Journal of bioinformatics最新文献_第3页

Software patents in Bioinformatics 生物信息学中的软件专利

Journal of bioinformatics Pub Date : 2006-06-15 DOI: 10.1093/bioinformatics/btl166

A. Valencia, A. Bateman

{"title":"Software patents in Bioinformatics","authors":"A. Valencia, A. Bateman","doi":"10.1093/bioinformatics/btl166","DOIUrl":"https://doi.org/10.1093/bioinformatics/btl166","url":null,"abstract":"Bioinformatics has published papers describing new software for over 20 years (Nilsson and Klein 1985). During this time the world of software has changed considerably particularly with the irresistible rise of initiatives to build freely accessible software as has opening access to data resources. The Internet and the Web have also changed the way we use and distribute software. This social and technical revolution is also changing the structure of the relations between commercial and academic software-based activities , for which patents and software protection are key elements. In this and the following issue we publish two editorials addressing the general topics of software accessibility, patents and intellectual property. In this issue, Steven L. Salzberg and John Quackenbush (past and present Associate Editors, respectively) present one perspective on the issue. In the next issue another of our Associate Editors, Jonathan D. Wren will put forward a different perspective. We welcome additional contributions to this discussion from our readership, which will help the journal in the process of adapting our publication guidelines to better serve the development of Bioinformatics. (1985) SEQ-ED: an interactive computer program for editing, analysis and storage of long DNA sequences.","PeriodicalId":90576,"journal":{"name":"Journal of bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2006-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75863423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Bioinformatics - The new home for protein sequence motifs 生物信息学-蛋白质序列基序的新家园

Journal of bioinformatics Pub Date : 2006-01-01 DOI: 10.1093/bioinformatics/bti755

A. Bateman

{"title":"Bioinformatics - The new home for protein sequence motifs","authors":"A. Bateman","doi":"10.1093/bioinformatics/bti755","DOIUrl":"https://doi.org/10.1093/bioinformatics/bti755","url":null,"abstract":"Protein domains and sequence motifs have been very influential in the field of molecular biology. These units are the common currency of protein structure and function. The Protein Sequence Motifs series in Trends in Biochemical Sciences was an extremely popular forum to publish these results, but sadly the journal published the final one in 2004 (McEntyre and Gibson 2004). Bioinformatics is well placed to publish reports of novel protein domains and over the past year we have published reports of the MEDs and PocR domains (Anantharaman and Aravind, 2005), the G5 domain (Bateman et al., 2005), the Why domain (Ciccarelli and Bork 2005) and the OCRE domain (Callebaut and Mornon 2005). In this issue we publish the PilZ domain (pronounced ‘pills’) by Amikam and Galperin (2005). This manuscript strongly suggests that the PilZ domain mediates binding to c-di-GMP a universal bacterial second messenger. Because the PilZ is found in hundreds of bacterial proteins this work will have a large impact in understanding bacteria. I would like to invite you to submit your next novel domain finding as a Discovery Note to Bioinformatics. We will also consider papers that describe the unification of existing protein families and domains into a larger superfamily. Discovery notes are papers intended for the reporting of biologically interesting discoveries using computational techniques. Discovery notes can be up to 4 journal pages length. The instructions to authors can be found at the following URL: http://www.oxfordjournals.org/bioinformatics/ for_authors/general.html If you would like a quick assessment of your domain discovery please send me a pre-submission enquiry outlining the domain and the biological significance of the finding.","PeriodicalId":90576,"journal":{"name":"Journal of bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80030755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

An update from the Bioinformatics Editors 来自生物信息学编辑的更新

Journal of bioinformatics Pub Date : 2005-12-15 DOI: 10.1093/bioinformatics/bti768

A. Bateman, A. Valencia

引用次数: 0

The Fifth Georgia Tech - Oak Ridge National Laboratory International Conference in Bioinformatics: in silico Biology, Computational Genomics and Evolutionary Biology 第五届佐治亚理工学院-橡树岭国家实验室生物信息学国际会议:硅生物学、计算基因组学和进化生物学

Journal of bioinformatics Pub Date : 2005-02-01 DOI: 10.1093/bioinformatics/bti1207

M. Borodovsky, A. Rzhetsky, D. Frishman

引用次数: 0

Increasing the Impact of Bioinformatics 增加生物信息学的影响

Journal of bioinformatics Pub Date : 2005-01-01 DOI: 10.1093/bioinformatics/bti185

A. Valencia, A. Bateman

引用次数: 6

New Leadership for Bioinformatics 生物信息学的新领导

Journal of bioinformatics Pub Date : 2004-08-12 DOI: 10.1093/bioinformatics/bth403

A. Bateman, A. Valencia

引用次数: 2

Guest Editor Preface: Plant & Animal Genome (PAG) Meeting Bioinformatics Session Paper Competition 客座编辑序言:植物与动物基因组(PAG)会议生物信息学会议论文竞赛

Journal of bioinformatics Pub Date : 2004-01-22 DOI: 10.1093/bioinformatics/bth016

