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  1. Successfully automated sigmoidal curve fitting is highly challenging when applied to large data sets. In this paper, we describe a robust algorithm for fitting sigmoid dose-response curves by estimating four p...

    Authors: Thuy Tuong Nguyen, Kyungmin Song, Yury Tsoy, Jin Yeop Kim, Yong-Jun Kwon, Myungjoo Kang and Michael Adsetts Edberg Hansen
    Citation: Source Code for Biology and Medicine 2014 9:27
  2. In a typical study of the genetics of a complex human disease, many different analysis programs are used, to test for linkage and association. This requires extensive and careful data reformatting, as many of ...

    Authors: Robert V Baron, Charles Kollar, Nandita Mukhopadhyay and Daniel E Weeks
    Citation: Source Code for Biology and Medicine 2014 9:26
  3. Whole genomes, whole exomes and transcriptomes of tumour samples are sequenced routinely to identify the drivers of cancer. The systematic sequencing and analysis of tumour samples, as well other oncogenomic e...

    Authors: Mike Gavrielides, Simon J Furney, Tim Yates, Crispin J Miller and Richard Marais
    Citation: Source Code for Biology and Medicine 2014 9:25
  4. Researchers usually employ bar graphs to show two groups of data, which can be easily manipulated to yield false impressions. To some extent, scatterplot can retain the real data values and the spread of the d...

    Authors: Yong Xu, Fuquan Zhang, Guoqiang Wang, Hongbao Cao, Zaohuo Cheng and Yin Yao Shugart
    Citation: Source Code for Biology and Medicine 2014 9:23
  5. Commonly when designing studies, researchers propose to measure several independent variables in a regression model, a subset of which are identified as the main variables of interest while the rest are retain...

    Authors: David Keith Williams and Zoran Bursac
    Citation: Source Code for Biology and Medicine 2014 9:24
  6. The analysis of a series of experimental data is an essential procedure in virtually every field of research. The information contained in the data is extracted by fitting the experimental data to a mathematic...

    Authors: Christoph Wiedemann, Peter Bellstedt and Matthias Görlach
    Citation: Source Code for Biology and Medicine 2014 9:21
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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

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

  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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

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

  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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