scDC: single cell differential composition analysis.

abstract：BACKGROUND:For many types of analyses, data about gene structure and locations of non-coding regions of genes are required. Although a vast amount of genomic sequence data is available, precise annotation of genes is lacking behind. Finding the corresponding gene of a given protein sequence by means of conventional too...

journal_title：BMC bioinformatics

authors： Keller O,Odronitz F,Stanke M,Kollmar M,Waack S

更新日期：2008-06-13 00:00:00

abstract：BACKGROUND:Automated protein function prediction methods are the only practical approach for assigning functions to genes obtained from model organisms. Many of the previously reported function annotation methods are of limited utility for fungal protein annotation. They are often trained only to one species, are not a...

journal_title：BMC bioinformatics

authors： Jung J,Yi G,Sukno SA,Thon MR

更新日期：2010-04-29 00:00:00

abstract：BACKGROUND:The computation of phylogenetic trees on the same set of species that are based on different orthologous genes can lead to incongruent trees. One possible explanation for this behavior are interspecific hybridization events recombining genes of different species. An important approach to analyze such events ...

journal_title：BMC bioinformatics

authors： Albrecht B

更新日期：2015-07-30 00:00:00

abstract：BACKGROUND:The inference of homology between proteins is a key problem in molecular biology The current best approaches only identify approximately 50% of homologies (with a false positive rate set at 1/1000). RESULTS:We present Homology Induction (HI), a new approach to inferring homology. HI uses machine learning to...

journal_title：BMC bioinformatics

authors： Karwath A,King RD

更新日期：2002-04-23 00:00:00

abstract：BACKGROUND:Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematica...

journal_title：BMC bioinformatics

authors： Chain B,Bowen H,Hammond J,Posch W,Rasaiyaah J,Tsang J,Noursadeghi M

更新日期：2010-06-24 00:00:00

abstract：BACKGROUND:Chemical cross-linking is used for protein-protein contacts mapping and for structural analysis. One of the difficulties in cross-linking studies is the analysis of mass-spectrometry data and the assignment of the site of cross-link incorporation. The difficulties are due to higher charges of fragment ions, ...

journal_title：BMC bioinformatics

authors： Jaiswal M,Crabtree N,Bauer MA,Hall R,Raney KD,Zybailov BL

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:High-throughput sequencing technologies, such as the Illumina Genome Analyzer, are powerful new tools for investigating a wide range of biological and medical questions. Statistical and computational methods are key for drawing meaningful and accurate conclusions from the massive and complex datasets generat...

journal_title：BMC bioinformatics

authors： Bullard JH,Purdom E,Hansen KD,Dudoit S

更新日期：2010-02-18 00:00:00

abstract：BACKGROUND:Short oligonucleotide arrays have several probes measuring the expression level of each target transcript. Therefore the selection of probes is a key component for the quality of measurements. However, once probes have been selected and synthesized on an array, it is still possible to re-evaluate the results...

journal_title：BMC bioinformatics

authors： Gautier L,Møller M,Friis-Hansen L,Knudsen S

更新日期：2004-08-14 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNA) are regulatory genes that target and repress other RNA molecules via sequence-specific binding. Several biological processes are regulated across many organisms by evolutionarily conserved miRNAs. Plants and invertebrates employ their miRNA in defense against viruses by targeting and degrad...

journal_title：BMC bioinformatics

authors： Carl JW Jr,Trgovcich J,Hannenhalli S

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Reliable prediction of antibody, or B-cell, epitopes remains challenging yet highly desirable for the design of vaccines and immunodiagnostics. A correlation between antigenicity, solvent accessibility, and flexibility in proteins was demonstrated. Subsequently, Thornton and colleagues proposed a method for ...

