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  1. Content type: Software

    In proteomics studies, liquid chromatography tandem mass spectrometry data (LC-MS/MS) is quantified by spectral counts or by some measure of ion abundance. Downstream comparative analysis of protein content (e...

    Authors: Daniel A. Machlab, Gabriel Velez, Alexander G. Bassuk and Vinit B. Mahajan

    Citation: Source Code for Biology and Medicine 2018 13:3

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  2. Content type: Methodology

    The segment overlap score (SOV) has been used to evaluate the predicted protein secondary structures, a sequence composed of helix (H), strand (E), and coil (C), by comparing it with the native or reference se...

    Authors: Tong Liu and Zheng Wang

    Citation: Source Code for Biology and Medicine 2018 13:1

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  3. 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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  4. 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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  5. 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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  6. 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

  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. Content type: Methodology

    Neuromusculoskeletal modeling and simulation enable investigation of the neuromusculoskeletal system and its role in human movement dynamics. These methods are progressively introduced into daily clinical prac...

    Authors: Alice Mantoan, Claudio Pizzolato, Massimo Sartori, Zimi Sawacha, Claudio Cobelli and Monica Reggiani

    Citation: Source Code for Biology and Medicine 2015 10:12

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  19. Content type: Research

    Inference of gene networks from expression data is an important problem in computational biology. Many algorithms have been proposed for solving the problem efficiently. However, many of the available implemen...

    Authors: Maciej Fronczuk, Adrian E. Raftery and Ka Yee Yeung

    Citation: Source Code for Biology and Medicine 2015 10:11

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  20. Content type: Software

    It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in...

    Authors: Connor H. Fortin, Katharina V. Schulze and Gregory A. Babbitt

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

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  21. Content type: Software

    High-throughput primer design is routinely performed in a wide number of molecular applications including genotyping specimens using traditional PCR techniques as well as assembly PCR, nested PCR, and primer w...

    Authors: Damien M. O’Halloran

    Citation: Source Code for Biology and Medicine 2015 10:8

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  22. Content type: Research

    Malaria has been a major life threatening mosquito borne disease from long since. Unavailability of any effective vaccine and recent emergence of multi drug resistant strains of malaria pathogen Plasmodium falcip...

    Authors: Md. Anayet Hasan, Md. Habibul Hasan Mazumder, Afrin Sultana Chowdhury, Amit Datta and Md. Arif Khan

    Citation: Source Code for Biology and Medicine 2015 10:7

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  23. Content type: Software

    MicroRNA expression can be quantified using sequencing techniques or commercial microRNA-expression arrays. Recently, the AgiMicroRna R-package was published that enabled systematic preprocessing and statistical ...

    Authors: Maarten LJ Coonen, Daniel HJ Theunissen, Jos CS Kleinjans and Danyel GJ Jennen

    Citation: Source Code for Biology and Medicine 2015 10:4

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  24. Content type: Software

    The study of biological membranes using Molecular Dynamics has become an increasingly popular means by which to investigate the interactions of proteins, peptides and potentials with lipid bilayers. These inte...

    Authors: Matthew Carr and Cait E MacPhee

    Citation: Source Code for Biology and Medicine 2015 10:3

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  25. Content type: Methodology

    The graphical visualization of gene expression data using heatmaps has become an integral component of modern-day medical research. Heatmaps are used extensively to plot quantitative differences in gene expres...

    Authors: Bohdan B Khomtchouk, Derek J Van Booven and Claes Wahlestedt

    Citation: Source Code for Biology and Medicine 2014 9:30

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  26. Content type: Methodology

    Eelgrass is a cosmopolitan seagrass species that provides important ecological services in coastal and near-shore environments. Despite its relevance, loss of eelgrass habitats is noted worldwide. Restoration ...

    Authors: Héctor Echavarría-Heras, Cecilia Leal-Ramírez, Enrique Villa-Diharce and Oscar Castillo

    Citation: Source Code for Biology and Medicine 2014 9:29

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  27. Content type: Research

    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

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  28. Content type: Software review

    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

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  29. Content type: Methodology

    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

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  30. Content type: Software review

    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

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  31. Content type: Methodology

    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

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  32. Content type: Software review

    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

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