Works by Garmire, Lana X

Results: 33

Co-detection and sequencing of genes and transcripts from the same single cells facilitated by a microfluidics platform.

Published in:

Scientific Reports, 2014, p. 1, doi. 10.1038/srep06485

By:

Lin Han;
Xiaoyuan Zi;
Garmire, Lana X.;
Yu Wu;
Weissman, Sherman M.;
Xinghua Pan;
Rong Fan

Publication type:

Article

Maternal plasma lipids are involved in the pathogenesis of preterm birth.

Published in:

GigaScience, 2022, v. 11, p. 1, doi. 10.1093/gigascience/giac004

By:

Chen, Yile;
He, Bing;
Liu, Yu;
Aung, Max T;
Rosario-Pabón, Zaira;
Vélez-Vega, Carmen M;
Alshawabkeh, Akram;
Cordero, José F;
Meeker, John D;
Garmire, Lana X

Publication type:

Article

Lilikoi V2.0: a deep learning–enabled, personalized pathway-based R package for diagnosis and prognosis predictions using metabolomics data.

Published in:

GigaScience, 2021, v. 10, n. 1, p. 1, doi. 10.1093/gigascience/giaa162

By:

Fang, Xinying;
Liu, Yu;
Ren, Zhijie;
Du, Yuheng;
Huang, Qianhui;
Garmire, Lana X

Publication type:

Article

Lilikoi: an R package for personalized pathway-based classification modeling using metabolomics data.

Published in:

GigaScience, 2018, v. 7, n. 12, p. N.PAG, doi. 10.1093/gigascience/giy136

By:

Al-Akwaa, Fadhl M;
Yunits, Breck;
Huang, Sijia;
Alhajaji, Hassam;
Garmire, Lana X

Publication type:

Article

Predicting interval from diagnosis to delivery in preeclampsia using electronic health records.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-58437-7

By:

Yang, Xiaotong;
Ballard, Hailey K.;
Mahadevan, Aditya D.;
Xu, Ke;
Garmire, David G.;
Langen, Elizabeth S.;
Lemas, Dominick J.;
Garmire, Lana X.

Publication type:

Article

Mentorship is not co-authorship: a revisit to mentorship.

Published in:

2021

By:

Garmire, Lana X.

Publication type:

Editorial

From Hawaii to PECASE award: tips of success from a female bioinformatician.

Published in:

2019

By:

Garmire, Lana X.

Publication type:

Editorial

DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1837-6

By:

Arisdakessian, Cédric;
Poirion, Olivier;
Yunits, Breck;
Zhu, Xun;
Garmire, Lana X.

Publication type:

Article

Placentas delivered by pre-pregnant obese women have reduced abundance and diversity in the microbiome.

Published in:

FASEB Journal, 2021, v. 35, n. 4, p. 1, doi. 10.1096/fj.202002184RR

By:

Benny, Paula A.;
Al-Akwaa, Fadhl M.;
Dirkx, Corbin;
Schlueter, Ryan J.;
Wolfgruber, Thomas K.;
Chern, Ingrid Y.;
Hoops, Suzie;
Knights, Dan;
Garmire, Lana X.

Publication type:

Article

Cox-nnet v2.0: improved neural-network-based survival prediction extended to large-scale EMR data.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2772, doi. 10.1093/bioinformatics/btab046

By:

Wang, Di;
Jing, Zheng;
He, Kevin;
Garmire, Lana X.

Publication type:

Article

Single-cell RNA-seq data have prevalent blood contamination but can be rescued by Originator, a computational tool separating single-cell RNA-seq by genetic and contextual information.

Published in:

Genome Biology, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s13059-025-03495-9

By:

Unjitwattana, Thatchayut;
Huang, Qianhui;
Yang, Yiwen;
Tao, Leyang;
Yang, Youqi;
Zhou, Mengtian;
Du, Yuheng;
Garmire, Lana X.

Publication type:

Article

Maternal cardiovascular-related single nucleotide polymorphisms, genes, and pathways associated with early-onset preeclampsia.

