Rajasree Menon

Summary

Affiliation: University of Michigan
Country: USA

Publications

  1. pmc Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers
    Rajasree Menon
    Center for Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109 2218, United States
    J Proteome Res 10:5503-11. 2011
  2. pmc A mouse plasma peptide atlas as a resource for disease proteomics
    Qing Zhang
    Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Genome Biol 9:R93. 2008
  3. pmc Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers
    Rajasree Menon
    Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109 2218, USA
    Cancer Res 70:3440-9. 2010
  4. pmc Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics
    Damian Fermin
    Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA
    Genome Biol 7:R35. 2006
  5. ncbi request reprint Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project
    Marcin Adamski
    University of Michigan, Ann Arbor, MI 48109 2218, USA
    Proteomics 5:3246-61. 2005
  6. pmc Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer
    Rajasree Menon
    Center for Computational Medicine and Biology and Pediatric Endocrinology, University of Michigan, 100 Washtenaw Avenue, Palmer Commons, Ann Arbor, MI 48109, USA
    Cancer Res 69:300-9. 2009
  7. pmc Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data
    Ridvan Eksi
    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS Comput Biol 9:e1003314. 2013
  8. pmc Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology
    Gilbert S Omenn
    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 2218, USA
    J Proteomics 90:28-37. 2013
  9. pmc Identification of alternatively spliced transcripts using a proteomic informatics approach
    Rajasree Menon
    Center for Computational Medicine and Biology and National Center for Integrative Biomedical Informatics, University of Michigan, Ann Arbor, MI, USA
    Methods Mol Biol 696:319-26. 2011
  10. doi request reprint Genome-Wide Functional Annotation of Human Protein-Coding Splice Variants Using Multiple Instance Learning
    Bharat Panwar
    Department of Computational Medicine and Bioinformatics, Department of Internal Medicine, Department of Human Genetics and School of Public Health, and Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan 48109, United States
    J Proteome Res 15:1747-53. 2016

