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Lana Garmire, PhD

Faculty RankAssistant Professor
InstitutionUniversity of Hawaii
AddressUniversity of Hawaii Cancer Center
701 Ilalo St
Honolulu HI 96813
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    R01HD084633     (GARMIRE, LANA X)Aug 19, 2016 - Jul 31, 2021
    An Integrative Omics Approach to Identify Biomarkers Related to Preeclampsia and Breast Cancer Risks
    Role: Principal Investigator

    K01ES025434     (GARMIRE, LANA X)Apr 1, 2019 - Jun 30, 2020
    An Integrative Bioinformatics Approach to Study Single Cancer Cell Heterogeneity
    Role: Principal Investigator

    R01LM012373     (GARMIRE, LANA X)Jul 19, 2019 - Aug 31, 2021
    An Integrative Bioinformatics Platform with Application in Single Cancer Cells
    Role: Principal Investigator

    R01LM012907     (GARMIRE, LANA X)Sep 21, 2019 - May 31, 2022
    DR. EPS: Drug Repurposing for Extended Patient Survival
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    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. Li H, Huang Q, Liu Y, Garmire LX. Single cell transcriptome research in human placenta. Reproduction. 2020 12; 160(6):R155-R167. PMID: 33112783.
      Citations:    Fields:    
    2. Brito JJ, Li J, Moore JH, Greene CS, Nogoy NA, Garmire LX, Mangul S. Corrigendum to: Recommendations to enhance rigor and reproducibility in biomedical research. Gigascience. 2020 Sep 17; 9(9). PMID: 32940333.
      Citations:    Fields:    
    3. He B, Garmire L. Prediction of repurposed drugs for treating lung injury in COVID-19. F1000Res. 2020; 9:609. PMID: 32934806.
      Citations: 3     Fields:    Translation:HumansCellsPHPublic Health
    4. Brito JJ, Li J, Moore JH, Greene CS, Nogoy NA, Garmire LX, Mangul S. Recommendations to enhance rigor and reproducibility in biomedical research. Gigascience. 2020 Jun 01; 9(6). PMID: 32479592.
      Citations: 1     Fields:    
    5. Du Y, Huang Q, Arisdakessian C, Garmire LX. Evaluation of STAR and Kallisto on Single Cell RNA-Seq Data Alignment. G3 (Bethesda). 2020 05 04; 10(5):1775-1783. PMID: 32220951.
      Citations:    Fields:    
    6. He B, Garmire L. Prediction of repurposed drugs for treating lung injury in COVID-19. ArXiv. 2020 Mar 30. PMID: 32550243.
    7. Chen B, Garmire L, Calvisi DF, Chua MS, Kelley RK, Chen X. Publisher Correction: Harnessing big 'omics' data and AI for drug discovery in hepatocellular carcinoma. Nat Rev Gastroenterol Hepatol. 2020 Mar 11. PMID: 32161375.
      Citations:    Fields:    
    8. Schlueter RJ, Al-Akwaa FM, Benny PA, Gurary A, Xie G, Jia W, Chun SJ, Chern I, Garmire LX. Prepregnant Obesity of Mothers in a Multiethnic Cohort Is Associated with Cord Blood Metabolomic Changes in Offspring. J Proteome Res. 2020 04 03; 19(4):1361-1374. PMID: 31975597.
      Citations:    Fields:    
    9. Benny PA, Alakwaa FM, Schlueter RJ, Lassiter CB, Garmire LX. A review of omics approaches to study preeclampsia. Placenta. 2020 03; 92:17-27. PMID: 32056783.
      Citations: 2     Fields:    
    10. Chen B, Garmire L, Calvisi DF, Chua MS, Kelley RK, Chen X. Harnessing big 'omics' data and AI for drug discovery in hepatocellular carcinoma. Nat Rev Gastroenterol Hepatol. 2020 04; 17(4):238-251. PMID: 31900465.
      Citations: 4     Fields:    Translation:HumansAnimalsCells
    11. Liu Q, Ha MJ, Bhattacharyya R, Garmire L, Baladandayuthapani V. Network-Based Matching of Patients and Targeted Therapies for Precision Oncology. Pac Symp Biocomput. 2020; 25:623-634. PMID: 31797633.
      Citations:    Fields:    
    12. Garmire LX. From Hawaii to PECASE award: tips of success from a female bioinformatician. Genome Biol. 2019 12 12; 20(1):271. PMID: 31831020.
      Citations:    Fields:    Translation:Humans
    13. Arisdakessian C, Poirion O, Yunits B, Zhu X, Garmire LX. DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data. Genome Biol. 2019 10 18; 20(1):211. PMID: 31627739.
