Front Matter (PDF) - Briefings in Bioinformatics - Oxford Journals

earthsomberΒιοτεχνολογία

29 Σεπ 2013 (πριν από 4 χρόνια και 1 μήνα)

115 εμφανίσεις

Briefi ngs in Bioinformatics Volume 12 • Number 6 • November 2011
Briefi ngs in

Bioinformatics
Volume 12 • Number 6 • November 2011
Contents
547 Editorial
Paolo Romano, Rosalba Giugno and Alfredo Pulvirenti
Special Issue Papers
549 Tools and collaborative environments for bioinformatics research
Paolo Romano, Rosalba Giugno and Alfredo Pulvirenti
562 Knowledge sharing and collaboration in translational research, and the DC-THERA
Directory
Andrea Splendiani, Michaela Gündel, Jonathan M. Austyn, Duccio Cavalieri, Ciro Scognamiglio
and Marco Brandizi
576 Social pathway annotation: extensions of the systems biology metabolic modelling
assistant
Ismael Navas-Delgado, Alejandro Real-Chicharro, Miguel Ángel Medina,
Francisca Sánchez-Jiménez and José F. Aldana-Montes
588 myMIR: a genome-wide microRNA targets identifi cation and annotation tool
Dario Corrada, Federica Viti, Ivan Merelli, Cristina Battaglia and Luciano Milanesi
601 RNA tertiary structure prediction with ModeRNA
Magdalena Rother, Kristian Rother, Tomasz Puton and Janusz M. Bujnicki
614 Computational challenges of sequence classifi cation in microbiomic data
Paolo Ribeca and Gabriel Valiente
Non Special Issue Papers
626 Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking
efforts
Adam M. Szalkowski and Christoph D. Schmid
634 Exon array data analysis using Affymetrix power tools and R statistical software
Helen E. Lockstone
645 Toward microRNA-mediated gene regulatory networks in plants
Yijun Meng, Chaogang Shao and Ming Chen
(Contents continued on inside of back cover)
Volume 12 • Number 6 • November 2011
print issn 1467-5463
online issn 1477-4054
Special Issue: Collaborative Bioinformatics and RNA Analysis
Briefi ngs in

