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James J. Cai - Publications

Affiliations: 
2000-2002 Microbiology University of Hong Kong, Downingtown, Hong Kong Island, Hong Kong 
 2006-2010 Biology Stanford University, Palo Alto, CA 
 2010- VIBS Texas A & M University, College Station, TX, United States 
Area:
Single-cell Biology, Machine Learning, Quantum Computing
Website:
https://cailab-tamu.github.io/
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55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Xu Q, Li G, Osorio D, Zhong Y, Yang Y, Lin YT, Zhang X, Cai JJ. scInTime: A Computational Method Leveraging Single-Cell Trajectory and Gene Regulatory Networks to Identify Master Regulators of Cellular Differentiation. Genes. 13. PMID 35205415 DOI: 10.3390/genes13020371  0.649
2022 Pinson MR, Chung DD, Mahnke AH, Salem NA, Osorio D, Nair V, Payne EA, Del Real JJ, Cai JJ, Miranda RC. Gag-like proteins: Novel mediators of prenatal alcohol exposure in neural development. Alcoholism, Clinical and Experimental Research. PMID 35187673 DOI: 10.1111/acer.14796  0.564
2021 Yang Y, Osorio D, Davidson LA, Han H, Mullens DA, Jayaraman A, Safe S, Ivanov I, Cai JJ, Chapkin RS. Single-cell RNA Sequencing Reveals How the Aryl Hydrocarbon Receptor Shapes Cellular Differentiation Potency in the Mouse Colon. Cancer Prevention Research (Philadelphia, Pa.). PMID 34815312 DOI: 10.1158/1940-6207.CAPR-21-0378  0.605
2021 Osorio D, Kuijjer ML, Cai JJ. rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. Bioinformatics (Oxford, England). PMID 34320637 DOI: 10.1093/bioinformatics/btab549  0.605
2020 Osorio D, Zhong Y, Li G, Huang JZ, Cai JJ. scTenifoldNet: A Machine Learning Workflow for Constructing and Comparing Transcriptome-wide Gene Regulatory Networks from Single-Cell Data. Patterns (New York, N.Y.). 1: 100139. PMID 33336197 DOI: 10.1016/j.patter.2020.100139  0.632
2020 Kumar V, Ivens A, Goodall Z, Meehan J, Doharey PK, Hillhouse A, Hurtado DO, Cai JJ, Zhang X, Schnaufer A, Cruz-Reyes J. Site-specific and mRNA-specific control of accurate mRNA editing by a helicase complex in trypanosomes. Rna (New York, N.Y.). PMID 32873716 DOI: 10.1261/Rna.076513.120  0.315
2020 Osorio D, Cai JJ. Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA sequencing data quality control. Bioinformatics (Oxford, England). PMID 32840568 DOI: 10.1093/Bioinformatics/Btaa751  0.611
2020 Eldridge R, Osorio D, Amstalden K, Edwards C, Young CR, Cai JJ, Konganti K, Hillhouse A, Threadgill DW, Welsh CJ, Brinkmeyer-Langford C. Antecedent presentation of neurological phenotypes in the Collaborative Cross reveals four classes with complex sex-dependencies. Scientific Reports. 10: 7918. PMID 32404926 DOI: 10.1038/S41598-020-64862-Z  0.573
2020 Huang G, Osorio D, Guan J, Ji G, Cai JJ. Overdispersed gene expression in schizophrenia. Npj Schizophrenia. 6: 9. PMID 32245959 DOI: 10.1038/s41537-020-0097-5  0.612
2019 Osorio D, Yu X, Zhong Y, Li G, Yu P, Serpedin E, Huang JZ, Cai JJ. Single-Cell Expression Variability Implies Cell Function. Cells. 9. PMID 31861624 DOI: 10.3390/Cells9010014  0.666
2019 Cai JJ. scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis. Bioinformatics (Oxford, England). PMID 31697351 DOI: 10.1093/Bioinformatics/Btz830  0.439
