Publications

(B: Book Chapters; C: Conference papers; J: Journal papers; P: Posters; T: Technical Reports.)

Underlined names are current and previous lab members in Shi Lab.

Google Scholar citations

2017

J26. "Bayesian Network Construction and Genotype-Phenotype Inference Using GWAS Statistics", Zhang L, Pan Q, Wang Y, Wu X, and Shi X, in submission.

J25. "Secure Cloud-Delegated Genetic Testing for Personalized Medicine with Genetic Biomarker Hiding", Han J, Jung T, Li X-Y, and Shi X, in submission.

J24. "A Deep Auto-encoder Model for Gene Expression Prediction", Xie R, Wen J, Quitadamo A, Cheng J,  and Shi X, in submission.

J23. "Nonparametric Detection of Anomalous Data via Kernel Mean Embedding", Zou S, Liang Y, Poor H.V., and Shi X, in revision.

B1. "Data-Driven Approaches for Detecting Anomalous Data Streams", Zou S, Liang Y, Poor H.V., and Shi X, to appear in the book of "Biomedical Signal Processing in Big Data".

J22. "An Empirical Bayesian Elastic Nets Method for Epistasis Analysis of microRNAs on Pathological Stages in Colon Cancer", Wen JQuitadamo A, Hall B, and Shi X, in press, BMC Genomics, 2017. (EBEN-Epistasis: Github Link for Data and Code).

C24. "Constructing an Integrative MicroRNA eQTL Network on Ovarian Cancer: A Label Propagation Approach Utilizing Multiple Networks", Hall B, Quitadamo A, and Shi X, in Proceedings of the 13th International Symposium on Bioinformatics Research and Applications (ISBRA2016, Track 2 paper), Honolulu, Hawaii, May 29 - June 1, 2017.

C23. "Lightweight Mutual Authentication among Sensors in Body Area Networks through Physical Unclonable Functions, Xie L, Wang W, Shi X and Qin T, in Proceedings of  IEEE International Conference on Communications (2017) Communication and Information Systems Security Symposium, Paris, France, May 21-25, 2017.

P17. "Covariate-aware models for high-order epistasis analysis in yeast", Wen J, and Shi X, the Biology of Genomes, Cold Spring Harbor, NY, May 9-13, 2017 (poster).

P16. "An Integrative Analysis of Philadelphia-like Acute Lymphoblastic Leukemia", Nodzak C, Lopes Centoducatte G, Quitadamo A, Yunes Andres J, and Shi X,  the Biology of Genomes, Cold Spring Harbor, NY, May 9-13, 2017 (poster).

2016

C22. "A Predictive Model of Gene Expression Using a Deep Learning Framework", Xie R, Quitadamo A, Cheng J,  and Shi X, in Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016), Dec 15-18, 2016 (invitation of journal submission to BMC Genomics special issue).

C21. "Building Bayesian Networks from GWAS Statistics Based on Independence of Causal Influence", Zhang L, Pan Q, Wu X, and Shi X, in Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016), Dec 15-18, 2016 (short paper).

J21. "An Overview of Human Genetic Privacy", Shi X and Wu X, Annals of NY Academy of Sciences, 2016, DOI: 10.1111/nyas.13211.

P15. "Visualizing Linguistic Relationships of Uto-Aztecan Languages and Bantu Languages", Xue M, Ford C, Whiteley P, Janies D, Shi X and Wheeler W, The 115th American Athoropological Association(AAA) Annual Meeting, Minneapolis, MN, November 16 - 20, 2016 (poster).

T1. "Infringement of Individual Privacy via Mining GWAS Statistics", Y Wang, X Wu, X Shi, Technical Report DPL-2014-004, University of Arkansas, 2016.

C20. “Infringement of Individual Privacy via Mining Differentially Private GWAS Statistics”, Wang Y, Wen J, Wu X, and Shi X, In Proceedings of the 2nd International Conference on Big Data Computing and Communication (BIGCOM 2016), July 29-31, 2016, Shenyang, Liaoni, China, Springer Lecture Notes in Computer Science, Volume 9784, p355-366.

