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  1. Analysis of DNA microarray data takes as input spot intensity measurements from scanner software and returns differential expression of genes between two conditions, together with a statistical significance as...

    Authors: Allan A Sioson, Shrinivasrao P Mane, Pinghua Li, Wei Sha, Lenwood S Heath, Hans J Bohnert and Ruth Grene
    Citation: BMC Bioinformatics 2006 7:215
    Content type: Research article Published on:

  2. The environmental sequencing of the Sargasso Sea has introduced a huge new resource of genomic information. Unlike the protein sequences held in the current searchable databases, the Sargasso Sea sequences ori...

    Authors: Michael L Tress, Domenico Cozzetto, Anna Tramontano and Alfonso Valencia
    Citation: BMC Bioinformatics 2006 7:213
    Content type: Research article Published on:

  3. Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxo...

    Authors: Jacob Köhler, Katherine Munn, Alexander Rüegg, Andre Skusa and Barry Smith
    Citation: BMC Bioinformatics 2006 7:212
    Content type: Methodology article Published on:

  4. Gene expression microarray experiments are expensive to conduct and guidelines for acceptable quality control at intermediate steps before and after the samples are hybridised to chips are vague. We conducted ...

    Authors: Lesley Jones, Darlene R Goldstein, Gareth Hughes, Andrew D Strand, Francois Collin, Stephen B Dunnett, Charles Kooperberg, Aaron Aragaki, James M Olson, Sarah J Augood, Richard LM Faull, Ruth Luthi-Carter, Valentina Moskvina and Angela K Hodges
    Citation: BMC Bioinformatics 2006 7:211
    Content type: Methodology article Published on:

  5. Large-scale genetic mapping projects require data management systems that can handle complex phenotypes and detect and correct high-throughput genotyping errors, yet are easy to use.

    Authors: Simon Fiddy, David Cattermole, Dong Xie, Xiao Yuan Duan and Richard Mott
    Citation: BMC Bioinformatics 2006 7:210
    Content type: Database Published on:

  6. We present a general approach to perform association analyses in pedigrees of arbitrary size and structure, which also allows for a mixture of pedigree members and independent individuals to be analyzed togeth...

    Authors: Kristina Allen-Brady, Jathine Wong and Nicola J Camp
    Citation: BMC Bioinformatics 2006 7:209
    Content type: Software Published on:

  7. Due to the functional importance of intrinsically disordered proteins or protein regions, prediction of intrinsic protein disorder from amino acid sequence has become an area of active research as witnessed in...

    Authors: Kang Peng, Predrag Radivojac, Slobodan Vucetic, A Keith Dunker and Zoran Obradovic
    Citation: BMC Bioinformatics 2006 7:208
    Content type: Software Published on:

  8. After complete sequencing of a number of genomes the focus has now turned to proteomics. Advanced proteomics technologies such as two-hybrid assay, mass spectrometry etc. are producing huge data sets of protei...

    Authors: Md Altaf-Ul-Amin, Yoko Shinbo, Kenji Mihara, Ken Kurokawa and Shigehiko Kanaya
    Citation: BMC Bioinformatics 2006 7:207
    Content type: Methodology article Published on:

  9. Current classification of protein folds are based, ultimately, on visual inspection of similarities. Previous attempts to use computerized structure comparison methods show only partial agreement with curated ...

    Authors: Vichetra Sam, Chin-Hsien Tai, Jean Garnier, Jean-Francois Gibrat, Byungkook Lee and Peter J Munson
    Citation: BMC Bioinformatics 2006 7:206
    Content type: Research article Published on:

  10. Simulation of DNA-microarray data serves at least three purposes: (i) optimizing the design of an intended DNA microarray experiment, (ii) comparing existing pre-processing and processing methods for best anal...

    Authors: Casper J Albers, Ritsert C Jansen, Jan Kok, Oscar P Kuipers and Sacha AFT van Hijum
    Citation: BMC Bioinformatics 2006 7:205
    Content type: Software Published on:

  11. Trait heterogeneity, which exists when a trait has been defined with insufficient specificity such that it is actually two or more distinct traits, has been implicated as a confounding factor in traditional st...

    Authors: Tricia A Thornton-Wells, Jason H Moore and Jonathan L Haines
    Citation: BMC Bioinformatics 2006 7:204
    Content type: Research article Published on:

  12. New analysis methods are being developed to integrate data from transcriptome, proteome, interactome, metabolome, and other investigative approaches. At the same time, existing methods are being modified to se...

    Authors: Pınar Pir, Betül Kırdar, Andrew Hayes, Z İlsen Önsan, Kutlu Ö Ülgen and Stephen G Oliver
    Citation: BMC Bioinformatics 2006 7:203
    Content type: Research article Published on:

  13. Prostate cancer is one of the leading causes of cancer illness and death among men in the United States and world wide. There is an urgent need to discover good biomarkers for early clinical diagnosis and trea...

