Elana J. Fertig

Also affiliated with University of Baltimore

Medicine

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 3%percentile

0.958Author DataRank

Indexed papers

2in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 2 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Intercellular signaling dynamics from a single cell atlas of the biomaterials response

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.24.218537

Top 38%

0.499DataRank

Top 38%13 citations

David R. Maestas, Jin Han, James I. Andorko, Patrick Cahan, Elana J. Fertig +3 more

Papers

Driven by 106 papers — median percentile 60. Top paper: “HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers”.

HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers

Oncogene(2020)10.1038/s41388-020-01431-8

N/A

2.5DataRank · unranked

100 citations

Daria A. Gaykalova, Theresa Guo, Alexander V. Favorov, Elana J. Fertig, Pablo Tamayo +18 more

Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines

British Journal of Cancer(2020)10.1038/s41416-020-0851-5

N/A

1.8DataRank · unranked

57 citations

Fernando T. Zamunér, Emily F. Davis-Marcisak, Gaurav Sharma, Michael Considine, Jawara Allen +4 more

A field guide to cultivating computational biology

PLOS Biology(2021)10.1371/journal.pbio.3001419

N/A

1.3DataRank · unranked

22 citations

Casey S. Greene, Piero Carninci, Benilton S. Carvalho, Michiel de Hoon, Stacey D. Finley +11 more

Entinostat in combination with nivolumab in metastatic pancreatic ductal adenocarcinoma: a phase 2 clinical trial

Nature Communications(2024)10.1038/s41467-024-52528-7

N/A

1.0DataRank · unranked

42 citations

Ludmila Danilova, Jennifer N. Durham, Courtney B. Betts, Leslie Cope, Dimitrios N. Sidiropoulos +19 more

Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories

Cell(2025)10.1016/j.cell.2025.06.048

N/A

0.945DataRank · unranked

45 citations

Daniel Bergman, Heber L. Rocha, David Zhou, Eric Cramer, Ian C. McLean +42 more

CD4 T cell–activating neoantigens enhance personalized cancer vaccine efficacy

JCI Insight(2023)10.1172/jci.insight.174027

N/A

0.921DataRank · unranked

34 citations

Gabriella Longway, Jacob T. Mitchell, Lalitya Andaloori, Emily F. Davis-Marcisak, Fangluo Chen +15 more

Transfer Learning Reveals Cancer-Associated Fibroblasts Are Associated with Epithelial–Mesenchymal Transition and Inflammation in Cancer Cells in Pancreatic Ductal Adenocarcinoma

Cancer Research(2024)10.1158/0008-5472.can-23-1660

N/A

0.867DataRank · unranked

44 citations

Benedict Kinny‐Köster, Joseph A. Tandurella, Jacob T. Mitchell, Dimitrios N. Sidiropoulos, Melanie Loth +29 more

Transfer learning between preclinical models and human tumors identifies a conserved NK cell activation signature in anti-CTLA-4 responsive tumors

Genome Medicine(2021)10.1186/s13073-021-00944-5

N/A

0.848DataRank · unranked

24 citations

Allison A. Fitzgerald, Michael D. Kessler, Ludmila Danilova, Elizabeth M. Jaffee, Neeha Zaidi +3 more

Integrating single cell sequencing with a spatial quantitative systems pharmacology model spQSP for personalized prediction of triple-negative breast cancer immunotherapy response

ImmunoInformatics(2021)10.1016/j.immuno.2021.100002

N/A

0.844DataRank · unranked

31 citations

Chang Gong, Álvaro Ruiz-Martínez, Hanwen Wang, Emily F. Davis-Marcisak, Atul Deshpande +3 more

Enter the Matrix: Factorization Uncovers Knowledge from Omics

Trends in Genetics(2018)10.1016/j.tig.2018.07.003

N/A

0.837DataRank · unranked

264 citations

Raman Arora, Alexander V. Favorov, Lana X. Garmire, Casey S. Greene, Loyal A. Goff +7 more

Multi-omic analyses of changes in the tumor microenvironment of pancreatic adenocarcinoma following neoadjuvant treatment with anti-PD-1 therapy

Cancer Cell(2022)10.1016/j.ccell.2022.10.001

N/A

0.778DataRank · unranked

178 citations

Joseph A. Tandurella, Jessica Gai, Qingfeng Zhu, Su Jin Lim, Dwayne L. Thomas +26 more

Evaluation of Cyclophosphamide/GVAX Pancreas Followed by Listeria-Mesothelin (CRS-207) with or without Nivolumab in Patients with Pancreatic Cancer

