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Digital Pathology Analysis Quantifies Spatial Heterogeneity of CD3, CD4, CD8, CD20, and FoxP3 Immune Markers in Triple-Negative Breast Cancer.
Published in:
Frontiers in Physiology, 2020, v. 11, p. N.PAG, doi. 10.3389/fphys.2020.583333
By:
- Mi, Haoyang;
- Gong, Chang;
- Sulam, Jeremias;
- Fertig, Elana J.;
- Szalay, Alexander S.;
- Jaffee, Elizabeth M.;
- Stearns, Vered;
- Emens, Leisha A.;
- Cimino-Mathews, Ashley M.;
- Popel, Aleksander S.
Publication type:
Article
Transfer learning between preclinical models and human tumors identifies a conserved NK cell activation signature in anti-CTLA-4 responsive tumors.
Published in:
Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-021-00944-5
By:
- Davis-Marcisak, Emily F.;
- Fitzgerald, Allison A.;
- Kessler, Michael D.;
- Danilova, Ludmila;
- Jaffee, Elizabeth M.;
- Zaidi, Neeha;
- Weiner, Louis M.;
- Fertig, Elana J.
Publication type:
Article
A preliminary analysis of interleukin-1 ligands as potential predictive biomarkers of response to cetuximab.
Published in:
Biomarker Research, 2019, v. 7, n. 1, p. N.PAG, doi. 10.1186/s40364-019-0164-0
By:
- Espinosa-Cotton, Madelyn;
- Fertig, Elana J.;
- Stabile, Laura P.;
- Gaither-Davis, Autumn;
- Bauman, Julie E.;
- Schmitz, Sandra;
- Gibson-Corley, Katherine N.;
- Cheng, Yinwen;
- Jensen, Isaac J.;
- Badovinac, Vladimir P.;
- Laux, Douglas;
- Simons, Andrean L.
Publication type:
Article
Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways.
Published in:
Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02363-6
By:
- Ho, Won Jin;
- Erbe, Rossin;
- Danilova, Ludmila;
- Phyo, Zaw;
- Bigelow, Emma;
- Stein-O'Brien, Genevieve;
- Thomas II, Dwayne L.;
- Charmsaz, Soren;
- Gross, Nicole;
- Woolman, Skylar;
- Cruz, Kayla;
- Munday, Rebecca M.;
- Zaidi, Neeha;
- Armstrong, Todd D.;
- Sztein, Marcelo B.;
- Yarchoan, Mark;
- Thompson, Elizabeth D.;
- Jaffee, Elizabeth M.;
- Fertig, Elana J.
Publication type:
Article
Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence.
Published in:
Genome Medicine, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13073-023-01218-y
By:
- Zhang, Shuming;
- Yuan, Long;
- Danilova, Ludmila;
- Mo, Guanglan;
- Zhu, Qingfeng;
- Deshpande, Atul;
- Bell, Alexander T. F.;
- Elisseeff, Jennifer;
- Popel, Aleksander S.;
- Anders, Robert A.;
- Jaffee, Elizabeth M.;
- Yarchoan, Mark;
- Fertig, Elana J.;
- Kagohara, Luciane T.
Publication type:
Article
Expression Microarray Analysis Reveals Alternative Splicing of <i>LAMA3</i> and <i>DST</i> Genes in Head and Neck Squamous Cell Carcinoma.
Published in:
PLoS ONE, 2014, v. 9, n. 3, p. 1, doi. 10.1371/journal.pone.0091263
By:
- Li, Ryan;
- Ochs, Michael F.;
- Ahn, Sun Mi;
- Hennessey, Patrick;
- Tan, Marietta;
- Soudry, Ethan;
- Gaykalova, Daria A.;
- Uemura, Mamoru;
- Brait, Mariana;
- Shao, Chunbo;
- Westra, William;
- Bishop, Justin;
- Fertig, Elana J.;
- Califano, Joseph A.
Publication type:
Article
Preferential Activation of the Hedgehog Pathway by Epigenetic Modulations in HPV Negative HNSCC Identified with Meta-Pathway Analysis.
Published in:
PLoS ONE, 2013, v. 8, n. 11, p. 1, doi. 10.1371/journal.pone.0078127
By:
- Fertig, Elana J.;
- Markovic, Ana;
- Danilova, Ludmila V.;
- Gaykalova, Daria A.;
- Cope, Leslie;
- Chung, Christine H.;
- Ochs, Michael F.;
- Califano, Joseph A.
