Park CY, Wong AK, Greene CS, Rowland J, Guan Y, Bongo LA, Burdine RD, Troyanskaya OG.  2013.  Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.. PLoS Comput Biol. 9(3):e1002957.

Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WKyu et al..  2008.  A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.. Genome Biol. 9 Suppl 1:S2.

Quang D, Guan Y, Parker SCJ.  2018.  YAMDA: thousandfold speedup of EM-based motif discovery using deep learning libraries and GPU. Bioinformatics. Oct 15;34(20):3578-3580. doi: 10.1093/bioinformatics/bty396

Ramani B, Panwar B, Moore LR, Wang B, Huang R, Guan Y, Paulson HL.  2017.  Comparison of spinocerebellar ataxia type 3 mouse models identifies early gain-of-function, cell-autonomous transcriptional changes in oligodendrocytes.. Hum Mol Genet.. (Sep 1;26(17):3362-3374, doi:10.1093/hmg/ddx224)

Shi L, Lin Y-H, Sierant MC, Zhu F, Cui S, Guan Y, Sartor MA, Tanabe O, Lim K-C, Engel JDouglas.  2014.  Developmental transcriptome analysis of human erythropoiesis.. Hum Mol Genet. 23(17):4528-42.

Shi L, Sierant MC, Gurdziel K, Zhu F, Cui S, Kolodziej KE, Strouboulis J, Guan Y, Tanabe O, Lim K-C et al..  2014.  Biased, Non-equivalent Gene-Proximal and -Distal Binding Motifs of Orphan Nuclear Receptor TR4 in Primary Human Erythroid Cells.. PLoS Genet. 10(5):e1004339.

Siddiqui O, Zhang H, Guan Y, Omenn G.  2018.  Chromosome 17 Missing Proteins: Recent Progress and Future Directions as part of the Next-50MP Challenge. Journal of Proteome Research. doi: 10.1021/acs.jproteome.8b00442. [Epub ahead of print]

Sieberts SK, Zhu F, García-García J, others, Eksi R, others, Li H, others, Guan Y, Mangravite LM.  2016.  Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.. Nat Commun. 7:12460.

Tang M, Gao C, Goutman S, Kalinin A, Mukherjee B, Guan Y, Dinov I.  2018.  Model-based and Model-free Techniques for Amyotrophic Lateral Sclerosis Diagnostic Prediction and Patient Clustering. Neuroinformatics. Nov 20. doi: 10.1007/s12021-018-9406-9

Wong AK, Park CY, Greene CS, Bongo LA, Guan Y, Troyanskaya OG.  2012.  IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.. Nucleic Acids Res. 40(Web Server issue):W484-90.

Yang Z-K, Niu Y-F, Ma Y-H, Xue J, Zhang M-H, Yang W-D, Liu J-S, Lu S-H, Guan Y, Li H-Y.  2013.  Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation.. Biotechnol Biofuels. 6(1):67.

Zhang H, Zhu F, Dodge H, Higgins G, Omenn G, Guan Y.  2018.  A similarity-based approach to leverage multi-cohort medical data on the diagnosis and prognosis of Alzheimer's disease. Gigascience. Jul 11. doi: 10.1093/gigascience/giy085

Zhu F, Panwar B, Guan Y.  2015.  Algorithms for modeling global and context-specific functional relationship networks.. Brief Bioinform.

Zhu F, Panwar B, Dodge HH, Li H, Hampstead BM, Albin RL, Paulson HL, Guan Y.  2016.  COMPASS: A computational model to predict changes in MMSE scores 24-months after initial assessment of Alzheimer's disease.. Sci Rep. 6:34567.

Zhu F, Shi L, Li H, Eksi R, Engel JDouglas, Guan Y.  2014.  Modeling Dynamic Functional Relationship Networks and Application to Ex Vivo Human Erythroid Differentiation.. Bioinformatics.

Zhu F, Guan Y.  2014.  Predicting Dynamic Signaling Network Response under Unseen Perturbations.. Bioinformatics.

Zhu F, Shi L, Engel JDouglas, Guan Y.  2015.  Regulatory network inferred using expression data of small sample size: application and validation in erythroid system.. Bioinformatics.