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  1. Transcriptional regulation is a key mechanism in the functioning of the cell, and is mostly effected through transcription factors binding to specific recognition motifs located upstream of the coding region o...

    Authors: Davide Corà, Ferdinando Di Cunto, Paolo Provero, Lorenzo Silengo and Michele Caselle
    Citation: BMC Bioinformatics 2004 5:57
    Content type: Research article Published on:

  2. The Distributed Annotation System (DAS) allows merging of DNA sequence annotations from multiple sources and provides a single annotation view. A straightforward way to establish a DAS annotation server is to ...

    Authors: Vincent Negre and Christoph Grunau
    Citation: BMC Bioinformatics 2004 5:55
    Content type: Software Published on:

  3. The detection of small yet statistically significant differences in gene expression in spotted DNA microarray studies is an ongoing challenge. Meeting this challenge requires careful examination of the perform...

    Authors: Jeffrey P Townsend
    Citation: BMC Bioinformatics 2004 5:54
    Content type: Software Published on:

  4. Several aspects of microarray data analysis are dependent on identification of genes expressed at or near the limits of detection. For example, regression-based normalization methods rely on the premise that m...

    Authors: Igor Dozmorov, Nicholas Knowlton, Yuhong Tang and Michael Centola
    Citation: BMC Bioinformatics 2004 5:53
    Content type: Methodology article Published on:

  5. An increasing number of whole viral and bacterial genomes are being sequenced and deposited in public databases. In parallel to the mounting interest in whole genomes, the number of whole genome analyses softw...

    Authors: Srikanth Celamkoti, Sashidhara Kundeti, Anjan Purkayastha, Raja Mazumder, Charles Buck and Donald Seto
    Citation: BMC Bioinformatics 2004 5:52
    Content type: Software Published on:

  8. To examine interactions among the angiotensin converting enzyme (ACE) insertion/deletion, plasminogen activator inhibitor-1 (PAI-1) 4G/5G, and tissue plasminogen activator (t-PA) insertion/deletion gene polymorph...

    Authors: Christopher S Coffey, Patricia R Hebert, Marylyn D Ritchie, Harlan M Krumholz, J Michael Gaziano, Paul M Ridker, Nancy J Brown, Douglas E Vaughan and Jason H Moore
    Citation: BMC Bioinformatics 2004 5:49
    Content type: Research article Published on:

  11. Once specific genes are identified through high throughput genomics technologies there is a need to sort the final gene list to a manageable size for validation studies. The triaging and sorting of genes often...

    Authors: Guohui Zhou, Xinyu Wen, Hang Liu, Michael J Schlicht, Martin J Hessner, Peter J Tonellato and Milton W Datta
    Citation: BMC Bioinformatics 2004 5:46
    Content type: Software Published on:

  13. Computer programs for the generation of multiple sequence alignments such as "Clustal W" allow detection of regions that are most conserved among many sequence variants. However, even for regions that are equa...

    Authors: Olga V Matveeva, Brian T Foley, Vladimir A Nemtsov, Raymond F Gesteland, Senya Matsufuji, John F Atkins, Aleksey Y Ogurtsov and Svetlana A Shabalina
    Citation: BMC Bioinformatics 2004 5:44
    Content type: Methodology article Published on:

  14. The explosion in biological information creates the need for databases that are easy to develop, easy to maintain and can be easily manipulated by annotators who are most likely to be biologists. However, depl...

    Authors: J Daniel Navarro, Naveen Talreja, Suraj Peri, BM Vrushabendra, BP Rashmi, N Padma, Vineeth Surendranath, Chandra Kiran Jonnalagadda, PS Kousthub, Nandan Deshpande, K Shanker and Akhilesh Pandey
    Citation: BMC Bioinformatics 2004 5:43
    Content type: Software Published on:

  15. To identify differentially expressed genes across experimental conditions in oligonucleotide microarray experiments, existing statistical methods commonly use a summary of probe-level expression data for each ...

