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Roderic Guigó

Research Profile

Occupations

Genes & Molecular Sequences

Chemicals & Drugs

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Evolution, Molecular

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Publications

TOP 3
Felice-Alessio Bava; Claudia Ben-Dov; Carolina Eliscovich; Pedro G Ferreira; Roderic Guigó; Belen Miñana; Juan Valcárcel; Raúl Méndez
CPEB1 coordinates alternative 3'-UTR formation with translational regulation.
David G Knowles; Angelika Merkel; Maik Röder; Roderic Guigó
Grape RNA-Seq analysis pipeline environment.
Dmitri D Pervouchine; David G Knowles; Roderic Guigó
Intron-centric estimation of alternative splicing from RNA-seq data.

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All Publications

2013: Felice-Alessio Bava; Claudia Ben-Dov; Carolina Eliscovich; Pedro G Ferreira; Roderic Guigó; Belen Miñana; Juan Valcárcel; Raúl Méndez
CPEB1 coordinates alternative 3'-UTR formation with translational regulation.
Nature 2013;495(7439):121-5.
2013: David G Knowles; Angelika Merkel; Maik Röder; Roderic Guigó
Grape RNA-Seq analysis pipeline environment.
Bioinformatics (Oxford, England) 2013;29(5):614-21.
2013: Dmitri D Pervouchine; David G Knowles; Roderic Guigó
Intron-centric estimation of alternative splicing from RNA-seq data.
Bioinformatics (Oxford, England) 2013;29(2):273-4.
2012: Santiago Marco-Sola; Roderic Guigó; Michael Sammeth; Paolo Ribeca
The GEM mapper: fast, accurate and versatile alignment by filtration.
Nature methods 2012;9(12):1185-8.
2012: Thasso Griebel; Roderic Guigó; Vincent Lacroix; Emanuele Raineri; Paolo Ribeca; Benedikt Zacher; Michael Sammeth
Modelling and simulating generic RNA-Seq experiments with the flux simulator.
Nucleic acids research 2012;40(20):10073-83.
2012: Thomas Derrien; Sarah Djebali; Thomas R Gingeras; Jose M Gonzalez; Gregory Guernec; James B Brown; Giovanni Bussotti; piero carninci; Carrie A Davis; Jennifer Harrow; Tim J Hubbard; Rory Johnson; David G Knowles; Julien Lagarde; Timo Lassmann; Leonard Lipovich; David Martin; Angelika Merkel; Cédric Notredame; Xiaoan Ruan; Yijun Ruan; Ramin Shiekhattar; Andrea Tanzer; Mark Thomas; Hagen Tilgner; Lavanya Veeravalli; Roderic Guigó
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.
Genome research 2012;22(9):1775-89.
2012: Cédric Howald; Tim J Hubbard; Felix Kokocinski; Stephen Searle; Andrea Tanzer; Jan-Hinnerk Vogel; Nathalie Walters; Simon White; Bronwen L Aken; Jacqueline Chrast; Thomas Derrien; Adam Frankish; Jose M Gonzalez; Roderic Guigó; Jennifer Harrow; Thibaut Hourlier; Alexandre Reymond
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.
Genome research 2012;22(9):1698-710.
2012: Chao Cheng; Carrie A Davis; Sarah Djebali; Xianjun Dong; Roger Alexander; Ewan Birney; piero carninci; Thomas R Gingeras; Roderic Guigó; Timo Lassman; Jing Leng; Renqiang Min; Joel S Rozowsky; Yijun Ruan; Michael Snyder; Zhiping Weng; Koon-Kiu Yan; Kevin Yip; Mark Gerstein
Understanding transcriptional regulation by integrative analysis of transcription factor binding data.
Genome research 2012;22(9):1658-67.
2012: Hagen Tilgner; Rory Johnson; David G Knowles; Michael Snyder; Sudipto Chakrabortty; João Curado; Carrie A Davis; Sarah Djebali; Thomas R Gingeras; Roderic Guigó
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs.