Bioinformatics
www.bib.oxfordjournals.org
BIB-12(6)Cover.indd 1
BIB-12(6)Cover.indd 1 11/16/2011 6:23:27 PM
11/16/2011 6:23:27 PM
Editorial Board
EDITOR
Martin Bishop
CNR-ITB Institute of Biomedical
Technologies,Italy
NORTHAMERICAN
ASSOCIATE EDITOR
Russ B.Altman
Stanford University,USA
EDITORIALOFFICE
Sophie Gilmour
Editorial Assistant,UK
EDITORIAL BOARD
Teresa K.Attwood
University of Manchester,UK
Mark Borodovsky
Georgia Institute of Technology,USA
Anne-Laure Boulesteix
University of Munich
Vladimir Brusic
Dana-Farber Cancer Institute,
USA
TimClark
Harvard University & Massachusetts
General Hospital,USA
Jo Dicks
John Innes Centre,UK
Werner Dubitzky
University of Ulster,Northern Ireland
Wendy Filsell
Unilever,UK
Donald Gilbert
Indiana University,USA
Winston Hide
SANBI,South Africa
Charlie Hodgman
University of Nottingham,UK
Rod Hubbard
University of York,UK
I.King Jordan
Georgia Institute of Technology,USA
Jacob Koehler
University of Tromsø,Norway
Jack Leunissen
Wageningen University,
The Netherlands
Mingyao Li
University of Pennsylvania
Jingchu Luo
Peking University,China
Shuangge Ma
School of Public Health Yale University,
USA
Scott Markel
SciTegic Inc.,USA
Tommaso Mazza
The Microsoft Research - University of
Trento CoSBi
Haruki Nakamara
Institute for Protein Research,
Osaka University
Indra Neil Sarkar
University of Vermont
Graziano Pesole
University of Bari,Italy
Sandor Pongor
International Centre for Genetic
Engineering and Biotechnology,Italy
Dennis Quan
IBM Thomas J.Watson Research
Center,USA
Shoba Ranganathan
Macquarie University,Australia
Keith Robison
Codon Devices,USA
Igor Rogozin
National Center for Biotechnology
Information,National Institutes
of Health,USA
Fritz Roth
Harvard Medical School/BCMP Dept.,
USA
Cathal Seoighe
IIDMIM,Medical School,University of
Cape Town,South Africa
OlgaTroyanskaya
Lewis-Sigler Institute for Integrative
Genomics,USA
Thomas Werner
Genomatix Software GmbH,
Germany
MathewWoodwark
AstraZeneca,UK
BOOKREVIEWS EDITOR
Sean Mooney
Associate Professor
Buck Institute for Age Research
8001 Redwood Blvd.
Novato,CA 94945
USA
Briefings in Bioinformatics
www.bib.oxfordjournals.org
SUBSCRIPTION
INFORMATION
A subscription to Briefings in Bioinformatics
comprises 6 issues.All prices include post-
age,and for subscribers outside the UK
delivery is by Standard Air.Briefings in
Bioinformatics Advance Access contains
papers that have recently been accepted
but have not yet been included within an
issue.
Annual subscription rates
(Volume12,6 Issues,2011)
I
NSTITUTIONAL
Print editionandsite-wide online
access:»472/US$943/E708
Print editiononly:»432/US$865/E649
Site-wideonlineaccessonly:
»393/US$786/E590
P
ERSONAL
Print edition (includesfreeonline
access):»229/US$457/E343
Please note:US$ rate applies to US
& Canada,Euros applies to Europe,
UK» appliestoUKandRest of World.
Theremaybyother subscriptionrates
available;foracompletelisting,pleasevisit
www.oxfordjournals.org/our_journals/bib/
access_purchase/price_list.html.
Full prepayment,in the correct currency,is
required for all orders.Orders are regarded
as firm and payments are not refundable.
Subscriptions are accepted and entered
on a complete volume basis.Claims cannot
be considered more than FOUR months
after publication or date of order,whichever
is later.All subscriptions in Canada
are subject to GST.Subscriptions in the EU
maybesubject toEuropeanVAT.If registered,
please supply details to avoid unnecessary
charges.For subscriptions that include
online versions,a proportion of the
subscription price may be subject to UK
VAT.Personal rate subscriptions are
only available if payment is made by
personal cheque or credit card and delivery
istoaprivateaddress.
FORFURTHERINFORMATION,
PLEASE CONTACT:
Journals Customer Service Department,
Oxford University Press,Great Clarendon
Street,Oxford OX2 6DP,UK.
E-mail:jnls.cust.serv@oup.com.
Tel (andanswerphoneoutsidenormal
workinghours):þ44 (0)1865 353907.
Fax:þ44 (0)1865 353485.
INTHEUS,PLEASE CONTACT:
Journals Customer Service Department,
Oxford University Press,2001 Evans Road,
Cary,NC 27513,USA.E-mail:jnlorders@
oxfordjournals.org.Tel (and answerphone
outsidenormal workinghours):800 8527323
(toll-freein USA/Canada).
Fax:919 6771714.
INJAPAN,PLEASE CONTACT:
Journals Customer Services,
Oxford University Press,4-5-10-8F,
Shiba,Minato-ku,Tokyo,108-8386,
Japan.Email:custserv.jp@oup.com
Tel:(03) 5444 5858.
Fax:(03) 34542929.
METHODS OF PAYMENT:
(i) Cheque (payable to Oxford University
Press,to Oxford University Press,
Cashiers Office,Great Clarendon Street,
Oxford OX2 6DP,UK) in GB» Sterling
(drawnona UKbank),US$ Dollars (drawnon
a US bank),or EUEEuros.(ii) Bank transfer
to Barclays Bank Plc,Oxford Group Office,
Oxford (bank sort code 20-65-18) (UK),
overseasonly Swift code BARCGB22
(GB» Sterlingtoaccount no.70299332,
IBANGB89BARC20651870299332;
US$ Dollarstoaccount no.66014600,
IBANGB27BARC20651866014600;
EUEEurostoaccount no.78923655,
IBANGB16BARC20651878923655).
(iii) Credit card (Mastercard,Visa,
Switchor American Express).
Briefings in Bioinformatics is published
six times a year in January,March,May,
July,September and November by Oxford
University Press,Oxford,UK.Annual sub-
scriptionpriceis »454/US$908/E681.
Briefings in Bioinformatics is distributed
by Mercury International,365 Blair Road,
Avenel,NJ 07001,USA.Periodicals postage
paid at Rahway,NJ and at additional entry
points.
US Postmaster:Send address changes
to Briefings in Bioinformatics,c/o Mercury
International,365 Blair Road,Avenel,
NJ 07001,USA.
SUPPLEMENTS,REPRINTS
ANDCORPORATE SALES
For requests from industry and companies
regardingsupplements,bulk articlereprints,
sponsored subscriptions,translation oppor-
tunities for previously published material,
and corporate online opportunities,please
e-mail special.sales@oxfordjournals.org,
fax þ44 (0)1865 353774 or visit www.oxford
journals.org/jnls/sales.
PERMISSIONS
For information on how to request permis-
sions to reproduce articles/information from
thisjournal,pleasevisit www.oxfordjournals.
org/jnls/permissions.
ADVERTISING
Advertising,inserts and artwork enquiries
should be addressed to Advertising and
Special Sales,Oxford Journals,Oxford
University Press,Great Clarendon Street,
Oxford,OX2 6DP,UK.Tel:þ44 (0)1865
354767.Fax:þ44 (0)1865 353774.E-mail:
jnlsadvertising@oxfordjournals.org.
DISCLAIMER
Statements of fact andopinioninthearticles
in Briefings in Bioinformatics are those of
the respective authors and contributors and
not of Bioinformatics or Oxford University
Press.Neither Oxford University Press nor
Briefings in Bioinformatics make any repre-
sentation,express or implied,in respect of
the accuracy of the material in this journal
andcannot accept anylegal responsibilityor
liability for any errors or omissions that may
be made.The reader should make his/her
own evaluation as to the appropriateness or
otherwise of any experimental technique
described.
￿2011Briefingsin Bioinformatics.
All rightsreserved;nopart of thispublication
may be reproduced,stored in a retrieval
system,or transmitted in any formor byany
means,electronic,mechanical,photocopy-
ing,recording,or otherwise without prior
written permission of the Publishers,or a
licence permitting restricted copying issued
in the UK by the Copyright Licensing
Agency Ltd,90 Tottenham Court Road,
London W1P 9HE,or in the USA by the
Copyright Clearance Center,222 Rosewood
Drive,Danvers,MA01923.
Typeset by Glyph International,Bangalore,
India.
Printed by C.O.S.Printers Pte Ltd,Singapore.