Publication type:
Article
Quantifying the Dynamics of Coupled Networks of Switches and Oscillators.
Published in:
PLoS ONE, 2012, v. 7, n. 1, p. 1, doi. 10.1371/journal.pone.0029497
By:
- Francis, Matthew R.;
- Fertig, Elana J.
Publication type:
Article
Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.
Published in:
2019
By:
- Ando, Mizuo;
- Saito, Yuki;
- Xu, Guorong;
- Bui, Nam Q.;
- Medetgul-Ernar, Kate;
- Pu, Minya;
- Fisch, Kathleen;
- Ren, Shuling;
- Sakai, Akihiro;
- Fukusumi, Takahito;
- Liu, Chao;
- Haft, Sunny;
- Pang, John;
- Mark, Adam;
- Gaykalova, Daria A.;
- Guo, Theresa;
- Favorov, Alexander V.;
- Yegnasubramanian, Srinivasan;
- Fertig, Elana J.;
- Ha, Patrick
Publication type:
Correction Notice
Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-09937-w
By:
- Ando, Mizuo;
- Saito, Yuki;
- Xu, Guorong;
- Bui, Nam Q.;
- Medetgul-Ernar, Kate;
- Pu, Minya;
- Fisch, Kathleen;
- Ren, Shuling;
- Sakai, Akihiro;
- Fukusumi, Takahito;
- Liu, Chao;
- Haft, Sunny;
- Pang, John;
- Mark, Adam;
- Gaykalova, Daria A.;
- Guo, Theresa;
- Favorov, Alexander V.;
- Yegnasubramanian, Srinivasan;
- Fertig, Elana J.;
- Ha, Patrick
Publication type:
Article
Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-09937-w
By:
- Ando, Mizuo;
- Saito, Yuki;
- Xu, Guorong;
- Bui, Nam Q.;
- Medetgul-Ernar, Kate;
- Pu, Minya;
- Fisch, Kathleen;
- Ren, Shuling;
- Sakai, Akihiro;
- Fukusumi, Takahito;
- Liu, Chao;
- Haft, Sunny;
- Pang, John;
- Mark, Adam;
- Gaykalova, Daria A.;
- Guo, Theresa;
- Favorov, Alexander V.;
- Yegnasubramanian, Srinivasan;
- Fertig, Elana J.;
- Ha, Patrick
Publication type:
Article
Ten quick tips for deep learning in biology.
Published in:
PLoS Computational Biology, 2022, v. 18, n. 3, p. 1, doi. 10.1371/journal.pcbi.1009803
By:
- Lee, Benjamin D.;
- Gitter, Anthony;
- Greene, Casey S.;
- Raschka, Sebastian;
- Maguire, Finlay;
- Titus, Alexander J.;
- Kessler, Michael D.;
- Lee, Alexandra J.;
- Chevrette, Marc G.;
- Stewart, Paul Allen;
- Britto-Borges, Thiago;
- Cofer, Evan M.;
- Yu, Kun-Hsing;
- Carmona, Juan Jose;
- Fertig, Elana J.;
- Kalinin, Alexandr A.;
- Signal, Brandon;
- Lengerich, Benjamin J.;
- Triche Jr., Timothy J.;
- Boca, Simina M.
Publication type:
Article
Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer.
Published in:
Scientific Reports, 2019, v. 9, n. 1, p. N.PAG, doi. 10.1038/s41598-019-51018-x
By:
- Flam, Emily L.;
- Danilova, Ludmila;
- Kelley, Dylan Z.;
- Stavrovskaya, Elena;
- Guo, Theresa;
- Considine, Michael;
- Qian, Jiang;
- Califano, Joseph A.;
- Favorov, Alexander;
- Fertig, Elana J.;
- Gaykalova, Daria A.
Publication type:
Article
Aberrant expression of CPSF1 promotes head and neck squamous cell carcinoma via regulating alternative splicing.
Published in:
PLoS ONE, 2020, p. 1, doi. 10.1371/journal.pone.0233380
By:
- Sakai, Akihiro;
- Ando, Mizuo;
- Fukusumi, Takahito;
- Ren, Shuling;
- Liu, Chao;
- Qualliotine, Jesse;
- Haft, Sunny;
- Sadat, Sayed;
- Saito, Yuki;
- Guo, Theresa W.;
- Xu, Guorong;
- Sasik, Roman;
- Fisch, Kathleen M.;
- Gutkind, J. Silvio;
- Fertig, Elana J.;
- Molinolo, Alfredo A.;
- Califano, Joseph A.
