DOCSLIB.ORG

Editorial News Issue 7 • 2014

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Editorial News Issue 7 • 2014 EDITORIAL NEWS ISSUE 7 • 2014 01001010001100001010000101000100001111100 10100010010010001001000101101001111101010Welcome to the 2014 Bioinformatics Editorial Newsletter Bioinformatics continues to go from strength to strength thanks to our authors, 10001010101001010100001010100101010100100reviews, board members and editors. We would like to take this opportunity to thank everyone who has supported the journal this year. Submissions have increased again to nearly 2300 in 2014, and we appreciate the support from reviewers to help us 10101010010101001001000100000010111101001process these papers. More authors are choosing to publish their papers under an open access licence, with uptake reaching 27% in 2014. 00010100100010101001010100100101000110000As always we very much welcome your suggestions for new developments, review or editorial topics, and feedback on any aspect of the journal. 10100001010001000011111001010001001001000Best regards The Bioinformatics Editor team, [email protected] 10010001011010011111010100010101010010101 Editorial Office and Reviews Update 00001010100101010100100101010010101001010Production Update Reviews published this year have covered topics including: 100100100010000001011110100100010100100012014 f Toward better understanding of artifacts in variant calling from high-coverage samples (http://bioinformatics.oxfordjournals.org/ 01010010101010010100101Submissions 2295 content/30/20/2843.abstract) f Challenges in RNA virus bioinformatics (http://bioinformatics.oxfordjournals.org/ Acceptance rate 33% 1011 content/30/13/1793.abstract) Algorithms and tools for protein–protein Time from submission to first f 37 days interaction networks clustering, with decision (average) 101 a special focus on population-based stochastic methods (http://bioinformatics. Advance Access online publication 5 days oxfordjournals.org/content/30/10/1343. 10 time (average) abstract) 1 Issue publication time (average) 49 days Optional open access uptake 27% 0100101000110000101000010100010000111110 0101000100100100010010001011010011111010 Here are the top 10 cited articles published in 2014: 1010001010101001010100001010100101010100Title Authors Issue Pages Citations RAxML version 8: a tool for 1001010101001010100100100010000001011110phylogenetic analysis and post- Stamatakis, Alexandros 9 1312 87 analysis of large phylogenies 1001000101001000101010010101001001010001Trimmomatic: a flexible trimmer for Bolger, Anthony M.; Lohse, Marc; 15 2114 38 Illumina sequence data Usadel, Bjoern 1000010100001010001000011111001010001001 Combining evolutionary information extracted from frequency profiles Liu, Bin; Zhang, Deyuan; Xu, 4 472 32 with sequence-based kernels for Ruifeng; et al. 0010001001000101101001111101010001010101protein remote homology detection iNuc-PseKNC: a sequence-based 0010101000010101001010101001001010100101predictor for predicting nucleosome Guo, Shou-Hui; Deng, En-Ze; Xu, 11 1522 25 positioning in genomes with pseudo Li-Qin; et al. 0100101010010010001000000101111010010001k-tuple nucleotide composition Causal analysis approaches in Kraemer, Andreas; Green, Jeff; 4 523 25 01001000101010010101010010100101Ingenuity Pathway Analysis Pollard, Jack, Jr.; et al. InterProScan 5: genome-scale pro- Jones, Philip; Binns, David; 9 1236 19 1011tein function classification Chang, Hsin-Yu; et al. DIYABC v2.0: a software to make approximate Bayesian computation inferences about population Cornuet, Jean-Marie; Pudlo, 8 1187 19 history using single nucleotide Pierre; Veyssier, Julien; et al. polymorphism, DNA sequence and microsatellite data featureCounts: an efficient general Liao, Yang; Smyth, Gordon K.; purpose program for assigning 7 923 16 Shi, Wei