Skip to main content

Articles

Page 171 of 249

  1. The development of high-throughput laboratory techniques created a demand for computer-assisted result analysis tools. Many of these techniques return lists of genes whose interpretation requires finding relev...

    Authors: Joel P Arrais, João Fernandes, João Pereira and José Luís Oliveira
    Citation: BMC Bioinformatics 2010 11:389
    Content type: Software Published on:

  5. All infectious disease oriented clinical diagnostic assays in use today focus on detecting the presence of a single, well defined target agent or a set of agents. In recent years, microarray-based diagnostics ...

    Authors: Adam F Allred, Guang Wu, Tuya Wulan, Kael F Fischer, Michael R Holbrook, Robert B Tesh and David Wang
    Citation: BMC Bioinformatics 2010 11:384
    Content type: Research article Published on:

  6. We study the usage of specific peptide platforms in protein composition. Using the pentapeptide as a unit of length, we find that in the universal proteome many pentapeptides are heavily repeated (even thousan...

    Authors: Giovanni Capone, Giuseppe Novello, Candida Fasano, Brett Trost, Mik Bickis, Anthony Kusalik and Darja Kanduc
    Citation: BMC Bioinformatics 2010 11:383
    Content type: Research article Published on:

  8. Accurate prediction of antigenic epitopes is important for immunologic research and medical applications, but it is still an open problem in bioinformatics. The case for discontinuous epitopes is even worse - ...

    Authors: Shide Liang, Dandan Zheng, Daron M Standley, Bo Yao, Martin Zacharias and Chi Zhang
    Citation: BMC Bioinformatics 2010 11:381
    Content type: Methodology article Published on:

  10. The development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences...

    Authors: Raphaël Helaers and Michel C Milinkovitch
    Citation: BMC Bioinformatics 2010 11:379
    Content type: Software Published on:

  11. The investigation of plant genome structure and evolution requires comprehensive characterization of repetitive sequences that make up the majority of higher plant nuclear DNA. Since genome-wide characterizati...

    Authors: Petr Novák, Pavel Neumann and Jiří Macas
    Citation: BMC Bioinformatics 2010 11:378
    Content type: Methodology article Published on:

  12. High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infras...

    Authors: David B Burdick, Chris C Cavnor, Jeremy Handcock, Sarah Killcoyne, Jake Lin, Bruz Marzolf, Stephen A Ramsey, Hector Rovira, Ryan Bressler, Ilya Shmulevich and John Boyle
    Citation: BMC Bioinformatics 2010 11:377
    Content type: Software Published on:

  13. Standardization of analytical approaches and reporting methods via community-wide collaboration can work synergistically with web-tool development to result in rapid community-driven expansion of online data r...

    Authors: Adam J Carroll, Murray R Badger and A Harvey Millar
    Citation: BMC Bioinformatics 2010 11:376
    Content type: Database Published on:

  14. The amount of available biological information is rapidly increasing and the focus of biological research has moved from single components to networks and even larger projects aiming at the analysis, modelling...

    Authors: Stephanie Heinen, Bernhard Thielen and Dietmar Schomburg
    Citation: BMC Bioinformatics 2010 11:375
    Content type: Database Published on:

  15. Accurate evaluation and modelling of residue-residue interactions within and between proteins is a key aspect of computational structure prediction including homology modelling, protein-protein docking, refine...

    Authors: Vladimir Potapov, Mati Cohen, Yuval Inbar and Gideon Schreiber
    Citation: BMC Bioinformatics 2010 11:374
    Content type: Methodology article Published on:

  16. A reliable extraction technique for resolving multiple spots in light or electron microscopic images is essential in investigations of the spatial distribution and dynamics of specific proteins inside cells an...

    Authors: Yoshitaka Kimori, Norio Baba and Nobuhiro Morone
    Citation: BMC Bioinformatics 2010 11:373
    Content type: Methodology article Published on:

  17. Sub-cellular structures interact in numerous direct and indirect ways in order to fulfill cellular functions. While direct molecular interactions crucially depend on spatial proximity, other interactions typicall...

    Authors: Jo A Helmuth, Grégory Paul and Ivo F Sbalzarini
    Citation: BMC Bioinformatics 2010 11:372
    Content type: Research article Published on:

  18. OFFGEL isoelectric focussing (IEF) has become a popular tool in proteomics to fractionate peptides or proteins. As a consequence there is a need for software solutions supporting data mining, interpretation an...

