2016-09-15
|
StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data
unknown status
| post
doi:10.1101/059584
|
2017-03-08
|
Epigenetic Regulation of Gene Expression in Cancer: Techniques, Resources, and Analysis
unknown status
| post
doi:10.1101/114025
|
2017-10-02
|
Enter the matrix: factorization uncovers knowledge from omics
unknown status
| post
doi:10.1101/196915
|
2018-05-25
|
REVA: a rank-based multi-dimensional measure of correlation
unknown status
| post
doi:10.1101/330498
|
2018-05-23
|
Combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer with CancerInSilico
unknown status
| post
doi:10.1101/328807
|
2018-01-12
|
Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer
published
| article-journal
doi:10.1093/bioinformatics/bty004
|
2018-07-27
|
Comprehensive analysis of retinal development at single cell resolution identifies NFI factors as essential for mitotic exit and specification of late-born cells
unknown status
| post
doi:10.1101/378950
|
2016-12-05
|
Splice Expression Variation Analysis (SEVA) for Inter-tumor Heterogeneity of Gene Isoform Usage in Cancer
unknown status
| post
doi:10.1101/091637
|
2018-08-20
|
Decomposing cell identity for transfer learning across cellular measurements, platforms, tissues, and species.
unknown status
| post
doi:10.1101/395004
|
2018-11-27
|
Expression variation analysis for tumor heterogeneity in single-cell RNA-sequencing data
unknown status
| post
doi:10.1101/479287
|
2019-08-08
|
Integrated single cell and bulk multi-omics reveals heterogeneity and early changes in pathways associated with cetuximab resistance in HNSCC sensitive cell lines
unknown status
| post
doi:10.1101/729384
|
2019-04-19
|
CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer
published
| article-journal
doi:10.1371/journal.pcbi.1006935
|
2020-05-31
|
A novel mechanism of natural killer cell response to anti-CTLA-4 therapy identified by integrative analysis of mouse and human tumors
unknown status
| post
doi:10.1101/2020.05.31.125625
|
2020-03-26
|
Cytokines secreted by stromal cells in TNBC microenvironment as potential targets for cancer therapy
published
| article-journal
doi:10.1080/15384047.2020.1739484
|
2020-10-15
|
CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures
published
| stub
| v1
| CC-BY
doi:10.6084/m9.figshare.c.5175367.v1
|
2020-10-15
|
CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures
published
| stub
| CC-BY
doi:10.6084/m9.figshare.c.5175367
|
2020-10-15
|
Additional file 1 of CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures
published
| component
| v1
| CC-BY
doi:10.6084/m9.figshare.13093744.v1
|
2020-10-15
|
Additional file 1 of CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures
published
| component
| CC-BY
doi:10.6084/m9.figshare.13093744
|
2021-02-03
|
Fibroblast activation protein regulates natural killer cell migration, extravasation and tumor infiltration
unknown status
| post
doi:10.1101/2021.02.03.429622
|
2021-08-11
|
Transfer learning between preclinical models and human tumors identifies a conserved NK cell activation signature in anti-CTLA-4 responsive tumors
published
| stub
| CC-BY
doi:10.6084/m9.figshare.c.5554421
|
2021-08-11
|
Transfer learning between preclinical models and human tumors identifies a conserved NK cell activation signature in anti-CTLA-4 responsive tumors
published
| stub
| v1
| CC-BY
doi:10.6084/m9.figshare.c.5554421.v1
|
2021-08-11
|
Additional file 2 of Transfer learning between preclinical models and human tumors identifies a conserved NK cell activation signature in anti-CTLA-4 responsive tumors
published
| dataset
| v1
| CC-BY
doi:10.6084/m9.figshare.15145877.v1
|
2021-08-11
|
Additional file 2 of Transfer learning between preclinical models and human tumors identifies a conserved NK cell activation signature in anti-CTLA-4 responsive tumors
published
| dataset
| CC-BY
doi:10.6084/m9.figshare.15145877
|
