[49] Edwin Baldwin, Jiali Han, Wenting Luo, Jin Zhou, Lingling An, Jian Liu, Helen Zhang, Haiquan Li*. On fusion methods for knowledge discovery from multi-omics datasets. Computational and Structural Biotechnology Journal 2020. doi:10.1016/j.csbj.2020.02.011.
[48] Yves A. Lussier, Atul Butte, Haiquan Li, Rong Chen, Jason H. Moore. Translational informatics of population Health: How large biomolecular and clinical datasets unite. Pacific Symposium on Biocomputing 24:455(2019). link
[47] Nima Pouladi, Ikbel Achour, Haiquan Li, Joanne Berghout, Colleen Kenost and Yves A Lussier. Biomechanisms of comorbidity: reviewing integrative analyses of multi-omics datasets and electronic health records. International Medical Informatics Association Yearbook of Medical Informatics 2016. pp 194-206. Invited. doi:10.15265/IY-2016-040
[46] Yves A. Lussier*, Haiquan Li*, Nima Pouladi and Qike Li. Accelerating precision biology and medicine with computational biology and bioinformatics. Genome Biology 15(9):450 (ISMB 2014 meeting report) doi:10.1186/s13059-014-0450-y.
[45] Yves A. Lussier and Haiquan Li. Hypothesis generation from heterogeneous datasets. Methods in Biomedical Informatics: A Pragmatic Approach. Elsevier Science, pp81-98, 2013. link.
[44] Yves A. Lussier, Haiquan Li, and Mark Maienschein-Cline. Conquering computational challenges of omics data and post-ENCODE paradigms. Genome Biology 14(8):310, 2013 (ISMB/ECCB 2013 meeting report). doi:10.1186/gb-2013-14-8-310. Highly accessed (ranked top 3 in access within 30 days of publication).
[43] Yves A. Lussier and Haiquan Li. The rise of translational bioinformatics. Genome Biology 13(8):319, 2012 (ISMB 2012 conference report). doi:10.1186/gb-2012-13-8-319 Highly accessed.
[42] Yves A Lussier and Haiquan Li. Breakthroughs in genomics data integration for predicting clinical outcome. Journal of Biomedical Informatics 45:1199-1201, 2012. doi:10.1016/j.jbi.2012.10.003
[41] Haiquan Li, Jinyan Li, Xuechun Zhao. Discovery of Interaction Sites from Protein Structures and Protein Interactions. Encyclopedia of Data Warehousing and Mining, 2nd Edition. IGI Global, pp.683-688, 2008.
[40] M. Melichar, K. Didan, A. Barreto-Muñoz, J. N. Duberstein, E. J. Hernández, T. Crimmins, Haiquan Li, M. Traphagen, K A. Thomas, P. Nagler. Random Forest Classification of Multitemporal Landsat 8 Spectral Data and Phenology Metrics for Land Cover Mapping in the Sonoran and Mojave Deserts. Remote Sensing 15(5): 1266, 2023.paperi
[39] Wenting Luo, Edwin Baldwin, Anna Yi Jiang, Shujuan Li, Bo Yang, Haiquan Li*. Effects of housing environments on COVID-19 transmission and mental health revealed by COVID-19 participant experience data from the All of Us research program in the USA: A case-control study. BMJ Open. 12:e0637144,2022.. paper
[38]Eugene H. Chang, Nima Pouladi, Stefano Guerra, Jana Jandova, Alexander Kim, Haiquan Li, Jianrong Li, Wayne Morgan, Debra A. Stern, Amanda L. Willis, Yves A. Lussier, Fernando D. Martinez.Epithelial cell responses to rhinovirus identify an early-life-onset asthma phenotype in adults. Journal of Allergy and Clinical Immunology 2022. paper
[37] Haiquan Li*, Edwin Baldwin, Xiang Zhang, Colleen Kenost, Wenting Luo, Elizabeth A. Calhoun, Lingling An, Charles L. Bennett*, Yves A. Lussier*. Comparison and Impact of COVID-19 for cancer patients: A survival analysis of fatality rate controlling for age, sex, and cancer type. BMJ Health & Care Informatics, invited, to appear. 2021. paper.
