@article{Abe&Mamitsuka97,
  author =   {Naoki Abe and Hiroshi Mamitsuka},
  title =    {Predicting Protein Secondary Structure Using Stochastic Tree Grammars},
  journal =  ML,
  volume =   {29},
  number =   {2-3},
  month =    {November},
  year =     {1997},
  pages =    {275--301},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Abe&Mamitsuka%20Predicting%20Protein%20Secondary%20Structure%20Using%20Stochastic%20Tree%20Grammars.pdf},
}

@inproceedings{Ahmed&al.05,
  author =   {Syed Toufeeq Ahmed and Deepthi Chidambaram and Hasan Davulcu and Chitta Baral},
  title =    {{InTex}: A Syntactic Role Driven Protein-Protein Interaction Extractor},
  booktitle =    ISMB-WS2005A,
  crossref =     {ISMB-WS2005A},
  pages = {54--61},
  year =     {2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Ahmed&al%20InTex%20-%20A%20Syntactic%20Role%20Driven%20Protein-Protein%20Interaction%20Extractor.pdf},
}

@article{Alako&al.05,
  title = {CoPub Mapper: mining MEDLINE based on search term co-publication},
  author = {Blaise T. Alako and Antoine Veldhoven and Sjozef van Baal and Rob Jelier and Stefan Verhoeven and Ton Rullmann and Jan Polman and Guido Jenster},
  issn = {1471-2105},
  journal = {BMC Bioinformatics},
  month = {March},
  number = {1},
  volume = {6},
  year = {2005},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Alako&al%20CoPub%20Mapper%20mining%20MEDLINE%20based%20on%20search%20term%20co-publication.pdf},
}



@article{Andrade&Bork00,
  title = {Automated extraction of information in molecular biology},
  author = {M. A. Andrade and P. Bork},
  issn = {0014-5793},
  journal = {FEBS Lett},
  month = {June},
  number = {1-2},
  pages = {12--17},
  volume = {476},
  year = {2000},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Andrade&Bork%20Automated%20extraction%20of%20information%20in%20molecular%20biology.pdf},
}

@inproceedings{Andrade&Valencia97,
  author = {M. A. Andrade and A. Valencia},
  title = {Automatic Annotation for Biological Sequences by Extraction of Keywords from {MEDLINE} Abstracts - Development of a Prototype System},
  booktitle =    ISMB1997,
  crossref = {ISMB1997},
  pages =        {25--32},
  year =         {1997},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Andrade&Valencia%20Automatic%20annotation%20for%20biological%20sequences%20by%20extraction%20of%20keywords%20from%20MEDLINE%20abstracts%20Development%20of%20a%20prototype%20system.pdf},
}

@article{Arazi&al.04,
  author =   {Arnon Arazi and Eshel Ben-Jacob and Uri Yechiali},
  title =    {Bridging Genetic Networks and Queueing Theory},
  journal =  {Physica A},
  volume =   {332},
  year =     {2004},
  pages =    {585--616},
  publisher =    {Elsevier},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Arazi&al%20Bridging%20Genetic%20Networks%20and%20Queueing%20Theory.pdf},
}

@inproceedings{Attwood&al.04,
  author =   {Teresa K. Attwood and Paul Bradley and Walter Daelemans and Luc Dehaspe and Frederique Durant and Melanie Hilario and Jee-Hyub Kim and Alex L. Mitchell and Johann Petrak and Violaine Pillet and Alexander K. Seewald and Kristof Van Belleghem and Anne-Lise Veuthey and Marc Zehnder},
  title =    {{BioMinT}: A Database Curator's Assitant for Biomedical Text Processing},
  booktitle =    ISMB-WS2004A,
  crossref =     {ISMB-WS2004A},
  year =     {2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Attwood&al%20BioMinT%20-%20A%20Database%20Curators%20Assitant%20for%20Biomedical%20Text%20Processing.pdf},
}

@article{Bader&Hogue02,
  author =       {G. D. Bader and C.W.V. Hogue},
  title =        {Analyzing Yeast Protein-Protein Interaction Data Obtained from Different Sources},
  journal =      {Nature Biotechnology},
  volume =       {20},
  pages =        {991--997},
  year =         {2002},
   month =                {October},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Bader&Hogue%20Analyzing%20yeast%20protein-protein%20interaction%20data%20obtained%20from%20different%20sources.pdf},
}

@inproceedings{Bailey&Elkan94,
  author =   {Timothy L. Bailey and Charles Elkan},
  title =    {Fitting a Mixture Model by Expectation Maximization to Discover Motifs in Biopolymers},
  booktitle =    {Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology (ISMB '94)},
  editor =   {Russ B. Altman and Douglas L. Brutlag and Peter D. Karp and Richard H. Lathrop and David B. Searls},
  month =    {August 14-17,},
  address =  {Stanford, California, USA},
  publisher =    AAAI,
  isbn =     {0-929280-68-7},
  pages =    {28--36},
  year =     {1994},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Bailey&Elkan%20Fitting%20a%20Mixture%20Model%20by%20Expectation%20Maximization%20to%20Discover%20Motifs%20in%20Biopolymers.pdf},
}

@inproceedings{Baldi&al.95,
  author =   {Pierre Baldi and S{\o}ren Brunak and Yves Chauvin and Jacob Engelbrecht and Anders Krogh},
  title =    {Periodic Sequence Patterns in Human Exons},
  pages =    {30--38},
  booktitle =    ISMB1995,
  year =     {1995},
  crossref =     {ISMB1995},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Baldi&al%20Periodic%20Sequence%20Patterns%20in%20Human%20Exons.pdf},
}

@article{Bean&Corn05,
  author =   {Carol A. Bean and Milton Corn},
  title =    {Extramural Funding Opportunities in Bioinformatics from the {National} {Library} of {Medicine}},
  journal =  JASIST,
  year =     {2005},
  volume =   {56},
  pages =    {551-556},
  number =   {5},
  month =    {March},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Bean&Corn%20Extramural%20Funding%20Opportunities%20in%20Bioinformatics.pdf},
}

@inproceedings{Ben-Hur&Noble05,
  author =   {Asa Ben-Hur and William Stafford Noble},
  title =    {Kernel Methods for Predicting Protein-Protein Interactions},
  pages =    {38--46},
  booktitle =    ISMB2005,
  year =     {2005},
  crossref =     {ISMB2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Ben-Hur&Noble%20Kernel%20Methods%20for%20Predicting%20Protein-Protein%20Interactions.pdf},
}

@article{Blaschke&Valencia01,
  author = {C. Blaschke and A. Valencia},
  title = {The Potential Use of {SUISEKI} as a Protein Interaction Discovery Tool},
  journal = {Genome Inform Ser Workshop Genome Inform.},
  volume = {12},
  pages = {123--134},
  year = {2001},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Blaschke&Valencia%20The%20potential%20use%20of%20SUISEKI%20as%20a%20protein%20interaction%20discovery%20tool.pdf},
}

@article{Blaschke&Valencia02,
  author = {C. Blaschke and A. Valencia},
  title = {The Frame-Based Module of the {SUISEKI} Information Extraction System},
  year = {2002},
  journal = {IEEE Intelligent Systems},
  volume = {17},
  pages = {14--20},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Blaschke&Valencia%20The%20frame-based%20module%20of%20the%20SUISEKI%20information%20extraction%20system.pdf},
}

@inproceedings{Blaschke&Valencia03,
  author =   {Christian Blaschke and Alfonso Valencia},
  title =    {{BioCreAtIvE}: Functional Extraction},
  booktitle =    ISMB-WS2003A,
  crossref =     {ISMB-WS2003A},
  year =     {2003},
  x-location =   {no},
}

@inproceedings{Blaschke&al.99,
  author =   {Christian Blaschke and Miguel A. Andrade and Christos A. Ouzounis and Alfonso Valencia},
  title =    {Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions},
  pages =    {60--67},
  booktitle =    ISMB1999,
  year =     {1999},
  crossref =     {ISMB1999},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Blaschke&al%20Automatic%20Extraction%20of%20Biological%20Information%20from%20Scientific%20Text%20Protein-Protein%20Interactions.pdf},
}

@inproceedings{Borgwardt&al.05,
  author =   {Karsten M. Borgwardt and Cheng Soon Ong and Stekan Sch{\"o}nauer and S. V. N. Vishwanathan and Alex J. Smola and Hans-Peter Kriegel},
  title =    {Protein Function Prediction via Graph Kernels},
  pages =    {47--56},
  booktitle =    ISMB2005,
  year =     {2005},
  crossref =     {ISMB2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Borgwardt&al%20Protein%20Function%20Prediction%20via%20Graph%20Kernels.pdf},
}

@article{Brent&Bruck06,
  author =   {Roger Brent and Jehoshua Bruck},
  title =    {Can Computers Help to Explain Biology},
  journal =  {Nature},
  pages =    {416--417},
  volume =   {440},
  month =    {March 23,},
  year =     {2006},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Brent&Bruck%20Can%20Computers%20Help%20to%20Explain%20Biology.pdf},
}

@misc{Briscoe97,
  author =   {Ted Briscoe},
  year =     {1997},
  title =    {Language Acquisition: The Bioprogram Hypothesis and the {Baldwin} {Effect}},
  type =     {Unpublished Manuscript},
  note =     {http://www.cl.cam.ac.uk/users/ejb/bioprogram.ps.gz},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Briscoe%20Language%20Acquisition%20The%20Bioprogram%20Hypothesis%20and%20the%20Baldwin%20Effect.pdf},
}

@article{Bruijn&Martin02,
  author = {Berry de Bruijn and Joel Martin},
  title = {Getting to the (C)ore of Knowledge: Mining Biomedical Literature},
  journal = {International Journal of Medical Informatics},
  volume = {67},
  number = {1-3},
  month = {December},
  year = {2002},
  pages = {7--18},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Bruijn&Martin%20Getting%20to%20the%20(C)ore%20of%20Knowledge%20-%20Mining%20Biomedical%20Literature.pdf},
}

@inproceedings{Bunescu&Mooney05,
              author = {Razvan C. Bunescu and Raymond J. Mooney},
              title = {Subsequence Kernels for Relation Extraction},
              booktitle = NIPS2005,
              year = {2005},
              crossref = {NIPS2005},
              x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Bunescu&Mooney%20Subsequence%20kernels%20for%20relation%20extraction.pdf},
}

@inproceedings{Bunescu&Mooney05a,
              author = {Razvan C. Bunescu and Raymond J. Mooney},
              title = {A Shortest Path Dependency Kernel for Relation Extraction},
              booktitle = HLT/EMNLP2005,
              year = {2005},
              month = {October},
              pages = {724--731},
              crossref = {HLT/EMNLP2005},
              x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Bunescu&Mooney%20A%20shortest%20path%20dependency%20kernel%20for%20relation%20extraction.pdf},
}

@unpublished{Bunescu&Mooney06,
             author = {Razvan C. Bunescu and Raymond J. Mooney},
             title = {Extracting Relations from Text: From Word Sequences to Dependency Paths},
             booktitle = {Text Mining and Natural Language Processing},
             editor = {Anne Kao and Steve Poteet},
             note = {Forthcoming},
             year = {2006},
             x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Bunescu&Mooney%20Extracting%20relations%20from%20text%20From%20word%20sequences%20to%20dependency%20paths.pdf},
}

@article{Bunescu&al.05,
  author = {Razvan Bunescu and Ruifang Ge and Rohit G. Kate and Edward M. Marcotte and Raymond J. Mooney and Arun K. Ramani and Yuk Wah Wong},
  title = {Comparative Experiments on Learning Information Extractors for Proteins and Their Interactions},
  journal = {Artificial Intelligence in Medicine},
  volume = {33},
  pages = {139--155},
  year = {2005},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Bunescu&al%20Comparative%20Experiments%20on%20Learning%20Information%20Extractors%20for%20Proteins%20and%20Their%20Interactions.pdf},
}

@article{Butte&Kohane06,
  author =   {Atul J. Butte and Isaac S. Kohane},
  title =    {Creation and Implications of a Phenome-Genome Network},
  journal =  {Nature Biotechnology},
  volume =   {24},
  pages =    {55--62},
  year =     {2006},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Butte&Kohane%20Creation%20and%20Implications%20of%20a%20Phenome-Genome%20Network.pdf},
}

@article{Chang&al.04,
  author =         {Jeffrey T. Chang and Hinrich Sch\"{u}tze and Russ B. Altman},
  title =         {{GAPSCORE}: Finding Gene and Protein Names One Word at a Time},
  year =         {2004},
  journal =         {Bioinformatics},
  volume =       {20},
  number =       {2},
  pages =        {216--225},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Chang&al%20GAPSCORE%20finding%20gene%20and%20protein%20names%20one%20word%20at%20a%20time.pdf},
}

@article{Chen&Sharp04,
    author = {Chen, H.  and Sharp, B. M. },
    journal = {BMC Bioinformatics},
    month = {October},
    number = {1},
    priority = {2},
    title = {Content-rich biological network constructed by mining PubMed abstracts.},
    volume = {5},
    year = {2004},
    x-location = {no},
}

@article{Chen&al06,
    author = {Chen, J.  and Hsu, W.  and Lee, M. L.  and Ng, S. K. },
    journal = {Bioinformatics},
    month = {August},
    number = {16},
    pages = {1998--2004},
    title = {Increasing confidence of protein interactomes using network topological metrics.},
    volume = {22},
    year = {2006},
    x-location = {no},
}

@article{Chen&al06b,
    author = {Chen, J. Y.  and Shen, C.  and Sivachenko, A. Y. },
    journal = {Pac Symp Biocomput},
    pages = {367--378},
    title = {Mining Alzheimer disease relevant proteins from integrated protein interactome data.},
    year = {2006},
    x-location = {no},
}

@incollection{Cohen&Hunter04,
  author =   {K. Bretonnel Cohen and Lawrence Hunter},
  title =    {Natural Language Processing and Systems Biology},
  editor =   {Werner Dubitzky and Francisco Azuaje},
  booktitle =    {Artificial Intelligence Methods and Tools for Systems Biology},
  year =     {2004},
  pages =    {147--174},
  isbn =     {1402028598},
  publisher =    {Springer Verlag},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Cohen&Hunter%20Natural%20Language%20Processing%20and%20Systems%20Biology.pdf},
}

@inproceedings{Cohen&al.03a,
  author =   {William W. Cohen and Richard Wang and Robert F. Murphy},
  title =    {Understanding Captions in Biomedical Publications},
  booktitle =    KDD2003,
  year =     {2003},
  pages =    {499--504},
  crossref =     {KDD2003},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Cohen&al%20Understanding%20Captions%20in%20Biomedical%20Publications.pdf},
}

