Skip to main content

Articles

Page 232 of 247

  1. The number of genes declared differentially expressed is a random variable and its variability can be assessed by resampling techniques. Another important stability indicator is the frequency with which a give...

    Authors: Xing Qiu, Yuanhui Xiao, Alexander Gordon and Andrei Yakovlev
    Citation: BMC Bioinformatics 2006 7:50
  2. Protein phosphorylation is an extremely important mechanism of cellular regulation. A large-scale study of phosphoproteins in a whole-cell lysate of Saccharomyces cerevisiae has previously identified 383 phosphor...

    Authors: Ross I Brinkworth, Alan L Munn and Boštjan Kobe
    Citation: BMC Bioinformatics 2006 7:47
  3. While gene duplication is known to be one of the most common mechanisms of genome evolution, the fates of genes after duplication are still being debated. In particular, it is presently unknown whether most du...

    Authors: Wen-Yu Chung, Reka Albert, Istvan Albert, Anton Nekrutenko and Kateryna D Makova
    Citation: BMC Bioinformatics 2006 7:46
  4. The development of algorithms to infer the structure of gene regulatory networks based on expression data is an important subject in bioinformatics research. Validation of these algorithms requires benchmark d...

    Authors: Tim Van den Bulcke, Koenraad Van Leemput, Bart Naudts, Piet van Remortel, Hongwu Ma, Alain Verschoren, Bart De Moor and Kathleen Marchal
    Citation: BMC Bioinformatics 2006 7:43
  5. Proteomics is the study of the proteome, and is critical to the understanding of cellular processes. Two central and related tasks of proteomics are protein identification and protein characterization. Many sm...

    Authors: Harald Barsnes, Svein-Ole Mikalsen and Ingvar Eidhammer
    Citation: BMC Bioinformatics 2006 7:42
  6. Experimental techniques such as DNA microarray, serial analysis of gene expression (SAGE) and mass spectrometry proteomics, among others, are generating large amounts of data related to genes and proteins at d...

    Authors: Monica Chagoyen, Pedro Carmona-Saez, Hagit Shatkay, Jose M Carazo and Alberto Pascual-Montano
    Citation: BMC Bioinformatics 2006 7:41
  7. The identification and characterization of genes that influence the risk of common, complex multifactorial disease primarily through interactions with other genes and environmental factors remains a statistica...

    Authors: Alison A Motsinger, Stephen L Lee, George Mellick and Marylyn D Ritchie
    Citation: BMC Bioinformatics 2006 7:39
  8. Members of a protein family often have highly conserved sequences; most of these sequences carry identical biological functions and possess similar three-dimensional (3-D) structures. However, enzymes with hig...

    Authors: Hao-Teng Chang, Tun-Wen Pai, Tan-chi Fan, Bo-Han Su, Pei-Chih Wu, Chuan-Yi Tang, Chun-Tien Chang, Shi-Hwei Liu and Margaret Dah-Tsyr Chang
    Citation: BMC Bioinformatics 2006 7:38
  9. With the ever-increasing number of gene sequences in the public databases, generating and analyzing multiple sequence alignments becomes increasingly time consuming. Nevertheless it is a task performed on a re...

    Authors: Xiao I Liu, Neeraj Korde, Ursula Jakob and Lars I Leichert
    Citation: BMC Bioinformatics 2006 7:37
  10. Mitochondria are sub-cellular organelles that have a central role in energy production and in other metabolic pathways of all eukaryotic respiring cells. In the last few years, with more and more genomes being...

    Authors: Domenico Catalano, Flavio Licciulli, Antonio Turi, Giorgio Grillo, Cecilia Saccone and Domenica D'Elia
    Citation: BMC Bioinformatics 2006 7:36
  11. High-density microarray technology is increasingly applied to study gene expression levels on a large scale. Microarray experiments rely on several critical steps that may introduce error and uncertainty in an...

    Authors: Kyoungmi Kim, Grier P Page, T Mark Beasley, Stephen Barnes, Katherine E Scheirer and David B Allison
    Citation: BMC Bioinformatics 2006 7:35
  12. Receptors and scaffold proteins possess a number of distinct domains and bind multiple partners. A common problem in modeling signaling systems arises from a combinatorial explosion of different states generat...

    Authors: Holger Conzelmann, Julio Saez-Rodriguez, Thomas Sauter, Boris N Kholodenko and Ernst D Gilles
    Citation: BMC Bioinformatics 2006 7:34
  13. There is an ever increasing rate of data made available on genetic variation, transcriptomes and proteomes. Similarly, a growing variety of bioinformatic programs are becoming available from many diverse sourc...

