Jingyi Jessica Li

Title(s)Professor, Statistics and Data Science
SchoolCollege of Letters and Science
ORCID ORCID Icon0000-0002-9288-5648 Additional info
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    Other Positions
    Title(s)Professor, Human Genetics

    Title(s)Professor, Computational Medicine

    Title(s)Professor, Biostatistics


    Collapse Biography 
    Collapse Education and Training
    University of California, Berkeley, California, U.S.A.Ph.D.05/2013Biostatistics
    Tsinghua University, Beijing, ChinaB.S.07/2007Biological Sciences
    Collapse Awards and Honors
    International Society for Computational Biology (ISCB)2023Overton Prize
    Committee of Presidents of Statistical Societies (COPSS)2023Emerging Leader Award
    Radcliffe Institute for Advanced Study at Harvard University2022  - 2023Radcliffe Fellowship
    MIT Technology Review2020MIT Technology Review 35 Innovators Under 35 China
    National Science Foundation2019CAREER Award
    UCLA David Geffen School of Medicine W.M. Keck Foundation2019Junior Faculty Award
    Alfred P. Sloan Foundation2018Sloan Research Fellowship
    International Chinese Statistical Association (ICSA) China Conference2018Junior Researcher Paper Award
    Johnson & Johnson2018Women in STEM2D Math Scholar Award
    PhRMA Foundation2017Research Starter Award in Informatics
    UCLA2016Faculty Research Grant / Trans-disciplinary Seed Grant
    Hellman Foundation2015Hellman Fellow
    UCLA2015Faculty Career Development Award
    Institute of International Studies, UC Berkeley2012International Dissertation Field Work Grant
    Cold Spring Harbor Asia Conferences2011Best Presentation Award
    UC Berkeley2010Outstanding Graduate Student Instructor Award
    Tsinghua University2007Distinguished Graduate of Class 2007

    Collapse Overview 
    Collapse Overview
    Jingyi Jessica Li, Professor of Statistics and Data Science (also affiliated with Biostatistics, Computational Medicine, and Human Genetics), leads a research group titled the Junction of Statistics and Biology at UCLA. With Ph.D. from UC Berkeley and B.S. from Tsinghua University, Dr. Li focuses on developing interpretable statistical methods for biomedical data. Her research delves into quantifying the central dogma, extracting hidden information from transcriptomics data, and ensuring statistical rigor in data analysis by employing synthetic negative controls. Recipient of multiple awards including the NSF CAREER Ward, Sloan Research Fellowship, ISCB Overton Prize, and COPSS Emerging Leaders Award, her contributions have gained recognition in the fields of computational biology and statistics.
    Collapse Websites

    Collapse Research 
    Collapse Research Activities and Funding
    Statistical methods for elucidating regulatory mechanisms and functional impacts of transcriptome variation at population and single-cell scales
    NIH R35GM140888Jun 1, 2021 - May 31, 2026
    Role: Principal Investigator
    Robust Identification and accurate quantification of RNA transcripts on a system wide scale
    NIH R01GM120507Sep 1, 2016 - May 31, 2022
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data. Genome Biol. 2024 May 23; 25(1):136. Wang W, Cen Y, Lu Z, Xu Y, Sun T, Xiao Y, Liu W, Li JJ, Wang C. PMID: 38783325; PMCID: PMC11112958.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    2. A genome-wide spectrum of tandem repeat expansions in 338,963 humans. Cell. 2024 Apr 25; 187(9):2336-2341.e5. Cui Y, Ye W, Li JS, Li JJ, Vilain E, Sallam T, Li W. PMID: 38582080; PMCID: PMC11065452.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    3. Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters. Nat Commun. 2024 Feb 26; 15(1):1753. Xia L, Lee C, Li JJ. PMID: 38409103; PMCID: PMC10897166.
      View in: PubMed   Mentions: 4     Fields:    
    4. scReadSim: a single-cell RNA-seq and ATAC-seq read simulator. Nat Commun. 2023 11 18; 14(1):7482. Yan G, Song D, Li JJ. PMID: 37980428; PMCID: PMC10657386.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    5. 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. 2023 11; 30(11):1246-1249. Zhang C, Zhang S, Li JJ. PMID: 37930802.
      View in: PubMed   Mentions:    Fields:    
    6. Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms. bioRxiv. 2023 Oct 11. Patowary A, Zhang P, Jops C, Vuong CK, Ge X, Hou K, Kim M, Gong N, Margolis M, Vo D, Wang X, Liu C, Pasaniuc B, Li JJ, Gandal MJ, de la Torre-Ubieta L. PMID: 36993726; PMCID: PMC10055310.
