Publications
Our contributions to RNA biology, computational methods, and beyond.
88 publications and preprints.
2026
A refined Saccharomyces cerevisiae reference transcriptome from Direct RNA Sequencing, with a reusable pipeline for UTR annotation updates
O Rossini, A Cleynen, NE Shirokikh
bioRxiv 2026.06.30.735557
dirCLIP profiles variant-specific RNA-protein interactions via nanopore long-read sequencing
Bahrudeen, Mohamed; Scaravilli, Mauro; Zahir, Zileena; Woodward, Katrina; Ahola, Timo; Ratnadiwakara, Madara; Kaslin, Jan; Loughlin, Fionna; Shirokikh, Nikolay E; Änkö, Minna-Liisa
bioRxiv 2026.01.22.701028
FracFixR: A compositional statistical framework for absolute proportion estimation between fractions in RNA sequencing data
A Cleynen, A Ravindran, NE Shirokikh
Bioinformatics 42(2), btaf615
Isoform-specific m6A deposition and coordinated splicing shape mammalian transcriptome evolution
Santos-Rodriguez, Gabriela; Srivastava, Akanksha; Ravindran, Agin; Oyelami, Favour O; Ip, Chi Kin; Gupta, Pallavi; Villanueva, Jeanette; King, Helen E; Grootveld, Abigail; Sneddon, Alexandra
Nature Communications
Multi-omic dissection of RNA control reveals convergent cis-regulatory programs during glucose starvation in yeast
Rossini, Orlane; Mahmud, Shafi; Shirokikh, Nikolay E; Cleynen, Alice
bioRxiv 2026.07.20.739609
TagGen: High-Performance Barcode Generator and Demultiplexer for High-Throughput and Long-Read Sequencing Applications
F Chowdhury, T Swain, R Shirokikh, D Rudler, A Fox, A Cleynen, ...
F1000Research 15, 642
The role of RNA modifications in cancer translational control
M Joy, A Cleynen, NE Shirokikh
RNA Biology 23, 1-39
VX: an AI-enabled desktop genome viewer and transcriptome browser with a programmable analysis framework
N Shirokikh, A Cleynen
bioRxiv 2026.05.17.725790
2025
Bayes-Adaptive Impulse Control of Piecewise-Deterministic Markov Processes
O Rossini, M Vinyals, A Cleynen, B de Saporta, R Sabbadin
Bridging impulse control of piecewise deterministic markov processes and markov decision processes: Frameworks, extensions, and open challenges
A Cleynen, B de Saporta, O Rossini, R Sabbadin, A Vernay
arXiv preprint arXiv:2501.04120
Controlled Hidden Semi‐Markov Models
A Cleynen, B de Saporta, O Rossini, R Sabbadin, A Vernay
A Comprehensive Guide to HSMM: Theory, Software, and Advanced Extensions …
Estimating relapse time distribution from longitudinal biomarker trajectories using iterative regression and continuous time Markov processes
A Cleynen, B de Saporta, A Vernay
arXiv preprint arXiv:2503.10448
SWARM resolves nanopore signal interference between RNA modification types and reveals splicing-shaped pseudouridylation
S Prodic, A Cleynen, S Mahmud, A Srivastava, A Ravindran, M Kanchi, ...