2019 Osorio D, Yu X, Yu P, Serpedin E, Cai JJ. Single-cell RNA sequencing of a European and an African lymphoblastoid cell line. Scientific Data. 6: 112. PMID 31273215 DOI: 10.1038/S41597-019-0116-4  0.668
2019 Guan J, Cai JJ, Ji G, Sham PC. Commonality in dysregulated expression of gene sets in cortical brains of individuals with autism, schizophrenia, and bipolar disorder. Translational Psychiatry. 9: 152. PMID 31127088 DOI: 10.1038/S41398-019-0488-4  0.359
2018 Lau SKP, Lo GCS, Chow FWN, Fan RYY, Cai JJ, Yuen KY, Woo PCY. Novel Partitivirus Enhances Virulence of and Causes Aberrant Gene Expression in Talaromyces marneffei. Mbio. 9. PMID 29895639 DOI: 10.1128/Mbio.00947-18  0.371
2018 Al Kawam A, Alshawaqfeh M, Cai JJ, Serpedin E, Datta A. Simulating variance heterogeneity in quantitative genome wide association studies. Bmc Bioinformatics. 19: 72. PMID 29589560 DOI: 10.1186/S12859-018-2061-1  0.402
2018 Brinkmeyer-Langford C, Chu C, Balog-Alvarez C, Yu X, Cai JJ, Nabity M, Kornegay JN. Expression profiling of disease progression in canine model of Duchenne muscular dystrophy. Plos One. 13: e0194485. PMID 29554127 DOI: 10.1371/Journal.Pone.0194485  0.366
2017 Guan J, Chen M, Ye C, Cai JJ, Ji G. AEGS: identifying aberrantly expressed gene sets for differential variability analysis. Bioinformatics (Oxford, England). PMID 29040376 DOI: 10.1093/Bioinformatics/Btx646  0.396
2016 Yang E, Wang G, Yang J, Zhou B, Tian Y, Cai JJ. Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action. Human Molecular Genetics. 25: 4911-4919. PMID 28171656 DOI: 10.1093/Hmg/Ddw314  0.429
2016 Yang E, Wang G, Yang J, Zhou B, Tian Y, Cai JJ. Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action. Human Molecular Genetics. PMID 27651397 DOI: 10.1093/hmg/ddw314  0.332
2016 Brinkmeyer-Langford C, Balog-Alvarez C, Cai JJ, Davis BW, Kornegay JN. Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy. Bmc Genomics. 17: 665. PMID 27549615 DOI: 10.1186/S12864-016-2948-Z  0.346
2016 Brinkmeyer-Langford CL, Guan J, Ji G, Cai JJ. Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains. Frontiers in Aging Neuroscience. 8: 183. PMID 27536236 DOI: 10.3389/Fnagi.2016.00183  0.36
2016 Guan J, Yang E, Yang J, Zeng Y, Ji G, Cai JJ. Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis. Human Genetics. PMID 27131873 DOI: 10.1007/S00439-016-1673-7  0.421
2015 Chacko N, Zhao Y, Yang E, Wang L, Cai JJ, Lin X. The lncRNA RZE1 Controls Cryptococcal Morphological Transition. Plos Genetics. 11: e1005692. PMID 26588844 DOI: 10.1371/Journal.Pgen.1005692  0.365
2015 Zeng Y, Wang G, Yang E, Ji G, Brinkmeyer-Langford CL, Cai JJ. Aberrant gene expression in humans. Plos Genetics. 11: e1004942. PMID 25617623 DOI: 10.1371/Journal.Pgen.1004942  0.452
2014 Yang E, Chow WN, Wang G, Woo PC, Lau SK, Yuen KY, Lin X, Cai JJ. Signature gene expression reveals novel clues to the molecular mechanisms of dimorphic transition in Penicillium marneffei. Plos Genetics. 10: e1004662. PMID 25330172 DOI: 10.1371/Journal.Pgen.1004662  0.432
2014 Wang G, Yang E, Smith KJ, Zeng Y, Ji G, Connon R, Fangue NA, Cai JJ. Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension. Frontiers in Genetics. 5: 312. PMID 25309574 DOI: 10.3389/Fgene.2014.00312  0.438
