Elana J. Fertig

According to our database, Elana J. Fertig authored at least 21 papers between 2010 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

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

Theinmozhi Arulraj, Hanwen Wang, Alberto Ippolito, Shuming Zhang, Elana J. Fertig, Aleksander S. Popel

Briefings Bioinform., 2024

2023

Transcriptomic forecasting with neural ordinary differential equations.

Rossin Erbe, Genevieve L. Stein-O'Brien, Elana J. Fertig

Patterns, August, 2023

2022

Ten quick tips for deep learning in biology.

Benjamin D. Lee, Anthony Gitter, Casey S. Greene, Sebastian Raschka, Finlay Maguire, Alexander J. Titus, Michael D. Kessler, Alexandra J. Lee, Marc G. Chevrette, Paul Allen Stewart, Thiago Britto-Borges, Evan M. Cofer, Kun-Hsing Yu, Juan Jose Carmona, Elana J. Fertig, Alexandr A. Kalinin, Brandon Signal, Benjamin J. Lengerich, Timothy J. Triche Jr., Simina M. Boca

PLoS Comput. Biol., 2022

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

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

Proceedings of the 21st IEEE International Conference on Machine Learning and Applications, 2022

2021

Ten Quick Tips for Deep Learning in Biology.

Benjamin D. Lee, Anthony Gitter, Casey S. Greene, Sebastian Raschka, Finlay Maguire, Alexander J. Titus, Michael D. Kessler, Alexandra J. Lee, Marc G. Chevrette, Paul Allen Stewart, Thiago Britto-Borges, Evan M. Cofer, Kun-Hsing Yu, Juan Jose Carmona, Elana J. Fertig, Alexandr A. Kalinin, Beth Signal, Benjamin J. Lengerich, Timothy J. Triche Jr., Simina M. Boca

CoRR, 2021

A field guide to cultivating computational biology.

Anne E. Carpenter, Casey S. Greene, Piero Carnici, Benilton S. Carvalho, Michiel de Hoon, Stacey D. Finley, Kim-Anh Lê Cao, Jerry S. H. Lee, Luigi Marchionni, Suzanne Sindi, Fabian J. Theis, Gregory P. Way, Jean Y. H. Yang, Elana J. Fertig

CoRR, 2021

2020

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

Thomas Sherman, Tiger Gao, Elana J. Fertig

BMC Bioinform., 2020

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

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

Bioinform., 2020

2019

CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer.

Thomas Sherman, Luciane T. Kagohara, Raymon Cao, Raymond Cheng, Matthew Satriano, Michael Considine, Gabriel Krigsfeld, Ruchira Ranaweera, Yong Tang, Sandra A. Jablonski, Genevieve L. Stein-O'Brien, Daria A. Gaykalova, Louis M. Weiner, Christine H. Chung, Elana J. Fertig

PLoS Comput. Biol., 2019

2018

Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer.

Bahman Afsari, Theresa Guo, Michael Considine, Liliana Florea, Luciane T. Kagohara, Genevieve L. Stein-O'Brien, Dylan Kelley, Emily Flam, Kristina D. Zambo, Patrick K. Ha, Donald Geman, Michael F. Ochs, Joseph A. Califano, Daria A. Gaykalova, Alexander V. Favorov, Elana J. Fertig

Bioinform., 2018

2017

PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.

Genevieve L. Stein-O'Brien, Jacob L. Carey, Waishing Lee, Michael Considine, Alexander V. Favorov, Emily Flam, Theresa Guo, Sijia Li, Luigi Marchionni, Thomas Sherman, Shawn Sivy, Daria A. Gaykalova, Ronald McKay, Michael F. Ochs, Carlo Colantuoni, Elana J. Fertig

Bioinform., 2017

StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data.

Elena D. Stavrovskaya, Tejasvi Niranjan, Elana J. Fertig, Sarah J. Wheelan, Alexander V. Favorov, Andrey A. Mironov

Bioinform., 2017

2015

AGA: Interactive pipeline for reproducible genomics analyses.

Michael Considine, Hilary S. Parker, Yingying Wei, Xaio Xia, Leslie Cope, Michael F. Ochs, Elana J. Fertig

F1000Research, 2015

switchBox: an R package for k-Top Scoring Pairs classifier development.

Bahman Afsari, Elana J. Fertig, Donald Geman, Luigi Marchionni

Bioinform., 2015

The estimation of dimensionality in gene expression data using Nonnegative Matrix Factorization.

Conor J. Kelton, Waishing Lee, Matthew Rusay, Ondrej Maxian, Elana J. Fertig, Michael F. Ochs

Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

2014

Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction.

Hilary S. Parker, Jeffrey T. Leek, Alexander V. Favorov, Michael Considine, Xiaoxin Xia, Sameer Chavan, Christine H. Chung, Elana J. Fertig

Bioinform., 2014

2012

Quantifying the Dynamics of Coupled Networks of Switches and Oscillators.

Matthew R. Francis, Elana J. Fertig

Proceedings of the Research in Computational Molecular Biology, 2012

Matrix factorization for transcriptional regulatory network inference.

Michael F. Ochs, Elana J. Fertig

Proceedings of the 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2012

Identifying context-specific transcription factor targets from prior knowledge and gene expression data.

Elana J. Fertig, Alexander V. Favorov, Michael F. Ochs

Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

2011

Cancer Systems Biology.

Elana J. Fertig, Ludmila V. Danilova, Michael F. Ochs

Proceedings of the Handbook of Statistical Bioinformatics., 2011

2010

CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.

Elana J. Fertig, Jie Ding, Alexander V. Favorov, Giovanni Parmigiani, Michael F. Ochs

Bioinform., 2010