BiosilicoPub Date : 2003-09-04DOI: 10.1016/S1478-5382(03)02357-6
Melanie R Nelson , Stephanie J Reisinger , Stephen G Henry
{"title":"Designing databases to store biological information","authors":"Melanie R Nelson , Stephanie J Reisinger , Stephen G Henry","doi":"10.1016/S1478-5382(03)02357-6","DOIUrl":"10.1016/S1478-5382(03)02357-6","url":null,"abstract":"<div><p>The increasing amount of data produced by large-scale biological experiments has highlighted the inadequacies of traditional scientific data management methods such as laboratory notebooks. Databases designed to store biological information are becoming increasingly common, but there is little guidance in the literature about the best practices of biological database design. This paper suggests best practices, and provides examples for the implementation of these practices.</p></div>","PeriodicalId":9227,"journal":{"name":"Biosilico","volume":"1 4","pages":"Pages 134-142"},"PeriodicalIF":0.0,"publicationDate":"2003-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1478-5382(03)02357-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76289879","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}
BiosilicoPub Date : 2003-09-04DOI: 10.1016/S1478-5382(03)02341-2
Ping Qiu
{"title":"Computational approaches for deciphering the transcriptional regulatory network by promoter analysis","authors":"Ping Qiu","doi":"10.1016/S1478-5382(03)02341-2","DOIUrl":"10.1016/S1478-5382(03)02341-2","url":null,"abstract":"<div><p>The rapid accumulation of complete genome sequences and the advance of high-throughput expression profiling technology have made a computational approach to the study of transcription regulation networks attractive and feasible. In this review, computational approaches to deciphering the transcriptional regulatory network, including promoter prediction, transcription factor binding site identification, combinatorial regulatory element predictions and transcription factor target gene identification are discussed. The role of comparative genomics in transcription regulatory region analysis is also reviewed.</p></div>","PeriodicalId":9227,"journal":{"name":"Biosilico","volume":"1 4","pages":"Pages 125-133"},"PeriodicalIF":0.0,"publicationDate":"2003-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1478-5382(03)02341-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88549363","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}
BiosilicoPub Date : 2003-09-04DOI: 10.1016/S1478-5382(03)02361-8
Mark Ragan
{"title":"Bioinformatics: a glimpse of the future","authors":"Mark Ragan","doi":"10.1016/S1478-5382(03)02361-8","DOIUrl":"10.1016/S1478-5382(03)02361-8","url":null,"abstract":"","PeriodicalId":9227,"journal":{"name":"Biosilico","volume":"1 4","pages":"Pages 119-120"},"PeriodicalIF":0.0,"publicationDate":"2003-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1478-5382(03)02361-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92704764","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}
BiosilicoPub Date : 2003-09-04DOI: 10.1016/S1478-5382(03)02367-9
Attul Butte
{"title":"Atul Butte discusses the divide between bioinformatics and the clinic","authors":"Attul Butte","doi":"10.1016/S1478-5382(03)02367-9","DOIUrl":"10.1016/S1478-5382(03)02367-9","url":null,"abstract":"<div><p>Atul Butte is an Assistant in Endocrinology and Informatics and Attending Physician at Children's Hospital, Boston, USA (<span>http://www.chip.org</span><svg><path></path></svg>), and is an Instructor in Paediatrics at Harvard Medical School (<span>http://www.harvard.edu</span><svg><path></path></svg>). He received his undergraduate degree in Computer Science from Brown University in 1991, and worked in several stints as a software engineer at Apple Computer and Microsoft Corporation. He graduated from the Brown University School of Medicine in 1995, during which he worked as a research fellow at National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK; <span>http://www.niddk.nih.gov</span><svg><path></path></svg>) through the Howard Hughes/NIH Research Scholars Program. He completed his residency in Paediatrics and Fellowship in Paediatric Endocrinology in 2001, both at Children's Hospital. During his research under Isaac Kohane (at Children's Hospital) he developed a novel methodology for analyzing large data sets of RNA expression, called Relevance Networks. His recent awards include the 2003 Emory University School of Medicine, Pathology Residents’ Choice Award, 2002 American Association for Clinical Chemistry Outstanding Speaker Award, 2002 Endocrine Society Travel Award based on presentation merit, 2001 American Association for Cancer Research Scholar-In-Training Award and the 2001 Lawson Wilkins Paediatric Endocrine Society Clinical Scholar Award.</p></div>","PeriodicalId":9227,"journal":{"name":"Biosilico","volume":"1 4","pages":"Pages 117-119"},"PeriodicalIF":0.0,"publicationDate":"2003-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1478-5382(03)02367-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85517148","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}