@inproceedings{Cohen&al.03b,
  title = {Extracting Information from Text and Images for Location Proteomics},
  author = {William W. Cohen and Zhenzhen Kou and Robert F. Murphy},
  booktitle = {Proceedings of the 3nd ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD 2003)},
  pages = {2--9},
  year = {2003},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Cohen&al%20Extracting%20information%20from%20text%20and%20images%20for%20location%20proteomics.pdf},
}

@article{Cooper&Kershenbaum05,
  title = {Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.},
  author = {James  W. Cooper and Aaron Kershenbaum},
  issn = {1471-2105},
  journal = {BMC Bioinformatics},
  month = {June},
  number = {1},
  volume = {6},
  year = {2005},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Cooper&Kershenbaum%20Discovery%20of%20protein-protein%20interactions%20using%20a%20combination%20of%20linguistic%20statistical%20and%20graphical%20information.pdf},
}

@inproceedings{Cohen&al.05,
  author =   {K. Bretonnel Cohen and Lynne Fox and Philip V. Ogren and Lawrence Hunter},
  title =    {Corpus Design for Biomedical Natural Language Processing},
  booktitle =    ISMB-WS2005A,
  crossref =     {ISMB-WS2005A},
  year =     {2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Cohen&al%20Corpus%20Design%20for%20Biomedical%20Natural%20Language%20Processing.pdf},
}

@article{Cohen04,
  author =   {Jacques Cohen},
  title =    {Bioinformatics - An Introduction for Computer Scientists},
  journal =  {ACM Computing Surveys},
  volume =   {36},
  number =   {2},
  year =     {2004},
  pages =    {122--158},
  publisher =    ACM,
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Cohen%20Bioinformatics%20-%20An%20Introduction%20for%20Computer%20Scientists.pdf},
}

@inproceedings{Cohen05,
  author =   {Aaron M. Cohen},
  title =    {Unsupervised Gene/Protein Named Entity Normalization Using Automatically Extracted Dictionaries},
  booktitle =    ISMB-WS2005A,
  crossref =     {ISMB-WS2005A},
  year =     {2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Cohen%20Unsupervised%20Gene-Protein%20Named%20Entity%20Normalization%20Using%20Automatically%20Extracted%20Dictionaries.pdf},
}

@article{Colizza&al.05,
        author = {Vittoria Colizza and Alessandro Flammini and Amos Maritan and Alessandro Vespignani},
        title = {Characterization and modeling of protein-protein interaction networks},
        journal = {Physica A},
        year = {2005},
        month = {July},
        volume = {352},
        number = {1},
        pages = {1--27},
        x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Colizza&al%20Characterization%20and%20modeling%20of%20protein-protein%20interaction%20networks.pdf},
}

@article{Corney&al.04,
  author = {David P. A. Corney and Bernard F. Buxton and William B. Langdon and David T. Jones},
  title = {{BioRAT}: Extracting Biological Information from Full-Length Papers},
  journal = {Bioinformatics},
  volume = {20},
  number = {17},
  pages = {3206--3213},
  year = {2004},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Corney&al%20BioRAT%20-%20Extracting%20Biological%20Information%20from%20Full-Length%20Papers.pdf},
}

@inproceedings{Craven&Kumlien99,
  author =   {Mark Craven and Johan Kumlien},
  title =    {Constructing Biological Knowledge Bases by Extracting Information from Text Sources},
  pages =    {77--86},
  booktitle =    ISMB1999,
  year =     {1999},
  crossref =     {ISMB1999},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Craven&Kumlien%20Constructing%20Biological%20Knowledge%20Bases%20by%20Extracting%20Information%20from%20Text%20Sources.pdf},
}

@inproceedings{Craven99,
  author =   {Mark Craven},
  title =    {Learning to Extract Relations from {MEDLINE}},
  booktitle =    AAAI-WS1999A,
  crossref =     {AAAI-WS1999A},
  year =     {1999},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Craven%20Learning%20to%20Extract%20Relations%20from%20MEDLINE.pdf},
}

@article{Daraselia&al.04,
  author =   {Nikolai Daraselia and Anton Yuryev and Sergei Egorov and Svetalana Novichkova and Alexander Nikitin and Ilya Mazo},
  title =    {Extracting Human Protein Interactions from {MEDLINE} Using a Full-Sentence Parser},
  volume =   {20},
  number =   {5},
  year =     {2004},
  pages =    {604--611},
  journal =  {Bioinformatics},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Daraselia&al%20Extracting%20Human%20Protein%20Interactions%20from%20MEDLINE%20Using%20a%20Full-Sentence%20Parser.pdf},
}

@inproceedings{Dingare&al.04,
  author =   {Shipra Dingare and Malvina Nissim and Jenny Finkel and Claire Grover and Christopher Manning},
  title =    {A System for Identifying Named Entities in Biomedical Text: How Results From Two Evaluations Reflect on Both the System and the Evaluations},
  booktitle =    ISMB-WS2004A,
  crossref =     {ISMB-WS2004A},
  year =     {2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Dingare&al%20A%20System%20for%20Identifying%20Names%20Entities%20in%20Biomedical%20Text.pdf},
}

@inproceedings{Dobrokhotov&al.03,
  author =   {Pavel B. Dobrokhotov and Cyril Goutte and Anne-Lisa Veuthey and Eric Gaussier},
  title =    {Combining {NLP} and Probabilistic Categorisation for Document and Term Selection for {SWISS-PROT} Medical Annotation},
  pages =    {91--94},
  booktitle =    ISMB2003,
  year =     {2003},
  crossref =     {ISMB2003},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Dobrokhotov&al%20Combining%20NLP%20and%20Probabilistic%20Categorisation%20for%20Document%20and%20Term%20Selection%20for%20SWISS-PROT%20Medical%20Annotation.pdf},
}

@inproceedings{Donaldson&al.03,
  author =   {Ian Donaldson and Joel Martin and Berry de Bruijn and Cheryl Wolting and Vicki Lay and Brigitte Tuekam and Shudong Zhang and Berivan Baskin and Gary D. Bader and Katerina Michalockova and Tony Pawson and Christopher W. V. Hogue},
  title =    {{PreBIND} and {Textomy} - Mining the Biomedical Literature for Protein-Protein Interactions Using a Support Vector Machine},
  booktitle =    ISMB-WS2003A,
  crossref =     {ISMB-WS2003A},
  year =     {2003},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Donaldson&al%20PreBIND%20and%20Textomy%20-%20Mining%20the%20Biomedical%20Literature%20for%20Protein-Protein%20Interactions%20Using%20a%20Support%20Vector%20Machine.pdf},
}

@book{Durbin&al.98,
  author =   {Richard Durbin and Sean R. Eddy and Anders Krogh and Graeme Mitchison},
  title =    {Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids},
  publisher =    CUP,
  year =     {1998},
  x-location =   {n/a},
}

@article{Erhardt&al.06,
  author = {Ram{\'o}n A-A. Erhardt and Reinhard Schneider and Christian Blaschke},
  title = {Status of Text-Mining Techniques Applied to Biomedical Text},
  journal = {Drug Discovery Today},
  volume = {11},
  number = {7-8},
  month = {April},
  year = {2006},
  pages = {315--325},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Erhardt&al%20Status%20of%20Text-Mining%20Techniques%20Applied%20to%20Biomedical%20Text.pdf},
}

@article{Erkan&Radev04,
  author    = {G\"{u}ne\c{s} Erkan and
               Dragomir R. Radev},
  title     = {LexRank: Graph-based Lexical Centrality as Salience in Text
               Summarization.},
  journal   = {Journal of Artificial Intelligence Research (JAIR)},
  volume    = {22},
  year      = {2004},
  pages     = {457--479},
  x-location = {no},
}

@inproceedings{Eskin&al.00,
  author =   {Eleazar Eskin and William Noble Grundy and Yoram Singer},
  title =    {Protein Family Classification Using Sparse {Markov} Transducers},
  pages =    {134--145},
  booktitle =    ISMB2000,
  year =     {2000},
  crossref =     {ISMB2000},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Eskin&al%20Protein%20Family%20Classification%20using%20Sparse%20Markov%20Transducers.pdf},
}

@inproceedings{Eskin&al.01,
  author =   {Eleazar Eskin and William Noble Grundy and Yoram Singer},
  title =    {Using Mixtures of Common Ancestors for Estimating the Probabilities of Discrete Events in Biological Sequences},
  pages =    {22--29},
  booktitle =    ISMB2001,
  year =     {2001},
  crossref =     {ISMB2001},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Eskin&al%20Using%20Mixtures%20of%20Common%20Ancestors%20for%20Estimating%20the%20Probabilities%20of%20Discrete%20Events%20in%20Biological%20Sequences.pdf},
}

@techreport{Felsenstein93,
  author =   {Joseph Felsenstein},
  title =    {{PHYLIP}: Phylogeny Inference Package},
  institution =  {Department of Genome Sciences, University of Washington},
  year =     {1995},
  note = {http://evolution.genetics.washington.edu/phylip/doc/main.html},
  x-location =   {no},
}


@article{Fenstermacher05,
  author =   {David Fenstermacher},
  title =    {Introduction to Bioinformatics},
  journal =  JASIST,
  year =     {2005},
  volume =   {56},
  pages =    {440--446},
  number =   {5},
  month =    {March},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Fenstermacher%20Introduction%20to%20Bioinformatics.pdf},
}

@article{Finkel&al.05,
  author =   {Jenny Finkel and Shipra Dingare and Christopher D. Manning and Malvina Nissim and Beatrice Alex and Claire Grover},
  journal =  {Bioinformatics},
  volume =   {6},
  year =     {2005},
  title =    {Exploring the Boundaries: Gene and Protein Identification in Biomedical Text},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Finkel&al%20Exploring%20the%20Boundaries%20-%20Gene%20and%20Protein%20Identification%20in.pdf},
}

@article{Fitch&Margoliash67,
  author =   {Walter M. Fitch and Emanuel Margoliash},
  title =    {Construction of Phylogenetic Trees},
  journal =  {Science},
  volume =   {155},
  number =   {3760},
  pages =    {279--284},
  month =    {January},
  year =     {1967},
  x-location =   {no},
}

@inproceedings{Friedman&al.01,
  author =   {Carol Friedman and Pauline Kra and Hong Yu and Michael Krauthammer and Andrey Rzhetsky},
  title =    {{GENIES}: A Natural-Language Processing System for the Extraction of Molecular Pathways from Journal Articles},
  pages =    {74--82},
  booktitle =    ISMB2001,
  year =     {2001},
  crossref =     {ISMB2001},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Friedman&al%20GENIES%20-%20A%20Natural-Language%20Processing%20System%20for%20the%20Extraction%20of%20Molecular%20Pathways%20from%20Journal%20Articles.pdf},
}

@article{Ginter&al.04a,
  author =   {Filip Ginter and Jorma Boberg and Jouni Jarvinen and Tapio Salakoski},
  title =    {New Techniques for Disambiguation in Natural Language and Their Application to Biological Text},
  journal =  JMLR,
  year =     {2004},
  volume =   {5},
  pages =    {605--621},
  month =    {June},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Ginter&etal%20New%20Techniques%20for%20Disambiguation.pdf},
}

@inproceedings{Ginter&al.04b,
  author =   {Filip Ginter and Tapio Pahikkala and Sampo Pyysalo and Jorma Boberg and Jouni J{\"a}rvinen and Tapio Salakoski},
  title =    {Extracting Protein-Protein Interaction Sentences by Applying Rough Set Data Analysis},
  booktitle =    {Proceedings of the Fourth International Conference on Rough Sets and Current Trends in Computing (RSCTC 2004)},
  editor =   {Shusaku Tsumoto and Roman Slowinski and Jan Komorowski and et al.},
  Series =       {Lecture Notes in Artificial Intelligence , Vol. 3066},
  publisher =    {Springer Verlag},
  pages =    {780--785},
  year =     {2004},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Ginter&al%20Extracting%20Protein-Protein%20Interaction%20Sentences%20by%20Applying%20Rough%20Set%20Data%20Analysis.pdf},
}

@inproceedings{Gionis&Mannila03,
  author =   {Aristides Gionis and Heikki Mannila},
  title =    {Finding Recurrent Sources in Sequences},
  booktitle =    {Seventh Annual Conference on Computational Biology (RECOMB'03)},
  address =  {Berlin, Germany},
  year =     {2003},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Gionis&Mannila%20Finding%20Recurrent%20Sources%20in%20Sequences.pdf},
}

@article{Goldberg&Roth03,
    author = {Goldberg, D. S.  and Roth, F. P. },
    journal = {Proc Natl Acad Sci U S A},
    month = {April},
    number = {8},
    pages = {4372--4376},
    title = {Assessing experimentally derived interactions in a small world.},
    volume = {100},
    year = {2003},
      x-location =   {no},
}

@article{Gonzalez&al07,
    author = {Graciela Gonzalez and Juan C. Uribe and Luis Tari and Colleen Brophy and Chitta Baral },
    journal = {Pacific Symposium on Biocomputing},
    pages = {28--39},
    title = {Mining Gene-Disease relationships from Biomedical Literature: Weighting Protein-Protein Interactions and Connectivity Measures},
    volume = {12},
    year = {2007},
    x-location =   {no},
}


@article{Grover&al.05,
        author = {Claire Grover and Mirella Lapata and Alex Lascarides},
        title = {A Comparison of Parsing Technologies for the Biomedical Domain},
        journal = NLE,
        year = {2005},
        month = {March},
        volume = {11},
        number = {1},
        pages = {27--65},
        x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Grover&al%20A%20comparison%20of%20parsing%20technologies%20for%20the%20biomedical%20domain.pdf},
}

@inproceedings{Gunduz&al.04,
  author =   {Cigdem Gunduz and Bulent Yener and S. Humayun Gultekin},
  title =    {The Cell-Graphs of Cancer},
  pages =    {145--151},
  booktitle =    ISMB2004,
  year =     {2004},
  crossref =     {ISMB2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Gunduz&al%20The%20Cell-Graphs%20of%20Cancer.pdf},
}

@book{Gusfield97,
  author =   {Dan Gusfield},
  title =    {Algorithms On Strings, Trees, and Sequences: Computer Science and Computational Biology},
  publisher =    CUP,
  year =     {1997},
  isbn =     {0521585198},
  x-location =   {n/a},
}

@inproceedings{Halperin&al.05,
  author =   {Eran Halperin and Gad Kimmel and Ron Shamir},
  title =    {Tag {SNP} Selection in Genotype Data for Maximizing {SNP} Prediction Accuracy},
  pages =    {195--203},
  booktitle =    ISMB2005,
  year =     {2005},
  crossref =     {ISMB2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Halperin&al%20Tag%20SNP%20Selection%20in%20Genotype%20Data%20for%20Maximizing%20SNP%20Prediction%20Accuracy.pdf},
}

@article{Hao&al.05,
  author = {Y. Hao and et al},
  title = {Discovering Patterns to Extract Protein-Protein Interactions from the Literature: Part {II}},
  year = {2005},
  journal = {Bioinformatics},
  volume = {21},
  pages = {3294--3300},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Hao&al%20Discovering%20Patterns%20to%20Extract%20Protein-Protein%20Interactions%20from%20the%20Literature%20Part%20II.pdf},
}