[36] Soumya Rajan, Amit Amin, Lingxiao Li, Delphine Rolland, Haiquan Li, Deukwoo Kwon, Mercedes Kweh, Artavazd Arumov, Evan Roberts, Aimin Yan, Venkatesha Basrur, Kojo Elenitoba-Johnson, Steven (Xi) Chen, Soham Puvvada, Yves Lussier, Daniel Bilbao, and Megan Lim and Jonathan Schatz. The Mechanism of Cancer Drug Addiction in ALK-Positive T-Cell Lymphoma. Oncogene Dec 5, 2019. doi:10.1038/s41388-019-1136-4
[35] Haiquan Li*, Jung Wei Fan, Francesca Vitali, Joanne Berghout, Dillon Aberasturi, Jianrong Li, Liam Wilson, Wesley Chiu, Minsu Pumajero, Jiali Han, Colleen Kenost, Pradeep C. Koripella, Nima Pouladi, Dean Billheimer, Edward J. Bedrick and Yves A. Lussier*. Novel disease syndromes unveiled by integra-tive multiscale network analysis of diseases sharing molecular effectors and comorbidities. BMC Medical Genomics 2018:11 (Suppl 6): 112.doi:10.1186/s12920-018-0428-9.
[34] Vincent Gardeux, Joanne Berghout, Ikbel Achour, A Grant Schissler, Qike Li, Colleen Kenost, Jianrong Li, Yuan Shang, Anthony Bosco, Donald Saner, Marilyn J Halonen, Daniel J Jackson, Haiquan Li*, Fernando D Martinez*, Yves A Lussier*. A genome-by-environment interaction classifier for precision medicine: personal transcriptome response to rhinovirus identifies children prone to asthma exacerbations. Journal of American Medical Informatics Association (JAMIA) 2017. doi:10.1093/jamia/ocx069.
[33] Qike Li, A. Grant Schissler, Vincent Gardeux, Ikbel Achour, Colleen Kenost, Joanne Berghout, Haiquan Li*, Hao Helen Zhang*, Yves A. Lussier*. N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes. BMC Medical Genomics . 2017 10(Suppl):27, doi:10.1186/s12920-017-0263-4.
[32] Qike Li, A. Grant Schissler, Vincent Gardeux, Joanne Berghout, Ikbel Achour, Colleen Kenost, Haiquan Li*, Hao Helen Zhang*, Yves A Lussier*. kMEn: analyzing noisy and bidirectional transcriptional pathway responses in single subjects. Journal of Biomedical Informatics 66:32-41, 2017. doi:10.1016/j.jbi.2016.12.009
[31] Haiquan Li, Ikbel Achour, Lisa Bastarache, Joanne Berghout, Vincent Gardux, Jianrong Li, Lisa Bastarache, Younghee Lee, Lorenzo Pesce, Xinan Yang, Kenneth S. Ramos, Ian Foster, Joshua C. Denny, Janson H. Moore, and Yves A. Lussier. Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions. npj Genomic Medicine 1:16006, 2016. doi:10.1038/npjgenmed.2016.6.
[30] A Grant Schissler, Qike Li, James Chen, Colleen Kenost, Ikbel Achour, D Dean Billheimer, Haiquan Li, Walter W Piegorsch, Yves A Lussier. Analysis of aggregated cell-cell statistical distance within pathways unveils therapeutic-resistance mechanisms in circulating tumor cells. Bioinformatics 32(12): i80-i89, 2016. doi:10.1093/bioinformatics/btw248. ISMB 2016 proceeding paper.