    Authors: Erdahl T Teber, Edward Crawford, Kent B Bolton, Derek Van Dyk, Peter R Schofield, Vimal Kapoor and W Bret Church
    Citation: BMC Bioinformatics 2006 7:33
  14. Gene expression profiling has become a useful biological resource in recent years, and it plays an important role in a broad range of areas in biology. The raw gene expression data, usually in the form of larg...

    Authors: Xian Wang, Ao Li, Zhaohui Jiang and Huanqing Feng
    Citation: BMC Bioinformatics 2006 7:32
  15. Analysis of High Throughput (HTP) Data such as microarray and proteomics data has provided a powerful methodology to study patterns of gene regulation at genome scale. A major unresolved problem in the post-ge...

    Authors: Ming Yi, Jay D Horton, Jonathan C Cohen, Helen H Hobbs and Robert M Stephens
    Citation: BMC Bioinformatics 2006 7:30
  16. The neighbor-joining method by Saitou and Nei is a widely used method for constructing phylogenetic trees. The formulation of the method gives rise to a canonical Θ(n3) algorithm upon which all existing implement...

    Authors: Thomas Mailund, Gerth S Brodal, Rolf Fagerberg, Christian NS Pedersen and Derek Phillips
    Citation: BMC Bioinformatics 2006 7:29
  17. Structural models determined by X-ray crystallography play a central role in understanding protein-protein interactions at the molecular level. Interpretation of these models requires the distinction between n...

    Authors: Hongbo Zhu, Francisco S Domingues, Ingolf Sommer and Thomas Lengauer
    Citation: BMC Bioinformatics 2006 7:27
  18. It is one of the ultimate goals for modern biological research to fully elucidate the intricate interplays and the regulations of the molecular determinants that propel and characterize the progression of vers...

    Authors: Xia Li, Shaoqi Rao, Wei Jiang, Chuanxing Li, Yun Xiao, Zheng Guo, Qingpu Zhang, Lihong Wang, Lei Du, Jing Li, Li Li, Tianwen Zhang and Qing K Wang
    Citation: BMC Bioinformatics 2006 7:26
  19. A variety of diseases are caused by chromosomal abnormalities such as aneuploidies (having an abnormal number of chromosomes), microdeletions, microduplications, and uniparental disomy. High density single nuc...

    Authors: Jason C Ting, Ying Ye, George H Thomas, Ingo Ruczinski and Jonathan Pevsner
    Citation: BMC Bioinformatics 2006 7:25
  20. In this work a simple method for the computation of relative similarities between homologous metabolic network modules is presented. The method is similar to classical sequence alignment and allows for the gen...

    Authors: Kyaw Tun, Pawan K Dhar, Maria Concetta Palumbo and Alessandro Giuliani
    Citation: BMC Bioinformatics 2006 7:24
  21. There are currently many different methods for processing and summarizing probe-level data from Affymetrix oligonucleotide arrays. It is of great interest to validate these methods and identify those that are ...

    Authors: Li-Xuan Qin, Richard P Beyer, Francesca N Hudson, Nancy J Linford, Daryl E Morris and Kathleen F Kerr
    Citation: BMC Bioinformatics 2006 7:23
  22. Trace or chromatogram files (raw data) are produced by automatic nucleic acid sequencing equipment or sequencers. Each file contains information which can be interpreted by specialised software to reveal the s...

    Authors: Alexei A Adzhubei, Jon K Laerdahl and Anna V Vlasova
    Citation: BMC Bioinformatics 2006 7:22
  23. A large variety of biological data can be represented by graphs. These graphs can be constructed from heterogeneous data coming from genomic and post-genomic technologies, but there is still need for tools aim...

    Authors: Patrick Durand, Laurent Labarre, Alain Meil, Jean-Louis Divol, Yves Vandenbrouck, Alain Viari and Jérôme Wojcik
    Citation: BMC Bioinformatics 2006 7:21
  24. A new method for the prediction of protein structural classes is constructed based on Rough Sets algorithm, which is a rule-based data mining method. Amino acid compositions and 8 physicochemical properties da...

    Authors: Youfang Cao, Shi Liu, Lida Zhang, Jie Qin, Jiang Wang and Kexuan Tang
    Citation: BMC Bioinformatics 2006 7:20
  25. Several high-throughput searches for ppotential natural antisense transcripts (NATs) have been performed recently, but most of the reports were focused on cis type. A thorough in silico analysis of human transcri...