Publication type:
Article
A field guide to cultivating computational biology.
Published in:
PLoS Biology, 2021, v. 19, n. 10, p. 1, doi. 10.1371/journal.pbio.3001419
By:
- Way, Gregory P.;
- Greene, Casey S.;
- Carninci, Piero;
- Carvalho, Benilton S.;
- de Hoon, Michiel;
- Finley, Stacey;
- Gosline, Sara J. C.;
- Lȇ Cao, Kim-Anh;
- Lee, Jerry S. H.;
- Marchionni, Luigi;
- Robine, Nicolas;
- Sindi, Suzanne S.;
- Theis, Fabian J.;
- Yang, Jean Y. H.;
- Carpenter, Anne E.;
- Fertig, Elana J.
Publication type:
Article
Computational methods and biomarker discovery strategies for spatial proteomics: a review in immuno-oncology.
Published in:
Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae421
By:
- Mi, Haoyang;
- Sivagnanam, Shamilene;
- Ho, Won Jin;
- Zhang, Shuming;
- Bergman, Daniel;
- Deshpande, Atul;
- Baras, Alexander S;
- Jaffee, Elizabeth M;
- Coussens, Lisa M;
- Fertig, Elana J;
- Popel, Aleksander S
Publication type:
Article
Leveraging multi-omics data to empower quantitative systems pharmacology in immuno-oncology.
Published in:
Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae131
By:
- Arulraj, Theinmozhi;
- Wang, Hanwen;
- Ippolito, Alberto;
- Zhang, Shuming;
- Fertig, Elana J;
- Popel, Aleksander S
Publication type:
Article
Breast cancer cells condition lymphatic endothelial cells within pre-metastatic niches to promote metastasis.
Published in:
Nature Communications, 2014, v. 5, n. 9, p. 4715, doi. 10.1038/ncomms5715
By:
- Lee, Esak;
- Fertig, Elana J.;
- Jin, Kideok;
- Sukumar, Saraswati;
- Pandey, Niranjan B.;
- Popel, Aleksander S.
Publication type:
Article
Functional normalization of 450k methylation array data improves replication in large cancer studies.
Published in:
Genome Biology, 2014, v. 15, n. 12, p. 503, doi. 10.1186/s13059-014-0503-2
By:
- Fortin, Jean-Philippe;
- Labbe, Aurélie;
- Lemire, Mathieu;
- Zanke, Brent W;
- Hudson, Thomas J;
- Fertig, Elana J;
- Greenwood, Celia MT;
- Hansen, Kasper D
Publication type:
Article
Comparative mutational landscape analysis of patient-derived tumour xenografts.
Published in:
2017
By:
- Brait, Mariana;
- Izumchenko, Evgeny;
- Kagohara, Luciane T;
- Long, Samuel;
- Wysocki, Piotr T;
- Faherty, Brian;
- Fertig, Elana J;
- Khor, Tin Oo;
- Bruckheimer, Elizabeth;
- Baia, Gilson;
- Ciznadija, Daniel;
- Sloma, Ido;
- Ben-Zvi, Ido;
- Paz, Keren;
- Sidransky, David
Publication type:
journal article
OutSplice: A Novel Tool for the Identification of Tumor-Specific Alternative Splicing Events.
Published in:
BioMedInformatics, 2023, v. 3, n. 4, p. 853, doi. 10.3390/biomedinformatics3040053
By:
- Bendik, Joseph;
- Kalavacherla, Sandhya;
- Webster, Nicholas;
- Califano, Joseph;
- Fertig, Elana J.;
- Ochs, Michael F.;
- Carter, Hannah;
- Guo, Theresa
Publication type:
Article
Identification of methylated genes in salivary gland adenoid cystic carcinoma xenografts using global demethylation and methylation microarray screening.
Published in:
International Journal of Oncology, 2016, v. 49, n. 1, p. 225, doi. 10.3892/ijo.2016.3532
By:
- SHIZHANG LING;
- RETTIG, ELENI M.;
- TAN, MARIETTA;
- XIAOFEI CHANG;
- ZHIMING WANG;
- BRAIT, MARIANA;
- BISHOP, JUSTIN A.;
- FERTIG, ELANA J.;
- CONSIDINE, MICHAEL;
- WICK, MICHAEL J.;
- HA, PATRICK K.