Detail Information

Publications23

  1. pmc Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers
    Rajasree Menon
    Center for Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109 2218, United States
    J Proteome Res 10:5503-11. 2011
    ..These results demonstrate the feasibility of integrating proteomic analysis with structure-based conformational predictions of differentially expressed alternative splice variants in cancers and other conditions...
  2. pmc A mouse plasma peptide atlas as a resource for disease proteomics
    Qing Zhang
    Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Genome Biol 9:R93. 2008
    ..A major finding from this study is the identification of novel isoforms and transcript variants not previously predicted from genome analysis...
  3. pmc Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers
    Rajasree Menon
    Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109 2218, USA
    Cancer Res 70:3440-9. 2010
    ..The cancer-associated differentially expressed splice variant proteins offer novel biomarker candidates that may function in breast cancer progression or metastasis...
  4. pmc Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics
    Damian Fermin
    Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA
    Genome Biol 7:R35. 2006
    ....
  5. ncbi request reprint Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project
    Marcin Adamski
    University of Michigan, Ann Arbor, MI 48109 2218, USA
    Proteomics 5:3246-61. 2005
    ..Recommendations of the PPP for future large-scale proteomics endeavors are described...
  6. pmc Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer
    Rajasree Menon
    Center for Computational Medicine and Biology and Pediatric Endocrinology, University of Michigan, 100 Washtenaw Avenue, Palmer Commons, Ann Arbor, MI 48109, USA
    Cancer Res 69:300-9. 2009
    ..Our results show that, in a mouse model for human pancreatic cancer, novel and differentially expressed alternative splice isoforms are detectable in plasma and may be a source of candidate biomarkers...
  7. pmc Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data
    Ridvan Eksi
    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS Comput Biol 9:e1003314. 2013
    ..It is extendable to any base machine learner and other species with alternatively spliced isoforms, and shifts the current gene-centered function prediction to isoform-level predictions. ..
  8. pmc Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology
    Gilbert S Omenn
    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 2218, USA
    J Proteomics 90:28-37. 2013
    ..Here we review our work on differential expression of splice variant proteins in cancers and the feasibility of integrating proteomic analysis with structure-based conformational predictions of the differences between such isoforms...
  9. pmc Identification of alternatively spliced transcripts using a proteomic informatics approach
    Rajasree Menon
    Center for Computational Medicine and Biology and National Center for Integrative Biomedical Informatics, University of Michigan, Ann Arbor, MI, USA
    Methods Mol Biol 696:319-26. 2011
    ..This approach is suitable for human and mouse datasets. Application of the method is illustrated with a study of the Kras activation-Ink4/Arf deletion mouse model of human pancreatic ductal adenocarcinoma...
  10. doi request reprint Genome-Wide Functional Annotation of Human Protein-Coding Splice Variants Using Multiple Instance Learning
    Bharat Panwar
    Department of Computational Medicine and Bioinformatics, Department of Internal Medicine, Department of Human Genetics and School of Public Health, and Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan 48109, United States
    J Proteome Res 15:1747-53. 2016
    ..All predictions have been implemented in a web resource called "IsoFunc", which is freely available for the global scientific community through http://guanlab.ccmb.med.umich.edu/isofunc . ..
  11. pmc A Network of Splice Isoforms for the Mouse
    Hong Dong Li
    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States
    Sci Rep 6:24507. 2016
    ..We expect this work will become a useful resource for the mouse genetics community to understand gene functions. The network is publicly available at: http://guanlab.ccmb.med.umich.edu/isoformnetwork. ..
  12. pmc Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project
    Hong Dong Li
    Department of Computational Medicine and Bioinformatics, Department of Internal Medicine, Department of Human Genetics and School of Public Health, Department of Electrical Engineering and Computer Science University of Michigan, Ann Arbor, Michigan 48109, United States
    J Proteome Res 14:3484-91. 2015
    ..ccmb.med.umich.edu/hisonet). All MS/MS data were available at ProteomeXchange Web site (http://www.proteomexchange.org) through their identifiers (retina: PXD001242, placenta: PXD000754)...
  13. pmc MI-PVT: A Tool for Visualizing the Chromosome-Centric Human Proteome
    Bharat Panwar
    Department of Computational Medicine and Bioinformatics, Department of Internal Medicine, Department of Human Genetics and School of Public Health, Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan 48109, United States
    J Proteome Res 14:3762-7. 2015
    ..Our aim is to integrate extensive mass-spectrometric proteomic data into the tool to facilitate finding chromosome-centric protein expression and correlation across tissues...
  14. ncbi request reprint Evolutionary-conserved gene expression response profiles across mammalian tissues
    Ji Chen
    Bioinformatics Program, University of Michigan, Ann Arbor, Michigan 48109, USA
    OMICS 11:96-115. 2007
    ....
  15. pmc Computational Inferences of the Functions of Alternative/Noncanonical Splice Isoforms Specific to HER2+/ER-/PR- Breast Cancers, a Chromosome 17 C-HPP Study
    Rajasree Menon
    University of Michigan, 100 Washtenaw Avenue, Room 2044B, Palmer Commons, Ann Arbor, Michigan 48109, United States
    J Proteome Res 14:3519-29. 2015
    ..Further detailed analysis is warranted as these proteins could be explored as potential biomarkers and therapeutic targets for HER2+/ER-/PR- BC patients. ..
  16. pmc The emerging era of genomic data integration for analyzing splice isoform function
    Hong Dong Li
    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
    Trends Genet 30:340-7. 2014
    ....
  17. pmc Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence
    Hong Dong Li
    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
    Proteomics 14:2709-18. 2014
    ..This integrative proteogenomics approach can successfully identify principal isoforms that are responsible for the canonical functions of genes. ..
  18. ncbi request reprint Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database
    Gilbert S Omenn
    Internal Medicine, University of Michigan, Ann Arbor, MI 48109 0656, USA
    Proteomics 5:3226-45. 2005
    ....
  19. pmc Alternative splice variants, a new class of protein cancer biomarker candidates: findings in pancreatic cancer and breast cancer with systems biology implications
    Gilbert S Omenn
    University of Michigan Center for Computational Medicine and Bioinformatics and Michigan Proteomics Alliance for Cancer Research, Ann Arbor, MI 48109 2218, USA
    Dis Markers 28:241-51. 2010
    ..The same approach is being applied to human tumors, plasma, and cell line studies of other cancers...
  20. pmc Effects of Antioxidants in Human Cancers: Differential Effects on Non-Coding Intronic RNA Expression
    Shreya Menon
    Skyline High School, Ann Arbor, MI 48103, USA
    Antioxidants (Basel) 5:. 2016
    ..It is important to study this novel effect of antioxidant supplements in detail as it may have a significant role in disease progression. ..
  21. pmc A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines
    Gilbert S Omenn
    Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 2218, USA
    J Proteomics 107:103-12. 2014
    ..This article is part of a Special Issue entitled: 20Years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini , Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez. ..
  22. pmc Novel bioinformatics method for identification of genome-wide non-canonical spliced regions using RNA-Seq data
    Yongsheng Bai
    Department of Computational Medicine and Bioinformatics, and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America Morgridge Institute for Research, University of Wisconsin Madison, Madison, Wisconsin, United States of America
    PLoS ONE 9:e100864. 2014
    ..Strikingly, other examples of targeted, unconventional splicing of short mRNA regions have yet to be reported...
  23. pmc Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes
    Rajasree Menon
    Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
    J Proteome Res 13:212-27. 2014
    ....