Clinical Cancer Research(2020)10.1158/1078-0432.ccr-19-3978

N/A

0.756DataRank · unranked

153 citations

Todd S. Crocenzi, Jennifer N. Durham, Elizabeth A. Sugar, Annie A. Wu, Beth Onners +16 more

Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets

Nucleic Acids Research(2020)10.1093/nar/gkaa349

N/A

0.714DataRank · unranked

17 citations

Michael D. Kessler, Alexander V. Favorov, Hariharan Easwaran, Daria A. Gaykalova, Elana J. Fertig +1 more

Immunotherapy response induces divergent tertiary lymphoid structure morphologies in hepatocellular carcinoma

Nature Immunology(2024)10.1038/s41590-024-01992-w

N/A

0.695DataRank · unranked

102 citations

Won Jin Ho, Luciane T. Kagohara, Alexander A. Girgis, Sarah M. Shin, Ludmila Danilova +34 more

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

Journal for ImmunoTherapy of Cancer(2021)10.1136/jitc-2021-002837

N/A

0.661DataRank · unranked

81 citations

Shangzi Wang, Veena R. Agarwal, Emily F. Davis-Marcisak, Annie Zuo, Sandra A. Jablonski +9 more

Evaluating the impact of age on immune checkpoint therapy biomarkers

Cell Reports(2021)10.1016/j.celrep.2021.109599

N/A

0.659DataRank · unranked

80 citations

Zheyu Wang, Sharon Wu, Joanne Xiu, Neeha Zaidi, Jennifer La +20 more

Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways

Genome biology(2021)10.1186/s13059-021-02363-6

N/A

0.631DataRank · unranked

66 citations

Rossin Erbe, Ludmila Danilova, Zaw Phyo, Emma Bigelow, Genevieve L. Stein-O’Brien +14 more

Viral status, immune microenvironment and immunological response to checkpoint inhibitors in hepatocellular carcinoma

Journal for ImmunoTherapy of Cancer(2020)10.1136/jitc-2019-000394

N/A

0.624DataRank · unranked

63 citations

Ludmila Danilova, Su Jin Lim, Rohan Verma, Stephanie Xavier, James M. Leatherman +6 more

Entinostat Decreases Immune Suppression to Promote Antitumor Responses in a HER2+ Breast Tumor Microenvironment

Cancer Immunology Research(2022)10.1158/2326-6066.cir-21-0170

N/A

0.624DataRank · unranked

63 citations

Christine I. Rafie, Julie K. Jang, Sofi Castanon, Aaron G. Baugh, Edgar Gonzalez +21 more

Human Pancreatic Cancer Single-Cell Atlas Reveals Association of CXCL10+ Fibroblasts and Basal Subtype Tumor Cells

Clinical Cancer Research(2024)10.1158/1078-0432.ccr-24-2183

N/A

0.587DataRank · unranked

49 citations

Samantha B. Kemp, Kailee M. Hartway, Jacob T. Mitchell, Yuesong Wu, Samuel D. Zwernik +25 more

Entinostat, nivolumab and ipilimumab for women with advanced HER2-negative breast cancer: a phase Ib trial

Nature Cancer(2024)10.1038/s43018-024-00729-w

N/A

0.587DataRank · unranked

49 citations

Won Jin Ho, Ludmila Danilova, Joseph A. Tandurella, James M. Leatherman, Christine I. Rafie +22 more

A tumor-derived type III collagen-rich ECM niche regulates tumor cell dormancy

Research Square(2021)10.21203/rs.3.rs-580847/v1

N/A

0.564DataRank · unranked

42 citations

Ana Rita Nobre, Chandrani Mondal, Isrha Taha, Eduardo Farias, Elana J. Fertig +4 more

Individual variation in the emergence of anterior-to-posterior neural fates from human pluripotent stem cells

Stem Cell Reports(2024)10.1016/j.stemcr.2024.07.004

N/A

0.560DataRank · unranked

18 citations

Seungmae Seo, Genevieve L. Stein-O’Brien, Amritha Jaishankar, Kazuya Ogawa, Nicola Micali +19 more

Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces

Cell Systems(2023)10.1016/j.cels.2023.03.004

N/A

0.557DataRank · unranked

40 citations

Melanie Loth, Dimitrios N. Sidiropoulos, Shuming Zhang, Long Yuan, Alexander T.F. Bell +25 more

