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ORCIDElana J. Fertig
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2020 – today
- 2024
[j12]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)- 2023
- [j11]Rossin Erbe, Genevieve L. Stein-O'Brien, Elana J. Fertig:
Transcriptomic forecasting with neural ordinary differential equations. Patterns 4(8): 100793 (2023) - 2022
- [j10]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) - [c5]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: 1063-1070 - 2021
- [i3]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:
A field guide to cultivating computational biology. CoRR abs/2104.11364 (2021) - [i2]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 abs/2105.14372 (2021) - 2020
- [j9]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): 3592-3593 (2020) - [j8]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): 453 (2020)
2010 – 2019
- 2019
- [j7]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) - 2018
- [j6]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): 1859-1867 (2018) - 2017
- [j5]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): 1892-1894 (2017) - [j4]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): 3158-3165 (2017) - 2015
- [j3]Bahman Afsari, Elana J. Fertig, Donald Geman, Luigi Marchionni:
switchBox: an R package for k-Top Scoring Pairs classifier development. Bioinform. 31(2): 273-274 (2015) - [c4]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: 1642-1649 - [i1]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: 28 (2015) - 2014
- [j2]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): 2757-2763 (2014) - 2012
- [c3]Elana J. Fertig, Alexander V. Favorov, Michael F. Ochs:
Identifying context-specific transcription factor targets from prior knowledge and gene expression data. BIBM 2012: 1-6 - [c2]Michael F. Ochs, Elana J. Fertig:
Matrix factorization for transcriptional regulatory network inference. CIBCB 2012: 387-396 - [c1]Matthew R. Francis, Elana J. Fertig:
Quantifying the Dynamics of Coupled Networks of Switches and Oscillators. RECOMB 2012: 60-61 - 2011
- [p1]Elana J. Fertig, Ludmila V. Danilova, Michael F. Ochs:
Cancer Systems Biology. Handbook of Statistical Bioinformatics 2011: 533-565 - 2010
- [j1]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): 2792-2793 (2010)
Coauthor Index
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