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  1. One of the main goals in cancer studies including high-throughput microRNA (miRNA) and mRNA data is to find and assess prognostic signatures capable of predicting clinical outcome. Both mRNA and miRNA expressi...

    Authors: Stephan Gade, Christine Porzelius, Maria Fälth, Jan C Brase, Daniela Wuttig, Ruprecht Kuner, Harald Binder, Holger Sültmann and Tim Beißbarth
    Citation: BMC Bioinformatics 2011 12:488
    Content type: Research article Published on:

  2. Semantic relations increasingly underpin biomedical text mining and knowledge discovery applications. The success of such practical applications crucially depends on the quality of extracted relations, which c...

    Authors: Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman and Thomas C Rindflesch
    Citation: BMC Bioinformatics 2011 12:486
    Content type: Research article Published on:

  3. High-content, high-throughput RNA interference (RNAi) offers unprecedented possibilities to elucidate gene function and involvement in biological processes. Microscopy based screening allows phenotypic observa...

    Authors: Bettina Knapp, Ilka Rebhan, Anil Kumar, Petr Matula, Narsis A Kiani, Marco Binder, Holger Erfle, Karl Rohr, Roland Eils, Ralf Bartenschlager and Lars Kaderali
    Citation: BMC Bioinformatics 2011 12:485
    Content type: Research article Published on:

  4. Our goals are to develop a computational histopathology pipeline for characterizing tumor types that are being generated by The Cancer Genome Atlas (TCGA) for genomic association. TCGA is a national collaborat...

    Authors: Hang Chang, Gerald V Fontenay, Ju Han, Ge Cong, Frederick L Baehner, Joe W Gray, Paul T Spellman and Bahram Parvin
    Citation: BMC Bioinformatics 2011 12:484
    Content type: Methodology article Published on:

  5. Multimodal data, especially imaging and non-imaging data, is being routinely acquired in the context of disease diagnostics; however, computational challenges have limited the ability to quantitatively integra...

    Authors: Abhishek Golugula, George Lee, Stephen R Master, Michael D Feldman, John E Tomaszewski, David W Speicher and Anant Madabhushi
    Citation: BMC Bioinformatics 2011 12:483
    Content type: Methodology article Published on:

  6. The Immune Epitope Database (IEDB) project manually curates information from published journal articles that describe immune epitopes derived from a wide variety of organisms and associated with different dise...

    Authors: Emily Seymour, Rohini Damle, Alessandro Sette and Bjoern Peters
    Citation: BMC Bioinformatics 2011 12:482
    Content type: Research article Published on:

  8. Transcriptome sequencing (RNA-Seq) has become the assay of choice for high-throughput studies of gene expression. However, as is the case with microarrays, major technology-related artifacts and biases affect ...

    Authors: Davide Risso, Katja Schwartz, Gavin Sherlock and Sandrine Dudoit
    Citation: BMC Bioinformatics 2011 12:480
    Content type: Research article Published on:

  9. The nCounter analysis system (NanoString Technologies, Seattle, WA) is a technology that enables the digital quantification of multiplexed target RNA molecules using color-coded molecular barcodes and single-m...

    Authors: Christopher D Brumbaugh, Hyunsung J Kim, Mario Giovacchini and Nader Pourmand
    Citation: BMC Bioinformatics 2011 12:479
    Content type: Software Published on:

  10. An important application of high dimensional gene expression measurements is the risk prediction and the interpretation of the variables in the resulting survival models. A major problem in this context is the...

    Authors: Kai Kammers, Michel Lang, Jan G Hengstler, Marcus Schmidt and Jörg Rahnenführer
    Citation: BMC Bioinformatics 2011 12:478
    Content type: Research article Published on:

  11. Great strides have been made in the effective treatment of HIV-1 with the development of second-generation protease inhibitors (PIs) that are effective against historically multi-PI-resistant HIV-1 variants. N...

    Authors: Kathleen M Doherty, Priyanka Nakka, Bracken M King, Soo-Yon Rhee, Susan P Holmes, Robert W Shafer and Mala L Radhakrishnan
    Citation: BMC Bioinformatics 2011 12:477
    Content type: Research article Published on:

  12. A "phylogenetic profile" refers to the presence or absence of a gene across a set of organisms, and it has been proven valuable for understanding gene functional relationships and network organization. Despite...

