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2020 – today
- 2024
[j21]Yiling Elaine Chen
, Xinzhou Ge, Kyla Woyshner, Meilu McDermott, Antigoni Manousopoulou, Scott B. Ficarro, Jarrod A. Marto, Kexin Li, Leo David Wang, Jingyi Jessica Li:
APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control. Genom. Proteom. Bioinform. 22(1) (2024)- 2023
- [j20]Chihao Zhang, Shihua Zhang, Jingyi Jessica Li:
A Python Package itca for Information-Theoretic Classification Accuracy: A Criterion That Guides Data-Driven Combination of Ambiguous Outcome Labels in Multiclass Classification. J. Comput. Biol. 30(11): 1246-1249 (2023) - 2022
- [j19]Dongyuan Song, Nan Miles Xi, Jingyi Jessica Li, Lin Wang:
scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data. Bioinform. 38(11): 3126-3127 (2022) - [j18]Elvis Han Cui, Dongyuan Song, Weng Kee Wong, Jingyi Jessica Li:
Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime. Bioinform. 38(16): 3927-3934 (2022) - [j17]Tianyi Sun, Dongyuan Song, Wei Vivian Li, Jingyi Jessica Li:
Simulating Single-Cell Gene Expression Count Data with Preserved Gene Correlations by scDesign2. J. Comput. Biol. 29(1): 23-26 (2022) - [j16]Chihao Zhang, Yiling Elaine Chen, Shihua Zhang, Jingyi Jessica Li:
Information-theoretic Classification Accuracy: A Criterion that Guides Data-driven Combination of Ambiguous Outcome Labels in Multi-class Classification. J. Mach. Learn. Res. 23: 341:1-341:65 (2022) - [i4]Lijia Wang, Y. X. Rachel Wang, Jingyi Jessica Li, Xin Tong:
Hierarchical Neyman-Pearson Classification for Prioritizing Severe Disease Categories in COVID-19 Patient Data. CoRR abs/2210.02197 (2022) - 2021
- [j15]Yidan Eden Sun, Heather J. Zhou, Jingyi Jessica Li:
Bipartite tight spectral clustering (BiTSC) algorithm for identifying conserved gene co-clusters in two species. Bioinform. 37(9): 1225-1233 (2021) - [j14]Yixin Guo, Ziwei Xue, Ruihong Yuan, Jingyi Jessica Li, William A. Pastor, Wanlu Liu:
RAD: a web application to identify region associated differentially expressed genes. Bioinform. 37(17): 2741-2743 (2021) - [j13]Dongyuan Song, Kexin Li, Zachary Hemminger, Roy Wollman, Jingyi Jessica Li:
scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling. Bioinform. 37(Supplement): 358-366 (2021) - [j12]Jingyi Jessica Li, Yiling Elaine Chen, Xin Tong:
A flexible model-free prediction-based framework for feature ranking. J. Mach. Learn. Res. 22: 124:1-124:54 (2021) - [j11]Ning Wang, Diane Lefaudeux, Anup Mazumder, Jingyi Jessica Li, Alexander Hoffmann:
Identifying the combinatorial control of signal-dependent transcription factors. PLoS Comput. Biol. 17(6) (2021) - [i3]Chihao Zhang, Yiling Elaine Chen, Shihua Zhang, Jingyi Jessica Li:
Information-theoretic Classification Accuracy: A Criterion that Guides Data-driven Combination of Ambiguous Outcome Labels in Multi-class Classification. CoRR abs/2109.00582 (2021) - 2020
- [j10]Jingyi Jessica Li, Xin Tong:
Statistical Hypothesis Testing versus Machine Learning Binary Classification: Distinctions and Guidelines. Patterns 1(7): 100115 (2020) - [i2]Wei Vivian Li, Xin Tong, Jingyi Jessica Li:
Bridging Cost-sensitive and Neyman-Pearson Paradigms for Asymmetric Binary Classification. CoRR abs/2012.14951 (2020)
2010 – 2019
- 2019
- [j9]Wei Vivian Li, Jingyi Jessica Li:
A statistical simulator scDesign for rational scRNA-seq experimental design. Bioinform. 35(14): i41-i50 (2019) - [j8]Dat Duong, Wasi Uddin Ahmad, Eleazar Eskin, Kai-Wei Chang, Jingyi Jessica Li:
Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their Definitions. J. Comput. Biol. 26(1): 38-52 (2019) - [j7]Zahra S. Razaee, Arash A. Amini, Jingyi Jessica Li:
Matched Bipartite Block Model with Covariates. J. Mach. Learn. Res. 20: 34:1-34:44 (2019) - 2018
- [j6]Wei Vivian Li, Jingyi Jessica Li:
Modeling and analysis of RNA-seq data: a review from a statistical perspective. Quant. Biol. 6(3): 195-209 (2018) - 2017
- [j5]Sara M. Clifton, Chaeryon Kang, Jingyi Jessica Li, Qi Long, Nirmish Shah, Daniel M. Abrams:
Hybrid Statistical and Mechanistic Mathematical Model Guides Mobile Health Intervention for Chronic Pain. J. Comput. Biol. 24(7): 675-688 (2017) - [i1]Zahra S. Razaee, Arash A. Amini, Jingyi Jessica Li:
Matched bipartite block model with covariates. CoRR abs/1703.04943 (2017) - 2016
- [j4]Wei Vivian Li, Zahra S. Razaee, Jingyi Jessica Li:
Epigenome overlap measure (EPOM) for comparing tissue/cell types based on chromatin states. BMC Genom. 17(S-1): 10 (2016) - [j3]Yuting Ye, Jingyi Jessica Li:
NMFP: a non-negative matrix factorization based preselection method to increase accuracy of identifying mRNA isoforms from RNA-seq data. BMC Genom. 17(S-1): 11 (2016) - 2014
- [j2]Alan P. Boyle, Carlos L. Araya, Cathleen Brdlik, Philip Cayting, Chao Cheng, Yong Cheng, Kathryn Gardner, LaDeana W. Hillier, Judith Janette, Lixia Jiang, Dionna Kasper, Trupti Kawli, Pouya Kheradpour, Anshul Kundaje, Jingyi Jessica Li, Lijia Ma, Wei Niu, E. Jay Rehm, Joel S. Rozowsky, Matthew Slattery, Rebecca Spokony, Robert Terrell, Dionne Vafeados, Daifeng Wang, Peter Weisdepp, Yi-Chieh Wu, Dan Xie, Koon-Kiu Yan, Elise A. Feingold, Peter J. Good, Michael J. Pazin, Haiyan Huang, Peter J. Bickel, Steven E. Brenner, Valerie Reinke, Robert H. Waterston, Mark Gerstein, Kevin P. White, Manolis Kellis, Michael Snyder:
Comparative analysis of regulatory information and circuits across distant species Open. Nat. 512(7515): 453-456 (2014) - 2012
- [j1]Qinghui Gao, Christine Ho, Yingmin Jia, Jingyi Jessica Li, Haiyan Huang:
Biclustering of Linear Patterns In Gene Expression Data. J. Comput. Biol. 19(6): 619-631 (2012)
Coauthor Index
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