Elana J. Fertig

Publication Activity (10 Years)

Years Active: 2010-2024
Publications (10 Years): 12

Top Topics

Matrix Factorisation

Ordinary Differential Equations

Statistical Modeling

Top Venues

PLoS Comput. Biol.

Publications

Theinmozhi Arulraj, Hanwen Wang, Alberto Ippolito, Shuming Zhang, Elana J. Fertig, Aleksander S. Popel
Leveraging multi-omics data to empower quantitative systems pharmacology in immuno-oncology. Briefings Bioinform. 25 (3) (2024)
Rossin Erbe, Genevieve L. Stein-O'Brien, Elana J. Fertig
Transcriptomic forecasting with neural ordinary differential equations. Patterns 4 (8) (2023)
Bahman Afsari, Alexander V. Favorov, Elana J. Fertig, Leslie Cope
Regression Expression Variation Analysis (REVA): a rank-based multi-dimensional measure of correlation. ICMLA (2022)
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
Ten quick tips for deep learning in biology. PLoS Comput. Biol. 18 (3) (2022)
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
Ten Quick Tips for Deep Learning in Biology. CoRR (2021)
Anne E. Carpenter, Casey S. Greene, Piero Carnici, Benilton S. Carvalho, Michiel de Hoon, Stacey Finley, Kim-Anh Le Cao, Jerry S. H. Lee, Luigi Marchionni, Suzanne Sindi, Fabian J. Theis, Gregory P. Way, Jean Y. H. Yang, Elana J. Fertig
A field guide to cultivating computational biology. CoRR (2021)
Thomas Sherman, Tiger Gao, Elana J. Fertig
CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures. BMC Bioinform. 21 (1) (2020)
Gaurav Sharma, Carlo Colantuoni, Loyal A. Goff, Elana J. Fertig, Genevieve L. Stein-O'Brien
projectR: an R/Bioconductor package for transfer learning via PCA, NMF, correlation and clustering. Bioinform. 36 (11) (2020)
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
CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer. PLoS Comput. Biol. 15 (4) (2019)
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
Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer. Bioinform. 34 (11) (2018)
Elena D. Stavrovskaya, Tejasvi Niranjan, Elana J. Fertig, Sarah J. Wheelan, Alexander V. Favorov, Andrey A. Mironov
StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data. Bioinform. 33 (20) (2017)
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
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF. Bioinform. 33 (12) (2017)
Michael Considine, Hilary S. Parker, Yingying Wei, Xaio Xia, Leslie Cope, Michael F. Ochs, Elana J. Fertig
AGA: Interactive pipeline for reproducible genomics analyses. F1000Research 4 (2015)
Bahman Afsari, Elana J. Fertig, Donald Geman, Luigi Marchionni
switchBox: an R package for k-Top Scoring Pairs classifier development. Bioinform. 31 (2) (2015)
Conor J. Kelton, Waishing Lee, Matthew Rusay, Ondrej Maxian, Elana J. Fertig, Michael F. Ochs
The estimation of dimensionality in gene expression data using Nonnegative Matrix Factorization. BIBM (2015)
Hilary S. Parker, Jeffrey T. Leek, Alexander V. Favorov, Michael Considine, Xiaoxin Xia, Sameer Chavan, Christine H. Chung, Elana J. Fertig
Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction. Bioinform. 30 (19) (2014)
Matthew R. Francis, Elana J. Fertig
Quantifying the Dynamics of Coupled Networks of Switches and Oscillators. RECOMB (2012)
Elana J. Fertig, Alexander V. Favorov, Michael F. Ochs
Identifying context-specific transcription factor targets from prior knowledge and gene expression data. BIBM (2012)
Michael F. Ochs, Elana J. Fertig
Matrix factorization for transcriptional regulatory network inference. CIBCB (2012)
Elana J. Fertig, Jie Ding, Alexander V. Favorov, Giovanni Parmigiani, Michael F. Ochs
CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data. Bioinform. 26 (21) (2010)