المؤلفون: Dongyuan Song (5792477), Jingyi Jessica Li (10726220)

مصطلحات موضوعية: Genetics, ill-posed p-values, cell pseudotime, well-calibrated p-values, cell state changes, PseudotimeDE, real-data applications, pseudotime inference uncertainty, gene expression, outputs well-calibrated p-values, RNA sequencing data Abstract, discovery rate control, RNA-sequencing data, pseudotime inference methods, DE gene identification method, Comprehensive simulations

Relation: https://figshare.com/articles/journal_contribution/Additional_file_1_of_PseudotimeDE_inference_of_differential_gene_expression_along_cell_pseudotime_with_well-calibrated_p-values_from_single-cell_RNA_sequencing_data/14516081

الاتاحة: https://doi.org/10.6084/m9.figshare.14516081.v1

المؤلفون: Dongyuan Song (5792477), Jingyi Jessica Li (10726220)

مصطلحات موضوعية: Genetics, ill-posed p-values, cell pseudotime, well-calibrated p-values, cell state changes, PseudotimeDE, real-data applications, pseudotime inference uncertainty, gene expression, outputs well-calibrated p-values, RNA sequencing data Abstract, discovery rate control, RNA-sequencing data, pseudotime inference methods, DE gene identification method, Comprehensive simulations

Relation: https://figshare.com/articles/journal_contribution/Additional_file_5_of_PseudotimeDE_inference_of_differential_gene_expression_along_cell_pseudotime_with_well-calibrated_p-values_from_single-cell_RNA_sequencing_data/14516096

الاتاحة: https://doi.org/10.6084/m9.figshare.14516096.v1

المؤلفون: Shaoyi Ji (3108864), Ze Yang (446151), Leonardi Gozali (10751729), Thomas Kenney (1828366), Arif Kocabas (10751732), Carolyn Jinsook Park (10751735), Mary Hynes (10751738)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Ecology, Developmental Biology, Cancer, Hematology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, cell state changes, transition states Mature mRNA molecules, site genomic elements, CDS ratios, Unbiased transcriptome analysis, gene ontology categories, UTR, cell-specific gene expression

Relation: https://figshare.com/articles/figure/Progenitor_cells_show_distinctive_3_UTR_CDS_patterns_/14543702

الاتاحة: https://doi.org/10.1371/journal.pone.0250669.g002

المؤلفون: Shaoyi Ji (3108864), Ze Yang (446151), Leonardi Gozali (10751729), Thomas Kenney (1828366), Arif Kocabas (10751732), Carolyn Jinsook Park (10751735), Mary Hynes (10751738)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Ecology, Developmental Biology, Cancer, Hematology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, cell state changes, transition states Mature mRNA molecules, site genomic elements, CDS ratios, Unbiased transcriptome analysis, gene ontology categories, UTR, cell-specific gene expression

Relation: https://figshare.com/articles/figure/3_UTR_CDS_ratios_change_with_cell_state_/14543708

الاتاحة: https://doi.org/10.1371/journal.pone.0250669.g004

المؤلفون: Shaoyi Ji (3108864), Ze Yang (446151), Leonardi Gozali (10751729), Thomas Kenney (1828366), Arif Kocabas (10751732), Carolyn Jinsook Park (10751735), Mary Hynes (10751738)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Ecology, Developmental Biology, Cancer, Hematology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, cell state changes, transition states Mature mRNA molecules, site genomic elements, CDS ratios, Unbiased transcriptome analysis, gene ontology categories, UTR, cell-specific gene expression

Relation: https://figshare.com/articles/figure/Gene_elements_and_EST_sequences_correlate_with_3_UTR_sequence_peaks_and_valleys_/14543717

الاتاحة: https://doi.org/10.1371/journal.pone.0250669.g007

المؤلفون: Shaoyi Ji (3108864), Ze Yang (446151), Leonardi Gozali (10751729), Thomas Kenney (1828366), Arif Kocabas (10751732), Carolyn Jinsook Park (10751735), Mary Hynes (10751738)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Ecology, Developmental Biology, Cancer, Hematology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, cell state changes, transition states Mature mRNA molecules, site genomic elements, CDS ratios, Unbiased transcriptome analysis, gene ontology categories, UTR, cell-specific gene expression

