Full Publication list: Please see our Google Scholar Citation Report Page for the full list of publications. Or use the keywords "Quan Long" and "Calgary" to search in PubMed for the works published by my research group in the University of Calgary.
Representative Publications: (Trainees in my group are Underlined; * = joint first authors; # = corresponding authors)
Statistical Genetics & Machine Learning:
He J, Antonyan L, Zhu H, Ardila K, Li Q, Enoma D, Zhang W, Liu A, Chekouo T, Cao B, MacDonald ME, Arnold P#, and Long Q#. (2024) “A statistical method for image-mediated association studies discovers genes and pathways associated with four brain disorders”. American Journal of Human Genetics. doi: 10.1016/j.ajhg.2023.11.006.
He J, Perera D, Wen W, Ping J, Li Q, Lyu L, Chen Z, Shu X, Long J, Cai Q, Shu XO, Yin Z, Zheng W, Long Q#, Guo X#. (2024) “Enhancing disease risk gene discovery by integrating transcription factor-linked trans-variants into transcriptome-wide association analyses”. Nucleic Acids Research. doi: 10.1093/nar/gkae1035.
Li Q*, Bian J*, Qian Y, Kossinna P, Gau C, Gordon P, Zhou X, Guo X, Yan J, Wu J#, Long Q#. (2024) “An expression-directed linear mixed model (edLMM) discovering low-effect genetic variants”. Genetics (Featured in the Apr issue). doi: 10.1093/genetics/iyae018.
He J, Wen W, Beeghly-Fadiel A, Chen Z, Cao C, Shu XO, Zheng W, Long Q#, Guo X#. (2022) “Integrating transcription factor occupancy with transcriptome-wide association analysis identifies susceptibility genes in human cancers”. Nature Communications. doi: 10.1038/s41467-022-34888-0.
Cao C, Kossinna P, Kwok D, Li Q, He J, Su L, Guo X, Zhang Q#, Long Q#. (2022) “Disentangling genetic feature selection and aggregation in transcriptome-wide association studies”. Genetics (Cover Feature of the Feb issue). doi: 10.1093/genetics/iyab216.
Cao C*, Ding B*, Li Q, Kwok D, Wu J#, Long Q#. (2021) “Power analysis of transcriptome-wide association studies: implications for practical protocol choice”. PLoS Genetics. doi: 10.1371/journal.pgen.1009405.
Cao C, Kwok D, Edie S, Li Q, Ding B, Kossinna P, Campbell S, Wu J, Greenberg M, Long Q#. (2021) “kTWAS: integrating kernel-machine with transcriptome-wide association studies improves statistical power and reveals novel genes”. Briefings in Bioinformatics. doi: 10.1093/bib/bbaa270.
Mak L*, Li M*, Cao C, Gordon P, Tarailo-Graovac M, Bousman C, Wang P, Long Q#. (2018) “SimPEL: Simulation-based Power Estimation for sequencing studies of Low-prevalence conditions”. Genetic Epidemiology. doi: 10.1002/gepi.22129.
Long Q*, Argmann C*, Houten SM, Huang T, Peng S, Zhao Y, Tu Z, The GTEx Consortium, Zhu J# (2016). "Inter-tissue coexpression network analysis reveals DPP4 as an important gene in heart to blood communication". Genome Medicine doi: 10.1186/s13073-016-0268-1.
Zhang Q#, Long Q#, Ott J. (2014) “AprioriGWAS, a new pattern mining strategy for detecting genetic variants associated with disease through interaction effects”. PLoS Computational Biology. doi: 10.1371/journal.pcbi.1003627.
Bioinformatic & Biostatistic Tools:
Perera D, Li E, Gordon PMK, van der Meer F, Lynch T, Gill J, Church DL, de Koning APJ, Huber CD, van Marle G#, Platt A#, Long Q# (2025) “Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell.” Nature Communications. doi: 10.1038/s41467-025-60988-8.
Perera D, Reisenhofer E, Hussein S, Higgins E, Huber CD#, Long Q#. (2023) “CATE: A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data”. Methods in Ecology and Evolution. doi: 10.1111/2041-210X.14168
Cao C*, He J*, Mak L*, Perera D, Wang J, Kwok D, Mourier T, Li M, Gavriliuc S, Greenberg M, Morrissy S, Sycuro L, Yang G, Jeffares D, Long Q# (2021) “Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding”. Molecular Biology & Evolution. doi: 10.1093/molbev/msab037.
Cao C, Greenberg M, Long Q#. (2021) "WgLink: reconstructing whole-genome viral haplotypes using L0+L1-regularization". Bioinformatics. doi: 10.1093/bioinformatics/btab076.
Xiong Z, Zhang Q, Platt A, Liao W, Shi X, de los Campos G, and Long Q#. (2019) “OCMA: Fast, memory-efficient factorization of prohibitively large relationship matrices”. G3: Genes, Genomes, Genetics. doi: 10.1534/g3.118.200908.
Cao C, Mak L, Jin G, Gordon P, Ye K, and Long Q#. (2019) “PRESM: Personalized Reference Editor for Somatic Mutation discovery in cancer genomics”. Bioinformatics. doi: 10.1093/bioinformatics/bty812.
Zhang Q, Tyler-Smith C#, Long Q#. (2015) “An extended Tajima’s D neutrality test incorporating SNP calling and imputation uncertainties”. Statistics and Its Interface. doi: 10.4310/SII.2015.v8.n4.a4.
Long Q*#, Zhang Q*, Vilhjalmsson BJ, Forai P, Seren Ü, Nordborg M. (2013) “JAWAMix5: an out-of-core HDF5-based java implementation of whole-genome association studies using mixed models”. Bioinformatics. doi: 10.1093/bioinformatics/btt122.
Long Q#, MacArthur D, Ning Z, and Tyler-Smith C. (2009) “HI: Haplotype Improver using paired-end short reads”. Bioinformatics. doi: 10.1093/bioinformatics/btp412.
Path-Finding Genomics:
Long Q*, Rabanal FA*, Meng D*, Huber CD*, Farlow A*, Platzer A, Zhang Q, Vilhjálmsson BJ, …, Hellmann I, Nordborg M# (2013). “Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden”. Nature Genetics. doi: 10.1038/ng.2678
Long Q as a listed participant of the GTEx Consortium. (2015) “The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans”. Science (Cover Article). doi: 10.1126/science.1262110.
Long Q as a listed participant of the 1,000 Genomes Project. (2010) “A map of human genome variation from population-scale sequencing”. Nature (Cover Article). doi: 10.1038/nature09534
Manuscripts submitted:
Li Q*, Bian J*, Weeraman J*, Zhang Z, Leung A, Ding QX, Chekouo T, Wu L, Yan J, Wu J#, Long Q#. (2025) “Autoencoder-transformed transcriptome improves genotype-phenotype association studies”. Accapted by IEEE Transactions on Computational Biology & Bioinformatics. Preprint: Biorxiv. Software: GitHub.
Li Q, Perera D, Chen Z, Wen W, Wang D, Yan J, Shu XO, Zheng W, Guo X#, Long Q#. (2025+) “Tissue-specific transfer-learning enables retasking of a general comprehensive model to a specific domain”. Submitted. (Preprint: Biorxiv)
Wang D*, Qian Y*, Ding QX, Greenberg M#, Long Q#. (2025+) “The Bias of Using Cross-Validation in Genomic Predictions and Its Correction”. Submitted. (Preprint: Biorxiv)
Software: Please refer to our GitHub for the bioinformatics and biostatistics tools.