    Authors: Leah Barrera, Chris Benner, Yong-Chuan Tao, Elizabeth Winzeler and Yingyao Zhou
    Citation: BMC Bioinformatics 2004 5:42
    Content type: Research article Published on:

  16. Alternative splicing is an efficient mechanism for increasing the variety of functions fulfilled by proteins in a living cell. It has been previously demonstrated that alternatively spliced regions often compr...

    Authors: Marc N Offman, Ramil N Nurtdinov, Mikhail S Gelfand and Dmitrij Frishman
    Citation: BMC Bioinformatics 2004 5:41
    Content type: Research article Published on:

  17. We present Pegasys – a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools.

    Authors: Sohrab P Shah, David YM He, Jessica N Sawkins, Jeffrey C Druce, Gerald Quon, Drew Lett, Grace XY Zheng, Tao Xu and BF Francis Ouellette
    Citation: BMC Bioinformatics 2004 5:40
    Content type: Software Published on:

  21. SNP genotyping typically incorporates a review step to ensure that the genotype calls for a particular SNP are correct. For high-throughput genotyping, such as that provided by the GenomeLab SNPstream® instrument...

    Authors: Ching Yu Austin Huang, Joel Studebaker, Anton Yuryev, Jianping Huang, Kathryn E Scott, Jennifer Kuebler, Shobha Varde, Steven Alfisi, Craig A Gelfand, Mark Pohl and Michael T Boyce-Jacino
    Citation: BMC Bioinformatics 2004 5:36
    Content type: Methodology article Published on:

  23. The biological interpretation of even a simple microarray experiment can be a challenging and highly complex task. Here we present a new method (Iterative Group Analysis) to facilitate, improve, and accelerate...

    Authors: Rainer Breitling, Anna Amtmann and Pawel Herzyk
    Citation: BMC Bioinformatics 2004 5:34
    Content type: Methodology article Published on:

  26. Functional genomics studies are yielding information about regulatory processes in the cell at an unprecedented scale. In the yeast S. cerevisiae, DNA microarrays have not only been used to measure the mRNA abund...

    Authors: Feng Gao, Barrett C Foat and Harmen J Bussemaker
    Citation: BMC Bioinformatics 2004 5:31
    Content type: Research article Published on:

  28. Integral membrane proteins constitute about 20–30% of all proteins in the fully sequenced genomes. They come in two structural classes, the α-helical and the β-barrel membrane proteins, demonstrating different...

    Authors: Pantelis G Bagos, Theodore D Liakopoulos, Ioannis C Spyropoulos and Stavros J Hamodrakas
    Citation: BMC Bioinformatics 2004 5:29
    Content type: Research article Published on:

  29. SUPFAM database is a compilation of superfamily relationships between protein domain families of either known or unknown 3-D structure. In SUPFAM, sequence families from Pfam and structural families from SCOP ...

    Authors: Shashi B Pandit, Rana Bhadra, VS Gowri, S Balaji, B Anand and N Srinivasan
    Citation: BMC Bioinformatics 2004 5:28
    Content type: Database Published on:

  30. All known genomes code for a large number of transcription factors. It is important to develop methods that will reveal how these transcription factors act on a genome wide level, that is, through what target ...

    Authors: Henry R Bigelow, Adam S Wenick, Allan Wong and Oliver Hobert
    Citation: BMC Bioinformatics 2004 5:27
    Content type: Software Published on:

  31. Recent technological advances in mass spectrometry pose challenges in computational mathematics and statistics to process the mass spectral data into predictive models with clinical and biological significance...

    Authors: Michael Wagner, Dayanand N Naik, Alex Pothen, Srinivas Kasukurti, Raghu Ram Devineni, Bao-Ling Adam, O John Semmes and George L Wright Jr
    Citation: BMC Bioinformatics 2004 5:26
    Content type: Research article Published on:

  32. Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but ...

    Authors: Remko de Knikker, Youjun Guo, Jin-long Li, Albert KH Kwan, Kevin Y Yip, David W Cheung and Kei-Hoi Cheung
    Citation: BMC Bioinformatics 2004 5:25
    Content type: Research article Published on:

  33. Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional ...