Published in:

PLoS ONE, 2019, v. 14, n. 9, p. 1, doi. 10.1371/journal.pone.0222672

By:

Benny, Paula;
Yamasato, Kelly;
Yunits, Breck;
Zhu, Xun;
Ching, Travers;
Garmire, Lana X.;
Berry, Marla J.;
Towner, Dena

Publication type:

Article

Genome-wide hypermethylation coupled with promoter hypomethylation in the chorioamniotic membranes of early onset pre-eclampsia.

Published in:

Molecular Human Reproduction, 2014, v. 20, n. 9, p. 885, doi. 10.1093/molehr/gau046

By:

Ching, Travers;
Song, Min-Ae;
Tiirikainen, Maarit;
Molnar, Janos;
Berry, Marla;
Towner, Dena;
Garmire, Lana X.

Publication type:

Article

Evaluation of STAR and Kallisto on Single Cell RNA-Seq Data Alignment.

Published in:

G3: Genes | Genomes | Genetics, 2020, v. 10, n. 5, p. 1775, doi. 10.1534/g3.120.401160

By:

Yuheng Du;
Qianhui Huang;
Arisdakessian, Cedric;
Garmire, Lana X.

Publication type:

Article

Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty.

Published in:

NPJ Precision Oncology, 2022, v. 6, n. 1, p. 1, doi. 10.1038/s41698-022-00283-7

By:

Badowski, Cedric;
He, Bing;
Garmire, Lana X.

Publication type:

Article

BML: a versatile web server for bipartite motif discovery.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab536

By:

Vahed, Mohammad;
Vahed, Majid;
Garmire, Lana X

Publication type:

Article

ASGARD is A Single-cell Guided Pipeline to Aid Repurposing of Drugs.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-36637-3

By:

He, Bing;
Xiao, Yao;
Liang, Haodong;
Huang, Qianhui;
Du, Yuheng;
Li, Yijun;
Garmire, David;
Sun, Duxin;
Garmire, Lana X.

Publication type:

Article

Prediction of spontaneous preterm birth using supervised machine learning on metabolomic data: A case–cohort study.

Published in:

BJOG: An International Journal of Obstetrics & Gynaecology, 2024, v. 131, n. 7, p. 908, doi. 10.1111/1471-0528.17723

By:

Al Ghadban, Yasmina;
Du, Yuheng;
Charnock‐Jones, D. Stephen;
Garmire, Lana X.;
Smith, Gordon C. S.;
Sovio, Ulla

Publication type:

Article

Five-Feature Models to Predict Preeclampsia Onset Time From Electronic Health Record Data: Development and Validation Study.

Published in:

Journal of Medical Internet Research, 2024, v. 26, p. 1, doi. 10.2196/48997

By:

Ballard, Hailey K;
Yang, Xiaotong;
Mahadevan, Aditya D;
Lemas, Dominick J;
Garmire, Lana X

Publication type:

Article

Non-coding yet non-trivial: a review on the computational genomics of lincRNAs.

Published in:

BioData Mining, 2015, v. 8, p. 1, doi. 10.1186/s13040-015-0075-z

By:

Ching, Travers;
Masaki, Jayson;
Weirather, Jason;
Garmire, Lana X.

Publication type:

Article

DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data.

Published in:

Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-021-00930-x

By:

Poirion, Olivier B.;
Jing, Zheng;
Chaudhary, Kumardeep;
Huang, Sijia;
Garmire, Lana X.

Publication type:

Article

A Novel Model to Combine Clinical and Pathway-Based Transcriptomic Information for the Prognosis Prediction of Breast Cancer.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 9, p. 1, doi. 10.1371/journal.pcbi.1003851

By:

Huang, Sijia;
Yee, Cameron;
Ching, Travers;
Yu, Herbert;
Garmire, Lana X.

Publication type:

Article

Using single nucleotide variations in single-cell RNA-seq to identify subpopulations and genotype-phenotype linkage.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-07170-5

By:

Poirion, Olivier;
Zhu, Xun;
Ching, Travers;
Garmire, Lana X.

Publication type:

Article

mirMark: a site-level and UTR-level classifier for miRNA target prediction.