      Citations: 18     Fields:    
    14. Benny P, Yamasato K, Yunits B, Zhu X, Ching T, Garmire LX, Berry MJ, Towner D. Maternal cardiovascular-related single nucleotide polymorphisms, genes, and pathways associated with early-onset preeclampsia. PLoS One. 2019; 14(9):e0222672. PMID: 31557190.
      Citations: 1     Fields:    Translation:Humans
    15. Olender J, Wang BD, Ching T, Garmire LX, Garofano K, Ji Y, Knox T, Latham P, Nguyen K, Rhim J, Lee NH. A Novel FGFR3 Splice Variant Preferentially Expressed in African American Prostate Cancer Drives Aggressive Phenotypes and Docetaxel Resistance. Mol Cancer Res. 2019 10; 17(10):2115-2125. PMID: 31266816.
      Citations:    Fields:    Translation:HumansAnimalsCells
    16. Taylor DM, Aronow BJ, Tan K, Bernt K, Salomonis N, Greene CS, Frolova A, Henrickson SE, Wells A, Pei L, Jaiswal JK, Whitsett J, Hamilton KE, MacParland SA, Kelsen J, Heuckeroth RO, Potter SS, Vella LA, Terry NA, Ghanem LR, Kennedy BC, Helbig I, Sullivan KE, Castelo-Soccio L, Kreigstein A, Herse F, Nawijn MC, Koppelman GH, Haendel M, Harris NL, Rokita JL, Zhang Y, Regev A, Rozenblatt-Rosen O, Rood JE, Tickle TL, Vento-Tormo R, Alimohamed S, Lek M, Mar JC, Loomes KM, Barrett DM, Uapinyoying P, Beggs AH, Agrawal PB, Chen YW, Muir AB, Garmire LX, Snapper SB, Nazarian J, Seeholzer SH, Fazelinia H, Singh LN, Faryabi RB, Raman P, Dawany N, Xie HM, Devkota B, Diskin SJ, Anderson SA, Rappaport EF, Peranteau W, Wikenheiser-Brokamp KA, Teichmann S, Wallace D, Peng T, Ding YY, Kim MS, Xing Y, Kong SW, Bönnemann CG, Mandl KD, White PS. The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Dev Cell. 2019 04 08; 49(1):10-29. PMID: 30930166.
      Citations: 5     Fields:    Translation:Humans
    17. Al-Akwaa FM, Yunits B, Huang S, Alhajaji H, Garmire LX. Lilikoi: an R package for personalized pathway-based classification modeling using metabolomics data. Gigascience. 2018 12 01; 7(12). PMID: 30535020.
      Citations: 4     Fields:    Translation:Humans
    18. Poirion O, Zhu X, Ching T, Garmire LX. Using single nucleotide variations in single-cell RNA-seq to identify subpopulations and genotype-phenotype linkage. Nat Commun. 2018 11 20; 9(1):4892. PMID: 30459309.
      Citations: 9     Fields:    Translation:Humans
    19. Chaudhary K, Poirion OB, Lu L, Huang S, Ching T, Garmire LX. Multimodal Meta-Analysis of 1,494 Hepatocellular Carcinoma Samples Reveals Significant Impact of Consensus Driver Genes on Phenotypes. Clin Cancer Res. 2019 01 15; 25(2):463-472. PMID: 30242023.
      Citations: 8     Fields:    Translation:HumansCells
    20. Stein-O'Brien GL, Arora R, Culhane AC, Favorov AV, Garmire LX, Greene CS, Goff LA, Li Y, Ngom A, Ochs MF, Xu Y, Fertig EJ. Enter the Matrix: Factorization Uncovers Knowledge from Omics. Trends Genet. 2018 10; 34(10):790-805. PMID: 30143323.
      Citations: 19     Fields:    Translation:Humans
    21. Poirion OB, Chaudhary K, Garmire LX. Deep Learning data integration for better risk stratification models of bladder cancer. AMIA Jt Summits Transl Sci Proc. 2018; 2017:197-206. PMID: 29888072.
    22. Ching T, Zhu X, Garmire LX. Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data. PLoS Comput Biol. 2018 04; 14(4):e1006076. PMID: 29634719.
      Citations: 21     Fields:    Translation:Humans
    23. Ching T, Garmire LX. Pan-cancer analysis of expressed somatic nucleotide variants in long intergenic non-coding RNA. Pac Symp Biocomput. 2018; 23:512-523. PMID: 29218910.