Genome research 2012;22(9):1616-25.
2012: Mar Gonzàlez-Porta; Miquel Calvo; Michael Sammeth; Roderic Guigó
Estimation of alternative splicing variability in human populations.
Genome research 2012;22(3):528-38.
2012: A M Kedzierska; M Drton; Roderic Guigó; M Casanellas
SPIn: model selection for phylogenetic mixtures via linear invariants.
Molecular biology and evolution 2012;29(3):929-37.
2012: Xianjun Dong; Mark Gerstein; Thomas R Gingeras; Melissa C Greven; Roderic Guigó; Anshul Kundaje; Ewan Birney; James B Brown; Chao Cheng; Sarah Djebali; Zhiping Weng
Modeling gene expression using chromatin features in various cellular contexts.
Genome biology 2012;13(9):R53.
2012: Thomas Derrien; Jordi Estellé; Roderic Guigó; David G Knowles; Santiago Marco Sola; Emanuele Raineri; Paolo Ribeca
Fast computation and applications of genome mappability.
PloS one 2012;7(1):e30377.
2011: Jonathan M Mudge; Alexandre Reymond; Cédric Howald; Tim Hubbard; Tyler Alioto; Thomas Derrien; Julio Fernandez-Banet; Adam Frankish; Roderic Guigó; Jennifer Harrow
The origins, evolution, and functional potential of alternative splicing in vertebrates.
Molecular biology and evolution 2011;28(10):2949-59.
2011: David Martin; Cristina Pantoja; Christian Valdes-Quezada; Eduardo Moltó; Fuencisla Matesanz; Ozren Bogdanović; Elisa de la Calle-Mustienes; Orlando Domínguez; Leila Taher; Mayra Furlan-Magaril; Antonio Alcina; Susana Cañón; María Fedetz; María A Blasco; Paulo S Pereira; Ivan Ovcharenko; Félix Recillas-Targa; Lluis Montoliu; Miguel Manzanares; Roderic Guigó; Manuel Serrano; Fernando Casares; Ana Fernández Miñán; José Luis Gómez-Skarmeta
Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes.
Nature structural & molecular biology 2011;18(6):708-14.
2011: Thomas Derrien; Roderic Guigó
[Long non-coding RNAs with enhancer-like function in human cells].
Médecine sciences : M/S 2011;27(4):359-61.
2011: Thomas Derrien; Roderic Guigó; Rory Johnson
The Long Non-Coding RNAs: A New (P)layer in the "Dark Matter".
Frontiers in genetics 2011;2():107.
2010: M Mariotti; Roderic Guigó
Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes.
Bioinformatics (Oxford, England) 2010;26(21):2656-63.
2010: Christoforos Nikolaou; Sonja Althammer; Miguel Beato; Roderic Guigó
Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae.
Epigenetics & chromatin 2010;3(1):20.
2009: Marcus Buschbeck; Iris Uribesalgo; Indra Wibowo; Pau Rué; David Martin; Arantxa Gutierrez; Lluís Morey; Roderic Guigó; Hernán López-Schier; Luciano Di Croce
The histone variant macroH2A is an epigenetic regulator of key developmental genes.
Nature structural & molecular biology 2009;16(10):1074-9.
2009: Hagen Tilgner; Christoforos Nikolaou; Sonja Althammer; Michael Sammeth; Miguel Beato; Juan Valcárcel; Roderic Guigó
Nucleosome positioning as a determinant of exon recognition.
Nature structural & molecular biology 2009;16(9):996-1001.
2009: Periklis Makrythanasis; Philipp Kapranov; Lucia Bartoloni; Alexandre Reymond; Samuel Deutsch; Roderic Guigó; France Denoeud; Jorg Drenkow; Colette Rossier; Francesca Ariani; Valeria Capra; Laurent Excoffier; Alessandra Renieri; Thomas Gingeras; Stylianos E Antonarakis
Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls.