2021-08-11
|
Additional file 1 of Transfer learning between preclinical models and human tumors identifies a conserved NK cell activation signature in anti-CTLA-4 responsive tumors
published
| component
| CC-BY
doi:10.6084/m9.figshare.15145874
|
2021-08-11
|
Additional file 1 of Transfer learning between preclinical models and human tumors identifies a conserved NK cell activation signature in anti-CTLA-4 responsive tumors
published
| component
| v1
| CC-BY
doi:10.6084/m9.figshare.15145874.v1
|
2021-08-27
|
Identifying Gene-wise Differences in Latent Space Projections Across Cell Types and Species in Single Cell Data using scProject
unknown status
| post
doi:10.1101/2021.08.25.457650
|
2021-07-29
|
From bench to bedside: single-cell analysis for cancer immunotherapy
published
| article-journal
doi:10.1016/j.ccell.2021.07.004
|
2021-09-01
|
Systemic inhibition of PTPN22 augments anticancer immunity
published
| article-journal
doi:10.1172/jci146950
|
2021-10-07
|
scatterHatch: an R/Bioconductor package for color blind accessible visualization of single-cell data
unknown status
| post
doi:10.1101/2021.10.07.463279
|
2021-10-07
|
A field guide to cultivating computational biology
published
| article-journal
doi:10.1371/journal.pbio.3001419
|
2021-08-11
|
Transfer learning between preclinical models and human tumors identifies a conserved NK cell activation signature in anti-CTLA-4 responsive tumors
published
| article-journal
| CC-BY
doi:10.1186/s13073-021-00944-5
|
2021
|
DPP inhibition alters the CXCR3 axis and enhances NK and CD8+ T cell infiltration to improve anti-PD1 efficacy in murine models of pancreatic ductal adenocarcinoma
published
| article-journal
| CC-BY-NC
doi:10.1136/jitc-2021-002837
|
2021-10-22
|
Editor's evaluation: Multiomic characterization of pancreatic cancer-associated macrophage polarization reveals deregulated metabolic programs driven by the GM-CSF–PI3K pathway
unknown status
| peer_review
| CC-BY
doi:10.7554/elife.73796.sa0
|
2022-02-04
|
Editor's evaluation: Regulation of protein complex partners as a compensatory mechanism in aneuploid tumors
unknown status
| peer_review
| CC-BY
doi:10.7554/elife.75526.sa0
|
2022-09-08
|
Model-informed experimental design recommendations for distinguishing intrinsic and acquired targeted therapeutic resistance in head and neck cancer
published
| article-journal
| CC-BY
doi:10.1038/s41540-022-00244-7
|
2022-08-03
|
Triple-negative breast cancer metastasis involves complex epithelial-mesenchymal transition dynamics and requires vimentin
published
| article-journal
doi:10.1126/scitranslmed.abn7571
|
2023-07-06
|
Transcriptomic forecasting with neural ordinary differential equations
published
| article-journal
| CC-BY-NC-ND
doi:10.1016/j.patter.2023.100793
|
2023-10-26
|
Immune landscape of tertiary lymphoid structures in hepatocellular carcinoma (HCC) treated with neoadjuvant immune checkpoint blockade
published
| unknown type
doi:10.1101/2023.10.16.562104
|
2024-03-13
|
MLL1 regulates cytokine-driven cell migration and metastasis
published
| article-journal
doi:10.1126/sciadv.adk0785
|
2024-04-08
|
Transfer learning reveals cancer-associated fibroblasts are associated with epithelial-mesenchymal transition and inflammation in cancer cells in pancreatic ductal adenocarcinoma
published
| article-journal
doi:10.1158/0008-5472.can-23-1660
|
2024-05-02
|
Supplemental Table 3: Pattern 7 Ordered Genes from Transfer Learning Reveals Cancer-Associated Fibroblasts Are Associated with Epithelial–Mesenchymal Transition and Inflammation in Cancer Cells in Pancreatic Ductal Adenocarcinoma
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.25735922.v1
|
2024-05-02
|
Supplementary Methods and Figures from Transfer Learning Reveals Cancer-Associated Fibroblasts Are Associated with Epithelial–Mesenchymal Transition and Inflammation in Cancer Cells in Pancreatic Ductal Adenocarcinoma
