Compositional Covariance Shrinkage and Regularised Partial Correlations

Authors: Jin, Suzanne, Notredame, Cedric, Erb, Ionas

Subject Terms: Statistics - Methodology, Statistics - Applications, G2F30, G2H20, G2P99

Access URL: http://arxiv.org/abs/2212.00496

Evolutionary analysis reveals the role of a non-catalytic domain of peptidyl arginine deiminase 2 in transcriptional regulation

Authors: Villanueva-Cañas, José Luis, Fernandez-Fuentes, Narcis, Saul, Dominik, Kosinsky, Robyn Laura, Teyssier, Catherine, Rogalska, Malgorzata Ewa, Pérez, Ferran Pegenaute, Oliva, Baldomero, Notredame, Cedric, Beato, Miguel, Sharma, Priyanka

Source: In iScience 19 April 2024 27(4)

Towards the accurate alignment of over a million protein sequences: Current state of the art

Authors: Santus, Luisa, Garriga, Edgar, Deorowicz, Sebastian, Gudyś, Adam, Notredame, Cedric

Source: In Current Opinion in Structural Biology June 2023 80

Highly significant improvement of protein sequence alignments with AlphaFold2

Authors: Baltzis, Athanasios, Mansouri, Leila, Jin, Suzanne, Langer, Björn E, Erb, Ionas, Notredame, Cedric

Source: Bioinformatics. 38(22):5007-5011

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100164935430.0x000001&indx=1&recIds=ETOCvdc_100164935430.0x000001

multistrap: boosting phylogenetic analyses with structural information.

Authors: Baltzis, Athanasios, Santus, Luisa, Langer, Björn E., Magis, Cedrik, de Vienne, Damien M., Gascuel, Olivier, Mansouri, Leila, Notredame, Cedric

Source: Nature Communications; 1/15/2025, Vol. 16 Issue 1, p1-14, 14p

Multiple Sequence Alignment Computation Using the T-Coffee Regressive Algorithm Implementation

Authors: Garriga, Edgar, Di Tommaso, Paolo, Magis, Cedrik, Erb, Ionas, Mansouri, Leila, Baltzis, Athanasios, Floden, Evan, Notredame, Cedric

Source: Methods in molecular biology. 2231:89-98

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN625406442&indx=1&recIds=ETOCRN625406442

Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty

Authors: Chatzou, Maria, Floden, Evan W., Di Tommaso, Paolo, Gascuel, Olivier, Notredame, Cedric

Source: Systematic Biology, 2018 Nov 01. 67(6), 997-1009.

Access URL: https://www.jstor.org/stable/26582223

Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools

Authors: Espinosa-Carrasco, Jose, Erb, Ionas, Hermoso Pulido, Toni, Ponomarenko, Julia, Dierssen, Mara, Notredame, Cedric

Source: In iScience 30 November 2018 9:244-257

Large multiple sequence alignments with a root-to-leaf regressive method

Authors: Garriga, Edgar, Di Tommaso, Paolo, Magis, Cedrik, Erb, Ionas, Mansouri, Leila, Baltzis, Athanasios, Laayouni, Hafid, Kondrashov, Fyodor, Floden, Evan, Notredame, Cedric

Source: Nature biotechnology. 37(12):1466-1470

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100193223251.0x000001&indx=1&recIds=ETOCvdc_100193223251.0x000001

Evolutionary Footprints Reveal Insights into Plant MicroRNA Biogenesis

Authors: Chorostecki, Uciel, Moro, Belen, Rojas, Arantxa M.L., Debernardi, Juan M., Schapire, Arnaldo L., Notredame, Cedric, Palatnik, Javier F.

Source: Plant Cell, 2017 Jun 01. 29(6), 1248-1261.

