SGPocket: A New Graph Convolutional Neural Network for Ligand-Protein Binding Site Prediction

Authors: Crampon, Kevin, Bourrasset, Cedric, Baud, Stephanie, Steffenel, Luiz Angelo

Contributors: Steffenel, Luiz Angelo, Laboratoire d'Informatique en Calcul Intensif et Image pour la Simulation (LICIIS), Université de Reims Champagne-Ardenne (URCA), Matrice Extracellulaire et Dynamique Cellulaire - UMR CNRS 7369 (MEDyC), Université de Reims Champagne-Ardenne (URCA)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS), Eviden

Source: Current Medicinal Chemistry. 32:5996-6006

Subject Terms: [INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 0101 mathematics, 01 natural sciences, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], 0104 chemical sciences

Access URL: https://pubmed.ncbi.nlm.nih.gov/38468517

CREMSA: compressed indexing of (ultra) large multiple sequence alignments

Authors: Salson, Mikaël, Boddaert, Arthur, Gueye, Awa Bousso, Bulteau, Laurent, Hernandez--Courbevoie, Yohan, Marchet, Camille, Pan, Nan, Will, Sebastian, Ponty, Yann

Contributors: Salson, Mikaël

Source: Bioinformatics

Subject Terms: Genome Sequence Analysis, Compression, Indexing, Multiple sequence alignment, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

File Description: application/pdf

Access URL: https://hal.science/hal-04910677v2/document
https://hal.science/hal-04910677v2
https://doi.org/10.1093/bioinformatics/btaf211

A Chimera Model for Motion Anticipation in the Retina and the Primary Visual Cortex

Authors: Emonet, Jérôme, Souihel, Selma, Di Volo, Matteo, Destexhe, Alain, Chavane, Frédéric, Cessac, Bruno

Contributors: Emonet, Jérôme

Source: Neural Computation. :1-50

Subject Terms: V1, Visual processing, [SCCO.NEUR] Cognitive science/Neuroscience, Lateral connectivity, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, Retina, Anticipation, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

File Description: application/pdf

Access URL: https://inria.hal.science/hal-04709925v2/document
https://doi.org/10.1162/neco.a.34
https://inria.hal.science/hal-04709925v2

Efficient GPU Computation of Large Protein Solvent-Excluded Surface

Authors: Cyprien Plateau–Holleville, Maxime Maria, Stéphane Mérillou, Matthieu Montes

Contributors: Plateau--Holleville, Cyprien, Synthèse et analyse d'images (XLIM-ASALI), XLIM (XLIM), Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS)-Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Génomique, bioinformatique et chimie moléculaire (GBCM), Conservatoire National des Arts et Métiers CNAM (CNAM), Institut universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), ANR-18-EURE-0017,TACTIC,Transverse Actions between advanced Ceramics & TIC(2018), European Project: 640283,H2020,ERC-2014-STG,VIDOCK(2015)

Source: IEEE Transactions on Visualization and Computer Graphics. 31:2101-2113

Subject Terms: Scientific visualization, [INFO.INFO-DC]Computer Science [cs]/Distributed, Molecular Biology/Structural Biology [q-bio.BM], [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], [INFO.INFO-GR] Computer Science [cs]/Graphics [cs.GR], Parallel, [INFO.INFO-GR]Computer Science [cs]/Graphics [cs.GR], [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, and Cluster Computing [cs.DC], Massively parallel algorithms, [INFO.INFO-DC] Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/38512738

A Comprehensive Framework for Unsupervised Deep Analysis of Tissue Bioarchitecture

Authors: Robert, Florian, Calovoulos, Alexia, Facq, Laurent, Decoeur, Fanny, Gontier, Etienne, Grosset, Christophe François, Denis de Senneville, Baudouin

Contributors: Denis De Senneville, Baudouin

Source: 2025 IEEE 38th International Symposium on Computer-Based Medical Systems (CBMS). :77-80

Subject Terms: [SDV] Life Sciences [q-bio], Segmentation, Bioarchitecture, [INFO] Computer Science [cs], Unsupervised learning, Scanning electron microscopy, Onconanotomy, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

File Description: application/pdf

Access URL: https://hal.science/hal-05036060v2

MCQR: Enhancing the Processing and Analysis of Quantitative Proteomics Data by Incorporating Chromatography and Mass Spectrometry Information

Authors: Balliau, Thierry, Frambourg, Anne, Langella, Olivier, Martin, Marie-Laure, Zivy, Michel, Blein-Nicolas, Mélisande

Contributors: Balliau, Thierry, Martin, Marie-Laure

Source: Journal of Proteome Research. 24:2861-2873

Subject Terms: quantitative proteomics, [SDV] Life Sciences [q-bio], statistical analysis, bioinformatics, quality control, data filtering, mass spectrometry, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/40391828
https://cnrs.hal.science/hal-05113649v1
https://hal.science/hal-05087344v1
https://doi.org/10.1021/acs.jproteome.4c01119

