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Gene Prediction: the End of the Beginning Comment Colin Semple
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central http://genomebiology.com/2000/1/2/reports/4012.1 Meeting report Gene prediction: the end of the beginning comment Colin Semple Address: Department of Medical Sciences, Molecular Medicine Centre, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK. E-mail: [email protected] Published: 28 July 2000 reviews Genome Biology 2000, 1(2):reports4012.1–4012.3 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2000/1/2/reports/4012 © GenomeBiology.com (Print ISSN 1465-6906; Online ISSN 1465-6914) Reducing genomes to genes reports A report from the conference entitled Genome Based Gene All ab initio gene prediction programs have to balance sensi- Structure Determination, Hinxton, UK, 1-2 June, 2000, tivity against accuracy. It is often only possible to detect all organised by the European Bioinformatics Institute (EBI). the real exons present in a sequence at the expense of detect- ing many false ones. Alternatively, one may accept only pre- dictions scoring above a more stringent threshold but lose The draft sequence of the human genome will become avail- those real exons that have lower scores. The trick is to try and able later this year. For some time now it has been accepted increase accuracy without any large loss of sensitivity; this deposited research that this will mark a beginning rather than an end. A vast can be done by comparing the prediction with additional, amount of work will remain to be done, from detailing independent evidence. -
Functional Effects Detailed Research Plan
GeCIP Detailed Research Plan Form Background The Genomics England Clinical Interpretation Partnership (GeCIP) brings together researchers, clinicians and trainees from both academia and the NHS to analyse, refine and make new discoveries from the data from the 100,000 Genomes Project. The aims of the partnerships are: 1. To optimise: • clinical data and sample collection • clinical reporting • data validation and interpretation. 2. To improve understanding of the implications of genomic findings and improve the accuracy and reliability of information fed back to patients. To add to knowledge of the genetic basis of disease. 3. To provide a sustainable thriving training environment. The initial wave of GeCIP domains was announced in June 2015 following a first round of applications in January 2015. On the 18th June 2015 we invited the inaugurated GeCIP domains to develop more detailed research plans working closely with Genomics England. These will be used to ensure that the plans are complimentary and add real value across the GeCIP portfolio and address the aims and objectives of the 100,000 Genomes Project. They will be shared with the MRC, Wellcome Trust, NIHR and Cancer Research UK as existing members of the GeCIP Board to give advance warning and manage funding requests to maximise the funds available to each domain. However, formal applications will then be required to be submitted to individual funders. They will allow Genomics England to plan shared core analyses and the required research and computing infrastructure to support the proposed research. They will also form the basis of assessment by the Project’s Access Review Committee, to permit access to data. -
Algorithms for Computational Biology 8Th International Conference, Alcob 2021 Missoula, MT, USA, June 7–11, 2021 Proceedings
Lecture Notes in Bioinformatics 12715 Subseries of Lecture Notes in Computer Science Series Editors Sorin Istrail Brown University, Providence, RI, USA Pavel Pevzner University of California, San Diego, CA, USA Michael Waterman University of Southern California, Los Angeles, CA, USA Editorial Board Members Søren Brunak Technical University of Denmark, Kongens Lyngby, Denmark Mikhail S. Gelfand IITP, Research and Training Center on Bioinformatics, Moscow, Russia Thomas Lengauer Max Planck Institute for Informatics, Saarbrücken, Germany Satoru Miyano University of Tokyo, Tokyo, Japan Eugene Myers Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany Marie-France Sagot Université Lyon 1, Villeurbanne, France