Relation: https://figshare.com/articles/figure/The_3_UTR_CDS_ratio_for_PpG_and_other_genes_changes_abruptly_at_the_boundary_between_the_Ki67_proliferative_zone_and_non-proliferative_zone_/14543705

الاتاحة: https://doi.org/10.1371/journal.pone.0250669.g003

المؤلفون: Shaoyi Ji (3108864), Ze Yang (446151), Leonardi Gozali (10751729), Thomas Kenney (1828366), Arif Kocabas (10751732), Carolyn Jinsook Park (10751735), Mary Hynes (10751738)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Ecology, Developmental Biology, Cancer, Hematology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, cell state changes, transition states Mature mRNA molecules, site genomic elements, CDS ratios, Unbiased transcriptome analysis, gene ontology categories, UTR, cell-specific gene expression

Relation: https://figshare.com/articles/figure/Unbiased_analysis_shows_that_Hi_3_UTR_CDS_genes_define_tissue_specific_properties_/14543714

الاتاحة: https://doi.org/10.1371/journal.pone.0250669.g006

المؤلفون: Shaoyi Ji (3108864), Ze Yang (446151), Leonardi Gozali (10751729), Thomas Kenney (1828366), Arif Kocabas (10751732), Carolyn Jinsook Park (10751735), Mary Hynes (10751738)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Ecology, Developmental Biology, Cancer, Hematology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, cell state changes, transition states Mature mRNA molecules, site genomic elements, CDS ratios, Unbiased transcriptome analysis, gene ontology categories, UTR, cell-specific gene expression

Relation: https://figshare.com/articles/figure/Widespread_differential_3_UTR_CDS_use_is_reflected_in_RNAseq_data_/14543711

الاتاحة: https://doi.org/10.1371/journal.pone.0250669.g005

المؤلفون: Dongyuan Song (5792477), Jingyi Jessica Li (10726220)

مصطلحات موضوعية: Genetics, ill-posed p-values, cell pseudotime, well-calibrated p-values, cell state changes, PseudotimeDE, real-data applications, pseudotime inference uncertainty, gene expression, outputs well-calibrated p-values, RNA sequencing data Abstract, discovery rate control, RNA-sequencing data, pseudotime inference methods, DE gene identification method, Comprehensive simulations

Relation: https://figshare.com/articles/dataset/Additional_file_3_of_PseudotimeDE_inference_of_differential_gene_expression_along_cell_pseudotime_with_well-calibrated_p-values_from_single-cell_RNA_sequencing_data/14516087

الاتاحة: https://doi.org/10.6084/m9.figshare.14516087.v1

المؤلفون: Dongyuan Song (5792477), Jingyi Jessica Li (10726220)

مصطلحات موضوعية: Genetics, ill-posed p-values, cell pseudotime, well-calibrated p-values, cell state changes, PseudotimeDE, real-data applications, pseudotime inference uncertainty, gene expression, outputs well-calibrated p-values, RNA sequencing data Abstract, discovery rate control, RNA-sequencing data, pseudotime inference methods, DE gene identification method, Comprehensive simulations

Relation: https://figshare.com/articles/dataset/Additional_file_2_of_PseudotimeDE_inference_of_differential_gene_expression_along_cell_pseudotime_with_well-calibrated_p-values_from_single-cell_RNA_sequencing_data/14516084

الاتاحة: https://doi.org/10.6084/m9.figshare.14516084.v1

المؤلفون: Dongyuan Song (5792477), Jingyi Jessica Li (10726220)

مصطلحات موضوعية: Genetics, ill-posed p-values, cell pseudotime, well-calibrated p-values, cell state changes, PseudotimeDE, real-data applications, pseudotime inference uncertainty, gene expression, outputs well-calibrated p-values, RNA sequencing data Abstract, discovery rate control, RNA-sequencing data, pseudotime inference methods, DE gene identification method, Comprehensive simulations

Relation: https://figshare.com/articles/dataset/Additional_file_4_of_PseudotimeDE_inference_of_differential_gene_expression_along_cell_pseudotime_with_well-calibrated_p-values_from_single-cell_RNA_sequencing_data/14516093

