Publications

2020 and in press

Wang Z, Li H, Guan Y. In Press. Machine Learning For Cancer Drug Combination. Clinical Pharmacology & Therapeutics.

Wu S, Li H, Quang D, Guan Y. In Press. Three-plane-assembled Deep Learning Segmentation of Gliomas. Radiology: Artificial Intelligence.

Mason M, Schinke C, Eng C, Towfic F, Gruber F, Dervan A, White B, Pratapa A, Guan Y, Chen H, Cui Y, et al. In Press. Multiple Myeloma DREAM Challenge Reveals Epigenetic Regulator PHF19 As Marker of Aggressive Disease. Leukemia.

Salcedo A., Tarabichi M., Espiritu S.M.G.,, Stuart J.M., Anastassiou D., Guan Y., Ewing A.D., Ellrott K., Wedge D.C. et al.. 2020. A community effort to create standards for evaluating tumor subclonal reconstruction. Nature Biotechnology. Jan;38(1):97-107. doi: 10.1038/s41587-019-0364-z. Epub 2020 Jan 9.

Rai V, Quang D, Erdos M, Cusanovich R, Daza R, Narisu N, Zou L, Didion J, Guan Y, Shendure J et al.. 2020. Single cell ATAC-seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures. Molecular Metabolism. 32, February 2020, Pages 109-121

2019

Guan Y. 2019. Waking up to data challenges. Nature Machine Intelligence. Jan 7 1 (1), 67

Li H, Quang D, Guan Y. 2019. Anchor: Trans-cell Type Prediction of Transcription Factor Binding Sites. Genome Research. 2019 Feb;29(2):281-292. doi: 10.1101/gr.237156.118. Epub 2018 Dec 19.

Guan Y, Zhang H, Quang D, Wang Z, Pappas D, Kremer J, Parker S, Zhu F. 2019. Machine learning to predict anti-TNF drug responses of rheumatoid arthritis patients by integrating clinical and genetic markers. Arthritis & Rheumatology. Jul 24. doi: 10.1002/art.41056. [Epub ahead of print]; (Highlights in Nat Rev Rheumatol. 2019 Oct 10. doi: 10.1038/s41584-019-0320-9.)

Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, al. et. 2019. Assessment of network module identification across complex diseases. Nature Methods. Sep;16(9):843-852. doi: 10.1038/s41592-019-0509-5. Epub 2019 Aug 30.

Menden MP, Wang D, Mason M, Szalai B, Bulusu KC, Guan Y, et al. 2019. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications. (10, Article number: 2674 (2019))

Li D, Balamurugan S, Yang YF, Zhang JW, Huang D, Zou LG, Yang WD, Liu JS, Guan Y, Li HY. 2019. Transcriptional regulation of microalgae for concurrent lipid overproduction and secretion. Science Advances. Jan 30;5(1):eaau3795. doi: 10.1126/sciadv.aau3795. eCollection 2019 Jan.

Al'Aref SJ, Anchouche K, Singh G, Slomka PJ, Kolli KK, Kumar A, others, Guan Y, Min JK. 2019. Clinical applications of machine learning in cardiovascular disease and its relevance to cardiac imaging.. Eur Heart J. Jun 21;40(24):1975-1986. doi: 10.1093/eurheartj/ehy404.

Zou Z, Zhang H, Guan Y, Zhang J. 2019. Deep residual neural networks resolve quartet molecular phylogenies. Molecular Biology and Evolution. Dec 23. pii: msz307. doi: 10.1093/molbev/msz307.

Li H, Siddiqui O, Zhang H, Guan Y. 2019. Joint Learning Improves Protein Abundance Prediction in Cancers. BMC Biology. Dec 23;17(1):107. doi: 10.1186/s12915-019-0730-9

Deng K, Li H, Guan Y. 2019. Treatment Stratification of Patients with Metastatic Castration-resistant Prostate Cancer by Machine Learning. iScience. Dec 26;23(2):100804. doi: 10.1016/j.isci.2019.100804.

