Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida.

abstract：BACKGROUND:Identifying protein complexes from protein-protein interaction (PPI) network is one of the most important tasks in proteomics. Existing computational methods try to incorporate a variety of biological evidences to enhance the quality of predicted complexes. However, it is still a challenge to integrate diffe...

journal_title：BMC bioinformatics

authors： Xu B,Li K,Zheng W,Liu X,Zhang Y,Zhao Z,He Z

更新日期：2018-12-20 00:00:00

abstract：BACKGROUND:Gene function annotations, which are associations between a gene and a term of a controlled vocabulary describing gene functional features, are of paramount importance in modern biology. Datasets of these annotations, such as the ones provided by the Gene Ontology Consortium, are used to design novel biologi...

journal_title：BMC bioinformatics

authors： Pinoli P,Chicco D,Masseroli M

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Microarray technologies produced large amount of data. The hierarchical clustering is commonly used to identify clusters of co-expressed genes. However, microarray datasets often contain missing values (MVs) representing a major drawback for the use of the clustering methods. Usually the MVs are not treated,...

journal_title：BMC bioinformatics

authors： de Brevern AG,Hazout S,Malpertuy A

更新日期：2004-08-23 00:00:00

abstract：BACKGROUND:Biomedical research projects deal with data management requirements from multiple sources like funding agencies' guidelines, publisher policies, discipline best practices, and their own users' needs. We describe functional and quality requirements based on many years of experience implementing data managemen...

journal_title：BMC bioinformatics

authors： Suhr M,Lehmann C,Bauer CR,Bender T,Knopp C,Freckmann L,Öst Hansen B,Henke C,Aschenbrandt G,Kühlborn LK,Rheinländer S,Weber L,Marzec B,Hellkamp M,Wieder P,Sax U,Kusch H,Nussbeck SY

更新日期：2020-12-17 00:00:00

abstract：BACKGROUND:Cell direct reprogramming technology has been rapidly developed with its low risk of tumor risk and avoidance of ethical issues caused by stem cells, but it is still limited to specific cell types. Direct reprogramming from an original cell to target cell type needs the cell similarity and cell specific regu...

journal_title：BMC bioinformatics

authors： Li L,Che D,Wang X,Zhang P,Rahman SU,Zhao J,Yu J,Tao S,Lu H,Liao M

更新日期：2019-03-04 00:00:00

abstract：BACKGROUND:Profile Hidden Markov Models (pHMMs) are a widely used tool for protein family research. Up to now, however, there exists no method to visualize all of their central aspects graphically in an intuitively understandable way. RESULTS:We present a visualization method that incorporates both emission and transi...

journal_title：BMC bioinformatics

authors： Schuster-Böckler B,Schultz J,Rahmann S

更新日期：2004-01-21 00:00:00

abstract：BACKGROUND:Polychromatic flow cytometry is a popular technique that has wide usage in the medical sciences, especially for studying phenotypic properties of cells. The high-dimensionality of data generated by flow cytometry usually makes it difficult to visualize. The naive solution of simply plotting two-dimensional g...

journal_title：BMC bioinformatics

authors： Raj S,Hussain F,Husein Z,Torosdagli N,Turgut D,Deo N,Pattanaik S,Chang CJ,Jha SK

更新日期：2017-06-07 00:00:00

abstract：BACKGROUND:Coalescent simulations have proven very useful in many population genetics studies. In order to arrive to meaningful conclusions, it is important that these simulations resemble the process of molecular evolution as much as possible. To date, no single coalescent program is able to simulate codon sequences s...

journal_title：BMC bioinformatics

authors： Arenas M,Posada D

更新日期：2007-11-20 00:00:00

abstract：BACKGROUND:Protein-protein interactions (PPIs) are of great importance in cellular systems of organisms, since they are the basis of cellular structure and function and many essential cellular processes are related to that. Most proteins perform their functions by interacting with other proteins, so predicting PPIs acc...

journal_title：BMC bioinformatics

authors： Liu L,Zhu X,Ma Y,Piao H,Yang Y,Hao X,Fu Y,Wang L,Peng J

更新日期：2020-12-16 00:00:00

abstract：BACKGROUND:Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing computational methods for the genome-wide "reverse engineering" of such networks have been successful only for lower eukaryotes with simple genomes. Here we present ARACNE, a n...