R. Bruskiewich

{"title":"Guest Editor Preface: Plant & Animal Genome (PAG) Meeting Bioinformatics Session Paper Competition","authors":"R. Bruskiewich","doi":"10.1093/bioinformatics/bth016","DOIUrl":"https://doi.org/10.1093/bioinformatics/bth016","url":null,"abstract":"In the field of science, not all experiments take place in the laboratory. In some cases, experiments can be organizational to explore a new way of doing things. Scientific workshops at the annual Plant & Animal Genome (PAG) conference in San Diego have traditionally followed a format of coordinator-invited presentations. Based on feedback from PAG meeting attendees in 2003 concerning the meeting’s bioinformatics workshops and inspired by the paper-driven format of other international bioinformatics meetings, a different workshop format for bioinformatics was proposed for 2004: an invited keynote speaker presenting a review of specified methodology in the field, followed by presentation of selected papers from a first ever PAG bioinformatics paper competition. The theme of the competitive papers was requested to be ‘bioinformatics applied to answer specific plant and/or animal genome research questions’. As an added incentive for prospective authors, the workshop organizer negotiated with Bioinformatics, to publish the keynote review paper and the five selected papers chosen by a formal process of peer review. I am now pleased to introduce these keynote and five selected papers of the competition, published in this special section of Bioinformatics:","PeriodicalId":90576,"journal":{"name":"Journal of bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2004-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77893830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Growth in Bioinformatics 生物信息学的发展

Journal of bioinformatics Pub Date : 2003-01-01 DOI: 10.1093/bioinformatics/19.1.1

C. Sander

引用次数: 27

The Fourth Georgia Tech-University of Georgia International Conference in Bioinformatics: in silico Biology, Biological Networks, from Genomics to Epidemiology (November 13-16, 2003, Atlanta, Georgia, USA) 第四届佐治亚理工大学生物信息学国际会议:从基因组学到流行病学的硅生物学、生物网络(2003年11月13-16日，美国佐治亚州亚特兰大)

Journal of bioinformatics Pub Date : 2003-01-01 DOI: 10.1093/bioinformatics/btg365

{"title":"The Fourth Georgia Tech-University of Georgia International Conference in Bioinformatics: in silico Biology, Biological Networks, from Genomics to Epidemiology (November 13-16, 2003, Atlanta, Georgia, USA)","authors":"","doi":"10.1093/bioinformatics/btg365","DOIUrl":"https://doi.org/10.1093/bioinformatics/btg365","url":null,"abstract":"Three previous bioinformatics meetings organized by Georgia Tech were held in Atlanta in 1997, 1999 and 2001 have attracted outstanding researchers from 14 countries around the globe and established this conference as a major academic forum for intensive and open exchange of new ideas. This year we again have invited many rising junior scientists to deliver plenary lectures on their discoveries made in silico, with many of these accomplishments driven by the explosion of genomic and proteomic data. The focus of the 2003 conference, in comparison with the previous ones, has shifted even further to the most complicated aspects of genomics and proteomics manifested by the impressive advances in creating consistent models of networks of cellular processes (http://opal. biology.gatech.edu/GeneMark/conference/). Other changes include the University of Georgia joining Georgia Tech as a co-organizer of the meeting and a move of the conference site to the brand new Georgia Tech Conference Center & Hotel opened in the Midtown area extension of Georgia Tech campus near the Atlanta Arts Center and the city’s historic area. Several papers presented at the conference are included in this current Special Issue of Bioinformatics, with their publication serving a parallel avenue of presentation for conference participants. Seven papers out of seventeen submitted manuscripts successfully passed peer review and were accepted for publication. The paper by Rocco and Critchlow describes a method for scanning the internet to identify web sites with particular functionalities and developing wrappers for automatic queries of those sites. They tested it on sites that perform BLAST searches and showed reasonable success at automatic classification and query submission. An important aspect of the work is the ability of the system to learn the appropriate queries. This is an important and very challenging problem and this paper offers interesting algorithmic ideas. Qian, Lin, Luscombe, Yu and Gerstein address the important and challenging computational problem of defining relationships between transcription factors (TFs) and their target genes. They apply support vector machines to microarray expression data to generate novel predictions from known interactions. Interestingly, their approach does not use DNA sequence information. Existing databases of experimentally confirmed TF-target pairs only contain positive examples, so the authors are careful to construct a balanced set of both positive and negative training data. The resulting database ofin silico predictions of TF-target pairs is a valuable complement to the information that can be derived from chromatin-immunoprecipitation microarray (‘ChIP on a chip’) experiments. Lukashin, Lukashev and Fuchs attack the problems of inference of topology of gene regulation networks that manifests itself in capricious patterns of gene expression in microarray experiments. They verify that genetic networks have many properties, such ","PeriodicalId":90576,"journal":{"name":"Journal of bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86464107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Journal Bioinformatics, key medium for computational biology 生物信息学杂志，计算生物学的关键媒介

Journal of bioinformatics Pub Date : 2002-01-01 DOI: 10.1093/bioinformatics/18.1.1

C. Sander

引用次数: 22