Ten quick tips for deep learning in biology

PLOS Computational Biology(2022)10.1371/journal.pcbi.1009803

N/A

0.550DataRank · unranked

38 citations

Anthony Gitter, Casey S. Greene, Sebastian Raschka, Finlay Maguire, Alexander J. Titus +16 more

Forecasting cancer: from precision to predictive medicine

Med(2021)10.1016/j.medj.2021.08.007

N/A

0.515DataRank · unranked

30 citations

Elizabeth M. Jaffee, Paul Macklin, Vered Stearns, Chenguang Wang, Elana J. Fertig

Intercellular signaling dynamics from a single cell atlas of the biomaterials response

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.24.218537

Top 38%

0.499DataRank

Top 38%13 citations

David R. Maestas, Jin Han, James I. Andorko, Patrick Cahan, Elana J. Fertig +3 more

Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS

Nature Protocols(2023)10.1038/s41596-023-00892-x

N/A

0.489DataRank · unranked

25 citations

Ashley Tsang, Jacob T. Mitchell, David Zhou, Julia Bowden, Emily F. Davis-Marcisak +13 more

Integrated immunological analysis of a successful conversion of locally advanced hepatocellular carcinoma to resectability with neoadjuvant therapy

Journal for ImmunoTherapy of Cancer(2020)10.1136/jitc-2020-000932

N/A

0.483DataRank · unranked

24 citations

Gaurav Sharma, Qingfeng Zhu, Genevieve L. Stein-O’Brien, Jennifer N. Durham, Robert A. Anders +8 more

Aberrant expression of CPSF1 promotes head and neck squamous cell carcinoma via regulating alternative splicing

PLoS ONE(2020)10.1371/journal.pone.0233380

N/A

0.483DataRank · unranked

24 citations

Mizuo Ando, Takahito Fukusumi, Shuling Ren, Chao Liu, Jesse R. Qualliotine +12 more

Ten challenges and opportunities in computational immuno-oncology

Journal for ImmunoTherapy of Cancer(2024)10.1136/jitc-2024-009721

N/A

0.471DataRank · unranked

11 citations

Alan D. Hutson, Mohammadhadi Khorrami, Vanessa D. Jönsson, Spencer R. Rosario, Jill S. Barnholtz‐Sloan +21 more

CD137 agonism enhances anti-PD1 induced activation of expanded CD8+ T cell clones in a neoadjuvant pancreatic cancer clinical trial

iScience(2024)10.1016/j.isci.2024.111569

Top 41%

0.459DataRank

Top 41%15 citations

Jacob T. Mitchell, Joseph A. Tandurella, Eric S. Christenson, Ludmila Danilova, Atul Deshpande +29 more

Antitumor T-cell Immunity Contributes to Pancreatic Cancer Immune Resistance

Cancer Immunology Research(2021)10.1158/2326-6066.cir-20-0272

N/A

0.442DataRank · unranked

18 citations

Zoe X. Malchiodi, Allison A. Fitzgerald, Annie Zuo, Shangzi Wang, Maha Moussa +10 more

Community-wide hackathons to identify central themes in single-cell multi-omics

Genome Biology(2021)10.1186/s13059-021-02433-9

N/A

0.436DataRank · unranked

15 citations

Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb +26 more

Multiomics Empowers Predictive Pancreatic Cancer Immunotherapy

The Journal of Immunology(2023)10.4049/jimmunol.2200660

N/A

0.434DataRank · unranked

17 citations

Elizabeth M. Jaffee, Elana J. Fertig, Janelle M. Montagne

Immune landscape of tertiary lymphoid structures in hepatocellular carcinoma (HCC) treated with neoadjuvant immune checkpoint blockade

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.16.562104

N/A

0.434DataRank · unranked

17 citations

Won Jin Ho, Luciane T. Kagohara, Alexander A. Girgis, Sarah M. Shin, Ludmila Danilova +29 more

Systems immunology spanning tumors, lymph nodes, and periphery

Cell Reports Methods(2023)10.1016/j.crmeth.2023.100670

N/A

0.403DataRank · unranked

9 citations

Won Jin Ho, Elizabeth M. Jaffee, Luciane T. Kagohara, Elana J. Fertig, Dimitrios N. Sidiropoulos

Spatial proteomics and transcriptomics reveal early immune cell organization in pancreatic intraepithelial neoplasia

JCI Insight(2025)10.1172/jci.insight.191595

N/A

0.368DataRank · unranked

10 citations

Jacob T. Mitchell, Sidharth Raghavan, Luciane T. Kagohara, Amanda L. Huff, Saurav D. Haldar +29 more

