Abstract：
BACKGROUND:Research related to cancer is vast, and continues in earnest in many directions. Due to the complexity of cancer, a better understanding of tumor growth dynamics can be gleaned from a dynamic computational model. We present a comprehensive, fully executable, spatial and temporal 3D computational model of the development of a cancerous tumor together with its environment. RESULTS:The model was created using Statecharts, which were then connected to an interactive animation front-end that we developed especially for this work, making it possible to visualize on the fly the on-going events of the system's execution, as well as the effect of various input parameters. We were thus able to gain a better understanding of, e.g., how different amounts or thresholds of oxygen and VEGF (vascular endothelial growth factor) affect the progression of the tumor. We found that the tumor has a critical turning point, where it either dies or recovers. If minimum conditions are met at that time, it eventually develops into a full, active, growing tumor, regardless of the actual amount; otherwise it dies. CONCLUSIONS:This brings us to the conclusion that the tumor is in fact a very robust system: changing initial values of VEGF and oxygen can increase the time it takes to become fully developed, but will not necessarily completely eliminate it.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Bloch N,Harel Ddoi
10.1186/s12859-016-1168-5subject
Has Abstractpub_date
2016-08-24 00:00:00pages
317issue
1issn
1471-2105pii
10.1186/s12859-016-1168-5journal_volume
17pub_type
杂志文章abstract：BACKGROUND:Genetic interaction profiles are highly informative and helpful for understanding the functional linkages between genes, and therefore have been extensively exploited for annotating gene functions and dissecting specific pathway structures. However, our understanding is rather limited to the relationship bet...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-11-343
更新日期：2010-06-24 00:00:00
abstract：BACKGROUND:Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings i...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-10-421
更新日期：2009-12-15 00:00:00
abstract：BACKGROUND:Copy number alterations (CNAs), due to their large impact on the genome, have been an important contributing factor to oncogenesis and metastasis. Detecting genomic alterations from the shallow-sequencing data of a low-purity tumor sample remains a challenging task. RESULTS:We introduce Accucopy, a method t...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-020-03924-5
更新日期：2021-01-15 00:00:00
abstract：BACKGROUND:Although many of the genic features in Mycobacterium abscessus have been fully validated, a comprehensive understanding of the regulatory elements remains lacking. Moreover, there is little understanding of how the organism regulates its transcriptomic profile, enabling cells to survive in hostile environmen...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-019-3042-8
更新日期：2019-09-10 00:00:00
abstract：BACKGROUND:Recently there has been a lot of interest in identifying modules at the level of genetic and metabolic networks of organisms, as well as in identifying single genes and reactions that are essential for the organism. A goal of computational and systems biology is to go beyond identification towards an explana...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-7-118
更新日期：2006-03-08 00:00:00
abstract：BACKGROUND:Microarray technology can acquire information about thousands of genes simultaneously. We analyzed published breast cancer microarray databases to predict five-year recurrence and compared the performance of three data mining algorithms of artificial neural networks (ANN), decision trees (DT) and logistic re...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-14-100
更新日期：2013-03-19 00:00:00
abstract：:Following publication of the original article [1], the author reported that there are several errors in the original article. ...
journal_title：BMC bioinformatics
pub_type： 杂志文章,已发布勘误
doi：10.1186/s12859-019-3318-z
更新日期：2020-01-22 00:00:00
abstract：BACKGROUND:Protein sequence motifs are by definition short fragments of conserved amino acids, often associated with a specific function. Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative description of functional motifs characterizing families of related sequences. ...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-6-164
更新日期：2005-06-29 00:00:00
abstract：BACKGROUND:Sequence mutations represent a driving force of adaptive evolution in bacterial pathogens. It is especially evident in reductive genome evolution where bacteria underwent lifestyles shifting from a free-living to a strictly intracellular or host-depending life. It resulted in loss-of-function mutations and/o...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-10-S1-S3
更新日期：2009-01-30 00:00:00
abstract：BACKGROUND:Identifying similarities between datasets is a fundamental task in data mining and has become an integral part of modern scientific investigation. Whether the task is to identify co-expressed genes in large-scale expression surveys or to predict combinations of gene knockouts which would elicit a similar phe...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-018-2210-6
更新日期：2018-06-11 00:00:00
abstract：BACKGROUND:The program InDeVal was originally developed to help researchers find known regions of insertion/deletion activity (with the exception of isolated single-base indels) in newly determined Poaceae trnL-F sequences and compare them with 533 previously determined sequences. It is supplied with input files design...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-5-173
更新日期：2004-10-29 00:00:00
abstract：BACKGROUND:Prioritizing genes according to their associations with a cancer allows researchers to explore genes in more informed ways. By far, Gene-centric or network-centric gene prioritization methods are predominated. Genes and their protein products carry out cellular processes in the context of functional modules....
