Medical abstract text mining papers

New
1. Associating Genes with Gene Ontology Codes Using a Maximum Entropy Analysis of Biomedical Literature
  - Soumya Raychaudhuri, Jeffrey T. Chang, Patrick D. Sutphin, and Russ B. Altman (2002)
  - 203.pdf
  - Intro to Max Entropy (PS)
2. ARROGANT: An application to manipulate large gene collections
  - Kulkarni et al, 2002
  - arrogant.pdf
3. A shallow parser based on closed-class words to capture relations in biomedical text
  - Gondy Leroy, Hsinchun Chen, and Jesse D. Martinez, Jan 2003
  - leroy.pdf
4. A vocabulary development and visualization tool based on natural language processing and the mining of textual patient reports
  - Carol Friedman, Hongfang Liu, and Lyudmila Shagina, May 2003
  - friedman_liu.pdf
PubGene
1. A literature network of human genes for high-throughput analysis of gene expression
  - T.K. Jenssen et.al, May 2001
  - pubgene_original.pdf
2. Associations betwee gene expressions in breast cancer and patient survival
  - T.K. Jenssen et. al, 2002
  - Jenssen_HumGenetic.pdf
3. Gene Expression Levels in Different Stages of Progression in Oral Squamous Cell Carcinoma
  - Kuo et. al, 2002
  - kuo jamia 2002.pdf
Gene-Disease Corellation
1. Analysis of Genomic and Proteomic Data Using Advanced Literature Mining
  - Hu et. al, Mar 2003
  - Hu.pdf
2. Association of genes to genetically inherited diseases using data mining
  - Perez-Iratxeta et.al
  - Perez-Iratxeta.pdf

Gene-Gene Relation
1. A method for finding communities of related genes
  - Wilkinson and Huberman, May 2003
  - wilkinson.pdf
2. Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network
  - Jonathan D. Wren and Harold R. Garner, 2003
  - wren_garner.pdf
3. Mining microarray expression data by literature profiling
  - Chaussabel and Sher, 2002
  - chaussabel.pdf
4. A literature network of human genes for high-throughput analysis of gene expression
  - Jenssen et. al, May 2001
  - pubgene_original.pdf
5. Use of keyword hierarchies to interpret gene expression patterns
  - Masys et. al, 2000
  - masys_welsh.pdf
6. Using text analysis to Identify Functionally Coherent Gene Groups
  - raychaudhuri.pdf
7. BioBibliometrics:Information retrieval and visualization from co-occurrences of gene names in medline abstracts
  - Stapley et.al, 2000
  - stapley.pdf
8. Identifying the Interaction between Genes and Gene Products Based on Frequently Seen Verbs in Medline Abstracts
  - Takeshi Sekimizu, Hyun S. Park, Jun'ichi Tsujii, 1998
  - sekimizu.pdf
9. Methods for Large-Scale Mining of Networks of Human Genes
  - Tor-Kristian Jenssen et.al
  - largescale.pdf

Protein Interactions
1. Automated extraction of information on protein-protein interactions from the biological literature
  - Ono et. al, 2000
  - ono.pdf
2. Mining literature for protein-protein interactions
  - Marcotte et.al, 2000
  - marcotte.pdf
3. Automatic Extraction of Protein Interactions from Scientific Abstracts
  - Thomas et.al, 2000
  - thomas.pdf
4. PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine
  - Donaldson et.al, 2003
  - preBIND_textomy.pdf
5. Computer-Assisted Generation of a Protein- Interaction Database for Nuclear Receptors
  - Albert et. al, 2003
  - albert.pdf
6. Extraction of protein interaction information from unstructured text using a context-free grammar
  - Joshua M. Temkin and Mark R. Gilder, Apr 2003
  - temkin.pdf

Protein Function
1. Protein Structures and Information Extraction from Biological Texts: The PASTA System
  - Gaizauskas et.al
  - gaizauskas_02.pdf

Gene relation to biological function
1. The computational analysis of scientific literature to define and recognize gene expression clusters
  - Soumya Raychaudhuri et. al, May 2003
  - raychaudhuri.pdf
2. Use of keword hierarchies to interpret gene expression patterns
  - Masys et.al, 2000
  - masys.pdf
3. Detecting gene relations from medline abstracts
  - Stephens et.al, 2001
  - stephens.pdf

Enzyme Binding
1. Mining Molecular Binding Terminology from Biomedical Text
  - Rindflesch et al.
  - rindflesch_hunter.pdf

Pathways (Full text search)
1. GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles

General
1. Mining the Biomedical Literature in the Genomic Era: An Overview
  - Shatkay and Feldman, Dec 2003
  - shatkay_feldman.pdf
2. Mining the bibliome: searching for a needle in a haystack? (report)
  - Les Grivell, 2002
  - grivell.pdf
3. Accomplishments and challenges in literature data mining for biology
  - Hirschman et.al, May 2002
  - hirschman.pdf
4. Genomics and Natural Language Processing
  - Mark D. Yandell and William H.Majoros, Aug 2002
  - yandell.pdf
5. Getting to the (c)ore of knowledge: mining biomedical literature
  - deBruijn.pdf
6. Toward Information Extraction: Identifying protein names from biological papers
  - K. Fukuda, T. Tsunoda, A. Tamura, T. Takagi, 1998
  - fukuda.pdf
7. Finding relevant references to genes and proteins in Medline using a Bayesian approach
  - Leonard, Colombe and Levy, May 2002
  - leonard.pdf
8. Mining MEDLINE: Abstracts, Sentences, Or Phrases?
  - J. Ding, D. Berleant, D. Nettleton, E. Wurtele, 2002
  - ding.pdf
9. Genes, Themes and Microarrays Using Information Retrieval for Large-Scale Gene Analysis
  - Hagit Shatkay, Stephen Edwards, W. John Wilbur, Mark Boguski, 2000
  - shatkay00genes.pdf