[29] Haiquan Li, Nima Pouladi, Ikbel Achour, Vincent Gardeux,Jianrong Li, Qike Li, Fernando Martinez, Joe GN Skip Garcia, Yves A Lussier.eQTL networks unveil enriched mRNA master integrators downstream of complex disease-associated SNPs . Journal of Biomedical Informatics 58:226-234, 2015. doi:10.1016/j.jbi.2015.10.010
[28] Grant A Schissler, Vincent Gardeux, Qike Li, Ikbel Achour, Haiquan Li, Walter W Piegorsch, Yves A Lussier. Dynaimc changes of RNA-sequencing expression for precision medicine: 'N-of-1-pathways' Mahalanobis distance within pathways of signle subjects predicts breast cancer survival. Bioinformatics 31(12):i293-i302,2015.doi:10.1093/bioinformatics/btv253, ISMB proceeding paper
[27]Hwanik Kim, Yves A Lussier, O Kyu Noh, Haiquan Li, Young-Taek Oh, Jaesung Heo. Prognostic implication of pulmonary function at the beginning of postoperative radiotherapy in non-small cell lung cancer. Radiotherapy and Oncology 113(3):374-378, 2014. paper
[26] Long Shuang Huang, Biji Mathew, Haiquan Li, Yutong Zhao, Shwu-Fan Ma, Imre Noth, Sekhar P. Reddy, Anantha Harijith,Peter V. Usatyuk, Evgeny V. Berdyshev, Naftali Kaminski, Tong Zhou, Wei Zhang, Yanmin Zhang, Jalees Rehman, Sainath R. Kotha, Travis O. Gurney, Narasimham L. Parinandi, Yves A. Lussier, Joe G.N.Garcia and Viswannathan Natarajan. The mitochondrial cardiolipin remodeling enzyme lysocardiolipin acyltransferase (LYCAT) is a novel target in pulmonary fibrosis. American Journal of Respiratory and Critical Care Medicine 189(11):1402-1415, 2014. doi:10.1164/rccm.201310-1917OC.
[25] Vincent Gardeux, Ikbel Achour, Mark Maienschein-Cline, Gurunadh Parinandi, Jianrong Li, Neil Bahroos, Haiquan Li, Joe Gn Garcia and Yves A Lussier. "N-of-1-pathways" unveils personal deregulated mechanisms from a single pair of RNA-seq samples: towards precision medicine. JAMIA 21(6):1015-1025,2014. doi:10.1136/amiajnl-2013-002519
[24] Xinan Yang, Yong Huang, Younghee Lee, Vincent Gardeux, Ikbel Achour, Kelly Regan, Ellen Rebman, Haiquan Li and Yves A Lussier. Insilico cancer cell versus stroma cellularity index computed from species-specific human and mouse transcriptome of xenograft models: towards accurate stroma targeting therapy assessment. BMC Medical Genomics 7:(Suppl 1):S2,2014. doi:10.1186/1755-8794-7-S1-S2. Presented at TBC 2013.