      Citations: 1     Fields:    Translation:HumansCells
    24. Ortega MA, Poirion O, Zhu X, Huang S, Wolfgruber TK, Sebra R, Garmire LX. Using single-cell multiple omics approaches to resolve tumor heterogeneity. Clin Transl Med. 2017 Dec 28; 6(1):46. PMID: 29285690.
    25. Zhu X, Wolfgruber TK, Tasato A, Arisdakessian C, Garmire DG, Garmire LX. Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists. Genome Med. 2017 Dec 05; 9(1):108. PMID: 29202807.
      Citations: 13     Fields:    
    26. Alakwaa FM, Chaudhary K, Garmire LX. Deep Learning Accurately Predicts Estrogen Receptor Status in Breast Cancer Metabolomics Data. J Proteome Res. 2018 01 05; 17(1):337-347. PMID: 29110491.
      Citations: 18     Fields:    Translation:Humans
    27. Chaudhary K, Poirion OB, Lu L, Garmire LX. Deep Learning-Based Multi-Omics Integration Robustly Predicts Survival in Liver Cancer. Clin Cancer Res. 2018 03 15; 24(6):1248-1259. PMID: 28982688.
      Citations: 76     Fields:    Translation:HumansCells
    28. Wang BD, Ceniccola K, Hwang S, Andrawis R, Horvath A, Freedman JA, Olender J, Knapp S, Ching T, Garmire L, Patel V, Garcia-Blanco MA, Patierno SR, Lee NH. Corrigendum: Alternative splicing promotes tumour aggressiveness and drug resistance in African American prostate cancer. Nat Commun. 2017 09 27; 8:16161. PMID: 28952599.
      Citations:    Fields:    
    29. Wang BD, Ceniccola K, Hwang S, Andrawis R, Horvath A, Freedman JA, Olender J, Knapp S, Ching T, Garmire L, Patel V, Garcia-Blanco MA, Patierno SR, Lee NH. Alternative splicing promotes tumour aggressiveness and drug resistance in African American prostate cancer. Nat Commun. 2017 06 30; 8:15921. PMID: 28665395.
      Citations: 23     Fields:    Translation:HumansAnimalsCells
    30. Huang S, Chaudhary K, Garmire LX. More Is Better: Recent Progress in Multi-Omics Data Integration Methods. Front Genet. 2017; 8:84. PMID: 28670325.
    31. Greene CS, Garmire LX, Gilbert JA, Ritchie MD, Hunter LE. Celebrating parasites. Nat Genet. 2017 03 30; 49(4):483-484. PMID: 28358134.
      Citations: 5     Fields:    Translation:Animals
    32. Yang J, Tanaka Y, Seay M, Li Z, Jin J, Garmire LX, Zhu X, Taylor A, Li W, Euskirchen G, Halene S, Kluger Y, Snyder MP, Park IH, Pan X, Weissman SM. Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors. Nucleic Acids Res. 2017 02 17; 45(3):1281-1296. PMID: 28003475.
      Citations: 15     Fields:    Translation:AnimalsCells
    33. Feng N, Wang Y, Zheng M, Yu X, Lin H, Ma RN, Shi O, Zheng X, Gao M, Yu H, Garmire L, Qian B. Genome-wide analysis of DNA methylation and their associations with long noncoding RNA/mRNA expression in non-small-cell lung cancer. Epigenomics. 2017 Jan 23. PMID: 28111977.
      Citations: 4     Fields:    
    34. Zhu X, Ching T, Pan X, Weissman SM, Garmire L. Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization. PeerJ. 2017; 5:e2888. PMID: 28133571.
    35. Garmire LX, Gliske S, Nguyen QC, Chen JH, Nemati S, VAN Horn JD, Moore JH, Shreffler C, Dunn M. THE TRAINING OF NEXT GENERATION DATA SCIENTISTS IN BIOMEDICINE. Pac Symp Biocomput. 2017; 22:640-645. PMID: 27897014.
      Citations: 2     Fields:    Translation:HumansPHPublic Health
    36. Lu L, McCurdy S, Huang S, Zhu X, Peplowska K, Tiirikainen M, Boisvert WA, Garmire LX. Time Series miRNA-mRNA integrated analysis reveals critical miRNAs and targets in macrophage polarization. Sci Rep. 2016 12 16; 6:37446. PMID: 27981970.
      Citations: 11     Fields:    Translation:AnimalsCells
    37. Feng N, Ching T, Wang Y, Liu B, Lin H, Shi O, Zhang X, Zheng M, Zheng X, Gao M, Zheng ZJ, Yu H, Garmire L, Qian B. Analysis of Microarray Data on Gene Expression and Methylation to Identify Long Non-coding RNAs in Non-small Cell Lung Cancer. Sci Rep. 2016 11 16; 6:37233. PMID: 27849024.