    Authors: David-Olivier D Azulay, Hendrik Neubert and Mireia Fernández Ocaña
    Citation: BMC Bioinformatics 2010 11:371
    Content type: Software Published on:

  20. Protein-DNA interaction constitutes a basic mechanism for the genetic regulation of target gene expression. Deciphering this mechanism has been a daunting task due to the difficulty in characterizing protein-b...

    Authors: Zhaohui S Qin, Jianjun Yu, Jincheng Shen, Christopher A Maher, Ming Hu, Shanker Kalyana-Sundaram, Jindan Yu and Arul M Chinnaiyan
    Citation: BMC Bioinformatics 2010 11:369
    Content type: Methodology article Published on:

  21. Microarray technology allows the simultaneous analysis of thousands of genes within a single experiment. Significance analyses of transcriptomic data ignore the gene dependence structure. This leads to correla...

    Authors: Yuna Blum, Guillaume Le Mignon, Sandrine Lagarrigue and David Causeur
    Citation: BMC Bioinformatics 2010 11:368
    Content type: Methodology article Published on:

  22. Nonnegative Matrix Factorization (NMF) is an unsupervised learning technique that has been applied successfully in several fields, including signal processing, face recognition and text mining. Recent applicat...

    Authors: Renaud Gaujoux and Cathal Seoighe
    Citation: BMC Bioinformatics 2010 11:367
    Content type: Software Published on:

  24. The study of protein-small molecule interactions is vital for understanding protein function and for practical applications in drug discovery. To benefit from the rapidly increasing structural data, it is esse...

    Authors: Ratna R Thangudu, Manoj Tyagi, Benjamin A Shoemaker, Stephen H Bryant, Anna R Panchenko and Thomas Madej
    Citation: BMC Bioinformatics 2010 11:365
    Content type: Research article Published on:

  27. Predicting metabolic sites is important in the drug discovery process to aid in rapid compound optimisation. No interactive tool exists and most of the useful tools are quite expensive.

    Authors: Lars Carlsson, Ola Spjuth, Samuel Adams, Robert C Glen and Scott Boyer
    Citation: BMC Bioinformatics 2010 11:362
    Content type: Methodology article Published on:

  28. Calibration of a microarray scanner is critical for accurate interpretation of microarray results. Shi et al. (BMC Bioinformatics, 2005, 6, Art. No. S11 Suppl. 2.) reported usage of a Full Moon BioSystems slide f...

    Authors: Alexander E Pozhitkov
    Citation: BMC Bioinformatics 2010 11:361
    Content type: Correspondence Published on:

  29. Molecular interaction networks can be efficiently studied using network visualization software such as Cytoscape. The relevant nodes, edges and their attributes can be imported in Cytoscape in various file for...

    Authors: Kris Laukens, Jens Hollunder, Thanh Hai Dang, Geert De Jaeger, Martin Kuiper, Erwin Witters, Alain Verschoren and Koenraad Van Leemput
    Citation: BMC Bioinformatics 2010 11:360
    Content type: Software Published on:

  31. Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as ...

    Authors: Wolfgang Hankeln, Pier Luigi Buttigieg, Dennis Fink, Renzo Kottmann, Pelin Yilmaz and Frank Oliver Glöckner
    Citation: BMC Bioinformatics 2010 11:358
    Content type: Software Published on:

  32. PDZ domain is a well-conserved, structural protein domain found in hundreds of signaling proteins that are otherwise unrelated. PDZ domains can bind to the C-terminal peptides of different proteins and act as ...

    Authors: Sibel Kalyoncu, Ozlem Keskin and Attila Gursoy
    Citation: BMC Bioinformatics 2010 11:357
    Content type: Research article Published on:

  33. Microarray measurements are susceptible to a variety of experimental artifacts, some of which give rise to systematic biases that are spatially dependent in a unique way on each chip. It is likely that such ar...

    Authors: High Seng Chai, Terry M Therneau, Kent R Bailey and Jean-Pierre A Kocher
    Citation: BMC Bioinformatics 2010 11:356
    Content type: Methodology article Published on:

  34. Transcriptional gene regulation is one of the most important mechanisms in controlling many essential cellular processes, including cell development, cell-cycle control, and the cellular response to variations...

    Authors: Marc Bailly-Bechet, Alfredo Braunstein, Andrea Pagnani, Martin Weigt and Riccardo Zecchina
    Citation: BMC Bioinformatics 2010 11:355
    Content type: Methodology article Published on:

  35. The analysis of oligonucleotide microarray data in pathogen surveillance and discovery is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each h...

