Selected from >50 peer-reviewed articles

  1. Chandrashekar P, Ahmadinejad N, Wang J, Sekulic A, Egan JB, Asmann YW, Kumar S, Mayley C, Liu L (2020) Somatic Selection Distinguishes Oncogenes and Tumor Suppressor Genes. Bioinformatics (in press)
  2. Guan X, Runger G, Liu L (2020) Dynamic Incorporation of Prior Knowledge from Multiple Domains in Biomarker Discovery. BMC Bioinformatics (in press).
  3. Liu L, Maxwell D, Patel R, Chandrashekar P, Gibson G, Kumar S. (2019) Biological relevance of predicted pathogenicity of noncoding variants. Nature Communications 10:330
  4. Liu L, Caselli R. (2018) Age stratification corrects bias in estimated hazards of APOE Genotype in Alzheimer’s disease. Alzheimer’s & Dementia TRCI 4:602–608
  5. Li C, Liu L, Dinu V. (2018) Pathways of topological rank analysis (potra): a novel method to detect pathways involved in cancer. PeerJ 6:e4571
  6. Liu L, Chang Y, Yang T, Noren DP, Amina Q, Kornblau S, Ye J. (2016) Evolution-informed Modeling Improves Outcome Prediction for Cancers. Evolutionary Applications 10(1):68-76
  7. Liu L, Tamura K, Sanderford M, Gray VE, Kumar S (2016) A Molecular Evolutionary Reference for the Human Variome. Molecular Biology and Evolution 33(1):245-54
  8. Gerek ZN, Liu L (co-first-author), Gerold K, Biparva P, Thomas ED, Kumar S. (2015) Evolutionary Diagnosis of non-synonymous variants involved in differential drug response. BMC Medical Genomics 8;Suppl 1:S6
  9. Kumar S, Liu L. (2014) No positive selection for G-allele in a p53 response element in Europeans. Cell 157(7):1497-1499
  10. Gray VE, Liu L (co-first-author), Nirankari R, Hornbeck P, Kumar S (2014) Signatures of natural selection on mutations of residues with multiple posttranslational modifications. Molecular Biology and Evolution 31(7):1641-5
  11. Liu L, Kumar S. (2013) Evolutionary balancing is critical for correctly forecasting disease associated amino acid variants. Molecular Biology and Evolution 30(6):1252-7
  12. Wellensiek BP, Larsen AC, Stephens B, Kukurba K, Waern K, Briones N, Liu L, Snyder M, Jacobs BL, Kumar S, Chaput JC. (2013) Genome-wide profiling of human cap-independent translation-enhancing elements. Nature Methods 10(8):747-50
  13. Kumar S, Sanderford M, Gray VE, Ye J, Liu L (2012) Evolutionary Diagnosis Method for Variants in Personal Exomes. Nature Methods 9(9):855-6
  14. Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ, Kumar S (2011) Human Genomic Disease Variants: A Neutral Evolutionary Explanation. Genome Research doi:10.1101/gr.133702.111
  15. Kumar S, Dudley JT, Filipski A, Liu L (2011) Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations. Trends in Genetics. 27(9):377-86.
  16. Sun Y, Cai YP, Liu L, Yu F, Farrell M, McKendree W, Farmerie WG. (2009) ESPRIT: estimating species richness using large collections of 16S rRNA shotgun sequences. Nucleic Acid Research 37(10):e76
  17. Moroz LL, Edwards JR, Puthanveettil SV, Kohn A, Ha T, Heyland A, Knudsen B, Sahni A, Yu F, Liu L, Jezzini S, Sadreyev R, Lovell P, Iannucculli W, Chen M, Nguyen T, Sheng H, Shaw R, Kalachikov S, Panchin Y, Farmerie WG, Russo JJ, Ju J, Kandel ER. (2006) The Neuronal Transcriptome of Aplysia californica: A Platform for the Neurogenomics of Defined Neurons, Neuronal Compartments and Neuronal Circuitry. Cell 127(7):1453-1467
  18. Cousins RJ, Blanchard RK, Popp MP, Liu L, Cao J, Moore JB and Green CL. (2003) A Global View of the Selectivity of Zinc Deprivation and Excess on Genes Expressed in Human THP-1 Mononuclear Cells. Proceedings of the National Academy of Science 100:6952-6957