Baulin Group

Eugene F. Baulin, PhD

Group Leader

Laboratory of RNA Algorithms
ORCID: 0000-0003-4694-9783

RESEARCH
MEMBERS OF THE GROUP
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GROUP LEADER
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Research interests

Functional RNA molecules have become recognized as major players in diverse cellular processes. A wide range of non-coding RNAs has been discovered, including catalytic ribozymes, ligand-binding riboswitches, long non-coding and intronic RNAs, all involved in various aspects of gene expression regulation. RNAs have driven breakthroughs such as mRNA vaccines and RNA-guided genome editing systems, significantly reshaping modern biology and medicine. RNAs often form complex structures that define their functioning, e.g., via binding to proteins or developing resistance to exonucleases. Studying RNA structure and its organization principles enables grasping the mechanisms underlying the folding of such RNAs, yielding crucial insights into RNA function, such as regulatory roles, interactions with proteins or small molecules, or involvement in disease pathways.

In the Laboratory of RNA Algorithms, we design innovative algorithms and tools to tackle the computational challenges of RNA structural studies and apply them to uncover insights into RNA biology. Our research focus includes the problems of RNA sequence and structure alignment, secondary structure prediction, motif search, and 3D structure prediction. Currently, we are developing ALTERNA, a method for simultaneous multiple sequence alignment and RNA secondary structure prediction from unaligned homologous sequences, which could derive pseudoknotted structures and alternative folds even from imperfect alignments.

Members of the group

	Name		Surname		Degree	E-mail
	Eugene		Baulin		PhD	e.baulin@imol.institute

Publications

2024

Bu, F., Adam, Y., Adamiak, R. W., Antczak, M., de Aquino, B. R. H., Badepally, N. G., Batey, R. T., Baulin, E.F., … & Miao, Z. (2024). RNA-Puzzles Round V: blind predictions of 23 RNA structures. Nature Methods, 1-13. 10.1038/s41592-024-02543-9
Badepally, N. G., de Moura, T. R., Purta, E., Baulin, E. F., & Bujnicki, J. M. (2024). Cryo-EM structure of raiA ncRNA from Clostridium reveals a new RNA 3D fold. Journal of Molecular Biology, 436(23), 168833. 10.1016/j.jmb.2024.168833
Baulin, E.F., Bohdan, D.R., Kowalski, D., Serwatka, M., Świerczyńska, J., Żyra, Z., & Bujnicki, J.M., (2024) ARTEM: a method for RNA tertiary motif identification with backbone permutations, and its example application to kink-turn-like motifs. bioRxiv. DOI: 10.1101/2024.05.31.596898
Bohdan, D. R., Bujnicki, J. M., & Baulin, E. F. (2024). ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment. Nucleic Acids Research, gkae758. 10.1093/nar/gkae758
de Moura, T. R., Purta, E., Bernat, A., Martín-Cuevas, E. M., Kurkowska, M., Baulin, E. F., … & Bujnicki, J. M. (2024). Conserved structures and dynamics in 5′-proximal regions of Betacoronavirus RNA genomes. Nucleic Acids Research, gkae144. 10.1093/nar/gkae144

2023

Bohdan, D. R., Nikolaev, G. I., Bujnicki, J. M., & Baulin, E. F. (2023). SQUARNA – an RNA secondary structure prediction method based on a greedy stem formation model. bioRxiv, 2023-08. 10.1101/2023.08.28.555103
Baulin, E. F., Mukherjee, S., … & Bujnicki, J. M. (2023). RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints. Proteins: Structure, Function, and Bioinformatics. 10.1002/prot.26575
Metelev, V. G., Baulin, E. F., & Bogdanov, A. A. (2023). Multiple Non-Canonical Base-Stacking Interactions as One of the Major Determinants of RNA Tertiary Structure Organization. Biochemistry (Moscow), 88(6), 792-800. 10.1134/S000629792306007X
Luo, B., Zhang, C., Ling, X., Mukherjee, S., Jia, G., Xie, J., Jia, X., Liu, L., Baulin, E.F., Luo, Y., Jiang, L., Dong, H., Wei, X., Bujnicki, J.M. & Su, Zh., (2023) Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing. Nature Catalysis, 6(4), pp.298-309. 10.1038/s41929-023-00934-3
Bohdan, D. R., Voronina, V. V., Bujnicki, J. M., & Baulin, E. F. (2023). A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures. Nucleic Acids Research, 51(16), 8367-8382. 10.1093/nar/gkad605

2021

Baulin EF. (2021) Features and Functions of the A-Minor Motif, the Most Common Motif in RNA Structure. Biochemistry (Moscow). Aug;86(8):952-61. 10.1134/S000629792108006X
Shalybkova AA, Mikhailova DS, Kulakovskiy IV, Fakhranurova LI, Baulin EF. (2021) Annotation of the local context of the RNA secondary structure improves the classification and prediction of A-minors. RNA. May 20:rna-078535. 10.1261/rna.078535.120

