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1

Nextflow enables reproducible computational workflows

Di Tommaso, Paolo, Chatzou, Maria, Floden, Evan W, Barja, Pablo Prieto, Palumbo, Emilio, Notredame, Cedric

Journal:

Nature Biotechnology

Year:

2017

Language:

english

File:

PDF, 1.86 MB

english, 2017

2

Ten steps to get started in Genome Assembly and Annotation

Dominguez Del Angel, Victoria, Hjerde, Erik, Sterck, Lieven, Capella-Gutierrez, Salvadors, Notredame, Cederic, Vinnere Pettersson, Olga, Amselem, Joelle, Bouri, Laurent, Bocs, Stephanie, Klopp, Christ

Journal:

Year:

2018

Language:

english

File:

PDF, 2.22 MB

english, 2018

3

Pertinence et expérience des dispositifs de veille et de recontact dans la prévention suicidaire auprès des enfants et des adolescents

Notredame, C.-E., Medjkane, F., Porte, A., Desobry, O., Ligier, F.

Journal:

Year:

2019

Language:

french

File:

PDF, 363 KB

french, 2019

4

Association between childhood trauma and multimodal early-onset hallucinations

Medjkane, François, Notredame, Charles-Edouard, Sharkey, Lucie, D'Hondt, Fabien, Vaiva, Guillaume, Jardri, Renaud

Journal:

The British Journal of Psychiatry

Year:

2020

Language:

english

File:

PDF, 311 KB

english, 2020

5

MULTICHANNEL SEQUENCE ANALYSIS APPLIED TO SOCIAL SCIENCE DATA

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

Journal:

Sociological Methodology

Year:

2010

Language:

english

File:

PDF, 768 KB

english, 2010

6

T-coffee: a novel method for fast and accurate multiple sequence alignment

Cédric Notredame, Desmond G Higgins, Jaap Heringa

Journal:

Journal of Molecular Biology

Year:

2000

Language:

english

File:

PDF, 278 KB

english, 2000

7

Macro-Based Cross Assemblers

Tavernier, K.R., Notredame, P.H.

Journal:

IEEE Transactions on Software Engineering

Year:

1980

Language:

english

File:

PDF, 1.51 MB

english, 1980

8

Validation d’une grille d’évaluation qualitative d’articles de presse écrite sur le suicide, dans le cadre du programme Papageno

Verzaux, S., Notredame, C.E., Pauwels, N., Danel, T., Vaiva, G., Walter, M.

Journal:

European Psychiatry

Year:

2015

Language:

french

File:

PDF, 76 KB

french, 2015

9

At least one more reason why

Notredame, Charles-Edouard, Grandgenèvre, Pierre, Vaiva, Guillaume, Séguin, Monique

Journal:

European Child & Adolescent Psychiatry

Year:

2017

Language:

english

File:

PDF, 661 KB

english, 2017

10

Factors Associated With Mental Health Disorders Among University Students in France Confined During the COVID-19 Pandemic

Wathelet, Marielle, Duhem, StÃ©phane, Vaiva, Guillaume, Baubet, Thierry, Habran, Enguerrand, Veerapa, Emilie, Debien, Christophe, Molenda, Sylvie, Horn, Mathilde, GrandgenÃ¨vre, Pierre, Notredame, Cha

Journal:

JAMA Network Open

Year:

2020

File:

PDF, 853 KB

2020

11

A user-friendly web portal for T-Coffee on supercomputers

Josep Rius, Fernando Cores, Francesc Solsona, Jano I van Hemert, Jos Koetsier, Cedric Notredame

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 875 KB

english, 2011

12

Exploring the gonad transcriptome of two extreme male pigs with RNA-seq

Anna Esteve-Codina, Robert Kofler, Nicola Palmieri, Giovanni Bussotti, Cedric Notredame, Miguel Pérez-Enciso

Journal:

Year:

2011

Language:

english

File:

PDF, 677 KB

english, 2011

13

Exploiting parallelism on progressive alignment methods

Miquel Orobitg, Fernando Guirado, Cedric Notredame, Fernando Cores

Journal:

The Journal of Supercomputing

Year:

2011

Language:

english

File:

PDF, 629 KB

english, 2011

14

Fibroblast-Derived Induced Pluripotent Stem Cells Show No Common Retroviral Vector Insertions

Florencio Varas, Matthias Stadtfeld, Luisa de Andres-Aguayo, Nimet Maherali, Alessandro di Tullio, Lorena Pantano, Cedric Notredame, Konrad Hochedlinger, Thomas Graf

Journal:

Year:

2009

Language:

english

File:

PDF, 367 KB

english, 2009

15

A Stochastic Model for Closed-Loop Preemptive Microprocessor I/O Organizations

Van Campenhout, J.M., Notredame, P.