Conditions for Cyclic Attractors for a Class of Discrete n-Dimensional Repressilators

Authors: Sun, Honglu, Folschette, Maxime, Magnin, Morgan, Tonello, Elisa

Contributors: Folschette, Maxime

Source: Lecture Notes in Computer Science ISBN: 9783032015693

Subject Terms: Interaction graph, Repressilators, Discrete regulatory networks, Attractors, Static analysis, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

File Description: application/pdf

Access URL: https://hal.science/hal-05236106v1/document
https://doi.org/10.1007/978-3-032-01570-9_10
https://hal.science/hal-05236106v1

A gap and synergy analysis of the European research infrastructure (RI) ecosystem: advancing the novel GRACE-RI dedicated to plant genetic resources

Authors: Domenico De Paola, Francesca Taranto, Soraya Mousavi, Francesco Mercati, Wilma Sabetta, Marina Tumolo, Sharif Islam, Roland Pieruschka, Andrea Scaloni, Anne-Francoise Adam-Blondon, Lorenzo Maggioni, Sandra Goritschnig, Filippo Guzzon, Massimo Ianigro, Giovanni Giuseppe Vendramin, Giovanni Giuliano, Gabriele Bucci

Contributors: ADAM-BLONDON, Anne-Françoise

Source: Annals of botany 136(2), 275-285 (2025). doi:10.1093/aob/mcaf092

Subject Terms: [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, plant genetic resources, GRACE-RI, Crop Diversity, ESFRI Roadmap, Research Infrastructure, GRACE-RI, Plant Genetic Resources, ex situ and in situ PGR conservation, Genebanks, Gap Analysis, Synergy Analysis, ESFRI roadmap, genebanks, [SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics, research infrastructure, Crop diversity, synergy analysis, ex situ and in situ PGR conservation, gap analysis, [SHS.GESTION] Humanities and Social Sciences/Business administration, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

File Description: application/pdf

Access URL: https://juser.fz-juelich.de/record/1043447
https://hal.science/hal-05222930v1
https://doi.org/10.1093/aob/mcaf092
https://hal.science/hal-05222930v1/document

Combining Molecular Docking and Pharmacophore Models Predicts Ligand Binding of Endocrine-Disrupting Chemicals to Nuclear Receptors

Authors: Sellami, Asma, Montes, Matthieu, Lagarde, Nathalie

Contributors: Lagarde, Nathalie

Source: Chemical Research in Toxicology. 38:672-685

Subject Terms: [SDV.MHEP.EM] Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, Binding Sites, Pharmacophore, Receptors, Cytoplasmic and Nuclear, Endocrine Disruptors, Ligands, endocrine disrupting chemicals, [SDV.TOX] Life Sciences [q-bio]/Toxicology, Molecular Docking Simulation, Nuclear receptors, Receptors, Androgen, docking, pharmacophores, Humans, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Protein Binding

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/40178351

Pervasive formation of double-stranded RNAs by overlapping sense/antisense transcripts in budding yeast mitosis and meiosis

Authors: Szachnowski, Ugo, Becker, Emmanuelle, Stuparevic, Igor, Wery, Maxime, Sallou, Olivier, Boudet, Matéo, Bretaudeau, Anthony, Morillon, Antonin, Primig, Michael

Contributors: Jonchère, Laurent, Institut Curie Paris, Dynamics, Logics and Inference for biological Systems and Sequences (Dyliss), Centre Inria de l'Université de Rennes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT), University of Zagreb, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Plateforme bioinformatique GenOuest Rennes, Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®-Centre Inria de l'Université de Rennes, Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Dynamique de l'information génétique : bases fondamentales et cancer (DIG CANCER), Institut Curie Paris -Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique EHESP (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes (Biosit : Biologie - Santé - Innovation Technologique), This study was in part funded by a postdoctoral fellowship by La Region Bretagne (SAD)and a Croatian Science Foundation Grant (IP-2022-10-6851) to Igor Stuparević, ANR('DNA-life' - ANR-15-CE12-0007) and ERC ('DARK' – consolidator grant) to AntoninMorillon, and La Ligue Contre le Cancer (CD35 and CD29) to Michael Primig. Inserm andthe University of Rennes provided further funding. High-throughput sequencing wasperformed by the ICGex NGS platform of the Curie Institute that was supported by grantsANR-10-EQPX-0003 (Equipex) and ANR-10-INBS-0009-08 (France Génomique Consortium) from the Agence Nationale de la Recherche ('Investissements d’Avenir' program), byITMO-Cancer Aviesan (Plan Cancer III) and by the SiRIC-Curie program (SiRIC GrantINCa-DGOS-465 and INCa-DGOSInserm_12554). Data management, quality control andprimary analysis were performed by the Bioinformatics platform of the Curie Institute., ANR-15-CE12-0007,DNA-Life,Impact de l'achitecture nucléaire sur la longévité(2015), ANR-10-EQPX-0003,ICGex,Equipement de biologie intégrative du cancer pour une médecine personnalisée(2010), ANR-10-INBS-0009,France Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), European Project: 616180,EC:FP7:ERC,ERC-2013-CoG,DARK(2014)

