R
Ruth Isserlin
Researcher at University of Toronto
Publications - 70
Citations - 11893
Ruth Isserlin is an academic researcher from University of Toronto. The author has contributed to research in topics: DNA methylation & Prostate cancer. The author has an hindex of 30, co-authored 70 publications receiving 9766 citations. Previous affiliations of Ruth Isserlin include Mount Sinai Hospital.
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Journal ArticleDOI
Integration of biological networks and gene expression data using Cytoscape
Melissa S. Cline,Michael E. Smoot,Ethan Cerami,Allan Kuchinsky,Nerius Landys,Christopher T. Workman,Rowan H. Christmas,Iliana Avila-Campilo,Iliana Avila-Campilo,Michael L. Creech,Benjamin Gross,Kristina Hanspers,Ruth Isserlin,Ryan Kelley,Sarah Killcoyne,Samad Lotia,Steven Maere,John H. Morris,Keiichiro Ono,Vuk Pavlovic,Alexander R. Pico,Aditya Vailaya,Peng-Liang Wang,Annette M. Adler,Bruce R. Conklin,Leroy Hood,Martin Kuiper,Chris Sander,Ilya Schmulevich,Benno Schwikowski,Guy J. Warner,Trey Ideker,Gary D. Bader +32 more
TL;DR: This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest.
Journal ArticleDOI
A draft map of the human proteome
Min-Sik Kim,Sneha M. Pinto,Derese Getnet,Raja Sekhar Nirujogi,Srikanth S. Manda,Raghothama Chaerkady,Anil K. Madugundu,Dhanashree S. Kelkar,Ruth Isserlin,Shobhit Jain,Joji Kurian Thomas,Babylakshmi Muthusamy,Pamela Leal-Rojas,Pamela Leal-Rojas,Praveen Kumar,Nandini A. Sahasrabuddhe,Lavanya Balakrishnan,Jayshree Advani,Bijesh George,Santosh Renuse,Lakshmi Dhevi N. Selvan,Arun H. Patil,Vishalakshi Nanjappa,Aneesha Radhakrishnan,Samarjeet Prasad,Tejaswini Subbannayya,Rajesh Raju,Manish Kumar,Sreelakshmi K. Sreenivasamurthy,Arivusudar Marimuthu,Gajanan Sathe,Sandip Chavan,Keshava K. Datta,Yashwanth Subbannayya,Apeksha Sahu,Soujanya D. Yelamanchi,Savita Jayaram,Pavithra Rajagopalan,Jyoti Sharma,Krishna R Murthy,Nazia Syed,Renu Goel,Aafaque Ahmad Khan,Sartaj Ahmad,Gourav Dey,Keshav Mudgal,Aditi Chatterjee,Tai-Chung Huang,Jun Zhong,Xinyan Wu,Patrick G. Shaw,Donald Freed,Muhammad Saddiq Zahari,Kanchan K Mukherjee,Subramanian Shankar,Anita Mahadevan,Henry H N Lam,Chris J. Mitchell,Susarla K. Shankar,Parthasarathy Satishchandra,John T. Schroeder,Ravi Sirdeshmukh,Anirban Maitra,Steven D. Leach,Charles G. Drake,Marc K. Halushka,T. S. Keshava Prasad,Ralph H. Hruban,Candace L. Kerr,Candace L. Kerr,Gary D. Bader,Christine A. Iacobuzio-Donahue,Harsha Gowda,Akhilesh Pandey +73 more
TL;DR: A draft map of the human proteome is presented using high-resolution Fourier-transform mass spectrometry to discover a number of novel protein-coding regions, which includes translated pseudogenes, non-c coding RNAs and upstream open reading frames.
Journal ArticleDOI
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
TL;DR: This work developed “Enrichment Map”, a network-based visualization method for gene-set enrichment results that is implemented as a freely available and user friendly plug-in for the Cytoscape network visualization software and is a significant advance in the interpretation of enrichment analysis.
Journal ArticleDOI
Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap
Jüri Reimand,Jüri Reimand,Ruth Isserlin,Veronique Voisin,Mike Kucera,Christian Tannus-Lopes,Asha Rostamianfar,Lina Wadi,Mona Meyer,Judy M. Y. Wong,Chao Xu,Daniele Merico,Gary D. Bader +12 more
TL;DR: This protocol describes pathway enrichment analysis of gene lists from RNA-seq and other genomics experiments using g:Profiler, GSEA, Cytoscape and EnrichmentMap software, and describes innovative visualization techniques.
Journal ArticleDOI
The Biomolecular Interaction Network Database and related tools 2005 update
C. Alfarano,C. E. Andrade,K. Anthony,Neil Bahroos,Martha Bajec,Ken Bantoft,Doron Betel,B. Bobechko,Kelly Boutilier,E. Burgess,K. Buzadzija,R. Cavero,C. D'Abreo,Ian Donaldson,D. Dorairajoo,Michel Dumontier,M. R. Dumontier,V. Earles,R. Farrall,Howard J. Feldman,E. Garderman,Y. Gong,R. Gonzaga,V. Grytsan,E. Gryz,V. Gu,E. Haldorsen,A. Halupa,Robin Haw,A. Hrvojic,L. Hurrell,Ruth Isserlin,F. Jack,F. Juma,Asim Khan,T. Kon,S. Konopinsky,V. Le,Eunjung Lee,San Ling,M. Magidin,J. Moniakis,J. Montojo,Susan Moore,Brenda Muskat,Ivan Ng,J. P. Paraiso,Belinda S. Parker,G. Pintilie,R. Pirone,John J. Salama,S. Sgro,T. Shan,Y. Shu,J. Siew,D. Skinner,Kevin A. Snyder,R. Stasiuk,D. Strumpf,Brigitte Tuekam,S. Tao,Z. Wang,Michelle White,R. Willis,Cheryl Wolting,S. Wong,A. Wrong,C. Xin,R. Yao,B. Yates,S. Zhang,K. Zheng,Tony Pawson,Benjamin Ouellette,Christopher W. V. Hogue +74 more
TL;DR: The Biomolecular Interaction Network Database (BIND) archives biomolecular interaction, reaction, complex and pathway information and provides users with methods to discover interactions and molecular mechanisms.