    Authors: Yuan-Yuan Li, Lei Qin, Zong-Ming Guo, Lei Liu, Hao Xu, Pei Hao, Jiong Su, Yixiang Shi, Wei-Zhong He and Yi-Xue Li
    Citation: BMC Bioinformatics 2006 7:18
  26. Methods for predicting protein function directly from amino acid sequences are useful tools in the study of uncharacterised protein families and in comparative genomics. Until now, this problem has been approa...

    Authors: Markus Brameier, Josien Haan, Andrea Krings and Robert M MacCallum
    Citation: BMC Bioinformatics 2006 7:16
  27. In recent years protein structure prediction methods using local structure information have shown promising improvements. The quality of new fold predictions has risen significantly and in fold recognition inc...

    Authors: Oliver Sander, Ingolf Sommer and Thomas Lengauer
    Citation: BMC Bioinformatics 2006 7:14
  28. Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. The integration and exchanging of the...

    Authors: Feng Li, Maoyu Li, Zhiqiang Xiao, Pengfei Zhang, Jianling Li and Zhuchu Chen
    Citation: BMC Bioinformatics 2006 7:13
  29. The choice of probe set algorithms for expression summary in a GeneChip study has a great impact on subsequent gene expression data analysis. Spiked-in cRNAs with known concentration are often used to assess t...

    Authors: Zihua Hu and Gail R Willsky
    Citation: BMC Bioinformatics 2006 7:12
  30. Various experimental techniques yield peptides that are biologically active but have unfavourable pharmacological properties. The design of structurally similar organic compounds, i.e. peptide mimetics, is a c...

    Authors: Andrean Goede, Elke Michalsky, Ulrike Schmidt and Robert Preissner
    Citation: BMC Bioinformatics 2006 7:11
  31. Benchmarking algorithms in structural bioinformatics often involves the construction of datasets of proteins with given sequence and structural properties. The SCOP database is a manually curated structural cl...

    Authors: James A Casbon, Gavin E Crooks and Mansoor AS Saqi
    Citation: BMC Bioinformatics 2006 7:10
  32. Single nucleotide polymorphisms (SNPs) are locations at which the genomic sequences of population members differ. Since these differences are known to follow patterns, disease association studies are facilitat...

    Authors: Staal A Vinterbo, Stephan Dreiseitl and Lucila Ohno-Machado
    Citation: BMC Bioinformatics 2006 7:8
  33. Expressed sequence tag (EST) datasets represent perhaps the largest collection of genetic information. ESTs can be exploited in a variety of biological experiments and analysis. Here we are interested in the d...

    Authors: Jie Zheng, Jan T Svensson, Kavitha Madishetty, Timothy J Close, Tao Jiang and Stefano Lonardi
    Citation: BMC Bioinformatics 2006 7:7
  34. Escherichia coli is the model organism for which our knowledge of its regulatory network is the most extensive. Over the last few years, our project has been collecting and curating the literature concerning E. c...

    Authors: Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Martín Peralta-Gil, Mónica I Peñaloza-Spínola, Agustino Martínez-Antonio, Peter D Karp and Julio Collado-Vides
    Citation: BMC Bioinformatics 2006 7:5
  35. Single nucleotide polymorphisms (SNP) constitute more than 90% of the genetic variation, and hence can account for most trait differences among individuals in a given species. Polymorphism detection software P...

    Authors: Lakshmi K Matukumalli, John J Grefenstette, David L Hyten, Ik-Young Choi, Perry B Cregan and Curtis P Van Tassell
    Citation: BMC Bioinformatics 2006 7:4
  36. Protein-protein interactions have traditionally been studied on a small scale, using classical biochemical methods to investigate the proteins of interest. More recently large-scale methods, such as two-hybrid...

    Authors: Pall F Jonsson, Tamara Cavanna, Daniel Zicha and Paul A Bates
    Citation: BMC Bioinformatics 2006 7:2

Featured videos

View featured videos from across the BMC-series journals

Annual Journal Metrics

  • 2022 Citation Impact
    3.0 - 2-year Impact Factor
    4.3 - 5-year Impact Factor
    0.938 - SNIP (Source Normalized Impact per Paper)
    1.100 - SJR (SCImago Journal Rank)

    2023 Speed
    19 days submission to first editorial decision for all manuscripts (Median)
    146 days submission to accept (Median)

    2023 Usage
    5,987,678 downloads
    4,858 Altmetric mentions 

Sign up for article alerts and news from this journal