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Source Code for Biology and Medicine

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  1. Content type: Software

    In science peer-reviewed publications serve as an important indicator of scientific excellence and productivity. Therefore, every scientist and institution must carefully maintain and update records of their s...

    Authors: Jörn Bethune, Lars Kraemer, Ingo Thomsen, Andreas Keller, David Ellinghaus and Andre Franke

    Citation: Source Code for Biology and Medicine 2017 12:5

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  2. Content type: Methodology

    Local field potentials (LFPs) evoked by sensory stimulation are particularly useful in electrophysiological research. For instance, spike timing and current transmembrane current flow estimated from LFPs recor...

    Authors: Maria Rubega, Claudia Cecchetto, Stefano Vassanelli and Giovanni Sparacino

    Citation: Source Code for Biology and Medicine 2017 12:3

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  3. Content type: Software

    Matched sequencing of both tumor and normal tissue is routinely used to classify variants of uncertain significance (VUS) into somatic vs. germline. However, assays used in molecular diagnostics focus on known...

    Authors: Markus Riester, Angad P. Singh, A. Rose Brannon, Kun Yu, Catarina D. Campbell, Derek Y. Chiang and Michael P. Morrissey

    Citation: Source Code for Biology and Medicine 2016 11:13

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  4. Content type: Software

    Next-generation sequencing is making it critical to robustly and rapidly handle genomic ranges within standard pipelines. Standard use-cases include annotating sequence ranges with gene or other genomic annota...

    Authors: Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei-Fei Liu and Paul C. Boutros

    Citation: Source Code for Biology and Medicine 2016 11:14

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    The Erratum to this article has been published in Source Code for Biology and Medicine 2017 12:1

  5. Content type: Software

    Next-generation sequencing can determine DNA bases and the results of sequence alignments are generally stored in files in the Sequence Alignment/Map (SAM) format and the compressed binary version (BAM) of it....

    Authors: Toshiki Takeuchi, Atsuo Yamada, Takashi Aoki and Kunihiro Nishimura

    Citation: Source Code for Biology and Medicine 2016 11:12

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  6. Content type: Software

    Whole exome sequencing (WES) has provided a means for researchers to gain access to a highly enriched subset of the human genome in which to search for variants that are likely to be pathogenic and possibly pr...

    Authors: Brigitte Glanzmann, Hendri Herbst, Craig J. Kinnear, Marlo Möller, Junaid Gamieldien and Soraya Bardien

    Citation: Source Code for Biology and Medicine 2016 11:10

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  7. Content type: Software

    Genomic deletions, inversions, and other rearrangements known collectively as structural variations (SVs) are implicated in many human disorders. Technologies for sequencing DNA provide a potentially rich sour...

    Authors: Caleb F. Davis, Deborah I. Ritter, David A. Wheeler, Hongmei Wang, Yan Ding, Shannon P. Dugan, Matthew N. Bainbridge, Donna M. Muzny, Pulivarthi H. Rao, Tsz-Kwong Man, Sharon E. Plon, Richard A. Gibbs and Ching C. Lau

    Citation: Source Code for Biology and Medicine 2016 11:8

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  8. Content type: Methodology

    The aim of this paper is to provide a general discussion, algorithm, and actual working programs of the deformation method for fast simulation of biological tissue formed by fibers and fluid. In order to demon...

    Authors: Ana Gabriella de Oliveira Sardinha, Ceres Nunes de Resende Oyama, Armando de Mendonça Maroja and Ivan F. Costa

    Citation: Source Code for Biology and Medicine 2016 11:7

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  9. Content type: Research

    Standardized schemas, databases, and public data repositories are needed for the studies of malaria vectors that encompass a remarkably diverse array of designs and rapidly generate large data volumes, often i...

    Authors: Samson S. Kiware, Tanya L. Russell, Zacharia J. Mtema, Alpha D. Malishee, Prosper Chaki, Dickson Lwetoijera, Javan Chanda, Dingani Chinula, Silas Majambere, John E. Gimnig, Thomas A. Smith and Gerry F. Killeen

    Citation: Source Code for Biology and Medicine 2016 11:4

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  10. Content type: Brief reports

    Quantitative co-localization studies strengthen the analysis of fluorescence microscopy-based assays and are essential for illustrating and understanding many cellular processes and interactions. In our earlie...

    Authors: Vasanth R. Singan and Jeremy C. Simpson

    Citation: Source Code for Biology and Medicine 2016 11:2

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  11. Content type: Research

    We previously presented a group theoretical model that describes psychiatric patient states or clinical data in a graded vector-like format based on modulo groups. Meanwhile, the Diagnostic and Statistical Manual...

    Authors: Jitsuki Sawamura, Shigeru Morishita and Jun Ishigooka

    Citation: Source Code for Biology and Medicine 2016 11:1

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  12. Content type: Methodology

    Optimal ranking of literature importance is vital in overcoming article overload. Existing ranking methods are typically based on raw citation counts, giving a sum of ‘inbound’ links with no consideration of c...

    Authors: Elliot J. Yates and Louise C. Dixon

    Citation: Source Code for Biology and Medicine 2015 10:16

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  13. Content type: Software

    One of the recent challenges of computational biology is development of new algorithms, tools and software to facilitate predictive modeling of big data generated by high-throughput technologies in biomedical ...

    Authors: Samad Jahandideh, Fatemeh Sharifi, Lukasz Jaroszewski and Adam Godzik

    Citation: Source Code for Biology and Medicine 2015 10:15

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  14. Content type: Software

    Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the majority of these are open source, few of ...

    Authors: Alexandros Kanterakis, Joël Kuiper, George Potamias and Morris A. Swertz

    Citation: Source Code for Biology and Medicine 2015 10:14

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  15. Content type: Software

    With the continued exponential growth in data volume, large-scale data mining and machine learning experiments have become a necessity for many researchers without programming or statistics backgrounds. WEKA (...

    Authors: Madison Flannery, David M. Budden and Alexandre Mendes

    Citation: Source Code for Biology and Medicine 2015 10:13

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