Inflammatory Signaling in Pancreatic Cancer Transfers Between a Single-cell RNA Sequencing Atlas and Co-Culture

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.14.500096

N/A

0.360DataRank · unranked

10 citations

Samantha Guinn, Joseph A. Tandurella, Jacob T. Mitchell, Dimitrios N. Sidiropoulos, Melanie Loth +24 more

Fibroblast activation protein regulates natural killer cell migration, extravasation and tumor infiltration

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.03.429622

N/A

0.330DataRank · unranked

6 citations

Rachael Maynard, Emily F. Davis-Marcisak, Apsra Nasir, Eric Glasgow, Sandra A. Jablonski +7 more

Career trajectories of MD-PhD physician scientists: The loss of women investigators

Cancer Cell(2024)10.1016/j.ccell.2024.04.006

N/A

0.292DataRank · unranked

6 citations

Lisa Gandy, Hanfei Qi, Elana J. Fertig, Amanda L. Blackford, Jennifer R. Grandis +1 more

Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R, and GenePattern Notebook implementations of CoGAPS

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.09.499398

N/A

0.292DataRank · unranked

6 citations

Ashley Tsang, Jacob T. Mitchell, Emily F. Davis-Marcisak, Thomas D. Sherman, Ted Liefeld +11 more

Enter the matrix: factorization uncovers knowledge from omics Names/Affiliations

bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/196915

N/A

0.269DataRank · unranked

5 citations

Raman Arora, Aedín C. Culhane, Alexander V. Favorov, Lana X. Garmire, Casey S. Greene +7 more

Antibody dependent cell-mediated cytotoxicity selection pressure induces diverse mechanisms of resistance

Cancer Biology & Therapy(2023)10.1080/15384047.2023.2269637

N/A

0.262DataRank · unranked

4 citations

Rossin Erbe, Yongwei Zhang, Theresa Guo, Zoe X. Malchiodi, Rachael Maynard +8 more

Analysis of immune checkpoint blockade biomarkers in elderly patients using large-scale cancer genomics data.

Journal of Clinical Oncology(2021)10.1200/jco.2021.39.15_suppl.2543

N/A

0.208DataRank · unranked

3 citations

Zheyu Wang, Sharon Wu, Joanne Xiu, Neeha Zaidi, Marc E. Lippman +12 more

Barcoding intracellular reverse transcription enables high-throughput phenotype-coupled T cell receptor analyses

Cell Reports Methods(2023)10.1016/j.crmeth.2023.100600

N/A

0.165DataRank · unranked

2 citations

Janelle M. Montagne, Thomas R. Nirschl, Emily F. Davis-Marcisak, Jeanette Johnson, Amanda L. Huff +10 more

Age-associated Senescent - T Cell Signaling Promotes Type 3 Immunity that Inhibits Regenerative Response

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.17.456641

N/A

0.165DataRank · unranked

2 citations

Christopher Cherry, Joscelyn C. Mejías, Anna Ruta, David R. Maestas, Alexis N. Peña +13 more

A field guide to cultivating computational biology

arXiv (Cornell University)(2021)10.48550/arxiv.2104.11364

N/A

0.104DataRank · unranked

1 citations

Casey S. Greene, Piero Carnici, Benilton S. Carvalho, Michiel de Hoon, Stacey D. Finley +9 more

Balancing ethical data sharing and open science for reproducible research in biomedical data science

Cell Reports Medicine(2025)10.1016/j.xcrm.2025.102080

N/A

0DataRank · unranked

5 citations

Allison Creason, Stuart S. Levine, Michael S. Noble, Anup A. Mahurkar, Owen White +2 more

Spatial profiling of human pancreatic ductal adenocarcinoma reveals molecular alterations associated with venous invasion

Science Translational Medicine(2025)10.1126/scitranslmed.ady7524

N/A

0DataRank · unranked

3 citations

Peter Chianchiano, Katsuya Hirose, Daniel James Salas-Escabillas, Doreen M. Zucha, Jacob T. Mitchell +12 more

Epigenetic profiling reveals key super-enhancer networks driving oncogenesis in HPV-positive HNSCC

iScience(2025)10.1016/j.isci.2025.113911

N/A

0DataRank · unranked

2 citations

Spencer S. Chan, Michael D. Kessler, Ilya E. Vorontsov, Andrey Loginov, Rossin Erbe +9 more