Source: RNA. 31:497-513

Subject Terms: long non-coding RNA, Mitosis, RNA, Fungal, [SDV.GEN] Life Sciences [q-bio]/Genetics, Saccharomyces cerevisiae, yeast, double-stranded RNA, Meiosis, antisense transcripts, Gene Expression Regulation, Fungal, double stranded RNA, Saccharomycetales, Budding yeast, RNA, Antisense, long noncoding RNA, RNA, Messenger, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], antisense RNA, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], RNA, Double-Stranded

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/39848697
https://hal.science/hal-04935733v1
https://hal.science/hal-04935733v1/document
https://doi.org/10.1261/rna.080290.124

Convergence of the Number of Period sets in Strings

Authors: Rivals, Eric, Sweering, Michelle, Wang, Pengfei

Contributors: Eric Rivals and Michelle Sweering and Pengfei Wang, Rivals, Eric

Source: Algorithmica. 87:690-711

Subject Terms: FOS: Computer and information sciences, Periodicity, Discrete Mathematics (cs.DM), upper bound, G.2.1, 0102 computer and information sciences, periodicity, 01 natural sciences, Asymptotic convergence, border, Computer Science - Data Structures and Algorithms, Data Structures and Algorithms (cs.DS), 0101 mathematics, Border, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], asymptotic convergence, MCS: 05-06, Discrete mathematics, Correlation, period, Combinatorics, Period, Autocorrelation, combinatorics, correlation, ddc:004, Upper bound, Computer Science - Discrete Mathematics

File Description: application/pdf

Access URL: http://arxiv.org/abs/2209.08926
https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2023.100
https://hal-lirmm.ccsd.cnrs.fr/lirmm-03780386v1
https://hal-lirmm.ccsd.cnrs.fr/lirmm-03780386v1/document
https://doi.org/10.4230/lipics.icalp.2023.100

Phylogenetic Network Diversity Parameterized by Reticulation Number and Beyond

Authors: Leo van Iersel, Mark Jones, Jannik Schestag, Celine Scornavacca, Mathias Weller

Contributors: Scornavacca, Celine

Source: Lecture Notes in Computer Science ISBN: 9783031949272

Subject Terms: [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

Access URL: https://hal.science/hal-04987366v1

Three-State Gene Expression Model Parameterized for Single-Cell Multi-omics Data

Authors: Peyric, Thibaut, Lepoutre, Thomas, Crombach, Anton, Guyet, Thomas

Contributors: Peyric, Thibaut

Source: Lecture Notes in Computer Science ISBN: 9783032014351

Subject Terms: Single cell RNA-Seq, Single cell ATAC-Seq, Biological system modeling, Gene regulation, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

Access URL: https://hal.science/hal-05180519v1
https://doi.org/10.1101/2025.07.16.665109

Predicting coarse-grained representations of biogeochemical cycles from metabarcoding data

Authors: Arnaud Belcour, Loris Megy, Sylvain Stephant, Caroline Michel, Sétareh Rad, Petra Bombach, Nicole Dopffel, Hidde de Jong, Delphine Ropers

Contributors: Arnaud, Belcour, Analyse, ingénierie et contrôle des micro-organismes (MICROCOSME), Centre Inria de l'Université Grenoble Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Grenoble Alpes (UGA), Laboratoire Interdisciplinaire de Physique Saint Martin d’Hères (LIPhy), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Grenoble Alpes Recherche-Infrastructure de CAlcul intensif et de Données (GRICAD), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP), Université Grenoble Alpes (UGA), Bureau de Recherches Géologiques et Minières (BRGM), Institut de Physique du Globe de Paris (IPGP (UMR_7154)), Institut national des sciences de l'Univers (INSU - CNRS)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Isodetect GmbH Leipzig, Company for Isotope Monitoring, Norwegian Research Center (NORCE), ANR-23-CETP-0002,HyLife,Risques microbiens liés au stockage souterrain de l'hydrogène en Europe(2023)

Source: Bioinformatics

Subject Terms: [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, [SDU.STU.GC] Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Bioinformatics of Microbes and Microbiomes, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

