T. Ching

发表

Genome-scale hypomethylation in the cord blood DNAs associated with early onset preeclampsia

Maarit Tiirikainen, Lana X Garmire, Travers Ching, 2015, Clinical Epigenetics.

Power analysis and sample size estimation for RNA-Seq differential expression

Lana X Garmire, Travers Ching, Sijia Huang, 2014, RNA.

Opportunities and obstacles for deep learning in biology and medicine [update in progress]

Anne E Carpenter, Srinivas C. Turaga, Brett K. Beaulieu-Jones, 2020 .

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

S. Weissman, Xinghua Pan, Xun Zhu, 2017, PeerJ.

Multimodal Meta-Analysis of 1,494 Hepatocellular Carcinoma Samples Reveals Significant Impact of Consensus Driver Genes on Phenotypes

Kumardeep Chaudhary, Sijia Huang, L. Garmire, 2018, Clinical Cancer Research.

Analysis of Microarray Data on Gene Expression and Methylation to Identify Long Non-coding RNAs in Non-small Cell Lung Cancer

B. Qian, Herbert Yu, L. Garmire, 2016, Scientific Reports.

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

Xun Zhu, Lana X Garmire, Mark Menor, 2014, Genome Biology.

Opportunities and obstacles for deep learning in biology and medicine

Anne E Carpenter, Srinivas C. Turaga, Brett K. Beaulieu-Jones, 2017, bioRxiv.

Characterization of Plant Glycoproteins: Analysis of Plant Glycopeptide Mass Spectrometry Data with plantGlycoMS, a Package in the R Statistical Computing Environment.

Margaret R. Baker, D. Tabb, Qing X. Li, 2018, Methods in molecular biology.

Site-Specific N-Glycosylation Characterization of Windmill Palm Tree Peroxidase Using Novel Tools for Analysis of Plant Glycopeptide Mass Spectrometry Data.

Margaret R. Baker, D. Tabb, Qing X. Li, 2016, Journal of proteome research.

Opportunities and obstacles for deep learning in biology and medicine: 2019 update

Anne E Carpenter, Srinivas C. Turaga, Brett K. Beaulieu-Jones, 2019 .

A Novel FGFR3 Splice Variant Preferentially Expressed in African American Prostate Cancer Drives Aggressive Phenotypes and Docetaxel Resistance

J. Rhim, N. Lee, L. Garmire, 2019, Molecular Cancer Research.

Phenotypic associations of consensus driver genes in hepatocellular carcinoma

L. Garmire, T. Ching, Olivier B. Poirion, 2017 .

Pan-Cancer Analyses Reveal Long Intergenic Non-Coding RNAs Relevant to Tumor Diagnosis, Subtyping and Prognosis

M. Tiirikainen, Herbert Yu, R. Fan, 2016, EBioMedicine.

Cometabolic degradation of blended biodiesel by Moniliella wahieum Y12T and Byssochlamys nivea M1

Qing X. Li, T. Ching, S. Masutani, 2017 .

Glycerol-assisted degradation of dibenzothiophene by Paraburkholderia sp. C3 is associated with polyhydroxyalkanoate granulation

Qing X. Li, T. Ching, B. Yoza, 2021, Chemosphere.

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

Xun Zhu, L. Garmire, T. Ching, 2019, PloS one.

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

S. Weissman, Xinghua Pan, Xun Zhu, 2017, PeerJ.

Analytical evaluation of the clonoSEQ Assay for establishing measurable (minimal) residual disease in acute lymphoblastic leukemia, chronic lymphocytic leukemia, and multiple myeloma

R. Emerson, M. Vignali, B. Howie, 2020, BMC Cancer.

Alternative splicing promotes tumour aggressiveness and drug resistance in African American prostate cancer

S. Knapp, M. Garcia-Blanco, N. Lee, 2017, Nature Communications.

Detecting heterogeneity in single-cell RNA-Seq 1 data by non-negative matrix factorization 2 3