David Sankoff University of Ottawa, Ottawa, Canada Ron Shamir Tel Aviv University, Ramat Aviv, Tel Aviv, Israel Terry Speed Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia Martin Vingron Max Planck Institute for Molecular Genetics, Berlin, Germany W. Eric Wong University of Texas at Dallas, Richardson, TX, USA More information about this subseries at http://www.springer.com/series/5381 Carlos Martín-Vide • Miguel A. Vega-Rodríguez • Travis Wheeler (Eds.) Algorithms for Computational Biology 8th International Conference, AlCoB 2021 Missoula, MT, USA, June 7–11, 2021 Proceedings 123 Editors Carlos Martín-Vide Miguel A. Vega-Rodríguez Rovira i Virgili University University of Extremadura Tarragona, Spain Cáceres, Spain Travis Wheeler University of Montana Missoula, MT, USA ISSN 0302-9743 ISSN 1611-3349 (electronic) Lecture Notes in Bioinformatics ISBN 978-3-030-74431-1 ISBN 978-3-030-74432-8 (eBook) https://doi.org/10.1007/978-3-030-74432-8 LNCS Sublibrary: SL8 – Bioinformatics © Springer Nature Switzerland AG 2021 This work is subject to copyright. -
Reconstructing Contiguous Regions of an Ancestral Genome
Downloaded from www.genome.org on December 5, 2006 Reconstructing contiguous regions of an ancestral genome Jian Ma, Louxin Zhang, Bernard B. Suh, Brian J. Raney, Richard C. Burhans, W. James Kent, Mathieu Blanchette, David Haussler and Webb Miller Genome Res. 2006 16: 1557-1565; originally published online Sep 18, 2006; Access the most recent version at doi:10.1101/gr.5383506 Supplementary "Supplemental Research Data" data http://www.genome.org/cgi/content/full/gr.5383506/DC1 References This article cites 20 articles, 11 of which can be accessed free at: http://www.genome.org/cgi/content/full/16/12/1557#References Open Access Freely available online through the Genome Research Open Access option. Email alerting Receive free email alerts when new articles cite this article - sign up in the box at the service top right corner of the article or click here Notes To subscribe to Genome Research go to: http://www.genome.org/subscriptions/ © 2006 Cold Spring Harbor Laboratory Press Downloaded from www.genome.org on December 5, 2006 Methods Reconstructing contiguous regions of an ancestral genome Jian Ma,1,5,6 Louxin Zhang,2 Bernard B. Suh,3 Brian J. Raney,3 Richard C. Burhans,1 W. James Kent,3 Mathieu Blanchette,4 David Haussler,3 and Webb Miller1 1Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA; 2Department of Mathematics, National University of Singapore, Singapore 117543; 3Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA; 4School of Computer Science, McGill University, Montreal, Quebec H3A 2B4, Canada This article analyzes mammalian genome rearrangements at higher resolution than has been published to date. -
Biocreative II.5 Workshop 2009 Special Session on Digital Annotations
BioCreative II.5 Workshop 2009 Special Session on Digital Annotations The purified IRF-4 was also The main role of BRCA2 shown to be capable of binding appears to involve regulating the DNA in a PU.1-dependent manner function of RAD51 in the repair by by electrophoretic mobility shift homologous recombination . analysis. brca2 irf4 We found that cells ex- Moreover, expression of pressing Olig2, Nkx2.2, and NG2 Carma1 induces phosphorylation were enriched among virus- of Bcl10 and activation of the infected, GFP-positive (GFP+) transcription factor NF-kappaB. cells. carma1 BB I O olig2 The region of VHL medi- The Rab5 effector ating interaction with HIF-1 alpha Rabaptin-5 and its isoform C R E A T I V E overlapped with a putative Rabaptin-5delta differ in their macromolecular binding site within ability to interact with the rsmallab5 the crystal structure. GTPase Rab4. vhl Translocation RCC, bearing We show that ERBB2-dependenterbb2 atf1 TFE3 or TFEB gene fusions, are Both ATF-1 homodimers and tfe3 medulloblastoma cell invasion and ATF-1/CREB heterodimers bind to recently recognized entities for prometastatic gene expression can the CRE but not to the related which risk factors have not been be blocked using the ERBB tyrosine phorbol ester response element. identified. kinase inhibitor OSI-774. C r i t i c a l A s s e s s m e n t o f I n f o r m a t i o n E x t r a c t i o n i n B i o l o g y October 7th - 9th, 2009 www.BioCreative.org BioCreative II.5 Workshop 2009 special session | Digital Annotations Auditorium of the Spanish National -