sequence reads to genomic features Protter: interactive protein feature Omasits, Ulrich; Ahrens, Chris- visualization and integration with 6 884 16 tian H.; Mueller, Sebastian; et al. experimental proteomic data Prokka: rapid prokaryotic genome Seemann, Torsten 14 2068 14 annotation 0100101000110000101000010100010000111110010100010010010 0010010001011010011111010101000101010100101010000101010 0101010100100101010100101010010010001000000101111010010 0100101000110000101000010100010000111110 0101000100100100010010001011010011111010 1010001010101001010100001010100101010100Conferences Bioinformatics has been represented at a number 1001010101001010100100100010000001011110of conferences this year, including of course ISMB 2014 in Boston, where the HiTSeq SIG was held as usual. Selected papers from HiTSeq can be found here: http://bioinformatics.oxfordjournals.org/ 1001000101001000101010010101001001010001content/30/24.toc#HITSEQPAPERS. 1000010100001010001000011111001010001001 IMPROVER Challenge special issue 0010001001000101101001111101010001010101Bioinformatics also published selected papers from the sbv IMPROVER Challenge, which can be found here: 0010101000010101001010101001001010100101http://bioinformatics.oxfordjournals.org/content/31/4 . 0100101010010010001000000101111010010001 New Impact Factor 01001000101010010101010010100101The Bioinformatics impact factor for 2014 was 4.621. The journal is ranked fourth in the Mathematical and Computational Biology category. 1011 4.621 ISCB articles Bioinformatics is an official journal of ISCB, and we have collected together the ISCB articles published in the journal over the past year (http://www. oxfordjournals.org/our_journals/bioinformatics/iscb_ articles.html). 0100101000110000101000010100010000111110010100010010010 0010010001011010011111010101000101010100101010000101010 0101010100100101010100101010010010001000000101111010010 0100101000110000101000010100010000111110 0101000100100100010010001011010011111010 1010001010101001010100001010100101010100Executive Editors John Hancock, UK Honorary Editors Janet Kelso, Germany Igor Jurisica, Canada Alex Bateman, UK Ivo Hofacker, Austria 1001010101001010100100100010000001011110Alfonso Valencia, Spain Martin Bishop, UK David Posada, Spain Cristos Ouzounis, Greece Associate Editors Burkhard Rost, USA Chris Sander, USA 1001000101001000101010010101001001010001Ziv Bar-Joseph, USA Anna Tramontano, Italy Gary Stormo, USA Inanc Birol, Canada Jonathan Wren, USA 1000010100001010001000011111001010001001Michael Brudno, Canada Robert Murphy, USA 0010001001000101101001111101010001010101 Editorial Board C Hodgman, UK P Park, USA 0010101000010101001010101001001010100101V Bafna, USA L Holm, Finland H Peng, USA S Brunak, Denmark W Huber, UK P Radivojac, USA 0100101010010010001000000101111010010001K A Crandall, USA T Ideker, USA C Sahinalp, Canada J Dopazo, Spain L Jensen, Germany C Seoighe, Irelend 01001000101010010101010010100101D Frishman, Germany A Navarro, Spain M Vingron, Germany D Higgins, Ireland C Ouzounis, UK 1011 How editorial board members can support Bioinformatics You can help us in a number of ways by: f acting as reviewers and identifying colleagues who might review manuscripts for the journal; f evaluating manuscripts in difficult cases where we need an extra solid opinion; f writing editorials and reviews, or suggesting review topics and authors; f contributing advice and ideas on the future development of the journal; f helping to raise awareness of the journal. We also see the Editorial Board as a good source of future Associate Editors, so if you would be interested in taking on such a role, let us know. 0100101000110000101000010100010000111110010100010010010 0010010001011010011111010101000101010100101010000101010 0101010100100101010100101010010010001000000101111010010.
