Chun-Nan Hsu • UCSD Profiles (original) (raw)

  1. Validation and expansion of Baveno VII criteria for cACLD and CSPH based on liver stiffness and platelet count: Correlation with risk of hepatic decompensation and death. Hepatology. 2025 Aug 01; 82(2):422-437. Vutien P, Barnard Giustini A, Kim NJ, Moon AM, Hsu CN, Mezzacappa C, Borgerding JA, Johnson KM, VoPham T, Berry K, Beste LA, Kaplan DE, Taddei TH, Ioannou GN. PMID: 39689352; PMCID: PMC12266799.
    View in: PubMed Mentions: 4 Fields:
    Translation:Humans
  2. RadBERT: Adapting Transformer-based Language Models to Radiology. Radiol Artif Intell. 2022 Jul; 4(4):e210258. Yan A, McAuley J, Lu X, Du J, Chang EY, Gentili A, Hsu CN. PMID: 35923376; PMCID: PMC9344353.
    View in: PubMed Mentions: 60 Fields:
  3. Federated learning for predicting clinical outcomes in patients with COVID-19. Nat Med. 2021 10; 27(10):1735-1743. Dayan I, Roth HR, Zhong A, Harouni A, Gentili A, Abidin AZ, Liu A, Costa AB, Wood BJ, Tsai CS, Wang CH, Hsu CN, Lee CK, Ruan P, Xu D, Wu D, Huang E, Kitamura FC, Lacey G, de Antônio Corradi GC, Nino G, Shin HH, Obinata H, Ren H, Crane JC, Tetreault J, Guan J, Garrett JW, Kaggie JD, Park JG, Dreyer K, Juluru K, Kersten K, Rockenbach MABC, Linguraru MG, Haider MA, AbdelMaseeh M, Rieke N, Damasceno PF, E Silva PMC, Wang P, Xu S, Kawano S, Sriswasdi S, Park SY, Grist TM, Buch V, Jantarabenjakul W, Wang W, Tak WY, Li X, Lin X, Kwon YJ, Quraini A, Feng A, Priest AN, Turkbey B, Glicksberg B, Bizzo B, Kim BS, Tor-Díez C, Lee CC, Hsu CJ, Lin C, Lai CL, Hess CP, Compas C, Bhatia D, Oermann EK, Leibovitz E, Sasaki H, Mori H, Yang I, Sohn JH, Murthy KNK, Fu LC, de Mendonça MRF, Fralick M, Kang MK, Adil M, Gangai N, Vateekul P, Elnajjar P, Hickman S, Majumdar S, McLeod SL, Reed S, Gräf S, Harmon S, Kodama T, Puthanakit T, Mazzulli T, de Lavor VL, Rakvongthai Y, Lee YR, Wen Y, Gilbert FJ, Flores MG, Li Q. PMID: 34526699; PMCID: PMC9157510.
    View in: PubMed Mentions: 190 Fields:
    Translation:HumansCells
  4. Antibody Watch: Text mining antibody specificity from the literature. PLoS Comput Biol. 2021 05; 17(5):e1008967. Hsu CN, Chang CH, Poopradubsil T, Lo A, William KA, Lin KW, Bandrowski A, Ozyurt IB, Grethe JS, Martone ME. PMID: 34043624; PMCID: PMC8189493.
    View in: PubMed Mentions: 2 Fields:
    Translation:HumansAnimals
  5. Increasing metadata coverage of SRA BioSample entries using deep learning-based named entity recognition. Database (Oxford). 2021 04 29; 2021. Klie A, Tsui BY, Mollah S, Skola D, Dow M, Hsu CN, Carter H. PMID: 33914028; PMCID: PMC8083811.
    View in: PubMed Mentions: 8 Fields:
  6. Federated Learning used for predicting outcomes in SARS-COV-2 patients. Res Sq. 2021 Jan 08. Flores M, Dayan I, Roth H, Zhong A, Harouni A, Gentili A, Abidin A, Liu A, Costa A, Wood B, Tsai CS, Wang CH, Hsu CN, Lee CK, Ruan C, Xu D, Wu D, Huang E, Kitamura F, Lacey G, César de Antônio Corradi G, Shin HH, Obinata H, Ren H, Crane J, Tetreault J, Guan J, Garrett J, Park JG, Dreyer K, Juluru K, Kersten K, Bezerra Cavalcanti Rockenbach MA, Linguraru M, Haider M, AbdelMaseeh M, Rieke N, Damasceno P, Cruz E Silva PM, Wang P, Xu S, Kawano S, Sriswasdi S, Park SY, Grist T, Buch V, Jantarabenjakul W, Wang W, Tak WY, Li X, Lin X, Kwon F, Gilbert F, Kaggie J, Li Q, Quraini A, Feng A, Priest A, Turkbey B, Glicksberg B, Bizzo B, Kim BS, Tor-Diez C, Lee CC, Hsu CJ, Lin C, Lai CL, Hess C, Compas C, Bhatia D, Oermann E, Leibovitz E, Sasaki H, Mori H, Yang I, Sohn JH, Keshava Murthy KN, Fu LC, Furtado de Mendonça MR, Fralick M, Kang MK, Adil M, Gangai N, Vateekul P, Elnajjar P, Hickman S, Majumdar S, McLeod S, Reed S, Graf S, Harmon S, Kodama T, Puthanakit T, Mazzulli T, de Lima Lavor V, Rakvongthai Y, Lee YR, Wen Y. PMID: 33442676; PMCID: PMC7805458.