Journal:

IEEE Transactions on Computers

Year:

1978

Language:

english

File:

PDF, 2.40 MB

english, 1978

16

Predicting phenotypic traits of prokaryotes from protein domain frequencies

Thomas Lingner, Stefanie Mühlhausen, Toni Gabaldón, Cedric Notredame, Peter Meinicke

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 353 KB

english, 2010

17

Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time

Dorota Retelska, Emmanuel Beaudoing, Cédric Notredame, C Victor Jongeneel, Philipp Bucher

Journal:

Year:

2007

Language:

english

File:

PDF, 1008 KB

english, 2007

18

Lipid-water interface mediates reversible ionophore conformational change

Robert Brasseur, Miguel Notredame, J.-M. Ruysschaert

Journal:

Biochemical and Biophysical Research Communications

Year:

1983

Language:

english

File:

PDF, 341 KB

english, 1983

19

Long Noncoding RNAs with Enhancer-like Function in Human Cells

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

Journal:

Year:

2010

Language:

english

File:

PDF, 945 KB

english, 2010

20

3DCoffee: Combining Protein Sequences and Structures within Multiple Sequence Alignments

Orla O'Sullivan, Karsten Suhre, Chantal Abergel, Desmond G Higgins, Cédric Notredame

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 417 KB

english, 2004

21

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

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

Journal:

Journal of Molecular Biology

Year:

2010

Language:

english

File:

PDF, 1.51 MB

english, 2010

22

AMPA: an automated web server for prediction of protein antimicrobial regions

Torrent, M., Di Tommaso, P., Pulido, D., Nogues, M. V., Notredame, C., Boix, E., Andreu, D.

Journal:

Year:

2012

Language:

english

File:

PDF, 130 KB

english, 2012

23

Segment-based multiple sequence alignment

Rausch, T., Emde, A.-K., Weese, D., Doring, A., Notredame, C., Reinert, K.

Journal:

Year:

2008

Language:

english

File:

PDF, 200 KB

english, 2008

24

Epistasis as the primary factor in molecular evolution

Breen, Michael S., Kemena, Carsten, Vlasov, Peter K., Notredame, Cedric, Kondrashov, Fyodor A.

Journal:

Year:

2012

Language:

english

File:

PDF, 112 KB

english, 2012

25

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

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

Journal:

Trends in Biochemical Sciences

Year:

2012

Language:

english

File:

PDF, 2.97 MB

english, 2012

26

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

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

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 388 KB

english, 2012

27

Recent progress in multiple sequence alignment: a survey

Notredame, Cédric

Journal:

Pharmacogenomics

Year:

2002

Language:

english

File:

PDF, 236 KB

english, 2002

28

Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures

Taly, Jean-Francois, Magis, Cedrik, Bussotti, Giovanni, Chang, Jia-Ming, Di Tommaso, Paolo, Erb, Ionas, Espinosa-Carrasco, Jose, Kemena, Carsten, Notredame, Cedric

Journal:

Bioentrepreneur

Year:

2011

Language:

english

File:

PDF, 2.23 MB

english, 2011

29

Identification of a novel microRNA (miRNA) from rice that targets an alternatively spliced transcript of the Nramp6 ( Natural resistance-associated macrophage protein 6 ) gene involved in pathogen resistance

Campo, Sonia, Peris-Peris, Cristina, Siré, Christelle, Moreno, Ana Beatriz, Donaire, Livia, Zytnicki, Matthias, Notredame, Cedric, Llave, César, San Segundo, Blanca

Journal:

New Phytologist

Year:

2013

Language:

english

File:

PDF, 1.13 MB

english, 2013

30

Breen et al. reply

Breen, Michael S., Kemena, Carsten, Vlasov, Peter K., Notredame, Cedric, Kondrashov, Fyodor A.

Journal:

Year:

2013

Language:

english

File:

PDF, 202 KB

english, 2013

31

Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package

Kemena, C., Bussotti, G., Capriotti, E., Marti-Renom, M. A., Notredame, C.

Journal:

Year:

2013

Language:

english

File:

PDF, 323 KB

english, 2013

32

[ACM Press the 20th European MPI Users' Group Meeting - Madrid, Spain (2013.09.15-2013.09.18)] Proceedings of the 20th European MPI Users' Group Meeting on - EuroMPI '13 - Scalability and accuracy improvements of consistency-based multiple sequence alignment tools

Orobitg, Miquel, Lladós, Jordi, Guirado, Fernando, Cores, Fernando, Notredame, Cedric

Year:

2013

Language:

english

File:

PDF, 5.99 MB

english, 2013

33

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

Di Tommaso, P., Moretti, S., Xenarios, I., Orobitg, M., Montanyola, A., Chang, J.-M., Taly, J.-F., Notredame, C.

Journal:

Nucleic Acids Research

Year:

2011

Language:

english

File:

PDF, 2.04 MB

english, 2011

34

L’étudiant en médecine, un apprenant en violence

Notredame, C.-E.

Journal:

Éthique & Santé

Year:

2013

Language:

french

File:

PDF, 385 KB

french, 2013

35

TCS: A New Multiple Sequence Alignment Reliability Measure to Estimate Alignment Accuracy and Improve Phylogenetic Tree Reconstruction

Chang, J.-M., Di Tommaso, P., Notredame, C.