S. Weissman, Xinghua Pan, Xun Zhu, 2017 .

Minimal Residual Disease Dynamics after Venetoclax-Obinutuzumab Treatment: Extended Off-Treatment Follow-up From the Randomized CLL14 Study

M. Hallek, S. Stilgenbauer, K. Kreuzer, 2021, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation

B. Bernstein, Y. Drier, B. Stockinger, 2015, Nature.

Single-Cell Transcriptomics Bioinformatics and Computational Challenges

Travers Ching, Xun Zhu, Olivier B. Poirion, 2016, Front. Genet..

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

L. Garmire, T. Ching, Jason L. Weirather, 2015, BioData Mining.

Pan-cancer analysis of expressed somatic nucleotide variants in long intergenic non-coding RNA

Lana X. Garmire, Travers Ching, L. Garmire, 2018, PSB.

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

D. Garmire, Xun Zhu, L. Garmire, 2014, Genome Biology.

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

Xun Zhu, L. Garmire, T. Ching, 2016, bioRxiv.

Using epigenomics data to predict gene expression in lung cancer

Sijia Huang, L. Garmire, T. Ching, 2015, BMC Bioinformatics.

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

Maarit Tiirikainen, Lana X Garmire, Travers Ching, 2014, Molecular human reproduction.

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

Xun Zhu, Lana X. Garmire, Travers Ching, 2018, PLoS Comput. Biol..

Quartet Analysis of Putative Horizontal Gene Transfer in Crenarchaeota

Qing X. Li, T. Ching, B. Yoza, 2014, Journal of Molecular Evolution.

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

Lana X. Garmire, Travers Ching, Herbert Yu, 2014, PLoS Comput. Biol..

Human DBR1 modulates the recycling of snRNPs to affect alternative RNA splicing and contributes to the suppression of cancer development

P. Fei, L. Garmire, T. Ching, 2017, Oncogene.

Multi-modal meta-analysis of 1494 hepatocellular carcinoma samples reveals vast impacts of consensus driver genes on phenotypes

Kumardeep Chaudhary, Sijia Huang, L. Garmire, 2017, bioRxiv.

Biodegradation of biodiesel and microbiologically induced corrosion of 1018 steel by Moniliella wahieum Y12

L. Hihara, Qing X. Li, T. Ching, 2016 .

Clonal Dynamics after Venetoclax-Obinutuzumab Therapy: Novel Insights from the Randomized, Phase 3 CLL14 Trial

M. Hallek, S. Stilgenbauer, K. Kreuzer, 2020 .

Genome-scale hypomethylation in the cord blood DNAs associated with early onset preeclampsia

M. Tiirikainen, L. Garmire, T. Ching, 2015, Clinical Epigenetics.

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

Lana X. Garmire, Travers Ching, Jayson Masaki, 2015, BioData Mining.

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

Xun Zhu, L. Garmire, T. Ching, 2016, bioRxiv.

Multimodal, broadly neutralizing antibodies against SARS-CoV-2 identified by high-throughput native pairing of BCRs from bulk B cells.

Charles W. Linkem, Y. Liang, A. Carbo, 2023, Cell chemical biology.

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

Xun Zhu, Lana X Garmire, Travers Ching, 2016, Nature Communications.

Power analysis and sample size estimation for RNA-Seq differential expression

L. Garmire, T. Ching, Sijia Huang, 2014, RNA.

Using epigenomics data to predict gene expression in lung cancer

Lana X. Garmire, Travers Ching, Jeffery Li, 2015, BMC Bioinformatics.

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

Travers Ching, Xun Zhu, Lana X. Garmire, 2016, bioRxiv.

Quartet Analysis of Putative Horizontal Gene Transfer in Crenarchaeota

T. Ching, Qing X. Li, B. Yoza, 2013, Journal of Molecular Evolution.