    Authors: Chaolin Zhang, Hai-Ri Li, Jian-Bing Fan, Jessica Wang-Rodriguez, Tracy Downs, Xiang-Dong Fu and Michael Q Zhang
    Citation: BMC Bioinformatics 2006 7:202
    Content type: Research article Published on:

  15. Gene expression microarray technology permits the analysis of global gene expression profiles. The amount of sample needed limits the use of small excision biopsies and/or needle biopsies from human or animal ...

    Authors: Rachel IM van Haaften, Blanche Schroen, Ben JA Janssen, Arie van Erk, Jacques JM Debets, Hubert JM Smeets, Jos FM Smits, Arthur van den Wijngaard, Yigal M Pinto and Chris TA Evelo
    Citation: BMC Bioinformatics 2006 7:200
    Content type: Research article Published on:

  17. Two-dimensional gel electrophoresis (2DE) is a powerful technique to examine post-translational modifications of complexly modulated proteins. Currently, spot detection is a necessary step to assess relations ...

    Authors: Werner Van Belle, Nina Ånensen, Ingvild Haaland, Øystein Bruserud, Kjell-Arild Høgda and Bjørn Tore Gjertsen
    Citation: BMC Bioinformatics 2006 7:198
    Content type: Methodology article Published on:

  18. Like microarray-based investigations, high-throughput proteomics techniques require machine learning algorithms to identify biomarkers that are informative for biological classification problems. Feature selec...

    Authors: Xuegong Zhang, Xin Lu, Qian Shi, Xiu-qin Xu, Hon-chiu E Leung, Lyndsay N Harris, James D Iglehart, Alexander Miron, Jun S Liu and Wing H Wong
    Citation: BMC Bioinformatics 2006 7:197
    Content type: Methodology article Published on:

  19. Biological databases and pathway knowledgebases are proliferating rapidly. We are developing software tools for computer-aided hypothesis design and evaluation, and we would like our tools to take advantage of...

    Authors: Stephen A Racunas, Nigam H Shah and Nina V Fedoroff
    Citation: BMC Bioinformatics 2006 7:196
    Content type: Research article Published on:

  20. Biological processes are mediated by networks of interacting genes and proteins. Efforts to map and understand these networks are resulting in the proliferation of interaction data derived from both experiment...

    Authors: Svetlana Pacifico, Guozhen Liu, Stephen Guest, Jodi R Parrish, Farshad Fotouhi and Russell L Finley Jr
    Citation: BMC Bioinformatics 2006 7:195
    Content type: Database Published on:

  21. There are many methods for analyzing microarray data that group together genes having similar patterns of expression over all conditions tested. However, in many instances the biologically important goal is to...

    Authors: Joseph C Roden, Brandon W King, Diane Trout, Ali Mortazavi, Barbara J Wold and Christopher E Hart
    Citation: BMC Bioinformatics 2006 7:194
    Content type: Software Published on:

  23. Monoclonal antibodies are used extensively throughout the biomedical sciences for detection of antigens, either in vitro or in vivo. We, for example, have used them for quantitation of proteins on "reverse-phase"...

    Authors: Sylvia M Major, Satoshi Nishizuka, Daisaku Morita, Rick Rowland, Margot Sunshine, Uma Shankavaram, Frank Washburn, Daniel Asin, Hosein Kouros-Mehr, David Kane and John N Weinstein
    Citation: BMC Bioinformatics 2006 7:192
    Content type: Database Published on:

  25. The high-density oligonucleotide microarray (GeneChip) is an important tool for molecular biological research aiming at large-scale detection of small nucleotide polymorphisms in DNA and genome-wide analysis o...

    Authors: Leandro Hermida, Olivier Schaad, Philippe Demougin, Patrick Descombes and Michael Primig
    Citation: BMC Bioinformatics 2006 7:190
    Content type: Database Published on:

  26. Hidden Markov Models (HMMs) have been extensively used in computational molecular biology, for modelling protein and nucleic acid sequences. In many applications, such as transmembrane protein topology predict...

    Authors: Pantelis G Bagos, Theodore D Liakopoulos and Stavros J Hamodrakas
    Citation: BMC Bioinformatics 2006 7:189
    Content type: Methodology article Published on:

  27. A large number of bioinformatics applications in the fields of bio-sequence analysis, molecular evolution and population genetics typically share input/ouput methods, data storage requirements and data analysi...

    Authors: Julien Dutheil, Sylvain Gaillard, Eric Bazin, Sylvain Glémin, Vincent Ranwez, Nicolas Galtier and Khalid Belkhir
    Citation: BMC Bioinformatics 2006 7:188
    Content type: Software Published on:

  31. Understanding the relationship between gene expression changes, enzyme activity shifts, and the corresponding physiological adaptive response of organisms to environmental cues is crucial in explaining how cel...

