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  1. It has recently become possible to rapidly and accurately detect epigenetic signatures in bacterial genomes using third generation sequencing data. Monitoring the speed at which a single polymerase inserts a b...

    Authors: Noam D Beckmann, Sashank Karri, Gang Fang and Ali Bashir
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  2. Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $106 prize...

    Authors: Milad Gholami, Aryan Arbabi, Ali Sharifi-Zarchi, Hamidreza Chitsaz and Mehdi Sadeghi
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  3. Merging the forward and reverse reads from paired-end sequencing is a critical task that can significantly improve the performance of downstream tasks, such as genome assembly and mapping, by providing them wi...

    Authors: Sunyoung Kwon, Byunghan Lee and Sungroh Yoon
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  4. Interest in de novo genome assembly has been renewed in the past decade due to rapid advances in high-throughput sequencing (HTS) technologies which generate relatively short reads resulting in highly fragmented ...

    Authors: James Lindsay, Hamed Salooti, Ion Măndoiu and Alex Zelikovsky
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  5. Metatranscriptomic sequencing is a highly sensitive bioassay of functional activity in a microbial community, providing complementary information to the metagenomic sequencing of the community. The acquisition...

    Authors: Wazim Mohammed Ismail, Yuzhen Ye and Haixu Tang
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  6. Recent advances in RNA sequencing (RNA-Seq) technology have offered unprecedented scope and resolution for transcriptome analysis. However, precise quantification of mRNA abundance and identification of differ...

    Authors: Jinghua Gu, Xiao Wang, Leena Halakivi-Clarke, Robert Clarke and Jianhua Xuan
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  7. Recent work identified the fundamental limits on the information requirements in terms of read length and coverage depth required for successful de novo genome reconstruction from shotgun sequencing data, based o...

    Authors: Ka-Kit Lam, Asif Khalak and David Tse
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  8. There is a widening gap between the throughput of massive parallel sequencing machines and the ability to analyze these sequencing data. Traditional assembly methods requiring long execution time and large amo...

    Authors: Jintao Meng, Bingqiang Wang, Yanjie Wei, Shengzhong Feng and Pavan Balaji
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  9. Recent advances in deep digital sequencing have unveiled an unprecedented degree of clonal heterogeneity within a single tumor DNA sample. Resolving such heterogeneity depends on accurate estimation of fractio...

    Authors: Xian Fan, Wanding Zhou, Zechen Chong, Luay Nakhleh and Ken Chen
    Citation: BMC Bioinformatics 2014 15:299
    Content type: Methodology article Published on:

  10. DNA-binding proteins are vital for the study of cellular processes. In recent genome engineering studies, the identification of proteins with certain functions has become increasingly important and needs to be...

    Authors: Li Song, Dapeng Li, Xiangxiang Zeng, Yunfeng Wu, Li Guo and Quan Zou
    Citation: BMC Bioinformatics 2014 15:298
    Content type: Research article Published on:

  11. Vitamins are typical ligands that play critical roles in various metabolic processes. The accurate identification of the vitamin-binding residues solely based on a protein sequence is of significant importance...

    Authors: Dong-Jun Yu, Jun Hu, Hui Yan, Xi-Bei Yang, Jing-Yu Yang and Hong-Bin Shen
    Citation: BMC Bioinformatics 2014 15:297
    Content type: Research article Published on:

  12. Human leukocyte antigen (HLA) genes are critical genes involved in important biomedical aspects, including organ transplantation, autoimmune diseases and infectious diseases. The gene family contains the most ...

    Authors: Chia-Jung Chang, Pei-Lung Chen, Wei-Shiung Yang and Kun-Mao Chao
    Citation: BMC Bioinformatics 2014 15:296
    Content type: Methodology article Published on:

  13. The sensitivity of Optical Coherence Tomography (OCT) images to identify retinal tissue morphology characterized by early neural loss from normal healthy eyes is tested by calculating structural information an...