@inproceedings{Harkema&al.04,
  author =   {Henk Harkema and Ian Roberts and Rob Gaizauskus and Mark Hepple},
  title =    {A {Web} Service for Biomedical Term Look-Up},
  booktitle =    ISMB-WS2004A,
  crossref =     {ISMB-WS2004A},
  year =     {2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Harkema&al%20A%20Web%20Service%20for%20Biomedical%20Term%20Look-Up.pdf},
}

@article{Hirschman&al.05,
  title = {Overview of BioCreAtIvE: critical assessment of information extraction for biology},
  author = {L. Hirschman and A. Yeh and C. Blaschke and A. Valencia},
  issn = {1471-2105},
  journal = {BMC Bioinformatics},
  volume = {6 Suppl 1},
  year = {2005},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Hirschman&al%20Overview%20of%20BioCreAtIvE%20critical%20assessment%20of%20information%20extraction%20for%20biology.pdf},
}

@inproceedings{Hatzivassiloglou&al.01,
  author =   {Vasileios Hatzivassiloglou and Pablo A. Dubou{\'e} and Andrey Rzhetsky},
  title =    {Disambiguating Proteins, Genes, and {RNA} in Text: A Machine Learning Approach},
  pages =    {97--106},
  booktitle =    ISMB2001,
  year =     {2001},
  crossref =     {ISMB2001},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Hatzivassiloglou&al%20Disambiguating%20Proteins,%20Genes,%20and%20RNA%20in%20Text%20-%20A%20Machine%20Learning%20Approach.pdf},
}

@article{Hemminger&al.05,
  author =   {Bradley M. Hemminger and Trish Losi and Anne Bauers},
  title =    {Survey of Bioinformatics Programs in the United States},
  journal =  JASIST,
  year =     {2005},
  volume =   {56},
  pages =    {529--537},
  number =   {5},
  month =    {March},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Hemminger&al%20Survey%20of%20Bioinfomatics%20Programs.pdf},
}

@article{Hermjakob&al.04,
  author = {Henning Hermjakob and Luisa Montecchi-Palazzi and Chris Lewington and Sugath Mudali and Samuel Kerrien and Sandra Orchard and Martin Vingron and Bernd Roechert and Peter Roepstorff and Alfonso Valencia and Hanah Margalit and John Armstrong and Amos Bairoch and Gianni Cesareni and David Sherman and Rolf Apweiler},
  year = {2004},
  title = {{IntAct}: An Open Source Molecular Interaction Database},
  journal = {Nucleic Acids Research},
  volume = {32},
  pages = {452--455},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Hermjakob&al%20IntAct%20an%20open%20source%20molecular%20interaction%20database.pdf},
}

@article{Hristovski&al.05,
  title = {Using literature-based discovery to identify disease candidate genes},
  author = {D. Hristovski and B. Peterlin and J. A. Mitchell and S. M. Humphrey},
  issn = {1386-5056},
  journal = {Int J Med Inform},
  month = {March},
  number = {2-4},
  pages = {289--298},
  volume = {74},
  year = {2005},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Hristovski&al%20Using%20literature-based%20discovery%20to%20identify%20disease%20candidate%20genes.pdf},
}

@article{Hersh02,
  author =   {William Hersh},
  title =    {{TREC} Genomics Pre-Track Workshop Report},
  pages =    {81--82},
  journal =  {SIGIR Forum},
  volume =   {36},
  number =   {2},
  year =     {2002},
  publisher =    ACM,
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Hersh%20TREC%20Genomics%20Pre-Track%20Workshop%20Report.pdf},
}

@article{Hirschman&al.02,
  author =   {Lynette Hirschman and Jong C. Park and Junichi Tsujii and Limsoon Wong and Cathy H. Wu},
  title =    {Accomplishments and Challenges in Literature Data Mining for Biology},
  journal =  {Bioinformatics},
  year =     {2002},
  volume =       {18},
  number =       {12},
  pages =        {1553--1561},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Hirschman&al%20Accomplishments%20and%20challenges%20in%20literature%20data%20mining%20for%20biology.pdf},
}

@article{Hoffman&Valencia03,
  author = {R. Hoffmann and A. Valencia},
  title = {Protein Interaction: Same Network, Different Hubs},
  year = {2003},
  journal = {Trends Genet.},
  volume = {19},
   number = {12},
   month = {December},
  pages = {681--683},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Hoffmann&Valencia%20Protein%20interaction%20same%20network,%20different%20hubs.pdf},
}

@article{Hoffmann&Valencia04,
  title = {A gene network for navigating the literature},
  author = {R. Hoffmann and A. Valencia},
  journal = {Nature Genet.},
  pages = {664},
  volume = {36},
  year = {2004},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Hoffmann&Valencia%20A%20gene%20network%20for%20navigating%20the%20literature.pdf},
}

@article{Hoffman&Valencia05,
    author = {Hoffmann, R.  and Valencia, A. },
    journal = {Bioinformatics},
    month = {September},
    title = {Implementing the iHOP concept for navigation of biomedical literature.},
    pages = {ii252--ii258},
    volume = {21 Suppl 2},
    year = {2005},
    x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Hoffmann&Valencia%20Implementing%20the%20iHOP%20concept%20for%20navigation%20of%20biomedical%20literature.pdf},
}



@article{Homayouni&al.05,
  author =   {Ramin Homayouni and Kevin Heinrich and Lai Wei and Michael W. Berry},
  title =    {Gene Clustering by Latent Semantic Indexing of {MEDLINE} Abstracts},
  journal =  {Bioinformatics},
  year =     {2005},
  volume =   {21},
  pages =    {104--115},
  number =   {1},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Homayouni&etal%20Gene%20Clustering%20by%20Latent%20Semantic.pdf},
}

@article{Hu05,
    author = {X. Hu},
    journal = {Int. J. Bioinformatics Research and Applications},
    volume = {1},
    number = {1},
    pages = {81--101},
    title = {Mining and analyzing acale-free protein-protein interaction network},
    year = {2005},
    x-location =     {no},
}

@inproceedings{Hu&al.05,
  author =   {Haiyan Hu and Xifeng Yan and Yu Huang and Jiawei Han and Xianghong Jasmine Zhou},
  title =    {Mining Coherent Dense Subgraphs Across Massive Biological Networks for Functional Discovery},
  pages =    {213--221},
  booktitle =    ISMB2005,
  year =     {2005},
  crossref =     {ISMB2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Hu&al%20Mining%20Coherent%20Dense%20Subgraphs%20Across%20Massive%20Biological%20Networks%20for%20Functional%20Discovery.pdf},
}

@article{Huang&al.04,
  author =   {Minlie Huang and Xiaoyan Zhu and Yu Hao and Donald G. Payan and Kunbin Qu and Ming Li},
  title =    {Discovering Patterns to Extract Protein-Protein Interactions from Full Texts},
  journal =  {Bioinformatics},
  year =     {2004},
  volume =       {20},
  number =       {18},
  pages =        {3604--3612},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Huang&al%20Discovering%20Patterns%20to%20Extract%20Protein-Protein%20Interactions%20from%20Full%20Texts.pdf},
}

@inproceedings{Humphreys&al.00,
  author =       {K. Humphreys and G. Demetriou and and R. Gaizauskas},
  title =        {Two Applications of Information Extraction to Biological Science Journal Articles: Enzyme Interactions and Protein Structures},
  booktitle =    {Proceedings of Pacific Symposium on Biocomputing (PSB-00)},
  year =         {2000},
   pages =                {502--513},
  address =      {Honolulu, Hawaii, USA},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Humphreys&al%20Two%20applications%20of%20information%20extraction%20to%20biological%20science%20journal%20articles%20Enzyme%20interactions%20and%20protein%20structures.pdf},
}

@inproceedings{Humphreys&al.99,
  author =   {Kevin Humphreys and George Demetriou and Robert Galizauskas},
  title =    {Information Extraction from Biological Science Journal Articles},
  booktitle =    IJCAI-WS1999B,
  year =     {1999},
  crossref = {IJCAI-WS1999B},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Humphreys&al%20Information%20Extraction%20from%20Biological%20Science%20Journal%20Articles.pdf},
}

@inproceedings{Ie&al.05,
  author =   {Eugene Ie and Jason Weston and William Stafford Noble and Christina Leslie},
  title =    {Multi-Class Protein Fold Detection Using Adaptive Codes},
  booktitle =    ICML2005,
  year =     {2005},
  crossref =     {ICML2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Ie&al%20Multi-Class%20Protein%20Fold%20Detection%20using%20Adaptive%20Codes.pdf},
}

@inproceedings{Iliopoulos&al.01,
  author =       {I. Iliopoulos and A. J. Enright and C. A. Ouzounis},
  title =        {Textquest: Document Clustering of {Medline} Abstracts for Concept Discovery in Molecular Biology},
  booktitle =    {Proceedings of Pacific Symposium on Biocomputing (PSB-01)},
  pages =        {384--395},
  year =         {2001},
  address =      {Honolulu, Hawaii, USA},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Iliopoulos&al%20Textquest%20Document%20clustering%20of%20Medline%20abstraction%20for%20concept%20discovery%20in%20molecular%20biology.pdf},
}

@article{Ito&al.00,
  author =   {Takashi Ito and Kosuke Tashiro and Shigeru Muta and Ritsuko Ozawa and Tomoko Chiba and Mayumi Nishizawa and Kiyoshi Yamamoto and Satoru Kuhara and Yoshiyuki Sakaki},
  title =    {Toward a Protein-Protein Interaction Map of the Budding Yeast: A Comprehensive System to Examine Two-Hybrid Interactions in All Possible Combinations Between Yeast Proteins},
  journal =  PNAS,
  year =     {2000},
  volume =   {97},
  pages =    {1143--1147},
  number =   {3},
  month =    {February 1,},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Ito&etal%20Toward%20a%20Portein-protein%20Interaction%20Map.pdf},
}

@inproceedings{Jaakkola&al.99,
  author =   {Tommi Jaakkola and Mark Diekhans and David Haussler},
  title =    {Using the {Fisher} Kernel Method to Detect Remote Protein Homologies},
  pages =    {149--158},
  booktitle =    ISMB1999,
  year =     {1999},
  crossref =     {ISMB1999},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Jaakkola&al%20Using%20the%20Fisher%20Kernel%20Method%20to%20Detect%20Remote%20Protein%20Homologies.pdf},
}

@article{Jang&al.06,
  title = {Finding the evidence for protein-protein interactions from PubMed abstracts},
  author = {Hyunchul Jang and Jaesoo Lim and Joon-Ho Lim and Soo-Jun Park and Kyu-Chul Lee and Seon-Hee Park},
  journal = {Bioinformatics},
  month = {July},
  number = {14},
  pages = {e220-e226},
  volume = {22},
  year = {2006},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Jang&al%20Finding%20the%20evidence%20for%20protein-protein%20interactions%20from%20PubMed%20abstracts.pdf},
}

@article{Jensen&al.06,
  author = {Lars Juhl Jensen and Jasmin Saric and Peer Bork},
  title = {Literature Mining for the Biologist: From Information Retrieval to Biological Discovery},
  journal = {Nature Reviews Genetics},
  volume = {7},
  month = {February},
  year = {2006},
  pages = {119--129},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Jensen&al%20Literature%20Mining%20for%20the%20Biologist%20-%20From%20Information%20Retrieval%20to%20Biological%20Discovery.pdf},
}

@article{Jeong&al00,
    author = {Jeong, H.  and Tombor, B.  and Albert, R.  and Oltvai, Z. N.  and Barabási, A. L. },
    journal = {Nature},
    month = {October},
    number = {6804},
    pages = {651--654},
    title = {The large-scale organization of metabolic networks.},
    volume = {407},
    year = {2000},
    x-location = {no},
}

@article{Jeong&al.01,
        author = {H. Jeong and S.P. Mason and A.L. Barab\'{a}si and Z.N. Oltvai},
        title = {Lethality and centrality in protein networks},
        journal = {Nature},
        year = {2001},
        month = {May 3,},
        volume = {411},
        number = {6833},
        pages = {41--42},
        x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Jeong&al%20Lethality%20and%20centrality%20in%20protein%20networks.pdf},
}

@inproceedings{Joslyn&al.04,
  author =   {Cliff A. Joslyn and Susan M. Mniszewski and Andy Fulmer and Gary Heaton},
  title =    {The Gene Ontology Categorizer},
  pages =    {169--177},
  booktitle =    ISMB2004,
  year =     {2004},
  crossref =     {ISMB2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Joslyn&al%20The%20Gene%20Ontology%20Categorizer.pdf},
}

@inproceedings{Jothi&al.05,
  author =   {Raja Jothi and Maricel G. Kann and Teresa M. Przytycka},
  title =    {Predicting Protein-Protein Interaction by Searching Evolutionary Tree Automorphism Space},
  pages =    {241--250},
  booktitle =    ISMB2005,
  year =     {2005},
  crossref =     {ISMB2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Jothi&al%20Predicting%20Protein-Protein%20Interaction%20by%20Searching%20Evolutionary%20Tree%20Automorphism%20Space.pdf},
}

@article{Kim&al.06,
  title = {BioContrasts: extracting and exploiting proteinprotein contrastive relations from biomedical literature},
  author = {Jung-Jae Kim and Zhuo Zhang and Jong  C. Park and See-Kiong Ng},
  issn = {1367-4803},
  journal = {Bioinformatics},
  month = {March},
  number = {5},
  pages = {597--605},
  publisher = {Oxford University Press},
  note = {http://www.ingentaconnect.com/content/oup/cabios/2006/00000022/00000005/art00597},
  volume = {22},
  year = {2006},
  x-location = {no},
}

@inproceedings{Kaplan&Linial04,
  author =   {Noam Kaplan and Michal Linial},
  title =    {False Annotations of Proteins: Automatic Detection via Keyword-Based Clustering},
  booktitle =    ISMB2004,
  year =     {2004},
  crossref =     {ISMB2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Kaplan&Linial%20False%20Annotations%20of%20Proteins%20-%20Automatic%20Detection%20via%20Keyword-Based%20Clustering.pdf},
}

@article{Karp00,
  author =   {Peter D. Karp},
  title =    {An Ontology for Biological Function Based on Molecular Interactions},
  journal =  {Bioinformatics},
  year =     {2000},
  volume =       {16},
  number =       {3},
  pages =        {269--285},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Karp%20An%20ontology%20for%20biological%20function%20based%20on%20molecular%20interactions.pdf},
}

@inproceedings{Katrenko&Adriaans06,
              author = {Sophia Katrenko and Pieter Adriaans},
              title = {Learning Relations from Biomedical Corpora Using Dependency Tree Levels},
              booktitle = {Proceedings of the Fifteenth Dutch-Belgian Conference on Machine Learning},
              year = {2006},
              month = {May 12,},
              x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Katrenko&Adriaans%20Learning%20relations%20from%20biomedical%20corpora%20using%20dependency%20tree%20levels.pdf},
}

