Publications



2016

Lai D.; Meyer I.M.
A comprehensive comparison of general RNA-RNA interaction prediction methods
Nucleic Acids Research 44 (7): e61 (2016-04-20)



2015

Mazloomian A.; Meyer I.M.
Genome-wide identification and characterisation of tissue-specific RNA editing events in D. melanogaster and their potential role in regulating alternative splicing
RNA Biology 12 (12): 1391-1401 (2015-12)



Zhu J.Y.; Meyer I.M.
Four RNA families with functional transient structures
RNA Biology 12 (1): 5-20 (2015)



2014

Lai D.; Meyer I.M.
e-RNA: a collection of web servers for comparative RNA structure prediction and visualisation
Nucleic Acids Research 42 (Web Server issue): W373-W376 (2014-07-01)



2013

Lai D.; Proctor J.R.; Meyer I.M.
On the importance of cotranscriptional RNA structure formation
RNA 19 (11): 1461-1473 (2013-11)



Zhu J.Y.A.; Steif A.; Proctor J.R.; Meyer I.M.
Transient RNA structure features are evolutionarily conserved and can be computationally predicted
Nucleic Acids Research 41 (12): 6273-6285 (2013-07-08)



Proctor J.R.; Meyer I.M.
COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account
Nucleic Acids Research 41 (9): e102 (2013-05)



2012

Steif A.; Meyer I.M.
The hok mRNA family
RNA Biology 9 (12): 1399-1404 (2012-12-01)



Lai D.; Proctor J.R.; Zhu J.Y.A.; Meyer I.M.
R-CHIE: a web server and R package for visualizing RNA secondary structures
Nucleic Acids Research 40 (12): e95 (2012-07)



Shah S.P.; Roth A.; Goya R.; Oloumi A.; Ha G.; Zhao Y.; Turashvili G.; Ding J.; Tse K.; Haffari G.; Bashashati A.; Prentice L.M.; Khattra J.; Burleigh A.; Yap D.; Bernard V.; McPherson A.; Shumansky K.; Crisan A.; Giuliany R.; Heravi-Moussavi A.; Rosner J.; Lai D.; Birol I.; Varhol R.; Tam A.; Dhalla N.; Zeng T.; Ma K.; Chan S.K.; Griffith M.; Moradian A.; Cheng S.W.G.; Morin G.B.; Watson P.; Gelmon K.; Chia S.; Chin S.F.; Curtis C.; Rueda O.M.; Pharoah P.D.; Damaraju S.; Mackey J.; Hoon K.; Harkins T.; Tadigotla V.; Sigaroudinia M.; Gascard P.; Tlsty T.; Costello J.F.; Meyer I.M.; Eaves C.J.; Wasserman W.W.; Jones S.; Huntsman D.; Hirst M.; Caldas C.; Marra M.A.; Aparicio S.
The clonal and mutational evolution spectrum of primary triple-negative breast cancers
Nature 486 (7403): 395-399 (2012-06-21)



2011

Goya R.; Meyer I.M.; Marra M.A.
Applications of high-throughput sequencing
Bioinformatics for High Throughput Sequencing : 27-53 (2011-09-22)



Morin R.D.; Mendez-Lago M.; Mungall A.J.; Goya R.; Mungall K.L.; Corbett R.D.; Johnson N.A.; Severson T.M.; Chiu R.; Field M.; Jackman S.; Krzywinski M.; Scott D.W.; Trinh D.L.; Tamura-Wells J.; Li S.; Firme M.R.; Rogic S.; Griffith M.; Chan S.; Yakovenko O.; Meyer I.M.; Zhao E.Y.; Smailus D.; Moksa M.; Chittaranjan S.; Rimsza L.; Brooks-Wilson A.; Spinelli J.J.; Ben-Neriah S.; Meissner B.; Woolcock B.; Boyle M.; McDonald H.; Tam A.; Zhao Y.; Delaney A.; Zeng T.; Tse K.; Butterfield Y.; Birol I.; Holt R.; Schein J.; Horsman D.E.; Moore R.; Jones S.J.M.; Connors J.M.; Hirst M.; Gascoyne R.D.; Marra M.A.
Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma
Nature 476 (7360): 298-303 (2011-08-18)



