Publications

2017

Emad A, Cairns J, Kalari KR, Wang L, Sinha S. Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance. Genome Biol. 2017 Aug 11;18(1):153. PMID: 28800781

Zhang Y*, Manjunath M*, Zhang S, Chasman D, Roy S, Song JS. Integrative genomic analysis predicts causative cis-regulatory mechanisms of the breast cancer-associated genetic variant rs4415084. Cancer Res. 2018 Jan 19. pii: canres.3486.2017. *co-first authors. PMID: 29351903

Ping P, Watson K, Han J, Bui A. Individualized Knowledge Graph: A Viable Informatics Path to Precision Medicine. Circ Res. 2017 Mar 31;120(7):1078-1080. doi: 10.1161/CIRCRESAHA.116.310024. PMID: 28360346

Kim M, KimY, Qian L, Song JS. TeachEnG: a Teaching Engine for Genomics. 2017 Oct 15;33(20):3296-3298. PMID: 29028264

Hanson C, Cairns J, Wang L, Sinha S. Principled Multi-Omic Analysis Reveals Gene Regulatory Mechanisms Of Phenotype Variation. bioRxiv. 2017. Genome Research (In Revision)

2016

Siddiqui T, Ren X, Parameswaran A, Han J. FacetGist: Collective Extraction of Document Facets in Large Technical Corpora. Proc ACM Int Conf Inf Knowl Manag. 2016 Oct;2016:871-880. doi: 10.1145/2983323.2983828. PubMed PMID: 28210517

Joglekar M, Garcia-Molina H, Parameswaran A. Interactive Data Exploration with Smart Drill-Down. Proc Int Conf Data Eng. 2016 May;2016:906-917. doi: 10.1109/ICDE.2016.7498300. Epub 2016 Jun 23. PubMed PMID: 28210096

Zhang C, Zhang K, Yuan Q, Zhang L, Hanratty T, Han J. GMove: Group-Level Mobility Modeling Using Geo-Tagged Social Media. KDD. 2016 Aug;2016:1305-1314. doi: 10.1145/2939672.2939793. PubMed PMID: 28163978

Shang J, Peng J, Han J. MACFP: Maximal Approximate Consecutive Frequent Pattern Mining under Edit Distance. Proc SIAM Int Conf Data Min. 2016 May;2016:558-566. doi: 10.1137/1.9781611974348.63. PubMed PMID: 28174677

Cheng Q, Shang J, Juen J, Han J, Schatz B. Mining Discriminative Patterns to Predict Health Status for Cardiopulmonary Patients. ACM BCB. 2016 Oct;2016:41-49. doi: 10.1145/2975167.2975171. PubMed PMID: 28174760

Shang J, Tong W, Peng J, Han J. DPClass: An Effective but Concise Discriminative Patterns-Based Classification Framework. Proc SIAM Int Conf Data Min. 2016 May;2016:567-575. doi: 10.1137/1.9781611974348.64. PubMed PMID: 28163983

Gao Y, Parameswaran A. Squish: Near-Optimal Compression for Archival of Relational Datasets. KDD. 2016 Aug;2016:1575-1584. doi: 10.1145/2939672.2939867. PubMed PMID: 28180028

Cairns J, Ung CY, da Rocha EL, Zhang C, Correia C, Weinshilboum R, Wang L, Li H. A network-based phenotype mapping approach to identify genes that modulate drug response phenotypes. Sci Rep. 2016 Nov 14;6:37003. doi: 10.1038/srep37003. PubMed PMID: 27841317

Maddox M, Goehring D, Elmore AJ, Madden S, Parameswaran A, Deshpande A. Decibel: The Relational Dataset Branching System. Proceedings VLDB Endowment. 2016 May;9(9):624-635. doi: 10.14778/2947618.2947619. PubMed PMID: 28149668

Blatti C, Sinha S. Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks. Bioinformatics. 2016 Jul 15;32(14):2167-75. doi: 10.1093/bioinformatics/btw151. Epub 2016 Mar 19. PubMed PMID: 27153592

Wang S, Qu M, Peng J. PROSNET: INTEGRATING HOMOLOGY WITH MOLECULAR NETWORKS FOR PROTEIN FUNCTION PREDICTION. Pac Symp Biocomput. 2016;22:27-38. PubMed PMID: 27896959

Das Sarma A, Parameswaran A, Widom J. Towards Globally Optimal Crowdsourcing Quality Management: The Uniform Worker Setting. Proc ACM SIGMOD Int Conf Manag Data. 2016 Jun-Jul;2016:47-62. doi: 10.1145/2882903.2882953. PubMed PMID: 28149000

2015

Vartak M, Rahman S, Madden S, Parameswaran A, Polyzotis N. SeeDB: Efficient Data-Driven Visualization Recommendations to Support Visual Analytics. Proceedings VLDB Endowment. 2015 Sep;8(13):2182-2193. PubMed PMID: 26779379; PubMed Central PMCID: PMC4714568.

Joglekar M, Garcia-Molina H, Parameswaran A. Smart Drill-Down: A New Data Exploration Operator. Proceedings VLDB Endowment. 2015 Aug;8(12):1928-1931. PubMed PMID: 26844008; PubMed Central PMCID: PMC4734647.

Sarma AD, Jain A, Nandi A, Parameswaran A, Widom J. Surpassing Humans and Computers with JellyBean: Crowd-Vision-Hybrid Counting Algorithms. Proc AAAI Conf Hum Comput Crowdsourc. 2015 Nov;2015:178-187. PubMed PMID: 26844304; PubMed Central PMCID: PMC4734649.