Load more

Recommended publications
  • Ismb/Eccb 2015
    Research Collection Journal Article ISMB/ECCB 2015 Author(s): Moreau, Yves; Beerenwinkel, Niko Publication Date: 2015 Permanent Link: https://doi.org/10.3929/ethz-b-000102416 Originally published in: Bioinformatics 31(12), http://doi.org/10.1093/bioinformatics/btv303 Rights / License: Creative Commons Attribution-NonCommercial 4.0 International This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library Bioinformatics, 31, 2015, i1–i2 doi: 10.1093/bioinformatics/btv303 ISMB/ECCB 2015 Editorial ISMB/ECCB 2015 This special issue of Bioinformatics serves as the proceedings of the 175 external reviewers recruited as sub-reviewers by program com- joint 23rd annual meeting of Intelligent Systems for Molecular mittee members. Table 1 provides a summary of the areas, area Biology (ISMB) and 14th European Conference on Computational chairs and a review summary by area. The conference used a two- Biology (ECCB), which took place in Dublin, Ireland, July 10–14, tier review system—a continuation and refinement of a process that 2015 (http://www.iscb.org/ismbeccb2015). ISMB/ECCB 2015, the begun with ISMB/ECCB 2013 in an effort to better ensure thorough official conference of the International Society for Computational and fair reviewing. Under the revised process, each of the 241 sub- Biology (ISCB, http://www.iscb.org/), was accompanied by nine missions was first reviewed by at least three expert referees, with a Special Interest Group meetings of 1 or 2 days each, and two satel- subset receiving between four and six reviews, as needed. lite meetings.
    [Show full text]
  • Department of Energy Office of Health and Environmental Research SEQUENCING the HUMAN GENOME Summary Report of the Santa Fe Workshop March 3-4, 1986
    Department of Energy Office of Health and Environmental Research SEQUENCING THE HUMAN GENOME Summary Report of the Santa Fe Workshop March 3-4, 1986 Los Alamos National Laboratory Los Alamos Los Alamos, New Mexico 87545 Los Alamos National Laboratory is operated by the University of California for the United States Department of Energy under contract W-7405-ENG-36. DEPARTMENT OF ENERGY OFFICE OF HEALTH AND ENVIRONMENTAL RESEARCH SEQUENCING THE HUMAN GENOME SUMMARY REPORT ON THE SANTA FE WORKSHOP (MARCH 3-4, 1986) Executive Summary. The following is a summary of the Santa Fe Workshop held on March 3 and 4, 1986. The workshop was sponsored by the Office of Health and Environmental Research (OHER) and Los Alamos National Laboratory (LANL) and dedicated to examining the feasibility, advisability, and approaches to sequencing the human genome. The workshop considered four principal topics: I. Technologies to be employed. II. Expected benefits. III. Architecture of the enterprise. IV. Participants and funding. I . Technology The participants of the workshop foresaw extraordinary and continuing progress in the efficiency and accuracy of mapping, ordering , and sequencing technologies. They suggested that a coordinated analysis of the human genome begin with the task of ordering overlapping recombinant DNA fragments obtained from purified human chromosomes that would provide an infrastructure for sequencing activity. At the same time, they support in-depth evaluation of current and developing strategies for sequencing including possible applications of automation and robotics that would minimize the time and cost of sequencing. II. Benefits The socio-political and health benefits, and the benefit:cost ratio were seen as highly favorable not only for human health, but in addition for the development of new diagnostic, preventative and therapeutic tools, jobs, and industries.
    [Show full text]
  • Mapping Our Genes—Genome Projects: How Big? How Fast?
    Mapping Our Genes—Genome Projects: How Big? How Fast? April 1988 NTIS order #PB88-212402 Recommended Citation: U.S. Congress, Office of Technology Assessment, Mapping Our Genes-The Genmne Projects.’ How Big, How Fast? OTA-BA-373 (Washington, DC: U.S. Government Printing Office, April 1988). Library of Congress Catalog Card Number 87-619898 For sale by the Superintendent of Documents U.S. Government Printing Office, Washington, DC 20402-9325 (order form can be found in the back of this report) Foreword For the past 2 years, scientific and technical journals in biology and medicine have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part of the public agenda. The debate involves science, technol- ogy, and politics. Congress is responsible for ‘(writing the rules” of what various Federal agencies do and for funding their work. This report surveys the points made so far in the debate, focusing on those that most directly influence the policy options facing the U.S. Congress, The House Committee on Energy and Commerce requested that OTA undertake the project. The House Committee on Science, Space, and Technology, the Senate Com- mittee on Labor and Human Resources, and the Senate Committee on Energy and Natu- ral Resources also asked OTA to address specific points of concern to them. Congres- sional interest focused on several issues: ● how to assess the rationales for conducting human genome projects, ● how to fund human genome projects (at what level and through which mech- anisms), ● how to coordinate the scientific and technical programs of the several Federal agencies and private interests already supporting various genome projects, and ● how to strike a balance regarding the impact of genome projects on international scientific cooperation and international economic competition in biotechnology.