2014 Chang CL, Cai JJ, Huang SY, Cheng PJ, Chueh HY, Hsu SY. Adaptive human CDKAL1 variants underlie hormonal response variations at the enteroinsular axis. Plos One. 9: e105410. PMID 25222615 DOI: 10.1371/Journal.Pone.0105410  0.345
2014 Wang G, Yang E, Mandhan I, Brinkmeyer-Langford CL, Cai JJ. Population-level expression variability of mitochondrial DNA-encoded genes in humans European Journal of Human Genetics. 22: 1093-1099. PMID 24398800 DOI: 10.1038/Ejhg.2013.293  0.447
2014 Wang G, Yang E, Brinkmeyer-Langford CL, Cai JJ. Additive, Epistatic, and Environmental Effects Through the Lens of Expression Variability QTL in a Twin Cohort Genetics. 196: 413-425. PMID 24298061 DOI: 10.1534/Genetics.113.157503  0.394
2013 Yang E, Wang G, Woo PC, Lau SK, Chow WN, Chong KT, Tse H, Kao RY, Chan CM, Che X, Yuen KY, Cai JJ. Unraveling the molecular basis of temperature-dependent genetic regulation in Penicillium marneffei. Eukaryotic Cell. 12: 1214-24. PMID 23851338 DOI: 10.1128/Ec.00159-13  0.382
2013 Chang CL, Semyonov J, Cheng PJ, Huang SY, Park JI, Tsai HJ, Lin CY, Grützner F, Soong YK, Cai JJ, Hsu SY. Widespread divergence of the CEACAM/PSG genes in vertebrates and humans suggests sensitivity to selection. Plos One. 8: e61701. PMID 23613906 DOI: 10.1371/Journal.Pone.0061701  0.409
2013 Hulse AM, Cai JJ. Genetic Variants Contribute to Gene Expression Variability in Humans Genetics. 193: 95-108. PMID 23150607 DOI: 10.1534/Genetics.112.146779  0.441
2012 Yang E, Hulse AM, Cai JJ. Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus. Evolutionary Bioinformatics. 8: 623-644. PMID 23225993 DOI: 10.4137/Ebo.S10372  0.443
2012 Brinkmeyer-Langford CL, Cai JJ, Gill CA, Skow LC. Microsatellite variation in the equine MHC. Animal Genetics. 44: 267-75. PMID 23051181 DOI: 10.1111/Age.12003  0.309
2011 Woo PC, Lau SK, Liu B, Cai JJ, Chong KT, Tse H, Kao RY, Chan CM, Chow WN, Yuen KY. Draft genome sequence of Penicillium marneffei strain PM1. Eukaryotic Cell. 10: 1740-1. PMID 22131218 DOI: 10.1128/Ec.05255-11  0.352
2011 Chang CL, Cai JJ, Cheng PJ, Chueh HY, Hsu SY. Identification of metabolic modifiers that underlie phenotypic variations in energy-balance regulation. Diabetes. 60: 726-34. PMID 21300845 DOI: 10.2337/Db10-1331  0.327
2011 Shen S, Lin L, Cai JJ, Jiang P, Kenkel EJ, Stroik MR, Sato S, Davidson BL, Xing Y. Widespread establishment and regulatory impact of Alu exons in human genes. Proceedings of the National Academy of Sciences of the United States of America. 108: 2837-42. PMID 21282640 DOI: 10.1073/Pnas.1012834108  0.422
2011 Lu ZX, Jiang P, Cai JJ, Xing Y. Context-dependent robustness to 5' splice site polymorphisms in human populations. Human Molecular Genetics. 20: 1084-96. PMID 21224255 DOI: 10.1093/Hmg/Ddq553  0.311
2011 Chang CL, Cai JJ, Lo C, Amigo J, Park JI, Hsu SY. Adaptive selection of an incretin gene in Eurasian populations. Genome Research. 21: 21-32. PMID 20978139 DOI: 10.1101/Gr.110593.110  0.334
2010 Cai JJ, Borenstein E, Petrov DA. Broker genes in human disease. Genome Biology and Evolution. 2: 815-25. PMID 20937604 DOI: 10.1093/Gbe/Evq064  0.402
2010 Tse H, Cai JJ, Tsoi HW, Lam EP, Yuen KY. Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes. Bmc Genomics. 11: 491. PMID 20828396 DOI: 10.1186/1471-2164-11-491  0.303