Computational Biology and Bioinformatics
Vol. 30 ISMB 2014, pages i1–i2 BIOINFORMATICS EDITORIAL doi:10.1093/bioinformatics/btu304 Editorial This special issue of Bioinformatics serves as the proceedings of The conference used a two-tier review system, a continuation the 22nd annual meeting of Intelligent Systems for Molecular and refinement of a process begun with ISMB 2013 in an effort Biology (ISMB), which took place in Boston, MA, July 11–15, to better ensure thorough and fair reviewing. Under the revised 2014 (http://www.iscb.org/ismbeccb2014). The official confer- process, each of the 191 submissions was first reviewed by at least ence of the International Society for Computational Biology three expert referees, with a subset receiving between four and (http://www.iscb.org/), ISMB, was accompanied by 12 Special eight reviews, as needed. These formal reviews were frequently Interest Group meetings of one or two days each, two satellite supplemented by online discussion among reviewers and Area meetings, a High School Teachers Workshop and two half-day Chairs to resolve points of dispute and reach a consensus on tutorials. Since its inception, ISMB has grown to be the largest each paper. Among the 191 submissions, 29 were conditionally international conference in computational biology and bioinfor- accepted for publication directly from the first round review Downloaded from matics. It is expected to be the premiere forum in the field for based on an assessment of the reviewers that the paper was presenting new research results, disseminating methods and tech- clearly above par for the conference. A subset of 16 papers niques and facilitating discussions among leading researchers, were viewed as potentially in the top tier but raised significant practitioners and students in the field. -
Duplication, Deletion, and Rearrangement in the Mouse and Human Genomes
Evolution’s cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes W. James Kent*†, Robert Baertsch*, Angie Hinrichs*, Webb Miller‡, and David Haussler§ *Center for Biomolecular Science and Engineering and §Howard Hughes Medical Institute, Department of Computer Science, University of California, Santa Cruz, CA 95064; and ‡Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802 Edited by Michael S. Waterman, University of Southern California, Los Angeles, CA, and approved July 11, 2003 (received for review April 9, 2003) This study examines genomic duplications, deletions, and rear- depending on details of definition and method. The length rangements that have happened at scales ranging from a single distribution of synteny blocks was found to be consistent with the base to complete chromosomes by comparing the mouse and theory of random breakage introduced by Nadeau and Taylor (8, human genomes. From whole-genome sequence alignments, 344 9) before significant gene order data became available. In recent large (>100-kb) blocks of conserved synteny are evident, but these comparisons of the human and mouse genomes, rearrangements are further fragmented by smaller-scale evolutionary events. Ex- of Ն100,000 bases were studied by comparing 558,000 highly cluding transposon insertions, on average in each megabase of conserved short sequence alignments (average length 340 bp) genomic alignment we observe two inversions, 17 duplications within 300-kb windows. An estimated 217 blocks of conserved (five tandem or nearly tandem), seven transpositions, and 200 synteny were found, formed from 342 conserved segments, with deletions of 100 bases or more. This includes 160 inversions and 75 length distribution roughly consistent with the random breakage duplications or transpositions of length >100 kb. -
BIOINFORMATICS Doi:10.1093/Bioinformatics/Btq499