PIVOT: an open-source tool for multi-omic spatial data registration

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.06.08.658506

N/A

0DataRank · unranked

4 citations

Valentina Matos Romero, Ian Reucroft, Margaret Eminizer, Donald Kramer, Daniela Higuera +19 more

Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.02.651747

N/A

0DataRank · unranked

1 citations

Orian Stapleton, Kavita Krishnan, Sushma Nagaraj, Dmitrijs Lvovs, Christopher Cherry +13 more

Automated Quality Control of Time-Course Imaging from 3D in vitro cultures

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.03.31.646437

N/A

0DataRank · unranked

0 citations

Tamara Y. Lopez-Vidal, Jeanette Johnson, Vania Wang, Daniel Bergman, Ashani T. Weeraratna +6 more

Informatics at the Frontier of Cancer Research

Cancer Research(2025)10.1158/0008-5472.can-24-2829

N/A

0DataRank · unranked

0 citations

Taxiarchis Botsis, Pablo G. Cámara, Lauren Ciotti, Lee Cooper, Jeremy Goecks +19 more

Fibroblast activation protein promotes natural killer cell invasion and tumor infiltration

The Journal of Immunology(2025)10.1093/jimmun/vkaf279

N/A

0DataRank · unranked

0 citations

Allison A. Fitzgerald, Emily F. Davis-Marcisak, Apsra Nasir, Shira E. Eisman, Eric Glasgow +10 more

Comparative assessment of physiochemical metrics for the clustering of adaptive immune receptor repertoires

Nucleic Acids Research(2025)10.1093/nar/gkaf1156

N/A

0DataRank · unranked

0 citations

Amanda L. Huff, Emily F. Davis-Marcisak, Theron Palmer, Hanzhi Wang, Luciane T. Kagohara +12 more

Temporal reassignment and correspondence evaluation with quality control for time-course imaging of 3D cell culture

Cell Reports Methods(2025)10.1016/j.crmeth.2025.101237

N/A

0DataRank · unranked

0 citations

Tamara Y. Lopez-Vidal, Jeanette Johnson, Vania Wang, Daniel Bergman, Ashani T. Weeraratna +6 more

Antigen-presenting cancer-associated fibroblasts in pancreatic ductal adenocarcinoma differentially regulate Treg phenotype and function via CXCL9 and CCL22 3293

The Journal of Immunology(2025)10.1093/jimmun/vkaf283.1109

N/A

0DataRank · unranked

0 citations

Jacob T. Mitchell, Meredith Wetzel, Nicole Groß, Lalitya Andaloori, Kathryn L. Howe +9 more

Community-wide hackathons to identify central themes in single-cell multi-omics

UNC Libraries(2025)10.17615/96cj-z232

N/A

0DataRank · unranked

0 citations

Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb +26 more

A cell-state axis underlying colonization in carcinomas with implications for metastasis risk prediction and interception

Cell Reports(2025)10.1016/j.celrep.2025.116701

N/A

0DataRank · unranked

0 citations

Zijie Li, Rachel K. Dveirin, Jeff Lin, Weixiang Fang, Shihan Wu +7 more

Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics

Genome Biology(2021)10.1186/s13059-021-02468-y

N/A

0DataRank · unranked

0 citations

Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb +26 more

Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics

UNC Libraries(2025)10.17615/vzc0-qk25

N/A

0DataRank · unranked

0 citations

Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb +26 more

projectR: an R/Bioconductor package for transfer learning via PCA, NMF, correlation and clustering

Bioinformatics(2020)10.1093/bioinformatics/btaa183

N/A

0DataRank · unranked

84 citations

Carlo Colantuoni, Loyal A. Goff, Elana J. Fertig, Genevieve L. Stein-O’Brien, Gaurav Sharma

Digital Pathology Analysis Quantifies Spatial Heterogeneity of CD3, CD4, CD8, CD20, and FoxP3 Immune Markers in Triple-Negative Breast Cancer

Frontiers in Physiology(2020)10.3389/fphys.2020.583333

N/A

0DataRank · unranked

79 citations

Chang Gong, Jeremias Sulam, Elana J. Fertig, Alexander S. Szalay, Elizabeth M. Jaffee +5 more

CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures

BMC Bioinformatics(2020)10.1186/s12859-020-03796-9

N/A

0DataRank · unranked

39 citations

Tiger Gao, Elana J. Fertig, Thomas D. Sherman

Variation of Human Neural Stem Cells Generating Organizer States In Vitro before Committing to Cortical Excitatory or Inhibitory Neuronal Fates