2020

Baulin, E., Metelev, V., & Bogdanov, A. (2020). Base-intercalated and base-wedged stacking elements in 3D-structure of RNA and RNA–protein complexes. Nucleic acids research, 48(15), 8675-8685. 10.1093/nar/gkaa610
Baulin E.F., Kulakovskiy I.V., Roytberg M.A., Astakhova T.V. (2020) Brain-related genes are specifically enriched with long phase 1 introns. PLoS ONE 10.1371/journal.pone.0233978

2016

Baulin, E ., Yacovlev, V., Khachko, D., Spirin, S., & Roytberg, M. (2016). URS DataBase: universe of RNA structures and their motifs. Database, baw085. 10.1093/database/baw085
Zanegina, O., Kirsanov, D., Baulin, E., Karyagina, A., Alexeevski, A., & Spirin, S. (2016). An updated version of NPIDB includes new classifications of DNA–protein complexes and their families. Nucleic acids research, 44(D1), D144-D153. 10.1093/nar/gkv1339

About Group Leader

Dr. Eugene F. Baulin completed his PhD in Mathematical Biology and Bioinformatics in 2021 under the supervision of Prof. Mikhail A. Roytberg and Prof. Ivan V. Kulakovskiy at the Moscow Institute of Physics and Technology, Russia, where he studied the interplay between the secondary structure and tertiary interactions and motifs in structured RNA molecules. He then joined the group of Prof. Janusz M. Bujnicki at IIMCB in Warsaw, Poland, as a postdoctoral researcher, where he was involved in developing computational methods for the analysis, modeling, and prediction of nucleic acid structures and their complexes. He joined IMOL in 2024 as a principal investigator.

Funding

2024

National Science Centre, OPUS 27: “Using ALTERNA to resolve the causality dilemma between RNA multiple sequence alignment and RNA secondary structure” (2024/53/B/NZ2/02718), leader: Eugene F. Baulin.

2022

EMBO Postdoctoral Fellowship: “Exploring RNA folds and remote evolutionary relationships with an improved structural similarity search method”. @Janusz Bujnicki lab, IIMCB in Warsaw.

2021

Russian Science Foundation grant: “Annotated atlas of long-range tertiary interactions in non-coding RNA structures”. Gratefully declined.

Resources

Our works

RNA Secondary Structure Prediction

SQUARNA – an RNA secondary structure prediction method based on a greedy stem formation model. DOI: 10.1101/2023.08.28.555103 (available via pip install)

RNA 3D Structure Alignment

ARTEM – a tool for RNA tertiary motif search. DOI: 10.1093/nar/gkad605
ARTEMIS – a tool for RNA 3D structure alignment. DOI: 10.1093/nar/gkae758 (Demo, Tutorial)

Other Tools and Datasets

urslib2 – a Python library for processing RNA structure data from PDB/mmCIF files & DSSR annotations. DOI: 10.1093/nar/gkad605
LORA – A dataset of long-range RNA 3D modules. DOI: 10.1093/nar/gkad605
ARTEM-KT – A dataset of kink-turn-like RNA 3D modules. DOI: 10.1101/2024.05.31.596898

RNA-related hints

Expect ~80% of all Mg ions in RNA-containing 3D structures to be garbage
Rfam families of riboswitches are usually aptamer-only and don’t include the platforms

Not our works, but still good 🙂

RNA CoSSMos – a database of RNA 3D loop motifs. DOI: 10.1093/database/baz153
JAR3D – scoring RNA loop sequences against known 3D motifs. DOI: 10.1093/nar/gkw453
ModeRNA – a tool for comparative modeling of RNA 3D structure. DOI: 10.1093/bioinformatics/btr400
SimRNA – a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories. DOI: 10.1093/nar/gkae356
QRNAS – software tool for refinement of nucleic acid structures. DOI: 10.1186/s12900-019-0103-1
RNAComposer – an automated template-based RNA structure modeling server. DOI: 10.1007/978-1-4939-6433-8_13
Rclick – a tool for topology-independent RNA 3D structure alignment. DOI: 10.1093/nar/gkw819
US-align – a unified protocol to compare 3D structures of different macromolecules. DOI: 10.1038/s41592-022-01585-1
RNA3DHub – RNA Structure Atlas, RNA 3D Motif Atlas, and Representative RNA Sets. DOI: 10.1016/j.ymeth.2016.04.025
DSSR – Dissecting the spatial structure of RNA, annotation of RNA interactions. DOI: 10.1093/nar/gkv716

RNA-related Wikipedia pages