@inproceedings{Katrenko&al.05,
  author = {S. Katrenko and et al},
  title = {Learning Biological Interactions from {Medline} Abstracts},
  year = {2005},
  booktitle = ICML2005,
  crossref = {ICML2005},
  x-location = {no},
}

@inproceedings{Kayaalp&al.03,
  title = {Methods for accurate retrieval of {MEDLINE} citations in functional genomics},
  author = {Mehmet Kayaalp and Alan R. Aronson and Susanne M. Humphrey and Nicholas C. Ide and Lorraine K. Tanabe and Lawrence H. Smith and Dina Demner-Fushman and Russell R. Loane and James G. Mork and Olivier Bodenreider},
  booktitle = {TREC 2003},
  pages = {441-450},
  year = {2003},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Kayaalp&al%20Methods%20for%20accurate%20retrieval%20of%20MEDLINE%20citations%20in%20functional%20genomics.pdf},
}

@inproceedings{Kim&al.02,
  author =   {Jin-Dong Kim and Yuka Tateisi and Jun'ichi Tsujii and Tomoko Ohta},
  title =    {Corpus-Based Approach to Biological Entity Recognition},
  booktitle =    ISMB-WS2002A,
  crossref =     {ISMB-WS2002A},
  year =     {2002},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Kim&al%20Corpus-Based%20Approach%20to%20Biological%20Entity%20Recognition.pdf},
}

@inproceedings{Kim&al.03,
  author =   {Jin-Dong Kim and Tomoko Ohta and Yuka Tateisi and Jun'ichi Tsujii},
  title =    {{GENIA} Corpus - A Semantically Annotated Corpus for Bio-Textmining},
  pages =    {180--182},
  booktitle =    ISMB2003,
  year =     {2003},
  crossref =     {ISMB2003},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Kim&al%20GENIA%20Corpus%20-%20A%20Semantically%20Annotated%20Corpus%20for%20Bio-Textmining.pdf},
}

@article{Koike&al.03,
  author =       {A. Koike and Y. Kobayashi and T. Takagi},
  title =        {Kinase Pathway Database: An Integrated Protein-Kinase and {NLP}-Based Protein-Interaction Resource},
  journal =      {Genome Research},
  volume =       {13},
  pages =        {1231--1243},
  year =         {2003},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Koike&al%20Kinase%20pathway%20database%20An%20integrated%20protein-Kinase%20and%20NLP-based%20Protein-interaction%20resource.pdf},
}

@inproceedings{Kors&al.05,
  author =   {Jan A. Kors and Martijn J. Schuemie and Bob J. A. Schijvenaars and Marc Weeber and Barend Mons},
  title =    {Combination of Genetic Databases Improving Identification of Genes and Proteins in Text},
  booktitle =    ISMB-WS2005A,
  crossref =     {ISMB-WS2005A},
  year =     {2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Kors&al%20Combining%20of%20Genetic%20Databases%20Improves%20Identification%20of%20Genes%20and%20Proteins%20in%20Text.pdf},
}

@inproceedings{Kou&al.05,
  author =   {Zhenzhen Kou and William W. Cohen and Robert F. Murphy},
  title =    {High-Recall Protein Entity Recognition Using a Dictionary},
  pages =    {266--273},
  booktitle =    ISMB2005,
  year =     {2005},
  crossref =     {ISMB2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Kou&al%20High-Recall%20Protein%20Entity%20Recognition%20Using%20a%20Dictionary.pdf},
}

@inproceedings{Koyuturk&al.04,
  author =   {Mehmet Koyut{\"u}rk and Ananth Grama and Wojciech Szpankowski},
  title =    {An Efficient Algorithm for Detecting Frequent Subgraphs in Biological Networks},
  pages =    {200--207},
  booktitle =    ISMB2004,
  year =     {2004},
  crossref =     {ISMB2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Koyuturk&al%20An%20Efficient%20Algorithm%20for%20Detecting%20Frequent%20Subgraphs%20in%20Biological%20Networks.pdf},
}

@article{Krallinger&Valencia05,
  title = {Text-mining and information-retrieval services for molecular biology},
  author = {M. Krallinger and A. Valencia},
  journal = {Genome Biol.},
  pages = {224},
  volume = {6},
  year = {2005},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Krallinger&Valencia%20Text-mining%20and%20information-retrieval%20services%20for%20molecular%20biology.pdf},
}

@inproceedings{Krauthammer&al.02,
  author =   {Michael Krauthammer and Pauline Kra and Ivan Iossifov and Shawn M. Gomez and George Hripcsak and Vasileios Hatzivassiloglou and Carol Friedman and Andrey Rzhetsky},
  title =    {Of Truth and Pathways: Chasing Bits of Information Through Myriads of Articles},
  pages =    {249--257},
  booktitle =    ISMB2002,
  year =     {2002},
  crossref =     {ISMB2002},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Krauthammer&al%20Of%20Truth%20and%20Pathways%20-%20Chasing%20Bits%20of%20Information%20Through%20Myriads%20of%20Articles.pdf},
}

@article{Krogel&Scheffer04,
  author =   {Mark-A. Krogel and Tobias Scheffer},
  title =    {Multi-Relational Learning, Text Mining, and Semi-Supervised Learning for Functional Genomics},
  journal =  ML,
  volume =   {57},
  number =   {1-2},
  month =    {October},
  year =     {2004},
  pages =    {61--81},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Krogel&Scheffer%20Multi-Relational%20Learning,%20Text%20Mining,%20and%20Semi-Supervised%20Learning%20for.pdf},
}

@article{Kuang&al.05,
  author =   {Rui Kuang and Jason Weston and WIlliam Stafford Noble and Christina Leslie},
  title =    {Motif-Based Protein Ranking by Network Propagation},
  journal =  {Bioinformatics},
  volume =   {21},
  number =   {19},
  pages =    {3711--3718},
  year =     {2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Kuang&al%20Motif-based%20protein%20ranking%20by%20network%20propagation.pdf},
}

@inproceedings{Kulick&al.03,
  author =   {Seth Kulick and Mark Liberman and Martha Palmer and Andrew Schein},
  title =    {Shallow Semantic Annotation of Biomedical Corpora for Information Extraction},
  booktitle =    ISMB-WS2003A,
  crossref =     {ISMB-WS2003A},
  year =     {2003},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Kulick&al%20Shallow%20Semantic%20Annotation%20of%20Biomedical%20Corpora%20for%20Information%20Extraction.pdf},
}

@article{Kuonen03,
  author =   {D. Kuonen},
  year =     {2003},
  title =    {Challenges in bioinformatics for statistical data miners},
  journal =  {Bulletin of the Swiss Statistical Society},
  volume =       {46},
  pages =        {10--17},
   month =                {October},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Kuonen%20Challenges%20in%20bioinformatics%20for%20statistical%20data%20miners.pdf},
}

@inproceedings{Lease&Charniak05,
  author =   {Matthew Lease and Eugene Charniak},
  title =    {Parsing Biomedical Literature},
  booktitle =    {Proceedings of the Second International Joint Conference on Natural Language Processing},
  year =     {2005},
  pages =    {58--69},
  month =    {October 11-13,},
  address =  {Jeju Island, Korea},
  publisher =    {Springer-Verlag},
  editor =   {R. Dale and K.-F. Wong and J. Su and O. Y. Kwong},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Lease&Charniak%20Parsing%20Biomedical%20Literature.pdf},
}

@inproceedings{Lee&Park02,
  author =   {Jin-bok Lee and Jong C. Park},
  title =    {Text Data Mining for Automatic Gene Ontology Extension},
  booktitle =    ISMB-WS2002A,
  crossref =     {ISMB-WS2002A},
  year =     {2002},
  x-location =   {no},
}

@inproceedings{Ling&al06,
  author    = {Xu Ling and
               Jing Jiang and
               Xin He and
               Qiaozhu Mei and
               ChengXiang Zhai and
               Bruce R. Schatz},
  title     = {Automatically Generating Gene Summaries from Biomedical
               Literature.},
  booktitle = {Pacific Symposium on Biocomputing},
  year      = {2006},
  pages     = {40-51},
  x-location =   {no},
}

@article{Masys&al.01,
  title = {Use of keyword hierarchies to interpret gene expression patterns},
  author = {D. R. Masys and J. B. Welsh and J. Lynn Fink and M. Gribskov and I. Klacansky and J. Corbeil},
  issn = {1367-4803},
  journal = {Bioinformatics},
  month = {April},
  number = {4},
  pages = {319--326},
  volume = {17},
  year = {2001},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Masys&al%20Use%20of%20keyword%20hierarchies%20to%20interpret%20gene%20expression%20patterns.pdf},
}

@article{Mcdermott&al05,
    author = {Mcdermott, Jason   and Bumgarner, Roger   and Samudrala, Ram  },
    journal = {Bioinformatics},
    month = {August},
    number = {15},
    pages = {3217--3226},
    publisher = {Oxford University Press},
    title = {Functional annotation from predicted protein interaction networks},
    volume = {21},
    year = {2005},
      x-location = {no},
}

@article{Leroy&Chen05,
  author =   {Gondy Leroy and Hsinchun Chen},
  title =    {Genescene: An Ontology-Enhanced Integration of Linguistic and Co-Occurrence based Relations in Biomedical Texts},
  journal =  JASIST,
  year =     {2005},
  volume =   {56},
  pages =    {457--468},
  number =   {5},
  month =    {March},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Leroy&Chen%20Genescene%20An%20Ontology-Enhanced%20Integration.pdf},
}

@article{Leslie&Kuang04,
  author =   {C. Leslie and R. Kuang},
  title =    {Fast String Kernels Using Inexact Matching for Protein Sequences},
  journal =  JMLR,
  volume =   {5},
  pages =    {1435--1455},
  month =    {November},
  year =     {2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Leslie&Kuang%20Fast%20String%20Kernels%20using%20Inexact%20Matching%20for%20Protein%20Sequences.pdf},
}

@article{Light&al.04,
  author =       {M. Light and X. Y. Qiu and P. Srinivasan},
  title =        {The Language of Bioscience: Facts, Speculations, and Statements in Between},
  journal =      {HLT Biolink},
  year =         {2004},
   pages =                {17--24},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Light&al%20The%20language%20of%20bioscience%20Facts,%20speculations,%20and%20statements%20in%20between.pdf},
}

@inproceedings{Lu&al.06,
  author = {Zhiyong Lu and K. Bretonnel Cohen and Lawrence Hunter},
  title = {Finding {GeneRIFs} via Gene Ontology Annotations},
  booktitle = {Proceedings of the Pacific Symposium on Biocomputing},
  volume = {11},
  pages = {52--63},
  year = {2006},
  address = {Maui, Hawaii},
  month = {January 3-7,},
  publisher = {World Scientific Publishing Co. Pte. Ltd.},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Lu&al%20Finding%20GeneRIFs%20via%20Gene%20Ontology%20Annotations.pdf},
}

@inproceedings{Mani&al.04,
  author =   {Inderjeet Mani and Zhangzhi Hu and Cathy Wu and Seok Bae Jang and Ken Samuel and Matthew Krause and Jon Phillips},
  title =    {Protein Name Tagging Guidelines: Lessons Learned},
  booktitle =    ISMB-WS2004A,
  crossref =     {ISMB-WS2004A},
  year =     {2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Mani&al%20Protein%20Name%20Tagging%20Guidelines%20-%20Lessons%20Learned.pdf},
}

@article{Mao&al.06,
  author =   {Fenglou Mao and Zhengchang Su and Victor Olman and Phuongan Dam and Zhijie Liu and Ying Xu},
  title =    {Mapping of Orthologous Genes in the Context of Biological Pathways: An Application of Integer Programming},
  journal =  PNAS,
  month =    {January 3,},
  year =     {2006},
  volume =   {103},
  number =   {1},
  pages =    {129--134},
  publisher =    {National Academy of Sciences},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Mao&al%20Mapping%20of%20Orthologous%20Genes%20in%20the%20Context%20of%20Biological%20Pathways%20-%20An%20Application%20of%20Integer%20Programming.pdf},
}

@article{Marcotte&al.01,
  author =       {E. M. Marcotte and I. Xenarios and D. Eisenberg},
  title =        {Mining Literature for Protein-Protein Interactions},
  journal =      {Bioinformatics},
  volume =       {17},
  pages =        {359--363},
  year =         {2001},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Marcotte&al%20Mining%20Literature%20for%20Protein-Protein%20Interactions.pdf},
}

@article{McDonald&Pereira05,
  title =    {Identifying Gene and Protein Mentions in Text Using Conditional Random Fields},
  author =   {Ryan McDonald and Fernando Pereira},
  journal =  {BMC Bioinformatics},
  year =     {2005},
  volume =   {6},
  number =   {Suppl 1},
  pages =    {S6},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/McDonald&Pereira%20Identifying%20Gene%20and%20Protein%20Mentions%20in%20Text%20Using%20Conditional%20Random%20Fields.pdf},
}

@article{McDonald&al.04,
  author =   {Daniel M. McDonald and Hsinchun Chen and Hua Su and Byron B. Marshall},
  title =    {Extracting Gene Pathway Relations Using a Hybrid Grammar: The {Arizona} Relation Parser},
  journal =  {Bioinformatics},
  year =     {2004},
  volume =       {20},
  number =       {18},
  pages =        {3370--3378},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/McDonald&al%20Extracting%20gene%20pathway%20relations%20using%20a%20hybrid%20grammar%20the%20Arizona%20Relation%20Parser.pdf},
}

@inproceedings{Mettu&al.05,
  author =   {Ramgopal R. Mettu and Ryan H. Lilien and Bruce Randall Donald},
  title =    {High-Throughput Inference of Protein-Protein Interfaces from Unassigned {NMR} Data},
  pages =    {292--301},
  booktitle =    ISMB2005,
  year =     {2005},
  crossref =     {ISMB2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Mettu&al%20High-Throughput%20Inference%20of%20Protein-Protein%20Interfaces%20from%20Unassigned%20NMR%20Data.pdf},
}

@inproceedings{Middendorf&al.04,
  author =   {Manuel Middendorf and Anshul Kundaje and Chris Wiggins and Yoav Freund and Christina Leslie},
  title =    {Predicting Genetic Regulatory Response Using Classification},
  pages =    {232--240},
  booktitle =    ISMB2004,
  year =     {2004},
  crossref =     {ISMB2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Middendorf&al%20Predicting%20Genetic%20Regulatory%20Response%20Using%20Classification.pdf},
}