Cell Reports(2020)10.1016/j.celrep.2020.107599

N/A

0DataRank · unranked

35 citations

Suel–Kee Kim, Marcelo Diaz-Bustamante, Genevieve L. Stein-O’Brien, Seungmae Seo, Joo Heon Shin +18 more

Extracellular Vesicles Released by Tumor Endothelial Cells Spread Immunosuppressive and Transforming Signals Through Various Recipient Cells

Frontiers in Cell and Developmental Biology(2020)10.3389/fcell.2020.00698

N/A

0DataRank · unranked

24 citations

Enrica Favaro, Ludmila Danilova, Elana J. Fertig, Alexander V. Favorov, Luciane T. Kagohara +9 more

Transfer learning between preclinical models and human tumors identifies conserved NK cell activation signature in anti-CTLA-4 responsive tumors

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.31.125625

N/A

0DataRank · unranked

9 citations

Allison A. Fitzgerald, Michael D. Kessler, Ludmila Danilova, Elizabeth M. Jaffee, Neeha Zaidi +3 more

nearBynding: A flexible pipeline characterizing protein binding to local RNA structure

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.24.352591

N/A

0DataRank · unranked

1 citations

Alexander V. Favorov, Elana J. Fertig, Anthony K. L. Leung, Veronica F. Busa

Inferring causal molecular networks: empirical assessment through a community-based effort

UNC Libraries(2020)10.17615/j5nb-5n89

N/A

0DataRank · unranked

0 citations

Steven M. Hill, Daoud Meerzaman, Venkateshan Kannan, Bahman Afsari, Takeshi Hase +95 more

Dynamics in hybrid complex systems of switches and oscillators

UNC Libraries(2020)10.17615/x6g0-ht94

N/A

0DataRank · unranked

0 citations

Dane Taylor, Juan Guillermo Restrepo, Elana J. Fertig

A tumor-derived type III collagen-rich ECM niche regulates tumor cell dormancy

Nature Cancer(2021)10.1038/s43018-021-00291-9

N/A

0DataRank · unranked

303 citations

Ana Rita Nobre, Chandrani Mondal, Isra Taha, Eduardo Farias, Elana J. Fertig +4 more

Systemic inhibition of PTPN22 augments anticancer immunity

Journal of Clinical Investigation(2021)10.1172/jci146950

N/A

0DataRank · unranked

53 citations

Sarah Croessmann, Jianping Lin, Zaw Phyo, Soren Charmsaz, Ludmila Danilova +18 more

Newly Identified Members of FGFR1 Splice Variants Engage in Cross-talk with AXL/AKT Axis in Salivary Adenoid Cystic Carcinoma

Cancer Research(2021)10.1158/0008-5472.can-20-1780

N/A

0DataRank · unranked

20 citations

Hyun-Su Kim, Brandon Leonard, Shizhang Ling, Bhumsuk Keam, Luigi Marchionni +7 more

Forecasting cellular states: from descriptive to predictive biology via single-cell multiomics

Current Opinion in Systems Biology(2021)10.1016/j.coisb.2021.03.008

N/A

0DataRank · unranked

17 citations

Michaela C. Ainslie, Elana J. Fertig, Genevieve L. Stein-O’Brien

Spatial correlation statistics enable transcriptome-wide characterization of RNA structure binding

Cell Reports Methods(2021)10.1016/j.crmeth.2021.100088

N/A

0DataRank · unranked

11 citations

Alexander V. Favorov, Elana J. Fertig, Anthony K. L. Leung, Veronica F. Busa

Feasibility and efficacy of neoadjuvant cabozantinib and nivolumab in patients with borderline resectable or locally advanced hepatocellular carcinoma (HCC).

Journal of Clinical Oncology(2021)10.1200/jco.2021.39.3_suppl.335

N/A

0DataRank · unranked

22 citations

Qingfeng Zhu, Jennifer N. Durham, Nicole Groß, Soren Charmsaz, James M. Leatherman +14 more

Expression bias in retinoic acid responsive genes defines variations in neural differentiation of human pluripotent stem cells

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.17.435870

N/A

0DataRank · unranked

0 citations

Seungmae Seo, Genevieve L. Stein-O’Brien, Amritha Jaishankar, Kazuya Ogawa, Nicola Micali +18 more

scatterHatch: an R/Bioconductor package for generating colorblind-friendly scatter plots for single-cell data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.07.463279