bioRxiv 2025.12.18.695332
Translon: a single term for translated regions
Świrski, Michał I; Tierney, Jack AS; Albà, M Mar; Andreev, Dmitry E; Aspden, Julie L; Atkins, John F; Bassani-Sternberg, Michal; Berry, Marla J; Biffo, Stefano; Boris-Lawrie, Kathleen
Nature methods 22(10), 2002-2006
2024
A Monte-Carlo planning strategy for medical follow-up optimization: Illustration on multiple myeloma data
B de Saporta, A Thierry d’Argenlieu, R Sabbadin, A Cleynen
PloS one 19 (12), e0315661
Biochemical-free enrichment or depletion of RNA classes in real-time during direct RNA sequencing with RISER
Sneddon, Alexandra; Ravindran, Agin; Shanmuganandam, Somasundhari; Kanchi, Madhu; Hein, Nadine; Jiang, Simon; Shirokikh, Nikolay; Eyras, Eduardo
Nature Communications 15(1), 4422
Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress
Horvath, Attila; Janapala, Yoshika; Woodward, Katrina; Mahmud, Shafi; Cleynen, Alice; Gardiner, Elizabeth E; Hannan, Ross D; Eyras, Eduardo; Preiss, Thomas; Shirokikh, Nikolay E
Nucleic Acids Research 52(13), 7925-7946
Deep reinforcement learning for controlled piecewise deterministic Markov process in cancer treatment follow-up
A Cleynen, B de Saporta, O Rossini, R Sabbadin, M Vinyals
PFIA
Defining Therapeutic Epitranscriptome of Multiple Myeloma for Accurate Subtyping and Personalized Prognostics
A Cleynen, A Ravindran, D Talaulikar, E Eyras, N Shirokikh
Blood 144, 4652
Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation
Smith, Aaron B; Ganguly, Diep R; Moore, Marten; Bowerman, Andrew F; Janapala, Yoshika; Shirokikh, Nikolay E; Pogson, Barry J; Crisp, Peter A
The Plant Journal 117(3), 818-839
High-Accuracy RNA Integrity Definition for Unbiased Transcriptome Comparisons with INDEGRA
A Cleynen, A Ravindran, A Sethi, B Kumar, T Javaid, S Mahmud, ...
bioRxiv 2024.12.12.627949
Predicting Yeast Translation Efficiency from RNA Modification and Degradation Features: A Machine Learning Approach
Rossini, Orlane; Cleynen, Alice; Shirokikh, Nikolay E; Mahmud, Shafi
Journees de Biostatistique 2024
Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications
Acera Mateos, P; J Sethi, A; Ravindran, A; Srivastava, A; Woodward, K; Mahmud, S; Kanchi, M; Guarnacci, M; Xu, J; WS Yuen, Z
Nature Communications 15(1), 3899
R2Dtool: integration and visualization of isoform-resolved RNA features
Sethi, Aditya J; Acera Mateos, Pablo; Hayashi, Rippei; Shirokikh, Nikolay E; Eyras, Eduardo
Bioinformatics 40(8), btae495
RNA Multi-Omics to Reveal New Targets in Mounting DLBCL and B-ALL Drug Resistance
N Muntasir, A Ravindran, S Mahmud, M Joy, J Perera, A Chowdhery, ...
Blood 144, 6258
Substrate diversity of NSUN enzymes and links of 5-methylcytosine to mRNA translation and turnover
Guarnacci, Marco; Zhang, Pei-Hong; Kanchi, Madhu; Hung, Yu-Ting; Lin, Hanrong; Shirokikh, Nikolay E; Yang, Li; Preiss, Thomas
Life science alliance 7(9)
2023
An example of medical treatment optimization under model uncertainty
A Cleynen, B de Saporta, O Rossini, R Sabbadin
Applied Probability Society Conference
An Improved Method for Purification of the Residual Bodies from the Seminiferous Tubules of Mice
Apu, Mohd Nazmul Hasan; Shirokikh, Nikolay E; Khochbin, Saadi; Soboleva, Tatiana A
Current Protocols 3(11), e920
Contrôle dynamique stochastique: une approche à base de modèles semi-Markov Application à l'optimisation d'un traitement médical
A Cleynen, B de Saporta, O Rossini, R Sabbadin
8èmes rencontres de statistique
In multiple myeloma, high-risk secondary genetic events observed at relapse are present from diagnosis in tiny, undetectable subclonal populations
R Lannes, M Samur, A Perrot, C Mazzotti, M Divoux, T Cazaubiel, X Leleu, ...