الاتاحة: https://doi.org/10.6084/m9.figshare.14516093.v1

المؤلفون: Neal G. Ravindra (9443558), Mia Madel Alfajaro (10319201), Victor Gasque (10319204), Nicholas C. Huston (10319207), Han Wan (502172), Klara Szigeti-Buck (10319210), Yuki Yasumoto (685821), Allison M. Greaney (10319213), Victoria Habet (10319216), Ryan D. Chow (10319219), Jennifer S. Chen (10319222), Jin Wei (424761), Renata B. Filler (8677386), Bao Wang (488990), Guilin Wang (37620), Laura E. Niklason (2429191), Ruth R. Montgomery (8551191), Stephanie C. Eisenbarth (10319225), Sidi Chen (127044), Adam Williams (5459639), Akiko Iwasaki (397932), Tamas L. Horvath (10319228), Ellen F. Foxman (10319231), Richard W. Pierce (2516263), Anna Marie Pyle (7305956), David van Dijk (239963), Craig B. Wilen (8677404)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Immunology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, type III interferons, cell state changes, cell tropism, COVID, epithelial cell types, Coronavirus Disease 2019, SARS-CoV -2 infection, FDA, IFN, HBEC, RNA, IL, ISG, ALI, Severe Acute Respiratory Syndrome C.

Relation: https://figshare.com/articles/figure/DEGs_across_different_cell_types_/14232797

الاتاحة: https://doi.org/10.1371/journal.pbio.3001143.s003

المؤلفون: Neal G. Ravindra (9443558), Mia Madel Alfajaro (10319201), Victor Gasque (10319204), Nicholas C. Huston (10319207), Han Wan (502172), Klara Szigeti-Buck (10319210), Yuki Yasumoto (685821), Allison M. Greaney (10319213), Victoria Habet (10319216), Ryan D. Chow (10319219), Jennifer S. Chen (10319222), Jin Wei (424761), Renata B. Filler (8677386), Bao Wang (488990), Guilin Wang (37620), Laura E. Niklason (2429191), Ruth R. Montgomery (8551191), Stephanie C. Eisenbarth (10319225), Sidi Chen (127044), Adam Williams (5459639), Akiko Iwasaki (397932), Tamas L. Horvath (10319228), Ellen F. Foxman (10319231), Richard W. Pierce (2516263), Anna Marie Pyle (7305956), David van Dijk (239963), Craig B. Wilen (8677404)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Immunology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, type III interferons, cell state changes, cell tropism, COVID, epithelial cell types, Coronavirus Disease 2019, SARS-CoV -2 infection, FDA, IFN, HBEC, RNA, IL, ISG, ALI, Severe Acute Respiratory Syndrome C.

Relation: https://figshare.com/articles/dataset/The_individual_numerical_values_for_the_following_figure_panels_Figs_1B_1C_1D_1E_1F_1G_2A_2B_2C_3A_3B_3C_3D_4A_4B_4C_4D_4E_4F_4G_4H_4I_5A_5B_5C_5D_6B_6C_and_6D_and_S1A_S1B_S1C_S1D_S1E_S2A_S2B_S2C_S2D_S3A_S3B_S3C_S4A_S4B_S4C_and_S4D_Figs_/14232803

الاتاحة: https://doi.org/10.1371/journal.pbio.3001143.s005

المؤلفون: Neal G. Ravindra (9443558), Mia Madel Alfajaro (10319201), Victor Gasque (10319204), Nicholas C. Huston (10319207), Han Wan (502172), Klara Szigeti-Buck (10319210), Yuki Yasumoto (685821), Allison M. Greaney (10319213), Victoria Habet (10319216), Ryan D. Chow (10319219), Jennifer S. Chen (10319222), Jin Wei (424761), Renata B. Filler (8677386), Bao Wang (488990), Guilin Wang (37620), Laura E. Niklason (2429191), Ruth R. Montgomery (8551191), Stephanie C. Eisenbarth (10319225), Sidi Chen (127044), Adam Williams (5459639), Akiko Iwasaki (397932), Tamas L. Horvath (10319228), Ellen F. Foxman (10319231), Richard W. Pierce (2516263), Anna Marie Pyle (7305956), David van Dijk (239963), Craig B. Wilen (8677404)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Immunology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, type III interferons, cell state changes, cell tropism, COVID, epithelial cell types, Coronavirus Disease 2019, SARS-CoV -2 infection, FDA, IFN, HBEC, RNA, IL, ISG, ALI, Severe Acute Respiratory Syndrome C.

