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  1. MALINA is a web service for bioinformatic analysis of whole-genome metagenomic data obtained from human gut microbiota sequencing. As input data, it accepts metagenomic reads of various sequencing technologies...

    Authors: Alexander V Tyakht, Anna S Popenko, Maxim S Belenikin, Ilya A Altukhov, Alexander V Pavlenko, Elena S Kostryukova, Oksana V Selezneva, Andrei K Larin, Irina Y Karpova and Dmitry G Alexeev
    Citation: Source Code for Biology and Medicine 2012 7:13
  2. Models written in description languages such as CellML are becoming a popular solution to the handling of complex cellular physiological models in biological function simulations. However, in order to fully si...

    Authors: Florencio Rusty Punzalan, Yoshiharu Yamashita, Naoki Soejima, Masanari Kawabata, Takao Shimayoshi, Hiroaki Kuwabara, Yoshitoshi Kunieda and Akira Amano
    Citation: Source Code for Biology and Medicine 2012 7:11
  3. Identification of canonical pathways through enrichment of differentially expressed genes in a given pathway is a widely used method for interpreting gene lists generated from high-throughput experimental stud...

    Authors: Bhaskar Dutta, Anders Wallqvist and Jaques Reifman
    Citation: Source Code for Biology and Medicine 2012 7:10
  4. Computer simulation has been an important technique to capture the dynamics of biochemical networks. In most networks, however, few kinetic parameters have been measured in vivo because of experimental complex...

    Authors: Kentaro Inoue, Kazuhiro Maeda, Yuki Kato, Shinpei Tonami, Shogo Takagi and Hiroyuki Kurata
    Citation: Source Code for Biology and Medicine 2012 7:9
  5. Laboratories engaged in computational biology or bioinformatics frequently need to run lengthy, multistep, and user-driven computational jobs. Each job can tie up a computer for a few minutes to several days, ...

    Authors: Daniel Jaschob and Michael Riffle
    Citation: Source Code for Biology and Medicine 2012 7:8
  6. The Portable Document Format (PDF) is the most commonly used file format for online scientific publications. The absence of effective means to extract text from these PDF files in a layout-aware manner present...

    Authors: Cartic Ramakrishnan, Abhishek Patnia, Eduard Hovy and Gully APC Burns
    Citation: Source Code for Biology and Medicine 2012 7:7
  7. The SAMtools utilities comprise a very useful and widely used suite of software for manipulating files and alignments in the SAM and BAM format, used in a wide range of genetic analyses. The SAMtools utilities...

    Authors: Ricardo H Ramirez-Gonzalez, Raoul Bonnal, Mario Caccamo and Daniel MacLean
    Citation: Source Code for Biology and Medicine 2012 7:6
  8. In scientific computing, Fortran was the dominant implementation language throughout most of the second part of the 20th century. The many tools accumulated during this time have been difficult to integrate wi...

    Authors: Ralf W Grosse-Kunstleve, Thomas C Terwilliger, Nicholas K Sauter and Paul D Adams
    Citation: Source Code for Biology and Medicine 2012 7:5
  9. The assembly of next-generation short-read sequencing data can result in a fragmented non-contiguous set of genomic sequences. Therefore a common step in a genome project is to join neighbouring sequence regio...

    Authors: Michael D Barton and Hazel A Barton
    Citation: Source Code for Biology and Medicine 2012 7:4
  10. Although published material exists about the skills required for a successful bioinformatics career, strangely enough no work to date has addressed the matter of how to excel at not being a bioinformatician. A se...

    Authors: Manuel Corpas, Segun Fatumo and Reinhard Schneider
    Citation: Source Code for Biology and Medicine 2012 7:3
  11. Authors: Cameron Neylon, Jan Aerts, C Titus Brown, Simon J Coles, Les Hatton, Daniel Lemire, K Jarrod Millman, Peter Murray-Rust, Fernando Perez, Neil Saunders, Nigam Shah, Arfon Smith, Gaël Varoquaux and Egon Willighagen
    Citation: Source Code for Biology and Medicine 2012 7:2
  12. There is a significant demand for creating pipelines or workflows in the life science discipline that chain a number of discrete compute and data intensive analysis tasks into sophisticated analysis procedures...

    Authors: Adam A Hunter, Andrew B Macgregor, Tamas O Szabo, Crispin A Wellington and Matthew I Bellgard
    Citation: Source Code for Biology and Medicine 2012 7:1
  13. Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in the minimum amount of space. As biologists are face...

