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  1. Direct comparison of 2D images is computationally inefficient due to the need for translation, rotation, and scaling of the images to evaluate their similarity. In many biological applications, such as digital...

    Authors: Julian S. DeVille, Daisuke Kihara and Atilla Sit
    Citation: Source Code for Biology and Medicine 2020 15:1
  2. Protein 3D structure is the support of its function. Comparison of 3D protein structures provides insight on their evolution and their functional specificities and can be done efficiently via protein structure...

    Authors: Guilhem Faure, Agnel Praveen Joseph, Pierrick Craveur, Tarun J. Narwani, Narayanaswamy Srinivasan, Jean-Christophe Gelly, Joseph Rebehmed and Alexandre G. de Brevern
    Citation: Source Code for Biology and Medicine 2019 14:5
  3. Next-generation sequencing (NGS) technologies have revolutionarily reshaped the landscape of ’-omics’ research areas. They produce a plethora of information requiring specific knowledge in sample preparation, ...

    Authors: Delfina Malandrino, Ilaria Manno, Alberto Negro, Andrea Petta, Luigi Serra, Concita Cantarella and Vittorio Scarano
    Citation: Source Code for Biology and Medicine 2019 14:4
  4. Due to the technological progress in Next Generation Sequencing (NGS), the amount of genomic data that is produced daily has seen a tremendous increase. This increase has shifted the bottleneck of genomic proj...

    Authors: Achraf El Allali and Mariam Arshad
    Citation: Source Code for Biology and Medicine 2019 14:3
  5. Resolving population genetic structure is challenging, especially when dealing with closely related or geographically confined populations. Although Principal Component Analysis (PCA)-based methods and genomic...

    Authors: Kridsadakorn Chaichoompu, Fentaw Abegaz, Sissades Tongsima, Philip James Shaw, Anavaj Sakuntabhai, Luísa Pereira and Kristel Van Steen
    Citation: Source Code for Biology and Medicine 2019 14:2
  6. Application of microarrays in omics technologies enables quantification of many biomolecules simultaneously. It is widely applied to observe the positive or negative effect on biomolecule activity in perturbed...

    Authors: Veer Singh Marwah, Giovanni Scala, Pia Anneli Sofia Kinaret, Angela Serra, Harri Alenius, Vittorio Fortino and Dario Greco
    Citation: Source Code for Biology and Medicine 2019 14:1
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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

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

  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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