Journal of Clinical Oncology 41 (9), 1695-1702
Local tree methods for classification: a review and some dead ends
A Cleynen, L Raynal, JM Marin
Computo
Numerical method for solving impulse control problems in partially observed piecewise deterministic Markov processes
A Cleynen, B De Saporta
Advances in Applied Probability, 1-32
Pathways of Early Evolution From the Perspectives of a Riboreplisome–The Ultimate RNA Machine of Life
Shirokikh, Nikolay
Preprints.org, 202305.0415
RNA machines
Shirokikh, Nikolay E; Jensen, Kirk Blomquist; Thakor, Nehal
Frontiers in Genetics 14, 1290420
2022
Language-informed basecalling architecture for nanopore direct rna sequencing
Sneddon, Alexandra; Mateos, Pablo Acera; Shirokikh, Nikolay; Eyras, Eduardo
Proceedings of Machine Learning Research 200, 150-165
Le paradoxe des anniversaires
A Cleynen, H Queffelec
Images des mathématiques
Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells
Shirokikh, Nikolay E
Critical reviews in biochemistry and molecular biology 57(3), 261-304
Unsupervized identification of prognostic copy-number alterations using segmentation and lasso regularization
A Cleynen, H Avet-Loiseau, J Corre
bioRxiv 2022.12.14.520497
2021
Rapid in vivo fixation and isolation of translational complexes from eukaryotic cells
Janapala, Yoshika; Woodward, Katrina; Lee, Jiwon; Rug, Melanie; Preiss, Thomas; Shirokikh, Nikolay E
Journal of Visualized Experiments(178)
Translational control in cell ageing: an update
Woodward, Katrina; Shirokikh, Nikolay E
Biochemical Society Transactions 49(6), 2853-2869
2020
Evaluation of mineralogy per geological layers by Approximate Bayesian Computation
V Bruned, A Cleynen, A Mas, S Wlodarczyk
SPE Journal 25 (05), 2418-2432
Rapport de conjoncture 2019: CID 51 Modélisation mathématique, informatique et physique pour les sciences du vivant
F Picard, M Ferro, A Cleynen, M Doumic, X Duchemin, G Fertin, J Filee, ...
Comité national de la recherche scientifique
Selective translation complex profiling reveals staged initiation and co-translational assembly of initiation factor complexes
Wagner, Susan; Herrmannová, Anna; Hronová, Vladislava; Gunišová, Stanislava; Sen, Neelam D; Hannan, Ross D; Hinnebusch, Alan G; Shirokikh, Nikolay E; Preiss, Thomas; Valášek, Leoš Shivaya
Molecular cell 79(4), 546-560. e7
2019
Control of translation at the initiation phase during glucose starvation in yeast
Janapala, Yoshika; Preiss, Thomas; Shirokikh, Nikolay E
International Journal of Molecular Sciences 20(16), 4043
Insights into the biogenesis and potential functions of exonic circular RNA
Ragan, Chikako; Goodall, Gregory J; Shirokikh, Nikolay E; Preiss, Thomas
Scientific reports 9(1), 2048
Migration of small ribosomal subunits on the 5′ untranslated regions of capped messenger RNA
Shirokikh, Nikolay E; Dutikova, Yulia S; Staroverova, Maria A; Hannan, Ross D; Preiss, Thomas
International Journal of Molecular Sciences 20(18), 4464
2018
Change-point detection for piecewise deterministic Markov processes
A Cleynen, B De Saporta
Automatica 97, 234-247
Dysregulated IL-18 is a key driver of immunosuppression and a possible therapeutic target in the multiple myeloma microenvironment
K Nakamura, S Kassem, A Cleynen, ML Chretien, C Guillerey, EM Putz, ...
Cancer cell 33 (4), 634-648. e5
Long intergenic non-coding RNAs have an independent impact on survival in multiple myeloma
MK Samur, S Minvielle, A Gulla, M Fulciniti, A Cleynen, A Aktas Samur, ...
Leukemia 32 (12), 2626-2635
Multiple myeloma clonal evolution in homogeneously treated patients
J Corre, A Cleynen, S Robiou du Pont, L Buisson, N Bolli, M Attal, ...
Leukemia 32 (12), 2636-2647
Nucleotide excision repair is a potential therapeutic target in multiple myeloma
R Szalat, MK Samur, M Fulciniti, M Lopez, P Nanjappa, A Cleynen, K Wen, ...
Leukemia 32 (1), 111-119
Translation initiation by cap‐dependent ribosome recruitment: recent insights and open questions
Shirokikh, Nikolay E; Preiss, Thomas
WIREs RNA 9(4), e1473
Variable BCL2/BCL2L1 ratio in multiple myeloma with t (11; 14)
A Cleynen, M Samur, A Perrot, L Buisson, S Maheo, M Fulciniti, M Attal, ...