      View in: PubMed   Mentions:
    7. How the Monty Hall problem is similar to the false discovery rate in high-throughput data analysis. Nat Biotechnol. 2023 06; 41(6):754-755. Li JJ. PMID: 37198440; PMCID: PMC11078861.
      View in: PubMed   Mentions:    Fields:    
    8. scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics. Nat Biotechnol. 2024 Feb; 42(2):247-252. Song D, Wang Q, Yan G, Liu T, Sun T, Li JJ. PMID: 37169966; PMCID: PMC11182337.
      View in: PubMed   Mentions: 15     Fields:    
    9. Functional characterization of age-dependent p16 epimutation reveals biological drivers and therapeutic targets for colorectal cancer. J Exp Clin Cancer Res. 2023 May 04; 42(1):113. Yang L, Chen X, Lee C, Shi J, Lawrence EB, Zhang L, Li Y, Gao N, Jung SY, Creighton CJ, Li JJ, Cui Y, Arimura S, Lei Y, Li W, Shen L. PMID: 37143122; PMCID: PMC10157929.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    10. METTL3-Mediated m6A Modification Controls Splicing Factor Abundance and Contributes to Aggressive CLL. Blood Cancer Discov. 2023 05 01; 4(3):228-245. Wu Y, Jin M, Fernandez M, Hart KL, Liao A, Ge X, Fernandes SM, McDonald T, Chen Z, Röth D, Ghoda LY, Marcucci G, Kalkum M, Pillai RK, Danilov AV, Li JJ, Chen J, Brown JR, Rosen ST, Siddiqi T, Wang L. PMID: 37067905; PMCID: PMC10150290.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    11. Transcriptomic congruence analysis for evaluating model organisms. Proc Natl Acad Sci U S A. 2023 02 07; 120(6):e2202584120. Zong W, Rahman T, Zhu L, Zeng X, Zhang Y, Zou J, Liu S, Ren Z, Li JJ, Sibille E, Lee AV, Oesterreich S, Ma T, Tseng GC. PMID: 36730203; PMCID: PMC9963430.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    12. PCA outperforms popular hidden variable inference methods for molecular QTL mapping. Genome Biol. 2022 10 11; 23(1):210. Zhou HJ, Li L, Li Y, Li W, Li JJ. PMID: 36221136; PMCID: PMC9552461.
      View in: PubMed   Mentions: 4     Fields:    
    13. Machine learning predicts improvement of functional outcomes in traumatic brain injury patients after inpatient rehabilitation. Front Rehabil Sci. 2022; 3:1005168. Say I, Chen YE, Sun MZ, Li JJ, Lu DC. PMID: 36211830; PMCID: PMC9535093.
      View in: PubMed   Mentions: 3  
    14. Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime. Bioinformatics. 2022 08 10; 38(16):3927-3934. Cui EH, Song D, Wong WK, Li JJ. PMID: 35758616; PMCID: PMC9991897.
      View in: PubMed   Mentions: 1     Fields:    
    15. scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data. Bioinformatics. 2022 05 26; 38(11):3126-3127. Song D, Xi NM, Li JJ, Wang L. PMID: 35426898; PMCID: PMC9991884.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    16. Exaggerated false positives by popular differential expression methods when analyzing human population samples. Genome Biol. 2022 03 15; 23(1):79. Li Y, Ge X, Peng F, Li W, Li JJ. PMID: 35292087; PMCID: PMC8922736.
      View in: PubMed   Mentions: 59     Fields:    Translation:Humans
    17. The interplay between translational efficiency, poly(A) tails, microRNAs, and neuronal activation. RNA. 2022 06; 28(6):808-831. Eisen TJ, Li JJ, Bartel DP. PMID: 35273099; PMCID: PMC9074895.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    18. Statistics or biology: the zero-inflation controversy about scRNA-seq data. Genome Biol. 2022 01 21; 23(1):31. Jiang R, Sun T, Song D, Li JJ. PMID: 35063006; PMCID: PMC8783472.
