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  3. The 5'-terminal cap structure plays an important role in many aspects of mRNA metabolism. Capping enzymes encoded by viruses and pathogenic fungi are attractive targets for specific inhibitors. There is a larg...

    Authors: Janusz M Bujnicki, Marcin Feder, Monika Radlinska and Leszek Rychlewski
    Citation: BMC Bioinformatics 2001 2:2
    Content type: Research article Published on:

  4. We apply a new machine learning method, the so-called Support Vector Machine method, to predict the protein structural class. Support Vector Machine method is performed based on the database derived from SCOP,...

    Authors: Yu-Dong Cai, Xiao-Jun Liu, Xue-biao Xu and Guo-Ping Zhou
    Citation: BMC Bioinformatics 2001 2:3
    Content type: Research article Published on:

  5. Leucine-rich repeats are one of the more common modules found in proteins. The leucine-rich repeat consensus motif is LxxLxLxxNxLxxLxxLxxLxx- where the first 11–12 residues are highly conserved and the remaind...

    Authors: Colin W Ward and Thomas PJ Garrett
    Citation: BMC Bioinformatics 2001 2:4
    Content type: Research article Published on:

  6. Prediction of protein structures is one of the fundamental challenges in biology today. To fully understand how well different prediction methods perform, it is necessary to use measures that evaluate their pe...

    Authors: Susana Cristobal, Adam Zemla, Daniel Fischer, Leszek Rychlewski and Arne Elofsson
    Citation: BMC Bioinformatics 2001 2:5
    Content type: Research article Published on:

  8. Currently, most genome annotation is curated by centralized groups with limited resources. Efforts to share annotations transparently among multiple groups have not yet been satisfactory.

    Authors: Robin D Dowell, Rodney M Jokerst, Allen Day, Sean R Eddy and Lincoln Stein
    Citation: BMC Bioinformatics 2001 2:7
    Content type: Research article Published on:

  11. Most profile and motif databases strive to classify protein sequences into a broad spectrum of protein families. The next step of such database studies should include the development of classification systems ...

    Authors: Kevin Truong and Mitsuhiko Ikura
    Citation: BMC Bioinformatics 2002 3:1
    Content type: Methodology article Published on:

  12. Comparative analysis of RNA sequences is the basis for the detailed and accurate predictions of RNA structure and the determination of phylogenetic relationships for organisms that span the entire phylogenetic...

    Authors: Jamie J Cannone, Sankar Subramanian, Murray N Schnare, James R Collett, Lisa M D'Souza, Yushi Du, Brian Feng, Nan Lin, Lakshmi V Madabusi, Kirsten M Müller, Nupur Pande, Zhidi Shang, Nan Yu and Robin R Gutell
    Citation: BMC Bioinformatics 2002 3:2
    Content type: Research article Published on:

  14. We provide a systematic study of the sources of variability in expression profiling data using 56 RNAs isolated from human muscle biopsies (34 Affymetrix MuscleChip arrays), and 36 murine cell culture and tiss...

    Authors: Marina Bakay, Yi-Wen Chen, Rehannah Borup, Po Zhao, Kanneboyina Nagaraju and Eric P Hoffman
    Citation: BMC Bioinformatics 2002 3:4
    Content type: Research article Published on:

  15. Analysis of any newly sequenced bacterial genome starts with the identification of protein-coding genes. Despite the accumulation of multiple complete genome sequences, which provide useful comparisons with cl...

    Authors: Stéphanie Bocs, Antoine Danchin and Claudine Médigue
    Citation: BMC Bioinformatics 2002 3:5
    Content type: Research article Published on:

  16. For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define...

    Authors: Jonas S Almeida and Susana Vinga
    Citation: BMC Bioinformatics 2002 3:6
    Content type: Methodology article Published on:

  17. Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational metho...

    Authors: Michele Caselle, Ferdinando Di Cunto and Paolo Provero
    Citation: BMC Bioinformatics 2002 3:7
    Content type: Methodology article Published on:

  18. Pattern matching is the core of bioinformatics; it is used in database searching, restriction enzyme mapping, and finding open reading frames. It is done repeatedly over increasingly long sequences, thus codes...