Li H-D, Bai T, Sandford E, Burmeister M, Guan Y. 2019. BaiHui: Cross-species Brain-specific Network Built with Hundreds of Hand-curated Datasets. Bioinformatics. (Jul 15;35(14):2486-2488. doi: 10.1093/bioinformatics/bty1001.)

Li H, Guan Y. 2019. Machine Learning Empowers Phosphoproteome Prediction in Cancers. Bioinformatics. Aug 13. pii: btz639. doi: 10.1093/bioinformatics/btz639. [Epub ahead of print] PMID: 31410451

Jiang YQ, Xiong JH, Li HY,, Guan Y, Gu H, Sun JF. 2019. Recognizing Basal Cell Carcinoma on Smartphone-Captured Digital Histopathology Images with Deep Neural Network. British Journal of Dermatology. Apr 24. doi: 10.1111/bjd.18026. [Epub ahead of print]

Li H, Hu S, Neamati N, Guan Y. 2019. TAIJI: Approaching Experimental Replicates-Level Accuracy for Drug Synergy Prediction. Bioinformatics. Jul 1;35(13):2338-2339. doi: 10.1093/bioinformatics/bty955.

Tang M, Gao C, Goutman S, Kalinin A, Mukherjee B, Guan Y, Dinov I. 2019. Model-based and Model-free Techniques for Amyotrophic Lateral Sclerosis Diagnostic Prediction and Patient Clustering. Neuroinformatics. Jul;17(3):407-421. doi: 10.1007/s12021-018-9406-9.

Sun C, Li H, Mills R, Guan Y. 2019. Prognostic Model for Multiple Myeloma Progression Integrating Gene Expression and Clinical Features. GigaScience. Dec 1;8(12). pii: giz153. doi: 10.1093/gigascience/giz153.

2018

Li H, Li T, Quang D, Guan Y. 2018. Network propagation predicts drug synergy in cancers. Cancer Research. Sep 15;78(18):5446-5457. doi: 10.1158/0008-5472.CAN-18-0740. Epub 2018 Jul 27.

Li H, Panwar B, Omenn GS, Guan Y. 2018. Accurate Prediction of Personalized Olfactory Perception from Large-Scale Chemoinformatic Features.. Gigascience. Feb 1;7(2). doi: 10.1093/gigascience/gix127.

Duda M, Zhang H, Li HD, Wall DP, Burmeister M, Guan Y. 2018. Brain-specific functional relationship networks inform autism spectrum disorder gene prediction.. Transl Psychiatry. . 8(1(56))

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]

Causey JL, Ashby C, Walker K, Wang ZP, Yang M, Guan Y, Moore JH, Huang X. 2018. DNAp: A Pipeline for DNA-seq Data Analysis. Sci Rep.. (May 1;8(1):6793. doi: 10.1038/s41598-018-25022-6.)

Hosoya T, Li H, Ku CJ, Wu Q, Guan Y, Engel JD. 2018. High throughput single cell sequencing of both T-cell-receptor-beta alleles. Journal of Immunology. (Dec 1;201(11):3465-3470. doi: 10.4049/jimmunol.1800774. Epub 2018 Oct 31.)

Guan Y, Li T, Zhang HJ, Zhu F, Omenn GS. 2018. Prioritizing Predictive Biomarkers for Gene Essentiality in Cancer Cells with mRNA Expression Data and DNA Copy Number Profile. Bioinformatics. 2018 Dec 1;34(23):3975-3982. doi: 10.1093/bioinformatics/bty467.

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

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

2017

Keller A, Gerkin RC, Guan Y, Dhurandhar A, Turu G, Szalai B, Mainland JD, Ihara Y, Yu CW, Wolfinger R et al.. 2017. Predicting human olfactory perception from chemical features of odor molecules.. Science. Feb 20. pii: eaal2014. doi: 10.1126/science.aal2014.

Li H-D, Zhang Y, Guan Y, Menon R, Omenn GS. 2017. Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks.. Methods Mol Biol.. (1558):415-436.

Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A. 2017. A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.. Cell Syst.. Nov 22;5(5):485-497.e3. doi: 10.1016/j.cels.2017.09.004. Epub 2017 Oct 4.

