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  1. Software

    goSTAG: gene ontology subtrees to tag and annotate genes within a set

    Over-representation analysis (ORA) detects enrichment of genes within biological categories. Gene Ontology (GO) domains are commonly used for gene/gene-product annotation. When ORA is employed, often times the...

    Brian D. Bennett and Pierre R. Bushel

    Source Code for Biology and Medicine 2017 12:6

    Published on: 13 April 2017

  2. Software

    LitDB - Keeping Track of Research Papers From Your Institute Made Simple

    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...

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

    Source Code for Biology and Medicine 2017 12:5

    Published on: 21 March 2017

  3. Methodology

    Algorithm and software to automatically identify latency and amplitude features of local field potentials recorded in electrophysiological investigation

    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...

    Maria Rubega, Claudia Cecchetto, Stefano Vassanelli and Giovanni Sparacino

    Source Code for Biology and Medicine 2017 12:3

    Published on: 7 February 2017

  4. Software

    PureCN: copy number calling and SNV classification using targeted short read sequencing

    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...

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

    Source Code for Biology and Medicine 2016 11:13

    Published on: 15 December 2016

  5. Software

    A bedr way of genomic interval processing

    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...

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

    Source Code for Biology and Medicine 2016 11:14

    Published on: 15 December 2016

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

  6. Software

    A new tool for prioritization of sequence variants from whole exome sequencing data

    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...

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

    Source Code for Biology and Medicine 2016 11:10

    Published on: 1 July 2016

  7. Software

    SV-STAT accurately detects structural variation via alignment to reference-based assemblies

    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...

    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

    Source Code for Biology and Medicine 2016 11:8

    Published on: 18 June 2016

  8. Methodology

    Implementation and clinical application of a deformation method for fast simulation of biological tissue formed by fibers and fluid

    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...

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

    Source Code for Biology and Medicine 2016 11:7

    Published on: 15 April 2016

  9. Software

    MM2S: personalized diagnosis of medulloblastoma patients and model systems

    Medulloblastoma (MB) is a highly malignant and heterogeneous brain tumour that is the most common cause of cancer-related deaths in children. Increasing availability of genomic data over the last decade had re...

    Deena M.A. Gendoo and Benjamin Haibe-Kains

    Source Code for Biology and Medicine 2016 11:6

    Published on: 11 April 2016

  10. Research

    A generic schema and data collection forms applicable to diverse entomological studies of mosquitoes

    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...

    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

    Source Code for Biology and Medicine 2016 11:4

    Published on: 28 March 2016

  11. Brief reports

    Implementation of the Rank-Weighted Co-localization (RWC) algorithm in multiple image analysis platforms for quantitative analysis of microscopy images

    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...

    Vasanth R. Singan and Jeremy C. Simpson

    Source Code for Biology and Medicine 2016 11:2

    Published on: 16 February 2016

  12. Research

    Symmetrical treatment of “Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition”, for major depressive disorders

    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...

    Jitsuki Sawamura, Shigeru Morishita and Jun Ishigooka

    Source Code for Biology and Medicine 2016 11:1

    Published on: 19 January 2016

  13. Methodology

    PageRank as a method to rank biomedical literature by importance

    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...

    Elliot J. Yates and Louise C. Dixon

    Source Code for Biology and Medicine 2015 10:16

    Published on: 9 December 2015

  14. Software

    FlexDM: Simple, parallel and fault-tolerant data mining using WEKA

    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 (...

    Madison Flannery, David M. Budden and Alexandre Mendes

    Source Code for Biology and Medicine 2015 10:13

    Published on: 17 November 2015

  15. Methodology

    MOtoNMS: A MATLAB toolbox to process motion data for neuromusculoskeletal modeling and simulation

    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...

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

    Source Code for Biology and Medicine 2015 10:12

    Published on: 16 November 2015

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