Publication type:
Article
Generating colorblind- friendly scatter plots for single- cell data.
Published in:
eLife, 2023, p. 1, doi. 10.7554/eLife.82128
By:
- Guha, Tejas;
- Fertig, Elana J.;
- Deshpande, Atul
Publication type:
Article
Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma.
Published in:
International Journal of Cancer, 2016, v. 139, n. 2, p. 373, doi. 10.1002/ijc.30081
By:
- Guo, Theresa;
- Gaykalova, Daria A.;
- Considine, Michael;
- Wheelan, Sarah;
- Pallavajjala, Aparna;
- Bishop, Justin A;
- Westra, William H.;
- Ideker, Trey;
- Koch, Wayne M;
- Khan, Zubair;
- Fertig, Elana J.;
- Califano, Joseph A.
Publication type:
Article
NF-κB and stat3 transcription factor signatures differentiate HPV-positive and HPV-negative head and neck squamous cell carcinoma.
Published in:
International Journal of Cancer, 2015, v. 137, n. 8, p. 1879, doi. 10.1002/ijc.29558
By:
- Gaykalova, Daria A.;
- Manola, Judith B.;
- Ozawa, Hiroyuki;
- Zizkova, Veronika;
- Morton, Kathryn;
- Bishop, Justin A.;
- Sharma, Rajni;
- Zhang, Chi;
- Michailidi, Christina;
- Considine, Michael;
- Tan, Marietta;
- Fertig, Elana J.;
- Hennessey, Patrick T.;
- Ahn, Julie;
- Koch, Wayne M.;
- Westra, William H.;
- Khan, Zubair;
- Chung, Christine H.;
- Ochs, Michael F.;
- Califano, Joseph A.
Publication type:
Article
Correction: 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.
Published in:
2020
By:
- Kagohara, Luciane T.;
- Zamuner, Fernando;
- Davis-Marcisak, Emily F.;
- Sharma, Gaurav;
- Considine, Michael;
- Allen, Jawara;
- Yegnasubramanian, Srinivasan;
- Gaykalova, Daria A.;
- Fertig, Elana J.
Publication type:
corrected article
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.
Published in:
British Journal of Cancer, 2020, v. 123, n. 1, p. 101, doi. 10.1038/s41416-020-0851-5
By:
- Kagohara, Luciane T.;
- Zamuner, Fernando;
- Davis-Marcisak, Emily F.;
- Sharma, Gaurav;
- Considine, Michael;
- Allen, Jawara;
- Yegnasubramanian, Srinivasan;
- Gaykalova, Daria A.;
- Fertig, Elana J.
Publication type:
Article
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.
Published in:
2020
By:
- Kagohara, Luciane T.;
- Zamuner, Fernando;
- Davis-Marcisak, Emily F.;
- Sharma, Gaurav;
- Considine, Michael;
- Allen, Jawara;
- Yegnasubramanian, Srinivasan;
- Gaykalova, Daria A.;
- Fertig, Elana J.
Publication type:
journal article
Analysis of gene expression of secreted factors associated with breast cancer metastases in breast cancer subtypes.
Published in:
Scientific Reports, 2015, p. 12133, doi. 10.1038/srep12133
By:
- Fertig, Elana J.;
- Lee, Esak;
- Pandey, Niranjan B.;
- Popel, Aleksander S.
Publication type:
Article
Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets.
Published in:
Nucleic Acids Research, 2020, v. 48, n. 12, p. e68, doi. 10.1093/nar/gkaa349
By:
- Erbe, Rossin;
- Kessler, Michael D;
- Favorov, Alexander V;
- Easwaran, Hariharan;
- Gaykalova, Daria A;
- Fertig, Elana J
Publication type:
Article
Evaluation of a Strategy for the Assimilation of Satellite Radiance Observations with the Local Ensemble Transform Kalman Filter.
Published in:
Monthly Weather Review, 2011, v. 139, n. 6, p. 1932, doi. 10.1175/2010MWR3515.1
By:
- Aravééquia, Joséé A.;
- Szunyogh, Istvan;
- Fertig, Elana J.;
- Kalnay, Eugenia;
- Kuhl, David;
- Kostelich, Eric J.
Publication type:
Article
A Random Forest Genomic Classifier for Tumor Agnostic Prediction of Response to Anti-PD1 Immunotherapy.