File Description: application/pdf

Access URL: https://inria.hal.science/hal-04938367v2
https://doi.org/10.1093/bioinformatics/btaf230
https://inria.hal.science/hal-04938367v2/document

SpecPeptidOMS Directly and Rapidly Aligns Mass Spectra on Whole Proteomes and Identifies Peptides That Are Not Necessarily Tryptic: Implications for Peptidomics

Authors: Benoist, Émile, Jean, Géraldine, Rogniaux, Hélène, Fertin, Guillaume, Tessier, Dominique

Contributors: Nantes Université, Bibliothèque universitaire

Source: Journal of Proteome Research. 24:2159-2172

Subject Terms: Proteomics, Mass spectrometry, Proteome, [INFO.INFO-DS] Computer Science [cs]/Data Structures and Algorithms [cs.DS], Dynamic programming, Mass Spectrometry, Peptide Fragments, HEK293 Cells, Tandem Mass Spectrometry, MS2 spectra, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Humans, Trypsin, Amino Acid Sequence, Peptidomics, Peptides, Sequence Alignment, Algorithms, Software, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/40146164

Partition Based Algorithms for Rearrangement Distances With Flexible Intergenic Regions

Authors: Gabriel Siqueira, Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Géraldine Jean, Guillaume Fertin, Zanoni Dias

Contributors: Institute of Computing Campinas (IC), Universidade Estadual de Campinas = University of Campinas (UNICAMP), Laboratoire des Sciences du Numérique de Nantes (LS2N), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT)-NANTES UNIVERSITÉ - École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT), LS2N_combi

Source: IEEE Transactions on Computational Biology and Bioinformatics. 22:455-468

Subject Terms: [INFO.INFO-CC]Computer Science [cs]/Computational Complexity [cs.CC], Rearrangement Distance, Bioinformatics, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], Genomics, Transforms, Approximation algorithms, Partitioning algorithms, Computational biology, Reversal, Intergenic Regions, Transposition, Heuristic algorithms, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Partition

Access URL: https://pubmed.ncbi.nlm.nih.gov/39316499

Enhancing fluorescence correlation spectroscopy with machine learning to infer anomalous molecular motion

Authors: Quiblier, Nathan, Rye, Jan-Michael, Leclerc, Pierre, Truong, Henri, Hannou, Abdelkrim, Héliot, Laurent, Berry, Hugues

Contributors: Berry, Hugues

Source: Biophysical Journal. 124:844-856

Subject Terms: Machine Learning, Diffusion, Motion, machine learning, Spectrometry, Fluorescence, [PHYS.PHYS.PHYS-BIO-PH] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], random motions, cell biophysics, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/39921256
https://inria.hal.science/hal-04650578v2/document
https://inria.hal.science/hal-04650578v2
https://doi.org/10.1016/j.bpj.2025.01.026

Has AlphaFold3 achieved success for RNA?

Authors: Bernard, Clément, Postic, Guillaume, Ghannay, Sahar, Tahi, Fariza

Contributors: Davesne, Frédéric

Source: Acta Crystallogr D Struct Biol

Subject Terms: [INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], Models, Molecular, deep learning, RNA, Nucleic Acid Conformation, Computational Biology, 3D RNA structure, Ccp4, AlphaFold3, structure quality assessment, Software, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

Access URL: https://pubmed.ncbi.nlm.nih.gov/39868559

Semi-supervised segmentation of RNA 3D structures using density-based clustering

Authors: Le, Quoc Khang, Angel, Eric, Tahi, Fariza, Postic, Guillaume

Contributors: Davesne, Frédéric

Source: Computational and Structural Biotechnology Journal. 27:3966-3984

Subject Terms: [INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], semi-supervised segmentation, RNA conformation, lncRNAs, 3D domains, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

Access URL: https://univ-evry.hal.science/hal-05250691v1
https://doi.org/10.1016/j.csbj.2025.08.037

Endhered Patterns in Matchings and RNA

Authors: Célia Biane, Greg Hampikian, Sergey Kirgizov, Khaydar Nurligareev

Contributors: Kirgizov, Sergey

Source: Journal of Computational Biology. 32:28-46

Subject Terms: [MATH.MATH-CO] Mathematics [math]/Combinatorics [math.CO], FOS: Computer and information sciences, [INFO.INFO-DM] Computer Science [cs]/Discrete Mathematics [cs.DM], Quantitative Biology - Biomolecules, Discrete Mathematics (cs.DM), FOS: Biological sciences, FOS: Mathematics, Mathematics - Combinatorics, Biomolecules (q-bio.BM), Combinatorics (math.CO), [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Computer Science - Discrete Mathematics

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/39714916
http://arxiv.org/abs/2404.18802
https://hal.science/hal-04563757v2
https://hal.science/hal-04563757v2/document