Human mutation 2009;30(9):E866-79.
2009: Sergi Castellano; Aida M Andrés; Elena Bosch; Mònica Bayes; Roderic Guigó; Andrew G Clark
Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins.
Molecular biology and evolution 2009;26(9):2031-40.
2009: Mònica Arman; Noemí Aguilera-Montilla; Virgínia Mas; Amaya Puig-Kröger; Miguel Pignatelli; Roderic Guigó; Angel-Luis Corbí; Francisco Lozano
The human CD6 gene is transcriptionally regulated by RUNX and Ets transcription factors in T cells.
Molecular immunology 2009;46(11-12):2226-35.
2009: Miguel Pignatelli; Florenci Serras; Andrés Moya; Roderic Guigó; Montserrat Corominas
CROC: finding chromosomal clusters in eukaryotic genomes.
Bioinformatics (Oxford, England) 2009;25(12):1552-3.
2009: Joan-Marc Servitja; Miguel Pignatelli; Miguel A Maestro; Carina Cardalda; Sylvia F Boj; Juanjo Lozano; Enrique Blanco; Amàlia Lafuente; Mark I McCarthy; Lauro Sumoy; Roderic Guigó; Jorge Ferrer
Hnf1alpha (MODY3) controls tissue-specific transcriptional programs and exerts opposed effects on cell growth in pancreatic islets and liver.
Molecular and cellular biology 2009;29(11):2945-59.
2009: Charles E Chapple; Roderic Guigó; Alain Krol
SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements.
Bioinformatics (Oxford, England) 2009;25(5):674-5.
2009: Gautier Koscielny; Vincent Le Texier; Chellappa Gopalakrishnan; Vasudev Kumanduri; Jean-Jack Riethoven; Francesco Nardone; Eleanor Stanley; Christine Fallsehr; Oliver Hofmann; Meelis Kull; Eoghan Harrington; Stéphanie Boué; Eduardo Eyras; Mireya Plass; Fabrice Lopez; William Ritchie; Virginie Moucadel; Takeshi Ara; Heike Pospisil; Alexander Herrmann; Jens G Reich; Roderic Guigó; Peer Bork; Magnus von Knebel Doeberitz; Jaak Vilo; Winston Hide; Rolf Apweiler; Thangavel Alphonse Thanaraj; Daniel Gautheret
ASTD: The Alternative Splicing and Transcript Diversity database.
Genomics 2009;93(3):213-20.
2009: Jennifer Harrow; Alinda Nagy; Alexandre Reymond; Tyler Alioto; Laszlo Patthy; Stylianos E Antonarakis; Roderic Guigó
Identifying protein-coding genes in genomic sequences.
Genome biology 2009;10(1):201.
2008: Sarah Djebali; Philipp Kapranov; Sylvain Foissac; Julien Lagarde; Alexandre Reymond; Catherine Ucla; Carine Wyss; Jorg Drenkow; Erica Dumais; Ryan R Murray; Chenwei Lin; David Szeto; France Denoeud; Miquel Calvo; Adam Frankish; Jennifer Harrow; Periklis Makrythanasis; Marc Vidal; Kourosh Salehi-Ashtiani; Stylianos E Antonarakis; Thomas Gingeras; Roderic Guigó
Efficient targeted transcript discovery via array-based normalization of RACE libraries.
Nature methods 2008;5(7):629-35.
2008: Maria Piqué; José Manuel López; Sylvain Foissac; Roderic Guigó; Raúl Méndez
A combinatorial code for CPE-mediated translational control.
Cell 2008;132(3):434-48.
2008: Enrique Blanco; Miguel Pignatelli; Sergi Beltran; Adrià Punset; Silvia Pérez-Lluch; Florenci Serras; Roderic Guigó; Montserrat Corominas
Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila.
Genome biology 2008;9(9):R134.