Relation: https://figshare.com/articles/figure/DEG_analysis_in_ciliated_cells_at_different_time_points_/14232800

الاتاحة: https://doi.org/10.1371/journal.pbio.3001143.s004

المؤلفون: Neal G. Ravindra (9443558), Mia Madel Alfajaro (10319201), Victor Gasque (10319204), Nicholas C. Huston (10319207), Han Wan (502172), Klara Szigeti-Buck (10319210), Yuki Yasumoto (685821), Allison M. Greaney (10319213), Victoria Habet (10319216), Ryan D. Chow (10319219), Jennifer S. Chen (10319222), Jin Wei (424761), Renata B. Filler (8677386), Bao Wang (488990), Guilin Wang (37620), Laura E. Niklason (2429191), Ruth R. Montgomery (8551191), Stephanie C. Eisenbarth (10319225), Sidi Chen (127044), Adam Williams (5459639), Akiko Iwasaki (397932), Tamas L. Horvath (10319228), Ellen F. Foxman (10319231), Richard W. Pierce (2516263), Anna Marie Pyle (7305956), David van Dijk (239963), Craig B. Wilen (8677404)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Immunology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, type III interferons, cell state changes, cell tropism, COVID, epithelial cell types, Coronavirus Disease 2019, SARS-CoV -2 infection, FDA, IFN, HBEC, RNA, IL, ISG, ALI, Severe Acute Respiratory Syndrome C.

Relation: https://figshare.com/articles/dataset/The_raw_data_used_to_generate_Fig_6B_6C_and_6D_/14232812

الاتاحة: https://doi.org/10.1371/journal.pbio.3001143.s007

المؤلفون: Neal G. Ravindra (9443558), Mia Madel Alfajaro (10319201), Victor Gasque (10319204), Nicholas C. Huston (10319207), Han Wan (502172), Klara Szigeti-Buck (10319210), Yuki Yasumoto (685821), Allison M. Greaney (10319213), Victoria Habet (10319216), Ryan D. Chow (10319219), Jennifer S. Chen (10319222), Jin Wei (424761), Renata B. Filler (8677386), Bao Wang (488990), Guilin Wang (37620), Laura E. Niklason (2429191), Ruth R. Montgomery (8551191), Stephanie C. Eisenbarth (10319225), Sidi Chen (127044), Adam Williams (5459639), Akiko Iwasaki (397932), Tamas L. Horvath (10319228), Ellen F. Foxman (10319231), Richard W. Pierce (2516263), Anna Marie Pyle (7305956), David van Dijk (239963), Craig B. Wilen (8677404)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Immunology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, type III interferons, cell state changes, cell tropism, COVID, epithelial cell types, Coronavirus Disease 2019, SARS-CoV -2 infection, FDA, IFN, HBEC, RNA, IL, ISG, ALI, Severe Acute Respiratory Syndrome C.

Relation: https://figshare.com/articles/figure/The_raw_images_for_Fig_2D_/14232815

الاتاحة: https://doi.org/10.1371/journal.pbio.3001143.s008

المؤلفون: Neal G. Ravindra (9443558), Mia Madel Alfajaro (10319201), Victor Gasque (10319204), Nicholas C. Huston (10319207), Han Wan (502172), Klara Szigeti-Buck (10319210), Yuki Yasumoto (685821), Allison M. Greaney (10319213), Victoria Habet (10319216), Ryan D. Chow (10319219), Jennifer S. Chen (10319222), Jin Wei (424761), Renata B. Filler (8677386), Bao Wang (488990), Guilin Wang (37620), Laura E. Niklason (2429191), Ruth R. Montgomery (8551191), Stephanie C. Eisenbarth (10319225), Sidi Chen (127044), Adam Williams (5459639), Akiko Iwasaki (397932), Tamas L. Horvath (10319228), Ellen F. Foxman (10319231), Richard W. Pierce (2516263), Anna Marie Pyle (7305956), David van Dijk (239963), Craig B. Wilen (8677404)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Immunology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, type III interferons, cell state changes, cell tropism, COVID, epithelial cell types, Coronavirus Disease 2019, SARS-CoV -2 infection, FDA, IFN, HBEC, RNA, IL, ISG, ALI, Severe Acute Respiratory Syndrome C.