Blood 132 (26), 2778-2780
2017
Expressed fusion gene landscape and its impact in multiple myeloma
A Cleynen, R Szalat, M Kemal Samur, S Robiou du Pont, L Buisson, ...
Nature communications 8 (1), 1893
Genomics of multiple myeloma
S Robiou du Pont, A Cleynen, C Fontan, M Attal, N Munshi, J Corre, ...
Journal of Clinical Oncology 35 (9), 963-967
Model selection for the segmentation of multiparameter exponential family distributions
A Cleynen, É Lebarbier
Electronic Journal of Statistics
Optimal stopping for change-point detection of Piecewise Deterministic Markov Processes
A Cleynen, B De Saporta
CT 2017-SIAM Conference on Control and Its Applications
Translation complex profile sequencing to study the in vivo dynamics of mRNA–ribosome interactions during translation initiation, elongation and termination
Shirokikh, Nikolay E; Archer, Stuart K; Beilharz, Traude H; Powell, David; Preiss, Thomas
Nature protocols 12(4), 697-731
2016
Comparing change-point location in independent series
A Cleynen, S Robin
Statistics and Computing 26 (1), 263-276
Dynamics of ribosome scanning and recycling revealed by translation complex profiling
Archer, Stuart K; Shirokikh, Nikolay E; Beilharz, Traude H; Preiss, Thomas
Nature 535(7613), 570-574
Inference in finite state space non parametric hidden Markov models and applications
É Gassiat, A Cleynen, S Robin
Statistics and Computing 26 (1), 61-71
Segmentor3isback: a fast segmentation algorithm
A Cleynen, G Rigaill, M Koskas
Segmentor3IsBack, R package version 2
2015
Differentially expressed and prognostically significant lincrnas may impact immune system and tumor progression in multiple myeloma (MM)
MK Samur, A Gulla, A Cleynen, F Magrangeas, S Minvielle, KC Anderson, ...
Blood 126 (23), 2989-2989
Dysregulated Nucleotide Excision Repair (NER) Is a New Target in Multiple Myeloma
R Szalat, MK Samur, A Cleynen, A Calkins, M Dreze, YT Tai, S Minvielle, ...
Blood 126 (23), 4187
Probe‐directed degradation (PDD) for flexible removal of unwanted cDNA sequences from RNA‐Seq libraries
Archer, Stuart K; Shirokikh, Nikolay E; Preiss, Thomas
Current protocols in human genetics 85(1), 11.15. 1-11.15. 36
Probing the closed-loop model of mRNA translation in living cells
Archer, Stuart K; Shirokikh, Nikolay E; Hallwirth, Claus V; Beilharz, Traude H; Preiss, Thomas
RNA biology 12(3), 248-254
Role of additional chromosomal changes in the prognostic value of t (4; 14) and del (17p) in multiple myeloma: the IFM experience
B Hebraud, F Magrangeas, A Cleynen, V Lauwers-Cances, ML Chretien, ...
Blood 125 (13), 2095-2100
The fusion gene landscape in Multiple Myeloma, with clinical impact
A Cleynen, R Szalat, MK Samur, G Parmigiani, NC Munshi, ...
Blood 126 (23), 835-835
Understanding the role of hyperdiploidy in myeloma prognosis: which trisomies really matter?
ML Chretien, J Corre, V Lauwers-Cances, F Magrangeas, A Cleynen, ...
Blood 126 (25), 2713-2719
2014
Comparing segmentation methods for genome annotation based on rna-seq data
A Cleynen, S Dudoit, S Robin
Journal of Agricultural, Biological, and Environmental Statistics 19 (1 …
Fast estimation of the Integrated Completed Likelihood criterion for change-point detection problems with applications to Next-Generation Sequencing data
A Cleynen, TM Luong, G Rigaill, G Nuel
Signal processing 98, 233-242
Frequent Igh fusion transcripts with clinical impact in multiple myeloma
A Cleynen, R Szalat, MK Samur, N Rashid, G Parmigiani, NC Munshi, ...
