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  1. Content type: Software

    To date, many genomic and pathway-related tools and databases have been developed to analyze microarray data. In published web-based applications to date, however, complex pathways have been displayed with sta...

    Authors: Deyun Pan, Ning Sun, Kei-Hoi Cheung, Zhong Guan, Ligeng Ma, Matthew Holford, Xingwang Deng and Hongyu Zhao

    Citation: BMC Bioinformatics 2003 4:56

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  2. Content type: Research article

    The genome of the avian adenovirus Chicken Embryo Lethal Orphan (CELO) has two terminal regions without detectable homology in mammalian adenoviruses that are left without annotation in the initial analysis. S...

    Authors: Stefan Washietl and Frank Eisenhaber

    Citation: BMC Bioinformatics 2003 4:55

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  3. Content type: Research article

    We describe the E-RFE method for gene ranking, which is useful for the identification of markers in the predictive classification of array data. The method supports a practical modeling scheme designed to avoi...

    Authors: Cesare Furlanello, Maria Serafini, Stefano Merler and Giuseppe Jurman

    Citation: BMC Bioinformatics 2003 4:54

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  4. Content type: Software

    The availability of increasing amounts of sequence data from completely sequenced genomes boosts the development of new computational methods for automated genome annotation and comparative genomics. Therefore...

    Authors: Georgios S Vernikos, Christos G Gkogkas, Vasilis J Promponas and Stavros J Hamodrakas

    Citation: BMC Bioinformatics 2003 4:53

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  5. Content type: Software

    Biological data resources have become heterogeneous and derive from multiple sources. This introduces challenges in the management and utilization of this data in software development. Although efforts are und...

    Authors: Scott D Zuyderduyn and Steven JM Jones

    Citation: BMC Bioinformatics 2003 4:51

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  6. Content type: Software

    Eval is a flexible tool for analyzing the performance of gene annotation systems. It provides summaries and graphical distributions for many descriptive statistics about any set of annotations, regardless of t...

    Authors: Evan Keibler and Michael R Brent

    Citation: BMC Bioinformatics 2003 4:50

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  7. Content type: Research article

    Conventionally, the first step in analyzing the large and high-dimensional data sets measured by microarrays is visual exploration. Dendrograms of hierarchical clustering, self-organizing maps (SOMs), and mult...

    Authors: Samuel Kaski, Janne Nikkilä, Merja Oja, Jarkko Venna, Petri Törönen and Eero Castrén

    Citation: BMC Bioinformatics 2003 4:48

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  8. Content type: Methodology article

    The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the utility of any prediction is complet...

    Authors: GPS Raghava, Stephen MJ Searle, Patrick C Audley, Jonathan D Barber and Geoffrey J Barton

    Citation: BMC Bioinformatics 2003 4:47

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  9. Content type: Research article

    Large-scale protein interaction maps provide a new, global perspective with which to analyse protein function. PSIMAP, the Protein Structural Interactome Map, is a database of all the structurally observed int...

    Authors: Dan Bolser, Panos Dafas, Richard Harrington, Jong Park and Michael Schroeder

    Citation: BMC Bioinformatics 2003 4:45

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  10. Content type: Methodology article

    For many RNA molecules, secondary structure rather than primary sequence is the evolutionarily conserved feature. No programs have yet been published that allow searching a sequence database for homologs of a ...

    Authors: Robert J Klein and Sean R Eddy

    Citation: BMC Bioinformatics 2003 4:44

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  11. Content type: Research article

    The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes fro...

    Authors: Roman L Tatusov, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Boris Kiryutin, Eugene V Koonin, Dmitri M Krylov, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Sridhar Rao, Sergei Smirnov, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin…

    Citation: BMC Bioinformatics 2003 4:41

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  12. Content type: Software

    In the last years several high-throughput cDNA sequencing projects have been funded worldwide with the aim of identifying and characterizing the structure of complete novel human transcripts. However some of t...

    Authors: Coral del Val, Karl-Heinz Glatting and Sandor Suhai

    Citation: BMC Bioinformatics 2003 4:39

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  13. Content type: Software

    We present Delila-genome, a software system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by scanning genomic sequences with inf...

    Authors: Sashidhar Gadiraju, Carrie A Vyhlidal, J Steven Leeder and Peter K Rogan

    Citation: BMC Bioinformatics 2003 4:38

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  14. Content type: Research article

    Genomic studies of complex tissues pose unique analytical challenges for assessment of data quality, performance of statistical methods used for data extraction, and detection of differentially expressed genes...

    Authors: Hanga C Galfalvy, Loubna Erraji-Benchekroun, Peggy Smyrniotopoulos, Paul Pavlidis, Steven P Ellis, J John Mann, Etienne Sibille and Victoria Arango

    Citation: BMC Bioinformatics 2003 4:37

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  15. Content type: Methodology article

    A potential benefit of profiling of tissue samples using microarrays is the generation of molecular fingerprints that will define subtypes of disease. Hierarchical clustering has been the primary analytical to...

    Authors: Mark Smolkin and Debashis Ghosh

    Citation: BMC Bioinformatics 2003 4:36

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  16. Content type: Database

    The problem of functional annotation based on homology modeling is primary to current bioinformatics research. Researchers have noted regularities in sequence, structure and even chromosome organization that a...