      View in: PubMed   Mentions: 57     Fields:    
    19. Simulating Single-Cell Gene Expression Count Data with Preserved Gene Correlations by scDesign2. J Comput Biol. 2022 01; 29(1):23-26. Sun T, Song D, Li WV, Li JJ. PMID: 35020490; PMCID: PMC8812500.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    20. Clipper: p-value-free FDR control on high-throughput data from two conditions. Genome Biol. 2021 10 11; 22(1):288. Ge X, Chen YE, Song D, McDermott M, Woyshner K, Manousopoulou A, Wang N, Li W, Wang LD, Li JJ. PMID: 34635147; PMCID: PMC8504070.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    21. RAD: a web application to identify region associated differentially expressed genes. Bioinformatics. 2021 Sep 09; 37(17):2741-2743. Guo Y, Xue Z, Yuan R, Li JJ, Pastor WA, Liu W. PMID: 33532827.
      View in: PubMed   Mentions: 6     Fields:    
    22. The concurrence of DNA methylation and demethylation is associated with transcription regulation. Nat Commun. 2021 09 06; 12(1):5285. Shi J, Xu J, Chen YE, Li JS, Cui Y, Shen L, Li JJ, Li W. PMID: 34489442; PMCID: PMC8421433.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansAnimalsCells
    23. Protocol for executing and benchmarking eight computational doublet-detection methods in single-cell RNA sequencing data analysis. STAR Protoc. 2021 09 17; 2(3):100699. Xi NM, Li JJ. PMID: 34382023; PMCID: PMC8339294.
      View in: PubMed   Mentions: 5     Fields:    
    24. scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling. Bioinformatics. 2021 07 12; 37(Suppl_1):i358-i366. Song D, Li K, Hemminger Z, Wollman R, Li JJ. PMID: 34252925; PMCID: PMC8275345.
      View in: PubMed   Mentions: 4     Fields:    
    25. mbImpute: an accurate and robust imputation method for microbiome data. Genome Biol. 2021 06 28; 22(1):192. Jiang R, Li WV, Li JJ. PMID: 34183041; PMCID: PMC8240317.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    26. Identifying the combinatorial control of signal-dependent transcription factors. PLoS Comput Biol. 2021 06; 17(6):e1009095. Wang N, Lefaudeux D, Mazumder A, Li JJ, Hoffmann A. PMID: 34166361; PMCID: PMC8263068.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    27. Postoperative Admission of Adult Craniotomy Patients to the Neuroscience Ward Reduces Length of Stay and Cost. Neurosurgery. 2021 06 15; 89(1):85-93. Sun MZ, Babayan D, Chen JS, Wang MM, Naik PK, Reitz K, Li JJ, Pouratian N, Kim W. PMID: 33862627.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    28. Bipartite tight spectral clustering (BiTSC) algorithm for identifying conserved gene co-clusters in two species. Bioinformatics. 2021 06 09; 37(9):1225-1233. Sun YE, Zhou HJ, Li JJ. PMID: 32814973; PMCID: PMC8599197.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    29. scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured. Genome Biol. 2021 05 25; 22(1):163. Sun T, Song D, Li WV, Li JJ. PMID: 34034771; PMCID: PMC8147071.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansAnimalsCells
    30. A flexible model-free prediction-based framework for feature ranking. J Mach Learn Res. 2021 May; 22. Li JJ, Chen YE, Tong X. PMID: 35321091; PMCID: PMC8939838.
      View in: PubMed   Mentions:
    31. PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data. Genome Biol. 2021 04 29; 22(1):124. Song D, Li JJ. PMID: 33926517; PMCID: PMC8082818.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    32. A new bioinformatics tool to recover missing gene expression in single-cell RNA sequencing data. J Mol Cell Biol. 2021 04 10; 13(1):1-2. Li JJ. PMID: 32997747; PMCID: PMC8035987.
      View in: PubMed   Mentions: 1     Fields:    
    33. Network Modeling in Biology: Statistical Methods for Gene and Brain Networks. Stat Sci. 2021 Feb; 36(1):89-108. Wang YXR, Li L, Li JJ, Huang H. PMID: 34305304; PMCID: PMC8296984.
      View in: PubMed   Mentions: 3  
    34. Cellular Heterogeneity-Adjusted cLonal Methylation (CHALM) improves prediction of gene expression. Nat Commun. 2021 01 15; 12(1):400. Xu J, Shi J, Cui X, Cui Y, Li JJ, Goel A, Chen X, Issa JP, Su J, Li W. PMID: 33452255; PMCID: PMC7811027.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    35. Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data. Cell Syst. 2021 02 17; 12(2):176-194.e6. Xi NM, Li JJ. PMID: 33338399; PMCID: PMC7897250.