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.25735919.v1
|
2024-05-02
|
Supplemental Table 1: Pancreas Gene Markers from Transfer Learning Reveals Cancer-Associated Fibroblasts Are Associated with Epithelial–Mesenchymal Transition and Inflammation in Cancer Cells in Pancreatic Ductal Adenocarcinoma
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.25735931
|
2024-05-28
|
Natural killer cells associate with epithelial cells in the pancreatic ductal adenocarcinoma tumor microenvironment
published
| post
doi:10.1101/2024.05.23.593868
|
2024-08-06
|
Phosphodiesterase-5 inhibition collaborates with vaccine-based immunotherapy to reprogram myeloid cells in pancreatic ductal adenocarcinoma
published
| article-journal
| CC-BY
doi:10.1172/jci.insight.179292
|
2024-09-27
|
Supplementary Data Table 1 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.27119035
|
2024-09-27
|
Supplementary Equations from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.27119032
|
2024-09-27
|
Supplementary Movie 3 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.27119020
|
2024-10-25
|
Immunotherapy response induces divergent tertiary lymphoid structure morphologies in hepatocellular carcinoma
published
| article-journal
doi:10.1038/s41590-024-01992-w
|
2020-10-25
|
nearBynding: A flexible pipeline characterizing protein binding to local RNA structure
unknown status
| post
doi:10.1101/2020.10.24.352591
|
2020-10-14
|
CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures
published
| article-journal
| CC-BY
doi:10.1186/s12859-020-03796-9
|
2022-01-04
|
The use of machine learning to discover regulatory networks controlling biological systems
published
| article-journal
doi:10.1016/j.molcel.2021.12.011
|
2022-03-24
|
Ten quick tips for deep learning in biology
published
| article-journal
| CC-BY
doi:10.1371/journal.pcbi.1009803
|
2022-07-11
|
Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R, and GenePattern Notebook implementations of CoGAPS
unknown status
| post
doi:10.1101/2022.07.09.499398
|
2022-11-24
|
Author response: Generating colorblind-friendly scatter plots for single-cell data
unknown status
| peer_review
| CC-BY
doi:10.7554/elife.82128.sa2
|
2023-06-01
|
Boosting Single-Cell RNA Sequencing Analysis with Simple Neural Attention
published
| unknown type
doi:10.1101/2023.05.29.542760
|
2023-09-17
|
Digitize your Biology! Modeling multicellular systems through interpretable cell behavior
published
| unknown type
doi:10.1101/2023.09.17.557982
|
2023-12-19
|
Fibroblast activation protein regulates natural killer cell migration, extravasation and tumor infiltration
published
| unknown type
doi:10.21203/rs.3.rs-3706465/v1
|
2023-11-21
|
Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS
published
| article-journal
doi:10.1038/s41596-023-00892-x
|
2024-05-02
|
Supplementary Methods and Figures from Transfer Learning Reveals Cancer-Associated Fibroblasts Are Associated with Epithelial–Mesenchymal Transition and Inflammation in Cancer Cells in Pancreatic Ductal Adenocarcinoma
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.25735919
|
2024-05-02
|
Supplemental Table 2: Pattern 1 Pathways from Transfer Learning Reveals Cancer-Associated Fibroblasts Are Associated with Epithelial–Mesenchymal Transition and Inflammation in Cancer Cells in Pancreatic Ductal Adenocarcinoma
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.25735925.v1
|
2024-05-02
|
Data from Transfer Learning Reveals Cancer-Associated Fibroblasts Are Associated with Epithelial–Mesenchymal Transition and Inflammation in Cancer Cells in Pancreatic Ductal Adenocarcinoma
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.c.7213937
|
2024-05-21
|
Virtual patient analysis identifies strategies to improve the performance of predictive biomarkers for PD-1 blockade
published
| unknown type
doi:10.1101/2024.05.21.595235
|
2024-07-15
|
Is There a Mathematician on Board?