    Authors: Caroline Baroukh, Sherry L Jenkins, Ruth Dannenfelser and Avi Ma'ayan
    Citation: Source Code for Biology and Medicine 2011 6:15
  14. With ever-increasing numbers of microbial genomes being sequenced, efficient tools are needed to perform strain-level identification of any newly sequenced genome. Here, we present the SNP identification for s...

    Authors: Ravi Vijaya Satya, Nela Zavaljevski and Jaques Reifman
    Citation: Source Code for Biology and Medicine 2011 6:14
  15. Current sequencing technology makes it practical to sequence many samples of a given organism, raising new challenges for the processing and interpretation of large genomics data sets with associated metadata....

    Authors: Marc E Colosimo, Matthew W Peterson, Scott Mardis and Lynette Hirschman
    Citation: Source Code for Biology and Medicine 2011 6:13
  16. We previously developed the DBRF-MEGN (d ifference-b ased r egulation f inding-m inimum e quivalent g ene n etwork) method, which deduces the most parsimonious signed directed graphs (SDGs) consistent with expres...

    Authors: Koji Kyoda, Kotaro Baba, Hiroaki Kitano and Shuichi Onami
    Citation: Source Code for Biology and Medicine 2011 6:12
  17. Recent developments in sequencing technologies have given the opportunity to sequence many bacterial genomes with limited cost and labor, compared to previous techniques. However, a limiting step of genome seq...

    Authors: Marco Galardini, Emanuele G Biondi, Marco Bazzicalupo and Alessio Mengoni
    Citation: Source Code for Biology and Medicine 2011 6:11
  18. Use of missing genotype imputations and haplotype reconstructions are valuable in genome-wide association studies (GWASs). By modeling the patterns of linkage disequilibrium in a reference panel, genotypes not...

    Authors: Kazuharu Misawa and Naoyuki Kamatani
    Citation: Source Code for Biology and Medicine 2011 6:10
  19. Laboratory Information Management Systems (LIMS) are an increasingly important part of modern laboratory infrastructure. As typically very sophisticated software products, LIMS often require considerable resou...

    Authors: Timothy G Bath, Selcuk Bozdag, Vackar Afzal and Daniel Crowther
    Citation: Source Code for Biology and Medicine 2011 6:9
  20. Creating a user friendly web based application which executes an R script allows physicians, epidemiologists, and others unfamiliar with the statistical language to perform powerful statistical analyses easily...

    Authors: Richard Newton, Andrew Deonarine and Lorenz Wernisch
    Citation: Source Code for Biology and Medicine 2011 6:6
  21. With the advent of high throughput genomics and high-resolution imaging techniques, there is a growing necessity in biology and medicine for parallel computing, and with the low cost of computing, it is now co...

    Authors: Kenneth S Kompass, Thomas J Hoffmann and John S Witte
    Citation: Source Code for Biology and Medicine 2011 6:4
  22. Cluster analysis methods have been extensively researched, but the adoption of new methods is often hindered by technical barriers in their implementation and use. WebGimm is a free cluster analysis web-servic...

    Authors: Vineet K Joshi, Johannes M Freudenberg, Zhen Hu and Mario Medvedovic
    Citation: Source Code for Biology and Medicine 2011 6:3
  23. Next Generation Sequencing (NGS) technology generates tens of millions of short reads for each DNA/RNA sample. A key step in NGS data analysis is the short read alignment of the generated sequences to a refere...

    Authors: Guorong Xu, Nan Deng, Zhiyu Zhao, Thair Judeh, Erik Flemington and Dongxiao Zhu
    Citation: Source Code for Biology and Medicine 2011 6:2
  24. Protein-protein interactions are crucially important for cellular processes. Knowledge of these interactions improves the understanding of cell cycle, metabolism, signaling, transport, and secretion. Informati...

    Authors: Chandra Sekhar Pedamallu and Janos Posfai
    Citation: Source Code for Biology and Medicine 2010 5:8
  25. Gaggle Tool Creator (GTC) is a web application which provides access to public annotation, interaction, orthology, and genomic data for hundreds of organisms, and enables instant analysis of the data using man...

    Authors: Dan Tenenbaum, J Christopher Bare and Nitin S Baliga
    Citation: Source Code for Biology and Medicine 2010 5:7
  26. The use of haplotype-based association tests can improve the power of genome-wide association studies. Since the observed genotypes are unordered pairs of alleles, haplotype phase must be inferred. However, es...