2008: Charles E Chapple; Roderic Guigó
Relaxation of selective constraints causes independent selenoprotein extinction in insect genomes.
PloS one 2008;3(8):e2968.
2008: Michael Sammeth; Sylvain Foissac; Roderic Guigó
A general definition and nomenclature for alternative splicing events.
PLoS computational biology 2008;4(8):e1000147.
2008: Zhiping Weng; Roderic Guigó
In silico meets in vivo.
Genome biology 2008;9(2):302.
2008: Sergi Castellano; Vadim N Gladyshev; Roderic Guigó; Marla J Berry
SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.
Nucleic acids research 2008;36(Database issue):D332-8.
2007: Arnaud Kerhornou; Roderic Guigó
BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations.
Bioinformatics (Oxford, England) 2007;23(14):1831-3.
2007: Enrique Blanco; Genís Parra; Roderic Guigó
Using geneid to identify genes.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2007;Chapter 4():Unit 4.3.
2007: Stefan Washietl; Jakob S Pedersen; Jan O Korbel; Claudia Stocsits; Andreas R Gruber; Jorg Hackermuller; Jana Hertel; Manja Lindemeyer; Kristin Reiche; Andrea Tanzer; Catherine Ucla; Carine Wyss; Stylianos E Antonarakis; France Denoeud; Julien Lagarde; Jorg Drenkow; Philipp Kapranov; Thomas Gingeras; Roderic Guigó; Michael Snyder; Mark Gerstein; Alexandre Reymond; Ivo L Hofacker; Peter F Stadler
Structured RNAs in the ENCODE selected regions of the human genome.
Genome research 2007;17(6):852-64.
2007: Deyou Zheng; Adam Frankish; Robert Baertsch; Philipp Kapranov; Alexandre Reymond; Siew Woh Choo; Yontao Lu; France Denoeud; Stylianos E Antonarakis; Michael Snyder; Yijun Ruan; Chia-Lin Wei; Thomas Gingeras; Roderic Guigó; Jennifer Harrow; Mark Gerstein
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.
Genome research 2007;17(6):839-51.
2007: France Denoeud; Philipp Kapranov; Catherine Ucla; Adam Frankish; Robert Castelo; Jorg Drenkow; Julien Lagarde; Tyler Alioto; Caroline Manzano; Jacqueline Chrast; Sujit Dike; Carine Wyss; Charlotte N Henrichsen; Nancy Holroyd; Mark C Dickson; Ruth Taylor; Zahra Hance; Sylvain Foissac; Richard Myers; Jane Rogers; Tim Hubbard; Jennifer Harrow; Roderic Guigó; Thomas Gingeras; Stylianos E Antonarakis; Alexandre Reymond
Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.
Genome research 2007;17(6):746-59.
2007: Joel S Rozowsky; Daniel Newburger; Fred Sayward; Jiaqian Wu; Greg Jordan; Jan O Korbel; Ugrappa Nagalakshmi; Jin Yang; Deyou Zheng; Roderic Guigó; Thomas Gingeras; Sherman Weissman; Perry Miller; Michael Snyder; Mark Gerstein
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.
Genome research 2007;17(6):732-45.
2007: Stephen Tanner; Zhouxin Shen; Julio Ng; Liliana Florea; Roderic Guigó; Steven P Briggs; Vineet Bafna
Improving gene annotation using peptide mass spectrometry.
Genome research 2007;17(2):231-9.
2007: Enrique Blanco; Roderic Guigó; Xavier Messeguer
Multiple non-collinear TF-map alignments of promoter regions.
BMC bioinformatics 2007;8():138.
2006: Roderic Guigó; Juan Valcárcel
Unweaving the meanings of messenger RNA sequences.
Molecular cell 2006;23(2):150-1.
2006: Enrique Blanco; Xavier Messeguer; Temple F Smith; Roderic Guigó
Transcription factor map alignment of promoter regions.
PLoS computational biology 2006;2(5):e49.