Access URL: https://www.jstor.org/stable/90011028

CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis

Authors: Ounzain, Samir, Micheletti, Rudi, Arnan, Carme, Plaisance, Isabelle, Cecchi, Dario, Schroen, Blanche, Reverter, Ferran, Alexanian, Michael, Gonzales, Christine, Ng, Shi Yan, Bussotti, Giovanni, Pezzuto, Iole, Notredame, Cedric, Heymans, Stephane, Guigó, Roderic, Johnson, Rory, Pedrazzini, Thierry

Source: In Journal of Molecular and Cellular Cardiology December 2015 89 Part A:98-112

High Performance computing improvements on bioinformatics consistency-based multiple sequence alignment tools

Authors: Orobitg, Miquel, Guirado, Fernando, Cores, Fernando, Llados, Jordi, Notredame, Cedric

Source: In Parallel Computing February 2015 42:18-34

Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania.

Authors: Cuypers, Bart^1,2, Meysman, Pieter², Erb, Ionas³, Bittremieux, Wout⁴, Valkenborg, Dirk^5,6, Baggerman, Geert^6,7, Mertens, Inge^6,7, Sundar, Shyam⁸, Khanal, Basudha⁹, Notredame, Cedric³, Dujardin, Jean-Claude^1,10, jcdujardin@itg.be, Domagalska, Malgorzata A.¹, jcdujardin@itg.be, Laukens, Kris², jcdujardin@itg.be

Source: PLoS Pathogens; 9/23/2022, Vol. 18 Issue 9, p1-23, 23p

Improved definition of the mouse transcriptome via targeted RNA sequencing

Authors: Bussotti, Giovanni, Leonardi, Tommaso, Clark, Michael B., Mercer, Tim R., Crawford, Joanna, Malquori, Lorenzo, Notredame, Cedric, Dinger, Marcel E., Mattick, John S., Enright, Anton J.

Source: Genome research. 26(5):705-716

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN606192317&indx=1&recIds=ETOCRN606192317

An improved understanding of TNFL/TNFR interactions using structure-based classifications

Authors: Magis, Cedrik, van der Sloot, Almer M., Serrano, Luis, Notredame, Cedric

Source: In Trends in Biochemical Sciences September 2012 37(9):353-363

MULTICHANNEL SEQUENCE ANALYSIS APPLIED TO SOCIAL SCIENCE DATA

Authors: Gauthier, Jacques-Antoine, Widmer, Eric D., Bucher, Philipp, Notredame, Cédric

Source: Sociological Methodology, 2010 Jan 01. 40, 1-38.

Access URL: https://www.jstor.org/stable/41336881

Long Noncoding RNAs with Enhancer-like Function in Human Cells

Authors: Ørom, Ulf Andersson, Derrien, Thomas, Beringer, Malte, Gumireddy, Kiranmai, Gardini, Alessandro, Bussotti, Giovanni, Lai, Fan, Zytnicki, Matthias, Notredame, Cedric, Huang, Qihong, Guigo, Roderic, Shiekhattar, Ramin

Source: In Cell 1 October 2010 143(1):46-58

T-RMSD: A Fine-grained, Structure-based Classification Method and its Application to the Functional Characterization of TNF Receptors

Authors: Magis, Cedrik, Stricher, François, van der Sloot, Almer M., Serrano, Luis, Notredame, Cedric

Source: In Journal of Molecular Biology 2010 400(3):605-617

Phylogenetic and functional characterization of water bears (Tardigrada) tubulins.

Authors: Novotná Floriančičová, Kamila, Baltzis, Athanasios, Smejkal, Jiří, Czerneková, Michaela, Kaczmarek, Łukasz, Malý, Jan, Notredame, Cedric, Vinopal, Stanislav

Source: Scientific Reports; 3/30/2023, Vol. 13 Issue 1, p1-13, 13p

Subject Terms: TARDIGRADA, TUBULINS, CENTRIOLES, CYTOSKELETON, MICROTUBULES, CENTROSOMES

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

Authors: Chang Jia-Ming, Di Tommaso Paolo, Taly Jean-François, Notredame Cedric

Source: BMC Bioinformatics, Vol 13, Iss Suppl 4, p S1 (2012)

Subject Terms: Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/8adc409df8e54c66a00bd63b0401b101