    Authors: Ester Vilaprinyo, Rui Alves and Albert Sorribas
    Citation: BMC Bioinformatics 2006 7:184
    Content type: Research article Published on:

  32. The identification of biologically interesting genes in a temporal expression profiling dataset is challenging and complicated by high levels of experimental noise. Most statistical methods used in the literat...

    Authors: Veronica Vinciotti, Xiaohui Liu, Rolf Turk, Emile J de Meijer and Peter AC 't Hoen
    Citation: BMC Bioinformatics 2006 7:183
    Content type: Research article Published on:

  33. The binding between peptide epitopes and major histocompatibility complex proteins (MHCs) is an important event in the cellular immune response. Accurate prediction of the binding between short peptides and th...

    Authors: Wen Liu, Xiangshan Meng, Qiqi Xu, Darren R Flower and Tongbin Li
    Citation: BMC Bioinformatics 2006 7:182
    Content type: Research article Published on:

  34. Array-based comparative genome hybridization (aCGH) is a tool for rapid comparison of genomes from different bacterial strains. The purpose of such analysis is to detect highly divergent or absent genes in a s...

    Authors: Lars Snipen, Dirk Repsilber, Ludvig Nyquist, Andreas Ziegler, Ågot Aakra and Are Aastveit
    Citation: BMC Bioinformatics 2006 7:181
    Content type: Research article Published on:

  38. Existing large-scale metabolic models of sequenced organisms commonly include enzymatic functions which can not be attributed to any gene in that organism. Existing computational strategies for identifying suc...

    Authors: Peter Kharchenko, Lifeng Chen, Yoav Freund, Dennis Vitkup and George M Church
    Citation: BMC Bioinformatics 2006 7:177
    Content type: Methodology article Published on:

  39. Systems biologists work with many kinds of data, from many different sources, using a variety of software tools. Each of these tools typically excels at one type of analysis, such as of microarrays, of metabol...

    Authors: Paul T Shannon, David J Reiss, Richard Bonneau and Nitin S Baliga
    Citation: BMC Bioinformatics 2006 7:176
    Content type: Software Published on:

  41. The imprint of natural selection on gene sequences is often difficult to detect. A plethora of methods have been devised to detect genetic changes due to selective processes. However, many of those methods dep...

    Authors: Vicente Arnau, Miguel Gallach, J Ignasi Lucas and Ignacio Marín
    Citation: BMC Bioinformatics 2006 7:174
    Content type: Software Published on:

  42. Non-coding RNAs (ncRNAs) have a multitude of roles in the cell, many of which remain to be discovered. However, it is difficult to detect novel ncRNAs in biochemical screens. To advance biological knowledge, c...

    Authors: Andrew V Uzilov, Joshua M Keegan and David H Mathews
    Citation: BMC Bioinformatics 2006 7:173
    Content type: Research article Published on:

  43. The design of oligonucleotides and PCR primers for studying large genomes is complicated by the redundancy of sequences. The eukaryotic genomes are particularly difficult to study due to abundant repeats. The ...

    Authors: Reidar Andreson, Eric Reppo, Lauris Kaplinski and Maido Remm
    Citation: BMC Bioinformatics 2006 7:172
    Content type: Software Published on:

  44. Scientific literature is a source of the most reliable and comprehensive knowledge about molecular interaction networks. Formalization of this knowledge is necessary for computational analysis and is achieved ...

    Authors: Anton Yuryev, Zufar Mulyukov, Ekaterina Kotelnikova, Sergei Maslov, Sergei Egorov, Alexander Nikitin, Nikolai Daraselia and Ilya Mazo
    Citation: BMC Bioinformatics 2006 7:171
    Content type: Methodology article Published on:

  46. The three major mechanisms that regulate transcript formation involve the selection of alternative sites for transcription start (TS), splicing, and polyadenylation. Currently there are efforts that collect da...

    Authors: Vincent Le Texier, Jean-Jack Riethoven, Vasudev Kumanduri, Chellappa Gopalakrishnan, Fabrice Lopez, Daniel Gautheret and Thangavel Alphonse Thanaraj
    Citation: BMC Bioinformatics 2006 7:169
    Content type: Database Published on:

  47. Successful realization of a "systems biology" approach to analyzing cells is a grand challenge for our understanding of life. However, current modeling approaches to cell simulation are labor-intensive, manual...

    Authors: Kazuharu Arakawa, Yohei Yamada, Kosaku Shinoda, Yoichi Nakayama and Masaru Tomita
    Citation: BMC Bioinformatics 2006 7:168
    Content type: Research article Published on:

  48. Both direct and indirect interactions determine molecular recognition of ligands by proteins. Indirect interactions can be defined as effects on recognition controlled from distant sites in the proteins, e.g. ...

    Authors: Peteris Prusis, Staffan Uhlén, Ramona Petrovska, Maris Lapinsh and Jarl ES Wikberg
    Citation: BMC Bioinformatics 2006 7:167
    Content type: Research article Published on:

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