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  1. Content type: Brief reports

    For over 400 years, due to the reassortment of their segmented genomes, influenza viruses evolve extremely quickly and cause devastating epidemics. This reassortment arises because two flu viruses can infect t...

    Authors: Michel Petitjean and Anne Vanet

    Citation: Source Code for Biology and Medicine 2014 9:18

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  2. Content type: Brief reports

    A growing spectrum of applications for natural and synthetic polymers, whether in industry or for biomedical research, demands for fast and universally applicable tools to determine the mechanical properties o...

    Authors: Guillaume Lamour, Julius B Kirkegaard, Hongbin Li, Tuomas PJ Knowles and Jörg Gsponer

    Citation: Source Code for Biology and Medicine 2014 9:16

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  3. Content type: Research

    Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic...

    Authors: Natapol Pornputtapong, Kwanjeera Wanichthanarak, Avlant Nilsson, Intawat Nookaew and Jens Nielsen

    Citation: Source Code for Biology and Medicine 2014 9:17

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  4. Content type: Software review

    The NCBI Entrez Gene and PubMed databases contain a wealth of high-quality information about genes for many different organisms. The NCBI Entrez online web-search interface is convenient for simple manual sear...

    Authors: Daniel J Park, Tú Nguyen-Dumont, Sori Kang, Karin Verspoor and Bernard J Pope

    Citation: Source Code for Biology and Medicine 2014 9:15

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  5. Content type: Research

    Information management systems are essential to capture data be it for public health and human disease, sustainable agriculture, or plant and animal biosecurity. In public health, the term patient registry is ...

    Authors: Matthew I Bellgard, Lee Render, Maciej Radochonski and Adam Hunter

    Citation: Source Code for Biology and Medicine 2014 9:14

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  6. Content type: Brief reports

    The fundamental challenge in optimally aligning homologous sequences is to define a scoring scheme that best reflects the underlying biological processes. Maximising the overall number of matches in the alignm...

    Authors: Neda Zamani, Görel Sundström, Marc P Höppner and Manfred G Grabherr

    Citation: Source Code for Biology and Medicine 2014 9:12

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  7. Content type: Software review

    Methylation plotter is a Web tool that allows the visualization of methylation data in a user-friendly manner and with publication-ready quality. The user is asked to introduce a file containing the methylatio...

    Authors: Izaskun Mallona, Anna Díez-Villanueva and Miguel A Peinado

    Citation: Source Code for Biology and Medicine 2014 9:11

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  8. Content type: Commentary

    A multi-million dollar research initiative involving the National Institutes of Health (NIH), Wellcome Trust and African scientists has been launched. The initiative, referred to as H3Africa, is an acronym tha...

    Authors: Moses P Adoga, Segun A Fatumo and Simon M Agwale

    Citation: Source Code for Biology and Medicine 2014 9:10

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  9. Content type: Research

    Myotis species of bats such as the Indiana Bat and Little Brown Bat are facing population declines because of White-nose syndrome (WNS). These species also face threats from anthropogenic activities such as wind ...

    Authors: Richard A Erickson, Wayne E Thogmartin and Jennifer A Szymanski

    Citation: Source Code for Biology and Medicine 2014 9:9

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    The Erratum to this article has been published in Source Code for Biology and Medicine 2014 9:122

  10. Content type: Software review

    The development of Next Generation Sequencing (NGS) during the last decade has created an unprecedented amount of sequencing data, as well as the ability to rapidly sequence specimens of interest. Read-based B...

    Authors: Jesus Enrique Herrera-Galeano, Kenneth G Frey, Regina Z Cer, Alfred J Mateczun, Kimberly A Bishop-Lilly and Vishwesh P Mokashi

    Citation: Source Code for Biology and Medicine 2014 9:7

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  11. Content type: Brief reports

    A well-known problem in cluster analysis is finding an optimal number of clusters reflecting the inherent structure of the data. PFClust is a partitioning-based clustering algorithm capable, unlike many widely...