N/A

0DataRank · unranked

0 citations

Elana J. Fertig, Atul Deshpande, Tejas Guha

The use of machine learning to discover regulatory networks controlling biological systems

Molecular Cell(2022)10.1016/j.molcel.2021.12.011

N/A

0DataRank · unranked

42 citations

Jessica Gore, Kelly Gemmill, Daria A. Gaykalova, Elana J. Fertig, Rossin Erbe

Engineered bispecific antibodies targeting the interleukin-6 and -8 receptors potently inhibit cancer cell migration and tumor metastasis

Molecular Therapy(2022)10.1016/j.ymthe.2022.07.008

N/A

0DataRank · unranked

29 citations

Michelle N. Karl, Wentao Wang, Bartholomew Starich, Haotian Tan, Ashley Kiemen +9 more

Integrated T cell cytometry metrics for immune-monitoring applications in immunotherapy clinical trials

JCI Insight(2022)10.1172/jci.insight.160398

N/A

0DataRank · unranked

17 citations

Genevieve L. Stein-O’Brien, Ludmila Danilova, Nicole Groß, Soren Charmsaz, Stephanie Xavier +7 more

Model-informed experimental design recommendations for distinguishing intrinsic and acquired targeted therapeutic resistance in head and neck cancer

npj Systems Biology and Applications(2022)10.1038/s41540-022-00244-7

N/A

0DataRank · unranked

16 citations

Constance J. Reznik, Ruchira S. Ranaweera, Feifei Song, Christine H. Chung, Elana J. Fertig +2 more

PanIN and CAF Transitions in Pancreatic Carcinogenesis Revealed with Spatial Data Integration

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.16.500312

N/A

0DataRank · unranked

15 citations

Jacob T. Mitchell, Ashley Kiemen, Kohei Fujikura, Helen Fedor, Bonnie Gambichler +15 more

Transfer learning of an in vivo- derived senescence signature identifies conserved and tissue-specific senescence across species and diverse pathologies

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.22.485297

N/A

0DataRank · unranked

1 citations

James I. Andorko, Kavita Krishnan, Joscelyn C. Mejías, Helen Nguyễn, Katlin B. Stivers +19 more

Using Mathematical Modeling to Distinguish Intrinsic and Acquired Targeted Therapeutic Resistance in Head and Neck Cancer

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.18.481078

N/A

0DataRank · unranked

0 citations

Constance J. Reznik, Ruchira S. Ranaweera, Feifei Song, Christine H. Chung, Elana J. Fertig +2 more

Transfer learning identifies in vivo senescence heterogeneity and contributions to vascularization and matrix production across species and diverse pathologies

Research Square(2022)10.21203/rs.3.rs-1847932/v1

N/A

0DataRank · unranked

0 citations

James I. Andorko, Kavita Krishnan, Joscelyn C. Mejías, Helen Nguyễn, Katlin B. Stivers +21 more

Regression Expression Variation Analysis (REVA): a rank-based multi-dimensional measure of correlation

(2022)10.1109/icmla55696.2022.00176

N/A

0DataRank · unranked

0 citations

Alexander V. Favorov, Elana J. Fertig, Leslie Cope, Bahman Afsari

Transfer learning in a biomaterial fibrosis model identifies in vivo senescence heterogeneity and contributions to vascularization and matrix production across species and diverse pathologies

GeroScience(2023)10.1007/s11357-023-00785-7

N/A

0DataRank · unranked

66 citations

James I. Andorko, Kavita Krishnan, Joscelyn C. Mejías, Helen Nguyễn, Katlin B. Stivers +21 more

Morphology-guided transcriptomic analysis of human pancreatic cancer organoids reveals microenvironmental signals that enhance invasion

Journal of Clinical Investigation(2023)10.1172/jci162054

N/A

0DataRank · unranked

24 citations

Hildur Knútsdóttir, Fatemeh Shojaeian, Michael G. Lerner, Maria F. Wissler, Elodie Henriet +15 more

Age‐associated Senescent – T Cell Signaling Promotes Type 3 Immunity that Inhibits the Biomaterial Regenerative Response

Advanced Materials(2023)10.1002/adma.202310476

N/A

0DataRank · unranked

17 citations

Christopher Cherry, Joscelyn C. Mejías, Kavita Krishnan, Anna Ruta, David R. Maestas +15 more

Informing virtual clinical trials of hepatocellular carcinoma with spatial multi-omics analysis of a human neoadjuvant immunotherapy clinical trial

