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. 
ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0000-0002-4048-3479
BMC Bioinformatics 6
: 231.
19 September 2005
BMC Molecular Biology
Co-transcriptional folding is encoded within RNA genes.
Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479 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. ORCID: https://orcid.org/0000-0002-4048-3479 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. ORCID: https://orcid.org/0000-0002-4048-3479 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. ORCID: https://orcid.org/0000-0003-4964-0685, 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. ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0000-0002-4048-3479 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. ORCID: https://orcid.org/0000-0002-4419-2839, Ing-Simmons, E. ORCID: https://orcid.org/0000-0002-0394-2429, Stefanov, S. ORCID: https://orcid.org/0000-0003-4341-8725, Flyamer, I., Dorado Garcia, H. ORCID: https://orcid.org/0000-0002-2578-3350, Schöpflin, R., Henssen, A.G. ORCID: https://orcid.org/0000-0003-1534-778X, 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. ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0000-0002-0840-0784, Wahle, P. ORCID: https://orcid.org/0000-0002-4728-806X, Werner, S. ORCID: https://orcid.org/0000-0001-8350-2417, Jungreis, I., Menzel, P. ORCID: https://orcid.org/0000-0003-4964-0685, Shukla, C.J., Abreu, R.L.P., Irizarry, R.A., Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479, Kellis, M. and Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102
Development 146
(6): dev175265.
28 March 2019
European Physical Journal C
The Cambridge jet algorithm: Features and applications.
Bentvelsen, S. and Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0000-0002-7667-8462, 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. ORCID: https://orcid.org/0000-0003-4964-0685, 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. ORCID: https://orcid.org/0000-0002-4048-3479, 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. ORCID: https://orcid.org/0000-0002-6568-4138, 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. ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0000-0002-4048-3479 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. ORCID: https://orcid.org/0000-0002-4048-3479, 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. ORCID: https://orcid.org/0000-0002-4048-3479, 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. ORCID: https://orcid.org/0000-0002-4048-3479, 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. ORCID: https://orcid.org/0000-0002-9634-7353, Wang, X. ORCID: https://orcid.org/0000-0002-7572-6354, Eichelbaum, K., Sadewasser, A. ORCID: https://orcid.org/0000-0002-8491-3952, Husic, I., Paki, K., Budt, M., Hergeselle, M., Vetter, B., Hou, J., Chen, W. ORCID: https://orcid.org/0000-0003-3263-1627, Wiebusch, L. ORCID: https://orcid.org/0000-0002-7210-6731, Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479, Wolff, T. ORCID: https://orcid.org/0000-0001-7688-236X and Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751
Nature Communications 10
(1): 5518.
4 December 2019
Nucleic Acids Research
DuplexDiscoverer: a computational method for the analysis of experimental duplex RNA-RNA interaction data.
Semenchenko, E. ORCID: https://orcid.org/0009-0007-5306-076X, Tsybulsky, V. ORCID: https://orcid.org/0009-0002-4141-6291 and Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479
Nucleic Acids Research 53
(7): gkaf266.
April 2025
e-RNA: a collection of web-servers for the prediction and visualisation of RNA secondary structure and their functional features.
Tsybulskyi, V. ORCID: https://orcid.org/0009-0002-4141-6291, Semenchenko, E. ORCID: https://orcid.org/0009-0007-5306-076X and Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0000-0003-4341-8725 and Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0009-0002-4141-6291 and Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0009-0002-4141-6291, Mounir, M. and Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0000-0002-4048-3479
Nucleic Acids Research 40
(12): e95.
July 2012
HMMCONVERTER 1.0: a toolbox for hidden Markov models.
Lam, T.Y. and Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0000-0002-4048-3479, 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. ORCID: https://orcid.org/0000-0002-4048-3479 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. ORCID: https://orcid.org/0000-0002-4048-3479, 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. ORCID: https://orcid.org/0000-0002-4048-3479 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. ORCID: https://orcid.org/0000-0002-4048-3479, 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. ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0000-0002-4048-3479 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. ORCID: https://orcid.org/0000-0002-4048-3479
RNA 19
(11): 1461-1473.
November 2013
RNA Biology
Transcriptional dynamics of microRNAs and their targets during Drosophila neurogenesis.
Menzel, P. ORCID: https://orcid.org/0000-0003-4964-0685, McCorkindale, A.L. ORCID: https://orcid.org/0000-0002-0840-0784, Stefanov, S.R. ORCID: https://orcid.org/0000-0003-4341-8725, Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102 and Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0000-0002-4048-3479
RNA Biology 12
(12): 1391-1401.