      Citations: 7     Fields:    Translation:HumansCells
    38. Poirion OB, Zhu X, Ching T, Garmire L. Single-Cell Transcriptomics Bioinformatics and Computational Challenges. Front Genet. 2016; 7:163. PMID: 27708664.
    39. Wei R, De Vivo I, Huang S, Zhu X, Risch H, Moore JH, Yu H, Garmire LX. Meta-dimensional data integration identifies critical pathways for susceptibility, tumorigenesis and progression of endometrial cancer. Oncotarget. 2016 Aug 23; 7(34):55249-55263. PMID: 27409342.
      Citations: 7     Fields:    Translation:Humans
    40. Huang S, Kou L, Furuya H, Yu C, Goodison S, Kattan MW, Garmire L, Rosser CJ. A Nomogram Derived by Combination of Demographic and Biomarker Data Improves the Noninvasive Evaluation of Patients at Risk for Bladder Cancer. Cancer Epidemiol Biomarkers Prev. 2016 09; 25(9):1361-6. PMID: 27383773.
      Citations: 2     Fields:    Translation:Humans
    41. Huang S, Chong N, Lewis NE, Jia W, Xie G, Garmire LX. Novel personalized pathway-based metabolomics models reveal key metabolic pathways for breast cancer diagnosis. Genome Med. 2016 Mar 31; 8(1):34. PMID: 27036109.
      Citations: 33     Fields:    Translation:Humans
    42. Ching T, Peplowska K, Huang S, Zhu X, Shen Y, Molnar J, Yu H, Tiirikainen M, Fogelgren B, Fan R, Garmire LX. Pan-Cancer Analyses Reveal Long Intergenic Non-Coding RNAs Relevant to Tumor Diagnosis, Subtyping and Prognosis. EBioMedicine. 2016 May; 7:62-72. PMID: 27322459.
      Citations: 12     Fields:    Translation:HumansCells
    43. Ching T, Masaki J, Weirather J, Garmire LX. Non-coding yet non-trivial: a review on the computational genomics of lincRNAs. BioData Min. 2015; 8:44. PMID: 26697116.
    44. Xie G, Zhou B, Zhao A, Qiu Y, Zhao X, Garmire L, Shvetsov YB, Yu H, Yen Y, Jia W. Lowered circulating aspartate is a metabolic feature of human breast cancer. Oncotarget. 2015 Oct 20; 6(32):33369-81. PMID: 26452258.
      Citations: 13     Fields:    Translation:HumansCells
    45. Gagliani N, Amezcua Vesely MC, Iseppon A, Brockmann L, Xu H, Palm NW, de Zoete MR, Licona-Limón P, Paiva RS, Ching T, Weaver C, Zi X, Pan X, Fan R, Garmire LX, Cotton MJ, Drier Y, Bernstein B, Geginat J, Stockinger B, Esplugues E, Huber S, Flavell RA. Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation. Nature. 2015 Jul 09; 523(7559):221-5. PMID: 25924064.
      Citations: 193     Fields:    Translation:AnimalsCells
    46. Li J, Ching T, Huang S, Garmire LX. Using epigenomics data to predict gene expression in lung cancer. BMC Bioinformatics. 2015; 16 Suppl 5:S10. PMID: 25861082.
      Citations: 12     Fields:    Translation:HumansCells
    47. Ching T, Ha J, Song MA, Tiirikainen M, Molnar J, Berry MJ, Towner D, Garmire LX. Genome-scale hypomethylation in the cord blood DNAs associated with early onset preeclampsia. Clin Epigenetics. 2015; 7:21. PMID: 25806090.
      Citations: 14     Fields:    
    48. Han L, Zi X, Garmire LX, Wu Y, Weissman SM, Pan X, Fan R. Co-detection and sequencing of genes and transcripts from the same single cells facilitated by a microfluidics platform. Sci Rep. 2014 Sep 26; 4:6485. PMID: 25255798.
      Citations: 18     Fields:    Translation:HumansCells
    49. Ching T, Huang S, Garmire LX. Power analysis and sample size estimation for RNA-Seq differential expression. RNA. 2014 Nov; 20(11):1684-96. PMID: 25246651.
      Citations: 64     Fields:    Translation:HumansAnimals
    50. Huang S, Yee C, Ching T, Yu H, Garmire LX. A novel model to combine clinical and pathway-based transcriptomic information for the prognosis prediction of breast cancer. PLoS Comput Biol. 2014 Sep; 10(9):e1003851. PMID: 25233347.