      View in: PubMed   Mentions: 62     Fields:    Translation:Humans
    36. DORGE: Discovery of Oncogenes and tumoR suppressor genes using Genetic and Epigenetic features. Sci Adv. 2020 11; 6(46). Lyu J, Li JJ, Su J, Peng F, Chen YE, Ge X, Li W. PMID: 33177077; PMCID: PMC7673741.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    37. Integrin-Src-YAP1 signaling mediates the melanoma acquired resistance to MAPK and PI3K/mTOR dual targeted therapy. Mol Biomed. 2020 Nov 10; 1(1):12. Yu C, Zhang M, Song J, Zheng X, Xu G, Bao Y, Lan J, Luo D, Hu J, Li JJ, Shi H. PMID: 35006410; PMCID: PMC8607431.
      View in: PubMed   Mentions: 14  
    38. Statistical Hypothesis Testing versus Machine Learning Binary Classification: Distinctions and Guidelines. Patterns (N Y). 2020 Oct 09; 1(7):100115. Li JJ, Tong X. PMID: 33073257; PMCID: PMC7546185.
      View in: PubMed   Mentions: 7  
    39. AIDE: annotation-assisted isoform discovery with high precision. Genome Res. 2019 12; 29(12):2056-2072. Li WV, Li S, Tong X, Deng L, Shi H, Li JJ. PMID: 31694868; PMCID: PMC6886511.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    40. Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes. Genome Biol. 2019 08 09; 20(1):162. Li JJ, Chew GL, Biggin MD. PMID: 31399036; PMCID: PMC6689182.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    41. EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences. Nucleic Acids Res. 2019 07 26; 47(13):e77. Ge X, Zhang H, Xie L, Li WV, Kwon SB, Li JJ. PMID: 31045217; PMCID: PMC6648345.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    42. A statistical simulator scDesign for rational scRNA-seq experimental design. Bioinformatics. 2019 07 15; 35(14):i41-i50. Li WV, Li JJ. PMID: 31510652; PMCID: PMC6612870.
      View in: PubMed   Mentions: 28     Fields:    
    43. Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their Definitions. J Comput Biol. 2019 01; 26(1):38-52. Duong D, Ahmad WU, Eskin E, Chang KW, Li JJ. PMID: 30383443; PMCID: PMC6350067.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimals
    44. Modeling and analysis of RNA-seq data: a review from a statistical perspective. Quant Biol. 2018 Sep; 6(3):195-209. Li WV, Li JJ. PMID: 31456901; PMCID: PMC6711375.
      View in: PubMed   Mentions: 27  
    45. Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution. Cell. 2018 05 03; 173(4):1014-1030.e17. Burke JE, Longhurst AD, Merkurjev D, Sales-Lee J, Rao B, Moresco JJ, Yates JR, Li JJ, Madhani HD. PMID: 29727661; PMCID: PMC5940017.
      View in: PubMed   Mentions: 19     Fields:    Translation:AnimalsCells
    46. MSIQ: JOINT MODELING OF MULTIPLE RNA-SEQ SAMPLES FOR ACCURATE ISOFORM QUANTIFICATION. Ann Appl Stat. 2018 Mar; 12(1):510-539. Li WV, Zhao A, Zhang S, Li JJ. PMID: 29731954; PMCID: PMC5935499.
      View in: PubMed   Mentions: 3  
    47. An accurate and robust imputation method scImpute for single-cell RNA-seq data. Nat Commun. 2018 03 08; 9(1):997. Li WV, Li JJ. PMID: 29520097; PMCID: PMC5843666.
      View in: PubMed   Mentions: 263     Fields:    Translation:HumansAnimals
    48. Neyman-Pearson classification algorithms and NP receiver operating characteristics. Sci Adv. 2018 02; 4(2):eaao1659. Tong X, Feng Y, Li JJ. PMID: 29423442; PMCID: PMC5804623.
      View in: PubMed   Mentions: 11     Fields:    
    49. Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis. Proc Natl Acad Sci U S A. 2018 01 30; 115(5):E1069-E1074. Zhang Y, Harris CJ, Liu Q, Liu W, Ausin I, Long Y, Xiao L, Feng L, Chen X, Xie Y, Chen X, Zhan L, Feng S, Li JJ, Wang H, Zhai J, Jacobsen SE. PMID: 29339507; PMCID: PMC5798360.