Published in:
Cancer Informatics, 2022, v. 21, p. 1, doi. 10.1177/11769351221136081
By:
- Bigelow, Emma;
- Saria, Suchi;
- Piening, Brian;
- Curti, Brendan;
- Dowdell, Alexa;
- Weerasinghe, Roshanthi;
- Bifulco, Carlo;
- Urba, Walter;
- Finkelstein, Noam;
- Fertig, Elana J.;
- Baras, Alex;
- Zaidi, Neeha;
- Jaffee, Elizabeth;
- Yarchoan, Mark
Publication type:
Article
Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination.
Published in:
Cancer Informatics, 2016, n. 15, p. 15, doi. 10.4137/CIN.S32468
By:
- Stansfield, John C.;
- Rusay, Matthew;
- Shan, Roger;
- Kelton, Conor;
- Gaykalova, Daria A.;
- Fertig, Elana J.;
- Califano, Joseph A.;
- Ochs, Michael F.
Publication type:
Article
Learning Dysregulated Pathways in Cancers from Differential Variability Analysis.
Published in:
Cancer Informatics, 2014, n. 13, p. 61, doi. 10.4137/CIN.S14066
By:
- Afsari, Bahman;
- Geman, Donald;
- Fertig, Elana J.
Publication type:
Article
Hypoxia induces ROS-resistant memory upon reoxygenation in vivo promoting metastasis in part via MUC1-C.
Published in:
Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-51995-2
By:
- Godet, Inês;
- Oza, Harsh H.;
- Shi, Yi;
- Joe, Natalie S.;
- Weinstein, Alyssa G.;
- Johnson, Jeanette;
- Considine, Michael;
- Talluri, Swathi;
- Zhang, Jingyuan;
- Xu, Reid;
- Doctorman, Steven;
- Mbulaiteye, Delma;
- Stein-O'Brien, Genevieve;
- Kagohara, Luciane T.;
- Santa-Maria, Cesar A.;
- Fertig, Elana J.;
- Gilkes, Daniele M.
Publication type:
Article
Triple-negative breast cancer metastasis involves complex epithelial-mesenchymal transition dynamics and requires vimentin.
Published in:
Science Translational Medicine, 2022, v. 14, n. 656, p. 1, doi. 10.1126/scitranslmed.abn7571
By:
- Grasset, Eloïse M.;
- Dunworth, Matthew;
- Sharma, Gaurav;
- Loth, Melanie;
- Tandurella, Joseph;
- Cimino-Mathews, Ashley;
- Gentz, Melissa;
- Bracht, Sydney;
- Haynes, Meagan;
- Fertig, Elana J.;
- Ewald, Andrew J.
Publication type:
Article
Epigenetic regulation of gene expression in cancer: techniques, resources and analysis.
Published in:
Briefings in Functional Genomics, 2018, v. 17, n. 1, p. 49, doi. 10.1093/bfgp/elx018
By:
- Kagohara, Luciane T.;
- Stein-O'Brien, Genevieve L.;
- Kelley, Dylan;
- Flam, Emily;
- Wick, Heather C.;
- Danilova, Ludmila V.;
- Easwaran, Hariharan;
- Favorov, Alexander V.;
- Qian, Jiang;
- Gaykalova, Daria A.;
- Fertig, Elana J.
Publication type:
Article
Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS.
Published in:
Nature Protocols, 2023, v. 18, n. 12, p. 3690, doi. 10.1038/s41596-023-00892-x
By:
- Johnson, Jeanette A. I.;
- Tsang, Ashley P.;
- Mitchell, Jacob T.;
- Zhou, David L.;
- Bowden, Julia;
- Davis-Marcisak, Emily;
- Sherman, Thomas;
- Liefeld, Ted;
- Loth, Melanie;
- Goff, Loyal A.;
- Zimmerman, Jacquelyn W.;
- Kinny-Köster, Ben;
- Jaffee, Elizabeth M.;
- Tamayo, Pablo;
- Mesirov, Jill P.;
- Reich, Michael;
- Fertig, Elana J.;
- Stein-O'Brien, Genevieve L.
Publication type:
Article
Gene expression signatures modulated by epidermal growth factor receptor activation and their relationship to cetuximab resistance in head and neck squamous cell carcinoma.
Published in:
BMC Genomics, 2012, v. 13, n. 1, p. 160, doi. 10.1186/1471-2164-13-160
By:
- Fertig, Elana J.;
- Qing Ren;
- Haixia Cheng;
- Hiromitsu Hatakeyama;
- Dicker, Adam P.;
- Rodeck, Ulrich;
- Considine, Michael;
- Ochs, Michael F.;
- Chung, Christine H.
