinchera, A. Tenenhaus, D. Wei, and A. O. Hero. "Globally Sparse PLS Regression". 7th International Conference on Partial Least Squares and Related Methods (PLS), 2012.
  • T.-Y. Liu, A. Wiesel, C. W. Woods, A. Zaas, G. S. Ginsburg and A. O. Hero. " Learning Differential Gene Expression Signatures from Personalized High Throughput Screening". The Great Lakes Bioinformatics Conference, 2012.
  • T.-Y. Liu, L. Trinchera, A. Tenenhaus, D. Wei, and A. O. Hero. "A new criterion for sparse PLS regression". Compstat, 2012.

Past and Present Research Collaborators

  • Sarah A. Tishkoff, Alessia Ranciaro, Eric Mbunwe, Departments of Genetics and Biology, University of Pennsylvania.
  • Arun Wiita, Hector Huang, Dept Laboratory Medicine, University of California, San Francisco.
  • Jasper Rine, Anne Dodson, Dept Molecular and Cell Biology, University of California, Berkeley.
  • Indika Rajapakse, Dept Computational Medicine and Bioinformatics, University of Michigan.
  • Geoffrey S. Ginsburg, Center for Applied Genomics and Precision Medicine, Dept Medicine, Duke University.
  • Alexandre Dufour, Quantitative Image Analysis Unit, Institut Pasteur, France.
  • Jean-Christophe Olivo-Marin, Quantitative Image Analysis Unit, Institut Pasteur, France.
  • Laura Trinchera, Rouen Business School, Mont-Saint-Aignan, France.
  • Arthur Tenenhaus, Department of Signal Processing and Electronic Systems, Supélec, Gif-sur-Yvette, France.
  • Frank Bogun, Dept Cardiology, University of Michigan.