journal_title：BMC bioinformatics

authors： Margolin AA,Nemenman I,Basso K,Wiggins C,Stolovitzky G,Dalla Favera R,Califano A

更新日期：2006-03-20 00:00:00

abstract：BACKGROUND:Cancer is a complex disease which is characterized by the accumulation of genetic alterations during the patient's lifetime. With the development of the next-generation sequencing technology, multiple omics data, such as cancer genomic, epigenomic and transcriptomic data etc., can be measured from each indiv...

journal_title：BMC bioinformatics

authors： Wei PJ,Zhang D,Xia J,Zheng CH

更新日期：2016-12-23 00:00:00

abstract：BACKGROUND:Substitution matrices are key parameters for the alignment of two protein sequences, and consequently for most comparative genomics studies. The composition of biological sequences can vary importantly between species and groups of species, and classical matrices such as those in the BLOSUM series fail to ac...

journal_title：BMC bioinformatics

authors： Lemaitre C,Barré A,Citti C,Tardy F,Thiaucourt F,Sirand-Pugnet P,Thébault P

更新日期：2011-11-24 00:00:00

abstract：BACKGROUND:Genome-wide association studies (GWAS) of single nucleotide polymorphisms (SNPs) have been successful in identifying loci contributing genetic effects to a wide range of complex human diseases and quantitative traits. The traditional approach to GWAS analysis is to consider each phenotype separately, despite...

journal_title：BMC bioinformatics

authors： Mägi R,Suleimanov YV,Clarke GM,Kaakinen M,Fischer K,Prokopenko I,Morris AP

更新日期：2017-01-11 00:00:00

abstract：:We developed a new computational technique called Step-Level Differential Response (SLDR) to identify genetic regulatory relationships. Our technique takes advantages of functional genomics data for the same species under different perturbation conditions, therefore complementary to current popular computational techn...

journal_title：BMC bioinformatics

authors： Yue Z,Wan P,Huang H,Xie Z,Chen JY

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments where adjacent segments have different properties, such as different mean values. Despite dozens of algorithms developed to address this problem in genomics research, methods with...

journal_title：BMC bioinformatics

authors： Girimurugan SB,Liu Y,Lung PY,Vera DL,Dennis JH,Bass HW,Zhang J

更新日期：2018-04-11 00:00:00

abstract：BACKGROUND:In bioinformatics community, many tasks associate with matching a set of protein query sequences in large sequence datasets. To conduct multiple queries in the database, a common used method is to run BLAST on each original querey or on the concatenated queries. It is inefficient since it doesn't exploit the...

journal_title：BMC bioinformatics

authors： Ge H,Sun L,Yu J

更新日期：2017-11-21 00:00:00

abstract：BACKGROUND:Computer simulation is a resource which can be employed to identify optimal breeding strategies to effectively and efficiently achieve specific goals in developing improved cultivars. In some instances, it is crucial to assess in silico the options as well as the impact of various crossing schemes and breedi...

journal_title：BMC bioinformatics

authors： Sun X,Mumm RH

更新日期：2016-02-06 00:00:00

abstract：BACKGROUND:Despite the widespread use of high throughput expression platforms and the availability of a desktop implementation of Gene Set Enrichment Analysis (GSEA) that enables non-experts to perform gene set based analyses, the availability of the necessary precompiled gene sets is rare for species other than human....

journal_title：BMC bioinformatics

authors： Powell JA

更新日期：2014-05-17 00:00:00

abstract：BACKGROUND:Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for such analysis but current tools are limited. RESULTS:We have developed InteractiVenn, a more flexible tool for interacting with Venn diagrams includin...

journal_title：BMC bioinformatics

authors： Heberle H,Meirelles GV,da Silva FR,Telles GP,Minghim R

更新日期：2015-05-22 00:00:00

abstract：BACKGROUND:Most state-of-the-art biomedical entity normalization systems, such as rule-based systems, merely rely on morphological information of entity mentions, but rarely consider their semantic information. In this paper, we introduce a novel convolutional neural network (CNN) architecture that regards biomedical e...