December 2015
Four RNA families with functional transient structures.
Zhu, J.Y. and Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479
RNA Biology 12
(1): 5-20.
2015
The hok mRNA family.
Steif, A. and Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479
RNA Biology 9
(12): 1399-1404.
1 December 2012
Viruses
Women in the European Virus Bioinformatics Center.
Hufsky, F. ORCID: https://orcid.org/0000-0002-9489-3182, Abecasis, A. ORCID: https://orcid.org/0000-0002-3903-5265, Agudelo-Romero, P. ORCID: https://orcid.org/0000-0002-3703-4111, Bletsa, M. ORCID: https://orcid.org/0000-0003-3184-6618, Brown, K. ORCID: https://orcid.org/0000-0002-8400-6922, Claus, C. ORCID: https://orcid.org/0000-0003-4962-6568, Deinhardt-Emmer, S. ORCID: https://orcid.org/0000-0003-4495-4052, Deng, L. ORCID: https://orcid.org/0000-0003-0225-0663, Friedel, C.C. ORCID: https://orcid.org/0000-0003-3569-4877, Gismondi, M.I. ORCID: https://orcid.org/0000-0002-2566-1169, Kostaki, E.G. ORCID: https://orcid.org/0000-0002-3346-0930, Kühnert, D. ORCID: https://orcid.org/0000-0002-5657-018X, Kulkarni-Kale, U. ORCID: https://orcid.org/0000-0002-1168-2479, Metzner, K.J. ORCID: https://orcid.org/0000-0003-4862-1503, Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479, Miozzi, L. ORCID: https://orcid.org/0000-0003-0410-8230, Nishimura, L. ORCID: https://orcid.org/0000-0003-2144-7867, Paraskevopoulou, S. ORCID: https://orcid.org/0000-0003-2608-2596, Pérez-Cataluña, A. ORCID: https://orcid.org/0000-0002-4784-8346, Rahlff, J. ORCID: https://orcid.org/0000-0002-2132-2709, Thomson, E. ORCID: https://orcid.org/0000-0003-1482-0889, Tumescheit, C. ORCID: https://orcid.org/0000-0002-7563-5575, van der Hoek, L. ORCID: https://orcid.org/0000-0003-2803-642X, Van Espen, L. ORCID: https://orcid.org/0000-0002-3870-4551, Vandamme, A.M. ORCID: https://orcid.org/0000-0002-6594-2766, Zaheri, M. ORCID: https://orcid.org/0000-0003-2777-835X, Zuckerman, N. ORCID: https://orcid.org/0000-0001-6074-2100 and Marz, M. ORCID: https://orcid.org/0000-0003-4783-8823
Viruses 14
(7): 1522.
12 July 2022
The International Virus Bioinformatics Meeting 2020.
Hufsky, F. ORCID: https://orcid.org/0000-0002-9489-3182, Beerenwinkel, N. ORCID: https://orcid.org/0000-0002-0573-6119, Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479, Roux, S. ORCID: https://orcid.org/0000-0002-5831-5895, Cook, G.M., Kinsella, C.M. ORCID: https://orcid.org/0000-0001-9865-4608, Lamkiewicz, K. ORCID: https://orcid.org/0000-0002-6375-6441, Marquet, M., Nieuwenhuijse, D.F. ORCID: https://orcid.org/0000-0003-1310-5031, Olendraite, I., Paraskevopoulou, S. ORCID: https://orcid.org/0000-0003-2608-2596, Young, F. ORCID: https://orcid.org/0000-0002-5236-1145, Dijkman, R. ORCID: https://orcid.org/0000-0003-0320-2743, Ibrahim, B. ORCID: https://orcid.org/0000-0001-7773-0122, Kelly, J., Le Mercier, P. ORCID: https://orcid.org/0000-0001-8528-090X, Marz, M., Ramette, A. ORCID: https://orcid.org/0000-0002-3437-4639 and Thiel, V. ORCID: https://orcid.org/0000-0002-5783-0887
Viruses 12
(12): 1398.
6 December 2020
bioRxiv
Investigating the concept of accessibility for predicting novel RNA-RNA interactions.
Reißer, S. ORCID: https://orcid.org/0000-0003-1224-6967 and Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479
bioRxiv
: 2021.06.03.446902.
3 June 2021
BIQ: a method for searching circular RNAs in transcriptome databases by indexing backsplice junctions.
Menzel, P. ORCID: https://orcid.org/0000-0003-4964-0685 and Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479
bioRxiv
: 556993.
25 February 2019
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