C19. "Epistasis Analysis of microRNAs in Colon Cancer Using Empirical Bayesian Elastic Nets", Wen JQuitadamo A, Hall B, and Shi X, In Proceedings of the 12th International Symposium on Bioinformatics Research and Applications (ISBRA2016, Track 2 paper), Minsky, Belaruse, June 6-8, 2016 (invited journal submission to BMC Genomics).

P14. "eQTL Analysis of Lung Adenocarcinoma Expression Subtypes", Quitadamo A, Desai H, and Shi X, the Biology of Genomes Meeting, Cold Spring Harbor, NY, May 10 - 14, 2016 (poster).

P13. "Apply Empirical Bayesian Elastic Net Method to microRNA Epistasis Analysis in Colon Cancer", Wen JQuitadamo A, Hall B, and Shi X, the Biology of Genomes Meeting, Cold Spring Harbor, NY, May 10 - 14, 2016 (poster).

P12. "Allele Specific Expression Analysis of Structural Variation in Human Populations", Wen J, Quitadamo A, and Shi X, the Biology of Genomes Meeting, Cold Spring Harbor, NY, May 10 - 14, 2016 (poster).

P11. "Method for Identifying BCR-ABL1-Like Pediatric Acute Lymphoblastic Leukemia", Lopes Centoducatte G, Bortolini Silveira A, Regina Brandalise S,  Quitadamo A, Shi X,  and Yunes Andres J, the 10th Biennial Childhood Leukemia Symposium, Athens, Greece, April 25-26, 2016 (poster).

J20. "Identifying microRNA and Gene Expression Networks Using Graph Communities", Hall B, Quitadamo A, and Shi X, Tsinghua Science and Technology. 2016. 21(2): 176-95.(EqtlCommunityDetection: Code, Github).

C18. "Sequential and Parallel LASSO: Novel Scalable Methods for eQTL Mapping", He A, Hall B, Wen J, Liang Y, and Shi X, In Proceedings of the 8th International Conference on Bioinformatics and Computational Biology (BICoB), April 4-6, 2016 Las Vegas, Nevada, USA. (seqParLASSO: code, GitHub).

P10. "An Integrative Network Mining Approach in Colorectal Cancer", Hall B, Quitadamo A, and Shi X, ACMG Clinical Genetics Meeting, Tampa, FL, March 8-12, 2016 (poster).

P9. "Network Driven Analysis of eQTLs in Lung Adenocarcinoma Subtypes", Quitadamo A, Desai H, and Shi X, ACMG Clinical Genetics Meeting, Tampa, FL, March 8-12, 2016 (poster).

C17. "Genetic Privacy: Risks, Ethics, and Protection Techniques", Shi X, and Wu X, In Proceedings of the Workshop on Data Science Learning and Applications to Biomedical and Health Sciences, p57-62, New York, NY, January 7-8, 2016 (invited journal submission to a special issue of the Annals of NY Academy of Sciences).

2015

J19. “An integrated map of structural variation in 2,504 human genomes”, Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson M, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam H, Mu XJ, Alkan C, Antaki D, Bae T, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer E-W, McCarthy S, Flicek P, Gibbs RA, Marth G, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Quitadamo A, Raeder B, Schadt E, Schlattl A, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu Y, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, The 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO, Nature, 2015. 562(7571): 75-81.

J18. "A Global Reference for Human Genetic Variation", The 1000 Genomes Project Consortium (Quitadamo A and Shi X are co-authors), Nature, 2015. 562(7571): 68-74.

P9. "An Integrative Approach to Constructing MicroRNA-Gene Networks in Ovarian Cancer", Quitadamo A, Hall B, and Shi X, The DARPA GRAPHS/SIMPLEX Workshop: Data, Algorithms and Problems on Graphs (DAPG 2015), New York, NY, September 28, 2015 (poster).

P8. "Sequential Parallel LASSO Models for eQTL Analysis", He A, Hall B, Wen J, Liang Y, and Shi X, In Proceedings of The 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB 2015), Atlanta, GA, September 9-12, 2015 (poster).

C16. "A Graph Community Approach to Constructing microRNA Networks", Hall B, Quitadamo A, and Shi X, In Proceedings of the 1st International Conference on Big Data Computing and Communication (BIGCOM 2015), August 1-3, 2015, Taiyuan, ShanXi, China. Springer Lecture Notes in Computer Science, Volume 9196, p283-293. (invited journal submission to Tsinghua Science and Technology)

J17. "A Sparse Learning Framework for Joint Effect Analysis of Copy Number Variants", Wang Z, Benika H, Xu J, and Shi X, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2015. PP(99):pp1-14 (CNVnet: Code, GitHub, SupplementaryTablesTCBB).