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-018-2216-0
更新日期：2018-06-05 00:00:00
abstract：BACKGROUND:Protein function in eukaryotic cells is often controlled in a cell cycle-dependent manner. Therefore, the correct assignment of cellular phenotypes to cell cycle phases is a crucial task in cell biology research. Nuclear proteins whose localization varies during the cell cycle are valuable and frequently use...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-015-0618-9
更新日期：2015-05-29 00:00:00
abstract：BACKGROUND:It has long been recognized that sensitivity analysis plays a key role in modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become a well-known platform for coding and sharing mathematical models of such processes. However, current SBML compatible software ...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-9-342
更新日期：2008-08-15 00:00:00
abstract：BACKGROUND:Wise et al. introduced a rank-based statistical technique for meta-analysis of genome scans, the Genome Scan Meta-Analysis (GSMA) method. Levinson et al. recently described two generalizations of the GSMA statistic: (i) a weighted version of the GSMA statistic, so that different studies could be ascribed dif...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-6-32
更新日期：2005-02-17 00:00:00
abstract：BACKGROUND:The identification of differentially expressed genes (DEGs) from Affymetrix GeneChips arrays is currently done by first computing expression levels from the low-level probe intensities, then deriving significance by comparing these expression levels between conditions. The proposed PL-LM (Probe-Level Linear ...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-7-391
更新日期：2006-08-25 00:00:00
abstract：BACKGROUND:The rapid development of structural genomics has resulted in many "unknown function" proteins being deposited in Protein Data Bank (PDB), thus, the functional prediction of these proteins has become a challenge for structural bioinformatics. Several sequence-based and structure-based methods have been develo...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-11-439
更新日期：2010-08-27 00:00:00
abstract：BACKGROUND:Finding common molecular interactions from different samples is essential work to understanding diseases and other biological processes. Coexpression networks and their modules directly reflect sample-specific interactions among genes. Therefore, identification of common coexpression network or modules may r...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-018-2193-3
更新日期：2018-06-13 00:00:00
abstract：BACKGROUND:Two important challenges in the analysis of molecular biology information are data (multi-omic information) integration and the detection of patterns across large scale molecular networks and sequences. They are are actually coupled beause the integration of omic information may provide better means to detec...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-018-2175-5
更新日期：2018-07-09 00:00:00
abstract：BACKGROUND:Drug combinations have the potential to improve efficacy while limiting toxicity. To robustly identify synergistic combinations, high-throughput screens using full dose-response surface are desirable but require an impractical number of data points. Screening of a sparse number of doses per drug allows to sc...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-019-2642-7
更新日期：2019-02-18 00:00:00
abstract：BACKGROUND:Many statistical methods have been proposed to identify disease biomarkers from gene expression profiles. However, from gene expression profile data alone, statistical methods often fail to identify biologically meaningful biomarkers related to a specific disease under study. In this paper, we develop a nove...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-9-416
更新日期：2008-10-06 00:00:00
abstract：BACKGROUND:Deep shotgun sequencing on next generation sequencing (NGS) platforms has contributed significant amounts of data to enrich our understanding of genomes, transcriptomes, amplified single-cell genomes, and metagenomes. However, deep coverage variations in short-read data sets and high sequencing error rates o...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-014-0357-3
更新日期：2014-11-19 00:00:00
abstract：BACKGROUND:The nucleosome is the fundamental packing unit of DNAs in eukaryotic cells. Its detailed positioning on the genome is closely related to chromosome functions. Increasing evidence has shown that genomic DNA sequence itself is highly predictive of nucleosome positioning genome-wide. Therefore a fast software t...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-11-346
更新日期：2010-06-24 00:00:00
abstract：BACKGROUND:Normalization is the process of removing non-biological sources of variation between array experiments. Recent investigations of data in gene expression databases for varying organisms and tissues have shown that the majority of expressed genes exhibit a power-law distribution with an exponent close to -1 (i...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-6-37
更新日期：2005-02-23 00:00:00
abstract：BACKGROUND:Protein-protein interactions (PPIs) play key roles in various cellular functions. In addition, some critical inter-species interactions such as host-pathogen interactions and pathogenicity occur through PPIs. Phytopathogenic bacteria infect hosts through attachment to host tissue, enzyme secretion, exopolysa...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-9-41
更新日期：2008-01-24 00:00:00
abstract：BACKGROUND:Protein aggregation is a significant problem in the biopharmaceutical industry (protein drug stability) and is associated medically with over 40 human diseases. Although a number of computational models have been developed for predicting aggregation propensity and identifying aggregation-prone regions in pro...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-14-314
更新日期：2013-10-28 00:00:00
abstract：BACKGROUND:This paper addresses the prediction of the free energy of binding of a drug candidate with enzyme InhA associated with Mycobacterium tuberculosis. This problem is found within rational drug design, where interactions between drug candidates and target proteins are verified through molecular docking simulatio...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-13-310
更新日期：2012-11-21 00:00:00
abstract：BACKGROUND:A phylogeny is the evolutionary history of a group of organisms. To date, sequence data is still the most used data type for phylogenetic reconstruction. Before any sequences can be used for phylogeny reconstruction, they must be aligned, and the quality of the multiple sequence alignment has been shown to a...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-10-S1-S11
更新日期：2009-01-30 00:00:00
abstract：BACKGROUND:Protein-protein interactions (PPIs) play important roles in various cellular processes. However, the low quality of current PPI data detected from high-throughput screening techniques has diminished the potential usefulness of the data. We need to develop a method to address the high data noise and incomplet...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-11-S7-S8
更新日期：2010-10-15 00:00:00
abstract：BACKGROUND:A metagenomic sample is a set of DNA fragments, randomly extracted from multiple cells in an environment, belonging to distinct, often unknown species. Unsupervised metagenomic clustering aims at partitioning a metagenomic sample into sets that approximate taxonomic units, without using reference genomes. Si...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-017-1466-6
更新日期：2017-03-14 00:00:00