@inproceedings{Mika&Rost04,
  author =   {Sven Mika and Burkhard Rost},
  title =    {Protein Names Precisely Peeled Off Free Text},
  pages =    {241--247},
  booktitle =    ISMB2004,
  year =     {2004},
  crossref =     {ISMB2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Mika&Rost%20Protein%20Names%20Precisely%20Peeled%20Off%20Free%20Text.pdf},
}

@article{Perez-Iratxeta&al.02,
  title = {Association of genes to genetically inherited diseases using data mining},
  author = {C. Perez-Iratxeta and P. Bork and M. A. Andrade},
  issn = {1061-4036},
  journal = {Nat Genet},
  month = {July},
  number = {3},
  pages = {316--319},
  volume = {31},
  year = {2002},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Perez-Iratxeta&al%20Association%20of%20genes%20to%20genetically%20inherited%20diseases%20using%20data%20mining.pdf},
}

@article{Perez-Iratxeta&al.05,
  title = {G2D: A Tool for Mining Genes Associated with Disease},
  author = {C. Perez-Iratxeta and Matthias Wjst and P. Bork and M. A. Andrade},
  issn = {1471-2156},
  journal = {BMC Genet},
  month = {August 22,},
  number = {1},
  volume = {6},
  year = {2005},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Perez-Iratxeta&al%20G2D%20a%20tool%20for%20mining%20genes%20associated%20with%20disease.pdf},
}

@inproceedings{Milward&al.04,
  author =   {David Milward and Marcus Bj{\"a}reland and William Hayes and Michelle Maxwell and Lisa {\"O}berg and Nick Tilford and James Thomas and Roger Hale and Sylvia Knight and Julie Barnes},
  title =    {Ontology-Based Interactive Information Extraction from Scientific Abstracts},
  booktitle =    ISMB-WS2004A,
  crossref =     {ISMB-WS2004A},
  year =     {2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Milward&al%20Ontology-Based%20Interactive%20Information%20Extraction%20from%20Scientific%20Abstracts.pdf},
}

@article{Mitsumori&al.06,
        author = {Tomohiro Mitsumori and Masaki Murata and Yasushi Fukuda and Kouichi Doi and Hirohumi Doi},
        title = {Extracting Protein-Protein Interaction Information from Biomedical Text with {SVM}},
        journal = {IEICE Transactions on Information and Systems},
        month = {August},
        year = {2006},
        volume = {E89-D},
        number = {8},
        pages = {2464--2466},
        x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Mitsumori&al%20Extracting%20protein-protein%20interaction%20information%20from%20biomedical%20text%20with%20SVM.pdf},
}

@inproceedings{Nakov&al.05,
  author =   {Preslav Nakov and Ariel Schwartz and Brian Wolf and Marti Hearst},
  title =    {Scaling Up {BioNLP}: Application of a Text Annotation Architecture to Noun Compound Bracketing},
  booktitle =    ISMB-WS2005A,
  crossref =     {ISMB-WS2005A},
  year =     {2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Nakov&al%20Scaling%20Up%20BioNLP%20-%20Application%20of%20a%20Text%20Annotation%20Architecture%20to%20Noun%20Compound%20Bracketing.pdf},
}

@inproceedings{Narayanaswamy&al.05,
  author =   {M. Narayanaswamy and K. E. Ravikumar and K. Vijay-Shanker},
  title =    {Beyond the Clause: Extraction of {Phosphorylation} Information from {MedLine} Abstracts},
  pages =    {319--327},
  booktitle =    ISMB2005,
  year =     {2005},
  crossref =     {ISMB2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Narayanaswamy&al%20Beyond%20the%20Clause%20-%20Extraction%20of%20Phosphorylation%20Information%20from%20MedLine%20Abstracts.pdf},
}

@article{Noble&al.05,
  author = {William Stafford Noble and Rui Kuang and Christina Leslie and Jason Weston},
  title = {Identifying Remote Protein Homologs by Network Propagation},
  journal = {FEBS Journal},
  volume = {272},
  number = {20},
  pages = {5119--5128},
  year = {2005},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Noble&al%20Identifying%20Remote%20Protein%20Homologs%20by%20Network%20Propagation.pdf},
}

@article{Novichkova&al.03,
  author =   {Svetlana Novichkova and Sergei Egorov and Nikolai Daraselia},
  title =    {{MedScan}, A Natural Language Processing Engine for {MEDLINE} Abstracts},
  journal =  {Bioinformatics},
  year =     {2003},
  volume =       {19},
  number =       {13},
  pages =        {1699--1706},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Novichkova&al%20MedScan,%20a%20natural%20language%20processing%20engine%20for%20MEDLINE%20abstracts.pdf},
}

@article{Nowak&Sigmund04,
  author =   {Martin A. Nowak and Karl Sigmund},
  title =    {Evolutionary Dynamics of Biological Games},
  year =     {2004},
  month =    {February 6,},
  volume =   {303},
  journal =  {Science},
  pages =    {793--799},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Nowak&Sigmund%20Evolutionary%20Dynamics%20of%20Biological%20Games.pdf},
}

@misc{Nusse04,
  author =       {R. Nusse},
  title =        {The {Wnt} Gene Homepage},
  institution =  {Howard Hughes Medical Institute},
  note = {http://www.stanford.edu/~rnusse/pathways/cell2.html},
  year =         {2004},
  x-location = {n/a},
}

@inproceedings{Ohta&al.97,
  author =   {Yoshihiro Ohta and Yasunori Yamamoto and Tomoko Okazaki and Ikuo Uchiyama and Toshihisa Takagi},
  title =    {Automatic Construction of Knowledge Base from Biological Papers},
  pages =    {218--225},
  booktitle =    ISMB1997,
  year =     {1997},
  crossref =     {ISMB1997},
  x-location =   {no},
}

@article{Ono&al.01,
  author = {T. Ono and et al},
  title = {Automated Extraction of Information on Protein-Protein Interactions from the Biological Literature},
  year = {2001},
  journal = {Bioinformatics},
  volume = {17},
  pages = {155--161},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Ono&al%20Automated%20Extraction%20of%20Information%20on%20Protein-Protein%20Interactions%20from%20the%20Biological%20Literature.pdf},
}

@article{Saric&al.05,
  title = {Extraction of regulatory gene/protein networks from Medline},
  author = {Jasmin Saric and Lars Juhl J. Jensen and Rossitza Ouzounova and Isabel Rojas and Peer Bork},
  issn = {1367-4803},
  journal = {Bioinformatics},
  month = {July},
  note = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=pubmed\&dopt=Abstract\&list_uids=16046493},
  year = {2005},
  x-location = {no},
}

@phdthesis{Otterbacher04,
  author =  {Jahna Otterbacher},
  title =   {Novelty and Change in Text},
  note = {PhD Dissertation Proposal},
  school =  {University of Michigan},
  month =   {December},
  year =    {2004},
x-location = {no},
}

@inproceedings{Park&al.02,
  author =   {Peter J. Park and Lu Tian and Isaac S. Kohane},
  title =    {Linking Gene Expression Data with Patient Survival Times Using Partial Least Squares},
  pages =    {120--127},
  booktitle =    ISMB2002,
  year =     {2002},
  crossref =     {ISMB2002},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Park&al%20Linking%20Gene%20Expression%20Data%20with%20Patient%20Survival%20Times%20Using%20Partial%20Least%20Squares.pdf},
}

@inproceedings{Proux&al.00,
  author =   {Denys Proux and Fran\c{c}ois Rechenmann and Laurent Julliard},
  title =    {A Pragmatic Information Extraction Strategy for Gathering Data on Genetic Interactions},
  pages =    {279--285},
  booktitle =    ISMB2000,
  year =     {2000},
  crossref =     {ISMB2000},
  x-location =   {no},
}

@inproceedings{Ramani&al.05,
  author =   {Arun Ramani and Edward Marcotte and Razvan Bunescu and Raymond Mooney},
  title =    {Using Biomedical Literature Mining to Consolidate the Set of Known Human Portein-Protein Interactions},
  booktitle =    ISMB-WS2005A,
  crossref =     {ISMB-WS2005A},
  year =     {2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Ramani&al%20Using%20Biomedical%20Literature%20Mining%20to%20Consolidate%20the%20Set%20of%20Known%20Human%20Portein-Protein%20Interactions.pdf},
}

@article{Rapp&Wheeler05,
        author = {Barbara A. Rapp and David L. Wheeler},
        title = {Bioinformatics Resources From the {National Center for Biotechnology Information}: An Integrated Foundation for Discovery},
        journal = JASIST,
        month = {March},
        year = {2005},
        volume = {56},
        number = {5},
        pages = {538--550},
        x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Rapp&Wheeler%20Bioinformatics%20resources%20from%20the%20National%20Center%20for%20Biotechnology%20Information%20An%20integrated%20foundation%20for%20discovery.pdf},
}

@article{Raychaudhuri&al.02,
  author =   {Soumya Raychaudhuri and Hinrich Sch{\"u}tze and Russ B. Altman},
  title =    {Using Text Analysis to Identify Functionally Coherent Gene Groups},
  journal =  {Genome Research},
  volume =   {12},
  number =   {10},
  pages =    {1582--1590},
  month =    {October},
  year =     {2002},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Raychaudhuri&al%20Using%20Text%20Analysis%20to%20Identify%20Functionally%20Coherent%20Gene%20Groups.pdf},
}

@inproceedings{Raychaudhuri&al.02a,
  author =   {Soumya Raychaudhuri and Hinrich Sch{\"u}tze and Russ B. Altman},
  title =    {Text Analysis of Scientific Literature Can Automatically Determine if a Group of Genes Share Common Biological Function},
  booktitle =    ISMB-WS2002A,
  crossref =     {ISMB-WS2002A},
  year =     {2002},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Raychaudhuri&al%20Text%20Analysis%20of%20Scientific%20Literature%20Can%20Automatically%20Determine%20if%20a%20Group%20of%20Genes%20Share.pdf},
}

@article{Raychaudhuri&al.03,
  author =   {Soumya Raychaudhuri and Hinrich Sch{\"u}tze and Russ B. Altman},
  title =    {Inclusion of Textual Documentation in the Analysis of Multidimensional Data Sets: Application to Gene Expression Data},
  journal =  ML,
  volume =   {52},
  number =   {1-2},
  month =    {July-August},
  year =     {2003},
  pages =    {119--145},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Raychaudhuri&al%20Inclusion%20of%20Textual%20Documentation%20in%20the%20Analysis%20of%20Multidimensional%20Data%20Sets.pdf},
}

@inproceedings{Reiss&Schwikowski04,
  author =   {David J. Reiss and Benno Schwikowski},
  title =    {Predicting Protein-Peptide Interactions Via a Network-Based Motif Sampler},
  pages =    {274--282},
  booktitle =    ISMB2004,
  year =     {2004},
  crossref =     {ISMB2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Reiss&Schwikowski%20Predicting%20Protein-Peptide%20Interactions%20Via%20a%20Network-Based%20Motif%20Sampler.pdf},
}

@inproceedings{Romano&al.06,
  title = {Investigating a Generic Paraphrase-based Approach for Relation Extraction},
  author = {Lorenza Romano and Milen Kouylekov and Idan Szpektor and Ido Dagan and Alberto Lavelli},
  booktitle = {11th Conference of the European Chapter of the Association for Computational Linguistics (EACL '06)},
  month = {April},
  pages = {409--416},
  publisher = {European Chapter of the Association for Computational Linguistics},
  year = {2006},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Romano&al%20Investigating%20a%20generic%20paraphrase-based%20approach%20for%20relation%20extraction.pdf},
}

@article{Shah&al.03,
  title = {Information extraction from full text scientific articles: where are the keywords?},
  author = {P. K. Shah and C. Perez-Iratxeta and P. Bork and M. A. Andrade},
  issn = {1471-2105},
  journal = {BMC Bioinformatics},
  month = {May 29,},
  number = {1},
  volume = {4},
  year = {2003},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Shah&al%20Information%20extraction%20from%20full%20text%20scientific%20articles%20Where%20are%20the%20keywords.pdf},
}

@inproceedings{Rosario&Hearst04,
  author =   {Barbara Rosario and Marti A. Hearst},
  title =    {Classifying Semantic Relations in Bioscience Texts},
  booktitle =    ACL2004,
  crossref =     {ACL2004},
  year =     {2004},
  pages =    {430--437},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Rosario&Hearst%20Classifying%20Semantic%20Relations%20in%20Bioscience%20Texts.pdf},
}

@article{Rzhetsky&al.04,
  author = {Andrey Rzhetsky and Ivan Iossifov and Tomohiro Koike and Michael Krauthammer and Pauline Kra and Mitzi Morris and Hong Yu and Pablo Ariel Dubou\'{e} and Wubin Weng and W. John Wilbur and Vasileios Hatzivassiloglou and Carol Friedman},
  title = {{GeneWays}: A System for Extracting, Analyzing, Visualizing, and Integrating Molecular Pathway Data},
  year = {2004},
  journal = {J Biomed Inform.},
  volume = {37},
  pages = {43--53},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Rzhetsky&al%20GeneWays%20A%20system%20for%20extracting,%20analyzing,%20visualizing,%20and%20integrating%20molecular%20pathway%20data.pdf},
}

@article{Santos&al.05,
  author =   {Carlos Santos and Daniela Eggle and David J. States},
  title =    {Wnt Pathway Curation Using Automated Natural Language Processing: Combining Statistical Methods with Partial and Full Parse for Knowledge Extraction},
  journal =  {Bioinformatics},
  volume =   {21},
  number =   {8},
  pages =    {1653--1658},
  year =     {2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Santos&al%20Wnt%20Pathway%20Curation%20using%20Automated%20Natural%20Language%20Processing%20-%20Combining%20Statistical%20Methods%20with%20Partial%20and%20Full%20Parse%20for.pdf},
}

@inproceedings{Schliep&al.03,
  author =   {Alexander Schliep and Alexander Schonhuth and Christine Steinhoff},
  title =    {Using Hidden {Markov} Models to Analyze Gene Expression Time Course Data},
  pages =    {255--263},
  booktitle =    ISMB2003,
  year =     {2003},
  crossref =     {ISMB2003},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Schliep&al%20Using%20Hidden%20Markov%20Models%20to%20Analyze%20Gene%20Expression%20Time%20Course%20Data.pdf},
}

@article{Schuemie&al.04,
  author = {M. J. Schuemie and M. Weeber and B. J. A. Schijvenaars and E. M. van Mulligen and C. C. van der Eijk and R. Jelier and B. Mons and J. A. Kors},
  title = {Distribution of Information in Biomedical Abstracts and Full-Text Publications},
  journal = {Bioinformatics},
  volume = {20},
  number = {16},
  year = {2004},
  pages = {2597--2604},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Schuemie&al%20Distribution%20of%20Information%20in%20Biomedical%20Abstracts%20and%20Full-Text%20Publications.pdf},
}