    Authors: Harry J Mangalam
    Citation: BMC Bioinformatics 2002 3:8
    Content type: Methodology article Published on:

  20. Escherichia coli guanine-N2 (m2G) methyltransferases (MTases) RsmC and RsmD modify nucleosides G1207 and G966 of 16S rRNA. They possess a common MTase domain in the C-terminus and a variable region in the N-termi...

    Authors: Janusz M Bujnicki and Leszek Rychlewski
    Citation: BMC Bioinformatics 2002 3:10
    Content type: Research article Published on:

  23. The BLAST algorithm compares biological sequences to one another in order to determine shared motifs and common ancestry. However, the comparison of all non-redundant (NR) sequences against all other NR sequen...

    Authors: Michel Dumontier and Christopher WV Hogue
    Citation: BMC Bioinformatics 2002 3:13
    Content type: Methodology article Published on:

  25. Authors: Jamie J Cannone, Sankar Subramanian, Murray N Schnare, James R Collett, Lisa M D'Souza, Yushi Du, Brian Feng, Nan Lin, Lakshmi V Madabusi, Kirsten M Müller, Nupur Pande, Zhidi Shang, Nan Yu and Robin R Gutell
    Citation: BMC Bioinformatics 2002 3:15
    Content type: Erratum Published on:

    The original article was published in BMC Bioinformatics 2002 3:2

  27. The biomedical community is developing new methods of data analysis to more efficiently process the massive data sets produced by microarray experiments. Systematic and global mathematical approaches that can ...

    Authors: David M Mutch, Alvin Berger, Robert Mansourian, Andreas Rytz and Matthew-Alan Roberts
    Citation: BMC Bioinformatics 2002 3:17
    Content type: Methodology article Published on:

  31. Post transcriptional gene silencing (PTGS) is a recently discovered phenomenon that is an area of intense research interest. Components of the PTGS machinery are being discovered by genetic and bioinformatics ...

    Authors: Alex Bateman
    Citation: BMC Bioinformatics 2002 3:21
    Content type: Research article Published on:

  32. DNA microarray technology is a powerful technique that was recently developed in order to analyze thousands of genes in a short time. Presently, microarrays, or chips, of the cDNA type and oligonucleotide type...

    Authors: Ravi Kothapalli, Sean J Yoder, Shrikant Mane and Thomas P Loughran Jr
    Citation: BMC Bioinformatics 2002 3:22
    Content type: Research article Published on:

  34. For many years, scientists believed that point mutations in genes are the genetic switches for somatic and inherited diseases such as cystic fibrosis, phenylketonuria and cancer. Some of these mutations likely...

    Authors: Sean D Mooney and Teri E Klein
    Citation: BMC Bioinformatics 2002 3:24
    Content type: Research article Published on:

  35. T-cells are key players in regulating a specific immune response. Activation of cytotoxic T-cells requires recognition of specific peptides bound to Major Histocompatibility Complex (MHC) class I molecules. MH...

    Authors: Pierre Dönnes and Arne Elofsson
    Citation: BMC Bioinformatics 2002 3:25
    Content type: Research article Published on:

  36. Molecular characterization has contributed to the understanding of the inception, progression, treatment and prognosis of cancer. Nucleic acid array-based technologies extend molecular characterization of tumo...

    Authors: Michael A Gieseg, Theresa Cody, Michael Z Man, Steven J Madore, Mark A Rubin and Eric P Kaldjian
    Citation: BMC Bioinformatics 2002 3:26
    Content type: Research article Published on:

  37. Identifying reliable oligonucleotide sequences for use in microarray experiments is a complex process. Two key issues are the accuracy of the input sequences and the specificity of the oligonucleotide sequences.

    Authors: Hao Chen and Burt M Sharp
    Citation: BMC Bioinformatics 2002 3:27
    Content type: Methodology article Published on:

  39. Gene expression analyses based on complex hybridization measurements have increased rapidly in recent years and have given rise to a huge amount of bioinformatic tools such as image analyses and cluster analys...