    Authors: Boris E Shakhnovich, John M Harvey, Steve Comeau, David Lorenz, Charles DeLisi and Eugene Shakhnovich

    Citation: BMC Bioinformatics 2003 4:34

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  17. Content type: Research article

    Microarray technology allows the monitoring of expression levels for thousands of genes simultaneously. This novel technique helps us to understand gene regulation as well as gene by gene interactions more sys...

    Authors: Taesung Park, Sung-Gon Yi, Sung-Hyun Kang, SeungYeoun Lee, Yong-Sung Lee and Richard Simon

    Citation: BMC Bioinformatics 2003 4:33

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  18. Content type: Methodology article

    Appropriate definitionof neural network architecture prior to data analysis is crucialfor successful data mining. This can be challenging when the underlyingmodel of the data is unknown. The goal of this study...

    Authors: Marylyn D Ritchie, Bill C White, Joel S Parker, Lance W Hahn and Jason H Moore

    Citation: BMC Bioinformatics 2003 4:28

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  19. Content type: Methodology article

    The development of large-scale gene expression profiling technologies is rapidly changing the norms of biological investigation. But the rapid pace of change itself presents challenges. Commercial microarrays ...

    Authors: Ashish Nimgaonkar, Despina Sanoudou, Atul J Butte, Judith N Haslett, Louis M Kunkel, Alan H Beggs and Isaac S Kohane

    Citation: BMC Bioinformatics 2003 4:27

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  20. Content type: Methodology article

    Microarray technology has become a very important tool for studying gene expression profiles under various conditions. Biologists often pool RNA samples extracted from different subjects onto a single microarr...

    Authors: Xuejun Peng, Constance L Wood, Eric M Blalock, Kuey Chu Chen, Philip W Landfield and Arnold J Stromberg

    Citation: BMC Bioinformatics 2003 4:26

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  21. Content type: Methodology article

    The gene regulatory information is hardwired in the promoter regions formed by cis-regulatory elements that bind specific transcription factors (TFs). Hence, establishing the architecture of plant promoters is fu...

    Authors: Ramana V Davuluri, Hao Sun, Saranyan K Palaniswamy, Nicole Matthews, Carlos Molina, Mike Kurtz and Erich Grotewold

    Citation: BMC Bioinformatics 2003 4:25

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  22. Content type: Research article

    Seattle Biomedical Research Institute (SBRI) as part of the Leishmania Genome Network (LGN) is sequencing chromosomes of the trypanosomatid protozoan species Leishmania major. At SBRI, chromosomal sequence is ann...

    Authors: Gautam Aggarwal, EA Worthey, Paul D McDonagh and Peter J Myler

    Citation: BMC Bioinformatics 2003 4:23

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  23. Content type: Methodology article

    To date, many of the methods for information extraction of biological information from scientific articles are restricted to the abstract of the article. However, full text articles in electronic version, whic...

    Authors: Parantu K Shah, Carolina Perez-Iratxeta, Peer Bork and Miguel A Andrade

    Citation: BMC Bioinformatics 2003 4:20

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  24. Content type: Methodology article

    DNA pooling is a technique to reduce genotyping effort while incurring only minor losses in accuracy of allele frequency estimates for single nucleotide polymorphism (SNP) markers.

    Authors: Josephine Hoh, Fumihiko Matsuda, Xu Peng, Daniela Markovic, Mark G Lathrop and Jurg Ott

    Citation: BMC Bioinformatics 2003 4:14

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  25. Content type: Methodology article

    Genes that are determined to be significantly differentially regulated in microarray analyses often appear to have functional commonalities, such as being components of the same biochemical pathway. This resul...

    Authors: Charles C Kim and Stanley Falkow

    Citation: BMC Bioinformatics 2003 4:12

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  26. Content type: Research article

    The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational method...

    Authors: Ian Donaldson, Joel Martin, Berry de Bruijn, Cheryl Wolting, Vicki Lay, Brigitte Tuekam, Shudong Zhang, Berivan Baskin, Gary D Bader, Katerina Michalickova, Tony Pawson and Christopher WV Hogue

    Citation: BMC Bioinformatics 2003 4:11

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  27. Content type: Research article

    There are several evolutionarily unrelated and structurally dissimilar superfamilies of S-adenosylmethionine (AdoMet)-dependent methyltransferases (MTases). A new superfamily (SPOUT) has been recently characte...

    Authors: Michal A Kurowski, Joanna M Sasin, Marcin Feder, Janusz Debski and Janusz M Bujnicki

    Citation: BMC Bioinformatics 2003 4:9

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  28. Content type: Research article

    Contradicting evidence has been presented in the literature concerning the effectiveness of empirical contact energies for fold recognition. Empirical contact energies are calculated on the basis of informatio...

    Authors: Marco Berrera, Henriette Molinari and Federico Fogolari

    Citation: BMC Bioinformatics 2003 4:8

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2018 Journal Metrics

  • Citation Impact
    2.511 - 2-year Impact Factor
    2.970 - 5-year Impact Factor
    0.855 - Source Normalized Impact per Paper (SNIP)
    1.374 - SCImago Journal Rank (SJR)


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