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)

Huang Z, Zhang H, Boss J, Goutman SA, Mukherjee B, Dinov ID, Guan Y. 2017. Complete hazard ranking to analyze right-censored data: An ALS survival study.. PLoS Comput Biol. Dec 18;13(12):e1005887. doi: 10.1371/journal.pcbi.1005887.

Ku CJ, Sekiguchi JM, Panwar B, Guan Y, Takahashi S, Yoh K, Maillard I, Hosoya T, Engel JD. 2017. GATA3 abundance is a critical determinant of T cell receptor beta allelic exclusion. Mol Cell Biol. Mar 20. pii: MCB.00052-17. doi: 10.1128/MCB.00052-17.

Panwar B, Omenn GS, Guan Y. 2017. miRmine: A Database of Human miRNA Expression Profiles.. Bioinformatics. Jan 19. pii: btx019. doi: 10.1093/bioinformatics/btx019.

2016

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.

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.

Allen GI, Amoroso N, Anghel C, others, Guan Y, others, Zhu F, Zhu H, Zhu S. 2016. Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.. Alzheimers Dement.

Menon S, Lu C, Menon R, Schwartz J, Guan Y. 2016. Effects of Antioxidants in Human Cancers: Differential Effects on Non-Coding Intronic RNA Expression.. Antioxidants (Basel) (The first author of this paper is a high-school trainee --now in Harvard-- in my lab, who entered the finalist of Intel Talent Search based on this piece of work.). 5(1)

Panwar B, Menon R, Eksi R, Li H, Omenn GS, Guan Y. 2016. Genome-wide Functional Annotation of Human Protein-coding Splice Variants Using Multiple Instance Learning.. J Proteome Res.

Hill SM, Heiser LM, Cokelaer T, Zhu F, others, Guan Y, others, Stolovitzky G, Saez-Rodriguez J, Mukherjee S. 2016. Inferring causal molecular networks: empirical assessment through a community-based effort.. Nat Methods. 13(4):310-8.

Li H-D, Menon R, Eksi R, Guerler A, Zhang Y, Omenn GS, Guan Y. 2016. A Network of Splice Isoforms for the Mouse.. Sci Rep. 6:24507.

Li H-D, Omenn GS, Guan Y. 2016. A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling.. Brief Bioinform.

Giorgetti E, Yu Z, Chua JP, Shimamura R, Zhao L, Zhu F, Venneti S, Pennuto M, Guan Y, Hung G et al.. 2016. Rescue of Metabolic Alterations in AR113Q Skeletal Muscle by Peripheral Androgen Receptor Gene Silencing.. Cell Rep. 17(1):125-36.

2015

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

Menon R, Panwar B, Eksi R, Kleer C, Guan Y, Omenn GS. 2015. Computational Inferences of the Functions of Alternative/Non-Canonical Splice Isoforms Specific to HER2+/ER-/PR- Breast Cancers, a Chromosome 17 C-HPP Study.. J Proteome Res.

Li H-D, Menon R, Govindarajoo B, Panwar B, Zhang Y, Omenn GS, Guan Y. 2015. Functional Networks of Highest-Connected Splice Isoforms, from the Chromosome 17 Human Proteome Project.. J Proteome Res.

Guan Y, Martini S, Mariani LH. 2015. Genes Caught In Flagranti: Integrating Renal Transcriptional Profiles With Genotypes and Phenotypes.. Semin Nephrol. 35(3):237-44.

Panwar B, Menon R, Eksi R, Omenn GS, Guan Y. 2015. MI-PTV: A Tool for Visualizing the Chromosome-centric Human Proteome.. J Proteome Res.

Li H-D, Omenn GS, Guan Y. 2015. MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse.. Database (Oxford). 2015:bav045.

Horvatovich P, Lundberg EK, Chen Y-J, Sung T-Y, He F, Nice EC, Goode RJA, Yu S, Ranganathan S, Baker MS et al.. 2015. A Quest for Missing Proteins: update 2015 on Chromosome-Centric Human Proteome Project.. J Proteome Res.

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.

2014

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.

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.

Li H-D, Menon R, Omenn GS, Guan Y. 2014. The emerging era of genomic data integration for analyzing splice isoform function.. Trends Genet. 30(8):340-347.

