Publications

2020:5

1. Nature methods

   Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition

   Ouyang Wei, Winsnes Casper F, Hjelmare Martin, Cesnik Anthony J, Åkesson Lovisa, Xu Hao, Sullivan Devin P, Dai Shubin, Lan Jun, Jinmo Park, others

   Nature methods 2020
2. NATURE METHODS

   Analysis of the Human Protein Atlas Image Classification competition (vol 54, pg 2112, 2019)

   Ouyang Wei, Winsnes Casper F, Hjelmare Martin, Cesnik Anthony J, Akesson Lovisa, Xu Hao, Sullivan Devin P, Dai Shubin, Lan Jun, Jinmo Park, others

   NATURE METHODS 2020
3. Nature Methods

   Author Correction: Analysis of the Human Protein Atlas Image Classification competition

   Ouyang Wei, Winsnes Casper F, Hjelmare Martin, Cesnik Anthony J, Åkesson Lovisa, Xu Hao, Sullivan Devin P, Dai Shubin, Lan Jun, Jinmo Park, others

   Nature Methods 2020
4. NATURE METHODS

   Analysis of the Human Protein Atlas Image Classification competition (vol 53, pg 961, 2019)

   Ouyang Wei, Winsnes Casper F, Hjelmare Martin, Cesnik Anthony J, Akesson Lovisa, Xu Hao, Sullivan Devin P, Dai Shubin, Lan Jun, Jinmo Park, others

   NATURE METHODS 2020
5. NATURE METHODS

   Analysis of the Human Protein Atlas Image Classification competition (vol 16, pg 1254, 2019)

   Ouyang Wei, Winsnes Casper F, Hjelmare Martin, Cesnik Anthony J, Akesson Lovisa, Xu Hao, Sullivan Devin P, Dai Shubin, Lan Jun, Jinmo Park, others

   NATURE METHODS 2020

2019:5

1. Genome biology

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

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

   Genome biology 2019
2. bioRxiv

   GranatumX: A community engaging and flexible software environment for single-cell analysis

   Zhu Xun, Yunits Breck, Wolfgruber Thomas, Liu Yu, Huang Qianhui, Poirion Olivier, Arisdakessian Cédric, Zhao Tianying, Garmire David, Garmire Lana

   bioRxiv 2019
3. BookChapter

   Data Analysis in Single-Cell RNA-Seq

   Zhu Xun, Garmire Lana X

   2019
4. PloS one

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

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

   PloS one 2019
5. Nature methods

   Analysis of the human protein atlas image classification competition

   Ouyang Wei, Winsnes Casper F, Hjelmare Martin, Cesnik Anthony J, Åkesson Lovisa, Xu Hao, Sullivan Devin P, Dai Shubin, Lan Jun, Jinmo Park, others

   Nature methods 2019

2018:2

1. PLoS computational b

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

   Ching Travers, Zhu Xun, Garmire Lana X

   PLoS computational biology 2018
2. Nature communication

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

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

   Nature communications 2018

2017:4

1. Genome medicine

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

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

   Genome medicine 2017
2. PeerJ

   Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization

   Zhu Xun, Ching Travers, Pan Xinghua, Weissman Sherman M, Garmire Lana

   PeerJ 2017
3. Nucleic acids resear

   Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors

   Yang Jennifer, Tanaka Yoshiaki, Seay Montrell, Li Zhen, Jin Jiaqi, Garmire Lana Xia, Zhu Xun, Taylor Ashley, Li Weidong, Euskirchen Ghia, others

   Nucleic acids research 2017
4. Clinical and transla

   Using single-cell multiple omics approaches to resolve tumor heterogeneity

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

   Clinical and translational medicine 2017

2016:6

1. Frontiers in genetic

   Single-cell transcriptomics bioinformatics and computational challenges

   Poirion Olivier B, Zhu Xun, Ching Travers, Garmire Lana

   Frontiers in genetics 2016
2. Oncotarget

   Meta-dimensional data integration identifies critical pathways for susceptibility, tumorigenesis and progression of endometrial cancer

   Wei Runmin, De Vivo Immaculata, Huang Sijia, Zhu Xun, Risch Harvey, Moore Jason H, Yu Herbert, Garmire Lana X

   Oncotarget 2016
3. EBioMedicine

   Pan-cancer analyses reveal long intergenic non-coding RNAs relevant to tumor diagnosis, subtyping and prognosis

   Ching Travers, Peplowska Karolina, Huang Sijia, Zhu Xun, Shen Yi, Molnar Janos, Yu Herbert, Tiirikainen Maarit, Fogelgren Ben, Fan Rong, others

   EBioMedicine 2016
4. Scientific reports

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

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

   Scientific reports 2016
5. bioRxiv

   Using Single Nucleotide Variations in Cancer Single-Cell RNA-Seq Data for Subpopulation Identification and Genotype-phenotype Linkage Analysis

   Poirion Olivier, Zhu Xun, Ching Travers, Garmire Lana

   bioRxiv 2016
6. bioRxiv

   Using Single Nucleotide Variations in Single-Cell RNA-Seq to Identify Tumor Subpopulations and Genotype-phenotype Linkage

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

   bioRxiv 2016