    Authors: Gábor Márk Somfai, Erika Tátrai, Lenke Laurik, Boglárka E Varga, Vera Ölvedy, William E Smiddy, Robert Tchitnga, Anikó Somogyi and Delia Cabrera DeBuc
    Citation: BMC Bioinformatics 2014 15:295
    Content type: Research article Published on:

  14. Masking of multiple sequence alignment blocks has become a powerful method to enhance the tree-likeness of the underlying data. However, existing masking approaches are insensitive to heterogeneous sequence di...

    Authors: Patrick Kück, Sandra A Meid, Christian Groß, Johann W Wägele and Bernhard Misof
    Citation: BMC Bioinformatics 2014 15:294
    Content type: Methodology article Published on:

  15. Venn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. They thus...

    Authors: Philippe Bardou, Jérôme Mariette, Frédéric Escudié, Christophe Djemiel and Christophe Klopp
    Citation: BMC Bioinformatics 2014 15:293
    Content type: Software Published on:

  16. Molecular dynamics (MD) simulations provide valuable insight into biomolecular systems at the atomic level. Notwithstanding the ever-increasing power of high performance computers current MD simulations face s...

    Authors: Benjamin Lutz, Claude Sinner, Stefan Bozic, Ivan Kondov and Alexander Schug
    Citation: BMC Bioinformatics 2014 15:292
    Content type: Software Published on:

  17. State-of-the-art protein-ligand docking methods are generally limited by the traditionally low accuracy of their scoring functions, which are used to predict binding affinity and thus vital for discriminating ...

    Authors: Hongjian Li, Kwong-Sak Leung, Man-Hon Wong and Pedro J Ballester
    Citation: BMC Bioinformatics 2014 15:291
    Content type: Research article Published on:

  19. Computational modeling transcription factor (TF) sequence specificity is an important research topic in regulatory genomics. A systematic comparison of 26 algorithms to learn TF-DNA binding specificity in in vitr...

    Authors: Junbai Wang
    Citation: BMC Bioinformatics 2014 15:289
    Content type: Research article Published on:

  20. Transcriptional regulation is normally based on the recognition by a transcription factor of a defined base sequence in a process of direct read-out. However, the nucleic acid secondary and tertiary structure ...

    Authors: David C Whitley, Valeria Runfola, Peter Cary, Liliya Nazlamova, Matt Guille and Garry Scarlett
    Citation: BMC Bioinformatics 2014 15:288
    Content type: Research article Published on:

  21. The development of digital imaging technology is creating extraordinary levels of accuracy that provide support for improved reliability in different aspects of the image analysis, such as content-based image ...

    Authors: Xin Qi, Daihou Wang, Ivan Rodero, Javier Diaz-Montes, Rebekah H Gensure, Fuyong Xing, Hua Zhong, Lauri Goodell, Manish Parashar, David J Foran and Lin Yang
    Citation: BMC Bioinformatics 2014 15:287
    Content type: Research article Published on:

  23. Text mining is increasingly used in the biomedical domain because of its ability to automatically gather information from large amount of scientific articles. One important task in biomedical text mining is re...

    Authors: Yifan Peng, Manabu Torii, Cathy H Wu and K Vijay-Shanker
    Citation: BMC Bioinformatics 2014 15:285
    Content type: Research article Published on:

  24. Short oligonucleotides can be used as markers to tag and track DNA sequences. For example, barcoding techniques (i.e. Multiplex Identifiers or Indexing) use short oligonucleotides to distinguish between reads fro...

    Authors: Scott M Yourstone, Derek S Lundberg, Jeffery L Dangl and Corbin D Jones
    Citation: BMC Bioinformatics 2014 15:284
    Content type: Software Published on:

  27. The use of short reads from High Throughput Sequencing (HTS) techniques is now commonplace in de novo assembly. Yet, obtaining contiguous assemblies from short reads is challenging, thus making scaffolding an imp...

    Authors: Kristoffer Sahlin, Francesco Vezzi, Björn Nystedt, Joakim Lundeberg and Lars Arvestad
    Citation: BMC Bioinformatics 2014 15:281
    Content type: Methodology article Published on:

  28. Chromatin immunoprecipitation (ChIP) followed by next-generation sequencing (ChIP-Seq) has been widely used to identify genomic loci of transcription factor (TF) binding and histone modifications. ChIP-Seq dat...