2010 Woo PCY, Tam EWT, Chong KTK, Cai JJ, Tung ETK, Ngan AHY, Lau SKP, Yuen KY. High diversity of polyketide synthase genes and the melanin biosynthesis gene cluster in Penicillium marneffei Febs Journal. 277: 3750-3758. PMID 20718860 DOI: 10.1111/J.1742-4658.2010.07776.X  0.392
2010 Cai JJ, Petrov DA. Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. Genome Biology and Evolution. 2: 393-409. PMID 20624743 DOI: 10.1093/Gbe/Evq019  0.393
2009 Cai JJ, Borenstein E, Chen R, Petrov DA. Similarly strong purifying selection acts on human disease genes of all evolutionary ages. Genome Biology and Evolution. 1: 131-44. PMID 20333184 DOI: 10.1093/Gbe/Evp013  0.399
2009 Woo PC, Lau SK, Tse H, Teng JL, Curreem SO, Tsang AK, Fan RY, Wong GK, Huang Y, Loman NJ, Snyder LA, Cai JJ, Huang JD, Mak W, Pallen MJ, et al. The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. Plos Genetics. 5: e1000416. PMID 19283063 DOI: 10.1371/Journal.Pgen.1000416  0.345
2009 Cai JJ, Macpherson JM, Sella G, Petrov DA. Pervasive hitchhiking at coding and regulatory sites in humans. Plos Genetics. 5: e1000336. PMID 19148272 DOI: 10.1371/Journal.Pgen.1000336  0.325
2008 Lin L, Shen S, Tye A, Cai JJ, Jiang P, Davidson BL, Xing Y. Diverse splicing patterns of exonized Alu elements in human tissues. Plos Genetics. 4: e1000225. PMID 18841251 DOI: 10.1371/Journal.Pgen.1000225  0.333
2008 Cai JJ. PGEToolbox: A Matlab Toolbox for Population Genetics and Evolution Journal of Heredity. 99: 438-440. PMID 18310616 DOI: 10.1093/Jhered/Esm127  0.334
2006 Cai JJ, Smith DK, Xia X, Yuen KY. MBEToolbox 2.0: an enhanced version of a MATLAB toolbox for molecular biology and evolution. Evolutionary Bioinformatics Online. 2: 179-82. PMID 19455210 DOI: 10.4137/Ebo.S0  0.554
2006 Cai JJ, Woo PC, Lau SK, Smith DK, Yuen KY. Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota. Journal of Molecular Evolution. 63: 1-11. PMID 16755356 DOI: 10.1007/S00239-004-0372-5  0.418
2006 Woo PC, Chong KT, Tse H, Cai JJ, Lau CC, Zhou AC, Lau SK, Yuen KY. Genomic and experimental evidence for a potential sexual cycle in the pathogenic thermal dimorphic fungus Penicillium marneffei. Febs Letters. 580: 3409-16. PMID 16714021 DOI: 10.1016/J.Febslet.2006.05.014  0.357
2005 Cai JJ, Smith DK, Xia X, Yuen KY. MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution. Bmc Bioinformatics. 6: 64. PMID 15780146 DOI: 10.1186/1471-2105-6-64  0.566
2005 Woo PC, Lau SK, Chu CM, Chan KH, Tsoi HW, Huang Y, Wong BH, Poon RW, Cai JJ, Luk WK, Poon LL, Wong SS, Guan Y, Peiris JS, Yuen KY. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. Journal of Virology. 79: 884-95. PMID 15613317 DOI: 10.1128/Jvi.79.2.884-895.2005  0.339
2003 Woo PC, Zhen H, Cai JJ, Yu J, Lau SK, Wang J, Teng JL, Wong SS, Tse RH, Chen R, Yang H, Liu B, Yuen KY. The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts. Febs Letters. 555: 469-77. PMID 14675758 DOI: 10.1016/S0014-5793(03)01307-3  0.339
2003 Yuen KY, Pascal G, Wong SS, Glaser P, Woo PC, Kunst F, Cai JJ, Cheung EY, Médigue C, Danchin A. Exploring the Penicillium marneffei genome. Archives of Microbiology. 179: 339-53. PMID 12640520 DOI: 10.1007/S00203-003-0533-8  0.38
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