Vol. 26 ECCB 2010, pages i409–i411 BIOINFORMATICS doi:10.1093/bioinformatics/btq499 ECCB 2010 Organization CONFERENCE CHAIR B. Comparative Genomics, Phylogeny, and Evolution Yves Moreau, Katholieke Universiteit Leuven, Belgium Martijn Huynen, Radboud University Nijmegen Medical Centre, The Netherlands PROCEEDINGS CHAIR Yves Van de Peer, Ghent University & VIB, Belgium Jaap Heringa, Free University of Amsterdam, The Netherlands C. Protein and Nucleotide Structure LOCAL ORGANIZING COMMITTEE Anna Tramontano, University of Rome ‘La Sapienza’, Italy Jan Gorodkin, University of Copenhagen, Denmark Yves Moreau, Katholieke Universiteit Leuven, Belgium Jaap Heringa, Free University of Amsterdam, The Netherlands D. Annotation and Prediction of Molecular Function Gert Vriend, Radboud University, Nijmegen, The Netherlands Yves Van de Peer, University of Ghent & VIB, Belgium Nir Ben-Tal, Tel-Aviv University, Israel Kathleen Marchal, Katholieke Universiteit Leuven, Belgium Fritz Roth, Harvard Medical School, USA Jacques van Helden, Université Libre de Bruxelles, Belgium Louis Wehenkel, Université de Liège, Belgium E. Gene Regulation and Transcriptomics Antoine van Kampen, University of Amsterdam & Netherlands Jaak Vilo, University of Tartu, Estonia Bioinformatics Center (NBIC) Zohar Yakhini, Agilent Laboratories, Tel-Aviv & the Tech-nion, Peter van der Spek, Erasmus MC, Rotterdam, The Netherlands Haifa, Israel STEERING COMMITTEE F. Text Mining, Ontologies, and Databases Michal Linial (Chair), Hebrew University, Jerusalem, Israel Alfonso Valencia, National -
BIOINFORMATICS ISCB NEWS Doi:10.1093/Bioinformatics/Btp280
Vol. 25 no. 12 2009, pages 1570–1573 BIOINFORMATICS ISCB NEWS doi:10.1093/bioinformatics/btp280 ISMB/ECCB 2009 Stockholm Marie-France Sagot1, B.J. Morrison McKay2,∗ and Gene Myers3 1INRIA Grenoble Rhône-Alpes and University of Lyon 1, Lyon, France, 2International Society for Computational Biology, University of California San Diego, La Jolla, CA and 3Howard Hughes Medical Institute Janelia Farm Research Campus, Ashburn, Virginia, USA ABSTRACT Computational Biology (http://www.iscb.org) was formed to take The International Society for Computational Biology (ISCB; over the organization, maintain the institutional memory of ISMB http://www.iscb.org) presents the Seventeenth Annual International and expand the informational resources available to members of the Conference on Intelligent Systems for Molecular Biology bioinformatics community. The launch of ECCB (http://bioinf.mpi- (ISMB), organized jointly with the Eighth Annual European inf.mpg.de/conferences/eccb/eccb.htm) 8 years ago provided for a Conference on Computational Biology (ECCB; http://bioinf.mpi- focus on European research activities in years when ISMB is held inf.mpg.de/conferences/eccb/eccb.htm), in Stockholm, Sweden, outside of Europe, and a partnership of conference organizing efforts 27 June to 2 July 2009. The organizers are putting the finishing for the presentation of a single international event when the ISMB touches on the year’s premier computational biology conference, meeting takes place in Europe every other year. with an expected attendance of 1400 computer scientists, The multidisciplinary field of bioinformatics/computational mathematicians, statisticians, biologists and scientists from biology has matured since gaining widespread recognition in the other disciplines related to and reliant on this multi-disciplinary early days of genomics research. -
Springer A++ Viewer
PublisherInfo PublisherName : BioMed Central PublisherLocation : London PublisherImprintName : BioMed Central European Virtual Institute for Genome Annotation receives €12 million ArticleInfo ArticleID : 4907 ArticleDOI : 10.1186/gb-spotlight-20040127-01 ArticleCitationID : spotlight-20040127-01 ArticleSequenceNumber : 259 ArticleCategory : Research news ArticleFirstPage : 1 ArticleLastPage : 2 RegistrationDate : 2004–1–27 ArticleHistory : OnlineDate : 2004–1–27 ArticleCopyright : BioMed Central Ltd2004 ArticleGrants : ArticleContext : 130594411 Genome Biology Email: [email protected] Janet Thornton, Director of the European Bioinformatics Institute(EBI; Hinxton, UK), is coordinator of the BioSapiens project. "The BioSapiens Network of Excellence ... will coordinate and focus excellent research in bioinformatics, by creating a Virtual Institute for Genome Annotation. The Institute will also establish a permanent European School of Bioinformatics, to train bioinformaticians and to encourage best practice in the exploitation of genome annotation data for biologists," she adds. The annotations will be integrated and made freely accessible via a web portal, and will be used to guide future experiments. Annotations will be integrated using the Open Source Distributed Annotation System(DAS) developed by Lincoln Stein and colleagues at Cold Spring Harbor Laboratory (USA) for exchanging genome annotations. "The development of methods, tools, and servers in close interaction with experimentalists is one feature that distinguishes the -