Relation: https://figshare.com/articles/dataset/The_raw_data_used_to_generate_S4A_S4B_S4C_and_S4D_Figs_/14232806

الاتاحة: https://doi.org/10.1371/journal.pbio.3001143.s006

المؤلفون: Neal G. Ravindra (9443558), Mia Madel Alfajaro (10319201), Victor Gasque (10319204), Nicholas C. Huston (10319207), Han Wan (502172), Klara Szigeti-Buck (10319210), Yuki Yasumoto (685821), Allison M. Greaney (10319213), Victoria Habet (10319216), Ryan D. Chow (10319219), Jennifer S. Chen (10319222), Jin Wei (424761), Renata B. Filler (8677386), Bao Wang (488990), Guilin Wang (37620), Laura E. Niklason (2429191), Ruth R. Montgomery (8551191), Stephanie C. Eisenbarth (10319225), Sidi Chen (127044), Adam Williams (5459639), Akiko Iwasaki (397932), Tamas L. Horvath (10319228), Ellen F. Foxman (10319231), Richard W. Pierce (2516263), Anna Marie Pyle (7305956), David van Dijk (239963), Craig B. Wilen (8677404)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Immunology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, type III interferons, cell state changes, cell tropism, COVID, epithelial cell types, Coronavirus Disease 2019, SARS-CoV -2 infection, FDA, IFN, HBEC, RNA, IL, ISG, ALI, Severe Acute Respiratory Syndrome C.

Relation: https://figshare.com/articles/figure/The_raw_images_for_Fig_3E_/14232818

الاتاحة: https://doi.org/10.1371/journal.pbio.3001143.s009

المؤلفون: Neal G. Ravindra (9443558), Mia Madel Alfajaro (10319201), Victor Gasque (10319204), Nicholas C. Huston (10319207), Han Wan (502172), Klara Szigeti-Buck (10319210), Yuki Yasumoto (685821), Allison M. Greaney (10319213), Victoria Habet (10319216), Ryan D. Chow (10319219), Jennifer S. Chen (10319222), Jin Wei (424761), Renata B. Filler (8677386), Bao Wang (488990), Guilin Wang (37620), Laura E. Niklason (2429191), Ruth R. Montgomery (8551191), Stephanie C. Eisenbarth (10319225), Sidi Chen (127044), Adam Williams (5459639), Akiko Iwasaki (397932), Tamas L. Horvath (10319228), Ellen F. Foxman (10319231), Richard W. Pierce (2516263), Anna Marie Pyle (7305956), David van Dijk (239963), Craig B. Wilen (8677404)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Immunology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, type III interferons, cell state changes, cell tropism, COVID, epithelial cell types, Coronavirus Disease 2019, SARS-CoV -2 infection, FDA, IFN, HBEC, RNA, IL, ISG, ALI, Severe Acute Respiratory Syndrome C.

Relation: https://figshare.com/articles/figure/SARS-CoV-2_tropism_in_primary_HBECs_reveals_ciliated_cells_as_primary_target_cells_/14232833

الاتاحة: https://doi.org/10.1371/journal.pbio.3001143.g003

المؤلفون: Neal G. Ravindra (9443558), Mia Madel Alfajaro (10319201), Victor Gasque (10319204), Nicholas C. Huston (10319207), Han Wan (502172), Klara Szigeti-Buck (10319210), Yuki Yasumoto (685821), Allison M. Greaney (10319213), Victoria Habet (10319216), Ryan D. Chow (10319219), Jennifer S. Chen (10319222), Jin Wei (424761), Renata B. Filler (8677386), Bao Wang (488990), Guilin Wang (37620), Laura E. Niklason (2429191), Ruth R. Montgomery (8551191), Stephanie C. Eisenbarth (10319225), Sidi Chen (127044), Adam Williams (5459639), Akiko Iwasaki (397932), Tamas L. Horvath (10319228), Ellen F. Foxman (10319231), Richard W. Pierce (2516263), Anna Marie Pyle (7305956), David van Dijk (239963), Craig B. Wilen (8677404)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Immunology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, type III interferons, cell state changes, cell tropism, COVID, epithelial cell types, Coronavirus Disease 2019, SARS-CoV -2 infection, FDA, IFN, HBEC, RNA, IL, ISG, ALI, Severe Acute Respiratory Syndrome C.

Relation: https://figshare.com/articles/figure/The_raw_images_for_Fig_3F_/14232824

الاتاحة: https://doi.org/10.1371/journal.pbio.3001143.s010