    Authors: Kazuharu Misawa and Naoyuki Kamatani
    Citation: Source Code for Biology and Medicine 2010 5:5
  27. Michigan's Department of Community Health (MDCH) is responsible for managing hospitals through the utilization of a Certificate of Need (CON) Commission. Regulation is achieved by limiting the number of beds a...

    Authors: Shaun A Langley, Steven P Fuller, Joseph P Messina, Ashton M Shortridge and Sue C Grady
    Citation: Source Code for Biology and Medicine 2010 5:4
  28. Meta-analysis is a major theme in biomedical research. In the present paper we introduce a package for R and Bioconductor that provides useful tools for performing this type of work. One idea behind the develo...

    Authors: Karl G Kugler, Laurin AJ Mueller and Armin Graber
    Citation: Source Code for Biology and Medicine 2010 5:3
  29. The manual counting of cells by microscopy is a commonly used technique across biological disciplines. Traditionally, hand tally counters have been used to track event counts. Although this method is adequate,...

    Authors: Charles C Kim and Joseph L DeRisi
    Citation: Source Code for Biology and Medicine 2010 5:1
  30. Visualization tools allow researchers to obtain a global view of the interrelationships between the probes or experiments of a gene expression (e.g. microarray) data set. Some existing methods include hierarchica...

    Authors: Raymond Wan, Larisa Kiseleva, Hajime Harada, Hiroshi Mamitsuka and Paul Horton
    Citation: Source Code for Biology and Medicine 2009 4:8
  31. Since more than a million single-nucleotide polymorphisms (SNPs) are analyzed in any given genome-wide association study (GWAS), performing multiple comparisons can be problematic. To cope with multiple-compar...

    Authors: Kazuharu Misawa and Naoyuki Kamatani
    Citation: Source Code for Biology and Medicine 2009 4:7
  32. Due to the advanced techniques in sequencing and fragment analysis, DNA sequencers and analyzers produce vast amounts of data within short time. To administrate the large data volume conveniently, efficient da...

    Authors: Justina Krawczyk, Alexander Goesmann, Ralf Nolte, Martin Werber and Bernd Weisshaar
    Citation: Source Code for Biology and Medicine 2009 4:4
  33. In molecular applications, virtual reality (VR) and immersive virtual environments have generally been used and valued for the visual and interactive experience – to enhance intuition and communicate excitemen...

    Authors: Jeremy N Block, David J Zielinski, Vincent B Chen, Ian W Davis, E Claire Vinson, Rachael Brady, Jane S Richardson and David C Richardson
    Citation: Source Code for Biology and Medicine 2009 4:3
  34. Information about protein interaction networks is fundamental to understanding protein function and cellular processes. Interaction patterns among proteins can suggest new drug targets and aid in the design of...

    Authors: Fiona Browne, Haiying Wang, Huiru Zheng and Francisco Azuaje
    Citation: Source Code for Biology and Medicine 2009 4:2
  35. Fungi from environmental samples are typically identified to species level through DNA sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region for use in BLAST-based similarity searches in th...

    Authors: R Henrik Nilsson, Gunilla Bok, Martin Ryberg, Erik Kristiansson and Nils Hallenberg
    Citation: Source Code for Biology and Medicine 2009 4:1
  36. The main problem in many model-building situations is to choose from a large set of covariates those that should be included in the "best" model. A decision to keep a variable in the model might be based on th...

    Authors: Zoran Bursac, C Heath Gauss, David Keith Williams and David W Hosmer
    Citation: Source Code for Biology and Medicine 2008 3:17
  37. Modern life sciences research increasingly relies on computational solutions, from large scale data analyses to theoretical modeling. Within the theoretical models Boolean networks occupy an increasing role as...

    Authors: István Albert, Juilee Thakar, Song Li, Ranran Zhang and Réka Albert
    Citation: Source Code for Biology and Medicine 2008 3:16
  38. Genomics and proteomics analyses regularly involve the simultaneous test of hundreds of hypotheses, either on numerical or categorical data. To correct for the occurrence of false positives, validation tests b...

    Authors: Anyela Camargo, Francisco Azuaje, Haiying Wang and Huiru Zheng
    Citation: Source Code for Biology and Medicine 2008 3:15
  39. Microarrays are becoming a very popular tool for microbial detection and diagnostics. Although these diagnostic arrays are much simpler when compared to the traditional transcriptome arrays, due to the high th...

    Authors: Joy Scaria, Aswathy Sreedharan and Yung-Fu Chang
    Citation: Source Code for Biology and Medicine 2008 3:14