2010

Lam T.Y.; Meyer I.M.
Efficient algorithms for training the parameters of hidden Markov models using stochastic expectation maximization (EM) training and Viterbi training
Algorithms for Molecular Biology 5: 38 (2010-12-09)



Wiebe N.J.P.; Meyer I.M.
TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures
PLoS Computational Biology 6 (6): e1000823 (2010-06-24)



2009

Lam T.Y.; Meyer I.M.
HMMCONVERTER 1.0: a toolbox for hidden Markov models
Nucleic Acids Research 37 (21): e139 (2009-11)



2008

Schoening J.C.; Streitner C.; Meyer I.M.; Gao Y.; Staiger D.
Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis
Nucleic Acids Research 36 (22): 6977-6987 (2008-12)



Pain A.; Boehme U.; Berry A.E.; Mungall K.; Finn R.D.; Jackson A.P.; Mourier T.; Mistry J.; Pasini E.M.; Aslett M.A.; Balasubrammaniam S.; Borgwardt K.; Brooks K.; Carret C.; Carver T.J.; Cherevach I.; Chillingworth T.; Clark T.G.; Galinski M.R.; Hall N.; Harper D.; Harris D.; Hauser H.; Ivens A.; Janssen C.S.; Keane T.; Larke N.; Lapp S.; Marti M.; Moule S.; Meyer I.M.; Ormond D.; Peters N.; Sanders M.; Sanders S.; Sargeant T.J.; Simmonds M.; Smith F.; Squares R.; Thurston S.; Tivey A.R.; Walker D.; White B.; Zuiderwijk E.; Churcher C.; Quail M.A.; Cowman A.F.; Turner C.M.R.; Rajandream MA; Kocken C.H.M.; Thomas A.W.; Newbold C.I.; Barrell B.G.; Berriman M.
The genome of the simian and human malaria parasite Plasmodium knowlesi
Nature 455 (7214): 799-803 (2008-10-09)



Meyer I.M.
Predicting novel RNA-RNA interactions
Current Opinion in Structural Biology 18 (3): 387-393 (2008-06)



2007

Meyer I.M.
A practical guide to the art of RNA gene prediction
Briefings in Bioinformatics 8 (6): 396-414 (2007-11)



Yen Z.C.; Meyer I.M.; Karalic S.; Brown C.J.
A cross-species comparison of X-chromosome inactivation in Eutheria
Genomics 90 (4): 453-463 (2007-10)



Meyer I.M.; Miklos I.
SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework
PLoS Computational Biology 3 (8): e149 (2007-08-10)



2005

Meyer I.M.; Miklos I.
Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs
Nucleic Acids Research 33 (19): 6338-6348 (2005-11-07)



Miklos I.; Meyer I.M.
A linear memory algorithm for Baum-Welch training
BMC Bioinformatics 6: 231 (2005-09-19)



Miklos I.; Meyer I.M.; Nagy B.
Moments of the Boltzmann distribution for RNA secondary structures
Bulletin of Mathematical Biology 67 (5): 1031-1047 (2005-09)



2004

Pedersen J.S.; Forsberg R.; Meyer I.M.; Hein J.
An evolutionary model for protein-coding regions with conserved RNA structure
Molecular Biology and Evolution 21 (10): 1913-1922 (2004-10)



Pedersen J.S.; Meyer I.M.; Forsberg R.; Simmonds P.; Hein J.
A comparative method for finding and folding RNA secondary structures within protein-coding regions
Nucleic Acids Research 32 (16): 4925-4936 (2004-09-24)



Meyer I.M.; Miklos I.
Co-transcriptional folding is encoded within RNA genes
BMC Molecular Biology 5: 10 (2004-08-06)



Meyer I.M.; Durbin R.
Gene structure conservation aids similarity based gene prediction
Nucleic Acids Research 32 (2): 776-783 (2004-02-04)



2002

Meyer I.M.; Durbin R.
Comparative ab initio prediction of gene structures using pair HMMs
Bioinformatics 18 (10): 1309-1318 (2002-10)



1998

Bentvelsen S.; Meyer I.
The Cambridge jet algorithm: Features and applications
European Physical Journal C 4 (4): 623-629 (1998-07)