Publication type:
Article
CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer.
Published in:
PLoS Computational Biology, 2019, v. 15, n. 5, p. 1, doi. 10.1371/journal.pcbi.1006935
By:
- Sherman, Thomas D.;
- Kagohara, Luciane T.;
- Cao, Raymon;
- Cheng, Raymond;
- Satriano, Matthew;
- Considine, Michael;
- Krigsfeld, Gabriel;
- Ranaweera, Ruchira;
- Tang, Yong;
- Jablonski, Sandra A.;
- Stein-O'Brien, Genevieve;
- Gaykalova, Daria A.;
- Weiner, Louis M.;
- Chung, Christine H.;
- Fertig, Elana J.
Publication type:
Article
Age‐associated Senescent – T Cell Signaling Promotes Type 3 Immunity that Inhibits the Biomaterial Regenerative Response.
Published in:
Advanced Materials, 2024, v. 36, n. 43, p. 1, doi. 10.1002/adma.202310476
By:
- Han, Jin;
- Cherry, Christopher;
- Mejías, Joscelyn C.;
- Krishnan, Kavita;
- Ruta, Anna;
- Maestas, David R.;
- Peña, Alexis N.;
- Nguyen, Helen Hieu;
- Nagaraj, Sushma;
- Yang, Brenda;
- Gray‐Gaillard, Elise F.;
- Rutkowski, Natalie;
- Browne, Maria;
- Tam, Ada J.;
- Fertig, Elana J.;
- Housseau, Franck;
- Ganguly, Sudipto;
- Moore, Erika M.;
- Pardoll, Drew M.;
- Elisseeff, Jennifer H.
Publication type:
Article
projectR: an R/Bioconductor package for transfer learning via PCA, NMF, correlation and clustering.
Published in:
Bioinformatics, 2020, v. 36, n. 11, p. 3592, doi. 10.1093/bioinformatics/btaa183
By:
- Sharma, Gaurav;
- Colantuoni, Carlo;
- Goff, Loyal A;
- Fertig, Elana J;
- Stein-O'Brien, Genevieve
Publication type:
Article
StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data.
Published in:
Bioinformatics, 2017, v. 33, n. 20, p. 3158, doi. 10.1093/bioinformatics/btx379
By:
- Stavrovskaya, Elena D.;
- Niranjan, Tejasvi;
- Fertig, Elana J.;
- Wheelan, Sarah J.;
- Favorov, Alexander V.;
- Mironov, Andrey A.
Publication type:
Article
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.
Published in:
Bioinformatics, 2017, v. 33, n. 12, p. 1892, doi. 10.1093/bioinformatics/btx058
By:
- Stein-O'Brien, Genevieve L.;
- Carey, Jacob L.;
- Wai Shing Lee;
- Considine, Michael;
- Favorov, Alexander V.;
- Flam, Emily;
- Guo, Theresa;
- Sijia Li;
- Marchionni, Luigi;
- Sherman, Thomas;
- Sivy, Shawn;
- Gaykalova, Daria A.;
- McKay, Ronald D.;
- Ochs, Michael F.;
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switchBox: an R package for k–Top Scoring Pairs classifier development.
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Bioinformatics, 2015, v. 31, n. 2, p. 273, doi. 10.1093/bioinformatics/btu622
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Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction.
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Bioinformatics, 2014, v. 30, n. 19, p. 2757, doi. 10.1093/bioinformatics/btu375
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- Fertig, Elana J.
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CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.
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Bioinformatics, 2010, v. 26, n. 21, p. 2792, doi. 10.1093/bioinformatics/btq503
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Model-informed experimental design recommendations for distinguishing intrinsic and acquired targeted therapeutic resistance in head and neck cancer.
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NPJ Systems Biology & Applications, 2022, v. 8, n. 1, p. 1, doi. 10.1038/s41540-022-00244-7
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- Gevertz, Jana L.
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Mechanistically detailed systems biology modeling of the HGF/Met pathway in hepatocellular carcinoma.
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NPJ Systems Biology & Applications, 2019, v. 5, n. 1, p. N.PAG, doi. 10.1038/s41540-019-0107-2
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Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance.
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Genome Medicine, 2018, v. 10, n. 1, p. N.PAG, doi. 10.1186/s13073-018-0545-2
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