P7. "A Network Ensemble of microRNA and Gene Expression in Ovarian Cancer", Hall B, Quitadamo A, and Shi X, The Biology of Genomes, Cold Spring Harbor Laboratory, May 5 - 9, 2015 (poster).

J16. "An Integrated Network of microRNA and Gene Expression in Ovarian Cancer", Quitadamo A, Tian L, Benika H, and Shi X, BMC Bioinformatics 2015, 16(Suppl 5):S5.

2014

J15. "Methods for Population Based eQTL Analysis in Human Genetics", Tian L, Quitadamo A, Lin F, Shi XTsinghua Science and Technology, 2014. 19(6): 624-634.

C15. "Unsupervised Nonparametric Anomaly Detection: A Kernel Method", Zou S, Liang Y, Poor H.V.,and  Shi X, In Proceedings of the 52nd Annual Allerton Conference on Communication, Control, and Computing (Allerton 2014), p836 - 841, Monticello, Illinois, October 1-3, 2014.

C14. "CNVnet: Combining Sparse Learning and Biological Networks to Capture Joint Effect of Copy Number Variants", Wang Z, Xu J, and Shi X, In Proceedings of The 5th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB 2014), p128-137, Newport Beach, CA, September 20-23, 2014 (CNVnet: Code, GitHub, SupplementaryTables) (ACM SigBio Best Student Paper Award, invited journal submission to IEEE/ACM TCBB).

P6. "A Network Approach for Integrative Analysis of Genomic Data in Ovarian Cancer", Quitadamo A, and Shi X, The 22nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2014, poster presentaion, selected for oral presentation), Boston, MA, July 11 - 15, 2014.

C13. "A microRNA-Gene Network in Ovarian Cancer from Genome-Wide QTL Analysis", Quitadamo A, Lin F, Tian L, and Shi X, The 10th International Symposium on Bioinformatics Research and Applications (ISBRA2014, Track 2 paper), Zhangjiajie, China, June 28-30, Springer LNBI 8492, p388, 2014 (invited journal submission to BMC Bioinformatics).

C12. "Kernel-Based Nonparametric Anomaly Detection", Zou S, Liang Y, Poor H.V.,and  Shi X, In Proceedings of the 15th IEEE International Workshop on Signal Processing Advances in Wireless Communications (SPAWC 2014), p224-228, Toronto, Canada, June 22-25, 2014.

P5. “Infringement of Individual Privacy via Mining GWAS Statistics”, Wang Y, Wu X, and Shi X, The Biology Of Genomes (poster presentation), Cold Spring Harbor, NY, May 6 - 10, 2014.

J14. “Finding Alternative eQTLs by Exploring Sparse Model Space”, Wang Z, Xu, J, and Shi X, Journal of Computational Biology (presented at RECOMB/ISCB RegSys 2013), May 2014, 21(5): 385-393. (Selected as Open Paper of the Day, Saturday, May 17, 2014, on both the Genetic Engineering & Biotechnology News, and the Mary Ann Liebert, Inc).

P4. “A Novel Method for Identifying OR Relationship in eQTL Mapping”, Wang Z, Xu, J, and Shi X, The 18th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2014, poster presentation), Pittsburgh, PA, April 2-5, 2014.

J13. "A network based method for analysis of lncRNA-disease associations and prediction of lncRNAs implicated in diseases.", Yang X, Gao L, Guo X, Shi X, Wu H, Song F, and Wang B. PLoS One. 2014 Jan 31;9(1):e87797.

2013

C11. “Using Aggregate Human Genome Data for Individual Identification”, Wang Y, Wu X, and Shi X, In Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013), p410-415, Shanghai, China, December 2013 (Best Paper Award).

C10.Finding Alternative eQTLs by Exploring Sparse Model Space”, Wang Z, Xu, J, and Shi X, In Proceedings of the RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges (RECOMB/ISCB RegSys 2013, oral presentation), Toronto, Canada, November 2013.