    Authors: David Adalsteinsson, David McMillen and Timothy C Elston
    Citation: BMC Bioinformatics 2004 5:24
    Content type: Software Published on:

  35. Genomic islands can be observed in many microbial genomes. These stretches of DNA have a conspicuous composition with regard to sequence or encoded functions. Genomic islands are assumed to be frequently acqui...

    Authors: Rainer Merkl
    Citation: BMC Bioinformatics 2004 5:22
    Content type: Methodology article Published on:

  37. Information obtained by DNA microarray technology gives a rough snapshot of the transcriptome state, i.e., the expression level of all the genes expressed in a cell population at any given time. One of the challe...

    Authors: Gaëlle Lelandais, Philippe Marc, Pierre Vincens, Claude Jacq and Stéphane Vialette
    Citation: BMC Bioinformatics 2004 5:20
    Content type: Software Published on:

  38. Tissue Microarrays (TMAs) have emerged as a powerful tool for examining the distribution of marker molecules in hundreds of different tissues displayed on a single slide. TMAs have been used successfully to va...

    Authors: Jules J Berman, Milton Datta, Andre Kajdacsy-Balla, Jonathan Melamed, Jan Orenstein, Kevin Dobbin, Ashok Patel, Rajiv Dhir and Michael J Becich
    Citation: BMC Bioinformatics 2004 5:19
    Content type: Methodology article Published on:

  41. Microarray and other high-throughput technologies are producing large sets of interesting genes that are difficult to analyze directly. Bioinformatics tools are needed to interpret the functional information i...

    Authors: Bing Zhang, Denise Schmoyer, Stefan Kirov and Jay Snoddy
    Citation: BMC Bioinformatics 2004 5:16
    Content type: Software Published on:

  43. Expressed Sequence Tag (EST) sequences are generally single-strand, single-pass sequences, only 200–600 nucleotides long, contain errors resulting in frame shifts, and represent different parts of their parent...

    Authors: Afshin Nadershahi, Scott C Fahrenkrug and Lynda BM Ellis
    Citation: BMC Bioinformatics 2004 5:14
    Content type: Research article Published on:

  44. Array comparative genomic hybridization (CGH) is a technique which detects copy number differences in DNA segments. Complete sequencing of the human genome and the development of an array representing a tiling...

    Authors: Bryan Chi, Ronald J deLeeuw, Bradley P Coe, Calum MacAulay and Wan L Lam
    Citation: BMC Bioinformatics 2004 5:13
    Content type: Software Published on:

  45. The proliferate nature of DNA microarray results have made it necessary to implement a uniform and quick quality control of experimental results to ensure the consistency of data across multiple experiments pr...

    Authors: Andreas Petri, Jan Fleckner and Mads Wichmann Matthiessen
    Citation: BMC Bioinformatics 2004 5:12
    Content type: Software Published on:

  47. Transcriptional regulation of cellular functions is carried out through a complex network of interactions among transcription factors and the promoter regions of genes and operons regulated by them.To better u...

    Authors: Radu Dobrin, Qasim K Beg, Albert-László Barabási and Zoltán N Oltvai
    Citation: BMC Bioinformatics 2004 5:10
    Content type: Research article Published on:

  48. Many proteomics initiatives require a seamless bioinformatics integration of a range of analytical steps between sample collection and systems modeling immediately assessable to the participants involved in th...

    Authors: Romesh Stanislaus, Liu Hong Jiang, Martha Swartz, John Arthur and Jonas S Almeida
    Citation: BMC Bioinformatics 2004 5:9
    Content type: Research article Published on:

  50. Profile Hidden Markov Models (pHMMs) are a widely used tool for protein family research. Up to now, however, there exists no method to visualize all of their central aspects graphically in an intuitively under...

    Authors: Benjamin Schuster-Böckler, Jörg Schultz and Sven Rahmann
    Citation: BMC Bioinformatics 2004 5:7
    Content type: Methodology article Published on:

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