Browse by Research Team

Algorithms for Molecular Biology

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

BMC Bioinformatics

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

BMC Molecular Biology

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

Bioinformatics

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

Bioinformatics for High Throughput Sequencing

Applications of high-throughput sequencing.
Goya, R., 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

Biotechnology Advances

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

Briefings in Bioinformatics

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

Bulletin of Mathematical Biology

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

Cells

Doxorubicin changes the spatial organization of the genome around active promoters.
Stefanova, M.E., Ing-Simmons, E., Stefanov, S., Flyamer, I., Dorado Garcia, H., Schöpflin, R., Henssen, A.G., Vaquerizas, J.M. and Mundlos, S.
Cells 12 (15): 2001. 4 August 2023

Current Opinion in Structural Biology

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

Development

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

European Physical Journal C

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

European Physical Journal Plus

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

Frontiers in Microbiology

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

Genomics

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

Journal of Statistical Mechanics: Theory and Experiment

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

Methods

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

Molecular Biology and Evolution

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

Nature

The clonal and mutational evolution spectrum of primary triple-negative breast cancers.
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. and Aparicio, S.
Nature 486 (7403): 395-399. 21 June 2012

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma.
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. and Marra, M.A.
Nature 476 (7360): 298-303. 18 August 2011

The genome of the simian and human malaria parasite Plasmodium knowlesi.
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. and Berriman, M.
Nature 455 (7214): 799-803. 9 October 2008

Nature Communications

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

Nucleic Acids Research

e-RNA: a collection of web-servers for the prediction and visualisation of RNA secondary structure and their functional features.
Tsybulskyi, V., 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

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

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

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

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., Steif, A., 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

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

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., Streitner, C., Meyer, I.M., Gao, Y. and Staiger, D.
Nucleic Acids Research 36 (22): 6977-6987. December 2008

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

PHAGE

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

PLoS Computational Biology

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

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

RNA

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

RNA Biology

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

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

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

Viruses

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

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

bioRxiv

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

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