RNAs are like these dots.
They evolve from each other.
But how?

Marcin Magnus, PhD
Computational RNA biologist at Harvard University, USA
I'm trying to understand the evolution and role of RNA and RNPs in biological systems using computational methods (machine learning, molecular dynamics, structure prediction) and experimental (yeast genetics, molecular biology) and codify this knowledge into predictive computational models that can be applied for future RNA therapeutics.

mqapRNA | EvoClustRNA | RNArchitecture | SimRNAweb | rna-tools | RNA Puzzles

RNA Club Warsaw | Do Science!


[GoogleScholar] [Publons] [GitHub]

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Get To Know My Science

A list of projects I've done with wonderful colleagues.

SimRNAweb

SimRNA is a method for RNA 3D structure modeling with optional restraints.

RNArchitecture

RNArchitecture is a structured ncRNAs, with focus on sequence and structure similarities.

NPDock

NPDock is a web server for modeling of RNA-protein and DNA-protein complex structures.

EvoClustRNA

Clustering routines of evolutionary conserved regions (helical regions) for RNA fold prediction.

Splicing modulation

Cwc15 stabilizes the spliceosomal catalytic interactions in the first-step conformation.

U6 RNA Dynamics

The lower U6-ISL stem is flexible and changes during spliceosomal catalysis. This feature is conserved across eukaryotes, in U6atac and domain V of group II introns.

rna-tools

A toolbox to analyze sequences, structures and simulations of RNA

RNA-Puzzles

A collective, CASP-like, experiment for blind RNA tertiary structure prediction.

mqapRNA

A quality prediction method for scoring RNA 3D models based on the deep learning.

Do Science!

Science Club. A place to discuss SCIENCE.

RNA Club Warsaw!

Do Science! Spin-off. A place to discuss RNA SCIENCE.

My Hacking Tools

emacs-env

Emacs is my rifle. There are many editors like it, but this one is mine. Without me, my rifle is useless. Without my rifle, I am useless. Check out some of the extensions: emacs-grammarly emacs-pdb-mode OrgModeClocking2Calendar garmin2orgmode

Geekbook

Fun to read & fun to write - eXtreme eXtendable note taking system for nerds/geeks (including scientists!) = beautiful html generator of your markdown-based notes.

Pocket-Plus-Calibre-Plugin

Calibre plugin for Pocket. Now, you get your articles organized by your Pocket tags, and way more...

pubmex

is a script to get a fancy/full paper title based on analysis of the file (can be also combined with macOS Finder)

$ pubmex.py sharp2017.pdf
Sharp.Hockfield.Convergence.The.future.health.Science.2017.pdf

Papers

Google Scholar: Citations 710, H-index: 12; Publons: Peer-review: 12 [as of 210428].

Selected papers

@ Stanford University, CA, USA & International Institute of Molecular and Cell Biology, Poland

RNA 3D Structure Prediction Using Multiple Sequence Alignment Information.
M. Magnus, K. Kappel, R. Das, and J. M. Bujnicki
BMC Bioinformatics, vol. 20, no. 1, pp. 512–15, Oct. 2019
https://github.com/mmagnus/EvoClustRNA

@ Warsaw University, Poland

Rearrangements within the U6 snRNA core at the transition between the two catalytic steps of splicing.
K. Eysmont, K. Matylla-Kulinska, A. Jaskulska, M. Magnus, and M. M. Konarska
Molecular Cell, vol. 75, no. 3, pp. 538–548.e3, Aug. 2019
https://github.com/mmagnus/rna-tools/tree/master/U6MolCell

@ International Institute of Molecular and Cell Biology, Poland & Warsaw University, Poland

RNA-Puzzles toolkit: A computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools.
M. Magnus, M. Antczak, P. Lukasiak, J. Wiedemann, T. Zok, J. M. Bujnicki, E. Westhof, M. Szachniuk, and Z. Miao
Nucleic Acid Research, vol. 48, no. 2, pp. 576–588, Jan. 2020
https://github.com/mmagnus/rna-tools

@ International Institute of Molecular Mechanisms and Machines, Polish Academy of Sciences, Warsaw, Poland

rna-tools.online – a Swiss army knife for RNA 3D modeling workflows
M. Magnus
Nucleic Acid Research, 10.1093/nar/gkac372, May 2022
https://rna-tools.online


Published:

