Novel domain expansion methods to improve the computational efficiency of the Chemical Master Equation solution for large biological networks.

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

authors： Fan X,Luo G,Huang YS

更新日期：2021-01-15 00:00:00

abstract：BACKGROUND:Testing the dependence of two variables is one of the fundamental tasks in statistics. In this work, we developed an open-source R package (knnAUC) for detecting nonlinear dependence between one continuous variable X and one binary dependent variables Y (0 or 1). RESULTS:We addressed this problem by using k...

journal_title：BMC bioinformatics

authors： Li Y,Liu X,Ma Y,Wang Y,Zhou W,Hao M,Yuan Z,Liu J,Xiong M,Shugart YY,Wang J,Jin L

更新日期：2018-11-22 00:00:00

abstract：BACKGROUND:Lung cancer is the leading cause of the largest number of deaths worldwide and lung adenocarcinoma is the most common form of lung cancer. In order to understand the molecular basis of lung adenocarcinoma, integrative analysis have been performed by using genomics, transcriptomics, epigenomics, proteomics an...

journal_title：BMC bioinformatics

authors： Zengin T,Önal-Süzek T

更新日期：2020-09-30 00:00:00

abstract：BACKGROUND:The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature thus represent an important way by which the efficiency of these processes can be improved. RESULTS:...

journal_title：BMC bioinformatics

authors： Müller HM,Van Auken KM,Li Y,Sternberg PW

更新日期：2018-03-09 00:00:00

abstract：BACKGROUND:The uncovering of genes linked to human diseases is a pressing challenge in molecular biology and precision medicine. This task is often hindered by the large number of candidate genes and by the heterogeneity of the available information. Computational methods for the prioritization of candidate genes can h...

journal_title：BMC bioinformatics

authors： Zampieri G,Tran DV,Donini M,Navarin N,Aiolli F,Sperduti A,Valle G

更新日期：2018-01-25 00:00:00

abstract：BACKGROUND:Understanding the relationship between gene expression changes, enzyme activity shifts, and the corresponding physiological adaptive response of organisms to environmental cues is crucial in explaining how cells cope with stress. For example, adaptation of yeast to heat shock involves a characteristic profil...

journal_title：BMC bioinformatics

authors： Vilaprinyo E,Alves R,Sorribas A

更新日期：2006-04-03 00:00:00

abstract：BACKGROUND:A relevant problem in drug design is the comparison and recognition of protein binding sites. Binding sites recognition is generally based on geometry often combined with physico-chemical properties of the site since the conformation, size and chemical composition of the protein surface are all relevant for ...

journal_title：BMC bioinformatics

authors： Bertolazzi P,Guerra C,Liuzzi G

更新日期：2010-09-29 00:00:00

abstract：BACKGROUND:Membrane transport proteins (transporters) play an essential role in every living cell by transporting hydrophilic molecules across the hydrophobic membranes. While the sequences of many membrane proteins are known, their structure and function is still not well characterized and understood, owing to the imm...

journal_title：BMC bioinformatics

authors： Alballa M,Butler G

更新日期：2020-04-23 00:00:00

abstract：BACKGROUND:Sequence motifs representing transcription factor binding sites (TFBS) are commonly encoded as position frequency matrices (PFM) or degenerate consensus sequences (CS). These formats are used to represent the characterised TFBS profiles stored in transcription factor databases, as well as to represent the po...

journal_title：BMC bioinformatics

authors： Kankainen M,Löytynoja A

更新日期：2007-06-08 00:00:00

abstract：BACKGROUND:For the development of genome assembly tools, some comprehensive and efficiently computable validation measures are required to assess the quality of the assembly. The mostly used N50 measure summarizes the assembly results by the length of the scaffold (or contig) overlapping the midpoint of the length-orde...

journal_title：BMC bioinformatics

authors： Mäkinen V,Salmela L,Ylinen J

更新日期：2012-10-03 00:00:00

abstract：BACKGROUND:Advances in sequencing and genotyping technologies are leading to the widespread availability of multi-species variation data, dense genotype data and large-scale resequencing projects. The 1000 Genomes Project and similar efforts in other species are challenging the methods previously used for storage and m...

journal_title：BMC bioinformatics

authors： Rios D,McLaren WM,Chen Y,Birney E,Stabenau A,Flicek P,Cunningham F

更新日期：2010-05-11 00:00:00

abstract：BACKGROUND:Automatic quantification of neuronal morphology from images of fluorescence microscopy plays an increasingly important role in high-content screenings. However, there exist very few freeware tools and methods which provide automatic neuronal morphology quantification for pharmacological discovery. RESULTS:T...

journal_title：BMC bioinformatics

authors： Ho SY,Chao CY,Huang HL,Chiu TW,Charoenkwan P,Hwang E

更新日期：2011-06-08 00:00:00

abstract：BACKGROUND:Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore that structurally similar proteins can share the same spatial arrangement of secondary structure eleme...

journal_title：BMC bioinformatics

authors： Kolbeck B,May P,Schmidt-Goenner T,Steinke T,Knapp EW

更新日期：2006-11-21 00:00:00

abstract：BACKGROUND:Microarrays permit biologists to simultaneously measure the mRNA abundance of thousands of genes. An important issue facing investigators planning microarray experiments is how to estimate the sample size required for good statistical power. What is the projected sample size or number of replicate chips need...

journal_title：BMC bioinformatics

authors： Page GP,Edwards JW,Gadbury GL,Yelisetti P,Wang J,Trivedi P,Allison DB

更新日期：2006-02-22 00:00:00

abstract：BACKGROUND:Protein structure prediction has achieved a lot of progress during the last few decades and a greater number of models for a certain sequence can be predicted. Consequently, assessing the qualities of predicted protein models in perspective is one of the key components of successful protein structure predict...