C9.Fine Mapping of Methylation Expression Quantitative Loci in Ovarian Cancer”, Shi X, In Proceedings of the 9th International Symposium on Bioinformatics Research and Applications (ISBRA 2013, Track 2 paper) Charlotte, NC, May 20-22, 2013. To appear in the Supplement of BMC Genetics, 2013.

2012

J12. “An Integrated Map of Genetic Variation from 1,092 Human Genomes”, The 1000 Genomes Project Consortium, Nature, 2012. 491: 56-65.

C8. “A Two-Graph Guided Multi-task Lasso Approach for eQTL Mapping”, Chen X*, Shi X* (co-first author), Xu X, Wang Z, Mills RE, Lee C, and Xu J, In Proceedings of the 15th International Conference of Artificial Intelligence and Statistics (AISTATS 2012), La Palma, Canary Islands, Journal of Machine Learning Research (JMLR) W&CP 22: 208-217, 2012 (Code, GitHub).

J11. “Extensive Genetic Diversity and Substructuring among Zebrafish Strains Revealed Through Copy Number Variant Analysis”, Brown KH*, Dobrinski KP*, Lee AS, Gokcumen O, Mills RE, Shi X, Chong W, Chen JY, Yoo P, David S, Petersond SM, Raj T, Choy KW, Stranger BE, Williamson RE, Zon LI, Freeman JL, and Lee C, Proceedings of the National Academy of Sciences of the USA (PNAS), 2012. 109(2):529-534 (cover article).

J10. “User Identification and Anonymization in 802.11 Wireless LANs”, Xu D, Wang Y, Shi X, and Yin X, Security and Communication Networks (Wiley), 2012. 5(1):15-27.

2011

J9. “Refinement of Primate CNV Hotspots Identifies Candidate Genomic Regions Evolving under Positive selection”, Gokcumen O*, Babb PL*, Iskow RC, Zhu Q, Shi X, Mills RE, Ionita-Laza I, Vallender EJ, Clark A, Johnson WE, Lee C, Genome Biology, 2011. 12:R52.

J8. “A Comprehensive Assessment of Array-Based Platforms and Calling Algorithms for Detection of Copy Number Variants”, Pinto D*, Darvishi K*, Shi X, Rigler D, Fitzgerald T, Lionel A, Thiruvahindrapuram B, MacDonald J, Mills R, Prasad A, Noonan K, Gribble S, Prigmore E, Donahoe P, Smith R, Park J.H, Hurles M, Carter N, Lee C, Scherer S, Feuk L, Nature Biotechnology, 2011. 29:512-520.

J7.“Mapping Copy Number Variation by Population-Scale Genome Sequencing”, Mills R*, Walter K*, Stewart C*, Handsaker R*, Chen K*, Alkan C*, Abyzov A*, Yoon S*, Ye K*, Cheetham R, Chinwalla A, Conrad D, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva L, Iqbal Z, Kang S, Kidd J, Konkel M, Korn J, Khurana E, Kural D, Lam H, Leng J, Li R, Li Y, Lin C, Luo R, Mu X, Nemesh J, Peckham H, Rausch T, Scally A, Shi X, Stromberg M, Stutz A, Urban A, Walker J, Wu J, Zhang Y, Zhang Z, Batzer M, Ding L, Marth G, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eicher E, Gerstein M, Hurles M, Lee C, McCarroll S, and Korbel J, and the 1000 Genomes Project, Nature, 2011. 470: 59-65.

J6. “Capacity of Data Collection in Randomly-Deployed Wireless Sensor Networks”, Chen S, Wang Y, Li X-Y, Shi X, ACM/Springer Wireless Networks (WINET), 2011. 17: 305-318.

2010

J5. “A Map of Human Genome Variation from Population Scale Sequencing”, The 1000 Genomes Project Consortium, Nature, 2010. 467: 1061-1073 (cover article).

C7. “802.11 User Anonymization”, Xu D, Wang Y, Shi X, and Yin X, In Proc. of the IEEE Global Telecommunications Conference (GlobeCom 2010), 1-5, Miami, FL, December 2010.

2009

C6. “Order-Optimal Data Collection in Wireless Sensor Networks: Delay and Capacity”, Chen S, Wang Y, Li X-Y, and Shi X, In Proc. of the 6th Annual IEEE Communications Society Conference on Sensor, Mesh, and Ad Hoc Communications and Networks (SECON 2009), 1-9, Rome, Italy, June 2009.