    Authors: Jike Cui, Todd F DeLuca, Jae-Yoon Jung and Dennis P Wall
    Citation: BMC Bioinformatics 2011 12:476
    Content type: Research article Published on:

  13. Epistasis is recognized fundamentally important for understanding the mechanism of disease-causing genetic variation. Though many novel methods for detecting epistasis have been proposed, few studies focus on ...

    Authors: Junliang Shang, Junying Zhang, Yan Sun, Dan Liu, Daojun Ye and Yaling Yin
    Citation: BMC Bioinformatics 2011 12:475
    Content type: Methodology article Published on:

  14. Interpretation of gene expression microarrays requires a mapping from probe set to gene. On many Affymetrix gene expression microarrays, a given gene may be detected by multiple probe sets, which may deliver i...

    Authors: Qiyuan Li, Nicolai J Birkbak, Balazs Gyorffy, Zoltan Szallasi and Aron C Eklund
    Citation: BMC Bioinformatics 2011 12:474
    Content type: Methodology article Published on:

  15. Today, an unprecedented volume of primary biodiversity data are being generated worldwide, yet significant amounts of these data have been and will continue to be lost after the conclusion of the projects task...

    Authors: Anthony Goddard, Nathan Wilson, Phil Cryer and Grant Yamashita
    Citation: BMC Bioinformatics 2011 12(Suppl 15):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 15

  16. Biodiversity informatics is a relatively new discipline extending computer science in the context of biodiversity data, and its development to date has not been uniform throughout the world. Digitizing effort ...

    Authors: Arturo H Ariño, Vishwas Chavan and Nick King
    Citation: BMC Bioinformatics 2011 12(Suppl 15):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 15

  17. A professional recognition mechanism is required to encourage expedited publishing of an adequate volume of 'fit-for-use' biodiversity data. As a component of such a recognition mechanism, we propose the devel...

    Authors: Peter Ingwersen and Vishwas Chavan
    Citation: BMC Bioinformatics 2011 12(Suppl 15):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 15

  18. Free and open access to primary biodiversity data is essential for informed decision-making to achieve conservation of biodiversity and sustainable development. However, primary biodiversity data are neither e...

    Authors: Vishwas Chavan and Lyubomir Penev
    Citation: BMC Bioinformatics 2011 12(Suppl 15):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 15

  19. Data are the evidentiary basis for scientific hypotheses, analyses and publication, for policy formation and for decision-making. They are essential to the evaluation and testing of results by peer scientists ...

    Authors: Tom Moritz, S Krishnan, Dave Roberts, Peter Ingwersen, Donat Agosti, Lyubomir Penev, Matthew Cockerill and Vishwas Chavan
    Citation: BMC Bioinformatics 2011 12(Suppl 15):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 15

  21. Next generation sequencing (NGS) enables a more comprehensive analysis of bacterial diversity from complex environmental samples. NGS data can be analysed using a variety of workflows. We test several simple a...

    Authors: Jorge Barriuso, Jose R Valverde and Rafael P Mellado
    Citation: BMC Bioinformatics 2011 12:473
    Content type: Research article Published on:

  22. Multiple Sequence Alignment (MSA) is a basic tool for bioinformatics research and analysis. It has been used essentially in almost all bioinformatics tasks such as protein structure modeling, gene and protein ...

    Authors: Xin Deng and Jianlin Cheng
    Citation: BMC Bioinformatics 2011 12:472
    Content type: Research article Published on:

  24. Protein side-chain packing problem has remained one of the key open problems in bioinformatics. The three main components of protein side-chain prediction methods are a rotamer library, an energy function and ...

    Authors: Md Shariful Islam Bhuyan and Xin Gao
    Citation: BMC Bioinformatics 2011 12(Suppl 14):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 14

  25. Prediction of protein-ligand binding sites is an important issue for protein function annotation and structure-based drug design. Nowadays, although many computational methods for ligand-binding prediction hav...

    Authors: Tianli Dai, Qi Liu, Jun Gao, Zhiwei Cao and Ruixin Zhu
    Citation: BMC Bioinformatics 2011 12(Suppl 14):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 14

  26. Various solutions have been introduced for the identification of post-translational modification (PTM) from tandem mass spectrometry (MS/MS) in proteomics field but the identification of peptide modifiers, suc...