journal_title：BMC bioinformatics

authors： Jing X,Dong Q

更新日期：2017-05-25 00:00:00

abstract：BACKGROUND:Visualization software can expose previously undiscovered patterns in genomic data and advance biological science. RESULTS:The Genoviz Software Development Kit (SDK) is an open source, Java-based framework designed for rapid assembly of visualization software applications for genomics. The Genoviz SDK frame...

journal_title：BMC bioinformatics

authors： Helt GA,Nicol JW,Erwin E,Blossom E,Blanchard SG Jr,Chervitz SA,Harmon C,Loraine AE

更新日期：2009-08-25 00:00:00

abstract：BACKGROUND:In omics data integration studies, it is common, for a variety of reasons, for some individuals to not be present in all data tables. Missing row values are challenging to deal with because most statistical methods cannot be directly applied to incomplete datasets. To overcome this issue, we propose a multip...

journal_title：BMC bioinformatics

authors： Voillet V,Besse P,Liaubet L,San Cristobal M,González I

更新日期：2016-10-03 00:00:00

abstract：BACKGROUND:The recent emergence of high-throughput automated image acquisition technologies has forever changed how cell biologists collect and analyze data. Historically, the interpretation of cellular phenotypes in different experimental conditions has been dependent upon the expert opinions of well-trained biologist...

journal_title：BMC bioinformatics

authors： Yin Z,Zhou X,Bakal C,Li F,Sun Y,Perrimon N,Wong ST

更新日期：2008-06-05 00:00:00

abstract：BACKGROUND:Non-coding RNAs gain more attention as their diverse roles in many cellular processes are discovered. At the same time, the need for efficient computational prediction of ncRNAs increases with the pace of sequencing technology. Existing tools are based on various approaches and techniques, but none of them p...

journal_title：BMC bioinformatics

authors： Raasch P,Schmitz U,Patenge N,Vera J,Kreikemeyer B,Wolkenhauer O

更新日期：2010-09-29 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:Microarray technology allows the analysis of genomic aberrations at an ever increasing resolution, making functional interpretation of these vast amounts of data the main bottleneck in routine implementation of high resolution array platforms, and emphasising the need for a centralised and easy to use CNV da...

journal_title：BMC bioinformatics

authors： Vandeweyer G,Reyniers E,Wuyts W,Rooms L,Kooy RF

更新日期：2011-01-05 00:00:00

abstract：BACKGROUND:Oscillatory genes, with periodic expression at the mRNA and/or protein level, have been shown to play a pivotal role in many biological contexts. However, with the exception of the circadian clock and cell cycle, only a few such genes are known. Detecting oscillatory genes from snapshot single-cell experimen...

journal_title：BMC bioinformatics

authors： Cutillo L,Boukouvalas A,Marinopoulou E,Papalopulu N,Rattray M

更新日期：2020-08-21 00:00:00

abstract：BACKGROUND:Observed co-expression of a group of genes is frequently attributed to co-regulation by shared transcription factors. This assumption has led to the hypothesis that promoters of co-expressed genes should share common regulatory motifs, which forms the basis for numerous computational tools that search for th...

journal_title：BMC bioinformatics

authors： Meng G,Mosig A,Vingron M

更新日期：2010-05-20 00:00:00

abstract：BACKGROUND:Kernel-based learning algorithms are among the most advanced machine learning methods and have been successfully applied to a variety of sequence classification tasks within the field of bioinformatics. Conventional kernels utilized so far do not provide an easy interpretation of the learnt representations i...

journal_title：BMC bioinformatics

authors： Meinicke P,Tech M,Morgenstern B,Merkl R

更新日期：2004-10-28 00:00:00

abstract：BACKGROUND:Comparison of metabolic networks is typically performed based on the organisms' enzyme contents. This approach disregards functional replacements as well as orthologies that are misannotated. Direct comparison of the structure of metabolic networks can circumvent these problems. RESULTS:Metabolic networks a...

journal_title：BMC bioinformatics

authors： Forst CV,Flamm C,Hofacker IL,Stadler PF

更新日期：2006-02-14 00:00:00

abstract：BACKGROUND:InterPro is a collection of protein signatures for the classification and automated annotation of proteins. Interproscan is a software tool that scans protein sequences against Interpro member databases using a variety of profile-based, hidden markov model and positional specific score matrix methods. It not...

journal_title：BMC bioinformatics

authors： Kelly RJ,Vincent DE,Friedberg I

更新日期：2010-12-21 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:The methodologies we use both enable and help define our research. However, as experimental complexity has increased the choice of appropriate methodologies has become an increasingly difficult task. This makes it difficult to keep track of available bioinformatics software, let alone the most suitable proto...

journal_title：BMC bioinformatics

authors： Eales JM,Pinney JW,Stevens RD,Robertson DL

更新日期：2008-09-01 00:00:00

abstract：BACKGROUND:Inferring gene regulatory network (GRN) has been an important topic in Bioinformatics. Many computational methods infer the GRN from high-throughput expression data. Due to the presence of time delays in the regulatory relationships, High-Order Dynamic Bayesian Network (HO-DBN) is a good model of GRN. Howeve...

journal_title：BMC bioinformatics

authors： Lo LY,Wong ML,Lee KH,Leung KS

更新日期：2015-11-25 00:00:00

abstract：BACKGROUND:Tumors have been hypothesized to be the result of a mixture of oncogenic events, some of which will be reflected in the gene expression of the tumor. Based on this hypothesis a variety of data-driven methods have been employed to decompose tumor expression profiles into component profiles, hypothetically lin...

journal_title：BMC bioinformatics

authors： van Vliet MH,Wessels LF,Reinders MJ

更新日期：2009-01-30 00:00:00