[22] RNA Puzzles V @ Nature Methods 2024

[21] SimRNAweb v2.0: A web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories @ Nucleic Acid Research 2024

[20] RNA3DB: A dataset for training and benchmarking deep learning models for RNA structure prediction
M. Szikszai, M. Magnus, S. Sanghi, S. Kadyan, N. Bouatta, E. Rivas
@biorxiv 2024

[19] RNA fragment assembly with experimental restraints.
G. Chojnowski, R. Zaborowski, M. Magnus, S. Mukherjee, and J. M. Bujnicki
@biorxiv 2021 Bioinformatics, Volume 39, Issue 9, September 2023
http://iimcb.genesilico.pl/rnamasonry

[18] RNA 3D structure comparison using RNA-Puzzles toolkit.
M. Magnus, Z. Miao
RNA Structure Prediction, 263-285, Jan 2023
https://github.com/mmagnus/rna-tools

[17] rna-tools.online – a Swiss army knife for RNA 3D modeling workflows.
M. Magnus
Nucleic Acid Research, 10.1093/nar/gkac372, May 2022
https://rna-tools.online

[16] RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.
Z. Miao, R. W. Adamiak, M. Antczak, M. J. Boniecki, J. M. Bujnicki, S.-J. Chen, C. Y. Cheng, Y. Cheng, F.-C. Chou, R. Das, N. V. Dokholyan, F. Ding, C. Geniesse, Y. Jiang, A. Joshi, A. Krokhotin, M. Magnus, O. Mailhot, F. Major, T. H. Mann, P. Piatkowski, R. Pluta, M. Popenda, J. Sarzynska, L. Sun, M. Szachniuk, S. Tian, J. Wang, J. Wang, A. M. Watkins, J. Wiedemann, Y. Xiao, X. Xu, J. D. Yesselman, D. Zhang, Y. Zhang, Z. Zhang, C. Zhao, P. Zhao, Y. Zhou, T. Zok, A. Zyła, A. Ren, R. T. Batey, B. L. Golden, L. Huang, D. M. Lilley, Y. Liu, D. J. Patel, and E. Westhof
RNA, [epub] 10.1261/rna.075341.120, May 2020

[15] RNA-Puzzles toolkit: A computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools.
M. Magnus, M. Antczak, P. Lukasiak, J. Wiedemann, T. Zok, J. M. Bujnicki, E. Westhof, M. Szachniuk, and Z. Miao
Nucleic Acid Research, vol. 48, no. 2, pp. 576–588, Jan. 2020
https://github.com/mmagnus/rna-tools

[14] RNA 3D Structure Prediction Using Multiple Sequence Alignment Information.
M. Magnus, K. Kappel, R. Das, and J. M. Bujnicki
BMC Bioinformatics, vol. 20, no. 1, pp. 512–15, Oct. 2019
https://github.com/mmagnus/EvoClustRNA

[13] Rearrangements within the U6 snRNA core at the transition between the two catalytic steps of splicing.
K. Eysmont, K. Matylla-Kulinska, A. Jaskulska, M. Magnus, and M. M. Konarska
Molecular Cell, vol. 75, no. 3, pp. 538–548.e3, Aug. 2019
https://github.com/mmagnus/rna-tools/tree/master/U6MolCell

[12] RNArchitecture: a database and a classification system of RNA families, with a focus on structural information.
P. Boccaletto, M. Magnus, C. Almeida, A. Zyła, A. Astha, R. Pluta, B. Bagiński, E. J. Jankowska, S. Dunin-Horkawicz, T. K. Wirecki, M. J. Boniecki, F. Stefaniak, and J. M. Bujnicki
Nucleic Acids Research, vol. 46, no. 1, pp. D202–D205, Jan. 2018
http://genesilico.pl/RNArchitecture

[11] RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.
Z. Miao, R. W. Adamiak, M. Antczak, R. T. Batey, A. J. Becka, M. Biesiada, M. J. Boniecki, J. M. Bujnicki, S.-J. Chen, C. Y. Cheng, F.-C. Chou, A. R. Ferré-D'Amaré, R. Das, W. K. Dawson, F. Ding, N. V. Dokholyan, S. Dunin-Horkawicz, C. G eniesse, K. Kappel, W. Kladwang, A. Krokhotin, G. E. Łach, F. Major, T. H. Mann, M. Magnus, K. Pachulska-Wieczorek, D. J. Patel, J. A. Piccirilli, M. Popenda, K. J. Purzycka, A. Ren, G. M. Rice, J. Santalucia, J. Sarzynska, M. Szachniuk, A. Tandon, J. J. Trausch, S. Tian, J. Wang, K. M. Weeks, B. Williams, Y. Xiao, X. Xu, D. Zhang, T. Zok, and E. Westhof
RNA, vol. 23, no. 5, pp. 655–672, May 2017