@article{Schwikowski&al00,
    author = {Schwikowski, B.  and Uetz, P.  and Fields, S. },
    journal = {Nat Biotechnol},
    month = {December},
    number = {12},
    pages = {1257--1261},
    title = {A network of protein-protein interactions in yeast.},
    volume = {18},
    year = {2000},
      x-location = {no},
}

@article{Searls02,
  author =   {David B. Searls},
  title =    {The Language of Genes},
  journal =  {Nature},
  year =     {2002},
  month =    {November},
  volume =   {420},
  pages =    {211--217},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Searls%20The%20Language%20of%20Genes.pdf},
}

@inproceedings{Segal&al.01,
  author =   {Eran Segal and Benjamin Taskar and Audrey Gasch and Nir Friedman and Daphne Koller},
  title =    {Rich Probabilistic Models for Gene Expression},
  pages =    {243--252},
  booktitle =    ISMB2001,
  year =     {2001},
  crossref =     {ISMB2001},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Segal&al%20Rich%20Probabilistic%20Models%20for%20Gene%20Expression.pdf},
}

@inproceedings{Segal&al.03,
  author =   {Eran Segal and Haidong Wang and Daphe Koller},
  title =    {Discovering Molecular Pathways from Protein Interaction and Gene Expression Data},
  pages =    {264--272},
  booktitle =    ISMB2003,
  year =     {2003},
  crossref =     {ISMB2003},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Segal&al%20Discovering%20Molecular%20Pathways%20from%20Protein%20Interaction%20and%20Gene%20Expression%20Data.pdf},
}

@inproceedings{Sehgal&Srinivasan05,
  author =   {Aditya Kumar Sehgal and Padmini Srinivasan},
  title =    {Manjal - A Text Mining System for {MEDLINE}},
  booktitle =    SIGIR2005,
  crossref =     {SIGIR2005},
  year =     {2005},
  pages =    {680--680},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Sehgal&Srinivasan%20Manjal%20-%20A%20Text%20Mining%20System%20for%20MEDLINE.pdf},
}

@inproceedings{Seki&Mostafa03,
  title = {A Probabilistic Model for Identifying Protein Names and their Name Boundaries},
  author = {Kazuhiro Seki and Javed Mostafa},
  booktitle = {In Proceedings of the 2nd IEEE-CS Bioinformatics Conference (CSB 2003)},
  month = {August},
  pages = {251--258},
  year = {2003},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Seki&Mostafa%20A%20probabilistic%20model%20for%20identifying%20protein%20names%20and%20their%20name%20boundaries.pdf},
}

@article{Seki&Mostafa05,
  author =   {Kazuhiro Seki and Javed Mostafa},
  title =    {A Hybrid Approach to Protein Name Identification in Biomedical Texts},
  journal =  IPM,
  year =     {2005},
  volume =   {41},
  pages =    {723--743},
  number =   {4},
  month =    {July},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Seki&Mostafa%20A%20Hybrid%20Approach%20to%20Protein%20Name%20Identification%20in.pdf},
}

@inproceedings{Seki&Mostafa05a,
  author =   {Kazuhiro Seki and Javed Mostafa},
  title =    {An Application of Text Categorization Methods to Gene Ontology Annotation},
  booktitle =    SIGIR2005,
  year =     {2005},
  crossref = {SIGIR2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Seki&Mostafa%20An%20Application%20of%20Text%20Categorization%20Methods%20to%20Gene%20Ontology%20Annotation.pdf},
}

@incollection{Seth&Edelman04,
  author =   {Anil K. Seth and Gerald M. Edelman},
  title =    {Theoretical Neuroanatomy: Analyzing the Structure,  Dynamics,and Function of Neuronal Networks},
  pages =    {483--511},
  note  =    {Lecture Notes in Physics - Volume 650},
  publisher =    {Springer Berlin/Heidelberg},
  year =     {2004},
  booktitle =    {Complex Networks},
  editor =   {Eli Ben-Naim and Hans Frauenfelder and Zoltan Toroczkai},
  isbn =     {3-540-22354-1},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Seth&Edelman%20Theoretical%20Neuroanatomy%20-%20Analyzing%20the%20Structure,%20%20Dynamics,and%20Function%20of%20Neuronal%20Networks.pdf},
}

@article{Settles05,
  title = {{ABNER}: an open source tool for automatically tagging genes, proteins, and other entity names in text},
  author = {B. Settles},
  journal = {Bioinformatics},
  pages = {3191--3192},
  volume = {21},
   number = {14},
  year = {2005},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Settles%20ABNER%20an%20open%20source%20tool%20for%20automatically%20tagging%20genes,%20proteins%20and%20other%20entity%20names%20in%20text.pdf},
}

@article{Shatkay&Feldman03,
  author =   {Hagit Shatkay and Ronen Feldman},
  title =    {Mining the Biomedical Literature in the Genomic Era: An Overview},
  journal =  {Journal of Computational Biology},
  month =    {December},
  year =     {2003},
  volume =   {10},
  number =   {6},
  pages =    {821--855},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Shatkay&Feldman%20Mining%20the%20Biomedical%20Literature%20in%20the%20Genomic%20Era%20-%20An%20Overview.pdf},
}

@inproceedings{Shatkay&al.05,
  author =   {Hagit Shatkay and A. Rzhetsky and W. J. Wilbur},
  title =    {Searching for High-Utility Text in the Biomedical Literature},
  booktitle =    ISMB-WS2005A,
  crossref =     {ISMB-WS2005A},
  year =     {2005},
  x-location =   {no},
}

@inproceedings{Smith&Cleary03,
  author =   {Tony C. Smith and John G. Cleary},
  title =    {Automatically Linking {MEDLINE} Abstracts to the Gene Ontology},
  booktitle =    ISMB-WS2003A,
  crossref =     {ISMB-WS2003A},
  year =     {2003},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Smith&Cleary%20Automatically%20Linking%20MEDLINE%20Abstracts%20to%20the%20Gene%20Ontology.pdf},
}

@inproceedings{Smith&al.05,
  author =   {L. H. Smith and L. Tanabe and T. Rindflesch and W. John Wilbur},
  title =    {{MedTag}: A Collection of Biomedical Annotations},
  booktitle =    ISMB-WS2005A,
  crossref =     {ISMB-WS2005A},
  year =     {2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Smith&al%20MedTag%20-%20A%20Collection%20of%20Biomedical%20Annotations.pdf},
}

@article{Sole&al.02,
        author = {Ricard V. Sol\'{e} and Romualdo Pastor-Satorras and Eric Smith and Thomas B. Kepler},
        title = {A model of large-scale proteome evolution},
        journal = {Advances in Complex Systems},
        year = {2002},
        volume = {5},
        number = {1},
        pages = {43--54},
        x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Sole&al%20A%20model%20of%20large-scale%20proteome%20evolution.pdf},
}

@article{Spirin&Mirny03,
    author = {Spirin, V.  and Mirny, L. A. },
    journal = {Proc Natl Acad Sci U S A},
    month = {October},
    number = {21},
    pages = {12123--12128},
    title = {Protein complexes and functional modules in molecular networks.},
    volume = {100},
    year = {2003},
      x-location = {no},
}

@inproceedings{Srinivasan&Libbus04,
  author =   {Padmini Srinivasan and Bisharah Libbus},
  title =    {Mining {MEDLINE} for Implicit Links Between Dietary Substances and Diseases},
  pages =    {290--296},
  booktitle =    ISMB2004,
  year =     {2004},
  crossref =     {ISMB2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Srinivasan&Libbus%20Mining%20MEDLINE%20for%20Implicit%20Links%20Between%20Dietary%20Substances%20and%20Diseases.pdf},
}

@article{Srinivasan04,
  author =   {Padmini Srinivasan},
  title =    {Text Mining: Generating Hypotheses from {MEDLINE}},
  journal =  JASIST,
  year =     {2004},
  volume =   {55},
  pages =    {396--413},
  number =   {5},
  month =    {March},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Srinivasan%20Text%20Mining%20Generating%20Hypotheses%20from%20Medline.pdf},
}

@inproceedings{Stephens&al.01,
  author =       {M. Stephens and M. Palakal and S. Mukhopadhyay and R. Raje and J. Mostafa},
  title =        {Detecting Gene Relations from {Medline} Abstracts},
  booktitle =    {Proceedings of Pacific Symposium on Biocomputing (PSB-01)},
  pages =        {483--495},
  year =         {2001},
  address =      {Honolulu, Hawaii, USA},
  x-location = {no},
}

@inproceedings{Subramaniam&al03,
    author = {Subramaniam, Venkata  L.  and Mukherjea, Sougata   and Kankar, Pankaj   and Srivastava, Biplav   and Batra, Vishal  S.  and Kamesam, Pasumarti  V.  and Kothari, Ravi  },
    booktitle = {CIKM '03: Proceedings of the twelfth international conference on Information and knowledge management},
    pages = {410--417},
    publisher = {ACM Press},
    title = {Information extraction from biomedical literature: methodology, evaluation and an application},
    year = {2003},
    x-location = {no},
}

@article{Sugiyama&al.03,
  author = {K. Sugiyama and et al},
  title = {Extracting Information on Protein-Protein Interactions from Biological Literature Based on Machine Learning Approaches},
  year = {2003},
  journal = {Genome Informatics},
  volume = {14},
  pages = {699--700},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Sugiyama&al%20Extracting%20Information%20on%20Protein-Protein%20Interactions%20from%20Biological%20Literature%20Based%20on%20Machine%20Learning%20Approaches.pdf},
}

@article{Suomela&Andrade05,
  title = {Ranking the whole {MEDLINE} database according to a large training set using text indexing},
  author = {B. P. Suomela and M. A. Andrade},
  journal = {BMC Bioinformatics},
  number = {75},
  volume = {6},
   month = {March 24,},
  year = {2005},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Suomela&Andrade%20Ranking%20the%20whole%20MEDLINE%20database%20according%20to%20a%20large%20training%20set%20using%20text%20indexing.pdf},
}

@inproceedings{Swanson&Smalheiser98,
  author =   {Don R. Swanson and Neil R. Smalheiser},
  title =    {Link Analyis of {MEDLINE} Titles as an Aid to Scientific Discovery},
  booktitle =    AAAI-FS1998A,
  crossref =     {AAAI-FS1998A},
  year =     {1998},
  pages =    {94--97},
  x-location =   {no},
}

@techreport{Talreja&al.04,
  author = {Rishi Talreja and Andrew Schein and Scott Winters and Lyle Ungar},
  title = {{GeneTaggerCRF}: An Entity Tagger for Recognizing Gene Names in Text},
  month = {May},
  year = {2004},
  institution = {PennBioIE - The Biomedical Information Extraction Project at the University of Pennsylvania},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Talreja&al%20GeneTaggerCRF%20-%20An%20Entity%20Tagger%20for%20Recognizing%20Gene%20Names%20in%20Text.pdf},
}

@article{Tanabe&Wilbur02,
  author = {Lorraine Tanabe and W. John Wilbur},
  title = {Tagging Gene and Protein Names in Biomedical Text},
  journal = {Bioinformatics},
  volume = {18},
  number = {8},
  year = {2002},
  pages = {1124--1132},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Tanabe&Wilbur%20Tagging%20Gene%20and%20Protein%20Names%20in%20Biomedical%20Text.pdf},
}

@article{Tanabe&al.05,
  title = {GENETAG: a tagged corpus for gene/protein named entity recognition},
  author = {L. Tanabe and N. Xie and L. H. Thom and W. Matten and W. J. Wilbur},
  journal = {BMC Bioinformatics},
  volume = {6 Suppl 1},
  year = {2005},
   month = {August 25,},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Tanabe&al%20GENETAG%20a%20tagged%20corpus%20for%20gene%20protein%20named%20entity%20recognition.pdf},
}

@inproceedings{Taskar04,
  author =   {Ben Taskar},
  title =    {A Framework for Learning with Combinatorial Output Structure and Applications to Protein Structure Prediction},
  booktitle =    NIPS-WS2004B,
  year =     {2004},
  crossref =     {NIPS-WS2004B},
  x-location =   {no},
}

@inproceedings{Tateisi&al.03,
  author =   {Yuka Tateisi and Tomoko Ohta and Jin-Dong Kim and Huaquing Hong and Su Jian and Jun-Ichi Tsujii},
  title =    {The {GENIA} Corpus: {MEDLINE} Abstracts Annotated with Linguistic Information},
  booktitle =    ISMB-WS2003A,
  crossref =     {ISMB-WS2003A},
  year =     {2003},
  x-location =   {no},
}

@article{Temkin&Gilder03,
  author =       {J. M. Temkin and M. R. Gilder},
  title =        {Extraction of Protein Interaction Information from Unstructured Text Using a Context-Free Grammar},
  journal =      {Bioinformatics},
  volume =       {19},
  pages =        {2046--2053},
  year =         {2003},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Temkin&Gilder%20Extraction%20of%20Protein%20Interaction%20Information%20from%20Unstructured%20Text%20Using%20a%20Context-Free%20Grammar.pdf},
}

@article{Torvik&al.05,
  author =   {Vetle I. Torvik and Marc Weeber and Don R. Swanson and Neil R. Smalheiser},
  title =    {A Probabilistic Similarity Metric for {MEDLINE} Records: A Model for Author Name Disambiguation},
  journal =  JASIST,
  year =     {2005},
  volume =   {56},
  pages =    {140--158},
  number =   {2},
  month =    {January 15,},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Torvik&al%20A%20Probabilistic%20Similarity%20Metric%20for%20Medline.pdf},
}

@article{Toshihide&al.99,
  author =   {Ono Toshihide and Hishigaki Haretsugu and Tanigami Akira and Takagi Toshihisa},
  year =     {1999},
  title =    {Automatic Extraction of Information on Protein-Protein Interaction from Scientific Literature},
  journal =  {Genome Informatics},
  volume =       {10},
  pages =        {296--297},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Toshihide&al%20Automatic%20Extraction%20of%20Information%20on%20Protein-Protein%20Interaction%20from%20Scientific%20Literature.pdf},
}

@inproceedings{Tsuda&Noble04,
  author =   {Koji Tsuda and William Noble},
  title =    {Learning Kernels from Biological Networks by Maximizing Entropy},
  pages =    {326--333},
  booktitle =    ISMB2004,
  year =     {2004},
  crossref =     {ISMB2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Tsuda&Noble%20Learning%20Kernels%20from%20Biological%20Networks%20by%20Maximizing%20Entropy.pdf},
}

@article{Vailaya&al.04,
  author = {Aditya Vailaya and Peter Bluvas and Robert Kincaid and Allan Kuchinsky and Michael Creech and and Annette Adler},
  title = {An Architecture for Biological Information Extraction and Representation},
  year = {2004},
  month = {December},
  journal = {Bioinformatics},
  x-location = {no},
}

@article{Vazquez&al.03,
        author = {Alexei V\'{a}zquez and Alessandro Flammini and Amos Maritan and Alessandro Vespignani},
        title = {Modeling of Protein Interaction Networks},
        journal = {ComPlexUs},
        year = {2003},
        month = {November},
        volume = {1},
        pages = {38--44},
        x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Vazquez&al%20Modeling%20of%20protein%20interaction%20networks.pdf},
}