BiosilicoPub Date : 2003-09-04DOI: 10.1016/S1478-5382(03)02359-X
Markus H.J. Seifert, Kristina Wolf, Daniel Vitt
{"title":"Virtual high-throughput in silico screening","authors":"Markus H.J. Seifert, Kristina Wolf, Daniel Vitt","doi":"10.1016/S1478-5382(03)02359-X","DOIUrl":"10.1016/S1478-5382(03)02359-X","url":null,"abstract":"<div><p><em>In silico</em> methods may benefit drug discovery and development significantly by saving an average of $130 million and 0.8 years per drug. Virtual high-throughput screening (vHTS) applies <em>in silico</em> approaches, such as docking and alignment, to large virtual molecular databases to enrich biologically active compounds in order to yield lead structures. In an industrial environment, the commonly used ligand-based and receptor-based methods outlined here need to be computationally faster to return the utmost benefit. Intelligent database searching using new fast feedback-driven screening methods appears to be particularly rewarding in terms of both cost and time benefits.</p></div>","PeriodicalId":9227,"journal":{"name":"Biosilico","volume":"1 4","pages":"Pages 143-149"},"PeriodicalIF":0.0,"publicationDate":"2003-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1478-5382(03)02359-X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76355767","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}
BiosilicoPub Date : 2003-09-04DOI: 10.1016/S1478-5382(03)02363-1
David Hodgson
{"title":"Is your software usable?","authors":"David Hodgson","doi":"10.1016/S1478-5382(03)02363-1","DOIUrl":"10.1016/S1478-5382(03)02363-1","url":null,"abstract":"<div><p>‘Ease-of-use…comes from conducting systematic usability engineering activities throughout the project lifecycle.’</p></div>","PeriodicalId":9227,"journal":{"name":"Biosilico","volume":"1 4","pages":"Pages 113-114"},"PeriodicalIF":0.0,"publicationDate":"2003-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1478-5382(03)02363-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79586690","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}
BiosilicoPub Date : 2003-07-01DOI: 10.1016/S1478-5382(03)02344-8
John R. Wakeley
{"title":"John Wakeley discusses theoretical population genetics","authors":"John R. Wakeley","doi":"10.1016/S1478-5382(03)02344-8","DOIUrl":"10.1016/S1478-5382(03)02344-8","url":null,"abstract":"<div><p>John R. Wakeley is Thomas D. Cabot Associate Professor of Biology at the Department of Organismic and Evolutionary Biology, Harvard University (<span>http://www.oeb.harvard.edu/</span><svg><path></path></svg>). His research is theoretical population genetics and molecular evolution, with a focus on the analysis of DNA sequence data, with particular interest in models of population subdivision and the divergence of populations and species. Prof. Wakeley develops statistical models to study genetic and demographic components in the evolution of subpopulations within species. Born in Berkeley, CA, USA, Wakeley obtained a BS and MS in Biology from Stanford University in 1989; he then went on to do a PhD in Integrative Biology from the University of California, Berkeley (1994). Following this, he went to the National Institute of Genetics in Mishima, Japan (1994–1995), then on to do an NIH postdoc at Rutgers University (1995–1998) and moved to Harvard in 1998.</p></div>","PeriodicalId":9227,"journal":{"name":"Biosilico","volume":"1 3","pages":"Pages 84-85"},"PeriodicalIF":0.0,"publicationDate":"2003-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1478-5382(03)02344-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80195227","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}
BiosilicoPub Date : 2003-07-01DOI: 10.1016/S1478-5382(03)02343-6
J.C. Louis
{"title":"Correcting ascertainment bias is no mere entertainment","authors":"J.C. Louis","doi":"10.1016/S1478-5382(03)02343-6","DOIUrl":"10.1016/S1478-5382(03)02343-6","url":null,"abstract":"","PeriodicalId":9227,"journal":{"name":"Biosilico","volume":"1 3","pages":"Pages 81-82"},"PeriodicalIF":0.0,"publicationDate":"2003-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1478-5382(03)02343-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77199608","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}
BiosilicoPub Date : 2003-07-01DOI: 10.1016/S1478-5382(03)02315-1
Sergey E. Ilyin, Albert Pinhasov, Anil H. Vaidya, Frank A. Amato, Jack Kauffman, Hong Xin, Patricia Andrade-Gordon, Carlos R. Plata-Salamán, Douglas E. Brenneman
{"title":"Emerging paradigms in applied bioinformatics","authors":"Sergey E. Ilyin, Albert Pinhasov, Anil H. Vaidya, Frank A. Amato, Jack Kauffman, Hong Xin, Patricia Andrade-Gordon, Carlos R. Plata-Salamán, Douglas E. Brenneman","doi":"10.1016/S1478-5382(03)02315-1","DOIUrl":"10.1016/S1478-5382(03)02315-1","url":null,"abstract":"","PeriodicalId":9227,"journal":{"name":"Biosilico","volume":"1 3","pages":"Pages 86-88"},"PeriodicalIF":0.0,"publicationDate":"2003-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1478-5382(03)02315-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76226754","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}
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