Blood 124 (21), 721
Long Intergenic Non-Coding RNAs (lincRNA) Impacts Biology and Clinical Outcome in Multiple Myeloma
MK Samur, N Rashid, A Cleynen, M Fulciniti, A Sperling, S Minvielle, ...
Blood 124 (21), 642
Segmentation of the Poisson and negative binomial rate models: a penalized estimator
A Cleynen, É Lebarbier
ESAIM: Probability and Statistics 18, 750-769
Segmentor3IsBack: an R package for the fast and exact segmentation of Seq-data
A Cleynen, M Koskas, E Lebarbier, G Rigaill, S Robin
Algorithms for Molecular Biology 9 (1), 6
Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage
Archer, Stuart K; Shirokikh, Nikolay E; Preiss, Thomas
BMC genomics 15(1), 401
2013
A penalized maximum likelihood estimator for the segmentation of RNA-Seq data
A Cleynen, E Lebarbier
Journées de Statistiques
Statistical Approaches for Segmentation: Application to Genome Annotation
A Cleynen
PhD thesis, Universite Paris-Sud (Paris XI)
2012
Leader sequences of eukaryotic mRNA can be simultaneously bound to initiating 80S ribosome and 40S ribosomal subunit
Sogorin, EA; Shirokikh, NE; Ibragimova, AM; Vasiliev, VD; Agalarov, S Ch; Spirin, AS
Biochemistry (Moscow) 77(4), 342-345
2011
Insight into the structural organization of the omega leader of TMV RNA: the role of various regions of the sequence in the formation of a compact structure of the omega RNA
Agalarov, Sultan C; Sogorin, Evgeny A; Shirokikh, Nikolay E; Spirin, Alexander S
Biochemical and biophysical research communications 404(1), 250-253
2010
Chemical and enzymatic probing of spatial structure of the omega leader of tobacco mosaic virus RNA
Shirokikh, NE; Agalarov, S Ch; Spirin, AS
Biochemistry (Moscow) 75(4), 405-411
Quantitative analysis of ribosome–mRNA complexes at different translation stages
Shirokikh, Nikolay E; Alkalaeva, Elena Z; Vassilenko, Konstantin S; Afonina, Zhanna A; Alekhina, Olga M; Kisselev, Lev L; Spirin, Alexander S
Nucleic acids research 38(3), e15-e15
2008
Poly (A) leader of eukaryotic mRNA bypasses the dependence of translation on initiation factors
Shirokikh, Nikolay E; Spirin, Alexander S
Proceedings of the National Academy of Sciences 105(31), 10738-10743
2007
Dissociation of eIF1 from the 40S ribosomal subunit is a key step in start codon selection in vivo
Cheung, Yuen-Nei; Maag, David; Mitchell, Sarah F; Fekete, Christie A; Algire, Mikkel A; Takacs, Julie E; Shirokikh, Nikolay; Pestova, Tatyana; Lorsch, Jon R; Hinnebusch, Alan G
Genes & development 21(10), 1217-1230
The leader sequence of tobacco mosaic virus RNA devoid of Watson–Crick secondary structure possesses a cooperatively melted, compact conformation
Kovtun, Alexey A; Shirokikh, Nikolay E; Gudkov, Anatoly T; Spirin, Alexander S
Biochemical and biophysical research communications 358(1), 368-372
2006
The fidelity of translation initiation: reciprocal activities of eIF1, IF3 and YciH
Lomakin, Ivan B; Shirokikh, Nikolay E; Yusupov, Marat M; Hellen, Christopher UT; Pestova, Tatyana V
The EMBO journal 25(1), 196-210
2005
The eIF1A C-terminal domain promotes initiation complex assembly, scanning and AUG selection in vivo
Fekete, Christie A; Applefield, Drew J; Blakely, Stephen A; Shirokikh, Nikolay; Pestova, Tatyana; Lorsch, Jon R; Hinnebusch, Alan G
The EMBO journal 24(20), 3588
Translation initiation by factor-independent binding of eukaryotic ribosomes to internal ribosomal entry sites
Pisarev, Andrey V; Shirokikh, Nikolay E; Hellen, Christopher UT
Comptes rendus biologies 328(7), 589-605