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Bioinformatics
VOLUME 28 NUMBER 18 SEPTEMBER 15 2012
MLSB 2012 PAPERS
Gene expression
Inferring epigenetic and transcriptional
regulation during blood cell development
with a mixture of sparse linear models
T.G.do Rego,H.G.Roider,F.A.T.de Carvalho
and I.G.Costa
Systems biology
Predicting drug–target interactions from
chemical and genomic kernels using
Bayesian matrix factorization
M.Gönen
Integrating literature-constrained and
data-driven inference of signalling
networks
F.Eduati,J.D.L.Rivas,B.D.Camillo,
G.Toffolo and J.Saez-Rodriguez
Efficient sampling for Bayesian inference
of conjunctive Bayesian networks
T.Sakoparnig and N.Beerenwinkel
Context-specific transcriptional regulatory
network inference from global gene
expression maps using double
two-way tt-tests
J.Qi and T.Michoel
Metabolite identification and molecular
fingerprint prediction through machine
learning
M.Heinonen,H.Shen,N.Zamboni and
J.Rousu
Network inference using steady-state data
and Goldbeter–koshland kinetics
C.J.Oates,B.T.Hennessy,Y.Lu,G.B.Mills
and S.Mukherjee
Data and text mining
Targeted retrieval of gene expression
measurements using regulatory models
E.Georgii,J.Salojärvi,M.Brosché,
J.Kangasjärvi and S.Kaski
ORIGINAL PAPERS
Genome analysis
A regression model for estimating DNA
copy number applied to capture
sequencing data
G.J.Rigaill,S.Cadot,R.J.C Kluin,Z.Xue,
R.Bernards,I.J.Majewski and L.F.A.Wessels
Sequence analysis
Fast and accurate read alignment for
resequencing
J.C.Mu,H.Jiang,A.Kiani,M.Mohiyuddin,
N.B.Asadi and W.H.Wong
Bioimage informatics
A bioimage informatics approach to
automatically extract complex fungal
networks
B.Obara,V.Grau and M.D.Fricker
APPLICATIONS NOTE
Sequence analysis
CBrowse:a SAM/BAM-based contig
browser for transcriptome assembly
visualization and analysis
P.Li,G.Ji,M.Dong,E.Schmidt,D.Lenox,
L.Chen,Q.Liu,L.Liu,J.Zhang and
C.Liang
SpliceSeq:a resource for analysis and
visualization of RNA-Seq data on
alternative splicing and its functional
impacts
M.C.Ryan,J.Cleland,R.Kim,W.C.Wong and
J.N.Weinstein
Phylogenetics
ANGES:reconstructing ANcestral
GEnomeS maps
B.R.Jones,A.Rajaraman,E.Tannier and
C.Chauve
Structural bioinformatics
RIBFIND:a web server for identifying
rigid bodies in protein structures and to
aid flexible fitting into cryo EM maps
A.P.Pandurangan and M.Topf
Structural bioinformatics
Cell-Dock:high-performance
protein–protein docking
C.Pons,D.Jiménez-González,C.González-
Álvarez,H.Servat,D.Cabrera-Benítez,
X.Aguilar and J.Fernández-Recio
Genetics and population analysis
GAPIT:genome association and prediction
integrated tool
A.E.Lipka,F.Tian,Q.Wang,J.Peiffer,M.Li,
P.J.Bradbury,M.A.Gore,E.S.Buckler and
Z.Zhang
Bioinformatics
VOLUME 28 NUMBER 18 SEPTEMBER 15 2012
www.bioinformatics.oxfordjournals.org
ISSN 1367-4803 (PRINT)
ISSN 1460-2059 (ONLINE)
continued inside back cover
Bioinformatics
VOLUME 28NUMBER 18SEPTEMBER152012PAGES 2297–2406
BIOINFO-28(18)Cover.qxd 8/29/12 2:09 PM Page 1
[10:18 14/8/2012 Bioinformatics-Bioinfo-28(18)IFC.tex] Page:2 1–2
BIOINFORMATICS
Executive Editors
Alex Bateman,UK Alfonso Valencia,Spain
Email:bioinformatics.editorialoffice@oup.com
Associate Editors
M.Albrecht,Germany (–2013)
J.Barrett,UK(–2014)
I.Birol,Canada (–2014)
M.Bishop,UK (–2012)
M.Brudno,Canada (–2014)
I.Hofacker (–2013)
T.Ideker,USA (–2012)
J.Kelso,Germany (–2013)
D.Posada,Spain (–2012)
G.Rätsch,USA (–2014)
B.Rost,USA (–2012)
A.Tramontano,Italy (–2013)
O.Troyanskaya,USA (–2014)
J.Wren,USA (–2014)
Editorial Office
bioinformatics.editorialoffice@oup.com
Editorial Board
V.Bafna,USA (–2014)
Z.Bar-Joseph,USA (–2014)
A.Brazma,UK (–2012)
S.Brunak,Denmark (–2014)
K.A.Crandall,USA (–2013)
J.Dopazo,Spain (–2013)
D.Frishman,Germany (–2013)
D.Higgins,Ireland (–2014)
C.Hodgman,UK (–2012)
L.Holm,Finland (–2012)
W.Huber,UK (–2013)
L.Jensen,Germany (–2013)
K.Karplus,USA (–2014)
T.Lengauer,Germany (–2011)
A.Navarro,Spain (–2013)
C.Ouzounis,UK (–2012)
I.Ovcharenko,USA (–2014)
P.Park,USA (–2014)
H.Peng,USA (–2014)
J.Quackenbush,USA (–2014)
P.Radivojac,USA (–2012)
I.Rigoutsos,USA (–2014)
D.Rocke,USA (–2014)
C.Sahinalp,Canada (–2014)
C.Seoighe,Ireland (–2012)
N.Srinivasan,India (–2014)
M.Vingron,Germany (–2014)
L.Wong,Singapore (–2012)
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