Publications by authors named "Ruth Isserlin"

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Gene-set enrichment analysis and visualization on the web using EnrichmentMap:RNASeq.
Max Franz, Christian T Lopes, Mike Kucera, Veronique Voisin, Ruth Isserlin

Bioinform Adv· September 2025

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Control of tissue development and cell diversity by cell cycle-dependent transcriptional filtering.
Maria Abou Chakra, Ruth Isserlin, Thinh N Tran, Gary D Bader

Elife· July 2021

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netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks.
Shraddha Pai, Philipp Weber, Ruth Isserlin, Hussam Kaka, Shirley Hui

F1000Res· April 2021

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Distinct DNA methylation patterns associated with treatment resistance in metastatic castration resistant prostate cancer.
Madonna R Peter, Misha Bilenky, Alastair Davies, Ruth Isserlin, Gary D Bader

Sci Rep· March 2021

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Dynamics of the cell-free DNA methylome of metastatic prostate cancer during androgen-targeting treatment.
Madonna R Peter, Misha Bilenky, Ruth Isserlin, Gary D Bader, Shu Yi Shen

Epigenomics· August 2020

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RCy3: Network biology using Cytoscape from within R.
Julia A Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R Pico

F1000Res· June 2020

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Single-cell transcriptomic profiling of the aging mouse brain.
Methodios Ximerakis, Scott L Lipnick, Brendan T Innes, Sean K Simmons, Xian Adiconis, Ruth Isserlin

Nat Neurosci· October 2019

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Bmi1 regulates human glioblastoma stem cells through activation of differential gene networks in CD133+ brain tumor initiating cells.
Parvez Vora, Mathieu Seyfrid, Chitra Venugopal, Maleeha A Qazi, Sabra Salim, Ruth Isserlin

J Neurooncol· July 2019

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netDx: interpretable patient classification using integrated patient similarity networks.
Shraddha Pai, Shirley Hui, Ruth Isserlin, Muhammad A Shah, Hussam Kaka

Mol Syst Biol· March 2019

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Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression.
Shivani Kamdar, Ruth Isserlin, Theodorus Van der Kwast, Alexandre R Zlotta, Gary D Bader

Clin Epigenetics· March 2019

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The Relative Contributions of Cell-Dependent Cortical Microcircuit Aging to Cognition and Anxiety.
Rammohan Shukla, Thomas D Prevot, Leon French, Ruth Isserlin, Brad R Rocco

Biol Psychiatry· February 2019

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Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap.
Jüri Reimand, Ruth Isserlin, Veronique Voisin, Mike Kucera, Christian Tannus-Lopes

Nat Protoc· February 2019

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Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities.
Alison E Casey, Ankit Sinha, Rajat Singhania, Julie Livingstone, Paul Waterhouse, Ruth Isserlin

J Cell Biol· August 2018

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Exercise-responsive phosphoproteins in the heart.
Hongbo Guo, Ruth Isserlin, Andrew Emili, Jatin G Burniston

J Mol Cell Cardiol· October 2017

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Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy.
Nehme El-Hachem, Deena M A Gendoo, Laleh Soltan Ghoraie, Zhaleh Safikhani, Petr Smirnov, Ruth Isserlin

Cancer Res· June 2017

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Global phosphoproteomic profiling reveals perturbed signaling in a mouse model of dilated cardiomyopathy.
Uros Kuzmanov, Hongbo Guo, Diana Buchsbaum, Jake Cosme, Cynthia Abbasi, Ruth Isserlin

Proc Natl Acad Sci U S A· November 2016

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Ectopic miR-125a Expression Induces Long-Term Repopulating Stem Cell Capacity in Mouse and Human Hematopoietic Progenitors.
Edyta E Wojtowicz, Eric R Lechman, Karin G Hermans, Erwin M Schoof, Erno Wienholds, Ruth Isserlin

Cell Stem Cell· September 2016

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AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations.
Mike Kucera, Ruth Isserlin, Arkady Arkhangorodsky, Gary D Bader

F1000Res· July 2016

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Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis.
Shivani N Kamdar, Linh T Ho, Ken J Kron, Ruth Isserlin, Theodorus van der Kwast

Clin Epigenetics· April 2016

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miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells.
Eric R Lechman, Bernhard Gentner, Stanley W K Ng, Erwin M Schoof, Peter van Galen, Ruth Isserlin

Cancer Cell· April 2016

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Cardioprotective Signature of Short-Term Caloric Restriction.
Hossein Noyan, Omar El-Mounayri, Ruth Isserlin, Sara Arab, Abdul Momen

PLoS One· March 2016

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miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells.
Eric R Lechman, Bernhard Gentner, Stanley W K Ng, Erwin M Schoof, Peter van Galen, Ruth Isserlin

Cancer Cell· February 2016

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Phosphoproteomic network analysis in the sea urchin Strongylocentrotus purpuratus reveals new candidates in egg activation.
Hongbo Guo, Ana Elisa Garcia-Vedrenne, Ruth Isserlin, Andrew Lugowski, Anthony Morada

Proteomics· December 2015

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Unbiased phosphoproteomic method identifies the initial effects of a methacrylic acid copolymer on macrophages.
Michael Dean Chamberlain, Laura A Wells, Alexandra Lisovsky, Hongbo Guo, Ruth Isserlin

Proc Natl Acad Sci U S A· August 2015

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A Call for Systematic Research on Solute Carriers.
Adrián César-Razquin, Berend Snijder, Tristan Frappier-Brinton, Ruth Isserlin, Gergely Gyimesi

Cell· July 2015

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