Ma Q, Ozel AB, Ramdas S, McGee B, Khoriaty R, Siemieniak D, Li H-D, Guan Y, Brody LC, Mills JL et al.. 2014. Genetic variants in PLG, LPA and SIGLEC 14 as well as smoking contribute to plasma plasminogen levels.. Blood.

Bethunaickan R, Berthier CC, Zhang W, Eksi R, Li H-D, Guan Y, Kretzler M, Davidson A. 2014. Identification of Stage-Specific Genes Associated With Lupus Nephritis and Response to Remission Induction in (NZB × NZW)F1 and NZM2410 Mice.. Arthritis Rheumatol. 66(8):2246-58.

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.

Omenn GS, Guan Y, Menon R. 2014. A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines.. J Proteomics. 107:103-12.

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

Li H-D, Menon R, Omenn GS, Guan Y. 2014. Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence.. Proteomics. (Hong-dong Li was selected as the winner of the AB SCIEX Young Investigator Award for this work.)

2013

Guan Y, Dunham MJ, Troyanskaya OG, Caudy AA. 2013. Comparative gene expression between two yeast species.. BMC Genomics. 14:33.

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.

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.

Caudy AA, Guan Y, Jia Y, Hansen C, DeSevo C, Hayes AP, Agee J, Alvarez-Dominguez JR, Arellano H, Barrett D et al.. 2013. A new system for comparative functional genomics of Saccharomyces yeasts.. Genetics. 195(1):275-87.

Eksi R, Li H-D, Menon R, Wen Y, Omenn GS, Kretzler M, Guan Y. 2013. Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data.. PLoS Comput Biol. 9(11):e1003314.

2012

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.

Guan Y, Gorenshteyn D, Burmeister M, Wong AK, Schimenti JC, Handel MAnn, Bult CJ, Hibbs MA, Troyanskaya OG. 2012. Tissue-specific functional networks for prioritizing phenotype and disease genes.. PLoS Comput Biol. 8(9):e1002694.

2011

Guan Y, Yao V, Tsui K, Gebbia M, Dunham MJ, Nislow C, Troyanskaya OG. 2011. Nucleosome-coupled expression differences in closely-related species.. BMC Genomics. 12:466.

2010

Guan Y, Ackert-Bicknell CL, Kell B, Troyanskaya OG, Hibbs MA. 2010. Functional genomics complements quantitative genetics in identifying disease-gene associations.. PLoS Comput Biol. 6(11):e1000991.

Guan Y, Dunham M, Caudy A, Troyanskaya O. 2010. Systematic planning of genome-scale experiments in poorly studied species.. PLoS Comput Biol. 6(3):e1000698.

2009

Guan Y, Ramalingam S, Nagegowda D, Taylor PWJ, Chye M-L. 2008. Brassica juncea chitinase BjCHI1 inhibits growth of fungal phytopathogens and agglutinates Gram-negative bacteria.. J Exp Bot. 59(12):3475-84.

Guan Y, Chye M-L. 2008. A Brassica juncea chitinase with two-chitin binding domains show anti-microbial properties against phytopathogens and Gram-negative bacteria.. Plant Signal Behav. 3(12):1103-5.

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.

2008

Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya OG. 2008. A genomewide functional network for the laboratory mouse.. PLoS Comput Biol. 4(9):e1000165.

Guan Y, Myers CL, Hess DC, Barutcuoglu Z, Caudy AA, Troyanskaya OG. 2008. Predicting gene function in a hierarchical context with an ensemble of classifiers.. Genome Biol. 9 Suppl 1:S3.

2007

Lui W-Y, Wong EWP, Guan Y, Lee WM. 2007. Dual transcriptional control of claudin-11 via an overlapping GATA/NF-Y motif: positive regulation through the interaction of GATA, NF-YA, and CREB and negative regulation through the interaction of Smad, HDAC1, and mSin3A.. J Cell Physiol. 211(3):638-48.

Guan Y, Dunham MJ, Troyanskaya OG. 2007. Functional analysis of gene duplications in Saccharomyces cerevisiae.. Genetics. 175(2):933-43.