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.11.553000

N/A

0DataRank · unranked

6 citations

Atul Deshpande, Babita K. Verma, Hanwen Wang, Hao‐Yang Mi, Long Yuan +9 more

Boosting Single-Cell RNA Sequencing Analysis with Simple Neural Attention

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.29.542760

N/A

0DataRank · unranked

2 citations

A. Ali Heydari, Elana J. Fertig, Suzanne Sindi, Katrina K. Hoyer, Oscar A. Davalos

Fibroblast activation protein regulates natural killer cell migration, extravasation and tumor infiltration

Research Square(2023)10.21203/rs.3.rs-3706465/v1

N/A

0DataRank · unranked

2 citations

Allison A. Fitzgerald, Rachael Maynard, Emily F. Davis-Marcisak, Apsra Nasir, Eric Glasgow +7 more

Data from Newly Identified Members of FGFR1 Splice Variants Engage in Cross-talk with AXL/AKT Axis in Salivary Adenoid Cystic Carcinoma

(2023)10.1158/0008-5472.c.6512485.v1

N/A

0DataRank · unranked

0 citations

Hyun‐Su Kim, Brandon Leonard, Shizhang Ling, Bhumsuk Keam, Luigi Marchionni +7 more

Data from Antitumor T-cell Immunity Contributes to Pancreatic Cancer Immune Resistance

(2023)10.1158/2326-6066.c.6550273.v1

N/A

0DataRank · unranked

0 citations

Zoe X. Malchiodi, Allison A. Fitzgerald, Annie Zuo, Shangzi Wang, Maha Moussa +10 more

PanIN and CAF transitions in pancreatic carcinogenesis revealed with spatial data integration

Cell Systems(2024)10.1016/j.cels.2024.07.001

N/A

0DataRank · unranked

52 citations

Jacob T. Mitchell, Ashley Kiemen, Melissa R. Lyman, Kohei Fujikura, Jae W. Lee +22 more

Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional regulation

Science Immunology(2024)10.1126/sciimmunol.adk4893

N/A

0DataRank · unranked

41 citations

Jennifer Tran, Pamela Wong, Changxu Fan, E. E. Schmidt, Bryan Fisk +24 more

Integration of Clinical Trial Spatial Multiomics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

Cancer Research(2024)10.1158/0008-5472.can-24-0943

N/A

0DataRank · unranked

35 citations

Atul Deshpande, Babita K. Verma, Hanwen Wang, Haoyang Mi, Long Yuan +9 more

Computational methods and biomarker discovery strategies for spatial proteomics: a review in immuno-oncology

Briefings in Bioinformatics(2024)10.1093/bib/bbae421

N/A

0DataRank · unranked

34 citations

Shamilene Sivagnanam, Won Jin Ho, Shuming Zhang, Daniel Bergman, Atul Deshpande +6 more

Virtual patient analysis identifies strategies to improve the performance of predictive biomarkers for PD-1 blockade

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2410911121

N/A

0DataRank · unranked

15 citations

Hanwen Wang, Atul Deshpande, Ravi Varadhan, Leisha A. Emens, Elizabeth M. Jaffee +4 more

Leveraging multi-omics data to empower quantitative systems pharmacology in immuno-oncology

Briefings in Bioinformatics(2024)10.1093/bib/bbae131

N/A

0DataRank · unranked

15 citations

Hanwen Wang, Alberto Ippolito, Shuming Zhang, Elana J. Fertig, Aleksander S. Popel +1 more

Phosphodiesterase-5 inhibition collaborates with vaccine-based immunotherapy to reprogram myeloid cells in pancreatic ductal adenocarcinoma

JCI Insight(2024)10.1172/jci.insight.179292

N/A

0DataRank · unranked

9 citations

Zhehao Zhang, Jacob T. Mitchell, Soren Charmsaz, Alexei Hernandez, Erin M. Coyne +17 more

Claudin 7 suppresses invasion and metastasis through repression of a smooth muscle actin program

The Journal of Cell Biology(2024)10.1083/jcb.202311002

N/A

0DataRank · unranked

4 citations

Rosela Golloshi, Chae Yun Cho, Yuqian Wang, Parker Stevenson, Genevieve L. Stein-O’Brien +3 more

Identifying a gene signature of metastatic potential by linking pre-metastatic state to ultimate metastatic fate

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.08.14.607813

N/A

0DataRank · unranked

0 citations

Zijie Li, Rachel Dveirin, Weixiang Fang, Hani Goodarzi, Elana J. Fertig +2 more

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