    View in: PubMed Mentions:
  7. Learning Visual-Semantic Embeddings for Reporting Abnormal Findings on Chest X-rays. Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing: Findings. 2020; 1954--1960. Ni, Jianmo and Hsu, Chun-nan and Gentili, Amilcare and McAuley, Julian. View Publication.
  8. A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans. PLoS One. 2019; 14(12):e0226771. Pendergrass SA, Buyske S, Jeff JM, Frase A, Dudek S, Bradford Y, Ambite JL, Avery CL, Buzkova P, Deelman E, Fesinmeyer MD, Haiman C, Heiss G, Hindorff LA, Hsu CN, Jackson RD, Lin Y, Le Marchand L, Matise TC, Monroe KR, Moreland L, North KE, Park SL, Reiner A, Wallace R, Wilkens LR, Kooperberg C, Ritchie MD, Crawford DC. PMID: 31891604; PMCID: PMC6938343.
    View in: PubMed Mentions: 9 Fields:
    Translation:Humans
  9. Challenges in the construction of knowledge bases for human microbiome-disease associations. Microbiome. 2019 09 05; 7(1):129. Badal VD, Wright D, Katsis Y, Kim HC, Swafford AD, Knight R, Hsu CN. PMID: 31488215; PMCID: PMC6728997.
    View in: PubMed Mentions: 20 Fields:
    Translation:Humans
  10. NormCo: Deep Disease Normalization for Biomedical Knowledge Base Construction. Automated Knowledge Base Construction Conference. 2019. Dustin Wright, Yannis Katsis, Raghav Mehta, Chun-Nan Hsu. . View Publication.
  11. Evaluation and accurate diagnoses of pediatric diseases using artificial intelligence. Nat Med. 2019 03; 25(3):433-438. Liang H, Tsui BY, Ni H, Valentim CCS, Baxter SL, Liu G, Cai W, Kermany DS, Sun X, Chen J, He L, Zhu J, Tian P, Shao H, Zheng L, Hou R, Hewett S, Li G, Liang P, Zang X, Zhang Z, Pan L, Cai H, Ling R, Li S, Cui Y, Tang S, Ye H, Huang X, He W, Liang W, Zhang Q, Jiang J, Yu W, Gao J, Ou W, Deng Y, Hou Q, Wang B, Yao C, Liang Y, Zhang S, Duan Y, Zhang R, Gibson S, Zhang CL, Li O, Zhang ED, Karin G, Nguyen N, Wu X, Wen C, Xu J, Xu W, Wang B, Wang W, Li J, Pizzato B, Bao C, Xiang D, He W, He S, Zhou Y, Haw W, Goldbaum M, Tremoulet A, Hsu CN, Carter H, Zhu L, Zhang K, Xia H. PMID: 30742121.
    View in: PubMed Mentions: 229 Fields:
    Translation:Humans
  12. Identifying and characterizing highly similar notes in big clinical note datasets. J Biomed Inform. 2018 06; 82:63-69. Gabriel RA, Kuo TT, McAuley J, Hsu CN. PMID: 29679685.
    View in: PubMed Mentions: 11 Fields:
    Translation:Humans
  13. Ensembles of NLP Tools for Data Element Extraction from Clinical Notes. AMIA Annu Symp Proc. 2016; 2016:1880-1889. Kuo TT, Rao P, Maehara C, Doan S, Chaparro JD, Day ME, Farcas C, Ohno-Machado L, Hsu CN. PMID: 28269947; PMCID: PMC5333200.
    View in: PubMed Mentions: 12 Fields:
    Translation:Humans
  14. Building a Natural Language Processing Tool to Identify Patients With High Clinical Suspicion for Kawasaki Disease from Emergency Department Notes. Acad Emerg Med. 2016 05; 23(5):628-36. Doan S, Maehara CK, Chaparro JD, Lu S, Liu R, Graham A, Berry E, Hsu CN, Kanegaye JT, Lloyd DD, Ohno-Machado L, Burns JC, Tremoulet AH, Pediatric Emergency Medicine Kawasaki Disease Research Group. PMID: 26826020; PMCID: PMC5031359.