    Authors: Huihuang Yan, Jared Evans, Mike Kalmbach, Raymond Moore, Sumit Middha, Stanislav Luban, Liguo Wang, Aditya Bhagwate, Ying Li, Zhifu Sun, Xianfeng Chen and Jean-Pierre A Kocher
    Citation: BMC Bioinformatics 2014 15:280
    Content type: Software Published on:

  30. UniFrac is a well-known tool for comparing microbial communities and assessing statistically significant differences between communities. In this paper we identify a discrepancy in the UniFrac methodology that...

    Authors: Jeffrey R Long, Vanessa Pittet, Brett Trost, Qingxiang Yan, David Vickers, Monique Haakensen and Anthony Kusalik
    Citation: BMC Bioinformatics 2014 15:278
    Content type: Correspondence Published on:

  31. The identification of protein-protein interaction sites is a computationally challenging task and important for understanding the biology of protein complexes. There is a rich literature in this field. A broad...

    Authors: Zhijie Dong, Keyu Wang, Truong Khanh Linh Dang, Mehmet Gültas, Marlon Welter, Torsten Wierschin, Mario Stanke and Stephan Waack
    Citation: BMC Bioinformatics 2014 15:277
    Content type: Methodology article Published on:

  32. Time series models can play an important role in disease prediction. Incidence data can be used to predict the future occurrence of disease events. Developments in modeling approaches provide an opportunity to...

    Authors: Michael J Kane, Natalie Price, Matthew Scotch and Peter Rabinowitz
    Citation: BMC Bioinformatics 2014 15:276
    Content type: Methodology article Published on:

  33. Small RNA sequencing is commonly used to identify novel miRNAs and to determine their expression levels in plants. There are several miRNA identification tools for animals such as miRDeep, miRDeep2 and miRDeep...

    Authors: Jiyuan An, John Lai, Atul Sajjanhar, Melanie L Lehman and Colleen C Nelson
    Citation: BMC Bioinformatics 2014 15:275
    Content type: Software Published on:

  34. Microarray technology, as well as other functional genomics experiments, allow simultaneous measurements of thousands of genes within each sample. Both the prediction accuracy and interpretability of a classif...

    Authors: Osama Mahmoud, Andrew Harrison, Aris Perperoglou, Asma Gul, Zardad Khan, Metodi V Metodiev and Berthold Lausen
    Citation: BMC Bioinformatics 2014 15:274
    Content type: Methodology article Published on:

  35. Recombination plays an important role in the maintenance of genetic diversity in many types of organisms, especially diploid eukaryotes. Recombination can be studied and used to map diseases. However, recombin...

    Authors: Ying Wang, Ying Zhou, Linfeng Li, Xian Chen, Yuting Liu, Zhi-Ming Ma and Shuhua Xu
    Citation: BMC Bioinformatics 2014 15:273
    Content type: Methodology article Published on:

  37. It has been widely realized that pathways rather than individual genes govern the course of carcinogenesis. Therefore, discovering driver pathways is becoming an important step to understand the molecular mech...

    Authors: Junhua Zhang, Ling-Yun Wu, Xiang-Sun Zhang and Shihua Zhang
    Citation: BMC Bioinformatics 2014 15:271
    Content type: Methodology article Published on:

  38. Dominance effect may play an important role in genetic variation of complex traits. Full featured and easy-to-use computing tools for genomic prediction and variance component estimation of additive and domina...

    Authors: Chunkao Wang, Dzianis Prakapenka, Shengwen Wang, Sujata Pulugurta, Hakizumwami Birali Runesha and Yang Da
    Citation: BMC Bioinformatics 2014 15:270
    Content type: Software Published on:

  39. In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modificati...

    Authors: Nishanth Ulhas Nair, Yu Lin, Ana Manasovska, Jelena Antic, Paulina Grnarova, Avinash Das Sahu, Philipp Bucher and Bernard ME Moret
    Citation: BMC Bioinformatics 2014 15:269
    Content type: Methodology article Published on:

  40. Extant genomes share regions where genes have the same order and orientation, which are thought to arise from the conservation of an ancestral order of genes during evolution. Such regions of so-called conserv...

