Browse by Research Team

Article

e-RNA: a collection of web-servers for the prediction and visualisation of RNA secondary structure and their functional features.
Tsybulskyi, V. and Semenchenko, E. and Meyer, I.M.
Nucleic Acids Research 51 (W1): W160-W167. 5 July 2023

CYCLeR - a novel tool for the full isoform assembly and quantification of circRNAs.
Stefanov, S.R. and Meyer, I.M.
Nucleic Acids Research 51 (2): e10. 25 January 2023

ShapeSorter: a fully probabilistic method for detecting conserved RNA structure features supported by SHAPE evidence.
Tsybulskyi, V. and Meyer, I.M.
Nucleic Acids Research 50 (15): e85. 26 August 2022

Women in the European Virus Bioinformatics Center.
Hufsky, F. and Abecasis, A. and Agudelo-Romero, P. and Bletsa, M. and Brown, K. and Claus, C. and Deinhardt-Emmer, S. and Deng, L. and Friedel, C.C. and Gismondi, M.I. and Kostaki, E.G. and Kühnert, D. and Kulkarni-Kale, U. and Metzner, K.J. and Meyer, I.M. and Miozzi, L. and Nishimura, L. and Paraskevopoulou, S. and Pérez-Cataluña, A. and Rahlff, J. and Thomson, E. and Tumescheit, C. and van der Hoek, L. and Van Espen, L. and Vandamme, A.M. and Zaheri, M. and Zuckerman, N. and Marz, M.
Viruses 14 (7): 1522. 12 July 2022

Analysis of correlation and ionization from pair distributions in many-electron systems.
López-Rosa, S. and Angulo, J. C. and Martín, A. L. and Antolín, J.
European Physical Journal Plus 136 (7): 763. 22 July 2021

CoBold: a method for identifying different functional classes of transient RNA structure features that can impact RNA structure formation in vivo.
Martín, A.L. and Mounir, M. and Meyer, I.M.
Nucleic Acids Research 49 (4): e19. 26 February 2021

The International Virus Bioinformatics Meeting 2020.
Hufsky, F. and Beerenwinkel, N. and Meyer, I.M. and Roux, S. and Cook, G.M. and Kinsella, C.M. and Lamkiewicz, K. and Marquet, M. and Nieuwenhuijse, D.F. and Olendraite, I. and Paraskevopoulou, S. and Young, F. and Dijkman, R. and Ibrahim, B. and Kelly, J. and Le Mercier, P. and Marz, M. and Ramette, A. and Thiel, V.
Viruses 12 (12): 1398. 6 December 2020

R-chie: a web server and R package for visualizing cis and trans RNA-RNA, RNA-DNA and DNA-DNA interactions.
Tsybulskyi, V. and Mounir, M. and Meyer, I.M.
Nucleic Acids Research 48 (18): e105. 9 October 2020

Bacteriophages: emerging applications in medicine, food, and biotechnology.
Sohail, H.A. and Coffey, A. and Debrowska, K. and Meyer, I.M. and Middelboe, M. and Sohail, M. and Clokie, M.R.J.
PHAGE 1 (2): 75-82. 16 June 2020

The dynamic proteome of influenza A virus infection identifies M segment splicing as a host range determinant.
Bogdanow, B. and Wang, X. and Eichelbaum, K. and Sadewasser, A. and Husic, I. and Paki, K. and Budt, M. and Hergeselle, M. and Vetter, B. and Hou, J. and Chen, W. and Wiebusch, L. and Meyer, I.M. and Wolff, T. and Selbach, M.
Nature Communications 10 (1): 5518. 4 December 2019

Modelling the DNA topology: the effect of the loop bending on G-quadruplex stability.
Bergues-Pupo, A.E. and Falo, F. and Fiasconaro, A.
Journal of Statistical Mechanics: Theory and Experiment 2019 (9): 094004. 2 September 2019

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs.
McCorkindale, A.L. and Wahle, P. and Werner, S. and Jungreis, I. and Menzel, P. and Shukla, C.J. and Abreu, R.L.P. and Irizarry, R.A. and Meyer, I.M. and Kellis, M. and Zinzen, R.P.
Development 146 (6): dev175265. 28 March 2019

Transcriptional dynamics of microRNAs and their targets during Drosophila neurogenesis.
Menzel, P. and McCorkindale, A.L. and Stefanov, S.R. and Zinzen, R.P. and Meyer, I.M.
RNA Biology 16 (1): 69-81. 20 January 2019

Sugar metabolism of the first thermophilic planctomycete thermogutta terrifontis: comparative genomic and transcriptomic approaches.
Elcheninov, A.G. and Menzel, P. and Gudbergsdottir, S.R. and Slesarev, A.I. and Kadnikov, V.V. and Krogh, A. and Bonch-Osmolovskaya, E.A. and Peng, X. and Kublanov, I.V.
Frontiers in Microbiology 8 : 2140. 2 November 2017

In silico methods for co-transcriptional RNA secondary structure prediction and for investigating alternative RNA structure expression.
Meyer, I.M.
Methods 120 : 3-16. 1 May 2017