    View in: PubMed Mentions: 24 Fields:
    Translation:Humans
  15. Weakly supervised learning of biomedical information extraction from curated data. BMC Bioinformatics. 2016 Jan 11; 17 Suppl 1:1. Jain S, Tumkur KR, Kuo TT, Bhargava S, Lin G, Hsu CN. PMID: 26817711; PMCID: PMC4847485.
    View in: PubMed Mentions: 13 Fields:
    Translation:Humans
  16. Citing a Data Repository: A Case Study of the Protein Data Bank. PLoS One. 2015; 10(8):e0136631. Huang YH, Rose PW, Hsu CN. PMID: 26317409; PMCID: PMC4552849.
    View in: PubMed Mentions: 11 Fields:
    Translation:Humans
  17. Analysis of metabolic syndrome components in >15 000 african americans identifies pleiotropic variants: results from the population architecture using genomics and epidemiology study. Circ Cardiovasc Genet. 2014 Aug; 7(4):505-13. Carty CL, Bhattacharjee S, Haessler J, Cheng I, Hindorff LA, Aroda V, Carlson CS, Hsu CN, Wilkens L, Liu S, Selvin E, Jackson R, North KE, Peters U, Pankow JS, Chatterjee N, Kooperberg C. PMID: 25023634; PMCID: PMC4142758.
    View in: PubMed Mentions: 28 Fields:
    Translation:Humans
  18. PombeX: robust cell segmentation for fission yeast transillumination images. PLoS One. 2013; 8(12):e81434. Peng JY, Chen YJ, Green MD, Sabatinos SA, Forsburg SL, Hsu CN. PMID: 24353754; PMCID: PMC3865994.
    View in: PubMed Mentions: 10 Fields:
    Translation:Animals
  19. Identification of latent biomarkers in hepatocellular carcinoma by ultra-deep whole-transcriptome sequencing. Oncogene. 2014 Sep 25; 33(39):4786-94. Lin KT, Shann YJ, Chau GY, Hsu CN, Huang CY. PMID: 24141781.
    View in: PubMed Mentions: 33 Fields:
    Translation:HumansCells
  20. Analysis of protein-protein interactions in cross-talk pathways reveals CRKL protein as a novel prognostic marker in hepatocellular carcinoma. Mol Cell Proteomics. 2013 May; 12(5):1335-49. Liu CH, Chen TC, Chau GY, Jan YH, Chen CH, Hsu CN, Lin KT, Juang YL, Lu PJ, Cheng HC, Chen MH, Chang CF, Ting YS, Kao CY, Hsiao M, Huang CY. PMID: 23397142; PMCID: PMC3650343.
    View in: PubMed Mentions: 17 Fields:
    Translation:HumansCells
  21. Phenome-wide association study (PheWAS) for detection of pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network. PLoS Genet. 2013; 9(1):e1003087. Pendergrass SA, Brown-Gentry K, Dudek S, Frase A, Torstenson ES, Goodloe R, Ambite JL, Avery CL, Buyske S, Bužková P, Deelman E, Fesinmeyer MD, Haiman CA, Heiss G, Hindorff LA, Hsu CN, Jackson RD, Kooperberg C, Le Marchand L, Lin Y, Matise TC, Monroe KR, Moreland L, Park SL, Reiner A, Wallace R, Wilkens LR, Crawford DC, Ritchie MD. PMID: 23382687; PMCID: PMC3561060.
    View in: PubMed Mentions: 109 Fields:
    Translation:Humans
  22. A ν-support vector regression based approach for predicting imputation quality. BMC Proc. 2012 Nov 13; 6 Suppl 7:S3. Huang YH, Rice JP, Saccone SF, Ambite JL, Arens Y, Tischfield JA, Hsu CN. PMID: 23173775; PMCID: PMC3504919.
    View in: PubMed Mentions: 1
  23. MetaMirClust: discovery of miRNA cluster patterns using a data-mining approach. Genomics. 2012 Sep; 100(3):141-8. Chan WC, Ho MR, Li SC, Tsai KW, Lai CH, Hsu CN, Lin WC. PMID: 22735742.
    View in: PubMed Mentions: 25 Fields:
    Translation:HumansAnimalsCells
  24. Ranking of multidimensional drug profiling data by fractional-adjusted bi-partitional scores. Bioinformatics. 2012 Jun 15; 28(12):i106-14. Hochbaum DS, Hsu CN, Yang YT. PMID: 22689749; PMCID: PMC3371864.