    Authors: Omar J Jabado, Sean Conlan, Phenix-Lan Quan, Jeffrey Hui, Gustavo Palacios, Mady Hornig, Thomas Briese and W Ian Lipkin
    Citation: BMC Bioinformatics 2010 11:354
    Content type: Methodology article Published on:

  36. Many high-throughput genomic experiments, such as Synthetic Genetic Array and yeast two-hybrid, use colony growth on solid media as a screen metric. These experiments routinely generate over 100,000 data point...

    Authors: John C Dittmar, Robert JD Reid and Rodney Rothstein
    Citation: BMC Bioinformatics 2010 11:353
    Content type: Software Published on:

  37. Protein-protein interactions are fundamental for the majority of cellular processes and their study is of enormous biotechnological and therapeutic interest. In recent years, a variety of computational approac...

    Authors: Albert Solernou and Juan Fernandez-Recio
    Citation: BMC Bioinformatics 2010 11:352
    Content type: Research article Published on:

  39. High-throughput methods for detecting protein-protein interactions enable us to obtain large interaction networks, and also allow us to computationally identify the associations of proteins as protein complexe...

    Authors: Yosuke Ozawa, Rintaro Saito, Shigeo Fujimori, Hisashi Kashima, Masamichi Ishizaka, Hiroshi Yanagawa, Etsuko Miyamoto-Sato and Masaru Tomita
    Citation: BMC Bioinformatics 2010 11:350
    Content type: Methodology article Published on:

  40. Phosphorylation events direct the flow of signals and metabolites along cellular protein networks. Current annotations of kinase-substrate binding events are far from complete. In this study, we scanned the en...

    Authors: Yichuan Liu and Aydin Tozeren
    Citation: BMC Bioinformatics 2010 11:349
    Content type: Research article Published on:

  42. DNA sequence comparison is a well-studied problem, in which two DNA sequences are compared using a weighted edit distance. Recent DNA sequencing technologies however observe an encoded form of the sequence, ra...

    Authors: Nils Homer, Stanley F Nelson and Barry Merriman
    Citation: BMC Bioinformatics 2010 11:347
    Content type: Research article Published on:

  43. The nucleosome is the fundamental packing unit of DNAs in eukaryotic cells. Its detailed positioning on the genome is closely related to chromosome functions. Increasing evidence has shown that genomic DNA seq...

    Authors: Liqun Xi, Yvonne Fondufe-Mittendorf, Lei Xia, Jared Flatow, Jonathan Widom and Ji-Ping Wang
    Citation: BMC Bioinformatics 2010 11:346
    Content type: Methodology article Published on:

  45. Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, t...

    Authors: Benjamin Chain, Helen Bowen, John Hammond, Wilfried Posch, Jane Rasaiyaah, Jhen Tsang and Mahdad Noursadeghi
    Citation: BMC Bioinformatics 2010 11:344
    Content type: Research article Published on:

  46. Genetic interaction profiles are highly informative and helpful for understanding the functional linkages between genes, and therefore have been extensively exploited for annotating gene functions and dissecti...

    Authors: Zhu-Hong You, Zheng Yin, Kyungsook Han, De-Shuang Huang and Xiaobo Zhou
    Citation: BMC Bioinformatics 2010 11:343
    Content type: Research article Published on:

  49. Pathogen diagnostic assays based on polymerase chain reaction (PCR) technology provide high sensitivity and specificity. However, the design of these diagnostic assays is computationally intensive, requiring h...

    Authors: Ravi Vijaya Satya, Kamal Kumar, Nela Zavaljevski and Jaques Reifman
    Citation: BMC Bioinformatics 2010 11:340
    Content type: Software Published on:

  50. Comparative analysis of gene expression profiling of multiple biological categories, such as different species of organisms or different kinds of tissue, promises to enhance the fundamental understanding of th...

    Authors: Wensheng Zhang, Andrea Edwards, Wei Fan, Dongxiao Zhu and Kun Zhang
    Citation: BMC Bioinformatics 2010 11:338
    Content type: Methodology article Published on:

Featured videos

View featured videos from across the BMC-series journals

Submit manuscript

Annual Journal Metrics

  • Citation Impact 2023
    Journal Impact Factor: 2.9
    5-year Journal Impact Factor: 3.6
    Source Normalized Impact per Paper (SNIP): 0.821
    SCImago Journal Rank (SJR): 1.005

    Speed 2023
    Submission to first editorial decision (median days): 12
    Submission to acceptance (median days): 146

    Usage 2023
    Downloads: 5,987,678
    Altmetric mentions: 4,858

Follow

Sign up for article alerts and news from this journal

BMC Bioinformatics

ISSN: 1471-2105

Contact us