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

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

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

e-RNA: a collection of web servers for comparative RNA structure prediction and visualisation.
Lai, D. and Meyer, I.M.
Nucleic Acids Research 42 (Web Server issue): W373-W376. 1 July 2014

Transient RNA structure features are evolutionarily conserved and can be computationally predicted.
Zhu, J.Y.A. and Steif, A. and Proctor, J.R. and Meyer, I.M.
Nucleic Acids Research 41 (12): 6273-6285. 8 July 2013

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

The hok mRNA family.
Steif, A. and Meyer, I.M.
RNA Biology 9 (12): 1399-1404. 1 December 2012

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

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

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

Efficient algorithms for training the parameters of hidden Markov models using stochastic expectation maximization (EM) training and Viterbi training.
Lam, T.Y. and Meyer, I.M.
Algorithms for Molecular Biology 5 : 38. 9 December 2010

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

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

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

The genome of the simian and human malaria parasite Plasmodium knowlesi.
Pain, A. and Boehme, U. and Berry, A.E. and Mungall, K. and Finn, R.D. and Jackson, A.P. and Mourier, T. and Mistry, J. and Pasini, E.M. and Aslett, M.A. and Balasubrammaniam, S. and Borgwardt, K. and Brooks, K. and Carret, C. and Carver, T.J. and Cherevach, I. and Chillingworth, T. and Clark, T.G. and Galinski, M.R. and Hall, N. and Harper, D. and Harris, D. and Hauser, H. and Ivens, A. and Janssen, C.S. and Keane, T. and Larke, N. and Lapp, S. and Marti, M. and Moule, S. and Meyer, I.M. and Ormond, D. and Peters, N. and Sanders, M. and Sanders, S. and Sargeant, T.J. and Simmonds, M. and Smith, F. and Squares, R. and Thurston, S. and Tivey, A.R. and Walker, D. and White, B. and Zuiderwijk, E. and Churcher, C. and Quail, M.A. and Cowman, A.F. and Turner, C.M.R. and Rajandream, MA and Kocken, C.H.M. and Thomas, A.W. and Newbold, C.I. and Barrell, B.G. and Berriman, M.
Nature 455 (7214): 799-803. 9 October 2008

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

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

Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs.
Meyer, I.M. and Miklos, I.
Nucleic Acids Research 33 (19): 6338-6348. 7 November 2005

A linear memory algorithm for Baum-Welch training.
Miklos, I. and Meyer, I.M.
BMC Bioinformatics 6 : 231. 19 September 2005

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

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

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

Co-transcriptional folding is encoded within RNA genes.
Meyer, I.M. and Miklos, I.
BMC Molecular Biology 5 : 10. 6 August 2004

Gene structure conservation aids similarity based gene prediction.
Meyer, I.M. and Durbin, R.
Nucleic Acids Research 32 (2): 776-783. 4 February 2004

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

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

Book Section

Deciphering the universe of RNA structures and trans RNA-RNA interactions of transcriptomes in vivo: from experimental protocols to computational analyses.
Stefanov, S.R. and Meyer, I.M.
In: Systems Biology. RNA Technologies . Springer, Cham, 173-216. ISBN 978-3-319-92966-8 2018

Applications of high-throughput sequencing.
Goya, R. and Meyer, I.M. and Marra, M.A.
In: Bioinformatics for High Throughput Sequencing. Springer, 27-53. ISBN 978-1-4614-0781-2 22 September 2011

Review

Discovering novel hydrolases from hot environments.
Wohlgemuth, R. and Littlechild, J. and Monti, D. and Schnorr, K. and van Rossum, T. and Siebers, B. and Menzel, P. and Kublanov, I.V. and Rike, A.G. and Skretas, G. and Szabo, Z. and Peng, X. and Young, M.J.
Biotechnology Advances 36 (8): 2077-2100. December 2018

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

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

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

Preprint

Investigating the concept of accessibility for predicting novel RNA-RNA interactions.
Reißer, S. and Meyer, I.M.
bioRxiv : 2021.06.03.446902. 3 June 2021

CYCLeR - a novel tool for the full isoform assembly and quantification of circRNAs.
Stefanov, S.R. and Meyer, I.M.
bioRxiv : 2021.04.27.441578. 28 April 2021

BIQ: A method for searching circular RNAs in transcriptome databases by indexing backsplice junctions.
Menzel, P. and Meyer, I.M.
bioRxiv : 556993. 25 February 2019

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs.
McCorkindale, A.L. and Wahle, P. and Werner, S. and Jungreis, I. and Menzel, P. and Shukla, C.J. and Lopes Pereira Abreu, R. and Irizarry, Rafael and Meyer, I. and Kellis, Manolis and Zinzen, R.P.
bioRxiv : 483461. 27 December 2018

The dynamic proteome of influenza A virus infection identifies M segment splicing as a host range determinant.
Bogdanow, B. and Eichelbaum, K. and Sadewasser, A. and Wang, X. and Husic, I. and Paki, K. and Hergeselle, M. and Vetter, B. and Hou, J. and Chen, W. and Wiebusch, L. and Meyer, I.M. and Wolff, T. and Selbach, M.
bioRxiv : 438176. 8 October 2018