@inproceedings{Verspoor04,
  author =   {Karin Verspoor},
  title =    {Towards a Semantic Lexicon for Biological Language Processing},
  booktitle =    ISMB-WS2004A,
  crossref =     {ISMB-WS2004A},
  year =     {2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Verspoor%20Towards%20a%20Semantic%20Lexicon%20for%20Biological%20Language%20Processing.pdf},
}

@inproceedings{Vert02,
  author =   {Jean-Philippe Vert},
  title =    {A Tree Kernel to Analyse Phylogenetic Profiles},
  pages =    {276--284},
  booktitle =    ISMB2002,
  year =     {2002},
  crossref =     {ISMB2002},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Vert%20A%20Tree%20Kernel%20to%20Analyse%20Phylogenetic%20Profiles.pdf},
}

@inproceedings{Vert04,
  author =   {Jean-Philippe Vert},
  title =    {Analysis and Inference of Gene Networks from Genomic Data},
  booktitle =    ISMB-WS2004B,
  crossref =     {ISMB-WS2004B},
  year =     {2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Vert%20Analysis%20and%20Inference%20of%20Gene%20Networks%20from%20Genomic%20Data.pdf},
}

@inproceedings{Vert05,
  author =   {Jean-Philippe Vert},
  title =    {Kernels for Protein Sequences},
  booktitle =    NIPS-WS2005F,
  year =     {2005},
  crossref =     {NIPS-WS2005F},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Vert%20Kernels%20for%20Protein%20Sequences.pdf},
}

@inproceedings{Wang&al.04,
  author =   {Haidong Wang and Eran Segal and Asa Ben-Hur and Daphne Koller and Douglas L. Brutlag},
  title =    {Identifying Protein-Protein Interaction Sites on a Genome-Wide Scale},
  booktitle =    NIPS2004,
  year =     {2004},
  pages =    {1465--1472},
  crossref = {NIPS2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Wang&al%20Identifying%20Protein-Protein%20Interaction%20Sites%20on%20a%20Genome-Wide%20Scale.pdf},
}

@inproceedings{Wang&al.05c,
  author =   {Hudong Wang and Shannon Bradshaw and Marc Light},
  title =    {Automatic Highlighting of Bioscience Literature},
  booktitle =    ISMB-WS2005A,
  crossref =     {ISMB-WS2005A},
  year =     {2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Wang&al%20Automatic%20Highlighting%20of%20Bioscience%20Literature.pdf},
}

@inproceedings{Wellner&al.05,
  author =   {Ben Wellner and Jos{\'e} Casta\~{n}o and James Pustejovsky},
  title =    {Adaptive String Similarity Metrics for Biomedical Reference Resolution},
  booktitle =    ISMB-WS2005A,
  crossref =     {ISMB-WS2005A},
  year =     {2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Wellner&al%20Adaptive%20String%20Similarity%20Metrics%20for%20Biomedical%20Reference%20Resolution.pdf},
}

@inproceedings{Wellner05,
  author =   {Ben Wellner},
  title =    {Weakly Supervised Learning Methods for Improving the Quality of Gene Name Normalization Data},
  booktitle =    ISMB-WS2005A,
  crossref =     {ISMB-WS2005A},
  year =     {2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Wellner%20Weakly%20Supervised%20Learning%20methods%20for%20Improving%20the%20Quality%20of%20Gene%20Name%20Normalization%20Data.pdf},
}

@article{Weston&al.04,
  author =   {Jason Weston and Andre Elisseeff and Dengyong Zhou and Christina Leslie and William S. Noble},
  title =    {Protein Ranking: From Local to Global Structure in the Protein Similarity Network},
  journal = PNAS,
  volume = {101},
  number = {17},
  pages = {6559--6563},
  year =     {2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Weston&al%20Protein%20Ranking%20-%20From%20Local%20to%20Global%20Structure%20in%20the%20Protein%20Similarity%20Network.pdf},
}

@inproceedings{Wieser&al.04,
  author =   {Daniela Wieser and Ernst Kretschmann and Rolf Apweiler},
  title =    {Filtering Erroneous Protein Annotation},
  pages =    {342--347},
  booktitle =    ISMB2004,
  year =     {2004},
  crossref =     {ISMB2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Wieser&al%20Filtering%20Erroneous%20Protein%20Annotation.pdf},
}

@article{Wilbur&Yang96,
  author =       {W. J. Wilbur and Y. Yang},
  title =        {An Analysis of Statistical Term Strength and Its Use in the Indexing and Retrieval of Molecular Biology Texts},
  journal =      {Computers in Biology and Medicine},
  volume =       {26},
    number =             {3},
  pages =        {209--222},
  year =         {1996},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Wilbur&Yang%20An%20analysis%20of%20statistical%20term%20strength%20and%20its%20use%20in%20the%20indexing%20and%20retrieval%20of%20molecular%20biology%20texts.pdf},
}

@article{Wilbur&al.06,
  author = {W. John Wilbur and Andrey Rzhetsky and Hagit Shatkay},
  title = {New Directions in Biomedical Text Annotation: Definitions, Guidelines and Corpus Construction},
  journal = {BMC Bioinformatics},
  year = {2006},
  month = {July 25,},
  volume = {7},
  number = {356},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Wilbur&al%20New%20Directions%20in%20Biomedical%20Text%20Annotation%20Definitions,%20Guidelines%20and%20Corpus%20Construction.pdf},
}

@inproceedings{Wilcox&al.00,
  author =   {Adam Wilcox and George Hripcsak and Carol Friedman},
  title =    {Using Knowledge Sources to Improve Classification of Medical Text Reports},
  booktitle =    KDD-WS2000A,
  year =     {2000},
  crossref = {KDD-WS2000A},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Wilcox&al%20Using%20Knowledge%20Sources%20to%20Improve%20Classification%20of%20Medical%20Text%20Reports.pdf},
}

@article{Williams05,
  author =   {Hugh E. Williams},
  title =    {Introduction to Genomic Information Retrieval},
  journal =  ACM-TOIS,
  year =     {2005},
  volume =   {23},
  pages =    {1--2},
  number =   {1},
  month =    {January},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Williams%20Introduction%20to%20Genomic%20IR.pdf},
}

@inproceedings{Wojcik&Schachter01,
  author =   {J{\'e}r{\^o}me Wojcik and Vincent Sch{\"a}chter},
  title =    {Protein-Protein Interaction Map Inference Using Interacting Domain Profile Pairs},
  pages =    {296--305},
  booktitle =    ISMB2001,
  year =     {2001},
  crossref =     {ISMB2001},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Wojcik&Schachter%20Protein-Protein%20Interaction%20Map%20Inference%20Using%20Interacting%20Domain%20Profile%20Pairs.pdf},
}

@article{Wuchty&al03,
    author = {Wuchty, S.  and Oltvai, Z. N.  and Barab‡si, A. L. },
    journal = {Nat Genet},
    month = {October},
    number = {2},
    pages = {176--179},
    title = {Evolutionary conservation of motif constituents in the yeast protein interaction network.},
    volume = {35},
    year = {2003},
      x-location =   {no},
}

@inproceedings{Yamanishi&al.04,
  author =   {Yoshihiro Yamanishi and Jean-Philippe Vert and Minoru Kanehisa},
  title =    {Protein Network Inference from Multiple Genomic Data: A Supervised Approach},
  pages =    {363--370},
  booktitle =    ISMB2004,
  year =     {2004},
  crossref =     {ISMB2004},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Yamanishi&al%20Protein%20Network%20Inference%20from%20Multiple%20Genomic%20Data%20-%20A%20Supervised%20Approach.pdf},
}

@inproceedings{Yan&al.05b,
  author =   {Xin Yan and Xue Li and Dawei Song},
  title =    {Document Re-Ranking by Generality in Bio-Medical Information Retrieval},
  booktitle =    WISE2005,
  year =     {2005},
  pages =    {376--389},
  crossref =     {WISE2005},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Yan&al%20Document%20Re-Ranking%20by%20Generality%20in%20Bio-Medical%20Information%20Retrieval.pdf},
}

@article{Yandell&Majors02,
  title = {Genomics and natural language processing},
  author = {M. D. Yandell and W. H. Majoros},
  journal = {Nature Rev. Genet.},
  pages = {601--610},
  volume = {3},
  year = {2002},
   month =  {August},
   x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Yandell&Majoros%20Genomics%20and%20natural%20language%20processing.pdf},
}

@inproceedings{Yeh&al.03a,
  author =   {Alexander S. Yeh and Lynette Hirschman and Alexander A. Morgan},
  title =    {Evaluation of Text Data Mining for Database Curation: Lessons Learned from the {KDD} {Challenge} {Cup}},
  pages =    {331--339},
  booktitle =    ISMB2003,
  year =     {2003},
  crossref =     {ISMB2003},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Yeh&al%20Evaluation%20of%20Text%20Data%20Mining%20for%20Database%20Curation%20-%20Lessons%20Learned%20from%20the%20KDD%20Challenge%20Cup.pdf},
}

@inproceedings{Yeh&al.03b,
  author =   {Alex Yeh and Lynette Hirschman and Alex Morgan},
  title =    {{BioCreAtIvE}: Entity Extraction},
  booktitle =    ISMB-WS2003A,
  crossref =     {ISMB-WS2003A},
  year =     {2003},
  x-location =   {no},
}



@inproceedings{Yi&al.03,
  author =   {Eunji Yi and Gary G. Lee and Soo-Jun Park},
  title =    {{HMM}-Based Protein Name Recognition with Edit Distance Using Automatically Annotated Corpus},
  booktitle =    ISMB-WS2003A,
  crossref =     {ISMB-WS2003A},
  year =     {2003},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Yi&al%20HMM-based%20protein%20name%20recognition%20with%20edit%20distance%20using%20automatically%20annotated%20corpus.pdf},
}


@inproceedings{Yona&al.98,
  author =   {Golan Yona and Nathan Linial and Naftali Tishby and Michal Linial},
  title =    {A Map of the Protein Space: An Automatic Hierarchical Classification of all Protein Sequences},
  pages =    {212--221},
  booktitle =    ISMB1998,
  year =     {1998},
  crossref =     {ISMB1998},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Yona&al%20A%20Map%20of%20the%20Protein%20Space%20-%20An%20Automatic%20Hierarchical%20Classification%20of%20all%20Protein%20Sequences.pdf},
}

@inproceedings{Yu&Agichtein03,
  author =   {Hong Yu and Eugene Agichtein},
  title =    {Extracting Synonymous Gene and Protein Terms from Biological Literature},
  pages =    {340--349},
  booktitle =    ISMB2003,
  year =     {2003},
  crossref =     {ISMB2003},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Yu&Agichtein%20Extracting%20Synonymous%20Gene%20and%20Protein%20Terms%20from%20Biological%20Literature.pdf},
}

@article{Yu&al.06,
        author = {Hong Yu and Won Kim and Vasileios Hatzivassiloglou and John Wilbur},
        title = {A large scale, corpus-based approach for automatically disambiguating biomedical abbreviations},
        journal = ACM-TOIS,
        month = {July},
        year = {2006},
        volume = {24},
        number = {3},
        pages = {380--404},
        x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Yu&al%20A%20large%20scale,%20corpus-based%20approach%20for%20automatically%20disambiguating%20biomedical%20abbreviations.pdf},
}

@article{Zaki&al.01,
  author =   {Mohammed J. Zaki and Shinichi Morishita and Isidore Rigoutsos},
  title =    {Report on {BIOKDD04}: {Workshop} on Data Mining in {Bioinformatics}},
  journal =  SIGKDD-EN,
  year =     {2004},
  volume =   {6},
  pages =    {153--154},
  number =   {2},
  publisher =    ACM,
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Zaki&al%20Report%20on%20BIOKDD04.pdf},
}

@article{Zanzoni&al.02,
  author = {Andreas Zanzoni and Luisa Montecchi-Palazzi and Michele Quondam and Gabriele Ausiello and Manuela Helmer-Citterich and Gianni Cesareni},
  title = {{MINT}: A {Molecular} {INTeraction} Database},
  journal = {FEBS Letters},
  month = {February 20,},
  volume = {513},
  number = {1},
  pages = {135--140},
  year = {2002},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Zanzoni&al%20MINT%20A%20Molecular%20INTeraction%20Database.pdf},
}

@article{Zhou&al.04,
  author =   {GuoDong Zhou and Jie Zhang and Jian Su and Dan Shen and ChewLim Tan},
  title =    {Recognizing Names in Biomedical Texts: A Machine Learning Approach},
  journal =  {Bioinformatics},
  volume =   {20},
  number =   {7},
  year =     {2004},
  pages =    {1178--1190},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Zhou&al%20Recognizing%20Names%20in%20Biomedical%20Texts%20A%20Machine%20Learning%20Approach.pdf},
}

@article{delSol&al.05,
  author = {Antonio del Sol and Hirotomo Fujihashi and Paul O'Meara},
  title = {Topology of small-world networks of protein-protein complex structures},
  journal = {Bioinformatics},
  year = {2005},
  month = {April 15,},
  volume = {21},
  number = {8},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/del%20Sol&al%20Topology%20of%20small-world%20networks%20of%20protein-protein%20complex%20structures.pdf},
}

@inproceedings{Hu&al.04,
  author = {Xiaohua Hu and Illhoi Yoo and Il-Yeol Song and Min Song and Jianchao Han and Mark Lechner},
  title = {Extracting and Mining Protein-Protein Interaction Network from Biomedical Literature},
  booktitle = {Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology},
  year = {2004},
  pages = {244--251},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Hu&al%20Extracting%20and%20mining%20protein-protein%20interaction%20network%20from%20biomedical%20literature.pdf},
}


@article{Tian&al.07,
  author = {Yuanyuan Tian and Richard C. McEachin and Carlos Santos and David J. States and Jignesh M. Patel},
  title = {{SAGA}: A subgraph matching tool for biological graphs},
  journal = {Bioinformatics},
  month = {January 15,},
  year = {2007},
  volume = {23},
  number = {2},
  pages = {232--239},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Tian&al%20SAGA%20-%20A%20subgraph%20matching%20tool%20for%20biological%20graphs.pdf},
}

@article{Hoffmann&Valencia03,
  author = {Robert Hoffmann and Alfonso Valencia},
  title = {Life cycles of successful genes},
  journal = {{TRENDS} in {Genetics}},
  month = {February},
  year = {2003},
  volume = {19},
  number = {2},
  pages = {79--81},
  x-location = {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Hoffmann&Valencia%20Life%20cycles%20of%20successful%20genes.pdf},
}