The 4Th Bologna Winter School: Hot Topics in Structural Genomics†
Comparative and Functional Genomics Comp Funct Genom 2003; 4: 394–396. Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.314 Conference Report The 4th Bologna Winter School: hot topics in structural genomics† Rita Casadio* Department of Biology/CIRB, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy *Correspondence to: Abstract Rita Casadio, Department of Biology/CIRB, University of The 4th Bologna Winter School on Biotechnologies was held on 9–15 February Bologna, Via Irnerio 42, 40126 2003 at the University of Bologna, Italy, with the specific aim of discussing recent Bologna, Italy. developments in bioinformatics. The school provided an opportunity for students E-mail: [email protected] and scientists to debate current problems in computational biology and possible solutions. The course, co-supported (as last year) by the European Science Foundation program on Functional Genomics, focused mainly on hot topics in structural genomics, including recent CASP and CAPRI results, recent and promising genome- Received: 3 June 2003 wide predictions, protein–protein and protein–DNA interaction predictions and Revised: 5 June 2003 genome functional annotation. The topics were organized into four main sections Accepted: 5 June 2003 (http://www.biocomp.unibo.it). Published in 2003 by John Wiley & Sons, Ltd. Predictive methods in structural Predictive methods in functional genomics genomics • Contemporary challenges in structure prediction • Prediction of protein function (Arthur Lesk, and the CASP5 experiment (John Moult, Uni- University of Cambridge, Cambridge, UK). versity of Maryland, Rockville, MD, USA). • Microarray data analysis and mining (Raf- • Contemporary challenges in structure prediction faele Calogero, University of Torino, Torino, (Anna Tramontano, University ‘La Sapienza’, Italy). -
Applications of Case-Based Reasoning in Molecular Biology
Articles Applications of Case-Based Reasoning in Molecular Biology Igor Jurisica and Janice Glasgow ■ Case-based reasoning (CBR) is a computational problems by recalling old problems and their reasoning paradigm that involves the storage and solutions and adapting these previous experi- retrieval of past experiences to solve novel prob- ences represented as cases. A case generally lems. It is an approach that is particularly relevant comprises an input problem, an output solu- in scientific domains, where there is a wealth of data but often a lack of theories or general princi- tion, and feedback in terms of an evaluation of ples. This article describes several CBR systems that the solution. CBR is founded on the premise have been developed to carry out planning, analy- that similar problems have similar solutions. sis, and prediction in the domain of molecular bi- Thus, one of the primary goals of a CBR system ology. is to find the most similar, or most relevant, cases for new input problems. The effective- ness of CBR depends on the quality and quan- tity of cases in a case base. In some domains, even a small number of cases provide good so- lutions, but in other domains, an increased number of unique cases improves problem- he domain of molecular biology can be solving capabilities of CBR systems because characterized by substantial amounts of there are more experiences to draw on. Howev- Tcomplex data, many unknowns, a lack of er, larger case bases can also decrease the effi- complete theories, and rapid evolution; rea- ciency of a system. The reader can find detailed soning is often based on experience rather descriptions of the CBR process and systems in than general knowledge.