    Authors: Chiyong Kang and Gwan-Su Yi
    Citation: BMC Bioinformatics 2011 12(Suppl 14):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 14

  27. Structural variations (SVs) change the structure of the genome and are therefore the causes of various diseases. Next-generation sequencing allows us to obtain a multitude of sequence data, some of which can b...

    Authors: Shin Suzuki, Tomohiro Yasuda, Yuichi Shiraishi, Satoru Miyano and Masao Nagasaki
    Citation: BMC Bioinformatics 2011 12(Suppl 14):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 14

  28. In the post-genomic era, transcriptomics and proteomics provide important information to understand the genomes. With fast development of high-throughput technology, more and more transcriptomics and proteomic...

    Authors: Guangyong Zheng, Haibo Wang, Chaochun Wei and Yixue Li
    Citation: BMC Bioinformatics 2011 12(Suppl 14):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 14

  29. It is important to understand the roles of C-type lectins in the immune system due to their ubiquity and diverse range of functions in animal cells. It has been observed that currently confirmed C-type lectins...

    Authors: Geoffrey Koh, Ariana Low, Daren Poh, Yujian Yao, Say Kong Ng, Victor Vai Tak Wong, Vincent Vagenende, Kong-Peng Lam and Dong-Yup Lee
    Citation: BMC Bioinformatics 2011 12(Suppl 14):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 14

  30. Renin has become an attractive target in controlling hypertension because of the high specificity towards its only substrate, angiotensinogen. The conversion of angiotensinogen to angiotensin I is the first an...

    Authors: Shalini John, Sundarapandian Thangapandian, Mahreen Arooj, Jong Chan Hong, Kwang Dong Kim and Keun Woo Lee
    Citation: BMC Bioinformatics 2011 12(Suppl 14):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 14

  31. Enumeration of chemical graphs satisfying given constraints is one of the fundamental problems in chemoinformatics and bioinformatics since it leads to a variety of useful applications including structure dete...

    Authors: Masaaki Shimizu, Hiroshi Nagamochi and Tatsuya Akutsu
    Citation: BMC Bioinformatics 2011 12(Suppl 14):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 14

  32. With the fast advances in nextgen sequencing technology, high-throughput RNA sequencing has emerged as a powerful and cost-effective way for transcriptome study. De novo assembly of transcripts provides an import...

    Authors: Qiong-Yi Zhao, Yi Wang, Yi-Meng Kong, Da Luo, Xuan Li and Pei Hao
    Citation: BMC Bioinformatics 2011 12(Suppl 14):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 14

  33. In contrast to the increasing number of the successful genome projects, there still remain many orphan metabolites for which their synthesis processes are unknown. Metabolites, including these orphan metabolit...

    Authors: Masaaki Kotera, Toshiaki Tokimatsu, Minoru Kanehisa and Susumu Goto
    Citation: BMC Bioinformatics 2011 12(Suppl 14):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 14

  34. The rapid accumulation of molecular sequence data, driven by novel wet-lab sequencing technologies, poses new challenges for large-scale maximum likelihood-based phylogenetic analyses on trees with more than 3...

    Authors: Fernando Izquierdo-Carrasco, Stephen A Smith and Alexandros Stamatakis
    Citation: BMC Bioinformatics 2011 12:470
    Content type: Research article Published on:

  36. Modern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those ...

    Authors: Angela Bauch, Izabela Adamczyk, Piotr Buczek, Franz-Josef Elmer, Kaloyan Enimanev, Pawel Glyzewski, Manuel Kohler, Tomasz Pylak, Andreas Quandt, Chandrasekhar Ramakrishnan, Christian Beisel, Lars Malmström, Ruedi Aebersold and Bernd Rinn
    Citation: BMC Bioinformatics 2011 12:468
    Content type: Software Published on:

  38. Multiple sequence alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addr...

    Authors: Scott Lloyd and Quinn O Snell
    Citation: BMC Bioinformatics 2011 12:466
    Content type: Research article Published on:

  39. Continuous time Markov chains (CTMCs) is a widely used model for describing the evolution of DNA sequences on the nucleotide, amino acid or codon level. The sufficient statistics for CTMCs are the time spent i...