published
| article-journal
doi:10.1158/0008-5472.can-24-1396
|
2024-09-27
|
Data from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.c.7403509
|
2024-09-27
|
Supplementary Movie 2 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.27119023
|
2024-09-27
|
Supplementary Movie 4 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.27119017
|
2024-09-28
|
Hypoxia induces ROS-resistant memory upon reoxygenation in vivo promoting metastasis in part via MUC1-C
published
| article-journal
| CC-BY-NC-ND
doi:10.1038/s41467-024-51995-2
|
2024-12-10
|
CD137 agonism enhances anti-PD1 induced activation of expanded CD8+ T cell clones in a neoadjuvant pancreatic cancer clinical trial
published
| article-journal
| CC-BY
doi:10.1016/j.isci.2024.111569
|
2021-10-22
|
Decision letter: Multiomic characterization of pancreatic cancer-associated macrophage polarization reveals deregulated metabolic programs driven by the GM-CSF–PI3K pathway
unknown status
| peer_review
| CC-BY
doi:10.7554/elife.73796.sa1
|
2022-03-25
|
Transfer learning of an in vivo-derived senescence signature identifies conserved and tissue-specific senescence across species and diverse pathologies
unknown status
| post
doi:10.1101/2022.03.22.485297
|
2022-02-04
|
Decision letter: Regulation of protein complex partners as a compensatory mechanism in aneuploid tumors
unknown status
| peer_review
| CC-BY
doi:10.7554/elife.75526.sa1
|
2022-02-04
|
Decision letter: Regulation of protein complex partners as a compensatory mechanism in aneuploid tumors
unknown status
| peer_review
| CC-BY
doi:10.7554/elife.75526.sa1
|
2022-10-10
|
Integrated T cell cytometry metrics for immune-monitoring applications in immunotherapy clinical trials
published
| article-journal
| CC-BY
doi:10.1172/jci.insight.160398
|
2022-12-16
|
Generating colorblind-friendly scatter plots for single-cell data
published
| article-journal
doi:10.7554/elife.82128
|
2023-05-04
|
Converging on a Cure: The Roads to Predictive Immunotherapy
published
| article-journal
doi:10.1158/2159-8290.cd-23-0277
|
2024-02-14
|
Entinostat, nivolumab and ipilimumab for women with advanced HER2-negative breast cancer: a phase Ib trial
published
| article-journal
doi:10.1038/s43018-024-00729-w
|
2024-04-07
|
Personalized neoantigen vaccine and pembrolizumab in advanced hepatocellular carcinoma: a phase 1/2 trial
published
| article-journal
doi:10.1038/s41591-024-02894-y
|
2024-05-02
|
Supplemental Table 3: Pattern 7 Ordered Genes from Transfer Learning Reveals Cancer-Associated Fibroblasts Are Associated with Epithelial–Mesenchymal Transition and Inflammation in Cancer Cells in Pancreatic Ductal Adenocarcinoma
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.25735922
|
2024-05-02
|
Supplemental Table 1: Pancreas Gene Markers from Transfer Learning Reveals Cancer-Associated Fibroblasts Are Associated with Epithelial–Mesenchymal Transition and Inflammation in Cancer Cells in Pancreatic Ductal Adenocarcinoma
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.25735931.v1
|
2024-05-02
|
Supplemental Table 2: Pattern 1 Pathways from Transfer Learning Reveals Cancer-Associated Fibroblasts Are Associated with Epithelial–Mesenchymal Transition and Inflammation in Cancer Cells in Pancreatic Ductal Adenocarcinoma
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.25735925
|
2024-05-02
|
Data from Transfer Learning Reveals Cancer-Associated Fibroblasts Are Associated with Epithelial–Mesenchymal Transition and Inflammation in Cancer Cells in Pancreatic Ductal Adenocarcinoma
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.c.7213937.v1
|
2024-06-11
|
Integration of Clinical Trial Spatial Multi-omics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery
published
| article-journal
doi:10.1158/0008-5472.can-24-0943
|
2024-08-17
|
Identifying a gene signature of metastatic potential by linking pre-metastatic state to ultimate metastatic fate
unknown status
| post
| CC-BY-NC-ND
doi:10.1101/2024.08.14.607813
|
2024-09-27
|
Supplementary Table 2 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.27119014
|
2024-09-27
|
Supplementary Figures from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.27119029
|
2024-09-27
|
Supplementary Movie 1 from Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery
unknown status
| post
| CC-BY
doi:10.1158/0008-5472.27119026
|
2024-10-04
|
A New Era of Data-Driven Cancer Research and Care: Opportunities and Challenges
published
| article-journal
| CC-BY
doi:10.1158/2159-8290.cd-24-1130
|
2024-10-29
|
SpliceMutr enables pan-cancer analysis of splicing-derived neoantigen burden in tumors
published
| article-journal
doi:10.1158/2767-9764.crc-23-0309
|
2024-11-12
|
Entinostat in combination with nivolumab in metastatic pancreatic ductal adenocarcinoma: a phase 2 clinical trial
published
| article-journal
doi:10.1038/s41467-024-52528-7
|
2025-01-23
|
Human Pancreatic Cancer Single-Cell Atlas Reveals Association of CXCL10+ Fibroblasts and Basal Subtype Tumor Cells
published
| article-journal
| CC-BY-NC-ND
doi:10.1158/1078-0432.ccr-24-2183
|
2024-06-28
|
Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional regulation
published
| article-journal
doi:10.1126/sciimmunol.adk4893
|