      Citations: 30     Fields:    Translation:HumansCells
    51. Ching T, Song MA, Tiirikainen M, Molnar J, Berry M, Towner D, Garmire LX. Genome-wide hypermethylation coupled with promoter hypomethylation in the chorioamniotic membranes of early onset pre-eclampsia. Mol Hum Reprod. 2014 Sep; 20(9):885-904. PMID: 24944161.
      Citations: 15     Fields:    Translation:HumansCells
    52. Yahirun JJ, Hamplová D. CHILDREN'S UNION STATUS AND CONTACT WITH MOTHERS: A CROSS-NATIONAL STUDY. Demogr Res. 2014 Jan-Jun; 30:1413-1444. PMID: 23021221.
      Citations: 164     Fields:    Translation:AnimalsCells
    53. Menor M, Ching T, Zhu X, Garmire D, Garmire LX. mirMark: a site-level and UTR-level classifier for miRNA target prediction. Genome Biol. 2014; 15(10):500. PMID: 25344330.
      Citations: 6     Fields:    
    54. Garmire LX, Subramaniam S. The poor performance of TMM on microRNA-Seq. RNA. 2013 Jun; 19(6):735-6. PMID: 23616641.
      Citations: 3     Fields:    Translation:Animals
    55. Hadd AG, Houghton J, Choudhary A, Sah S, Chen L, Marko AC, Sanford T, Buddavarapu K, Krosting J, Garmire L, Wylie D, Shinde R, Beaudenon S, Alexander EK, Mambo E, Adai AT, Latham GJ. Targeted, high-depth, next-generation sequencing of cancer genes in formalin-fixed, paraffin-embedded and fine-needle aspiration tumor specimens. J Mol Diagn. 2013 Mar; 15(2):234-47. PMID: 23321017.
      Citations: 79     Fields:    Translation:HumansCells
    56. Wu Y, Garmire LX, Fan R. Inter-cellular signaling network reveals a mechanistic transition in tumor microenvironment. Integr Biol (Camb). 2012 Dec; 4(12):1478-86. PMID: 23080410.
      Citations: 7     Fields:    Translation:HumansCells
    57. Colas AR, McKeithan WL, Cunningham TJ, Bushway PJ, Garmire LX, Duester G, Subramaniam S, Mercola M. Whole-genome microRNA screening identifies let-7 and mir-18 as regulators of germ layer formation during early embryogenesis. Genes Dev. 2012 Dec 01; 26(23):2567-79. PMID: 23152446.
      Citations: 24     Fields:    Translation:AnimalsCells
    58. Garmire LX, Subramaniam S. Evaluation of normalization methods in mammalian microRNA-Seq data. RNA. 2012 Jun; 18(6):1279-88. PMID: 22532701.
      Citations: 43     Fields:    Translation:Animals
    59. Garmire LX, Garmire DG, Huang W, Yao J, Glass CK, Subramaniam S. A global clustering algorithm to identify long intergenic non-coding RNA--with applications in mouse macrophages. PLoS One. 2011; 6(9):e24051. PMID: 21980340.
      Citations: 19     Fields:    Translation:HumansAnimalsCells
    60. Wang KC, Garmire LX, Young A, Nguyen P, Trinh A, Subramaniam S, Wang N, Shyy JY, Li YS, Chien S. Role of microRNA-23b in flow-regulation of Rb phosphorylation and endothelial cell growth. Proc Natl Acad Sci U S A. 2010 Feb 16; 107(7):3234-9. PMID: 20133741.
      Citations: 69     Fields:    Translation:HumansCells
    61. Garmire LX, Shen Z, Briggs S, Yeo G, Subramaniam S, Glass C. Regulatory network of microRNAs in RAW 264.7 macrophage cells. Annu Int Conf IEEE Eng Med Biol Soc. 2010; 2010:6198-201. PMID: 21097158.
    62. Garmire LX, Hunt CA. In silico methods for unraveling the mechanistic complexities of intestinal absorption: metabolism-efflux transport interactions. Drug Metab Dispos. 2008 Jul; 36(7):1414-24. PMID: 18436618.
      Citations: 1     Fields:    
    63. Garmire LX, Garmire DG, Hunt CA. An in silico transwell device for the study of drug transport and drug-drug interactions. Pharm Res. 2007 Dec; 24(12):2171-86. PMID: 17703347.
      Citations: 5     Fields:    Translation:HumansAnimalsCells
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