Zhuang H, Parameswaran A, Roth D, Han J. Debiasing Crowdsourced Batches. KDD. 2015 Aug;2015:1593-1602. PubMed PMID: 26713175; PubMed Central PMCID: PMC4691348.

Wan M, Ouyang Y, Kaplan L, Han J. Graph Regularized Meta-path Based Transductive Regression in Heterogeneous Information Network. Proc SIAM Int Conf Data Min. 2015 Apr-May;2015:918-926. PubMed PMID: 26705510; PubMed Central PMCID: PMC4688014.

Ren X, El-Kishky A, Wang C, Han J. Automatic Entity Recognition and Typing from Massive Text Corpora: A Phrase and Network Mining Approach. KDD. 2015 Aug;2015:2319-2320. PubMed PMID: 26705508; PubMed Central PMCID: PMC4688010.

Kordjamshidi P, Roth D, Wu H. Saul: Towards Declarative Learning Based Programming. IJCAI (U S). 2015 Jul;2015:1844-1851. PubMed PMID: 26635465; PubMed Central PMCID: PMC4666300.

Kim A, Blais E, Parameswaran A, Indyk P, Madden S, Rubinfeld R. Rapid Sampling for Visualizations with Ordering Guarantees.Proceedings VLDB Endowment. 2015 Jan;8(5):521-532. PubMed PMID: 26779380; PubMed Central PMCID: PMC4714571.

Bhardwaj A, Karger D, Subramanyam H, Deshpande A, Madden S, Wu E, Elmore A, Parameswaran A, Zhang R. Collaborative Data Analytics with DataHub. Proceedings VLDB Endowment. 2015 Aug;8(12):1916-1919. PubMed PMID: 26844007; PubMed Central PMCID: PMC4734646.

Sinha S, Song J, Weinshilboum R, Jongeneel V, Han J. KnowEnG: a knowledge engine for genomics. J Am Med Inform Assoc. 2015 Nov;22(6):1115-9. doi: 10.1093/jamia/ocv090. Epub 2015 Jul 23. PubMed PMID: 26205246; PubMed Central PMCID: PMC5009907.

Ren X, El-Kishky A, Wang C, Tao F, Voss CR, Ji H, Han J. ClusType: Effective Entity Recognition and Typing by Relation Phrase-Based Clustering. KDD. 2015 Aug;2015:995-1004. PubMed PMID: 26705503; PubMed Central PMCID: PMC4688017.

Zhi S, Han J, Gu Q. Robust Classification of Information Networks by Consistent Graph Learning. Mach Learn Knowl Discov Databases. 2015 Sep;9285:752-767. Epub 2015 Aug 29. PubMed PMID: 26705541; PubMed Central PMCID: PMC4688020.

Tao F, Zhao B, Fuxman A, Li Y, Han J. Leveraging Pattern Semantics for Extracting Entities in Enterprises. Proc Int World Wide Web Conf. 2015 May;2015:1078-1088. PubMed PMID: 26705540; PubMed Central PMCID: PMC4688019.

Liu J, Shang J, Wang C, Ren X, Han J. Mining Quality Phrases from Massive Text Corpora. Proc ACM SIGMOD Int Conf Manag Data. 2015 May-Jun;2015:1729-1744. PubMed PMID: 26705375; PubMed Central PMCID: PMC4688018.

Li Y, Li Q, Gao J, Su L, Zhao B, Fan W, Han J. On the Discovery of Evolving Truth. KDD. 2015 Aug;2015:675-684. PubMed PMID: 26705502; PubMed Central PMCID: PMC4688022.

Wang C, Liu X, Song Y, Han J. Towards Interactive Construction of Topical Hierarchy: A Recursive Tensor Decomposition Approach. KDD. 2015 Aug;2015:1225-1234. PubMed PMID: 26705505; PubMed Central PMCID: PMC4688012.

Zhang C, Zheng Y, Ma X, Han J. Assembler: Efficient Discovery of Spatial Co-evolving Patterns in Massive Geo-sensory Data.KDD. 2015 Aug;2015:1415-1424. PubMed PMID: 26705506; PubMed Central PMCID: PMC4688023.

Kordjamshidi P, Roth D, Moens MF. Structured learning for spatial information extraction from biomedical text: bacteria biotopes. BMC Bioinformatics. 2015 Apr 25;16:129. doi: 10.1186/s12859-015-0542-z. PubMed PMID: 25909637; PubMed Central PMCID: PMC4426185.

Wang S, Cho H, Zhai C, Berger B, Peng J. Exploiting ontology graph for predicting sparsely annotated gene function. Bioinformatics. 2015 Jun 15;31(12):i357-64. doi: 10.1093/bioinformatics/btv260. PubMed PMID: 26072504; PubMed Central PMCID: PMC4542782.

Stephens ZD, Lee SY, Faghri F, Campbell RH, Zhai C, Efron MJ, Iyer R, Schatz MC, Sinha S, Robinson GE. Big Data: Astronomical or Genomical? PLoS Biol. 2015 Jul 7;13(7):e1002195. doi: 10.1371/journal.pbio.1002195. eCollection 2015 Jul. PubMed PMID: 26151137; PubMed Central PMCID: PMC4494865.

Hanson C, Cairns J, Wang L, Sinha S. Computational discovery of transcription factors associated with drug response. Pharmacogenomics J. 2016 Nov;16(6):573-582. doi: 10.1038/tpj.2015.74. Epub 2015 Oct 27. PubMed PMID: 26503816; PubMed Central PMCID: PMC4848185.