journal_title：BMC bioinformatics

authors： Ponomarenko J,Bui HH,Li W,Fusseder N,Bourne PE,Sette A,Peters B

更新日期：2008-12-02 00:00:00

abstract：BACKGROUND:Knowledge of when and in which cells each gene is expressed across multicellular organisms is critical in understanding both gene function and regulation of cell type diversity. However, methods for measuring expression typically involve a trade-off between imaging-based methods, which give the precise locat...

journal_title：BMC bioinformatics

authors： Burdick JT,Murray JI

更新日期：2013-06-22 00:00:00

abstract：BACKGROUND:As a rule, peptides are more flexible and unstructured than proteins with their substantial stabilizing hydrophobic cores. Nevertheless, a few stably folding peptides have been discovered. This raises the question whether there may be more such peptides that are unknown as yet. These molecules could be helpf...

journal_title：BMC bioinformatics

authors： Gronwald W,Hohm T,Hoffmann D

更新日期：2008-02-19 00:00:00

abstract：BACKGROUND:Existing large-scale metabolic models of sequenced organisms commonly include enzymatic functions which can not be attributed to any gene in that organism. Existing computational strategies for identifying such missing genes rely primarily on sequence homology to known enzyme-encoding genes. RESULTS:We pres...

journal_title：BMC bioinformatics

authors： Kharchenko P,Chen L,Freund Y,Vitkup D,Church GM

更新日期：2006-03-29 00:00:00

abstract：BACKGROUND:Transcription factor binding sites (TFBSs) are crucial in the regulation of gene transcription. Recently, chromatin immunoprecipitation followed by cDNA microarray hybridization (ChIP-chip array) has been used to identify potential regulatory sequences, but the procedure can only map the probable protein-DNA...

journal_title：BMC bioinformatics

authors： Lu CC,Yuan WH,Chen TM

更新日期：2008-12-12 00:00:00

abstract：BACKGROUND:Microbial electrosynthesis and electro fermentation are techniques that aim to optimize microbial production of chemicals and fuels by regulating the cellular redox balance via interaction with electrodes. While the concept is known for decades major knowledge gaps remain, which make it hard to evaluate its ...

journal_title：BMC bioinformatics

authors： Kracke F,Krömer JO

更新日期：2014-12-30 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

authors： Ranjard L,Wong TKF,Rodrigo AG

更新日期：2020-01-22 00:00:00

abstract：BACKGROUND:Mass spectrometry based peptide mass fingerprints (PMFs) offer a fast, efficient, and robust method for protein identification. A protein is digested (usually by trypsin) and its mass spectrum is compared to simulated spectra for protein sequences in a database. However, existing tools for analyzing PMFs oft...

journal_title：BMC bioinformatics

authors： Kaltenbach HM,Wilke A,Böcker S

更新日期：2007-03-26 00:00:00

abstract：BACKGROUND:Many proteins contain conserved sequence patterns (motifs) that contribute to their functionality. The process of experimentally identifying and validating novel protein motifs can be difficult, expensive, and time consuming. A means for helping to identify in advance the possible function of a novel motif i...

journal_title：BMC bioinformatics

authors： Bristow F,He R,Van Domselaar G

更新日期：2011-09-26 00:00:00

abstract：BACKGROUND:Mixed models have a long and fruitful history in statistics. They are pertinent to genomics problems because they are highly versatile, accommodating a wide variety of situations within the same theoretical and algorithmic framework. RESULTS:Qxpak is a package for versatile statistical genomics, specificall...

journal_title：BMC bioinformatics

authors： Pérez-Enciso M,Misztal I

更新日期：2011-05-25 00:00:00

abstract：BACKGROUND:Common existing phylogenetic tree visualisation tools are not able to display readable trees with more than a few thousand nodes. These existing methodologies are based in two dimensional space. RESULTS:We introduce the idea of visualising phylogenetic trees in three dimensional hyperbolic space with the Wa...

