Gerstein Lab Publications

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Papers related to publishing, scientific communication and knowledge representation. This includes papers on text-mining and computer security, which impact greatly on scientific communication.


Structuring supplemental materials in support of reproducibility.
D Greenbaum, J Rozowsky, V Stodden, M Gerstein (2017). Genome Biol 18: 64.
 
 
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Temporal Dynamics of Collaborative Networks in Large Scientific Consortia.
D Wang, KK Yan, J Rozowsky, E Pan, M Gerstein (2016). Trends Genet 32: 251-3.
 
 
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Closure of the NCBI SRA and implications for the long-term future of genomics data storage.
D Lipman, P Flicek, S Salzberg, M Gerstein, R Knight (2011). Genome Biol 12: 402.
 
 
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The spread of scientific information: insights from the web usage statistics in PLoS article-level metrics.
KK Yan, M Gerstein (2011). PLoS One 6: e19917.
 
 
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Reproducible Research: Addressing the need for data and code sharing in computational science
Yale Law School Roundtable on Data and Code Sharing (2010). Computing in Science & Engineering 12(5): 8-13 (Sept/Oct).
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Structured digital tables on the Semantic Web: toward a structured digital literature.
KH Cheung, M Samwald, RK Auerbach, MB Gerstein (2010). Mol Syst Biol 6: 403.
 
 
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Getting started in text mining: part two.
A Rzhetsky, M Seringhaus, MB Gerstein (2009). PLoS Comput Biol 5: e1000411.
 
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Seeking a new biology through text mining.
A Rzhetsky, M Seringhaus, M Gerstein (2008). Cell 134: 9-13.
 
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Open access: taking full advantage of the content.
PE Bourne, JL Fink, M Gerstein (2008). PLoS Comput Biol 4: e1000037.
 
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Manually structured digital abstracts: a scaffold for automatic text mining.
M Seringhaus, M Gerstein (2008). FEBS Lett 582: 1170.
 
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Uncovering trends in gene naming.
MR Seringhaus, PD Cayting, MB Gerstein (2008). Genome Biol 9: 401.
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Semantic Web Approach to Database Integration in the Life Sciences
KH Cheung, AK Smith, KYL Yip, CJO Baker, MB Gerstein (2007). in Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences (eds. C Baker and K Cheung, Springer, NY), pp. 11-30
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Semantic Web Standards: Legal and Social Issues and Implications
D Greenbaum, M Gerstein (2007). in Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences (eds. C Baker and K Cheung, Springer, NY), pp. 413-433
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Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics.
A Smith, K Cheung, M Krauthammer, M Schultz, M Gerstein (2007). Bioinformatics 23: 3073-9.
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Structured digital abstract makes text mining easy.
M Gerstein, M Seringhaus, S Fields (2007). Nature 447: 142.
 
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RNAi development.
M Gerstein, SM Douglas (2007). PLoS Comput Biol 3: e80.
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Publishing perishing? Towards tomorrow's information architecture.
MR Seringhaus, MB Gerstein (2007). BMC Bioinformatics 8: 17.
 
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Chemistry Nobel rich in structure.
M Seringhaus, M Gerstein (2007). Science 315: 40-1.
 
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The Death of the Scientific Paper
Seringhaus M, Gerstein M (2006). The Scientist. 20(9): 25
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Data mining on the web.
A Smith, M Gerstein (2006). Science 314: 1682; author reply 1682.
 
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Tools needed to navigate landscape of the genome.
M Gerstein (2006). Nature 440: 740.
 
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Network security and data integrity in academia: an assessment and a proposal for large-scale archiving.
A Smith, D Greenbaum, SM Douglas, M Long, M Gerstein (2005). Genome Biol 6: 119.
 
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PubNet: a flexible system for visualizing literature derived networks.
SM Douglas, GT Montelione, M Gerstein (2005). Genome Biol 6: R80.
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Impediments to database interoperation: legal issues and security concerns.
D Greenbaum, A Smith, M Gerstein (2005). Nucleic Acids Res 33: D3-4.
 
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Computer security in academia-a potential roadblock to distributed annotation of the human genome.
D Greenbaum, SM Douglas, A Smith, J Lim, M Fischer, M Schultz, M Gerstein (2004). Nat Biotechnol 22: 771-2.
 
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An analysis of the present system of scientific publishing: what's wrong and where to go from here
D Greenbaum, J Lim, M Gerstein (2003). Interdiscip Sci Rev 28:293-302
 
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A universal legal framework as a prerequisite for database interoperability.
D Greenbaum, M Gerstein (2003). Nat Biotechnol 21: 979-82.
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Blurring the boundaries between scientific 'papers' and biological databases
M Gerstein, J Junker (2002). Nature Yearbook of Science and Technology 210-212 (ed. D Butler, Palgrave Macmillan Publishers)
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Interrelating different types of genomic data, from proteome to secretome: 'oming in on function.
D Greenbaum, NM Luscombe, R Jansen, J Qian, M Gerstein (2001). Genome Res 11: 1463-8.
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Annotation of the human genome.
M Gerstein (2000). Science 288: 1590.
 
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E-publishing on the Web: promises, pitfalls, and payoffs for bioinformatics.
M Gerstein (1999). Bioinformatics 15: 429-31.
 
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Forging links in an electronic paper chain.
M Gerstein (1999). Nature 398: 20.
 
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