Journal:

Molecular Biology and Evolution

Year:

2014

Language:

english

File:

PDF, 589 KB

english, 2014

36

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

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

Journal:

Parallel Computing

Year:

2015

Language:

english

File:

PDF, 987 KB

english, 2015

37

[IEEE 2012 IEEE International Symposium on Parallel & Distributed Processing (IPDPS) - Shanghai, China (2012.05.21-2012.05.25)] 2012 IEEE 26th International Parallel and Distributed Processing Symposium - Enhancing the Scalability of Consistency-based Progressive Multiple Sequences Alignment Applications

Orobitg, M., Cores, F., Guirado, F., Kemena, C., Notredame, C., Ripoll, A.

Year:

2012

Language:

english

File:

PDF, 1.02 MB

english, 2012

38

Pharmacological Assessment Defines Leishmania donovani Casein Kinase 1 as a Drug Target and Reveals Important Functions in Parasite Viability and Intracellular Infection

Rachidi, N., Taly, J. F., Durieu, E., Leclercq, O., Aulner, N., Prina, E., Pescher, P., Notredame, C., Meijer, L., Spath, G. F.

Journal:

Antimicrobial Agents and Chemotherapy

Year:

2014

Language:

english

File:

PDF, 3.27 MB

english, 2014

39

Upcoming challenges for multiple sequence alignment methods in the high-throughput era

Kemena, C., Notredame, C.

Journal:

Year:

2009

Language:

english

File:

PDF, 376 KB

english, 2009

40

COFFEE: an objective function for multiple sequence alignments

Notredame, C., Holm, L., Higgins, D. G.

Journal:

Year:

1998

Language:

english

File:

PDF, 224 KB

english, 1998

41

The iRMSD: a local measure of sequence alignment accuracy using structural information

Armougom, F., Moretti, S., Keduas, V., Notredame, C.

Journal:

Year:

2006

Language:

english

File:

PDF, 287 KB

english, 2006

42

APDB: a novel measure for benchmarking sequence alignment methods without reference alignments

O'Sullivan, O., Zehnder, M., Higgins, D., Bucher, P., Grosdidier, A., Notredame, C.

Journal:

Year:

2003

Language:

english

File:

PDF, 344 KB

english, 2003

43

STRIKE: evaluation of protein MSAs using a single 3D structure

Kemena, C., Taly, J.-F., Kleinjung, J., Notredame, C.

Journal:

Year:

2011

Language:

english

File:

PDF, 507 KB

english, 2011

44

BlastR--fast and accurate database searches for non-coding RNAs

Bussotti, G., Raineri, E., Erb, I., Zytnicki, M., Wilm, A., Beaudoing, E., Bucher, P., Notredame, C.

Journal:

Nucleic Acids Research

Year:

2011

Language:

english

File:

PDF, 3.04 MB

english, 2011

45

Use of ChIP-Seq data for the design of a multiple promoter-alignment method

Erb, I., Gonzalez-Vallinas, J. R., Bussotti, G., Blanco, E., Eyras, E., Notredame, C.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 4.12 MB

english, 2012

46

The Rhizome of Life: The Sympatric Rickettsia felis Paradigm Demonstrates the Random Transfer of DNA Sequences

Merhej, V., Notredame, C., Royer-Carenzi, M., Pontarotti, P., Raoult, D.

Journal:

Molecular Biology and Evolution

Year:

2011

Language:

english

File:

PDF, 1.45 MB

english, 2011

47

R-Coffee: a web server for accurately aligning noncoding RNA sequences

Moretti, S., Wilm, A., Higgins, D. G., Xenarios, I., Notredame, C.

Journal:

Nucleic Acids Research

Year:

2008

Language:

english

File:

PDF, 1.24 MB

english, 2008

48

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods

Moretti, S., Armougom, F., Wallace, I. M., Higgins, D. G., Jongeneel, C. V., Notredame, C.

Journal:

Nucleic Acids Research

Year:

2007

Language:

english

File:

PDF, 1.77 MB

english, 2007

49

Recovering accuracy methods for scalable consistency library

Lladós, Jordi, Guirado, Fernando, Cores, Fernando, Lérida, Josep Lluís, Notredame, Cedric

Journal:

The Journal of Supercomputing

Year:

2015

Language:

english

File:

PDF, 753 KB

english, 2015

50

Transcript profiling of jasmonate-elicited Taxus cells reveals a β-phenylalanine-CoA ligase

Ramírez-Estrada, Karla, Altabella, Teresa, Onrubia, Miriam, Moyano, Elisabeth, Notredame, Cedric, Osuna, Lidia, Vanden Bossche, Robin, Goossens, Alain, Cusido, Rosa M., Palazon, Javier

Journal:

Plant Biotechnology Journal

Year:

2015

Language:

english

File:

PDF, 1.84 MB

english, 2015

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