    Authors: Khadija Musayeva, Tristan Henderson, John BO Mitchell and Lazaros Mavridis

    Citation: Source Code for Biology and Medicine 2014 9:5

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  12. Content type: Software review

    We recently described Hi-Plex, a highly multiplexed PCR-based target-enrichment system for massively parallel sequencing (MPS), which allows the uniform definition of library size so that subsequent paired-end...

    Authors: Bernard J Pope, Tú Nguyen-Dumont, Fleur Hammet and Daniel J Park

    Citation: Source Code for Biology and Medicine 2014 9:3

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  13. Content type: Software review

    Cellular events play a central role in the understanding of biological processes and functions, providing insight on both physiological and pathogenesis mechanisms. Automatic extraction of mentions of such eve...

    Authors: David Campos, Quoc-Chinh Bui, Sérgio Matos and José Luís Oliveira

    Citation: Source Code for Biology and Medicine 2014 9:1

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  14. Content type: Brief reports

    Multiobjective sequence alignment brings the advantage of providing a set of alignments that represent the trade-off between performing insertion/deletions and matching symbols from both sequences. Each of the...

    Authors: Luís Paquete, Pedro Matias, Maryam Abbasi and Miguel Pinheiro

    Citation: Source Code for Biology and Medicine 2014 9:2

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  15. Content type: Software review

    Genome sequencing has become routine, however genome assembly still remains a challenge despite the computational advances in the last decade. In particular, the abundance of repeat elements in genomes makes i...

    Authors: Genivaldo GZ Silva, Bas E Dutilh, T David Matthews, Keri Elkins, Robert Schmieder, Elizabeth A Dinsdale and Robert A Edwards

    Citation: Source Code for Biology and Medicine 2013 8:23

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  16. Content type: Brief reports

    Molecular descriptors have been extensively used in the field of structure-oriented drug design and structural chemistry. They have been applied in QSPR and QSAR models to predict ADME-Tox properties, which sp...

    Authors: Andreas Dander, Laurin AJ Mueller, Ralf Gallasch, Stephan Pabinger, Frank Emmert-Streib, Armin Graber and Matthias Dehmer

    Citation: Source Code for Biology and Medicine 2013 8:22

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  17. Content type: Research

    Rare disease registries (RDRs) are an essential tool to improve knowledge and monitor interventions for rare diseases. If designed appropriately, patient and disease related information captured within them ca...

    Authors: Matthew Bellgard, Christophe Beroud, Kay Parkinson, Tess Harris, Segolene Ayme, Gareth Baynam, Tarun Weeramanthri, Hugh Dawkins and Adam Hunter

    Citation: Source Code for Biology and Medicine 2013 8:21

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    The Erratum to this article has been published in Source Code for Biology and Medicine 2014 9:4

  18. Content type: Software review

    Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisitio...

    Authors: Gert Wollny, Peter Kellman, María-Jesus Ledesma-Carbayo, Matthew M Skinner, Jean-Jaques Hublin and Thomas Hierl

    Citation: Source Code for Biology and Medicine 2013 8:20

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  19. Content type: Brief reports

    When acquiring simple three-dimensional (3d) trajectory data it is common to accumulate large coordinate data sets. In order to examine integrity and consistency of object tracking, it is often necessary to ra...

    Authors: Luke J Whitehorn, Frances M Hawkes and Ian AN Dublon

    Citation: Source Code for Biology and Medicine 2013 8:19

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  20. Content type: Software review

    Protein-protein interaction (PPI) plays a core role in cellular functions. Massively parallel supercomputing systems have been actively developed over the past few years, which enable large-scale biological pr...