[23] Younghee Lee+, Haiquan Li+, Jianrong Li+,Ellen Rebman+, Ikbel Achour, Kelly E Regan, Eric R. Gamazon, James L. Chen, Xinan Yang, Nancy J. Cox, Yves A. Lussier. Network Models of Genome-wide Association Studies Uncover the Topological Centrality of Protein Interactions in Complex Diseases. Journal of American Medical Informatics Association (JAMIA) 20:619-629, 2013. doi:10.1136/amiajnl-2012-001519
[22] James L. Chen, Alexander Hsu, Xinan Yang, Jianrong Li, Gurunadh Parinandi, Haiquan Li, Yves A. Lussier. Curation-Free Biomodules Mechanisms in Prostate Cancer Predict Recurrent Disease. BMC Medical Genomics 6 (Suppl 2):S4, 2013. doi:10.1186/1755-8794-6-S2-S4
[21] Haiquan Li+, Younghee Lee+, James L. Chen, Ellen Rebman, Jianrong Li, Yves A. Lussier. Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory. Journal of American Medical Informatics Association (JAMIA) 19 (2):295-305, 2012. doi:10.1136/amiajnl-2011-000482
[20] Kelly Regan+, Kanix Wang+, Emily Doughty+, Haiquan Li+, Jianrong Li+, Younghee Lee, Maricel Kann, Yves A. Lussier. Translating Mendelian and complex inheritance of Alzheimer’s genes for predicting unique personal genome variants. Journal of American Medical Informatics Association (JAMIA) 19 (2):306-316, 2012. doi:10.1136/amiajnl-2011-000656
[19] Yves A Lussier, Nikolai N Khodarev, Kelly Regan, Kimberly Corbin, Haiquan Li, Sabha Ganai, Sajid A Khan, Jennifer Generlich, Thomas E Darga, Hanli Fan, Oleksiy Karpenko, Philip B Paty, Mitchell C Posner, Steven J Chmura, Samuel Hellman, Mark K Ferguson, Weichselbaum RR. Oligo- and polymetastatic progression in lung metastasis (es) patients is associated with specific microRNAs. PloS One 7 (12):e50141. doi:10.1371/journal.pone.0050141.
[18] Zhentian Lei+, Haiquan Li+, Patrick Zhao and Lloyd W. Sumner. MET-IDEA version 2.06; Improved efficiency and additional functions for mass spectrometry-based metabolomics data processing. Metabolomics 8 (Suppl 1):S105-S110, 2012. doi:10.1007/s11306-012-0397-5
[17] Vagner A. Benedito, Haiquan Li, Xinbin Dai, Maren Wandrey, Ji He, Rakesh Kaudal, Ivone Torres-jerez, S. Karen Gomez, Marie J. Harrison, Yuhong Tang, Patrick X Zhao, Michael K. Udvardi. Genomic Inventory and Transcriptional analysis of Medicago Trucatula Transporters. Plant Physiology 152(3):1716-1730, 2010. doi:10.1104/pp.109.148684
[16] Haiquan Li, Vagner A. Benedito, Michael K. Udvardi and Patrick Xuechun Zhao. TransportTP: A Two-phase Classification Approach for Membrane Transporter Prediciton and Characterization. BMC Bioinformatics, 10:418, 2009x. doi:10.1186/1471-2105-10-418
[15] Haiquan Li, Xinbin Dai, Xuechun Zhao. A Nearest Neighbor Approach for Automated Transporter Prediction and Categorization from Protein Sequences. Bioinformatics 24(9): 1129-1136, 2008. doi:10.1093/bioinformatics/btn099
[14] Jinyan Li, Guimei Liu, Haiquan Li, Limsoon Wong. Maximal Bicliques Subgraphs and Closed Pattern Pairs of the Adjacency Matrix: A One-to-one Correspondence and Mining Algorithms. IEEE Transactions on Knowledge and Data Engineering (TKDE) 19(12):1625-1637,2007. paper. doi:10.1109/TKDE.2007.190660
[13] Haiquan Li, Jinyan Li, Limsoon Wong. Discovering Motif Pairs at Interaction Sites from Protein Sequences on a Proteome-wide Scale. Bioinformatics 22(8):989-996, 2006. doi:10.1093/bioinformatics/btl020
[12] Haiquan Li, Jinyan Li. Discovery of Stable and Significant Binding Motif Pairs from PDB Complexes and Protein Interaction Datasets. Bioinformatics 21(3):314-324, 2005. doi:10.1093/bioinformatics/bti019
[11] Jinyan Li and Haiquan Li. Using Fixed Point Theorems to Model the Binding in Protein-protein Interactions. IEEE Transactions on Knowledge and Data Engineering (TKDE) 17(8):1079-1087, 2005. paper. doi:10.1109/TKDE.2005.134
[10] Qike Li, Samir Rachid Zaim, Dillon Aberasturi, Joanne Berghout, Haiquan Li, Francesca Vitali, Colleen Kenost, Helen Hao Zhang, Yves A. Lussier. Interpretation of ‘Omics dynamics in a single subject using local estimates of dispersion between two transcriptomes. AMIA Annual Symposium 2019.