2006: Roderic Guigó; Paul Flicek; Josep F Abril; Alexandre Reymond; Julien Lagarde; France Denoeud; Stylianos E Antonarakis; Michael Ashburner; Vladimir Bajic; Ewan Birney; Robert Castelo; Eduardo Eyras; Catherine Ucla; Thomas Gingeras; Jennifer Harrow; Tim Hubbard; Suzanna E Lewis; Martin G Reese
EGASP: the human ENCODE Genome Annotation Assessment Project.
Genome biology 2006;7 Suppl 1():S2.1-31.
2006: Martin G Reese; Roderic Guigó
EGASP: Introduction.
Genome biology 2006;7 Suppl 1():S1.1-3.
2006: Loris Mularoni; Roderic Guigó; M Mar Albà
Mutation patterns of amino acid tandem repeats in the human proteome.
Genome biology 2006;7(4):R33.
2006: Enrique Blanco; Domènec Farré; M Mar Albà; Xavier Messeguer; Roderic Guigó
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.
Nucleic acids research 2006;34(Database issue):D63-7.
2006: Genís Parra; Alexandre Reymond; Noura Dabbouseh; Emmanouil T Dermitzakis; Robert Castelo; Timothy M Thomson; Stylianos E Antonarakis; Roderic Guigó
Tandem chimerism as a means to increase protein complexity in the human genome.
Genome research 2006;16(1):37-44.
2005: Sergi Castellano; Alexey V Lobanov; Charles Chapple; Sergey V Novoselov; Mario Albrecht; Deame Hua; Alain Lescure; Thomas Lengauer; Alain Krol; Vadim N Gladyshev; Roderic Guigó
Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(45):16188-93.
2005: José M Izquierdo; Nuria Majós; Sophie Bonnal; Concepción Martínez; Robert Castelo; Roderic Guigó; Daniel Bilbao; Juan Valcárcel
Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition.
Molecular cell 2005;19(4):475-84.
2005: Roderic Guigó; Martin G Reese
EGASP: collaboration through competition to find human genes.
Nature methods 2005;2(8):575-7.
2005: Núria López-Bigas; Benjamin Audit; Christos Ouzounis; Genís Parra; Roderic Guigó
Are splicing mutations the most frequent cause of hereditary disease?
FEBS letters 2005;579(9):1900-3.
2005: Kalin Taskov; Charles Chapple; Gregory V Kryukov; Sergi Castellano; Alexey V Lobanov; Konstantin V Korotkov; Roderic Guigó; Vadim N Gladyshev
Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome?
Nucleic acids research 2005;33(7):2227-38.
2005: Robert Castelo; Alexandre Reymond; Carine Wyss; Francisco Câmara; Genís Parra; Stylianos E Antonarakis; Roderic Guigó; Eduardo Eyras
Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.
Nucleic acids research 2005;33(6):1935-9.
2005: Josep F Abril; Robert Castelo; Roderic Guigó
Comparison of splice sites in mammals and chicken.
Genome research 2005;15(1):111-9.
2004: Robert Castelo; Roderic Guigó
Splice site identification by idlBNs.
Bioinformatics (Oxford, England) 2004;20 Suppl 1():i69-76.
2004: Jose Castresana; Roderic Guigó; M Mar Albà
Clustering of genes coding for DNA binding proteins in a region of atypical evolution of the human genome.
Journal of molecular evolution 2004;59(1):72-9.
2004: Michael R Brent; Roderic Guigó
Recent advances in gene structure prediction.
Current opinion in structural biology 2004;14(3):264-72.
2004: M Mar Albà; Roderic Guigó
Comparative analysis of amino acid repeats in rodents and humans.
Genome research 2004;14(4):549-54.
2004: Sergi Castellano; Sergey V Novoselov; Gregory V Kryukov; Alain Lescure; Enrique Blanco; Alain Krol; Vadim N Gladyshev; Roderic Guigó
Reconsidering the evolution of eukaryotic selenoproteins: a novel nonmammalian family with scattered phylogenetic distribution.