C5. “A Bayesian Approach to High-Throughput Biological Model Generation”, Shi X and Stevens R, In Proc. of the 1st Bioinformatics and Computational Biology Conference (BiCob 2009), Lecture Notes in Bioinformatics (Springer Verlag) 5462: 376-387, New Orleans, LA, April 2009.

C4. “Enhanced Feature Selection and Generation for 802.11 User Identification”, Xu D, Wang Y, and Shi X, In Proc. of The 18th International Conference on Computer Communications and Networks (ICCCN 2009), 1-6, San Francisco, CA, August 2009.

C3. “Self-Organizing Fault Tolerant Topology Control in Large-Scale Three-Dimensional Wireless Networks”, Wang Y, Cao L, Dahlberg T, Li F, and Shi X, ACM Transactions on Autonomous and Adaptive Systems (TAAS), 2009. 3:19.1-19.21.

2008 and earlier

T3. “System and Tools to Support a Bayesian Approach to Improving Large-Scale Metabolic Models”, Shi X, Ph.D. Dissertation, University of Chicago, December 2008.

P3. “A Bayesian Approach to Improve Genome-Scale Metabolic Models by the Integration of Biological and Topological Evidence”, Shi X, and Stevens R, In Proc. of the 7th Annual International Conference on Computational Systems Bioinformatics (CSB 2008, poster presentation), Stanford, CA, August 2008.

C2. “SWARM: A Scientific Workflow for Supporting Bayesian Approaches to Improve Metabolic Models”, Shi X and Stevens R, In Proc. of The 6th ACM/IEEE International Workshop on Challenges of Large Applications in Distributed Environments (CLADE 2008), 25-34, Boston, MA, March, 2008.

J4. “The National Microbial Pathogen Database Resource (NMPDR): A Genomics Platform Based on Subsystem Annotation”, McNeil L, Reich C, Aziz R, Bartels D, Cohoon M, Disz T, Edwards R, Gerdes S, Hwang K, Kubal M, Margaryan G, Meyer F, Mihalo W, Olsen G, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch G, Rodionov D, Shi X, Vassieva O, Vonstein V, Zagnitko O, Xia F, Zinner J, Overbeek R, Stevens R, Nucleic Acids Research, 2007.35:D347-D353.

P2. “An Infrastructure to Construct Genome-Scale Metabolic Models Automatically”, Shi X, and Stevens R, In Proc. of 7th International Conference on Systems Biology (ICSB 2006, poster presentation), Yokohama, Japan, Oct. 2006.

P1. “A Computational Drug Target and Drug Screening Pipeline”, Shi X, Xia F, Cohoon M, Gao H, Hwang K, Kubal M, Margaryan G, Zinner J, Disz T and Stevens R, In Proc. of the 7th International Conference on Systems Biology (ICSB 2006, poster presentation), Yokohama, Japan, Oct. 2006.

C1. “Efficient On-Demand Topology Control for Wireless Ad Hoc Networks”, Wang Y and Shi X, In Proc. of 14th IEEE International Conference on Computer Communications and Networks (ICCCN 2005), 159-164, San Diego, California, October 2005.

T2. “Extending Version Control to Track Scientific Results”, Shi X, Master Thesis, University of Chicago, August 2003.

T1. “Design and Implementation of a Visual CASE Platform Based on UML”, Shi X, Master Thesis, Beijing Institute of Technology, China, March 2001 (Chinese).

J3. “Data Storage Mechanism for a CASE Environment Supporting Visual Modeling”, Chen Y, Guo B, Shi X, and Zhao X, Journal of Beijing Institute of Technology, 2001. 21(2):220-224 (Chinese).

J2. “A Multi-View Modeling Mechanism Based on UML” with Chen Y, Shi X, Zhao X, and Liu R, Journal of Beijing Institute of Technology, 2001. 21(1):53-56 (Chinese).

J1. “Design and Implementation of a CASE Platform for Software Developing Process Based on UML” Chen Y, Shi X, and Zhao X, Journal of Beijing Institute of Technology, 2001. 21(1):48-52 (Chinese).