    View in: PubMed Mentions: Fields:
    Translation:AnimalsCells
  25. Automatic morphological subtyping reveals new roles of caspases in mitochondrial dynamics. PLoS Comput Biol. 2011 Oct; 7(10):e1002212. Peng JY, Lin CC, Chen YJ, Kao LS, Liu YC, Chou CC, Huang YH, Chang FR, Wu YC, Tsai YS, Hsu CN. PMID: 21998575; PMCID: PMC3188504.
    View in: PubMed Mentions: 82 Fields:
    Translation:AnimalsCells
  26. Soft tagging of overlapping high confidence gene mention variants for cross-species full-text gene normalization. BMC Bioinformatics. 2011 Oct 03; 12 Suppl 8:S6. Kuo CJ, Ling MH, Hsu CN. PMID: 22152021; PMCID: PMC3269941.
    View in: PubMed Mentions: 2 Fields:
  27. The gene normalization task in BioCreative III. BMC Bioinformatics. 2011 Oct 03; 12 Suppl 8:S2. Lu Z, Kao HY, Wei CH, Huang M, Liu J, Kuo CJ, Hsu CN, Tsai RT, Dai HJ, Okazaki N, Cho HC, Gerner M, Solt I, Agarwal S, Liu F, Vishnyakova D, Ruch P, Romacker M, Rinaldi F, Bhattacharya S, Srinivasan P, Liu H, Torii M, Matos S, Campos D, Verspoor K, Livingston KM, Wilbur WJ. PMID: 22151901; PMCID: PMC3269937.
    View in: PubMed Mentions: 71 Fields:
    Translation:HumansAnimals
  28. UMARS: Un-MAppable Reads Solution. BMC Bioinformatics. 2011 Feb 15; 12 Suppl 1:S9. Li SC, Chan WC, Lai CH, Tsai KW, Hsu CN, Jou YS, Chen HC, Chen CH, Lin WC. PMID: 21342592; PMCID: PMC3044317.
    View in: PubMed Mentions: 6 Fields:
    Translation:Cells
  29. Discovery and characterization of medaka miRNA genes by next generation sequencing platform. BMC Genomics. 2010 Dec 02; 11 Suppl 4:S8. Li SC, Chan WC, Ho MR, Tsai KW, Hu LY, Lai CH, Hsu CN, Hwang PP, Lin WC. PMID: 21143817; PMCID: PMC3005926.
    View in: PubMed Mentions: 26 Fields:
    Translation:AnimalsCells
  30. From NPC therapeutic target identification to potential treatment strategy. Mol Cancer Ther. 2010 Sep; 9(9):2511-23. Lan MY, Chen CL, Lin KT, Lee SA, Yang WL, Hsu CN, Wu JC, Ho CY, Lin JC, Huang CY. PMID: 20716640.
    View in: PubMed Mentions: 10 Fields:
    Translation:HumansCells
  31. A spectral graph theoretic approach to quantification and calibration of collective morphological differences in cell images. Bioinformatics. 2010 Jun 15; 26(12):i29-37. Lin YS, Lin CC, Tsai YS, Ku TC, Huang YH, Hsu CN. PMID: 20529919; PMCID: PMC2881379.
    View in: PubMed Mentions: 3 Fields:
    Translation:Cells
  32. Sequence features involved in the mechanism of 3' splice junction wobbling. BMC Mol Biol. 2010 May 07; 11:34. Tsai KW, Chan WC, Hsu CN, Lin WC. PMID: 20459675; PMCID: PMC2875228.
    View in: PubMed Mentions: 13 Fields:
    Translation:HumansCells
  33. Identification of homologous microRNAs in 56 animal genomes. Genomics. 2010 Jul; 96(1):1-9. Li SC, Chan WC, Hu LY, Lai CH, Hsu CN, Lin WC. PMID: 20347954.
    View in: PubMed Mentions: 60 Fields:
    Translation:HumansAnimalsCells
  34. NIPS 2009. Periodic Step Size Adaptation for Single Pass On-line Learning. 2009; 22:763-771. Hsu CN, Chang YM, Huang HS, Lee YJ. View Publication.
  35. Integrating high dimensional bi-directional parsing models for gene mention tagging. Bioinformatics. 2008 Jul 01; 24(13):i286-94. Hsu CN, Chang YM, Kuo CJ, Lin YS, Huang HS, Chung IF. PMID: 18586726; PMCID: PMC2718659.
    View in: PubMed Mentions: 39 Fields:
  36. FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. Nucleic Acids Res. 2006 Jul 01; 34(Web Server issue):W635-41. Yuan HY, Chiou JJ, Tseng WH, Liu CH, Liu CK, Lin YJ, Wang HH, Yao A, Chen YT, Hsu CN. PMID: 16845089; PMCID: PMC1538865.
    View in: PubMed Mentions: 255 Fields:

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