Elana J Fertig creator_3xycjhim35ekpnho7ajxogt7yq

Given name Elana
Surname Fertig

Releases

This creator has contributed to:

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
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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
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