    Authors: Christoph K Wierling, Matthias Steinfath, Thorsten Elge, Steffen Schulze-Kremer, Pia Aanstad, Matthew Clark, Hans Lehrach and Ralf Herwig
    Citation: BMC Bioinformatics 2002 3:29
    Content type: Research article Published on:

  40. Regulation of gene transcription is crucial for the function and development of all organisms. While gene prediction programs that identify protein coding sequence are used with remarkable success in the annot...

    Authors: Nikolaus Rajewsky, Massimo Vergassola, Ulrike Gaul and Eric D Siggia
    Citation: BMC Bioinformatics 2002 3:30
    Content type: Research article Published on:

  41. Expressed sequence tags (ESTs) are single pass reads from randomly selected cDNA clones. They provide a highly cost-effective method to access and identify expressed genes. However, they are often prone to seq...

    Authors: John Parkinson, David B Guiliano and Mark Blaxter
    Citation: BMC Bioinformatics 2002 3:31
    Content type: Research article Published on:

  42. SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally...

    Authors: Katerina Michalickova, Gary D Bader, Michel Dumontier, Hao Lieu, Doron Betel, Ruth Isserlin and Christopher WV Hogue
    Citation: BMC Bioinformatics 2002 3:32
    Content type: Methodology article Published on:

  43. We describe the development, validation, and use of a highly redundant 120,000 oligonucleotide microarray (MuscleChip) containing 4,601 probe sets representing 1,150 known genes expressed in muscle and 2,075 E...

    Authors: Rehannah HA Borup, Stefano Toppo, Yi-Wen Chen, Tanya M Teslovich, Gerolamo Lanfranchi, Giorgio Valle and Eric P Hoffman
    Citation: BMC Bioinformatics 2002 3:33
    Content type: Research article Published on:

  44. Intracellular signal transduction is achieved by networks of proteins and small molecules that transmit information from the cell surface to the nucleus, where they ultimately effect transcriptional changes. U...

    Authors: Martin Steffen, Allegra Petti, John Aach, Patrik D'haeseleer and George Church
    Citation: BMC Bioinformatics 2002 3:34
    Content type: Research article Published on:

  45. For effective exposition of biological information, especially with regard to analysis of large-scale data types, researchers need immediate access to multiple categorical knowledge bases and need summary info...

    Authors: Mark D Robinson, Jörg Grigull, Naveed Mohammad and Timothy R Hughes
    Citation: BMC Bioinformatics 2002 3:35
    Content type: Methodology article Published on:

  46. A method to evaluate and analyze the massive data generated by series of microarray experiments is of utmost importance to reveal the hidden patterns of gene expression. Because of the complexity and the high ...

    Authors: Junbai Wang, Jan Delabie, Hans Christian Aasheim, Erlend Smeland and Ola Myklebost
    Citation: BMC Bioinformatics 2002 3:36
    Content type: Research article Published on:

  47. Total sequence decomposition, using the web-based MASIA tool, identifies areas of conservation in aligned protein sequences. By structurally annotating these motifs, the sequence can be parsed into individual ...

    Authors: Catherine H Schein, Numan Özgün, Tadahide Izumi and Werner Braun
    Citation: BMC Bioinformatics 2002 3:37
    Content type: Research article Published on:

  48. Robustness of mathematical models of biochemical networks is important for validation purposes and can be used as a means of selecting between different competing models. Tools for quantifying parametric robus...

    Authors: Lan Ma and Pablo A Iglesias
    Citation: BMC Bioinformatics 2002 3:38
    Content type: Research article Published on:

  49. An organism's ability to adapt to its particular environmental niche is of fundamental importance to its survival and proliferation. In the largest study of its kind, we sought to identify and exploit the amin...

    Authors: Michel Dumontier, Katerina Michalickova and Christopher WV Hogue
    Citation: BMC Bioinformatics 2002 3:39
    Content type: Research article Published on:

  50. Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression ...

    Authors: Konrad Büssow, Steve Hoffmann and Volker Sievert
    Citation: BMC Bioinformatics 2002 3:40
    Content type: Methodology article Published on:

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