    Authors: Joseph MEX Lucas, Matthieu Muffato and Hugues Roest Crollius
    Citation: BMC Bioinformatics 2014 15:268
    Content type: Research article Published on:

  41. The phenome represents a distinct set of information in the human population. It has been explored particularly in its relationship with the genome to identify correlations for diseases. The phenome has been a...

    Authors: Halil Bisgin, Zhichao Liu, Hong Fang, Reagan Kelly, Xiaowei Xu and Weida Tong
    Citation: BMC Bioinformatics 2014 15:267
    Content type: Methodology article Published on:

  42. Natural Language Processing (NLP) has been shown effective to analyze the content of radiology reports and identify diagnosis or patient characteristics. We evaluate the combination of NLP and machine learning...

    Authors: Anne-Dominique Pham, Aurélie Névéol, Thomas Lavergne, Daisuke Yasunaga, Olivier Clément, Guy Meyer, Rémy Morello and Anita Burgun
    Citation: BMC Bioinformatics 2014 15:266
    Content type: Research article Published on:

  44. DNA barcodes are short unique sequences used to label DNA or RNA-derived samples in multiplexed deep sequencing experiments. During the demultiplexing step, barcodes must be detected and their position identif...

    Authors: Tilo Buschmann, Rong Zhang, Douglas E Brash and Leonid V Bystrykh
    Citation: BMC Bioinformatics 2014 15:264
    Content type: Research article Published on:

  45. Searching the orthologs of a given protein or DNA sequence is one of the most important and most commonly used Bioinformatics methods in Biology. Programs like BLAST or the orthology search engine Inparanoid c...

    Authors: Ines Wagner, Michael Volkmer, Malvika Sharan, Jose M Villaveces, Felix Oswald, Vineeth Surendranath and Bianca H Habermann
    Citation: BMC Bioinformatics 2014 15:263
    Content type: Software Published on:

  46. The use of sequencing technologies to investigate the microbiome of a sample can positively impact patient healthcare by providing therapeutic targets for personalized disease treatment. However, these samples...

    Authors: Allyson L Byrd, Joseph F Perez-Rogers, Solaiappan Manimaran, Eduardo Castro-Nallar, Ian Toma, Tim McCaffrey, Marc Siegel, Gary Benson, Keith A Crandall and William Evan Johnson
    Citation: BMC Bioinformatics 2014 15:262
    Content type: Methodology article Published on:

  47. Human epidermal growth factor receptor 2 (HER2) has an important role in cancer aggressiveness and poor prognosis. HER2 has been used as a drug target for cancers. In particular, to effectively treat HER2-posi...

    Authors: Wannarat Yim-im, Orathai Sawatdichaikul, Suwanna Semsri, Natharinee Horata, Wanwimon Mokmak, Sissades Tongsima, Apichart Suksamrarn and Kiattawee Choowongkomon
    Citation: BMC Bioinformatics 2014 15:261
    Content type: Research article Published on:

  48. Gene set analysis (GSA) methods test the association of sets of genes with phenotypes in gene expression microarray studies. While GSA methods on a single binary or categorical phenotype abounds, little attent...

    Authors: Xiaoming Wang, Saumyadipta Pyne and Irina Dinu
    Citation: BMC Bioinformatics 2014 15:260
    Content type: Methodology article Published on:

  49. Plant breeders use an increasingly diverse range of data types to identify lines with desirable characteristics suitable to be taken forward in plant breeding programmes. There are a number of key morphologica...

    Authors: Paul D Shaw, Martin Graham, Jessie Kennedy, Iain Milne and David F Marshall
    Citation: BMC Bioinformatics 2014 15:259
    Content type: Research article Published on:

  50. With the increasing pace of new Genetically Modified Organisms (GMOs) authorized or in pipeline for commercialization worldwide, the task of the laboratories in charge to test the compliance of food, feed or s...

    Authors: Dany Morisset, Petra Kralj Novak, Darko Zupanič, Kristina Gruden, Nada Lavrač and Jana Žel
    Citation: BMC Bioinformatics 2014 15:258
    Content type: Software Published on:

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