EMBO reports 2004;5(1):71-7.
2003: Josep F Abril; Roderic Guigó; Thomas Wiehe
gff2aplot: Plotting sequence comparisons.
Bioinformatics (Oxford, England) 2003;19(18):2477-9.
2003: Gregory V Kryukov; Sergi Castellano; Sergey V Novoselov; Alexey V Lobanov; Omid Zehtab; Roderic Guigó; Vadim N Gladyshev
Characterization of mammalian selenoproteomes.
Science (New York, N.Y.) 2003;300(5624):1439-43.
2003: Sergi Beltran; Enrique Blanco; Florenci Serras; Beatriz Pérez-Villamil; Roderic Guigó; Spyros Artavanis-Tsakonas; Montserrat Corominas
Transcriptional network controlled by the trithorax-group gene ash2 in Drosophila melanogaster.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(6):3293-8.
2003: Genís Parra; Pankaj Agarwal; Josep F Abril; Thomas Wiehe; James W Fickett; Roderic Guigó
Comparative gene prediction in human and mouse.
Genome research 2003;13(1):108-17.
2002: Gernot Glöckner; Ludwig Eichinger; Karol Szafranski; Justin A Pachebat; Alan T Bankier; Paul H Dear; Rüdiger Lehmann; Cornelia Baumgart; Genís Parra; Josep F Abril; Roderic Guigó; Kai Kumpf; Budi Tunggal; Edward Cox; Michael A Quail; Matthias Platzer; André Rosenthal; Angelika A Noegel
Sequence and analysis of chromosome 2 of Dictyostelium discoideum.
Nature 2002;418(6893):79-85.
2001: Thomas Wiehe; S Gebauer-Jung; Thomas Mitchell-Olds; Roderic Guigó
SGP-1: prediction and validation of homologous genes based on sequence alignments.
Genome research 2001;11(9):1574-83.
2001: Sergi Castellano; N Morozova; Marta Morey; M J Berry; Florenci Serras; Montserrat Corominas; Roderic Guigó
In silico identification of novel selenoproteins in the Drosophila melanogaster genome.
EMBO reports 2001;2(8):697-702.
2000: Thomas Wiehe; Roderic Guigó; W Miller
Genome sequence comparisons: hurdles in the fast lane to functional genomics.
Briefings in bioinformatics 2000;1(4):381-8.
2000: Timothy M Thomson; Juan Jose Lozano ; Noureddine Loukili; R Carrió; Florenci Serras; B Cormand; M Valeri; Víctor M Díaz; Josep F Abril; Moisès Burset; J Merino; Alfons Macaya; Montserrat Corominas; Roderic Guigó
Fusion of the human gene for the polyubiquitination coeffector UEV1 with Kua, a newly identified gene.
Genome research 2000;10(11):1743-56.
2000: Roderic Guigó; Pankaj Agarwal; Josep F Abril; Moisès Burset; J W Fickett
An assessment of gene prediction accuracy in large DNA sequences.
Genome research 2000;10(10):1631-42.
2000: Josep F Abril; Roderic Guigó
gff2ps: visualizing genomic annotations.
Bioinformatics (Oxford, England) 2000;16(8):743-4.
2000: Genís Parra; E Blanco; Roderic Guigó
GeneID in Drosophila.
Genome research 2000;10(4):511-5.
1998: Roderic Guigó
Assembling genes from predicted exons in linear time with dynamic programming.
Journal of computational biology : a journal of computational molecular cell biology 1998;5(4):681-702.
1997: Juan Jose Lozano ; E López-de-Briñas; Nuria B Centeno; Roderic Guigó; Ferran Sanz
Three-dimensional modelling of human cytochrome P450 1A2 and its interaction with caffeine and MeIQ.
Journal of computer-aided molecular design 1997;11(4):395-408.