Literature DB >> 18400772

EPO-KB: a searchable knowledge base of biomarker to protein links.

Jonathan L Lustgarten1, Chad Kimmel, Henrik Ryberg, William Hogan.   

Abstract

UNLABELLED: The knowledge base EPO-KB (Empirical Proteomic Ontology Knowledge Base) is based on an OWL ontology that represents current knowledge linking mass-to-charge (m/z) ratios to proteins on multiple platforms including Matrix Assisted Laser/Desorption Ionization (MALDI) and Surface Enhanced Laser/Desorption Ionization (SELDI)--Time of Flight (TOF). At present, it contains information on m/z ratio to protein links that were extracted from 120 published research papers. It has a web interface that allows researchers to query and retrieve putative proteins that correspond to a user-specified m/z ratio. EPO-KB also allows automated entry of additional m/z ratio to protein links and is expandable to the addition of gene to protein and protein to disease links. AVAILABILITY: http://www.dbmi.pitt.edu/EPO-KB

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Year:  2008        PMID： 18400772      PMCID： PMC2567111          DOI： 10.1093/bioinformatics/btn125

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  9 in total

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Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

2.  Monte Carlo estimation of the number of possible protein folds: effects of sampling bias and folds distributions.

Authors:  Hadas Leonov; Joseph S B Mitchell; Isaiah T Arkin
Journal:  Proteins       Date:  2003-05-15

3.  The use of plasma surface-enhanced laser desorption/ionization time-of-flight mass spectrometry proteomic patterns for detection of head and neck squamous cell cancers.

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Journal:  Clin Cancer Res       Date:  2004-07-15       Impact factor: 12.531

4.  Fractional factorial design for optimization of the SELDI protocol for human adipose tissue culture media.

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Journal:  Biotechnol Prog       Date:  2007 Jan-Feb

5.  Proteomic profiling of cerebrospinal fluid identifies biomarkers for amyotrophic lateral sclerosis.

Authors:  Srikanth Ranganathan; Eric Williams; Philip Ganchev; Vanathi Gopalakrishnan; David Lacomis; Leo Urbinelli; Kristyn Newhall; Merit E Cudkowicz; Robert H Brown; Robert Bowser
Journal:  J Neurochem       Date:  2005-12       Impact factor: 5.372

6.  Discovery of distinct protein profiles specific for lung tumors and pre-malignant lung lesions by SELDI mass spectrometry.

Authors:  Tatyana A Zhukov; Roy A Johanson; Alan B Cantor; Robert A Clark; Melvyn S Tockman
Journal:  Lung Cancer       Date:  2003-06       Impact factor: 5.705

7.  Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study.

Authors:  David J States; Gilbert S Omenn; Thomas W Blackwell; Damian Fermin; Jimmy Eng; David W Speicher; Samir M Hanash
Journal:  Nat Biotechnol       Date:  2006-03       Impact factor: 54.908

8.  From genomics to chemical genomics: new developments in KEGG.

Authors:  Minoru Kanehisa; Susumu Goto; Masahiro Hattori; Kiyoko F Aoki-Kinoshita; Masumi Itoh; Shuichi Kawashima; Toshiaki Katayama; Michihiro Araki; Mika Hirakawa
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

9.  The Universal Protein Resource (UniProt).

Authors: 
Journal:  Nucleic Acids Res       Date:  2006-11-16       Impact factor: 16.971
  9 in total
  9 in total

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Authors:  Jiye Ai; Barry Smith; David T Wong
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2.  Discovery and verification of amyotrophic lateral sclerosis biomarkers by proteomics.

Authors:  Henrik Ryberg; Jiyan An; Samuel Darko; Jonathan Llyle Lustgarten; Matt Jaffa; Vanathi Gopalakrishnan; David Lacomis; Merit Cudkowicz; Robert Bowser
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3.  Transfer learning of classification rules for biomarker discovery and verification from molecular profiling studies.

Authors:  Philip Ganchev; David Malehorn; William L Bigbee; Vanathi Gopalakrishnan
Journal:  J Biomed Inform       Date:  2011-05-06       Impact factor: 6.317

4.  Mass spectrometry-based analysis of therapy-related changes in serum proteome patterns of patients with early-stage breast cancer.

Authors:  Monika Pietrowska; Joanna Polanska; Lukasz Marczak; Katarzyna Behrendt; Elzbieta Nowicka; Maciej Stobiecki; Andrzej Polanski; Rafal Tarnawski; Piotr Widlak
Journal:  J Transl Med       Date:  2010-07-11       Impact factor: 5.531

5.  Serum apolipoproteins C-I and C-III are reduced in stomach cancer patients: results from MALDI-based peptidome and immuno-based clinical assays.

Authors:  Meital Cohen; Rami Yossef; Tamir Erez; Aleksandra Kugel; Michael Welt; Mark M Karpasas; Jonathan Bones; Pauline M Rudd; Julien Taieb; Herve Boissin; Dror Harats; Karin Noy; Yoram Tekoah; Rachel G Lichtenstein; Eitan Rubin; Angel Porgador
Journal:  PLoS One       Date:  2011-01-18       Impact factor: 3.240

6.  Identification of serum proteome signatures of locally advanced and metastatic gastric cancer: a pilot study.

Authors:  Agata Abramowicz; Anna Wojakowska; Agnieszka Gdowicz-Klosok; Joanna Polanska; Pawel Rodziewicz; Pawel Polanowski; Agnieszka Namysl-Kaletka; Monika Pietrowska; Jerzy Wydmanski; Piotr Widlak
Journal:  J Transl Med       Date:  2015-09-17       Impact factor: 5.531

7.  Microgeographic Proteomic Networks of the Human Colonic Mucosa and Their Association With Inflammatory Bowel Disease.

Authors:  Xiaoxiao Li; James LeBlanc; David Elashoff; Ian McHardy; Maomeng Tong; Bennett Roth; Andrew Ippoliti; Gildardo Barron; Dermot McGovern; Keely McDonald; Rodney Newberry; Thomas Graeber; Steve Horvath; Lee Goodglick; Jonathan Braun
Journal:  Cell Mol Gastroenterol Hepatol       Date:  2016-05-17

8.  Knowledge-based variable selection for learning rules from proteomic data.

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9.  Radiotherapy-related changes in serum proteome patterns of head and neck cancer patients; the effect of low and medium doses of radiation delivered to large volumes of normal tissue.

Authors:  Piotr Widłak; Monika Pietrowska; Joanna Polańska; Tomasz Rutkowski; Karol Jelonek; Magdalena Kalinowska-Herok; Agnieszka Gdowicz-Kłosok; Andrzej Wygoda; Rafał Tarnawski; Krzysztof Składowski
Journal:  J Transl Med       Date:  2013-12-05       Impact factor: 5.531
  9 in total

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