      View in: PubMed   Mentions: 32     Fields:    Translation:AnimalsCells
    50. Quantitating translational control: mRNA abundance-dependent and independent contributions and the mRNA sequences that specify them. Nucleic Acids Res. 2017 Nov 16; 45(20):11821-11836. Li JJ, Chew GL, Biggin MD. PMID: 29040683; PMCID: PMC5714229.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    51. Hybrid Statistical and Mechanistic Mathematical Model Guides Mobile Health Intervention for Chronic Pain. J Comput Biol. 2017 Jul; 24(7):675-688. Clifton SM, Kang C, Li JJ, Long Q, Shah N, Abrams DM. PMID: 28581814; PMCID: PMC5510708.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    52. Correspondence of D. melanogaster and C. elegans developmental stages revealed by alternative splicing characteristics of conserved exons. BMC Genomics. 2017 03 16; 18(1):234. Gao R, Li JJ. PMID: 28302059; PMCID: PMC5353869.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    53. Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states. Nucleic Acids Res. 2017 02 28; 45(4):1657-1672. Yang Y, Yang YT, Yuan J, Lu ZJ, Li JJ. PMID: 27980097; PMCID: PMC5389511.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    54. TROM: A Testing-Based Method for Finding Transcriptomic Similarity of Biological Samples. Stat Biosci. 2017 Jun; 9(1):105-136. Li WV, Chen Y, Li JJ. PMID: 28781712; PMCID: PMC5542419.
      View in: PubMed   Mentions: 10  
    55. NMFP: a non-negative matrix factorization based preselection method to increase accuracy of identifying mRNA isoforms from RNA-seq data. BMC Genomics. 2016 Jan 11; 17 Suppl 1:11. Ye Y, Li JJ. PMID: 26818007; PMCID: PMC4895266.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    56. Epigenome overlap measure (EPOM) for comparing tissue/cell types based on chromatin states. BMC Genomics. 2016 Jan 11; 17 Suppl 1:10. Li WV, Razaee ZS, Li JJ. PMID: 26817822; PMCID: PMC4895267.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    57. A quantitative proteomic analysis of cellular responses to high glucose media in Chinese hamster ovary cells. Biotechnol Prog. 2015 Jul-Aug; 31(4):1026-38. Liu Z, Dai S, Bones J, Ray S, Cha S, Karger BL, Li JJ, Wilson L, Hinckle G, Rossomando A. PMID: 25857574.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    58. Gene expression. Statistics requantitates the central dogma. Science. 2015 Mar 06; 347(6226):1066-7. Li JJ, Biggin MD. PMID: 25745146.
      View in: PubMed   Mentions: 81     Fields:    Translation:HumansAnimalsCells
    59. Comparative analysis of regulatory information and circuits across distant species. Nature. 2014 Aug 28; 512(7515):453-6. Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M. PMID: 25164757; PMCID: PMC4336544.
      View in: PubMed   Mentions: 96     Fields:    Translation:HumansAnimalsCells
    60. Comparative analysis of the transcriptome across distant species. Nature. 2014 Aug 28; 512(7515):445-8. Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R. PMID: 25164755; PMCID: PMC4155737.
      View in: PubMed   Mentions: 158     Fields:    Translation:HumansAnimalsCells
    61. Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data. Genome Res. 2014 Jul; 24(7):1086-101. Li JJ, Huang H, Bickel PJ, Brenner SE. PMID: 24985912; PMCID: PMC4079965.
      View in: PubMed   Mentions: 47     Fields:    Translation:AnimalsCells
    62. System wide analyses have underestimated protein abundances and the importance of transcription in mammals. PeerJ. 2014; 2:e270. Li JJ, Bickel PJ, Biggin MD. PMID: 24688849; PMCID: PMC3940484.
      View in: PubMed   Mentions: 145     Fields:    
    63. DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Proc Natl Acad Sci U S A. 2012 Dec 26; 109(52):21330-5. Fisher WW, Li JJ, Hammonds AS, Brown JB, Pfeiffer BD, Weiszmann R, MacArthur S, Thomas S, Stamatoyannopoulos JA, Eisen MB, Bickel PJ, Biggin MD, Celniker SE. PMID: 23236164; PMCID: PMC3535648.
      View in: PubMed   Mentions: 82     Fields:    Translation:AnimalsCells
    64. Biclustering of linear patterns in gene expression data. J Comput Biol. 2012 Jun; 19(6):619-31. Gao Q, Ho C, Jia Y, Li JJ, Huang H. PMID: 22697238; PMCID: PMC3375643.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    65. Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. Proc Natl Acad Sci U S A. 2011 Dec 13; 108(50):19867-72. Li JJ, Jiang CR, Brown JB, Huang H, Bickel PJ. PMID: 22135461; PMCID: PMC3250192.
      View in: PubMed   Mentions: 65     Fields:    Translation:Animals
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