journal_title：BMC bioinformatics

authors： Li H,Chen Q,Tang B,Wang X,Xu H,Wang B,Huang D

更新日期：2017-10-03 00:00:00

abstract：BACKGROUND:The BioCreative text mining evaluation investigated the application of text mining methods to the task of automatically extracting information from text in biomedical research articles. We participated in Task 2 of the evaluation. For this task, we built a system to automatically annotate a given protein wit...

journal_title：BMC bioinformatics

authors： Ray S,Craven M

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:Gene expression experiments are common in molecular biology, for example in order to identify genes which play a certain role in a specified biological framework. For that purpose expression levels of several thousand genes are measured simultaneously using DNA microarrays. Comparing two distinct groups of t...

journal_title：BMC bioinformatics

authors： Jung K,Friede T,Beissbarth T

更新日期：2011-07-15 00:00:00

abstract：BACKGROUND:Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological challenge for computational biology which consists in objectively extracting from these data the structu...

journal_title：BMC bioinformatics

authors： Boulos RE,Tremblay N,Arneodo A,Borgnat P,Audit B

更新日期：2017-04-11 00:00:00

abstract：BACKGROUND:Histopathology image analysis is a gold standard for cancer recognition and diagnosis. Automatic analysis of histopathology images can help pathologists diagnose tumor and cancer subtypes, alleviating the workload of pathologists. There are two basic types of tasks in digital histopathology image analysis: i...

journal_title：BMC bioinformatics

authors： Xu Y,Jia Z,Wang LB,Ai Y,Zhang F,Lai M,Chang EI

更新日期：2017-05-26 00:00:00

abstract：BACKGROUND:Gas chromatography coupled with mass spectrometry (GC-MS) is one of the technologies widely used for qualitative and quantitative analysis of small molecules. In particular, GC coupled to single quadrupole MS can be utilized for targeted analysis by selected ion monitoring (SIM). However, to our knowledge, t...

journal_title：BMC bioinformatics

authors： Ranjbar MR,Di Poto C,Wang Y,Ressom HW

更新日期：2015-08-19 00:00:00

abstract：BACKGROUND:Automated protein function prediction methods are needed to keep pace with high-throughput sequencing. With the existence of many programs and databases for inferring different protein functions, a pipeline that properly integrates these resources will benefit from the advantages of each method. However, int...

journal_title：BMC bioinformatics

authors： Yu C,Zavaljevski N,Desai V,Johnson S,Stevens FJ,Reifman J

更新日期：2008-01-25 00:00:00

abstract：BACKGROUND:The identification of protein coding regions (exons) in DNA sequences using signal processing techniques is an important component of bioinformatics and biological signal processing. In this paper, a new method is presented for the identification of exonic regions in DNA sequences. This method is based on th...

journal_title：BMC bioinformatics

authors： Abbasi O,Rostami A,Karimian G

更新日期：2011-11-03 00:00:00

abstract：BACKGROUND:Guide-trees are used as part of an essential heuristic to enable the calculation of multiple sequence alignments. They have been the focus of much method development but there has been little effort at determining systematically, which guide-trees, if any, give the best alignments. Some guide-tree constructi...

journal_title：BMC bioinformatics

authors： Sievers F,Hughes GM,Higgins DG

更新日期：2014-10-04 00:00:00

abstract：BACKGROUND:The rapid growth of protein-protein interaction (PPI) data has led to the emergence of PPI network analysis. Despite advances in high-throughput techniques, the interactomes of several model organisms are still far from complete. Therefore, it is desirable to expand these interactomes with ortholog-based and...

journal_title：BMC bioinformatics

authors： Lee SA,Chan CH,Tsai CH,Lai JM,Wang FS,Kao CY,Huang CY

更新日期：2008-12-12 00:00:00

abstract：BACKGROUND:With the growing availability of full-text articles online, scientists and other consumers of the life sciences literature now have the ability to go beyond searching bibliographic records (title, abstract, metadata) to directly access full-text content. Motivated by this emerging trend, I posed the followin...

journal_title：BMC bioinformatics

authors： Lin J

更新日期：2009-02-03 00:00:00