[9] Francesca Vitali, Joanne Berghout, Jungwei Fan, Jianrong Li, Qike Li, Haiquan Li*, Yves A Lussier*. Precision drug repurposing via convergent eQTL-based molecules and pathway targeting independent disease-associated polymorphisms. Pacific Symposium on Biocomputing (PSB) 24:308-319, 2019. Hawaii, 2019. paper
[8] Jiali Han, Jianrong Li, Ikbel Achour, Lorenzo Pesce, Ian Foster, Haiquan Li*, Yves A. Lussier*. Convergent downstream candidate mechanisms of distinct intergenic polymorphisms between co-classified diseases implicate epistasis among noncoding elements. Pacific Symposium on Biocomputing (PSB) , 23:524-535, Hawaii,2018. paper
[7] Young Ji Lee, Andew D. Boyd, Jianrong John Li, Vincent Gardeux, Colleen Kenost, Don Saner, Haiquan Li, Ivo Abraham, Jerry A. Krishnan, Yves A. Lussier. COPD hospitalization risk increased with distinct patterns of multiple systems comorbidities unveiled by network modelling. AMIA Annual Symposium 2014, pp 855-864, 2014.paper
[6] Alan Perez-rathke, Haiquan Li, Yves A Lussier. Interpreting personal transcriptomes: personalized mechanism-scale profiling of RNA-Seq data. Pacific Symposium of Biocomputing (PSB) 18:159-170, 2013, paper.
[5] Xinan Yang, Haiquan Li, Kelly Regan, Jianrong Li, Young Huang, H Rosie Xing and Yves A. Lussier. Towards Mechanism Classifiers: Expression-anchored Gene Ontology Signature Predicts Clinical Outcome in Lung Adenocarcinoma Patients. AMIA 2012 Annual Symposium, pp1040-1049, 2012. paper
[4] Jinyan Li, Haiquan Li, Limsoon Wong, Jian Pei, Guozhu Dong. Minimum Description Length (MDL) Principle: Generators are Preferable to Closed Patterns. Twenty-first National Conference on Artificial Intelligence (AAAI-06), Boston, pp. 409-414, 2006. paper
[3] Haiquan Li, Jinyan Li, Limsoon Wong, Mengling Feng, Yanpeng Tan. Relative Risk and Odds Ratio: A Data Mining Perspective. 24th Symposium on Principles of Database Systems (PODS). Baltimore, USA. pp 368-377, 2005. paper. doi:10.1145/1065167.1065215
[2] Jinyan Li, Haiquan Li, Donny Soh, Limsoon Wong. A Correspondence between Maximal Complete Bipartite Subgraphs and Closed Patterns. 9th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD), Portugal, pp 146-156, 2005. paper. doi:10.1007/11564126_18
[1] Haiquan Li, Jinyan Li, Soon Heng Tan, See-kiong Ng. Discovery of Binding Motif Pairs from Protein Complex Structural Data and Portein Interaction Sequence Data. The 9th Pacific Symposium on Biocomputing (PSB), Hawaii, pp 312-323, 2004. paper.
Haiquan Li, Ikbel Archour, Joanne Berghout, Yves A. Lussier. Pharmacogenomics of Intergenic Single-Nuclotide Polymorphisms and in Silio Modeling for Precision Therapy. patent document US Patent App. 16/342913. Doc# 20200051661 Feb 13, 2020
"Efficient Discovery of Binding Motif Pairs from Protein-protein Interactions", School of Computing, National University of Singapore.