    Authors: Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Takehiro Shimoda, Toshiyuki Sato, Takashi Ishida and Yutaka Akiyama

    Citation: Source Code for Biology and Medicine 2013 8:18

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  21. Content type: Brief reports

    The popular European Molecular Biology Open Software Suite (EMBOSS) currently contains over 400 tools used in various bioinformatics researches, equipped with sophisticated development frameworks for interoper...

    Authors: Hidetoshi Itaya, Kazuki Oshita, Kazuharu Arakawa and Masaru Tomita

    Citation: Source Code for Biology and Medicine 2013 8:17

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  22. Content type: Methodology

    The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, ...

    Authors: Erlend Hodneland, Tanja Kögel, Dominik Michael Frei, Hans-Hermann Gerdes and Arvid Lundervold

    Citation: Source Code for Biology and Medicine 2013 8:16

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  23. Content type: Methodology

    Electron Paramagnetic Resonance (EPR) is a non-destructive, non-invasive technique useful for the characterization of organic moieties in primitive carbonaceous matter related to the origin of life. The classi...

    Authors: Mathilde Bourbin, Yann Le Du, Laurent Binet and Didier Gourier

    Citation: Source Code for Biology and Medicine 2013 8:15

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  24. Content type: Methodology

    Traditional flow cytometry data analysis is largely based on interactive and time consuming analysis of series two dimensional representations of up to 20 dimensional data. Recent technological advances have i...

    Authors: Josef Spidlen, Aaron Barsky, Karin Breuer, Peter Carr, Marc-Danie Nazaire, Barbara Allen Hill, Yu Qian, Ted Liefeld, Michael Reich, Jill P Mesirov, Peter Wilkinson, Richard H Scheuermann, Rafick-Pierre Sekaly and Ryan R Brinkman

    Citation: Source Code for Biology and Medicine 2013 8:14

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  25. Content type: Commentary

    The suffix -ome conveys “comprehensiveness” in some way. The idea of the Corpasome started half-jokingly, acknowledging the efforts to sequence five members of my family. After the unexpected response from man...

    Authors: Manuel Corpas

    Citation: Source Code for Biology and Medicine 2013 8:13

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  26. Content type: Methodology

    Identifying and quantifying pathological changes in brain electrical activity is important for investigations of brain injury and neurological disease. An example is the development of epilepsy, a secondary co...

    Authors: Justin Sick, Eric Bray, Amade Bregy, W Dalton Dietrich, Helen M Bramlett and Thomas Sick

    Citation: Source Code for Biology and Medicine 2013 8:12

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  27. Content type: Research

    Processing and pattern recognition of myoelectric signals have been at the core of prosthetic control research in the last decade. Although most studies agree on reporting the accuracy of predicting predefined...

    Authors: Max Ortiz-Catalan, Rickard Brånemark and Bo Håkansson

    Citation: Source Code for Biology and Medicine 2013 8:11

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  28. Content type: Software review

    Surrogate variable analysis (SVA) is a powerful method to identify, estimate, and utilize the components of gene expression heterogeneity due to unknown and/or unmeasured technical, genetic, environmental, or ...

    Authors: Mehdi Pirooznia, Fayaz Seifuddin, Fernando S Goes, Jeffrey T Leek and Peter P Zandi

    Citation: Source Code for Biology and Medicine 2013 8:8

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  29. Content type: Brief reports

    The whole-genome sequences of many non-model organisms have recently been determined. Using these genome sequences, next-generation sequencing based experiments such as RNA-seq and ChIP-seq have been performed...

    Authors: Akiko Izawa and Jun Sese

    Citation: Source Code for Biology and Medicine 2013 8:6

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  30. Content type: Methodology

    In population association studies, standard methods of statistical inference assume that study subjects are independent samples. In genetic association studies, it is therefore of interest to diagnose undocume...

    Authors: Annick Nembot-Simo, Jinko Graham and Brad McNeney

    Citation: Source Code for Biology and Medicine 2013 8:5

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  31. Content type: Brief reports

    Large-scale sequence studies requiring BLAST-based analysis produce huge amounts of data to be parsed. BLAST parsers are available, but they are often missing some important features, such as keeping all infor...