    [Show full text]
  • Characterizing the Dna-Binding Site Specificities of Cis2his2 Zinc Fingers
    MQP-ID-DH-UM1 C H A R A C T E RI Z IN G T H E DN A-BINDIN G SI T E SPE C I F I C I T I ES O F C IS2H IS2 Z IN C F IN G E RS A Major Qualifying Project Report Submitted to the Faculty of the WORCESTER POLYTECHNIC INSTITUTE in partial fulfillment of the requirements for the Degrees of Bachelor of Science in Biochemistry and Biology and Biotechnology by _________________________ Heather Bell April 26, 2012 APPROVED: ____________________ ____________________ ____________________ Scot Wolfe, PhD Destin Heilman, PhD David Adams, PhD Gene Function and Exp. Biochemistry Biology and Biotech UMass Medical School WPI Project Advisor WPI Project Advisor MAJOR ADVISOR A BST R A C T The ability to modularly assemble Zinc Finger Proteins (ZFPs) as well as the wide variety of DNA sequences they can recognize, make ZFPs an ideal framework to design novel DNA-binding proteins. However, due to the complexity of the interactions between residues in the ZF recognition helix and the DNA-binding site there is currently no comprehensive recognition code that would allow for the accurate prediction of the DNA ZFP binding motifs or the design of novel ZFPs for a desired target site. Through the analysis of the DNA-binding site specificities of 98 ZFP clones, determined through a bacterial one-hybrid selection system, a predictive model was created that can accurately predict the binding site motifs of novel ZFPs. 2 T A B L E O F C O N T E N TS Signature Page ««««««««««««««««««««««««««« $EVWUDFW«««««««««««««««««««««««««««««« 7DEOHRI&RQWHQWV«««««««««««««««««««««««««« $FNQRZOHGJHPHQWV««««««««««««««««««««««««« %DFNJURXQG«««««««««««««««««««««««««««« Project Purpose «««««««««««««««««««««««««««15 0HWKRGV««««««««««««««««««««««««««««««16 5HVXOWV««««««««««««««««««««««««««««««21 'LVFXVVLRQ«««««««««««««««««««««««««««««28 Bibliograph\«««««««««««««««««««««««««««« 6XSSOHPHQWDO««««««««««««««««««««««««««« 3 A C K N O W L E D G E M E N TS I would like to thank Dr.
    [Show full text]
  • 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
    [Show full text]
  • 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.