journal_title：BMC bioinformatics

authors： Hughes T,Hyun Y,Liberles DA

更新日期：2004-04-29 00:00:00

abstract：BACKGROUND:Transposable elements (TEs) are DNA sequences that are able to move from their location in the genome by cutting or copying themselves to another locus. As such, they are increasingly recognized as impacting all aspects of genome function. With the dramatic reduction in cost of DNA sequencing, it is now poss...

journal_title：BMC bioinformatics

authors： Gilly A,Etcheverry M,Madoui MA,Guy J,Quadrana L,Alberti A,Martin A,Heitkam T,Engelen S,Labadie K,Le Pen J,Wincker P,Colot V,Aury JM

更新日期：2014-11-19 00:00:00

abstract：BACKGROUND:Many practical tasks in biomedicine require accessing specific types of information in scientific literature; e.g. information about the results or conclusions of the study in question. Several schemes have been developed to characterize such information in scientific journal articles. For example, a simple ...

journal_title：BMC bioinformatics

authors： Guo Y,Korhonen A,Liakata M,Silins I,Hogberg J,Stenius U

更新日期：2011-03-08 00:00:00

abstract：BACKGROUND:Complex networks are studied across many fields of science and are particularly important to understand biological processes. Motifs in networks are small connected sub-graphs that occur significantly in higher frequencies than in random networks. They have recently gathered much attention as a useful concep...

journal_title：BMC bioinformatics

authors： Kashani ZR,Ahrabian H,Elahi E,Nowzari-Dalini A,Ansari ES,Asadi S,Mohammadi S,Schreiber F,Masoudi-Nejad A

更新日期：2009-10-04 00:00:00

abstract：BACKGROUND:Recent studies have shown that copy number variations (CNVs) are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly ass...

journal_title：BMC bioinformatics

authors： Gai X,Perin JC,Murphy K,O'Hara R,D'arcy M,Wenocur A,Xie HM,Rappaport EF,Shaikh TH,White PS

更新日期：2010-02-04 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

authors： Amzallag A,Ramaswamy S,Benes CH

更新日期：2019-02-18 00:00:00

abstract：BACKGROUND:The scientific literature contains millions of microbial gene identifiers within the full text and tables, but these annotations rarely get incorporated into public sequence databases. We propose to utilize the Open Access (OA) subset of PubMed Central (PMC) as a gene annotation database and have developed a...

journal_title：BMC bioinformatics

authors： Stubben CJ,Challacombe JF

更新日期：2014-02-05 00:00:00

abstract：BACKGROUND:Computational and visual data analysis for genomics has traditionally involved a combination of tools and resources, of which the most ubiquitous consist of genome browsers, focused mainly on integrative visualization of large numbers of big datasets, and computational environments, focused on data modeling ...

journal_title：BMC bioinformatics

authors： Chelaru F,Corrada Bravo H

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:A common method for presenting and studying biological interaction networks is visualization. Software tools can enhance our ability to explore network visualizations and improve our understanding of biological systems, particularly when these tools offer analysis capabilities. However, most published networ...

journal_title：BMC bioinformatics

authors： Macpherson JI,Pinney JW,Robertson DL

更新日期：2009-03-26 00:00:00

abstract：BACKGROUND:Machine learning has been utilized to predict cancer drug response from multi-omics data generated from sensitivities of cancer cell lines to different therapeutic compounds. Here, we build machine learning models using gene expression data from patients' primary tumor tissues to predict whether a patient wi...

journal_title：BMC bioinformatics

authors： Clayton EA,Pujol TA,McDonald JF,Qiu P

更新日期：2020-09-30 00:00:00

abstract：BACKGROUND:We study the statistical properties of fragment coverage in genome sequencing experiments. In an extension of the classic Lander-Waterman model, we consider the effect of the length distribution of fragments. We also introduce a coding of the shape of the coverage depth function as a tree and explain how thi...

journal_title：BMC bioinformatics

authors： Evans SN,Hower V,Pachter L

更新日期：2010-08-18 00:00:00