Published in:

Genome Biology, 2014, v. 15, n. 10, p. 1, doi. 10.1186/s13059-014-0500-5

By:

Menor, Mark;
Ching, Travers;
Xun Zhu;
Garmire, David;
Garmire, Lana X.

Publication type:

Article

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists.

Published in:

Genome Medicine, 2017, v. 9, p. 1, doi. 10.1186/s13073-017-0492-3

By:

Xun Zhu;
Wolfgruber, Thomas K.;
Tasato, Austin;
Arisdakessian, Cédric;
Garmire, David G.;
Garmire, Lana X.

Publication type:

Article

Novel personalized pathway-based metabolomics models reveal key metabolic pathways for breast cancer diagnosis.

Published in:

Genome Medicine, 2016, v. 8, p. 1, doi. 10.1186/s13073-016-0289-9

By:

Sijia Huang;
Chong, Nicole;
Lewis, Nathan E.;
Wei Jia;
Guoxiang Xie;
Garmire, Lana X.

Publication type:

Article

Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data.

Published in:

PLoS Computational Biology, 2018, v. 14, n. 4, p. 1, doi. 10.1371/journal.pcbi.1006076

By:

Ching, Travers;
Zhu, Xun;
Garmire, Lana X.

Publication type:

Article

Using single‐cell multiple omics approaches to resolve tumor heterogeneity.

Published in:

Clinical & Translational Medicine, 2017, v. 6, n. 1, p. 1, doi. 10.1186/s40169-017-0177-y

By:

Ortega, Michael A.;
Poirion, Olivier;
Zhu, Xun;
Huang, Sijia;
Wolfgruber, Thomas K.;
Sebra, Robert;
Garmire, Lana X.

Publication type:

Article

Inter-cellular signaling network reveals a mechanistic transition in tumor microenvironment.

Published in:

Integrative Biology, 2012, v. 4, n. 12, p. 1478, doi. 10.1039/c2ib20044a

By:

Wu, Yu;
Garmire, Lana X.;
Fan, Rong

Publication type:

Article

A Global Clustering Algorithm to Identify Long Intergenic Non-Coding RNA - with Applications in Mouse Macrophages.

Published in:

PLoS ONE, 2011, v. 6, n. 9, p. 1, doi. 10.1371/journal.pone.0024051

By:

Garmire, Lana X.;
Garmire, David G.;
Huang, Wendy;
Yao, Joyee;
Glass, Christopher K.;
Subramaniam, Shankar

Publication type:

Article

Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation.

Published in:

Nature, 2015, v. 523, n. 7559, p. 221, doi. 10.1038/nature14452

By:

Gagliani, Nicola;
Vesely, Maria Carolina Amezcua;
Iseppon, Andrea;
Brockmann, Leonie;
Xu, Hao;
Palm, Noah W.;
de Zoete, Marcel R.;
Licona-Limón, Paula;
Paiva, Ricardo S.;
Ching, Travers;
Weaver, Casey;
Zi, Xiaoyuan;
Pan, Xinghua;
Fan, Rong;
Garmire, Lana X.;
Cotton, Matthew J.;
Drier, Yotam;
Bernstein, Bradley;
Geginat, Jens;
Stockinger, Brigitta

Publication type:

Article

Time Series miRNA-mRNA integrated analysis reveals critical miRNAs and targets in macrophage polarization.

Published in:

Scientific Reports, 2016, p. 37446, doi. 10.1038/srep37446

By:

Lu, Liangqun;
McCurdy, Sara;
Huang, Sijia;
Zhu, Xun;
Peplowska, Karolina;
Tiirikainen, Maarit;
Boisvert, William A.;
Garmire, Lana X.

Publication type:

Article

Heterogeneity of neutrophils and inflammatory responses in patients with COVID-19 and healthy controls.

Published in:

Frontiers in Immunology, 2022, v. 13, p. 01, doi. 10.3389/fimmu.2022.970287

By:

Jintao Xu;
Bing He;
Carver, Kyle;
Vanheyningen, Debora;
Parkin, Brian;
Garmire, Lana X.;
Olszewski, Michal A.;
Deng, Jane C.

Publication type:

Article