[10] SimRNAweb: a web server for RNA 3D structure modeling with optional restraints.
M. Magnus* , M. J. Boniecki*, W. K. Dawson, and J. M. Bujnicki
Nucleic Acids Research, vol. 44, no. 1, pp. W315–9, Jul. 2016
https://genesilico.pl/SimRNAweb

[9] Modeling of Protein-RNA Complex Structures Using Computational Docking Methods.
B. Madan, J. M. Kasprzak, I. Tuszyńska, M. Magnus, K. Szczepaniak, W. K. Dawson, and J. M. Bujnicki
Methods Mol. Biol., vol. 1414, no. 21, pp. 353–372, 2016

[8] RNA 3D Structure Modeling by Combination of Template-Based Method ModeRNA, Template-Free Folding with SimRNA, and Refinement with QRNAS.
P. Piatkowski, J. M. Kasprzak, D. Kumar, M. Magnus, G. Chojnowski, and J. M. Bujnicki
Methods Mol. Biol., vol. 1490, no. Suppl, pp. 217–235, 2016

[7] NPDock: a web server for protein-nucleic acid docking.
I. Tuszyńska, M. Magnus, K. Jonak, W. K. Dawson, and J. M. Bujnicki
Nucleic Acids Research, vol. 43, no. 1, pp. W425–30, Jul. 2015
http://genesilico.pl/NPDock

[6] RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.
Z. Miao, R. W. Adamiak, M.-F. Blanchet, M. J. Boniecki, J. M. Bujnicki, S.-J. Chen, C. Y. Cheng, G. Chojnowski, F.-C. Chou, P. Cordero, J. A. Cruz, A. R. Ferré-D'Amaré, R. Das, F. Ding, N. V. Dokholyan, S. Dunin-Horkawicz, W. Kladwang, A. Krokhotin, G. Lach, M. Magnus, F. Major, T. H. Mann, B. Masquida, D. Matelska, M. Meyer, A. Peselis, M. Popenda, K. J. Purzycka, A. Serganov, J. Stasiewicz, M. Szachniuk, A. Tandon, S. Tian, J. Wang, Y. Xiao, X. Xu, J. Zhang, P. Zhao, T. Zok, and E. Westhof
RNA, vol. 21, no. 6, pp. 1066–1084, Jun. 2015

[5] Computational modeling of protein-RNA complex structures.
I. Tuszyńska, D. Matelska, M. Magnus, G. Chojnowski, J. M. Kasprzak, L. P. Kozlowski, S. Dunin-Horkawicz, and J. M. Bujnicki
Methods, vol. 65, no. 3, pp. 310–319, Feb. 2014

[4] Computational modeling of RNA 3D structures, with the aid of experimental restraints.
M. Magnus*, D. Matelska*, G. Lach, G. Chojnowski, M. J. Boniecki, E. Purta, W. K. Dawson, S. Dunin-Horkawicz, and J. M. Bujnicki
RNA Biol, vol. 11, no. 5, pp. 522–536, 2014

[3] MetaLocGramN: A meta-predictor of protein subcellular localization for Gram-negative bacteria.
M. Magnus, M. Pawlowski, and J. M. Bujnicki
BBA - Proteins and Proteomics, vol. 1824, no. 12, pp. 1425–1433, Dec. 2012
http://genesilico.pl/MetaLocGramN/

[2] Structural bioinformatics of the human spliceosomal proteome.
I. Korneta, M. Magnus, and J. M. Bujnicki
Nucleic Acids Research, vol. 40, no. 15, pp. 7046–7065, Aug. 2012
http://iimcb.genesilico.pl/SpliProt3D

[1] Structures of MicroRNA Precursors.
P. Kozlowski, J. Starega-Roslan, M. Legacz, M. Magnus, and W. J. Krzyzosiak
Current Perspectives in microRNAs (miRNA), no. 1, Dordrecht: Springer, Dordrecht, 2008, pp. 1–16.