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Elana 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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last updated on 2024-05-08 21:00 CEST by the dblp team
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