@inproceedings{Janssens&al.07,

    author = {Frizo Janssens and Wolfgang Gl\"{a}nzel and Bart De Moor},

    title = {Dynamic hybrid clustering of bioinformatics by incorporating text mining and citation analysis},

    booktitle = {KDD '07: Proceedings of the 13th ACM SIGKDD international conference on Knowledge discovery and data mining},

    year = {2007},

    isbn = {978-1-59593-609-7},

    pages = {360--369},

    location = {San Jose, California, USA},

    doi = {http://doi.acm.org/10.1145/1281192.1281233},

    publisher = {ACM Press},

    address = {New York, NY, USA},

    x-location =   {yes},


  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Janssens&al%20Dynamic%20Hybrid%20Clustering%20of%20Bioinformatics%20by%20Incorporating%20Text%20Mining%20and%20Citation%20Analysis.pdf},

}


@article{Kim&al.07,

    author = {Jee-Hyub Kim and Alex Mitchell and Teresa K. Attwood and Melanie Hilario },

    title = { Learning to extract relations for protein annotation },

    journal = {Bioinformatics},

    volume = {23},

    year = {2007},

    pages = {i256--i263},

    x-location =   {yes},

  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Kim&al%20Learning%20to%20extract%20relations%20for%20protein%20annotation.pdf},

}



@article{Kolarik&al.07,

    author = {Corinna Kol{\'a}rik and Martin Hofmann-Apitius and Marc Zimmermann and Juliane Fluck},

    title = { Identification of new drug classification terms in textual resources },

    journal = { Bioinformatics},

    volume = {23},

    year = {2007},

    pages = {i264--i272 },

    x-location =   {yes},

  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Kolarik&al%20Identification%20of%20new%20druc%20classification%20terms%20in%20textual%20resources.pdf},

}


@article{Ling&al.07,

    author = {Xu Ling and Jing Jiang and Xin He and Qiaozhu Mei and Chengxiang Zhai and Bruce Schatz},

    title = {Generating gene summaries from biomedical literature: A study of semi-structured summarization},

    journal = {Inf. Process. Manage.},

    volume = {43},

    number = {6},

    year = {2007},

    issn = {0306-4573},

    pages = {1777--1791},

    publisher = {Pergamon Press, Inc.},

    address = {Tarrytown, NY, USA},

    x-location =   {yes},

  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Ling&al%20Generating%20Gene%20Summaries%20from%20Biomedical%20Literature%20A%20Study%20of%20Semi-Structured%20Summarization.pdf},

}


@inproceedings{Pandey&al.07,

    author = {Gaurav Pandey and Michael Steinbach and Rohit Gupta and Tushar Garg and Vipin Kumar},

    title = {Association analysis-based transformations for protein interaction networks: a function prediction case study},

    booktitle = {KDD '07: Proceedings of the 13th ACM SIGKDD international conference on Knowledge discovery and data mining},

    year = {2007},

    isbn = {978-1-59593-609-7},

    pages = {540--549},

    location = {San Jose, California, USA},

    doi = {http://doi.acm.org/10.1145/1281192.1281251},

    publisher = {ACM Press},

    address = {New York, NY, USA},

    x-location =   {yes},

  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Pandey&al%20Association%20Analysis-based%20Transformations%20for%20Protein%20Interaction%20Networks%20A%20Function%20Prediction%20Case%20Study.pdf},

}



@article{Reeve&al.07,

    author = {Lawrence H. Reeve and Hyoil Han and Ari D. Brooks},

    title = {The use of domain-specific concepts in biomedical text summarization},

    journal = {Inf. Process. Manage.},

    volume = {43},

    number = {6},

    year = {2007},

    issn = {0306-4573},

    pages = {1765--1776},

    publisher = {Pergamon Press, Inc.},

    address = {Tarrytown, NY, USA},

    x-location =   {n/a},

}



@article{Sanchez-Graillet&Poesio07,

    author = {Olivia Sanchez-Graillet and Massimo Poesio },

    title = {Negation of protein-protein interactions: analysis and extraction },

    journal = {Bioinformatics},

    volume = {23},

    year = {2007},

    pages = {i424--i432 },

    x-location =   {yes},


  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Graillet&Poesio%20Negation%20of%20protein-protein%20interactions%20analysis%20and%20extraction.pdf},

}







@article{Al-Mubaid&Singh05,
    author = {Hisham Al-Mubaid and Rajit K Singh},
    title = {A New Text Mining Approach for Finding Protein-to-Disease Associations},
    journal = {American Journal of Biochemistry and Biotechnology},
    volume = {1},
    number = {3},
    year = {2005},
    pages = {145--152},
      x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Al-Mubaid&Singh%20A%20New%20Text%20Mining%20Approach%20for%20Finding%20Protein-to-Disease%20Associations.pdf},

}



@inproceedings{Chen&al.06,
    author = {Jake Yue Chen and Changyu Shen and Andrey Y. Sivachenko},
    title = {MINING ALZHEIMER DISEASE RELEVANT PROTEINS FROM INTEGRATED PROTEIN INTERACTOME DATA},
    booktitle = {Pacific Symposium on Biocomputing},
    year = {2006},
    pages = {367--378},
    location = {Maui, Hawaii},
    doi = {doi:10.1142/9789812701626_0034},
    publisher = {World Scientific Publishing Co. Pte. Ltd.},
    x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/CHEN&al%20MINING%20ALZHEIMER%20DISEASE%20RELEVANT%20PROTEINS%20FROM%20INTEGRATED%20PROTEIN%20INTERACTOME%20DATA.pdf},

}



@inproceedings{Gonzalez&al.07,
    author = {Graciela Gonzalez and Juan C. Uribe and Luis Tari and Colleen Brophy and Chitta Baral},
    title = {MINING GENE-DISEASE RELATIONSHIPS FROM BIOMEDICAL LITERATURE: WEIGHTING PROTEIN-PROTEIN INTERACTIONS AND CONNECTIVITY MEASURES},
    booktitle = {Pacific Symposium on Biocomputing 2007},
    year = {2007},
    pages = {28-39},
    location = {Maui, Hawaii},
    x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/GONZALEZ&al%20MINING%20GENE-DISEASE%20RELATIONSHIPS%20FROM%20BIOMEDICAL%20LITERATURE%20WEIGHTING%20PROTEIN-PROTEIN%20INTERACTIONS%20AND%20CONNECTIVITY%20MEASURES.pdf},
}

@comment{AAAI papers about Adam Anthony and Marie desJardins}

@inproceedings{Hung&al.07,
  author    = {Hsieh-Chuan Hung and
               Richard Tzong-Han Tsai and
               Wen-Lian Hsu},
  title     = {Identifying Protein Interaction Abstracts with Contextual
               Bag of Words},
  booktitle = {AAAI 2007},
  year      = {2007},
  pages     = {1870--1871},
  crossref  = {AAAI2007},
  x-location =   {no},
}

@inproceedings{Lord&al.03,
  author    = {Phillip W. Lord and
               Robert D. Stevens and
               Andy Brass and
               Carole A. Goble},
  title     = {Semantic Similarity Measures as Tools for Exploring the
               Gene Ontology},
  booktitle = {Pacific Symposium on Biocomputing},
  year      = {2003},
  pages     = {601--612},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Lord&al%20Semantic%20Similarity%20Measures%20as%20Tools%20for%20Exploring%20the%20Gene%20Ontology.pdf},
}


@comment{papers from papers-2007}



@inproceedings{Nakov&al.04,
    author = {Preslav  I. Nakov and Schwartz S. Ariel and Hearst A. Marti},
    booktitle = {Workshop on Search and Discovery in Bioinformatics},
    year = {2004},
    title = {Citances: Citation Sentences for Semantic Analysis of Bioscience Text},
      x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Nakov&al%20Citances%20Citation%20Sentences%20for%20Semantic%20Analysis%20of%20Bioscience%20Text.pdf},

}

@inproceedings{Alex&al.07,
  title = {Recognising Nested Named Entities in Biomedical Text},
  author = { Beatrice Alex and Barry Haddow and Claire Grover  },
  year = {2007},
  booktitle = {BioNLP workshop at ACL 2007},
  publisher = {ACL},
  pages = {65-72},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Alex&al%20Recognising%20Nested%20Named%20Entities%20in%20Biomedical%20Text.pdf},


}

@article{Hoffmann&Valencia07,
    author = {Robert Hoffmann and Alfonso Valencia },
    journal = {Trends Genet},
    pages = {79--81},
    title = {Life Cycles of Successful Genes},
    year = {2007},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Hoffman&Valencia%20Life%20Cycles%20of%20Successful%20Genes.pdf},
}

@article{Melvin&al.07,
 author = {Iain Melvin and Eugene Ie and Jason Weston and William Stafford Noble and Christina Leslie},
 title = {Multi-class Protein Classification Using Adaptive Codes},
 journal = {J. Mach. Learn. Res.},
 volume = {8},
 year = {2007},
 issn = {1533-7928},
 pages = {1557--1581},
 publisher = {MIT Press},
 address = {Cambridge, MA, USA},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Melvin&al%20Multi-class%20Protein%20Classification%20Using%20Adaptive%20Codes.pdf},
}

@article{Torvik&Smalheiser07,
    author = {Vetle  I. Torvik and Neil  R. Smalheiser },
    journal = {Bioinformatics},
    keywords = {literature-based-discovery},
    month = {April},
    pages = {btm161+},
    title = {A quantitative model for linking two disparate sets of articles in MEDLINE},
    year = {2007},
  x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Torvik&Smalheiser%20A%20quantitative%20model%20for%20linking%20two%20disparate%20sets%20of%20articles%20in%20MEDLINE.pdf},
}

@misc{Cardona&al.07,
  author = {Gabriel Cardona and Francesc Rossello and Gabriel Valiente},
  title = {A Perl Package and an Alignment Tool for Phylogenetic Networks},
  year = {2007},
    x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Cardona&al%20A%20Perl%20Package%20and%20an%20Alignment%20Tool%20for%20Phylogenetic%20Networks.pdf},
}

@article{Lin&Wilbur07,
  author = {J. Lin and  W. J. Wilbur},
  title = {PubMed related articles: a probabilistic topic-based model for content similarity},
  journal = { BMC Bioinformatics},
  volume = {8},
  number = {1},
  month = {October},
  number = {30},
  year = {2007},
  pages = {423},
    x-location =   {yes},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Lin&Wilbur%20PubMed%20related%20articles%20a%20probabilistic%20topic-based%20model%20for%20content%20similarity.pdf},

}


@article{Albert05,

  author = {Reka Albert},

  title = {{Scale-free networks in cell biology}},

  journal = {J Cell Sci},

  volume = {118},

  number = {21},

  pages = {4947--4957},

  year = {2005},

  url = {%20%20http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Albert%20Scale-free%20networks%20in%20cell%20biology.pdf},

}

@article{Giot&al.03,

  author = {L. Giot and J.S. Bader and C. Brouwer and A. Chaudhuri and B. Kuang and Y. Li and Y.L. Hao and C.E. Ooi and B. Godwin and E. Vitols and G. Vijayadamodar and P. Pochart and H. Machineni and M. Welsh and Y. Kong and B. Zerhusen and R. Malcolm and Z. Varrone and A Collis and M. Minto and S. Burgess and L. McDaniel and E. Stimpson and F. Spriggs and J. Williams and K. Neurath and N. Ioime and M. Agee and E. Voss and K. Furtak and R. Renzulli and N. Aanensen and S. Carrolla and E. Bickelhaupt and Y. Lazovatsky and A. DaSilva and J. Zhong and C.A. Stanyon and R.L. Jr. Finley and K.P. White and M. Braverman and T. Jarvie and S. Gold and M. Leach and J. Knight and R.A. Shimkets and M.P. McKenna and J. Chant and J.M. Rothberg.},

  title = {A protein interaction map of Drosophila melanogaster},

  journal = {Science},

  month = {Dec 5},

  year = {2003},

  volume = {302},

  number = {5651},

  pages = {1727--1736},

  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Giot&al%20A%20Protein%20Interaction%20Map%20of%20Drosophila%20melanogaster.pdf},

}


@article{Hakes&al.08,

  author = {Luke Hakes and John W Pinney and David L. Robertson and Simon C Lovell},

  title = {Protein-protein interaction networks and biology{-}what's the connection?},

  journal = {Nature Biotechnology},

  volume = {26},

  pages = {69--72},

  year = {2008},

  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Hakes&al%20Protein-protein%20interaction%20networks%20and%20biology%20whats%20the%20connection.pdf},

}

@article{Barbarasi&Oltvai02,

  author = {Z. N. Oltvai and A. -L. Barbarasi},

  title = {Network Biology: Understanding the Cell's Functional Organization},

  journal = {Nature Reviews Genetics},

  volume = {5},

  pages = {101--113},

  year = {2004},

  url = {%20http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Barabasi&Oitvai%20Network%20Biology:%20Understanding%20the%20Cell's%20Funcional%20Organization.pdf},
}




@article{Plake&al.06,

  author = {Conrad Plake and Torsten Schiemann and Marcus Pankalla and Jorg Hakenberg and Ulf Leser},

  title = {{ALIBABA: PubMed as a graph}},

  journal = {Bioinformatics},

  volume = {},

  number = {},

  pages = {btl408},

  year = {2006},

  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Plake&al%20ALIBABA:%20PubMed%20as%20a%20graph.pdf},

}


@article{Tian&al.07a,

   author = {Yuanyuan Tian and Richard C. Mceachin and Carlos Santos and David J. States and Jignesh M. Patel},

   title = {SAGA: a subgraph matching tool for biological graphs},

   journal = {Bioinformatics},

   volume = {23},

   number = {2},

   year = {2007},

   issn = {1367-4803},

   pages = {232--239},

   publisher = {Oxford University Press},

   address = {Oxford, UK},

  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Tian&al%20SAGA:%20A%20subgraph%20matching%20tool%20for%20biological%20graphs.pdf},

 }

@article{Hearst&al.07,
    author = {Marti A  A. Hearst and Anna Divoli and Harendra Guturu and Alex Ksikes and Preslav Nakov and Michael A  A. Wooldridge and Jerry Ye},
    issn = {1460-2059},
    journal = {Bioinformatics},
    month = {June},
    title = {BioText Search Engine: beyond abstract search.},
    year = {2007},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Hearst&al%20BioText%20Search%20Engine%20beyond%20abstract%20search..pdf},
}

@article{Li&al.08,
 author = {Jiexun Li and Zhu Zhang and Xin Li and Hsinchun Chen},
 title = {Kernel-based learning for biomedical relation extraction},
 journal = {J. Am. Soc. Inf. Sci. Technol.},
 volume = {59},
 number = {5},
 year = {2008},
 issn = {1532-2882},
 pages = {756--769},
 publisher = {John Wiley \& Sons, Inc.},
 address = {New York, NY, USA},
  url = {http://tangra.si.umich.edu/clair/intranet/bibs/biobib/Li&Zhang%20Kernel%20based%20learning%20for%20biomedical%20relation%20extraction.pdf},
}