    Authors: Massimiliano Orsini and Simone Carcangiu

    Citation: Source Code for Biology and Medicine 2013 8:4

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  32. Content type: Software review

    Data processing in the bioinformatics field often involves the handling of diverse software programs in one workflow. The field is lacking a set of standards for file formats so that files have to be processed...

    Authors: Simon Barkow-Oesterreicher, Can Türker and Christian Panse

    Citation: Source Code for Biology and Medicine 2013 8:3

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  33. Content type: Methodology

    High–throughput (HT) technologies provide huge amount of gene expression data that can be used to identify biomarkers useful in the clinical practice. The most frequently used approaches first select a set of ...

    Authors: Grzegorz Zycinski, Annalisa Barla, Margherita Squillario, Tiziana Sanavia, Barbara Di Camillo and Alessandro Verri

    Citation: Source Code for Biology and Medicine 2013 8:2

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  34. Content type: Methodology

    MicroRNAs (miRNAs) constitute the largest family of noncoding RNAs involved in gene silencing and represent critical regulators of cell and tissue differentiation. Microarray expression profiling of miRNAs is ...

    Authors: Guy N Brock, Partha Mukhopadhyay, Vasyl Pihur, Cynthia Webb, Robert M Greene and M Michele Pisano

    Citation: Source Code for Biology and Medicine 2013 8:1

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  35. Content type: Software review

    MALINA is a web service for bioinformatic analysis of whole-genome metagenomic data obtained from human gut microbiota sequencing. As input data, it accepts metagenomic reads of various sequencing technologies...

    Authors: Alexander V Tyakht, Anna S Popenko, Maxim S Belenikin, Ilya A Altukhov, Alexander V Pavlenko, Elena S Kostryukova, Oksana V Selezneva, Andrei K Larin, Irina Y Karpova and Dmitry G Alexeev

    Citation: Source Code for Biology and Medicine 2012 7:13

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  36. Content type: Research

    Models written in description languages such as CellML are becoming a popular solution to the handling of complex cellular physiological models in biological function simulations. However, in order to fully si...

    Authors: Florencio Rusty Punzalan, Yoshiharu Yamashita, Naoki Soejima, Masanari Kawabata, Takao Shimayoshi, Hiroaki Kuwabara, Yoshitoshi Kunieda and Akira Amano

    Citation: Source Code for Biology and Medicine 2012 7:11

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  37. Content type: Research

    Identification of canonical pathways through enrichment of differentially expressed genes in a given pathway is a widely used method for interpreting gene lists generated from high-throughput experimental stud...

    Authors: Bhaskar Dutta, Anders Wallqvist and Jaques Reifman

    Citation: Source Code for Biology and Medicine 2012 7:10

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  38. Content type: Brief reports

    Computer simulation has been an important technique to capture the dynamics of biochemical networks. In most networks, however, few kinetic parameters have been measured in vivo because of experimental complex...

    Authors: Kentaro Inoue, Kazuhiro Maeda, Yuki Kato, Shinpei Tonami, Shogo Takagi and Hiroyuki Kurata

    Citation: Source Code for Biology and Medicine 2012 7:9

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  39. Content type: Software review

    Laboratories engaged in computational biology or bioinformatics frequently need to run lengthy, multistep, and user-driven computational jobs. Each job can tie up a computer for a few minutes to several days, ...

    Authors: Daniel Jaschob and Michael Riffle

    Citation: Source Code for Biology and Medicine 2012 7:8

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  40. Content type: Commentary

    Although published material exists about the skills required for a successful bioinformatics career, strangely enough no work to date has addressed the matter of how to excel at not being a bioinformatician. A se...

    Authors: Manuel Corpas, Segun Fatumo and Reinhard Schneider

    Citation: Source Code for Biology and Medicine 2012 7:3

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