    [Show full text]
  • 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
    [Show full text]
  • ISMB 99 August 6 – 10, 1999 Heidelberg, Germany the Seventh
    ______________________________________ Welcome to ISMB 99 August 6 – 10, 1999 Heidelberg, Germany The Seventh International Conference on Intelligent Systems for Molecular Biology ______________________________________ Final Program and Detailed Schedule Friday, August 6, 1999 Tutorial Day The tutorials will take place in the following rooms: 8:30 – 12:30 (Coffee break around 10:30) Tutorial #1 Trübnersaal Piere Baldi Probabilistic graphical models Tutorial #2 Robert-Schumann-Zimmer Douglas L. Brutlag Bioinformatics and Molecular Biology Tutorial #3 Ballsaal Martin Reese The challenge of annotating a complete eukaryotic genome: A case study in Drosophila melanogaster Tutorial #4 Gustav-Mahler-Zimmer Tandy Warnow Computational and statistical Junhyong Kim challenges involved in reconstructing evolutionary trees Tutorial #5 Sebastian-Münster-Saal Thomas Werner The biology and bioinformatics of regulatory regions in genomes Lunch (on this day served in "Grosser Saal" on the ground floor) 13:30 – 17:30 (Coffee break around 15:30) Tutorial #6 Sebastian-Münster-Saal Rob Miller EST Clustering Alan Christoffels Winston Hide Tutorial #7 Trübnersaal Kevin Karplus Getting the most out of hidden Markov Melissa Cline models Christian Barrett Tutorial #8 Robert-Schumann-Zimmer Arthur Lesk Sequence-structure relationships and evolutionary structure changes in proteins Tutorial #9 Gustav-Mahler-Zimmer David States PERL abstractions for databases and Brian Dunford distributed computing Shore Tutorial # 10 Ballsaal Zoltan Szallasi Genetic network analysis
    [Show full text]
  • 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
    [Show full text]
  • 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).
    [Show full text]
  • Dear Delegates,History of Productive Scientific Discussions of New Challenging Ideas and Participants Contributing from a Wide Range of Interdisciplinary fields
    3rd IS CB S t u d ent Co u ncil S ymp os ium Welcome To The 3rd ISCB Student Council Symposium! Welcome to the Student Council Symposium 3 (SCS3) in Vienna. The ISCB Student Council's mis- sion is to develop the next generation of computa- tional biologists. We would like to thank and ac- knowledge our sponsors and the ISCB organisers for their crucial support. The SCS3 provides an ex- citing environment for active scientific discussions and the opportunity to learn vital soft skills for a successful scientific career. In addition, the SCS3 is the biggest international event targeted to students in the field of Computational Biology. We would like to thank our hosts and participants for making this event educative and fun at the same time. Student Council meetings have had a rich Dear Delegates,history of productive scientific discussions of new challenging ideas and participants contributing from a wide range of interdisciplinary fields. Such meet- We are very happy to welcomeings have you proved all touseful the in ISCBproviding Student students Council and postdocs Symposium innovative inputsin Vienna. and an Afterincreased the network suc- cessful symposiums at ECCBof potential 2005 collaborators. in Madrid and at ISMB 2006 in Fortaleza we are determined to con- tinue our efforts to provide an event for students and young researchers in the Computational Biology community. Like in previousWe ar yearse extremely our excitedintention to have is toyou crhereatee and an the opportunity vibrant city of Vforienna students welcomes to you meet to our their SCS3 event. peers from all over the world for exchange of ideas and networking.
    [Show full text]
  • Download File
    Topics in Signal Processing: applications in genomics and genetics Abdulkadir Elmas Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2016 c 2016 Abdulkadir Elmas All Rights Reserved ABSTRACT Topics in Signal Processing: applications in genomics and genetics Abdulkadir Elmas The information in genomic or genetic data is influenced by various complex processes and appropriate mathematical modeling is required for studying the underlying processes and the data. This dissertation focuses on the formulation of mathematical models for certain problems in genomics and genetics studies and the development of algorithms for proposing efficient solutions. A Bayesian approach for the transcription factor (TF) motif discovery is examined and the extensions are proposed to deal with many interdependent parameters of the TF-DNA binding. The problem is described by statistical terms and a sequential Monte Carlo sampling method is employed for the estimation of unknown param- eters. In particular, a class-based resampling approach is applied for the accurate estimation of a set of intrinsic properties of the DNA binding sites. Through statistical analysis of the gene expressions, a motif-based computational approach is developed for the inference of novel regulatory networks in a given bacterial genome. To deal with high false-discovery rates in the genome-wide TF binding predictions, the discriminative learning approaches are examined in the context of sequence classification, and a novel mathematical model is introduced to the family of kernel-based Support Vector Machines classifiers. Furthermore, the problem of haplotype phasing is examined based on the genetic data obtained from cost-effective genotyping technologies.
    [Show full text]