    Authors: Paula Tataru and Asger Hobolth
    Citation: BMC Bioinformatics 2011 12:465
    Content type: Methodology article Published on:

  41. Our goal was to examine how various aspects of a gene signature influence the success of developing multi-gene prediction models. We inserted gene signatures into three real data sets by altering the expressio...

    Authors: Kenneth R Hess, Caimiao Wei, Yuan Qi, Takayuki Iwamoto, W Fraser Symmans and Lajos Pusztai
    Citation: BMC Bioinformatics 2011 12:463
    Content type: Research article Published on:

  42. Herpes Simplex Virus 1 and 2 causes several infections in humans including cold sores and encephalitis. Previous antiviral studies on herpes viruses have focussed on developing nucleoside analogues that can in...

    Authors: Abhinav Grover, Vibhuti Agrawal, Ashutosh Shandilya, Virendra S Bisaria and Durai Sundar
    Citation: BMC Bioinformatics 2011 12(Suppl 13):S22
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 13

  43. Cell divisions play critical roles in disease and development. The analysis of cell division phenotypes in high content image-based screening and time-lapse microscopy relies on automated nuclear segmentation ...

    Authors: Tie Hua Du, Wee Choo Puah and Martin Wasser
    Citation: BMC Bioinformatics 2011 12(Suppl 13):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 13

  44. Biological networks are constantly subjected to random perturbations, and efficient feedback and compensatory mechanisms exist to maintain their stability. There is an increased interest in building gene regul...

    Authors: Jagath C Rajapakse and Piyushkumar A Mundra
    Citation: BMC Bioinformatics 2011 12(Suppl 13):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 13

  45. A genetic interaction refers to the deviation of phenotypes from the expected when perturbing two genes simultaneously. Studying genetic interactions help clarify relationships between genes, such as compensat...

    Authors: Chien-Hsiang Hsu, Tse-Yi Wang, Hsueh-Ting Chu, Cheng-Yan Kao and Kuang-Chi Chen
    Citation: BMC Bioinformatics 2011 12(Suppl 13):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 13

  46. Many methods have been developed to infer and reason about molecular interaction networks. These approaches often yield networks with hundreds or thousands of nodes and up to an order of magnitude more edges. ...

    Authors: Christopher L Poirel, Clifford C Owens III and T M Murali
    Citation: BMC Bioinformatics 2011 12(Suppl 13):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 13

  47. This study assesses four predictive ecological models; Fuzzy Logic (FL), Recurrent Artificial Neural Network (RANN), Hybrid Evolutionary Algorithm (HEA) and multiple linear regressions (MLR) to forecast chloro...

    Authors: Sorayya Malek, Sharifah Mumtazah Syed Ahmad, Sarinder Kaur Kashmir Singh, Pozi Milow and Aishah Salleh
    Citation: BMC Bioinformatics 2011 12(Suppl 13):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 13

  48. PB1-F2 is a major virulence factor of influenza A. This protein is a product of an alternative reading frame in the PB1-encoding RNA segment 2. Its presence of is dictated by the presence or absence of prematu...

    Authors: David S DeLuca, Derin B Keskin, Guang Lan Zhang, Ellis L Reinherz and Vladimir Brusic
    Citation: BMC Bioinformatics 2011 12(Suppl 13):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 13

  49. DNA barcoding technology, which uses a short piece of DNA sequence to identify species, has wide ranges of applications. Until today, a universal DNA barcode marker for plants remains elusive. The rbc L and mat K...

    Authors: Chang Liu, Dong Liang, Ting Gao, Xiaohui Pang, Jingyuan Song, Hui Yao, Jianping Han, Zhihua Liu, Xiaojun Guan, Kun Jiang, Huan Li and Shilin Chen
    Citation: BMC Bioinformatics 2011 12(Suppl 13):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 13

  50. The 2011 International Conference on Bioinformatics (InCoB) conference, which is the annual scientific conference of the Asia-Pacific Bioinformatics Network (APBioNet), is hosted by Kuala Lumpur, Malaysia, is ...

    Authors: Shoba Ranganathan, Christian Schönbach, Janet Kelso, Burkhard Rost, Sheila Nathan and Tin Wee Tan
    Citation: BMC Bioinformatics 2011 12(Suppl 13):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 12 Supplement 13

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